From meghdad_saeedian at yahoo.com  Sun Jul  1 09:43:02 2012
From: meghdad_saeedian at yahoo.com (meghdad saeedian)
Date: Sun, 1 Jul 2012 00:43:02 -0700 (PDT)
Subject: [Pw_forum] Fw: Re: Problem in using GGA+U for the PbSe Calculation
Message-ID: <1341128582.8159.YahooMailClassic@web140606.mail.bf1.yahoo.com>

?
Dear Emine
?
before all, thanks for your consideration.
after that, 
?
>Ok so let me understand
that's right. you undrestand the problem precisely.?
?
>Please send more info on the configuration of your machine
architecture : x86_64
Linix Version : CentOS 5.5
Fortran Compiler : ifort version 12.1.0
Code?Version : espresso-5.0/
?
>you can attach them as well.
tabd.f90 & set_hubbard_l.f90 are attached
?
Thanks?
MS?

--- On Sun, 7/1/12, Emine Kucukbenli <kucukben at sissa.it> wrote:


From: Emine Kucukbenli <kucukben at sissa.it>
Subject: Re: [Pw_forum] Problem in using GGA+U for the PbSe Calculation
To: meghdad_saeedian at yahoo.com
Date: Sunday, July 1, 2012, 4:58 AM



Ok so let me understand,
Now we are talking about another machine, where the code compiles
successfully after the modifications to those two files, but gives the
"pseudo potential not yet inserted" error in runtime (in PbSe case),
even though you have supplied them in the lists we have mentioned
before.
I am sorry I find it a bit hard to understand why this would happen.
Please send more info on the configuration of your machine, version of
the code, compilers you use, so i can see if i can reproduce it. i am
also curious about the files you have modified. you can attach them as
well.
ciao
emine


Quoting meghdad saeedian <meghdad_saeedian at yahoo.com>:

> Dear Emine
>
> Iv changed ~/espresso-5.0/PW/src/tabd.f90 &
> ~/espresso-5.0/flib/set_hubbard_l.f90 in the another machine? and pw
> compiled correctly as below :
>
> .
> .
> .
> make[2]: Entering directory `/home/user25/espresso-5.0/PW/src'
> test -n "" && ( cd ../.. ; make -w? || exit 1) || :
> make[2]: Leaving directory `/home/user25/espresso-5.0/PW/src'
> if test -d tools ; then \
> ??? ( cd tools ; if test "make" = "" ; then make -w pwtools; \
> ??? else make -w ; fi ) ; fi ; \
>
> make[2]: Entering directory `/home/user25/espresso-5.0/PW/tools'
> test -n "" && ( cd ../.. ; make -w? || exit 1) || :
> make[2]: Leaving directory `/home/user25/espresso-5.0/PW/tools'
> make[1]: Leaving directory
>? `/home/user25/espresso-5.0/PW'
> [user25 at ce espresso-5.0]$
>
> in this machine, GGA+U for ZnO works well.
> But there is still the previous error for PbSe :(
>
> How can I trace the problem?
>
> Thanks
> MS
>
> --- On Sat, 6/30/12, Emine Kucukbenli <kucukben at sissa.it> wrote:
>
> From: Emine Kucukbenli <kucukben at sissa.it>
> Subject: Re: [Pw_forum] Fw: Re: Problem in using GGA+U for the PbSe
> Calculation
> To: meghdad_saeedian at yahoo.com
> Date: Saturday, June 30, 2012, 8:57 PM
>
> Dear Meghdad,
>> I didnt know that I should make it again.
> Good, now you know :)
>
>> what can I do now?
>
> A starting place would be, to think what the error message is trying
> to tell you "invalid character"
>? ?
> then [I am guessing but not 100% that is the problem], googling "non
> printable/control characters" for the editor you have used to edit the
> tabd.f90 code: MS Word, etc...
> ciao
> emine
>
>
> Quoting meghdad saeedian <meghdad_saeedian at yahoo.com>:
>
>> Dear Emine
>>
>> I didnt know that I should make it again.
>> Anyway, Iv done the below command:
>> $ make pw
>> then it give the following error:
>>
>> make[1]: Entering directory `/home/meghdad/espresso-4.3.2/PW'
>> test -n "" && ( cd .. ; make -w? || exit 1) || :
>> gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW
>> -I../include -I../iotk/src -I../Modules -I. -c set_hubbard_l.f90
>> gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW
>> -I../include -I../iotk/src
>? -I../Modules -I. -c tabd.f90
>> tabd.f90:1.1:
>>
>> \!
>> ?1
>> Error: Invalid character in name at (1)
>> make[1]: *** [tabd.o] Error 1
>> make[1]: Leaving directory `/home/meghdad/espresso-4.3.2/PW'
>> make: *** [pw] Error 2
>> meghdad at meghdad-Vostro-1320:
>>
>> what can I do now?
>>
>> MS
>>
>>
>>
>>
>> --- On Sat, 6/30/12, Emine Kucukbenli <kucukben at sissa.it> wrote:
>>
>> From: Emine Kucukbenli <kucukben at sissa.it>
>> Subject: Re: [Pw_forum] Problem in using GGA+U for the PbSe Calculation
>> To: meghdad_saeedian at yahoo.com
>> Date: Saturday, June 30, 2012, 7:11
>? PM
>>
>>
>>
>> Hi Meghdad,
>> seems you have done the necessary modifications to the code,
>> silly question but have you complied to code again (make pw?)
>> ciao
>> emine
>>
>> Quoting meghdad saeedian <meghdad_saeedian at yahoo.com>:
>>
>>> Dear all
>>>
>>> I want to use GGA+U to calculation of the energy gap of PbSe.
>>> So I put the value of the angular momentum in the
>>> PW/set_hubbard_l.f90? as below:
>>>
>>> ???? ! ... other elements
>>> ???? !
>>> ???? CASE( 'H' )
>>> ??????? !
>>> ??????? hubbard_l =? 0
>>>
>? ???????
>>> ? !
>>> ???? CASE( 'Pb' )
>>> ??????? !
>>> ??????? hubbard_l =? 2
>>> ??????? !
>>> ???? CASE( 'Se' )
>>> ??????? !
>>> ??????? hubbard_l =?
>>> ? 1
>>> ??????? !
>>> And the occupation number in the PW/tabd.f90 modified as below :
>>>
>>> ??? !
>>> ???? CASE( 'Pb'? )
>>> ??????? hubbard_occ = 10.d0
>>> ???? !
>>> ???? CASE( 'O', 'Se'? )
>>>
>? ??????? hubbard_occ = 4.d0
>>> ???? !
>>> ???? CASE( 'H'? )
>>> ??????? hubbard_occ = 1.d0
>>> ???? !
>>>
>>>
>>> Then the input file of PbSe is constructed as below:
>>> ?
>>> &control
>>> ??? calculation='vc-relax'
>>> ??? prefix='PbSe',
>>> ??? pseudo_dir ='/home/meghdad/espresso-4.3.2/pseudo/',
>>> ??? outdir='/home/meghdad/tmp/',
>>> ??? tstress = .true.
>>> ??? tprnfor =
>>> ? .true.
>>> ??? nstep=5000,
>>>
>>> ?/
>>> ?&system
>>> ??? ibrav= 1,? celldm(1) =11.716301129,
>>> ???
>? nat=? 2, ntyp= 2, nbnd=11,
>>> ??? ecutwfc =40,
>>> ??? lda_plus_u = .true.,
>>> ??? Hubbard_U(2) = 0.5,(this value is just for the run)
>>> ??? Hubbard_U(1) = 0.6,(this value is just for the run)
>>>
>>> ? /
>>> ?&electrons
>>> ??? conv_thr =? 1.0d-8
>>> ??? mixing_beta= 0.5
>>> ??? mixing_mode='plain'
>>> ??? diagonalization='cg'
>>> ?/
>>> ?&IONS
>>> ??? ion_dynamics='damp',
>>> ??? pot_extrapolation='second_order'
>>> ??? wfc_extrapolation='second_order'
>>> ?/
>>> ?&CELL
>>> ??? cell_dynamics='damp-w'
>>> ?/
>>>
>>> ATOMIC_SPECIES
>>>
>? ?Pb? 207.21???
>>> ? Pb.pbe-d-van.UPF
>>> ?Se? 78.96???? Se.pbe-van.UPF
>>>
>>> ATOMIC_POSITIONS (alat)
>>> Pb??? ?0.000000000?? 0.000000000?? 0.000000000
>>> Se??? ?0.5?????????? 0.5?????????? 0.5
>>>
>>> K_POINTS { automatic }
>>> ?8? 8? 8?? 0 0 0
>>>
>>> Im getting the following error:
>>>
>>> from set_hubbard_l : error #???????? 1
>>> ???? pseudopotential not yet inserted
>>>
>>> I was wondering if anyone could help me.
>>> Tanks in advance
>>>
>>> ?
>>> Meghdad Saeedian
>>> MSc
>? graduated from the University Of Tehran, Departemant Of Physics


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From degironc at sissa.it  Sun Jul  1 15:10:07 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sun, 01 Jul 2012 15:10:07 +0200
Subject: [Pw_forum] Fw: Re: Problem in using GGA+U for the PbSe
	Calculation
In-Reply-To: <1341128582.8159.YahooMailClassic@web140606.mail.bf1.yahoo.com>
References: <1341128582.8159.YahooMailClassic@web140606.mail.bf1.yahoo.com>
Message-ID: <4FF04C2F.4070909@sissa.it>

Dear meghdad saeedian
   the reported error appears to be in tabd.f90 ... in the lines 
starting with  an !
   however when using the tabd.f90 you sent i can compile the code with 
no error.
   it must be some special character that slipped in your file .. as the 
changes are simple you can try to reimplement them starting from a fresh 
version of tabd.f90...  or see if the attached file (which is just your 
version as received that works for me) is working now.

stefano


On 07/01/2012 09:43 AM, meghdad saeedian wrote:
>   
> Dear Emine
>   
> before all, thanks for your consideration.
> after that,
>   
>> Ok so let me understand
> that's right. you undrestand the problem precisely.
>   
>> Please send more info on the configuration of your machine
> architecture : x86_64
> Linix Version : CentOS 5.5
> Fortran Compiler : ifort version 12.1.0
> Code Version : espresso-5.0/
>   
>> you can attach them as well.
> tabd.f90 & set_hubbard_l.f90 are attached
>   
> Thanks
> MS
>
> --- On Sun, 7/1/12, Emine Kucukbenli <kucukben at sissa.it> wrote:
>
>
> From: Emine Kucukbenli <kucukben at sissa.it>
> Subject: Re: [Pw_forum] Problem in using GGA+U for the PbSe Calculation
> To: meghdad_saeedian at yahoo.com
> Date: Sunday, July 1, 2012, 4:58 AM
>
>
>
> Ok so let me understand,
> Now we are talking about another machine, where the code compiles
> successfully after the modifications to those two files, but gives the
> "pseudo potential not yet inserted" error in runtime (in PbSe case),
> even though you have supplied them in the lists we have mentioned
> before.
> I am sorry I find it a bit hard to understand why this would happen.
> Please send more info on the configuration of your machine, version of
> the code, compilers you use, so i can see if i can reproduce it. i am
> also curious about the files you have modified. you can attach them as
> well.
> ciao
> emine
>
>
> Quoting meghdad saeedian <meghdad_saeedian at yahoo.com>:
>
>> Dear Emine
>>
>> Iv changed ~/espresso-5.0/PW/src/tabd.f90 &
>> ~/espresso-5.0/flib/set_hubbard_l.f90 in the another machine  and pw
>> compiled correctly as below :
>>
>> .
>> .
>> .
>> make[2]: Entering directory `/home/user25/espresso-5.0/PW/src'
>> test -n "" && ( cd ../.. ; make -w  || exit 1) || :
>> make[2]: Leaving directory `/home/user25/espresso-5.0/PW/src'
>> if test -d tools ; then \
>>      ( cd tools ; if test "make" = "" ; then make -w pwtools; \
>>      else make -w ; fi ) ; fi ; \
>>
>> make[2]: Entering directory `/home/user25/espresso-5.0/PW/tools'
>> test -n "" && ( cd ../.. ; make -w  || exit 1) || :
>> make[2]: Leaving directory `/home/user25/espresso-5.0/PW/tools'
>> make[1]: Leaving directory
>>    `/home/user25/espresso-5.0/PW'
>> [user25 at ce espresso-5.0]$
>>
>> in this machine, GGA+U for ZnO works well.
>> But there is still the previous error for PbSe :(
>>
>> How can I trace the problem?
>>
>> Thanks
>> MS
>>
>> --- On Sat, 6/30/12, Emine Kucukbenli <kucukben at sissa.it> wrote:
>>
>> From: Emine Kucukbenli <kucukben at sissa.it>
>> Subject: Re: [Pw_forum] Fw: Re: Problem in using GGA+U for the PbSe
>> Calculation
>> To: meghdad_saeedian at yahoo.com
>> Date: Saturday, June 30, 2012, 8:57 PM
>>
>> Dear Meghdad,
>>> I didnt know that I should make it again.
>> Good, now you know :)
>>
>>> what can I do now?
>> A starting place would be, to think what the error message is trying
>> to tell you "invalid character"
>>    ?
>> then [I am guessing but not 100% that is the problem], googling "non
>> printable/control characters" for the editor you have used to edit the
>> tabd.f90 code: MS Word, etc...
>> ciao
>> emine
>>
>>
>> Quoting meghdad saeedian <meghdad_saeedian at yahoo.com>:
>>
>>> Dear Emine
>>>
>>> I didnt know that I should make it again.
>>> Anyway, Iv done the below command:
>>> $ make pw
>>> then it give the following error:
>>>
>>> make[1]: Entering directory `/home/meghdad/espresso-4.3.2/PW'
>>> test -n "" && ( cd .. ; make -w  || exit 1) || :
>>> gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW
>>> -I../include -I../iotk/src -I../Modules -I. -c set_hubbard_l.f90
>>> gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW
>>> -I../include -I../iotk/src
>>    -I../Modules -I. -c tabd.f90
>>> tabd.f90:1.1:
>>>
>>> \!
>>>   1
>>> Error: Invalid character in name at (1)
>>> make[1]: *** [tabd.o] Error 1
>>> make[1]: Leaving directory `/home/meghdad/espresso-4.3.2/PW'
>>> make: *** [pw] Error 2
>>> meghdad at meghdad-Vostro-1320:
>>>
>>> what can I do now?
>>>
>>> MS
>>>
>>>
>>>
>>>
>>> --- On Sat, 6/30/12, Emine Kucukbenli <kucukben at sissa.it> wrote:
>>>
>>> From: Emine Kucukbenli <kucukben at sissa.it>
>>> Subject: Re: [Pw_forum] Problem in using GGA+U for the PbSe Calculation
>>> To: meghdad_saeedian at yahoo.com
>>> Date: Saturday, June 30, 2012, 7:11
>>    PM
>>>
>>>
>>> Hi Meghdad,
>>> seems you have done the necessary modifications to the code,
>>> silly question but have you complied to code again (make pw?)
>>> ciao
>>> emine
>>>
>>> Quoting meghdad saeedian <meghdad_saeedian at yahoo.com>:
>>>
>>>> Dear all
>>>>
>>>> I want to use GGA+U to calculation of the energy gap of PbSe.
>>>> So I put the value of the angular momentum in the
>>>> PW/set_hubbard_l.f90  as below:
>>>>
>>>>       ! ... other elements
>>>>       !
>>>>       CASE( 'H' )
>>>>          !
>>>>          hubbard_l =  0
>>>>
>>           
>>>>    !
>>>>       CASE( 'Pb' )
>>>>          !
>>>>          hubbard_l =  2
>>>>          !
>>>>       CASE( 'Se' )
>>>>          !
>>>>          hubbard_l =
>>>>    1
>>>>          !
>>>> And the occupation number in the PW/tabd.f90 modified as below :
>>>>
>>>>      !
>>>>       CASE( 'Pb'  )
>>>>          hubbard_occ = 10.d0
>>>>       !
>>>>       CASE( 'O', 'Se'  )
>>>>
>>            hubbard_occ = 4.d0
>>>>       !
>>>>       CASE( 'H'  )
>>>>          hubbard_occ = 1.d0
>>>>       !
>>>>
>>>>
>>>> Then the input file of PbSe is constructed as below:
>>>>   
>>>> &control
>>>>      calculation='vc-relax'
>>>>      prefix='PbSe',
>>>>      pseudo_dir ='/home/meghdad/espresso-4.3.2/pseudo/',
>>>>      outdir='/home/meghdad/tmp/',
>>>>      tstress = .true.
>>>>      tprnfor =
>>>>    .true.
>>>>      nstep=5000,
>>>>
>>>>   /
>>>>   &system
>>>>      ibrav= 1,  celldm(1) =11.716301129,
>>>>     
>>    nat=  2, ntyp= 2, nbnd=11,
>>>>      ecutwfc =40,
>>>>      lda_plus_u = .true.,
>>>>      Hubbard_U(2) = 0.5,(this value is just for the run)
>>>>      Hubbard_U(1) = 0.6,(this value is just for the run)
>>>>
>>>>    /
>>>>   &electrons
>>>>      conv_thr =  1.0d-8
>>>>      mixing_beta= 0.5
>>>>      mixing_mode='plain'
>>>>      diagonalization='cg'
>>>>   /
>>>>   &IONS
>>>>      ion_dynamics='damp',
>>>>      pot_extrapolation='second_order'
>>>>      wfc_extrapolation='second_order'
>>>>   /
>>>>   &CELL
>>>>      cell_dynamics='damp-w'
>>>>   /
>>>>
>>>> ATOMIC_SPECIES
>>>>
>>     Pb  207.21
>>>>    Pb.pbe-d-van.UPF
>>>>   Se  78.96     Se.pbe-van.UPF
>>>>
>>>> ATOMIC_POSITIONS (alat)
>>>> Pb     0.000000000   0.000000000   0.000000000
>>>> Se     0.5           0.5           0.5
>>>>
>>>> K_POINTS { automatic }
>>>>   8  8  8   0 0 0
>>>>
>>>> Im getting the following error:
>>>>
>>>> from set_hubbard_l : error #         1
>>>>       pseudopotential not yet inserted
>>>>
>>>> I was wondering if anyone could help me.
>>>> Tanks in advance
>>>>
>>>>   
>>>> Meghdad Saeedian
>>>> MSc
>>    graduated from the University Of Tehran, Departemant Of Physics
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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From zafartariq2003 at yahoo.com  Sun Jul  1 16:33:57 2012
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Sun, 1 Jul 2012 07:33:57 -0700 (PDT)
Subject: [Pw_forum] Problem in using GGA+U for the PbSe Calculation
In-Reply-To: <mailman.3636.1341148210.9401.pw_forum@pwscf.org>
Message-ID: <1341153237.63783.YahooMailClassic@web121406.mail.ne1.yahoo.com>





	
	
	
	
	
	

Dear meghdad saeedian
I face the
same problem during last two days but I resolve it. your settings in
set_hubbard.f90 and tabed.f90 are right. Just comile it and replace
it with your older pw.x file and check the bath for bin directory.
I
try it for fedora 8 having compiler gfortran 4.1.2. But i hope that
it will works for higher version of gfortran and fedora.? 
Best
of LUCK

Muhammad Zafar

PhD Scholar

Department of Physics

The Islamia University of Bahawalpur,Pakistan

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From swetarekharam at gmail.com  Sun Jul  1 16:34:41 2012
From: swetarekharam at gmail.com (Swetarekha Ram)
Date: Sun, 1 Jul 2012 20:04:41 +0530
Subject: [Pw_forum] reg: phonon
Message-ID: <CAFsnUVZ6ZMmyC3wGQiyRMYAjh5PwTm0AR0NXNO92xdNSUOEp4w@mail.gmail.com>

Dear users,

   I am new to pwscf. I want to do the phonon-disperssion with
spin-orbit coupling.
But my doubt is ,
1. Is it compulsory that we have to choose the pseudo potential at
least for one atom of our system with spin-orbit.
If it so, then what we have to do if the corresponding pseudo
potential is not available,or we can use the UPF for all the atom.

2. For the phonon calculation, the filedyn file is writing in the xml
format if spin-orbit coupling is included, then how we will use this
for the asr calculation.

3. ASR calculation is applicable only for the Gamma point, or can we
use the asr calculation at the X or for other specific point in the
brillouin zone.


-- 
Swetarekha Ram,
Research Scholar,
Dept. of Physics,
IIT Hyderabad.

From sirok4 at gmail.com  Sun Jul  1 17:23:55 2012
From: sirok4 at gmail.com (David Furman)
Date: Sun, 1 Jul 2012 18:23:55 +0300
Subject: [Pw_forum] Total energy too low
Message-ID: <007f01cd579d$894561c0$9bd02540$@com>

Dear users,

 

I am new to Quantum Espresso and still in the stages of learning. I
calculated the total energy (SCF) of Europium oxide (cubic) at the
experimental

lattice length and at additional shorter lengths to get the equation of
state of the material.

 

The energies after each calculation are in the range of -1775 - (-1774) Ry,
which I believe is out of range and indicate probably something is wrong.

I have checked the unit cell appearance with xcrysden and it looks fine.

 

I've never met a system with energy low as on the order of minus a few
thousand Rydbergs. (I would expect something between 1-50 Rydbergs)

 

Has anybody encountered such a problem ? Anyone has a clue ? I'd be happy to
get some help .

 

Thanks

 

 

David Furman, Graduate Student | Fritz Haber Research Center for 

Molecular Dynamics, The Hebrew University of Jerusalem | +972-8656-8909

 

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From kucukben at sissa.it  Sun Jul  1 17:43:53 2012
From: kucukben at sissa.it (Emine Kucukbenli)
Date: Sun, 01 Jul 2012 17:43:53 +0200
Subject: [Pw_forum] Problem in using GGA+U for the PbSe Calculation
In-Reply-To: <1341153237.63783.YahooMailClassic@web121406.mail.ne1.yahoo.com>
References: <1341153237.63783.YahooMailClassic@web121406.mail.ne1.yahoo.com>
Message-ID: <20120701174353.Horde.bj_gUh8V4mxP8HA5dSanWSA@webmail.sissa.it>

Hi all,
just to update the thread,
I have checked Meghdad's pseudopotentials and one of them (Pb) was  
manually edited to have a different element name (P), probably "b" got  
deleted at some point by accident, P was not in the Hubbard U lists,  
so the code would still complain that "pseudo is not inserted yet"  
(and a good thing that it actually did otherwise it would be a garbage  
in garbage out situation.)
So the code is working, all is ok :)
ciao
emine


From degironc at sissa.it  Sun Jul  1 19:04:53 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sun, 01 Jul 2012 19:04:53 +0200
Subject: [Pw_forum] Total energy too low
In-Reply-To: <007f01cd579d$894561c0$9bd02540$@com>
References: <007f01cd579d$894561c0$9bd02540$@com>
Message-ID: <4FF08335.3020304@sissa.it>

if it is a cell with just a few atoms it's strange
how much is the energy of the isolated pseudo-atom when running ld1 ?

if something is wrong une possibility is that the pseudo has a ghost...
where does the Eu pseudo comes from ? have you tried to make a test for 
ghost using ld1 ?

stefano



On 07/01/2012 05:23 PM, David Furman wrote:
> Dear users,
>
>   
>
> I am new to Quantum Espresso and still in the stages of learning. I
> calculated the total energy (SCF) of Europium oxide (cubic) at the
> experimental
>
> lattice length and at additional shorter lengths to get the equation of
> state of the material.
>
>   
>
> The energies after each calculation are in the range of -1775 - (-1774) Ry,
> which I believe is out of range and indicate probably something is wrong.
>
> I have checked the unit cell appearance with xcrysden and it looks fine.
>
>   
>
> I've never met a system with energy low as on the order of minus a few
> thousand Rydbergs. (I would expect something between 1-50 Rydbergs)
>
>   
>
> Has anybody encountered such a problem ? Anyone has a clue ? I'd be happy to
> get some help .
>
>   
>
> Thanks
>
>   
>
>   
>
> David Furman, Graduate Student | Fritz Haber Research Center for
>
> Molecular Dynamics, The Hebrew University of Jerusalem | +972-8656-8909
>
>   
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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From gkucukdalyan at gmail.com  Sun Jul  1 19:08:20 2012
From: gkucukdalyan at gmail.com (Gulcin Tetiker)
Date: Sun, 1 Jul 2012 13:08:20 -0400
Subject: [Pw_forum] Charge density as a percentage
Message-ID: <4B15409B-5425-4293-9962-91562C9700A4@gmail.com>

Hi All, 

I was just wondering if it is possible to calculate the charge percentage of li- graphene system. What i mean is that being able to calculate the charge percentage of lithium and graphene separately in the whole lithium-graphene system. 

Regards,

Gulcin

From meghdad_saeedian at yahoo.com  Sun Jul  1 21:12:26 2012
From: meghdad_saeedian at yahoo.com (meghdad saeedian)
Date: Sun, 1 Jul 2012 12:12:26 -0700 (PDT)
Subject: [Pw_forum] Fw: Re: Problem in using GGA+U for the PbSe
	Calculation
In-Reply-To: <4FF04C2F.4070909@sissa.it>
Message-ID: <1341169946.95349.YahooMailClassic@web140603.mail.bf1.yahoo.com>

Dear all 
?
Emine solved my problem and it was the mistaken edit in the?pseudopotential of Pb which?Emine explained in the previous post.??
I sincerely thanks?Emine.?
?
MS

--- On Sun, 7/1/12, Stefano de Gironcoli <degironc at sissa.it> wrote:


From: Stefano de Gironcoli <degironc at sissa.it>
Subject: Re: [Pw_forum] Fw: Re: Problem in using GGA+U for the PbSe Calculation
To: pw_forum at pwscf.org
Date: Sunday, July 1, 2012, 5:40 PM




Dear meghdad saeedian
? the reported error appears to be in tabd.f90 ... in the lines starting with? an !
? however when using the tabd.f90 you sent i can compile the code with no error.
? it must be some special character that slipped in your file .. as the changes are simple you can try to reimplement them starting from a fresh version of tabd.f90...? or see if the attached file (which is just your version as received that works for me) is working now.
?
stefano


On 07/01/2012 09:43 AM, meghdad saeedian wrote:

?
Dear Emine
?
before all, thanks for your consideration.
after that, 
?

Ok so let me understand
that's right. you undrestand the problem precisely.?
?

Please send more info on the configuration of your machine
architecture : x86_64
Linix Version : CentOS 5.5
Fortran Compiler : ifort version 12.1.0
Code?Version : espresso-5.0/
?

you can attach them as well.
tabd.f90 & set_hubbard_l.f90 are attached
?
Thanks?
MS?

--- On Sun, 7/1/12, Emine Kucukbenli <kucukben at sissa.it> wrote:


From: Emine Kucukbenli <kucukben at sissa.it>
Subject: Re: [Pw_forum] Problem in using GGA+U for the PbSe Calculation
To: meghdad_saeedian at yahoo.com
Date: Sunday, July 1, 2012, 4:58 AM



Ok so let me understand,
Now we are talking about another machine, where the code compiles
successfully after the modifications to those two files, but gives the
"pseudo potential not yet inserted" error in runtime (in PbSe case),
even though you have supplied them in the lists we have mentioned
before.
I am sorry I find it a bit hard to understand why this would happen.
Please send more info on the configuration of your machine, version of
the code, compilers you use, so i can see if i can reproduce it. i am
also curious about the files you have modified. you can attach them as
well.
ciao
emine


Quoting meghdad saeedian <meghdad_saeedian at yahoo.com>:


Dear Emine

Iv changed ~/espresso-5.0/PW/src/tabd.f90 &
~/espresso-5.0/flib/set_hubbard_l.f90 in the another machine? and pw
compiled correctly as below :

.
.
.
make[2]: Entering directory `/home/user25/espresso-5.0/PW/src'
test -n "" && ( cd ../.. ; make -w? || exit 1) || :
make[2]: Leaving directory `/home/user25/espresso-5.0/PW/src'
if test -d tools ; then \
??? ( cd tools ; if test "make" = "" ; then make -w pwtools; \
??? else make -w ; fi ) ; fi ; \

make[2]: Entering directory `/home/user25/espresso-5.0/PW/tools'
test -n "" && ( cd ../.. ; make -w? || exit 1) || :
make[2]: Leaving directory `/home/user25/espresso-5.0/PW/tools'
make[1]: Leaving directory
? `/home/user25/espresso-5.0/PW'
[user25 at ce espresso-5.0]$

in this machine, GGA+U for ZnO works well.
But there is still the previous error for PbSe :(

How can I trace the problem?

Thanks
MS

--- On Sat, 6/30/12, Emine Kucukbenli <kucukben at sissa.it> wrote:

From: Emine Kucukbenli <kucukben at sissa.it>
Subject: Re: [Pw_forum] Fw: Re: Problem in using GGA+U for the PbSe
Calculation
To: meghdad_saeedian at yahoo.com
Date: Saturday, June 30, 2012, 8:57 PM

Dear Meghdad,

I didnt know that I should make it again.
Good, now you know :)


what can I do now?
A starting place would be, to think what the error message is trying
to tell you "invalid character"
? ?
then [I am guessing but not 100% that is the problem], googling "non
printable/control characters" for the editor you have used to edit the
tabd.f90 code: MS Word, etc...
ciao
emine


Quoting meghdad saeedian <meghdad_saeedian at yahoo.com>:


Dear Emine

I didnt know that I should make it again.
Anyway, Iv done the below command:
$ make pw
then it give the following error:

make[1]: Entering directory `/home/meghdad/espresso-4.3.2/PW'
test -n "" && ( cd .. ; make -w? || exit 1) || :
gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW
-I../include -I../iotk/src -I../Modules -I. -c set_hubbard_l.f90
gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW
-I../include -I../iotk/src
? -I../Modules -I. -c tabd.f90

tabd.f90:1.1:

\!
?1
Error: Invalid character in name at (1)
make[1]: *** [tabd.o] Error 1
make[1]: Leaving directory `/home/meghdad/espresso-4.3.2/PW'
make: *** [pw] Error 2
meghdad at meghdad-Vostro-1320:

what can I do now?

MS




--- On Sat, 6/30/12, Emine Kucukbenli <kucukben at sissa.it> wrote:

From: Emine Kucukbenli <kucukben at sissa.it>
Subject: Re: [Pw_forum] Problem in using GGA+U for the PbSe Calculation
To: meghdad_saeedian at yahoo.com
Date: Saturday, June 30, 2012, 7:11
? PM



Hi Meghdad,
seems you have done the necessary modifications to the code,
silly question but have you complied to code again (make pw?)
ciao
emine

Quoting meghdad saeedian <meghdad_saeedian at yahoo.com>:


Dear all

I want to use GGA+U to calculation of the energy gap of PbSe.
So I put the value of the angular momentum in the
PW/set_hubbard_l.f90? as below:

???? ! ... other elements
???? !
???? CASE( 'H' )
??????? !
??????? hubbard_l =? 0

? ???????


? !
???? CASE( 'Pb' )
??????? !
??????? hubbard_l =? 2
??????? !
???? CASE( 'Se' )
??????? !
??????? hubbard_l =?
? 1
??????? !
And the occupation number in the PW/tabd.f90 modified as below :

??? !
???? CASE( 'Pb'? )
??????? hubbard_occ = 10.d0
???? !
???? CASE( 'O', 'Se'? )

? ??????? hubbard_occ = 4.d0


???? !
???? CASE( 'H'? )
??????? hubbard_occ = 1.d0
???? !


Then the input file of PbSe is constructed as below:
?
&control
??? calculation='vc-relax'
??? prefix='PbSe',
??? pseudo_dir ='/home/meghdad/espresso-4.3.2/pseudo/',
??? outdir='/home/meghdad/tmp/',
??? tstress = .true.
??? tprnfor =
? .true.
??? nstep=5000,

?/
?&system
??? ibrav= 1,? celldm(1) =11.716301129,
???
? nat=? 2, ntyp= 2, nbnd=11,


??? ecutwfc =40,
??? lda_plus_u = .true.,
??? Hubbard_U(2) = 0.5,(this value is just for the run)
??? Hubbard_U(1) = 0.6,(this value is just for the run)

? /
?&electrons
??? conv_thr =? 1.0d-8
??? mixing_beta= 0.5
??? mixing_mode='plain'
??? diagonalization='cg'
?/
?&IONS
??? ion_dynamics='damp',
??? pot_extrapolation='second_order'
??? wfc_extrapolation='second_order'
?/
?&CELL
??? cell_dynamics='damp-w'
?/

ATOMIC_SPECIES

? ?Pb? 207.21???


? Pb.pbe-d-van.UPF
?Se? 78.96???? Se.pbe-van.UPF

ATOMIC_POSITIONS (alat)
Pb??? ?0.000000000?? 0.000000000?? 0.000000000
Se??? ?0.5?????????? 0.5?????????? 0.5

K_POINTS { automatic }
?8? 8? 8?? 0 0 0

Im getting the following error:

from set_hubbard_l : error #???????? 1
???? pseudopotential not yet inserted

I was wondering if anyone could help me.
Tanks in advance

?
Meghdad Saeedian
MSc
? graduated from the University Of Tehran, Departemant Of Physics




 
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum



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From degironc at sissa.it  Mon Jul  2 00:05:52 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 02 Jul 2012 00:05:52 +0200
Subject: [Pw_forum] Charge density as a percentage
In-Reply-To: <4B15409B-5425-4293-9962-91562C9700A4@gmail.com>
References: <4B15409B-5425-4293-9962-91562C9700A4@gmail.com>
Message-ID: <4FF0C9C0.3070907@sissa.it>

a post-processing tool that can be used for that purpose is the 
projwfc.x code (check for it in the PP subdirectory) which calculates 
the  density of state projected on the atomic orbitals.
consider however that any decomposition of density in atomic 
contributions is somehow arbitrary and
you should not believe too much in the precise numbers you obtain

stefano

On 07/01/2012 07:08 PM, Gulcin Tetiker wrote:
> Hi All,
>
> I was just wondering if it is possible to calculate the charge percentage of li- graphene system. What i mean is that being able to calculate the charge percentage of lithium and graphene separately in the whole lithium-graphene system.
>
> Regards,
>
> Gulcin
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



From 809997648 at qq.com  Mon Jul  2 13:24:21 2012
From: 809997648 at qq.com (=?gb18030?B?wdm358WqtdE=?=)
Date: Mon, 2 Jul 2012 19:24:21 +0800
Subject: [Pw_forum] Problem in  Bands of Graphene Nanoribbon
Message-ID: <tencent_5066B31E4BCBE587044537F8@qq.com>

Hi! All
 I'm trying to calculate the quantum conductance of quasi one dimension structure with Wannier90 and PWscf. 
 But the one dimension band structure of suppercell is weird: bands with high energy seem very "crowded".
 I meet this problem when calculating Al nanowire and graphene nanoribbon. It seems a computation error as
 energy seems to be limitted in a small range.
 I have raised the value of cutoff and distance between nanoribbons in directions perpendicular to transport,
 but results changed little.
 My friend plots the bands of graphene nanoribbon with fplo, which can be a reference I think.
  
 The input files and bands are in attachment.
  
 Thank you very much!
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From ytaghipour at aeoi.org.ir  Mon Jul  2 13:26:45 2012
From: ytaghipour at aeoi.org.ir (Yavar Taghipour Azar)
Date: Mon, 02 Jul 2012 15:56:45 +0430
Subject: [Pw_forum] augmentation charge importance in calculation of local
	dos
Message-ID: <WC20120702112645.6603FE@aeoi.org.ir>


 
Dear QE users

I want to divide my case to some boxes and analyze local dos for them; 
especially, I want to investigate contribution of different parts of cell 
near the band edges. 
I have used Ultra-soft Pseudopotentials in my calculations. By considering 
that augmentation charge contribution is not included in local dos 
calculations, is that led to losing some information about electronic 
structure? 
 
Thanks in advance.
 
 
-------------------------------------------
Yavar Taghipour
PhD Student
Physics Group, AEOI
Tehran-Iran
 
Email: ytaghipour at aeoi.org.ir
Phone: +98 (0) 21 82064556
-----------------------------------------------------------
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From nicola.marzari at epfl.ch  Mon Jul  2 13:58:13 2012
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Mon, 02 Jul 2012 13:58:13 +0200
Subject: [Pw_forum] Problem in  Bands of Graphene Nanoribbon
In-Reply-To: <tencent_5066B31E4BCBE587044537F8@qq.com>
References: <tencent_5066B31E4BCBE587044537F8@qq.com>
Message-ID: <4FF18CD5.1030207@epfl.ch>


Hi,

it's probably the opposite - what you are seeing are free-electron like
states, that are capture very well by plane waves and pwscf, but would 
not be described by localized orbitals method (and hence also challenges
to describe those in mlwfs).

			nicola



On 02/07/2012 13:24, ???? wrote:
> Hi! All
> I'm trying to calculate the quantum conductance of quasi one dimension
> structure with Wannier90 and PWscf.
> But the one dimension band structure of suppercell is weird: bands with
> high energy seem very "crowded".
> I meet this problem when calculating Al nanowire and graphene
> nanoribbon. It seems a computation error as
> energy seems to be limitted in a small range.
> I have raised the value of cutoff and distance between nanoribbons in
> directions perpendicular to transport,
> but results changed little.
> My friend plots the bands of graphene nanoribbon with fplo, which can be
> a reference I think.
> The input files and bands are in attachment.
> Thank you very much!
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


-- 

----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL



From ytaghipour at aeoi.org.ir  Mon Jul  2 14:26:39 2012
From: ytaghipour at aeoi.org.ir (Yavar Taghipour Azar)
Date: Mon, 02 Jul 2012 16:56:39 +0430
Subject: [Pw_forum] (no subject)
Message-ID: <WC20120702122639.540401@aeoi.org.ir>


 
Dear QE users

I want to divide my case to some boxes and analyze local dos for them; 
especially, I want to investigate contribution of different parts of cell 
near the band edges. 
I have used Ultra-soft Pseudopotentials in my calculations. By considering 
that augmentation charge contribution is not included in local dos 
calculations, is that led to losing some information about electronic 
structure? 
 
Thanks in advance.
 
 
-------------------------------------------
Yavar Taghipour Azar
PhD Student
Physics Group, AEOI
Tehran-Iran
 
Email: ytaghipour at aeoi.org.ir
Phone: +98 (0) 21 82064556
-----------------------------------------------------------
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From fratesi at mater.unimib.it  Mon Jul  2 14:39:11 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Mon, 02 Jul 2012 14:39:11 +0200
Subject: [Pw_forum] (no subject)
In-Reply-To: <WC20120702122639.540401@aeoi.org.ir>
References: <WC20120702122639.540401@aeoi.org.ir>
Message-ID: <4FF1966F.6050609@mater.unimib.it>

Dear Yavar,

you are going to miss the contribution of the augmentation charge to the 
|psi|^2. That is not important if you are interested in spacial regions 
far from any atom (small or zero overlap with the augmentation spheres); 
that might instead be important if you want a quantitative analysis in 
the atomic region. For the latter, however, the analysis of the 
atom-projected DOS could be much more useful (or you could implement 
augmentation charge contributions).

PS please write to the list only, not to personal addresses.

Guido


On 07/02/2012 02:26 PM, Yavar Taghipour Azar wrote:
>
> Dear QE users
>
> I want to divide my case to some boxes and analyze local dos for them;
> especially, I want to investigate contribution of different parts of cell
> near the band edges.
> I have used Ultra-soft Pseudopotentials in my calculations. By considering
> that augmentation charge contribution is not included in local dos
> calculations, is that led to losing some information about electronic
> structure?
>
> Thanks in advance.
>
>
> -------------------------------------------
> Yavar Taghipour Azar
> PhD Student
> Physics Group, AEOI
> Tehran-Iran
>
> Email: ytaghipour at aeoi.org.ir
> <javascript:top.openWin('/WorldClient.dll?Session=QQUMKJC&View=Compose&New=Yes&To=ytaghipour%40aeoi.org.ir','Compose',800,600,'yes');>
> Phone: +98 (0) 21 82064556
> -----------------------------------------------------------
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy

From ytaghipour at aeoi.org.ir  Mon Jul  2 14:46:49 2012
From: ytaghipour at aeoi.org.ir (Yavar Taghipour Azar)
Date: Mon, 02 Jul 2012 17:16:49 +0430
Subject: [Pw_forum] [***SPAM*** Score/Req: 10.00/5.0] Re:  (no subject)
In-Reply-To: <4FF1966F.6050609@mater.unimib.it>
References: <WC20120702122639.540401@aeoi.org.ir>
	<4FF1966F.6050609@mater.unimib.it>
Message-ID: <WC20120702124649.990402@aeoi.org.ir>

Dear Guido,

thanks for your consideration and good comments
 


-----Original Message-----
From: Guido Fratesi <fratesi at mater.unimib.it>
To: pw_forum at pwscf.org
Date: Mon, 02 Jul 2012 14:39:11 +0200
Subject: [***SPAM*** Score/Req: 10.00/5.0] Re: [Pw_forum] (no subject)


Dear Yavar,

you are going to miss the contribution of the augmentation charge to the 
|psi|^2. That is not important if you are interested in spacial regions 
far from any atom (small or zero overlap with the augmentation spheres); 
that might instead be important if you want a quantitative analysis in 
the atomic region. For the latter, however, the analysis of the 
atom-projected DOS could be much more useful (or you could implement 
augmentation charge contributions).

PS please write to the list only, not to personal addresses.

Guido


On 07/02/2012 02:26 PM, Yavar Taghipour Azar wrote:
>
> Dear QE users
>
> I want to divide my case to some boxes and analyze local dos for them;
> especially, I want to investigate contribution of different parts of cell
> near the band edges.
> I have used Ultra-soft Pseudopotentials in my calculations. By considering
> that augmentation charge contribution is not included in local dos
> calculations, is that led to losing some information about electronic
> structure?
>
> Thanks in advance.
>
>
> -------------------------------------------
> Yavar Taghipour Azar
> PhD Student
> Physics Group, AEOI
> Tehran-Iran
>
> Email: ytaghipour at aeoi.org.ir
> 
<javascript:top.openWin('/WorldClient.dll?Session=QQUMKJC&View=Compose&New=Yes&To=ytaghipour%40aeoi.org.ir','Compose',800,600,'yes');>
> Phone: +98 (0) 21 82064556
> -----------------------------------------------------------
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From giovanni.cantele at spin.cnr.it  Mon Jul  2 14:52:17 2012
From: giovanni.cantele at spin.cnr.it (Giovanni Cantele)
Date: Mon, 2 Jul 2012 14:52:17 +0200
Subject: [Pw_forum] Problem in  Bands of Graphene Nanoribbon
In-Reply-To: <tencent_5066B31E4BCBE587044537F8@qq.com>
References: <tencent_5066B31E4BCBE587044537F8@qq.com>
Message-ID: <563D381C-A731-4B58-916C-17C673FC3E7C@spin.cnr.it>


On Jul 2, 2012, at 1:24 PM, ???????? wrote:

> Hi! All
> I'm trying to calculate the quantum conductance of quasi one dimension structure with Wannier90 and PWscf.
> But the one dimension band structure of suppercell is weird: bands with high energy seem very "crowded".
> I meet this problem when calculating Al nanowire and graphene nanoribbon. It seems a computation error as
> energy seems to be limitted in a small range.
> I have raised the value of cutoff and distance between nanoribbons in directions perpendicular to transport,
> but results changed little.
> My friend plots the bands of graphene nanoribbon with fplo, which can be a reference I think.
>  
> The input files and bands are in attachment.
>  
> Thank you very much!
> <nscf.in><scf.in><bands.jpg><bands_fplo.jpg>_______________________________________________

It seems that your band structure is correct. If you want to look at higher energy bands, due to the presence of 
these "free-electron-like" states, you must increase nbnd.

The Wannier90 procedure might be useful to single out bands with a specific atomic character
(e.g. those deriving from the pz orbitals of C atoms). See, as an example, Fig. 2 of Nano Lett., 2009, 9 (10), pp 3425?C3429.
Giovanni




--

**** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it

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From 1009ukumar at gmail.com  Mon Jul  2 15:12:36 2012
From: 1009ukumar at gmail.com (Sonu Kumar)
Date: Mon, 2 Jul 2012 18:42:36 +0530
Subject: [Pw_forum] [***SPAM*** Score/Req: 10.00/5.0] Re: (no subject)
In-Reply-To: <WC20120702124649.990402@aeoi.org.ir>
References: <WC20120702122639.540401@aeoi.org.ir>
	<4FF1966F.6050609@mater.unimib.it>
	<WC20120702124649.990402@aeoi.org.ir>
Message-ID: <CAHePdfCUxccNRSV-3W1AtKroZ_Eq-6Jw+i=5d_GV9dFesW9Xeg@mail.gmail.com>

Dear all QE users and Prof. Guido Fratesi,

I have a doubt...
Electron localization function calculations does not make
much sense when using ultra-soft pseudopotentials.

Is it true? although USPP takes into account the charge removal due
to smoothness of pseudo states  by adding augmentation charges.

regards,
sonu

==========================================
Sonu Kumar
Phd Student,Physics Department
Indian Institute of Technology ,Delhi-110016, India
web:-http://www.iitd.ac.in/
==========================================



On Mon, Jul 2, 2012 at 6:16 PM, Yavar Taghipour Azar <ytaghipour at aeoi.org.ir
> wrote:

>  Dear Guido,
>
> thanks for your consideration and good comments
>
>
>
>
> -----Original Message-----
> From: Guido Fratesi <fratesi at mater.unimib.it>
> To: pw_forum at pwscf.org
> Date: Mon, 02 Jul 2012 14:39:11 +0200
> Subject: [***SPAM*** Score/Req: 10.00/5.0] Re: [Pw_forum] (no subject)
>
> Dear Yavar,
>
> you are going to miss the contribution of the augmentation charge to the
> |psi|^2. That is not important if you are interested in spacial regions
> far from any atom (small or zero overlap with the augmentation spheres);
> that might instead be important if you want a quantitative analysis in
> the atomic region. For the latter, however, the analysis of the
> atom-projected DOS could be much more useful (or you could implement
> augmentation charge contributions).
>
> PS please write to the list only, not to personal addresses.
>
> Guido
>
>
> On 07/02/2012 02:26 PM, Yavar Taghipour Azar wrote:
> >
> > Dear QE users
> >
> > I want to divide my case to some boxes and analyze local dos for them;
> > especially, I want to investigate contribution of different parts of cell
> > near the band edges.
> > I have used Ultra-soft Pseudopotentials in my calculations. By
> considering
> > that augmentation charge contribution is not included in local dos
> > calculations, is that led to losing some information about electronic
> > structure?
> >
> > Thanks in advance.
> >
> >
> > -------------------------------------------
> > Yavar Taghipour Azar
> > PhD Student
> > Physics Group, AEOI
> > Tehran-Iran
> >
> > Email: ytaghipour at aeoi.org.ir
> >
> <javascript:top.openWin('/WorldClient.dll?Session=QQUMKJC&View=Compose&New=Yes&To=ytaghipour%
> 40aeoi.org.ir','Compose',800,600,'yes');>
> > Phone: +98 (0) 21 82064556
> > -----------------------------------------------------------
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> --
> Guido Fratesi
>
> Dipartimento di Scienza dei Materiali
> Universita` degli Studi di Milano-Bicocca
> via Cozzi 53, 20125 Milano, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
>  http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From swetarekharam at gmail.com  Mon Jul  2 15:19:44 2012
From: swetarekharam at gmail.com (Swetarekha Ram)
Date: Mon, 2 Jul 2012 18:49:44 +0530
Subject: [Pw_forum] phonon
Message-ID: <CAFsnUVYOLi8fgARx1fnw_iy9HBEy0gPRsp4=m1t3ZgOtz+MMRQ@mail.gmail.com>

Dear users,

   I wrote this same previously, but I did not get any reply.
This time I am expecting some suggestion.

 I want to do the phonon-dispersion with
spin-orbit coupling.
But my doubt is ,
1. Is it compulsory that we have to choose the pseudo potential at
least for one atom of our system with spin-orbit.
If it so, then what we have to do if the corresponding pseudo
potential is not available,or we can use the UPF for all the atom.

2. For the phonon calculation, the filedyn file is writing in the xml
format if spin-orbit coupling is included, then how we will use this
for the asr calculation.

3. ASR calculation is applicable only for the Gamma point, or can we
use the asr calculation at the X or for other specific point in the
brillouin zone.

-- 
Swetarekha Ram,
Research Scholar,
Dept. of Physics,
IIT Hyderabad.

From martin.gmitra at gmail.com  Mon Jul  2 15:34:34 2012
From: martin.gmitra at gmail.com (Martin Gmitra)
Date: Mon, 2 Jul 2012 15:34:34 +0200
Subject: [Pw_forum] Problem in Bands of Graphene Nanoribbon
In-Reply-To: <563D381C-A731-4B58-916C-17C673FC3E7C@spin.cnr.it>
References: <tencent_5066B31E4BCBE587044537F8@qq.com>
	<563D381C-A731-4B58-916C-17C673FC3E7C@spin.cnr.it>
Message-ID: <CAG-DMb2K7VpRaACy8tqf3vRJLNLuDEzDBwDgN-YN8pHXQLwE5g@mail.gmail.com>

Hi!
Such "crowded" bands one sees also for film calculations. Comparing
to 2D codes (e.g. FLEUR) I have seen that increasing vacuum clears
the "crowded" high energy states.

Martin Gmitra

Spintronics group
Uni Regensburg, Germany


On Mon, Jul 2, 2012 at 2:52 PM, Giovanni Cantele
<giovanni.cantele at spin.cnr.it> wrote:
>
> On Jul 2, 2012, at 1:24 PM, ???? wrote:
>
> Hi! All
> I'm trying to calculate the quantum conductance of quasi one dimension
> structure with Wannier90 and PWscf.
> But the one dimension band structure of suppercell is weird: bands with high
> energy seem very "crowded".
> I meet this problem when calculating Al nanowire and graphene nanoribbon. It
> seems a computation error as
> energy seems to be limitted in a small range.
> I have raised the value of cutoff and distance between nanoribbons in
> directions perpendicular to transport,
> but results changed little.
> My friend plots the bands of graphene nanoribbon with fplo, which can be a
> reference I think.
>
> The input files and bands are in attachment.
>
> Thank you very much!
> <nscf.in><scf.in><bands.jpg><bands_fplo.jpg>_______________________________________________
>
>
> It seems that your band structure is correct. If you want to look at higher
> energy bands, due to the presence of
> these "free-electron-like" states, you must increase nbnd.
>
> The Wannier90 procedure might be useful to single out bands with a specific
> atomic character
> (e.g. those deriving from the pz orbitals of C atoms). See, as an example,
> Fig. 2 of Nano Lett., 2009, 9 (10), pp 3425?3429.
> Giovanni
>
>
>
>
> --
>
> **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Scienze Fisiche
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>                      http://www.nanomat.unina.it
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From fratesi at mater.unimib.it  Mon Jul  2 16:56:10 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Mon, 02 Jul 2012 16:56:10 +0200
Subject: [Pw_forum] [***SPAM*** Score/Req: 10.00/5.0] Re: (no subject)
In-Reply-To: <CAHePdfCUxccNRSV-3W1AtKroZ_Eq-6Jw+i=5d_GV9dFesW9Xeg@mail.gmail.com>
References: <WC20120702122639.540401@aeoi.org.ir>
	<4FF1966F.6050609@mater.unimib.it>
	<WC20120702124649.990402@aeoi.org.ir>
	<CAHePdfCUxccNRSV-3W1AtKroZ_Eq-6Jw+i=5d_GV9dFesW9Xeg@mail.gmail.com>
Message-ID: <4FF1B68A.9090308@mater.unimib.it>

Dear Sonu,
the thread was about the local density of states, not the ELF.
Guido

On 07/02/2012 03:12 PM, Sonu Kumar wrote:
> Dear all QE users and Prof. Guido Fratesi,
>
> I have a doubt...
> Electron localization function calculations does not make
> much sense when using ultra-soft pseudopotentials.
>
> Is it true? although USPP takes into account the charge removal due
> to smoothness of pseudo states  by adding augmentation charges.
>
> regards,
> sonu
>
> ==========================================
> Sonu Kumar
> Phd Student,Physics Department
> Indian Institute of Technology ,Delhi-110016, India
> web:-http://www.iitd.ac.in/
> ==========================================
>
>
>
> On Mon, Jul 2, 2012 at 6:16 PM, Yavar Taghipour Azar
> <ytaghipour at aeoi.org.ir <mailto:ytaghipour at aeoi.org.ir>> wrote:
>
>     Dear Guido,
>     thanks for your consideration and good comments
>
>         -----Original Message-----
>         From: Guido Fratesi <fratesi at mater.unimib.it
>         <mailto:fratesi at mater.unimib.it>>
>         To: pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>
>         Date: Mon, 02 Jul 2012 14:39:11 +0200
>         Subject: [***SPAM*** Score/Req: 10.00/5.0] Re: [Pw_forum] (no
>         subject)
>
>         Dear Yavar,
>
>         you are going to miss the contribution of the augmentation
>         charge to the
>         |psi|^2. That is not important if you are interested in spacial
>         regions
>         far from any atom (small or zero overlap with the augmentation
>         spheres);
>         that might instead be important if you want a quantitative
>         analysis in
>         the atomic region. For the latter, however, the analysis of the
>         atom-projected DOS could be much more useful (or you could
>         implement
>         augmentation charge contributions).
>
>         PS please write to the list only, not to personal addresses.
>
>         Guido
>
>
>         On 07/02/2012 02:26 PM, Yavar Taghipour Azar wrote:
>          >
>          > Dear QE users
>          >
>          > I want to divide my case to some boxes and analyze local dos
>         for them;
>          > especially, I want to investigate contribution of different
>         parts of cell
>          > near the band edges.
>          > I have used Ultra-soft Pseudopotentials in my calculations.
>         By considering
>          > that augmentation charge contribution is not included in
>         local dos
>          > calculations, is that led to losing some information about
>         electronic
>          > structure?
>          >
>          > Thanks in advance.
>          >
>          >
>          > -------------------------------------------
>          > Yavar Taghipour Azar
>          > PhD Student
>          > Physics Group, AEOI
>          > Tehran-Iran
>          >
>          > Email: ytaghipour at aeoi.org.ir <mailto:ytaghipour at aeoi.org.ir>
>          >
>         <javascript:top.openWin('/WorldClient.dll?Session=QQUMKJC&View=Compose&New=Yes&To=ytaghipour%40aeoi.org.ir
>         <http://40aeoi.org.ir>','Compose',800,600,'yes');>
>          > Phone: +98 (0) 21 82064556
>          > -----------------------------------------------------------
>          >
>          >
>          > _______________________________________________
>          > Pw_forum mailing list
>          > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>          > http://www.democritos.it/mailman/listinfo/pw_forum
>          >
>
>         --
>         Guido Fratesi
>
>         Dipartimento di Scienza dei Materiali
>         Universita` degli Studi di Milano-Bicocca
>         via Cozzi 53, 20125 Milano, Italy
>         _______________________________________________
>         Pw_forum mailing list
>         Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>         http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy

From baroni at sissa.it  Tue Jul  3 00:06:43 2012
From: baroni at sissa.it (Stefano Baroni)
Date: Tue, 3 Jul 2012 00:06:43 +0200
Subject: [Pw_forum] phonon
In-Reply-To: <CAFsnUVYOLi8fgARx1fnw_iy9HBEy0gPRsp4=m1t3ZgOtz+MMRQ@mail.gmail.com>
References: <CAFsnUVYOLi8fgARx1fnw_iy9HBEy0gPRsp4=m1t3ZgOtz+MMRQ@mail.gmail.com>
Message-ID: <A84F0070-56EF-4097-BDE5-C49FFAA51035@sissa.it>


On Jul 2, 2012, at 3:19 PM, Swetarekha Ram wrote:

> Dear users,
> 
>   I wrote this same previously, but I did not get any reply.
> This time I am expecting some suggestion.

???

SB

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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From yzunt at yahoo.com  Tue Jul  3 05:34:51 2012
From: yzunt at yahoo.com (Yusuf Zuntu)
Date: Mon, 2 Jul 2012 20:34:51 -0700 (PDT)
Subject: [Pw_forum] Ploting graphene energy band
Message-ID: <1341286491.53349.YahooMailNeo@web111213.mail.gq1.yahoo.com>

Dear QE Users

I am new with QE. I am following a default example for calculating/ploting band structure of simple graphene. The steps followed for relaxing, SCF? NSCF calculations using PWgui was successful.I donot understand the command (steps 4) on how to extract the band energy from graphene.band.out (after nscf calculation, step 3) to grapheneband.dat to be used for ploting the band sructure. following are the defaults steps followed:

1.try to
relax the crystal structure and get equilibrium
configuration.
?
?? (using PWgui
to open input file"graphene.rx.in")
??? 2.try a scf
calculation for further band calculation.
??? (using PWgui
to open input file "graphene.scf.in")
??? 3.try to
calculate band energy for arbitary wavevectors.
??? (using PWgui
to open input file "graphene.band.in")
??? 4.use
bands.x in PP dictionary to extract band energy from
graphene.band.out
to?????
????? grapheneband.dat.
????? (mpiexec -n 2 ./bands.x < graphene.bands.in
> graphene.bands.out)
??????Attention:
the number of CPU must be equal to?that of
pw.x
??????If
.dat file is not found, inspect graphene.band.out file. There will
give
?????? some?valuable?suggestion.
??? 5.use
grapheneband.dat to get picture.
??? ? (./plotband.x graphenebands.dat)
?? ?? Then, there will some question
I must answer.
?????????? First:Emin, Emax > (the energy range appear in
picture)
?????????? Second:output file (xmgr) >
?????????? ?????? skipping ...
?????????? ?????? output file (ps) >
????????????????? (choosing the type and giving a name of the picture)
?????????? Third:Efermi >? (giving the ferm
energy. This value can only obtaind after?
???????????????? I?check?the picture of energy
band)
?????????? Forth:deltaE, reference E (for tics)
???????????????? (deltaE is the major tick of y axis.
????????????????? reference E means the move the y axis. Traditional,
referenceE=Efermi)
?????????? Fifth:show the picture of energy band.
???????????????? ggv grapheneband

Thanks

Yusuf Zuntu
MSC candidate UPM malaysia
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From 1009ukumar at gmail.com  Tue Jul  3 06:09:32 2012
From: 1009ukumar at gmail.com (Sonu Kumar)
Date: Tue, 3 Jul 2012 09:39:32 +0530
Subject: [Pw_forum] [***SPAM*** Score/Req: 10.00/5.0] Re: (no subject)
In-Reply-To: <4FF1B68A.9090308@mater.unimib.it>
References: <WC20120702122639.540401@aeoi.org.ir>
	<4FF1966F.6050609@mater.unimib.it>
	<WC20120702124649.990402@aeoi.org.ir>
	<CAHePdfCUxccNRSV-3W1AtKroZ_Eq-6Jw+i=5d_GV9dFesW9Xeg@mail.gmail.com>
	<4FF1B68A.9090308@mater.unimib.it>
Message-ID: <CAHePdfD5Z2qf4iiuC08U7GSA_vcurw+h5-pNet6SkK55WxrEyA@mail.gmail.com>

I am sorry for asking the question at inappropriate/unsuitable thread.





==========================================
Sonu Kumar
Phd Student,Physics Department
Indian Institute of Technology ,Delhi-110016, India
web:-http://www.iitd.ac.in/
==========================================



On Mon, Jul 2, 2012 at 8:26 PM, Guido Fratesi <fratesi at mater.unimib.it>wrote:

> Dear Sonu,
> the thread was about the local density of states, not the ELF.
> Guido
>
> On 07/02/2012 03:12 PM, Sonu Kumar wrote:
> > Dear all QE users and Prof. Guido Fratesi,
> >
> > I have a doubt...
> > Electron localization function calculations does not make
> > much sense when using ultra-soft pseudopotentials.
> >
> > Is it true? although USPP takes into account the charge removal due
> > to smoothness of pseudo states  by adding augmentation charges.
> >
> > regards,
> > sonu
> >
> > ==========================================
> > Sonu Kumar
> > Phd Student,Physics Department
> > Indian Institute of Technology ,Delhi-110016, India
> > web:-http://www.iitd.ac.in/
> > ==========================================
> >
> >
> >
> > On Mon, Jul 2, 2012 at 6:16 PM, Yavar Taghipour Azar
> > <ytaghipour at aeoi.org.ir <mailto:ytaghipour at aeoi.org.ir>> wrote:
> >
> >     Dear Guido,
> >     thanks for your consideration and good comments
> >
> >         -----Original Message-----
> >         From: Guido Fratesi <fratesi at mater.unimib.it
> >         <mailto:fratesi at mater.unimib.it>>
> >         To: pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>
> >         Date: Mon, 02 Jul 2012 14:39:11 +0200
> >         Subject: [***SPAM*** Score/Req: 10.00/5.0] Re: [Pw_forum] (no
> >         subject)
> >
> >         Dear Yavar,
> >
> >         you are going to miss the contribution of the augmentation
> >         charge to the
> >         |psi|^2. That is not important if you are interested in spacial
> >         regions
> >         far from any atom (small or zero overlap with the augmentation
> >         spheres);
> >         that might instead be important if you want a quantitative
> >         analysis in
> >         the atomic region. For the latter, however, the analysis of the
> >         atom-projected DOS could be much more useful (or you could
> >         implement
> >         augmentation charge contributions).
> >
> >         PS please write to the list only, not to personal addresses.
> >
> >         Guido
> >
> >
> >         On 07/02/2012 02:26 PM, Yavar Taghipour Azar wrote:
> >          >
> >          > Dear QE users
> >          >
> >          > I want to divide my case to some boxes and analyze local dos
> >         for them;
> >          > especially, I want to investigate contribution of different
> >         parts of cell
> >          > near the band edges.
> >          > I have used Ultra-soft Pseudopotentials in my calculations.
> >         By considering
> >          > that augmentation charge contribution is not included in
> >         local dos
> >          > calculations, is that led to losing some information about
> >         electronic
> >          > structure?
> >          >
> >          > Thanks in advance.
> >          >
> >          >
> >          > -------------------------------------------
> >          > Yavar Taghipour Azar
> >          > PhD Student
> >          > Physics Group, AEOI
> >          > Tehran-Iran
> >          >
> >          > Email: ytaghipour at aeoi.org.ir <mailto:ytaghipour at aeoi.org.ir>
> >          >
> >
> <javascript:top.openWin('/WorldClient.dll?Session=QQUMKJC&View=Compose&New=Yes&To=ytaghipour%
> 40aeoi.org.ir
> >         <http://40aeoi.org.ir>','Compose',800,600,'yes');>
> >          > Phone: +98 (0) 21 82064556
> >          > -----------------------------------------------------------
> >          >
> >          >
> >          > _______________________________________________
> >          > Pw_forum mailing list
> >          > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >          > http://www.democritos.it/mailman/listinfo/pw_forum
> >          >
> >
> >         --
> >         Guido Fratesi
> >
> >         Dipartimento di Scienza dei Materiali
> >         Universita` degli Studi di Milano-Bicocca
> >         via Cozzi 53, 20125 Milano, Italy
> >         _______________________________________________
> >         Pw_forum mailing list
> >         Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >         http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >     _______________________________________________
> >     Pw_forum mailing list
> >     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >     http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> --
> Guido Fratesi
>
> Dipartimento di Scienza dei Materiali
> Universita` degli Studi di Milano-Bicocca
> via Cozzi 53, 20125 Milano, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From ytaghipour at aeoi.org.ir  Tue Jul  3 07:08:12 2012
From: ytaghipour at aeoi.org.ir (Yavar Taghipour Azar)
Date: Tue, 03 Jul 2012 09:38:12 +0430
Subject: [Pw_forum] [***SPAM*** Score/Req: 10.00/5.0] Re:
	[***SPAM***	Score/Req: 10.00/5.0] Re: (no subject)
In-Reply-To: <4FF1B68A.9090308@mater.unimib.it>
References: <WC20120702122639.540401@aeoi.org.ir>
	<4FF1966F.6050609@mater.unimib.it>
	<WC20120702124649.990402@aeoi.org.ir>
	<CAHePdfCUxccNRSV-3W1AtKroZ_Eq-6Jw+i=5d_GV9dFesW9Xeg@mail.gmail.com>
	<4FF1B68A.9090308@mater.unimib.it>
Message-ID: <WC20120703050812.180417@aeoi.org.ir>

Dear Guido,
 
When we use projwfc.x program to calculation of projected dos, summation on 
the all of projected dos on the all of atoms in unit cell, is in good 
agreement by total dos. But when we divide the unit cell into 2 parts and we 
use projwfc.x for calculation of local dos, the sum of two local dos columns 
is smaller than total dos. 
I will be very grateful ifyou can give me a suggestion or reference for more 
information about the origin of the difference between result of local dos 
and summation of projected dos in the same volume.
 
PS: I want to compare total and adsorbate-projected density of states, which 
one is correct method; summation over all projected dos on adsorbate atoms 
or calculation of local dos for the box which contains all of the atoms of 
adsorbate? 

Thanks in advance.
 
 
-------------------------------------------
Yavar Taghipour Azar
PhD Student
Physics Group, AEOI
Tehran-Iran
 
Email: ytaghipour at aeoi.org.ir
Phone: +98 (0) 21 82064556
-----------------------------------------------------------



-----Original Message-----
From: Guido Fratesi <fratesi at mater.unimib.it>
To: pw_forum at pwscf.org
Date: Mon, 02 Jul 2012 16:56:10 +0200
Subject: [***SPAM*** Score/Req: 10.00/5.0] Re: [Pw_forum] [***SPAM*** 
Score/Req: 10.00/5.0] Re: (no subject)


Dear Sonu,
the thread was about the local density of states, not the ELF.
Guido

On 07/02/2012 03:12 PM, Sonu Kumar wrote:
> Dear all QE users and Prof. Guido Fratesi,
>
> I have a doubt...
> Electron localization function calculations does not make
> much sense when using ultra-soft pseudopotentials.
>
> Is it true? although USPP takes into account the charge removal due
> to smoothness of pseudo states  by adding augmentation charges.
>
> regards,
> sonu
>
> ==========================================
> Sonu Kumar
> Phd Student,Physics Department
> Indian Institute of Technology ,Delhi-110016, India
> web:-http://www.iitd.ac.in/
> ==========================================
>
>
>
> On Mon, Jul 2, 2012 at 6:16 PM, Yavar Taghipour Azar
> <ytaghipour at aeoi.org.ir <mailto:ytaghipour at aeoi.org.ir>> wrote:
>
>     Dear Guido,
>     thanks for your consideration and good comments
>
>         -----Original Message-----
>         From: Guido Fratesi <fratesi at mater.unimib.it
>         <mailto:fratesi at mater.unimib.it>>
>         To: pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>
>         Date: Mon, 02 Jul 2012 14:39:11 +0200
>         Subject: [***SPAM*** Score/Req: 10.00/5.0] Re: [Pw_forum] (no
>         subject)
>
>         Dear Yavar,
>
>         you are going to miss the contribution of the augmentation
>         charge to the
>         |psi|^2. That is not important if you are interested in spacial
>         regions
>         far from any atom (small or zero overlap with the augmentation
>         spheres);
>         that might instead be important if you want a quantitative
>         analysis in
>         the atomic region. For the latter, however, the analysis of the
>         atom-projected DOS could be much more useful (or you could
>         implement
>         augmentation charge contributions).
>
>         PS please write to the list only, not to personal addresses.
>
>         Guido
>
>
>         On 07/02/2012 02:26 PM, Yavar Taghipour Azar wrote:
>          >
>          > Dear QE users
>          >
>          > I want to divide my case to some boxes and analyze local dos
>         for them;
>          > especially, I want to investigate contribution of different
>         parts of cell
>          > near the band edges.
>          > I have used Ultra-soft Pseudopotentials in my calculations.
>         By considering
>          > that augmentation charge contribution is not included in
>         local dos
>          > calculations, is that led to losing some information about
>         electronic
>          > structure?
>          >
>          > Thanks in advance.
>          >
>          >
>          > -------------------------------------------
>          > Yavar Taghipour Azar
>          > PhD Student
>          > Physics Group, AEOI
>          > Tehran-Iran
>          >
>          > Email: ytaghipour at aeoi.org.ir <mailto:ytaghipour at aeoi.org.ir>
>          >
>         
<javascript:top.openWin('/WorldClient.dll?Session=QQUMKJC&View=Compose&New=Yes&To=ytaghipour%40aeoi.org.ir
>         <http://40aeoi.org.ir>','Compose',800,600,'yes');>
>          > Phone: +98 (0) 21 82064556
>          > -----------------------------------------------------------
>          >
>          >
>          > _______________________________________________
>          > Pw_forum mailing list
>          > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>          > http://www.democritos.it/mailman/listinfo/pw_forum
>          >
>
>         --
>         Guido Fratesi
>
>         Dipartimento di Scienza dei Materiali
>         Universita` degli Studi di Milano-Bicocca
>         via Cozzi 53, 20125 Milano, Italy
>         _______________________________________________
>         Pw_forum mailing list
>         Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>         http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy
_______________________________________________
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From fratesi at mater.unimib.it  Tue Jul  3 09:40:47 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Tue, 03 Jul 2012 09:40:47 +0200
Subject: [Pw_forum] [***SPAM*** Score/Req: 10.00/5.0] Re: [***SPAM***
 Score/Req: 10.00/5.0] Re: (no subject)
In-Reply-To: <WC20120703050812.180417@aeoi.org.ir>
References: <WC20120702122639.540401@aeoi.org.ir>
	<4FF1966F.6050609@mater.unimib.it>
	<WC20120702124649.990402@aeoi.org.ir>
	<CAHePdfCUxccNRSV-3W1AtKroZ_Eq-6Jw+i=5d_GV9dFesW9Xeg@mail.gmail.com>
	<4FF1B68A.9090308@mater.unimib.it>
	<WC20120703050812.180417@aeoi.org.ir>
Message-ID: <4FF2A1FF.1090704@mater.unimib.it>

> But when we divide the unit cell into 2 parts
> and we use projwfc.x for calculation of local dos, the sum of two local
> dos columns is smaller than total dos.

You are probably using USPP and missing the augmentation charge 
contribution.

> I will be very grateful ifyou can give me a suggestion or reference for
> more information about the origin of the difference between result of
> local dos and summation of projected dos in the same volume.

These are two different concepts (below, psi_nk=bands; phi=atomic wfc):

PDOS_nlm: sum_nk weight(k) occupation(n,k) | <psi_n(k)|phi_nlm> |^2

LDOS_vol: sum_nk weight(k) occupation(n,k) \int_vol d3r |psi_n(k)(r)|^2

Try to figure out them, there's no reason why they would be the same. 
There's no "same volume" for PDOS and LDOS. Only the sum of all PDOS_nlm 
should equal the total DOS. Idem, the LDOS in the cell volume should be 
the total DOS but the augmentation contribution to |psi(r)| was not 
implemented.

> PS: I want to compare total and adsorbate-projected density of states,
> which one is correct method; summation over all projected dos on
> adsorbate atoms or calculation of local dos for the box which contains
> all of the atoms of adsorbate?

Keeping in mind that arbitrariness is present in both methods, and 
qualitative questions can be answered, I would use the PDOS. Try answer 
the questions: "what is THE box which contains all of the atoms of the 
adsorbate?" Can you? Or worse... "Do electrons belong to this atom?"

Guido

PS there's extensive literature on the subject of partitioning charge:
very recently, http://link.aps.org/doi/10.1103/PhysRevLett.108.166403

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy



From ytaghipour at aeoi.org.ir  Tue Jul  3 10:30:13 2012
From: ytaghipour at aeoi.org.ir (Yavar Taghipour Azar)
Date: Tue, 03 Jul 2012 13:00:13 +0430
Subject: [Pw_forum] [***SPAM*** Score/Req: 10.00/5.0] Re:
	[***SPAM***	Score/Req: 10.00/5.0] Re: [***SPAM*** Score/Req:
	10.00/5.0] Re: (no	subject)
In-Reply-To: <4FF2A1FF.1090704@mater.unimib.it>
References: <WC20120702122639.540401@aeoi.org.ir>
	<4FF1966F.6050609@mater.unimib.it>
	<WC20120702124649.990402@aeoi.org.ir>
	<CAHePdfCUxccNRSV-3W1AtKroZ_Eq-6Jw+i=5d_GV9dFesW9Xeg@mail.gmail.com>
	<4FF1B68A.9090308@mater.unimib.it>
	<WC20120703050812.180417@aeoi.org.ir>
	<4FF2A1FF.1090704@mater.unimib.it>
Message-ID: <WC20120703083013.33042F@aeoi.org.ir>

Dear Professor Fratesi,
 
Thank you so much for your helpful and instructive comments.
 
 
Sincerely, 

 
-------------------------------------------
Yavar Taghipour Azar
PhD Student
Physics Group, AEOI
Tehran-Iran
 
Email: ytaghipour at aeoi.org.ir
Phone: +98 (0) 21 82064556
-----------------------------------------------------------

-----Original Message-----
From: Guido Fratesi <fratesi at mater.unimib.it>
To: pw_forum at pwscf.org
Date: Tue, 03 Jul 2012 09:40:47 +0200
Subject: [***SPAM*** Score/Req: 10.00/5.0] Re: [Pw_forum] [***SPAM*** 
Score/Req: 10.00/5.0] Re: [***SPAM*** Score/Req: 10.00/5.0] Re: (no subject)


> But when we divide the unit cell into 2 parts
> and we use projwfc.x for calculation of local dos, the sum of two local
> dos columns is smaller than total dos.

You are probably using USPP and missing the augmentation charge 
contribution.

> I will be very grateful ifyou can give me a suggestion or reference for
> more information about the origin of the difference between result of
> local dos and summation of projected dos in the same volume.

These are two different concepts (below, psi_nk=bands; phi=atomic wfc):

PDOS_nlm: sum_nk weight(k) occupation(n,k) | <psi_n(k)|phi_nlm> |^2

LDOS_vol: sum_nk weight(k) occupation(n,k) \int_vol d3r |psi_n(k)(r)|^2

Try to figure out them, there's no reason why they would be the same. 
There's no "same volume" for PDOS and LDOS. Only the sum of all PDOS_nlm 
should equal the total DOS. Idem, the LDOS in the cell volume should be 
the total DOS but the augmentation contribution to |psi(r)| was not 
implemented.

> PS: I want to compare total and adsorbate-projected density of states,
> which one is correct method; summation over all projected dos on
> adsorbate atoms or calculation of local dos for the box which contains
> all of the atoms of adsorbate?

Keeping in mind that arbitrariness is present in both methods, and 
qualitative questions can be answered, I would use the PDOS. Try answer 
the questions: "what is THE box which contains all of the atoms of the 
adsorbate?" Can you? Or worse... "Do electrons belong to this atom?"

Guido

PS there's extensive literature on the subject of partitioning charge:
very recently, http://link.aps.org/doi/10.1103/PhysRevLett.108.166403

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy


_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From sohailphysics at yahoo.co.in  Thu Jul  5 08:53:53 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Thu, 5 Jul 2012 14:53:53 +0800 (SGT)
Subject: [Pw_forum] Pseudopotential for MoS2
Message-ID: <1341471233.4994.YahooMailClassic@web192202.mail.sg3.yahoo.com>

Dear Pw users

Can any body help me in getting the link to obtain pseudo potentials for MoS2
Both LDA and GGA

Thanks

Sohail
King Khalid University
Saudi Arabia
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From akohlmey at gmail.com  Thu Jul  5 09:37:58 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Thu, 5 Jul 2012 09:37:58 +0200
Subject: [Pw_forum] Pseudopotential for MoS2
In-Reply-To: <1341471233.4994.YahooMailClassic@web192202.mail.sg3.yahoo.com>
References: <1341471233.4994.YahooMailClassic@web192202.mail.sg3.yahoo.com>
Message-ID: <CADTmJ6GTTY4rRUL7Wxs34F5q2suMyAwmakXwkCFdZZ0t=Vf5xg@mail.gmail.com>

On Thu, Jul 5, 2012 at 8:53 AM, Sohail Ahmad <sohailphysics at yahoo.co.in> wrote:
>
> Dear Pw users
>
> Can any body help me in getting the link to obtain pseudo potentials for MoS2
> Both LDA and GGA


...and i want a pony for christmas.

how about you start with the ones that are provided on the Q-E homepage?

axel.

>
> Thanks
>
> Sohail
> King Khalid University
> Saudi Arabia
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



--
Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

From sohailphysics at yahoo.co.in  Thu Jul  5 09:54:47 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Thu, 5 Jul 2012 15:54:47 +0800 (SGT)
Subject: [Pw_forum] Pseudo potential MoS2
In-Reply-To: <mailman.1.1341474314.2526.pw_forum@pwscf.org>
Message-ID: <1341474887.31027.YahooMailClassic@web192203.mail.sg3.yahoo.com>

Dear Axel and users

I am looking for pseudo potential of Mo and S of pbe type

On QE web its available for S but not for Mo
For Mo,? it is pw91 type

I am worried , there would be a mismatch

I am new to QE and have not generated PP before

Thanks

Sohail 
King Khalid University
Saudi Arabia


--- On Thu, 5/7/12, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> wrote:

From: pw_forum-request at pwscf.org <pw_forum-request at pwscf.org>
Subject: Pw_forum Digest, Vol 61, Issue 11
To: pw_forum at pwscf.org
Date: Thursday, 5 July, 2012, 1:15 PM

Send Pw_forum mailing list submissions to
??? pw_forum at pwscf.org

To subscribe or unsubscribe via the World Wide Web, visit
??? http://www.democritos.it/mailman/listinfo/pw_forum
or, via email, send a message with subject or body 'help' to
??? pw_forum-request at pwscf.org

You can reach the person managing the list at
??? pw_forum-owner at pwscf.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Pw_forum digest..."


Today's Topics:

???1. Pseudopotential for MoS2 (Sohail Ahmad)
???2. Re: Pseudopotential for MoS2 (Axel Kohlmeyer)


----------------------------------------------------------------------

Message: 1
Date: Thu, 5 Jul 2012 14:53:53 +0800 (SGT)
From: Sohail Ahmad <sohailphysics at yahoo.co.in>
Subject: [Pw_forum] Pseudopotential for MoS2
To: Plane Wave <pw_forum at pwscf.org>
Message-ID:
??? <1341471233.4994.YahooMailClassic at web192202.mail.sg3.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Dear Pw users

Can any body help me in getting the link to obtain pseudo potentials for MoS2
Both LDA and GGA

Thanks

Sohail
King Khalid University
Saudi Arabia
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------------------------------

Message: 2
Date: Thu, 5 Jul 2012 09:37:58 +0200
From: Axel Kohlmeyer <akohlmey at gmail.com>
Subject: Re: [Pw_forum] Pseudopotential for MoS2
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
??? <CADTmJ6GTTY4rRUL7Wxs34F5q2suMyAwmakXwkCFdZZ0t=Vf5xg at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Thu, Jul 5, 2012 at 8:53 AM, Sohail Ahmad <sohailphysics at yahoo.co.in> wrote:
>
> Dear Pw users
>
> Can any body help me in getting the link to obtain pseudo potentials for MoS2
> Both LDA and GGA


...and i want a pony for christmas.

how about you start with the ones that are provided on the Q-E homepage?

axel.

>
> Thanks
>
> Sohail
> King Khalid University
> Saudi Arabia
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



--
Dr. Axel Kohlmeyer? akohlmey at gmail.com? http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.


------------------------------

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


End of Pw_forum Digest, Vol 61, Issue 11
****************************************
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From tkaloni at gmail.com  Thu Jul  5 09:57:28 2012
From: tkaloni at gmail.com (Thaneshwor Kaloni)
Date: Thu, 5 Jul 2012 10:57:28 +0300
Subject: [Pw_forum] Pw_forum Digest, Vol 61, Issue 11
In-Reply-To: <mailman.1.1341474314.2526.pw_forum@pwscf.org>
References: <mailman.1.1341474314.2526.pw_forum@pwscf.org>
Message-ID: <CABvS7Q+gQgkhB-X-Y95P+KJ8pYyudCSu9wQA0EBgU1o2ZrW=dA@mail.gmail.com>

>
> Dear Sohail,


Here you go!
http://www.quantum-espresso.org/?page_id=190



Date: Thu, 5 Jul 2012 14:53:53 +0800 (SGT)
> From: Sohail Ahmad <sohailphysics at yahoo.co.in>
> Subject: [Pw_forum] Pseudopotential for MoS2
> To: Plane Wave <pw_forum at pwscf.org>
> Message-ID:
>         <1341471233.4994.YahooMailClassic at web192202.mail.sg3.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Pw users
>
> Can any body help me in getting the link to obtain pseudo potentials for
> MoS2
> Both LDA and GGA
>
> Thanks
>
> Sohail
> King Khalid University
> Saudi Arabia
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://www.democritos.it/pipermail/pw_forum/attachments/20120705/6b10a538/attachment.html
>
> ------------------------------
>
>
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From giannozz at democritos.it  Thu Jul  5 09:59:09 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 5 Jul 2012 09:59:09 +0200
Subject: [Pw_forum] Pseudo potential MoS2
In-Reply-To: <1341474887.31027.YahooMailClassic@web192203.mail.sg3.yahoo.com>
References: <1341474887.31027.YahooMailClassic@web192203.mail.sg3.yahoo.com>
Message-ID: <139F42F5-3D83-4796-B65D-BDAC7DE61362@democritos.it>

The pseudopotential page in the quantum-espresso.org
web site contains many links to more pseudopotential tables

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From tkaloni at gmail.com  Thu Jul  5 12:47:28 2012
From: tkaloni at gmail.com (Thaneshwor Kaloni)
Date: Thu, 5 Jul 2012 13:47:28 +0300
Subject: [Pw_forum] error with spin polarized calculation with SOC
Message-ID: <CABvS7QLBmkFZZNbtG6XfV8mjnhvm9a-kD4T3eHVf=4oDjy9_8A@mail.gmail.com>

Dear QE Users,

I would like to perform spin polarized calculations with SOC.
I am receiving following errors. Could anyone please assist me?


**************************************
INPUT
***************************************
&control
    calculation='scf',
    restart_mode='from_scratch',
    prefix='C',
    pseudo_dir = '/home/kalonitp/code/pseudo/',
    outdir='t/',
    tefield = .true.
    dipfield = .true.
/
 &system
    ibrav = 4, a=3.86, b=3.86,
    c=15,cosac=0.0, cosbc=0.0, cosab=-0.5
    nat=2, ntyp=1, nbnd=10,
    ecutwfc =60,
    occupations='smearing',smearing='gaussian', degauss=0.05,
    lspinorb=.true.
    noncolin=.true.
    nspin=2,
    starting_magnetization=0.7
    london=.true.
    edir = 3
    eamp = 0.001
    emaxpos = 0.5
    eopreg = 0.1
/
 &ELECTRONS
    mixing_beta=0.7,
    conv_thr = 1.0D-6,
/
ATOMIC_SPECIES
Si    28.0855     Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (crystal)
Si      -0.001668875  -0.003337750   0.007491059
Si       0.331668875   0.663337750   0.037508941
K_POINTS {automatic}
8 8 1 0 0 0

******************************************************
OUTPUT
*************************************************************
     Program PWSCF v.4.3.1      starts on  5Jul2012 at 11:13:34

     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org",
     in publications or presentations arising from this work. More details
at
     http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

     Parallel version (MPI), running on    10 processors
     R & G space division:  proc/pool =   10

     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...
     Presently no symmetry can be used with electric field

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from iosys : error #         1
     noncolin .and. nspin==2 are conflicting flags
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

Best, Kaloni
*King Abdullah University of Science and
Technology<http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CE4QFjAA&url=http%3A%2F%2Fwww.kaust.edu.sa%2F&ei=onD1T-nUMY-EhQfu3MznBg&usg=AFQjCNHJzMdOUU1yTNpoXW5ZvxZP5_Xh4g&sig2=lyRtZOfF3o4sI2zekG6QnQ>
*KSA, Saudi Arabia
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From aycakiragasi at gmail.com  Thu Jul  5 13:04:54 2012
From: aycakiragasi at gmail.com (=?ISO-8859-9?B?QXnnYSBL/XJh8GFz/Q==?=)
Date: Thu, 5 Jul 2012 14:04:54 +0300
Subject: [Pw_forum] unit cell of Beta-GaSe crystal
Message-ID: <CAA_hC0kzFvoCceWXDkwoGhFXJqGJwF0XrNziMSGYTMZKmsbqGQ@mail.gmail.com>

Dear All Pw-users !

I'm a new pw user.
I want to calculate total energy of B-GaSe  crystal (hexagonal structure).
Altough I tried so hard, I couldn't set up unit cell of B-GaSe in Pwscf.
I couldn t see correct atomic structure of GaSe. I don t know where ? am
wrong.
Can anybody help me ! please !
I used parameters in the attached files. Also, my input file follow as

(lattice parameters a=3.73A  , c=15.919A,  z1=0.1003 and z2=0.1701


control
    calculation='scf'
    restart_mode='from_scratch',
    tstress = .true.
    tprnfor = .true.
    prefix='810-28',
    pseudo_dir = '/home/projet/pseudo/',
    outdir='/home/projet/tp/'
 /
 &system
    ibrav=0,
    celldm(1)=7.051,
    nat=8,
    ntyp=2,
    ecutwfc =50.0,
    ecutrho = 600.0,
 /
 &electrons
    diagonalization='david'
    conv_thr = 1.0e-6
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Se  1.0 Se_pz.upf
 Ga  1.0 Ga_pz.upf
ATOMIC_POSITIONS {alat}
Se -0.5     0.28867  0.1003
Ga  0.0     0.0      0.1701
Ga  0.0     0.0      0.3299
Se -0.5     0.28867  0.3997
Se  0.0     0.0      0.6003
Ga -0.5     0.28867  0.6701
Ga -0.5     0.28867  0.8299
Se  0.0     0.0      0.8997
K_POINTS {automatic}
6 6 6 0 0 0

CELL_PARAMETERS {hexagonal}
 1.0   0.0   0.0
 0.5   0.866 0.0
 0.0   0.0   4.26
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From cyrille.barreteau at cea.fr  Thu Jul  5 13:18:06 2012
From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille)
Date: Thu, 5 Jul 2012 11:18:06 +0000
Subject: [Pw_forum] RE :  error with spin polarized calculation with SOC
In-Reply-To: <CABvS7QLBmkFZZNbtG6XfV8mjnhvm9a-kD4T3eHVf=4oDjy9_8A@mail.gmail.com>
References: <CABvS7QLBmkFZZNbtG6XfV8mjnhvm9a-kD4T3eHVf=4oDjy9_8A@mail.gmail.com>
Message-ID: <6E80B49CBC3D9F4694B510228B88EE3C1ABB65@E-EXDAGE-A1.extra.cea.fr>

If you want to use SOC or do non-collinear caculation you should take nspin=4
(If you do not define nspin it will be automatically be set to 4)

  Cyrille



============================================================
Cyrille Barreteau                                 phone :      +33 (0)1 69 08 29 51
CEA Saclay                                       cellphone:   +33 (0)6 47 53 66 52
IRAMIS, SPCSI,  Bat. 462                fax :            +33 (0)1 69 08 84 46
91191 Gif sur Yvette Cedex               email:            cyrille.barreteau at cea.fr<mailto:cyrille.barreteau at cea.fr>
FRANCE
~~~~~~~~~~~~~~~~~~~~~~~~
Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/
==============================================================

________________________________
De : pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] de la part de Thaneshwor Kaloni [tkaloni at gmail.com]
Date d'envoi : jeudi 5 juillet 2012 12:47
? : pw_forum
Objet : [Pw_forum] error with spin polarized calculation with SOC

Dear QE Users,

I would like to perform spin polarized calculations with SOC.
I am receiving following errors. Could anyone please assist me?


**************************************
INPUT
***************************************
&control
    calculation='scf',
    restart_mode='from_scratch',
    prefix='C',
    pseudo_dir = '/home/kalonitp/code/pseudo/',
    outdir='t/',
    tefield = .true.
    dipfield = .true.
/
 &system
    ibrav = 4, a=3.86, b=3.86,
    c=15,cosac=0.0, cosbc=0.0, cosab=-0.5
    nat=2, ntyp=1, nbnd=10,
    ecutwfc =60,
    occupations='smearing',smearing='gaussian', degauss=0.05,
    lspinorb=.true.
    noncolin=.true.
    nspin=2,
    starting_magnetization=0.7
    london=.true.
    edir = 3
    eamp = 0.001
    emaxpos = 0.5
    eopreg = 0.1
/
 &ELECTRONS
    mixing_beta=0.7,
    conv_thr = 1.0D-6,
/
ATOMIC_SPECIES
Si    28.0855     Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (crystal)
Si      -0.001668875  -0.003337750   0.007491059
Si       0.331668875   0.663337750   0.037508941
K_POINTS {automatic}
8 8 1 0 0 0

******************************************************
OUTPUT
*************************************************************
     Program PWSCF v.4.3.1      starts on  5Jul2012 at 11:13:34

     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org",
     in publications or presentations arising from this work. More details at
     http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

     Parallel version (MPI), running on    10 processors
     R & G space division:  proc/pool =   10

     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...
     Presently no symmetry can be used with electric field

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from iosys : error #         1
     noncolin .and. nspin==2 are conflicting flags
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

Best, Kaloni
King Abdullah University of Science and Technology<http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CE4QFjAA&url=http%3A%2F%2Fwww.kaust.edu.sa%2F&ei=onD1T-nUMY-EhQfu3MznBg&usg=AFQjCNHJzMdOUU1yTNpoXW5ZvxZP5_Xh4g&sig2=lyRtZOfF3o4sI2zekG6QnQ>
KSA, Saudi Arabia
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From tkaloni at gmail.com  Thu Jul  5 13:27:29 2012
From: tkaloni at gmail.com (Thaneshwor Kaloni)
Date: Thu, 5 Jul 2012 14:27:29 +0300
Subject: [Pw_forum] RE : error with spin polarized calculation with SOC
In-Reply-To: <6E80B49CBC3D9F4694B510228B88EE3C1ABB65@E-EXDAGE-A1.extra.cea.fr>
References: <CABvS7QLBmkFZZNbtG6XfV8mjnhvm9a-kD4T3eHVf=4oDjy9_8A@mail.gmail.com>
	<6E80B49CBC3D9F4694B510228B88EE3C1ABB65@E-EXDAGE-A1.extra.cea.fr>
Message-ID: <CABvS7QJdBEKDnY4Rj7ZaxoBmeQLPRGS7hqGb09ki0ePo5y8kpA@mail.gmail.com>

Dear Professor Cyrille,

Thank you very much for your prompt and kind reply.
But still I am getting following kind of error with inclusion of nspin=4

 from iosys : error #         1
     LSDA not available with electric field


On Thu, Jul 5, 2012 at 2:18 PM, BARRETEAU Cyrille
<cyrille.barreteau at cea.fr>wrote:

>  If you want to use SOC or do non-collinear caculation you should take
> nspin=4
> (If you do not define nspin it will be automatically be set to 4)
>
>   Cyrille
>
>
>  ============================================================
> Cyrille Barreteau                                 phone :      +33 (0)1 69 08 29 51
> CEA Saclay                                       cellphone:   +33 (0)6 47 53 66 52
> IRAMIS, SPCSI,  Bat. 462                fax :            +33 (0)1 69 08 84 46
> 91191 Gif sur Yvette Cedex               email:            cyrille.barreteau at cea.fr
> FRANCE
> ~~~~~~~~~~~~~~~~~~~~~~~~
> Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/
> ==============================================================
>
>   ------------------------------
> *De :* pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] de la part
> de Thaneshwor Kaloni [tkaloni at gmail.com]
> *Date d'envoi :* jeudi 5 juillet 2012 12:47
> *? :* pw_forum
> *Objet :* [Pw_forum] error with spin polarized calculation with SOC
>
>   Dear QE Users,
>
>  I would like to perform spin polarized calculations with SOC.
> I am receiving following errors. Could anyone please assist me?
>
>
>  **************************************
> INPUT
> ***************************************
>  &control
>     calculation='scf',
>     restart_mode='from_scratch',
>     prefix='C',
>     pseudo_dir = '/home/kalonitp/code/pseudo/',
>     outdir='t/',
>     tefield = .true.
>     dipfield = .true.
> /
>  &system
>     ibrav = 4, a=3.86, b=3.86,
>     c=15,cosac=0.0, cosbc=0.0, cosab=-0.5
>     nat=2, ntyp=1, nbnd=10,
>     ecutwfc =60,
>     occupations='smearing',smearing='gaussian', degauss=0.05,
>     lspinorb=.true.
>     noncolin=.true.
>     nspin=2,
>     starting_magnetization=0.7
>     london=.true.
>     edir = 3
>     eamp = 0.001
>     emaxpos = 0.5
>     eopreg = 0.1
> /
>  &ELECTRONS
>     mixing_beta=0.7,
>     conv_thr = 1.0D-6,
> /
> ATOMIC_SPECIES
> Si    28.0855     Si.pbe-rrkj.UPF
> ATOMIC_POSITIONS (crystal)
> Si      -0.001668875  -0.003337750   0.007491059
> Si       0.331668875   0.663337750   0.037508941
> K_POINTS {automatic}
> 8 8 1 0 0 0
>
>  ******************************************************
> OUTPUT
> *************************************************************
>      Program PWSCF v.4.3.1      starts on  5Jul2012 at 11:13:34
>
>       This program is part of the open-source Quantum ESPRESSO suite
>      for quantum simulation of materials; please cite
>          "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>           URL http://www.quantum-espresso.org",
>      in publications or presentations arising from this work. More details
> at
>
> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
>
>       Parallel version (MPI), running on    10 processors
>      R & G space division:  proc/pool =   10
>
>       Current dimensions of program PWSCF are:
>      Max number of different atomic species (ntypx) = 10
>      Max number of k-points (npk) =  40000
>      Max angular momentum in pseudopotentials (lmaxx) =  3
>      Waiting for input...
>      Presently no symmetry can be used with electric field
>
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from iosys : error #         1
>      noncolin .and. nspin==2 are conflicting flags
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>       stopping ...
>
>  Best, Kaloni
>  *King Abdullah University of Science and Technology<http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CE4QFjAA&url=http%3A%2F%2Fwww.kaust.edu.sa%2F&ei=onD1T-nUMY-EhQfu3MznBg&usg=AFQjCNHJzMdOUU1yTNpoXW5ZvxZP5_Xh4g&sig2=lyRtZOfF3o4sI2zekG6QnQ>
> * KSA, Saudi Arabia
>



-- 
Best regards, Kaloni
Web page:
http://sa.linkedin.com/pub/thaneshwor-kaloni/18/955/238
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From dalcorso at sissa.it  Thu Jul  5 13:54:34 2012
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Thu, 05 Jul 2012 13:54:34 +0200
Subject: [Pw_forum] RE : error with spin polarized calculation with SOC
In-Reply-To: <CABvS7QJdBEKDnY4Rj7ZaxoBmeQLPRGS7hqGb09ki0ePo5y8kpA@mail.gmail.com>
References: <CABvS7QLBmkFZZNbtG6XfV8mjnhvm9a-kD4T3eHVf=4oDjy9_8A@mail.gmail.com>
	<6E80B49CBC3D9F4694B510228B88EE3C1ABB65@E-EXDAGE-A1.extra.cea.fr>
	<CABvS7QJdBEKDnY4Rj7ZaxoBmeQLPRGS7hqGb09ki0ePo5y8kpA@mail.gmail.com>
Message-ID: <1341489274.3868.2.camel@ulisse.cm.sissa.it>


On Thu, 2012-07-05 at 14:27 +0300, Thaneshwor Kaloni wrote:
> Dear Professor Cyrille,
> 
> 
> Thank you very much for your prompt and kind reply.
> But still I am getting following kind of error with inclusion of
> nspin=4 
> 
> 
>  from iosys : error #         1
>      LSDA not available with electric field

This option is not implemented. You cannot do a finite electric field
calculation with spin-orbit coupling.  

HTH

Andrea


> 
> 
> 
> On Thu, Jul 5, 2012 at 2:18 PM, BARRETEAU Cyrille
> <cyrille.barreteau at cea.fr> wrote:
>         If you want to use SOC or do non-collinear caculation you
>         should take nspin=4 
>         (If you do not define nspin it will be automatically be set to
>         4)
>         
>           Cyrille
>         
>         
>         ============================================================
>         Cyrille Barreteau                                 phone :      +33 (0)1 69 08 29 51
>         CEA Saclay                                       cellphone:   +33 (0)6 47 53 66 52
>         IRAMIS, SPCSI,  Bat. 462                fax :            +33 (0)1 69 08 84 46
>         91191 Gif sur Yvette Cedex               email:            cyrille.barreteau at cea.fr
>         FRANCE 
>         ~~~~~~~~~~~~~~~~~~~~~~~~ 
>         Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ 
>         ==============================================================
>         
>         ______________________________________________________________
>         De : pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org]
>         de la part de Thaneshwor Kaloni [tkaloni at gmail.com]
>         Date d'envoi : jeudi 5 juillet 2012 12:47
>         ? : pw_forum
>         Objet : [Pw_forum] error with spin polarized calculation with
>         SOC
>         
>         
>         
>         Dear QE Users,
>         
>         
>         I would like to perform spin polarized calculations with SOC.
>         I am receiving following errors. Could anyone please assist
>         me?
>         
>         
>         
>         
>         **************************************
>         INPUT
>         ***************************************
>         &control
>             calculation='scf',
>             restart_mode='from_scratch',
>             prefix='C',
>             pseudo_dir = '/home/kalonitp/code/pseudo/',
>             outdir='t/',
>             tefield = .true.
>             dipfield = .true.
>         /
>          &system
>             ibrav = 4, a=3.86, b=3.86,
>             c=15,cosac=0.0, cosbc=0.0, cosab=-0.5
>             nat=2, ntyp=1, nbnd=10,
>             ecutwfc =60, 
>             occupations='smearing',smearing='gaussian', degauss=0.05,
>             lspinorb=.true.
>             noncolin=.true.
>             nspin=2,
>             starting_magnetization=0.7
>             london=.true.
>             edir = 3            
>             eamp = 0.001  
>             emaxpos = 0.5
>             eopreg = 0.1
>         /
>          &ELECTRONS
>             mixing_beta=0.7,
>             conv_thr = 1.0D-6,
>         /
>         ATOMIC_SPECIES
>         Si    28.0855     Si.pbe-rrkj.UPF 
>         ATOMIC_POSITIONS (crystal)
>         Si      -0.001668875  -0.003337750   0.007491059
>         Si       0.331668875   0.663337750   0.037508941
>         K_POINTS {automatic}
>         8 8 1 0 0 0
>         
>         
>         ******************************************************
>         OUTPUT
>         *************************************************************
>              Program PWSCF v.4.3.1      starts on  5Jul2012 at
>         11:13:34 
>         
>         
>              This program is part of the open-source Quantum ESPRESSO
>         suite
>              for quantum simulation of materials; please cite
>                  "P. Giannozzi et al., J. Phys.:Condens. Matter 21
>         395502 (2009);
>                   URL http://www.quantum-espresso.org", 
>              in publications or presentations arising from this work.
>         More details at
>         
>          http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
>         
>         
>              Parallel version (MPI), running on    10 processors
>              R & G space division:  proc/pool =   10
>         
>         
>              Current dimensions of program PWSCF are:
>              Max number of different atomic species (ntypx) = 10
>              Max number of k-points (npk) =  40000
>              Max angular momentum in pseudopotentials (lmaxx) =  3
>              Waiting for input...
>              Presently no symmetry can be used with electric field
>         
>         
>          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>         %%%%%%%%%%%%%%%%%
>              from iosys : error #         1
>              noncolin .and. nspin==2 are conflicting flags
>          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>         %%%%%%%%%%%%%%%%%
>         
>         
>              stopping ...
>         
>         
>         Best, Kaloni 
>         King Abdullah University of Science and Technology
>         KSA, Saudi Arabia
> 
> 
> 
> 
> -- 
> Best regards, Kaloni
> Web page:
> http://sa.linkedin.com/pub/thaneshwor-kaloni/18/955/238
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Bonomea 265              Fax. 0039-040-3787249
I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it



From tkaloni at gmail.com  Thu Jul  5 13:59:55 2012
From: tkaloni at gmail.com (Thaneshwor Kaloni)
Date: Thu, 5 Jul 2012 14:59:55 +0300
Subject: [Pw_forum] RE : error with spin polarized calculation with SOC
In-Reply-To: <1341489274.3868.2.camel@ulisse.cm.sissa.it>
References: <CABvS7QLBmkFZZNbtG6XfV8mjnhvm9a-kD4T3eHVf=4oDjy9_8A@mail.gmail.com>
	<6E80B49CBC3D9F4694B510228B88EE3C1ABB65@E-EXDAGE-A1.extra.cea.fr>
	<CABvS7QJdBEKDnY4Rj7ZaxoBmeQLPRGS7hqGb09ki0ePo5y8kpA@mail.gmail.com>
	<1341489274.3868.2.camel@ulisse.cm.sissa.it>
Message-ID: <CABvS7Q+wXQENhYfSZMYnDtSziyCOwcn-VO3LYOdvVtwns8qpyw@mail.gmail.com>

Dear Andrea,

>This option is not implemented. You cannot do a finite electric >field
>calculation with spin-orbit coupling.


I have done electric field + SOC calculation already as suggested by
Professor Gabriele Sclauzero.
Now the question is how to get spin up and spin down bnads?

Best, Kaloni


On Thu, Jul 5, 2012 at 2:54 PM, Andrea Dal Corso <dalcorso at sissa.it> wrote:

>
> On Thu, 2012-07-05 at 14:27 +0300, Thaneshwor Kaloni wrote:
> > Dear Professor Cyrille,
> >
> >
> > Thank you very much for your prompt and kind reply.
> > But still I am getting following kind of error with inclusion of
> > nspin=4
> >
> >
> >  from iosys : error #         1
> >      LSDA not available with electric field
>
> This option is not implemented. You cannot do a finite electric field
> calculation with spin-orbit coupling.
>
> HTH
>
> Andrea
>
>
> >
> >
> >
> > On Thu, Jul 5, 2012 at 2:18 PM, BARRETEAU Cyrille
> > <cyrille.barreteau at cea.fr> wrote:
> >         If you want to use SOC or do non-collinear caculation you
> >         should take nspin=4
> >         (If you do not define nspin it will be automatically be set to
> >         4)
> >
> >           Cyrille
> >
> >
> >         ============================================================
> >         Cyrille Barreteau                                 phone :      +33
> (0)1 69 08 29 51
> >         CEA Saclay                                       cellphone:   +33
> (0)6 47 53 66 52
> >         IRAMIS, SPCSI,  Bat. 462                fax :            +33
> (0)1 69 08 84 46
> >         91191 Gif sur Yvette Cedex               email:
> cyrille.barreteau at cea.fr
> >         FRANCE
> >         ~~~~~~~~~~~~~~~~~~~~~~~~
> >         Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/
> >         ==============================================================
> >
> >         ______________________________________________________________
> >         De : pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org]
> >         de la part de Thaneshwor Kaloni [tkaloni at gmail.com]
> >         Date d'envoi : jeudi 5 juillet 2012 12:47
> >         ? : pw_forum
> >         Objet : [Pw_forum] error with spin polarized calculation with
> >         SOC
> >
> >
> >
> >         Dear QE Users,
> >
> >
> >         I would like to perform spin polarized calculations with SOC.
> >         I am receiving following errors. Could anyone please assist
> >         me?
> >
> >
> >
> >
> >         **************************************
> >         INPUT
> >         ***************************************
> >         &control
> >             calculation='scf',
> >             restart_mode='from_scratch',
> >             prefix='C',
> >             pseudo_dir = '/home/kalonitp/code/pseudo/',
> >             outdir='t/',
> >             tefield = .true.
> >             dipfield = .true.
> >         /
> >          &system
> >             ibrav = 4, a=3.86, b=3.86,
> >             c=15,cosac=0.0, cosbc=0.0, cosab=-0.5
> >             nat=2, ntyp=1, nbnd=10,
> >             ecutwfc =60,
> >             occupations='smearing',smearing='gaussian', degauss=0.05,
> >             lspinorb=.true.
> >             noncolin=.true.
> >             nspin=2,
> >             starting_magnetization=0.7
> >             london=.true.
> >             edir = 3
> >             eamp = 0.001
> >             emaxpos = 0.5
> >             eopreg = 0.1
> >         /
> >          &ELECTRONS
> >             mixing_beta=0.7,
> >             conv_thr = 1.0D-6,
> >         /
> >         ATOMIC_SPECIES
> >         Si    28.0855     Si.pbe-rrkj.UPF
> >         ATOMIC_POSITIONS (crystal)
> >         Si      -0.001668875  -0.003337750   0.007491059
> >         Si       0.331668875   0.663337750   0.037508941
> >         K_POINTS {automatic}
> >         8 8 1 0 0 0
> >
> >
> >         ******************************************************
> >         OUTPUT
> >         *************************************************************
> >              Program PWSCF v.4.3.1      starts on  5Jul2012 at
> >         11:13:34
> >
> >
> >              This program is part of the open-source Quantum ESPRESSO
> >         suite
> >              for quantum simulation of materials; please cite
> >                  "P. Giannozzi et al., J. Phys.:Condens. Matter 21
> >         395502 (2009);
> >                   URL http://www.quantum-espresso.org",
> >              in publications or presentations arising from this work.
> >         More details at
> >
> >
> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
> >
> >
> >              Parallel version (MPI), running on    10 processors
> >              R & G space division:  proc/pool =   10
> >
> >
> >              Current dimensions of program PWSCF are:
> >              Max number of different atomic species (ntypx) = 10
> >              Max number of k-points (npk) =  40000
> >              Max angular momentum in pseudopotentials (lmaxx) =  3
> >              Waiting for input...
> >              Presently no symmetry can be used with electric field
> >
> >
> >          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >         %%%%%%%%%%%%%%%%%
> >              from iosys : error #         1
> >              noncolin .and. nspin==2 are conflicting flags
> >          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >         %%%%%%%%%%%%%%%%%
> >
> >
> >              stopping ...
> >
> >
> >         Best, Kaloni
> >         King Abdullah University of Science and Technology
> >         KSA, Saudi Arabia
> >
> >
> >
> >
> > --
> > Best regards, Kaloni
> > Web page:
> > http://sa.linkedin.com/pub/thaneshwor-kaloni/18/955/238
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> --
> Andrea Dal Corso                    Tel. 0039-040-3787428
> SISSA, Via Bonomea 265              Fax. 0039-040-3787249
> I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it
>
>
>


-- 
Best regards, Kaloni
Web page:
http://sa.linkedin.com/pub/thaneshwor-kaloni/18/955/238
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From giannozz at democritos.it  Thu Jul  5 14:10:25 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 5 Jul 2012 14:10:25 +0200
Subject: [Pw_forum] unit cell of Beta-GaSe crystal
In-Reply-To: <CAA_hC0kzFvoCceWXDkwoGhFXJqGJwF0XrNziMSGYTMZKmsbqGQ@mail.gmail.com>
References: <CAA_hC0kzFvoCceWXDkwoGhFXJqGJwF0XrNziMSGYTMZKmsbqGQ@mail.gmail.com>
Message-ID: <F29595B1-FA06-40AE-9D25-617297A2A314@democritos.it>


On Jul 5, 2012, at 13:04 , Ay?a K?ra?as? wrote:

> Altough I tried so hard, I couldn't set up unit cell of B-GaSe in  
> Pwscf

had you tried so hard, you would have noticed that there is something
strange in the third column of your atomic positions: the numbers run
from 0.1 to 0.9 in units of the lattice parameter a=3.73A, while your
third lattice vector is c=15.9A long

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From dalcorso at sissa.it  Thu Jul  5 14:15:52 2012
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Thu, 05 Jul 2012 14:15:52 +0200
Subject: [Pw_forum] RE : error with spin polarized calculation with SOC
In-Reply-To: <CABvS7Q+wXQENhYfSZMYnDtSziyCOwcn-VO3LYOdvVtwns8qpyw@mail.gmail.com>
References: <CABvS7QLBmkFZZNbtG6XfV8mjnhvm9a-kD4T3eHVf=4oDjy9_8A@mail.gmail.com>
	<6E80B49CBC3D9F4694B510228B88EE3C1ABB65@E-EXDAGE-A1.extra.cea.fr>
	<CABvS7QJdBEKDnY4Rj7ZaxoBmeQLPRGS7hqGb09ki0ePo5y8kpA@mail.gmail.com>
	<1341489274.3868.2.camel@ulisse.cm.sissa.it>
	<CABvS7Q+wXQENhYfSZMYnDtSziyCOwcn-VO3LYOdvVtwns8qpyw@mail.gmail.com>
Message-ID: <1341490552.3868.12.camel@ulisse.cm.sissa.it>

You did an unsupported calculation by removing the error message.
The tefield case might work, while the lefield case is not implemented.
Please check the postprocessing tool bands.x to get the expectation
value of the spin for each band. This will tell you approximately which
bands have mainly spin up and which have mainly spin-down, but note that
with spin orbit, bands are not eigenstates of the spin.

HTH

Andrea

On Thu, 2012-07-05 at 14:59 +0300, Thaneshwor Kaloni wrote:
> Dear Andrea,
> 
> 
> >This option is not implemented. You cannot do a finite electric
> >field
> >calculation with spin-orbit coupling.
> 
> 
> I have done electric field + SOC calculation already as suggested by
> Professor Gabriele Sclauzero.
> Now the question is how to get spin up and spin down bnads?
> 
> 
> Best, Kaloni
> 
> 
> 
> 
> On Thu, Jul 5, 2012 at 2:54 PM, Andrea Dal Corso <dalcorso at sissa.it>
> wrote:
>         
>         On Thu, 2012-07-05 at 14:27 +0300, Thaneshwor Kaloni wrote:
>         > Dear Professor Cyrille,
>         >
>         >
>         > Thank you very much for your prompt and kind reply.
>         > But still I am getting following kind of error with
>         inclusion of
>         > nspin=4
>         >
>         >
>         >  from iosys : error #         1
>         >      LSDA not available with electric field
>         
>         
>         This option is not implemented. You cannot do a finite
>         electric field
>         calculation with spin-orbit coupling.
>         
>         HTH
>         
>         Andrea
>         
>         
>         >
>         >
>         >
>         > On Thu, Jul 5, 2012 at 2:18 PM, BARRETEAU Cyrille
>         > <cyrille.barreteau at cea.fr> wrote:
>         >         If you want to use SOC or do non-collinear
>         caculation you
>         >         should take nspin=4
>         >         (If you do not define nspin it will be automatically
>         be set to
>         >         4)
>         >
>         >           Cyrille
>         >
>         >
>         >
>         ============================================================
>         >         Cyrille Barreteau
>         phone :      +33 (0)1 69 08 29 51
>         >         CEA Saclay
>         cellphone:   +33 (0)6 47 53 66 52
>         >         IRAMIS, SPCSI,  Bat. 462                fax :
>              +33 (0)1 69 08 84 46
>         >         91191 Gif sur Yvette Cedex               email:
>                cyrille.barreteau at cea.fr
>         >         FRANCE
>         >         ~~~~~~~~~~~~~~~~~~~~~~~~
>         >         Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/
>         >
>         ==============================================================
>         >
>         
>         >
>         ______________________________________________________________
>         >         De : pw_forum-bounces at pwscf.org
>         [pw_forum-bounces at pwscf.org]
>         >         de la part de Thaneshwor Kaloni [tkaloni at gmail.com]
>         >         Date d'envoi : jeudi 5 juillet 2012 12:47
>         >         ? : pw_forum
>         >         Objet : [Pw_forum] error with spin polarized
>         calculation with
>         >         SOC
>         >
>         >
>         >
>         >         Dear QE Users,
>         >
>         >
>         >         I would like to perform spin polarized calculations
>         with SOC.
>         >         I am receiving following errors. Could anyone please
>         assist
>         >         me?
>         >
>         >
>         >
>         >
>         >         **************************************
>         >         INPUT
>         >         ***************************************
>         >         &control
>         >             calculation='scf',
>         >             restart_mode='from_scratch',
>         >             prefix='C',
>         >             pseudo_dir = '/home/kalonitp/code/pseudo/',
>         >             outdir='t/',
>         >             tefield = .true.
>         >             dipfield = .true.
>         >         /
>         >          &system
>         >             ibrav = 4, a=3.86, b=3.86,
>         >             c=15,cosac=0.0, cosbc=0.0, cosab=-0.5
>         >             nat=2, ntyp=1, nbnd=10,
>         >             ecutwfc =60,
>         >             occupations='smearing',smearing='gaussian',
>         degauss=0.05,
>         >             lspinorb=.true.
>         >             noncolin=.true.
>         >             nspin=2,
>         >             starting_magnetization=0.7
>         >             london=.true.
>         >             edir = 3
>         >             eamp = 0.001
>         >             emaxpos = 0.5
>         >             eopreg = 0.1
>         >         /
>         >          &ELECTRONS
>         >             mixing_beta=0.7,
>         >             conv_thr = 1.0D-6,
>         >         /
>         >         ATOMIC_SPECIES
>         >         Si    28.0855     Si.pbe-rrkj.UPF
>         >         ATOMIC_POSITIONS (crystal)
>         >         Si      -0.001668875  -0.003337750   0.007491059
>         >         Si       0.331668875   0.663337750   0.037508941
>         >         K_POINTS {automatic}
>         >         8 8 1 0 0 0
>         >
>         >
>         >
>         ******************************************************
>         >         OUTPUT
>         >
>         *************************************************************
>         >              Program PWSCF v.4.3.1      starts on  5Jul2012
>         at
>         >         11:13:34
>         >
>         >
>         >              This program is part of the open-source Quantum
>         ESPRESSO
>         >         suite
>         >              for quantum simulation of materials; please
>         cite
>         >                  "P. Giannozzi et al., J. Phys.:Condens.
>         Matter 21
>         >         395502 (2009);
>         >                   URL http://www.quantum-espresso.org",
>         >              in publications or presentations arising from
>         this work.
>         >         More details at
>         >
>         >
>          http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
>         >
>         >
>         >              Parallel version (MPI), running on    10
>         processors
>         >              R & G space division:  proc/pool =   10
>         >
>         >
>         >              Current dimensions of program PWSCF are:
>         >              Max number of different atomic species (ntypx)
>         = 10
>         >              Max number of k-points (npk) =  40000
>         >              Max angular momentum in pseudopotentials
>         (lmaxx) =  3
>         >              Waiting for input...
>         >              Presently no symmetry can be used with electric
>         field
>         >
>         >
>         >          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>         %%%%%%%%%%
>         >         %%%%%%%%%%%%%%%%%
>         >              from iosys : error #         1
>         >              noncolin .and. nspin==2 are conflicting flags
>         >          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>         %%%%%%%%%%
>         >         %%%%%%%%%%%%%%%%%
>         >
>         >
>         >              stopping ...
>         >
>         >
>         >         Best, Kaloni
>         >         King Abdullah University of Science and Technology
>         >         KSA, Saudi Arabia
>         >
>         >
>         >
>         >
>         > --
>         > Best regards, Kaloni
>         > Web page:
>         > http://sa.linkedin.com/pub/thaneshwor-kaloni/18/955/238
>         >
>         >
>         >
>         >
>         >
>         >
>         
>         > _______________________________________________
>         > Pw_forum mailing list
>         > Pw_forum at pwscf.org
>         > http://www.democritos.it/mailman/listinfo/pw_forum
>         --
>         Andrea Dal Corso                    Tel. 0039-040-3787428
>         SISSA, Via Bonomea 265              Fax. 0039-040-3787249
>         I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it
>         
>         
> 
> 
> 
> 
> -- 
> Best regards, Kaloni
> Web page:
> http://sa.linkedin.com/pub/thaneshwor-kaloni/18/955/238
> 
> 
> 
> 
> 
> 
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Bonomea 265              Fax. 0039-040-3787249
I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it



From manojnarayan86 at gmail.com  Thu Jul  5 14:24:18 2012
From: manojnarayan86 at gmail.com (manoj narayanan)
Date: Thu, 5 Jul 2012 17:54:18 +0530
Subject: [Pw_forum] core level shifting calculation
Message-ID: <CAFy9Os=9OsCGG8tgC6nkTZ0RPK+-iGrKbcROREK0Yx2RQVk0xQ@mail.gmail.com>

Dear pwscf users
                                       I was trying to calculate the core
level shifting of Al (111) and Cu surface using quantum espresso. Is it
necessary to use core excited pseudo potential or as in Z+1 approximation
or equivalent core approximation can we use another pseudo potential of
next atom , for example Si in case of Al and Zn for Cu ? Also when I ran a
 calculation for Al (using Si PP) in the output for initial state shift I
got a warning "BEWARE: shift with CC never tested !!! ". Can anyone please
tell me what it is and why it comes

Thank you all
Manoj Narayan Hela
Allahabad University
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From gabriele.sclauzero at epfl.ch  Thu Jul  5 14:28:11 2012
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Thu, 5 Jul 2012 14:28:11 +0200
Subject: [Pw_forum] RE : error with spin polarized calculation with SOC
In-Reply-To: <CABvS7Q+wXQENhYfSZMYnDtSziyCOwcn-VO3LYOdvVtwns8qpyw@mail.gmail.com>
References: <CABvS7QLBmkFZZNbtG6XfV8mjnhvm9a-kD4T3eHVf=4oDjy9_8A@mail.gmail.com>
	<6E80B49CBC3D9F4694B510228B88EE3C1ABB65@E-EXDAGE-A1.extra.cea.fr>
	<CABvS7QJdBEKDnY4Rj7ZaxoBmeQLPRGS7hqGb09ki0ePo5y8kpA@mail.gmail.com>
	<1341489274.3868.2.camel@ulisse.cm.sissa.it>
	<CABvS7Q+wXQENhYfSZMYnDtSziyCOwcn-VO3LYOdvVtwns8qpyw@mail.gmail.com>
Message-ID: <D0D7474C-DE03-44BD-9A7C-5CF9BEE02F4C@epfl.ch>

Dear Kaloni,

Il giorno 05/lug/2012, alle ore 13.59, Thaneshwor Kaloni ha scritto
> Dear Andrea,
> 
> >This option is not implemented. You cannot do a finite electric >field
> >calculation with spin-orbit coupling.
> 
> 
> I have done electric field + SOC calculation already as suggested by Professor Gabriele Sclauzero.

Since Berry phase is not available with SOC, I suggested you to try with the sawtooth potential method.
Mine was just a suggestion, I had not actually checked inside the code at that time. 
I wonder how you managed to do such calculation if the electric field is not implemented for nspin=4 (non collinear). 
In order to include SOC you need nspin=4.

By the way, this forum is rather informal, you do not need to address people with titles here (moreover I'm not a professor).



Regards,


GS

? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne







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From aycakiragasi at gmail.com  Thu Jul  5 14:43:04 2012
From: aycakiragasi at gmail.com (=?ISO-8859-9?B?QXnnYSBL/XJh8GFz/Q==?=)
Date: Thu, 5 Jul 2012 15:43:04 +0300
Subject: [Pw_forum] unit cell of Beta-GaSe crystal
In-Reply-To: <F29595B1-FA06-40AE-9D25-617297A2A314@democritos.it>
References: <CAA_hC0kzFvoCceWXDkwoGhFXJqGJwF0XrNziMSGYTMZKmsbqGQ@mail.gmail.com>
	<F29595B1-FA06-40AE-9D25-617297A2A314@democritos.it>
Message-ID: <CAA_hC0k+gz=any4azyQ1ymFfNvA58ESVS=hWVoG2Dj+LYjcM8g@mail.gmail.com>

Dear Paolo Giannozzi,

Thank you so much for your helps, I have solved problem and created the
structure.

2012/7/5 Paolo Giannozzi <giannozz at democritos.it>

>
> On Jul 5, 2012, at 13:04 , Ay?a K?ra?as? wrote:
>
> > Altough I tried so hard, I couldn't set up unit cell of B-GaSe in
> > Pwscf
>
> had you tried so hard, you would have noticed that there is something
> strange in the third column of your atomic positions: the numbers run
> from 0.1 to 0.9 in units of the lattice parameter a=3.73A, while your
> third lattice vector is c=15.9A long
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From giannozz at democritos.it  Thu Jul  5 15:32:19 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 5 Jul 2012 15:32:19 +0200
Subject: [Pw_forum] core level shifting calculation
In-Reply-To: <CAFy9Os=9OsCGG8tgC6nkTZ0RPK+-iGrKbcROREK0Yx2RQVk0xQ@mail.gmail.com>
References: <CAFy9Os=9OsCGG8tgC6nkTZ0RPK+-iGrKbcROREK0Yx2RQVk0xQ@mail.gmail.com>
Message-ID: <BAB7BFDE-96A5-4385-AB7A-E2F7BEDEB9FD@democritos.it>


On Jul 5, 2012, at 14:24 , manoj narayanan wrote:

> "BEWARE: shift with CC never tested !!! ". Can anyone please tell  
> me what it is

CC = core corrections: you are using pseudopotentials with non linear  
core corrections

> and why it comes

for the reason explained in the message itself.

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From d.tiana at bath.ac.uk  Thu Jul  5 21:17:39 2012
From: d.tiana at bath.ac.uk (Davide Tiana)
Date: Thu, 05 Jul 2012 20:17:39 +0100
Subject: [Pw_forum] I can't find the error :-(
Message-ID: <20120705201739.Horde.ZdWXaM1vlIJP9ehTZTC2DtA@webmail.bath.ac.uk>

Dear all,
sorry if I bother you with a silly pw input. I can't figure out why  
this input is wrong. Comparing with similar ones everything seems to  
be fine.
(I don't know if it is another clue but it can be open with no problem  
with PWgui).
Thanks in advanced for any helps you can give me.

where is the error in this input file?

&control
     calculation='relax',
     title='zigzag',
     wf_collect=.true.,
     outdir='./',
     prefix='zigzag',
     etot_conv_thr=5.0d-4,
     forc_conv_thr=1.0d-3,
  /
  &system
    ibrav=14,
    A=7.0008,
    B=9.7164,
    C=16.693,
    cosBC=?0.073568915,
    cosAC=?0.163584241,
    cosAB=?0.046461386,
    nat=53,
    ntyp=6,
    tot_charge=0.0,
    ecutwfc=45.0,
    ecutrho=450.0,
    nosym=.false.,
    nosym_evc=.false.,
    london=.true.,
    london_s6=0.75,
    london_rcut=200,
    occupations='smearing',
    smearing='marzari-vanderbilt'
    degauss=0.04
  /
  &electrons
    electron_maxstep=80,
    conv_thr=1.0d-6,
    mixing_mode='plain',
    mixing_beta=0.7,
    mixing_ndim=8,
    mixing_fixed_ns=0,
    diagonalization='david',
  /
  &ions
    ion_dynamics='bfgs',
    ion_positions='default',
    phase_space='full',
    pot_extrapolation='atomic',
    wfc_extrapolation='none',
    remove_rigid_rot=.false.,
    upscale=100.d0,
    bfgs_ndim=1,
    trust_radius_max=0.8D0,
    trust_radius_min=1.D-3,
    trust_radius_ini=0.5D0,
    w_1=0.01D0
    w_2=0.5D0
  /
  ATOMIC_SPECIES
    H  1.007   H.pw91-rrkjus.UPF
    C  12.011  C.pw91-n-rrkjus.UPF
    N  14.007  N.pw91-n-rrkjus.UPF
    O  15.999  O.pw91-n-rrkjus.UPF
    S  32.066  S.pw91-n-rrkjus.UPF
    Zn 65.409  Zn.pw91-dn-rrkjus.UPF
ATOMIC_POSITIONS (crystal)
Zn         0.578420  0.797930  0.245020
S          0.892900  0.754800  0.321720
S          0.532400  0.630140  0.359300
C          0.775600  0.651200  0.377600
C          0.893100  0.574400  0.441400
C          0.802500  0.499300  0.494300
C          1.092900  0.573600  0.448400
H          0.658484  0.497791  0.491135
H          1.162620  0.626518  0.411599
S          0.232700  0.793820  0.174940
S          0.513200  0.591440  0.145020
C          0.286200  0.648800  0.123000
C          0.138700  0.573400  0.060200
C          0.053700  0.395600 -0.051300
C          0.191700  0.466400  0.008600
H          0.093523  0.320982 -0.088598
H          0.329520  0.440313  0.014493
O          0.543300  0.972400  0.325600
C          0.401000  0.972900  0.360600
C          0.495200  1.200600  0.427500
C          0.202400  1.072700  0.453100
N          0.365000  1.076500  0.411100
H          0.312744  0.887449  0.347623
H          0.632077  1.173674  0.441456
H          0.461004  1.259340  0.474237
H          0.481812  1.253835  0.378051
H          0.200577  1.162451  0.486274
H          0.079775  1.057289  0.412588
H          0.213205  0.995558  0.489830
O          0.687700  0.922400  0.166600
C          0.597200  1.022500  0.140400
C          0.540300  1.212500  0.055600
C          0.818000  1.065600  0.046900
N          0.647900  1.095500  0.082600
H          0.481877  1.044650  0.166216
H          0.630783  1.296591  0.061083
H          0.437698  1.228952  0.089877
H          0.478294  1.192415 -0.002688
H          0.918244  1.143828  0.062698
H          0.781594  1.053830 -0.013740
H          0.871518  0.978618  0.067224
O          1.235300  0.156000  0.202600
C          1.085900  0.157600  0.233400
C          1.063400  0.403000  0.231000
C          0.820300  0.263900  0.285800
N          0.993400  0.269100  0.249500
H          1.037676  0.064331  0.245752
H          0.950768  0.458791  0.212031
H          1.143621  0.451642  0.281051
H          1.144441  0.391320  0.187189
H          0.711560  0.301097  0.248624
H          0.785186  0.165940  0.294816
H          0.844111  0.320974  0.339219
K_POINTS {automatic}
4 3 7 0 0 0



From mm2422 at cornell.edu  Thu Jul  5 21:30:43 2012
From: mm2422 at cornell.edu (MMS)
Date: Thu, 5 Jul 2012 15:30:43 -0400
Subject: [Pw_forum] Convergence issues with Bulk Magnesium
Message-ID: <CAB+vMKR5HSAkmQXxp_YxL5Q1vgONqGp0Wf82zAG87zXQSh+PtA@mail.gmail.com>

Hi,

I am trying to simulate bulk Mg in the hcp structure. Before beginning my
structural relaxation I wanted to test convergence of the energy values
with respect to ecutwfc. This is one of the input files.

&control
        calculation='scf'
        title='Mgscf'
        verbosity='high'
        restart_mode='from_scratch'
        prefix='Mg'
        tstress=.true.
        tprnfor=.true.
        pseudo_dir='./pseudo/'
        outdir='./'
/
&system
        ibrav=4
        celldm(1)=6.0
        celldm(3)=1.623
        nat=2
        ntyp=1
        nbnd=10
        ecutwfc=30
        ecutrho=240
        occupations='smearing'
        degauss=0.015
        smearing='mv'
/
&electrons
        diagonalization='david'
        mixing_mode='plain'
        mixing_beta=0.7
        conv_thr=1.0D-9
/
ATOMIC_SPECIES
Mg 24.305 Mg.pz-n-vbc.UPF
ATOMIC_POSITIONS {crystal}
Mg 1/3 2/3 1/4
Mg 2/3 1/3 3/4
K_POINTS {automatic}
6 6 4 0 0 0

I kept varying ecutwfc, and ecutrho was parametrized to be eight times
ecutwfc. I had used the perdew-zunger LDA pseudopotential.

Now the ecutwfc values versus the energy values in Rydberg are shown below
20 -4.28664244
30 -4.28693764
40 -4.28699724
50 -4.28701233
60 -4.28704753
70 -4.28717529
80 -4.28739243
90 -4.28771080
100 -4.28803666
110 -4.28853887
120 -4.28941450
130 -4.28990855
140 -4.29054764
150 -4.29142411
160 -4.29309040

What I notice is that the change in energy values (different between
successive values) initially start decreasing, but slowly start increasing
and oscillating but always positive, meaning that the energy was
continually decreasing. This doesnot help me conclude ecutwfc's convergence
point.

Now, I tried varying the degauss values and even tried increasing the k
points, but I still see the same behavior. Can I get some pointers in this
regard?

Meenakshi Sundaram
Graduate Student
Mechanical and Aerospace Engg.
Cornell
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From ttduyle at gmail.com  Thu Jul  5 21:43:05 2012
From: ttduyle at gmail.com (Duy Le)
Date: Thu, 5 Jul 2012 15:43:05 -0400
Subject: [Pw_forum] I can't find the error :-(
In-Reply-To: <20120705201739.Horde.ZdWXaM1vlIJP9ehTZTC2DtA@webmail.bath.ac.uk>
References: <20120705201739.Horde.ZdWXaM1vlIJP9ehTZTC2DtA@webmail.bath.ac.uk>
Message-ID: <CAF-j6z8Y1jmDTB1Rh0k5Vz8NzDKbsPNJG9FwZy8P0P-GW6xJCw@mail.gmail.com>

It is usually easier for pwscfers to help you if you post error messages as
well.

BTW, what are the question marks (?) in cosAB... standing for?

-D

----------------------------------------------------
Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Thu, Jul 5, 2012 at 3:17 PM, Davide Tiana <d.tiana at bath.ac.uk> wrote:

> Dear all,
> sorry if I bother you with a silly pw input. I can't figure out why
> this input is wrong. Comparing with similar ones everything seems to
> be fine.
> (I don't know if it is another clue but it can be open with no problem
> with PWgui).
> Thanks in advanced for any helps you can give me.
>
> where is the error in this input file?
>
> &control
>      calculation='relax',
>      title='zigzag',
>      wf_collect=.true.,
>      outdir='./',
>      prefix='zigzag',
>      etot_conv_thr=5.0d-4,
>      forc_conv_thr=1.0d-3,
>   /
>   &system
>     ibrav=14,
>     A=7.0008,
>     B=9.7164,
>     C=16.693,
>     cosBC=?0.073568915,
>     cosAC=?0.163584241,
>     cosAB=?0.046461386,
>     nat=53,
>     ntyp=6,
>     tot_charge=0.0,
>     ecutwfc=45.0,
>     ecutrho=450.0,
>     nosym=.false.,
>     nosym_evc=.false.,
>     london=.true.,
>     london_s6=0.75,
>     london_rcut=200,
>     occupations='smearing',
>     smearing='marzari-vanderbilt'
>     degauss=0.04
>   /
>   &electrons
>     electron_maxstep=80,
>     conv_thr=1.0d-6,
>     mixing_mode='plain',
>     mixing_beta=0.7,
>     mixing_ndim=8,
>     mixing_fixed_ns=0,
>     diagonalization='david',
>   /
>   &ions
>     ion_dynamics='bfgs',
>     ion_positions='default',
>     phase_space='full',
>     pot_extrapolation='atomic',
>     wfc_extrapolation='none',
>     remove_rigid_rot=.false.,
>     upscale=100.d0,
>     bfgs_ndim=1,
>     trust_radius_max=0.8D0,
>     trust_radius_min=1.D-3,
>     trust_radius_ini=0.5D0,
>     w_1=0.01D0
>     w_2=0.5D0
>   /
>   ATOMIC_SPECIES
>     H  1.007   H.pw91-rrkjus.UPF
>     C  12.011  C.pw91-n-rrkjus.UPF
>     N  14.007  N.pw91-n-rrkjus.UPF
>     O  15.999  O.pw91-n-rrkjus.UPF
>     S  32.066  S.pw91-n-rrkjus.UPF
>     Zn 65.409  Zn.pw91-dn-rrkjus.UPF
> ATOMIC_POSITIONS (crystal)
> Zn         0.578420  0.797930  0.245020
> S          0.892900  0.754800  0.321720
> S          0.532400  0.630140  0.359300
> C          0.775600  0.651200  0.377600
> C          0.893100  0.574400  0.441400
> C          0.802500  0.499300  0.494300
> C          1.092900  0.573600  0.448400
> H          0.658484  0.497791  0.491135
> H          1.162620  0.626518  0.411599
> S          0.232700  0.793820  0.174940
> S          0.513200  0.591440  0.145020
> C          0.286200  0.648800  0.123000
> C          0.138700  0.573400  0.060200
> C          0.053700  0.395600 -0.051300
> C          0.191700  0.466400  0.008600
> H          0.093523  0.320982 -0.088598
> H          0.329520  0.440313  0.014493
> O          0.543300  0.972400  0.325600
> C          0.401000  0.972900  0.360600
> C          0.495200  1.200600  0.427500
> C          0.202400  1.072700  0.453100
> N          0.365000  1.076500  0.411100
> H          0.312744  0.887449  0.347623
> H          0.632077  1.173674  0.441456
> H          0.461004  1.259340  0.474237
> H          0.481812  1.253835  0.378051
> H          0.200577  1.162451  0.486274
> H          0.079775  1.057289  0.412588
> H          0.213205  0.995558  0.489830
> O          0.687700  0.922400  0.166600
> C          0.597200  1.022500  0.140400
> C          0.540300  1.212500  0.055600
> C          0.818000  1.065600  0.046900
> N          0.647900  1.095500  0.082600
> H          0.481877  1.044650  0.166216
> H          0.630783  1.296591  0.061083
> H          0.437698  1.228952  0.089877
> H          0.478294  1.192415 -0.002688
> H          0.918244  1.143828  0.062698
> H          0.781594  1.053830 -0.013740
> H          0.871518  0.978618  0.067224
> O          1.235300  0.156000  0.202600
> C          1.085900  0.157600  0.233400
> C          1.063400  0.403000  0.231000
> C          0.820300  0.263900  0.285800
> N          0.993400  0.269100  0.249500
> H          1.037676  0.064331  0.245752
> H          0.950768  0.458791  0.212031
> H          1.143621  0.451642  0.281051
> H          1.144441  0.391320  0.187189
> H          0.711560  0.301097  0.248624
> H          0.785186  0.165940  0.294816
> H          0.844111  0.320974  0.339219
> K_POINTS {automatic}
> 4 3 7 0 0 0
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From janette.wong at mail.utoronto.ca  Thu Jul  5 21:35:19 2012
From: janette.wong at mail.utoronto.ca (Janet Wong)
Date: Thu, 5 Jul 2012 19:35:19 +0000
Subject: [Pw_forum] I can't find the error :-(
In-Reply-To: <20120705201739.Horde.ZdWXaM1vlIJP9ehTZTC2DtA@webmail.bath.ac.uk>
References: <20120705201739.Horde.ZdWXaM1vlIJP9ehTZTC2DtA@webmail.bath.ac.uk>
Message-ID: <6D3C4797C791254CB5D576BF880C82A6223ED11C@BY2PRD0310MB388.namprd03.prod.outlook.com>

Hi Davide,

I think the source of your errors are the following lines:
ATOMIC_POSITIONS (crystal) <-- I think those rounded brackets "()"should be the squiggly brackets '{}' instead, Although I am sure if that makes a difference.
cosBC=?0.073568915, <--- the "?" should not be there
cosAC=?0.163584241,
cosAB=?0.046461386,

Best,
Janet

Janet Wong
Graduate Student
University of Toronto, Canada
________________________________________
From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] on behalf of Davide Tiana [d.tiana at bath.ac.uk]
Sent: Thursday, July 05, 2012 3:17 PM
To: pw-mailing_list
Subject: [Pw_forum] I can't find the error :-(

Dear all,
sorry if I bother you with a silly pw input. I can't figure out why
this input is wrong. Comparing with similar ones everything seems to
be fine.
(I don't know if it is another clue but it can be open with no problem
with PWgui).
Thanks in advanced for any helps you can give me.

where is the error in this input file?

&control
     calculation='relax',
     title='zigzag',
     wf_collect=.true.,
     outdir='./',
     prefix='zigzag',
     etot_conv_thr=5.0d-4,
     forc_conv_thr=1.0d-3,
  /
  &system
    ibrav=14,
    A=7.0008,
    B=9.7164,
    C=16.693,
    cosBC=?0.073568915,
    cosAC=?0.163584241,
    cosAB=?0.046461386,
    nat=53,
    ntyp=6,
    tot_charge=0.0,
    ecutwfc=45.0,
    ecutrho=450.0,
    nosym=.false.,
    nosym_evc=.false.,
    london=.true.,
    london_s6=0.75,
    london_rcut=200,
    occupations='smearing',
    smearing='marzari-vanderbilt'
    degauss=0.04
  /
  &electrons
    electron_maxstep=80,
    conv_thr=1.0d-6,
    mixing_mode='plain',
    mixing_beta=0.7,
    mixing_ndim=8,
    mixing_fixed_ns=0,
    diagonalization='david',
  /
  &ions
    ion_dynamics='bfgs',
    ion_positions='default',
    phase_space='full',
    pot_extrapolation='atomic',
    wfc_extrapolation='none',
    remove_rigid_rot=.false.,
    upscale=100.d0,
    bfgs_ndim=1,
    trust_radius_max=0.8D0,
    trust_radius_min=1.D-3,
    trust_radius_ini=0.5D0,
    w_1=0.01D0
    w_2=0.5D0
  /
  ATOMIC_SPECIES
    H  1.007   H.pw91-rrkjus.UPF
    C  12.011  C.pw91-n-rrkjus.UPF
    N  14.007  N.pw91-n-rrkjus.UPF
    O  15.999  O.pw91-n-rrkjus.UPF
    S  32.066  S.pw91-n-rrkjus.UPF
    Zn 65.409  Zn.pw91-dn-rrkjus.UPF
ATOMIC_POSITIONS (crystal)
Zn         0.578420  0.797930  0.245020
S          0.892900  0.754800  0.321720
S          0.532400  0.630140  0.359300
C          0.775600  0.651200  0.377600
C          0.893100  0.574400  0.441400
C          0.802500  0.499300  0.494300
C          1.092900  0.573600  0.448400
H          0.658484  0.497791  0.491135
H          1.162620  0.626518  0.411599
S          0.232700  0.793820  0.174940
S          0.513200  0.591440  0.145020
C          0.286200  0.648800  0.123000
C          0.138700  0.573400  0.060200
C          0.053700  0.395600 -0.051300
C          0.191700  0.466400  0.008600
H          0.093523  0.320982 -0.088598
H          0.329520  0.440313  0.014493
O          0.543300  0.972400  0.325600
C          0.401000  0.972900  0.360600
C          0.495200  1.200600  0.427500
C          0.202400  1.072700  0.453100
N          0.365000  1.076500  0.411100
H          0.312744  0.887449  0.347623
H          0.632077  1.173674  0.441456
H          0.461004  1.259340  0.474237
H          0.481812  1.253835  0.378051
H          0.200577  1.162451  0.486274
H          0.079775  1.057289  0.412588
H          0.213205  0.995558  0.489830
O          0.687700  0.922400  0.166600
C          0.597200  1.022500  0.140400
C          0.540300  1.212500  0.055600
C          0.818000  1.065600  0.046900
N          0.647900  1.095500  0.082600
H          0.481877  1.044650  0.166216
H          0.630783  1.296591  0.061083
H          0.437698  1.228952  0.089877
H          0.478294  1.192415 -0.002688
H          0.918244  1.143828  0.062698
H          0.781594  1.053830 -0.013740
H          0.871518  0.978618  0.067224
O          1.235300  0.156000  0.202600
C          1.085900  0.157600  0.233400
C          1.063400  0.403000  0.231000
C          0.820300  0.263900  0.285800
N          0.993400  0.269100  0.249500
H          1.037676  0.064331  0.245752
H          0.950768  0.458791  0.212031
H          1.143621  0.451642  0.281051
H          1.144441  0.391320  0.187189
H          0.711560  0.301097  0.248624
H          0.785186  0.165940  0.294816
H          0.844111  0.320974  0.339219
K_POINTS {automatic}
4 3 7 0 0 0


_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum



From giannozz at democritos.it  Thu Jul  5 21:50:32 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 5 Jul 2012 21:50:32 +0200
Subject: [Pw_forum] I can't find the error :-(
In-Reply-To: <20120705201739.Horde.ZdWXaM1vlIJP9ehTZTC2DtA@webmail.bath.ac.uk>
References: <20120705201739.Horde.ZdWXaM1vlIJP9ehTZTC2DtA@webmail.bath.ac.uk>
Message-ID: <5888645A-7665-4C0A-BFD1-774073EB07A8@democritos.it>


On Jul 5, 2012, at 21:17 , Davide Tiana wrote:

> I can't figure out why this input is wrong

I can't figure out why you do not specify "what" is wrong

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Thu Jul  5 21:53:54 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 5 Jul 2012 21:53:54 +0200
Subject: [Pw_forum] I can't find the error :-(
In-Reply-To: <6D3C4797C791254CB5D576BF880C82A6223ED11C@BY2PRD0310MB388.namprd03.prod.outlook.com>
References: <20120705201739.Horde.ZdWXaM1vlIJP9ehTZTC2DtA@webmail.bath.ac.uk>
	<6D3C4797C791254CB5D576BF880C82A6223ED11C@BY2PRD0310MB388.namprd03.prod.outlook.com>
Message-ID: <D1BBFD53-F03B-4AC9-8B89-5CD788EB1F51@democritos.it>


On Jul 5, 2012, at 21:35 , Janet Wong wrote:

> ATOMIC_POSITIONS (crystal) <-- I think those rounded brackets "()"
> should be the squiggly brackets '{}' instead

it doesn't make any difference: the code looks for keywords in the line,
gnores everything else

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From faccin.giovani at gmail.com  Thu Jul  5 22:15:04 2012
From: faccin.giovani at gmail.com (Giovani Faccin)
Date: Thu, 5 Jul 2012 16:15:04 -0400
Subject: [Pw_forum] Convergence issues with Bulk Magnesium
In-Reply-To: <CAB+vMKR5HSAkmQXxp_YxL5Q1vgONqGp0Wf82zAG87zXQSh+PtA@mail.gmail.com>
References: <CAB+vMKR5HSAkmQXxp_YxL5Q1vgONqGp0Wf82zAG87zXQSh+PtA@mail.gmail.com>
Message-ID: <CAK-VqZC4SCkpXpD6ca0Ezp9tdvhXmn4DhBUJ3XT0+D2JqujDHQ@mail.gmail.com>

Hi Meenakshi,

Perhaps it's not converging because some other parameter's error is larger
than the wfc one. To check it out, you could try this:

ecutwfc=50;  ecutrho=500    (which are not very high neither very low)

and now check the convergence with respect to:
a) degauss value;
b) k-points
c) number of bands (try with bands = 40 once just to be sure).

That said, one thing that is not clear to me: when you built that table,
you have changed the value of ecutwfc. But for each ecutwfc, did you
recalculate the ecutrho so that ecutrho = 8-12 * ecutwfc on each
calculation?

Regards,

Giovani Faccin
UFMS / Brazil


2012/7/5 MMS <mm2422 at cornell.edu>

> Hi,
>
> I am trying to simulate bulk Mg in the hcp structure. Before beginning my
> structural relaxation I wanted to test convergence of the energy values
> with respect to ecutwfc. This is one of the input files.
>
> &control
>         calculation='scf'
>         title='Mgscf'
>         verbosity='high'
>         restart_mode='from_scratch'
>         prefix='Mg'
>         tstress=.true.
>         tprnfor=.true.
>         pseudo_dir='./pseudo/'
>         outdir='./'
> /
> &system
>         ibrav=4
>         celldm(1)=6.0
>         celldm(3)=1.623
>         nat=2
>         ntyp=1
>         nbnd=10
>         ecutwfc=30
>         ecutrho=240
>         occupations='smearing'
>         degauss=0.015
>         smearing='mv'
> /
> &electrons
>         diagonalization='david'
>         mixing_mode='plain'
>         mixing_beta=0.7
>         conv_thr=1.0D-9
> /
> ATOMIC_SPECIES
> Mg 24.305 Mg.pz-n-vbc.UPF
> ATOMIC_POSITIONS {crystal}
> Mg 1/3 2/3 1/4
> Mg 2/3 1/3 3/4
> K_POINTS {automatic}
> 6 6 4 0 0 0
>
> I kept varying ecutwfc, and ecutrho was parametrized to be eight times
> ecutwfc. I had used the perdew-zunger LDA pseudopotential.
>
> Now the ecutwfc values versus the energy values in Rydberg are shown below
> 20 -4.28664244
> 30 -4.28693764
> 40 -4.28699724
> 50 -4.28701233
> 60 -4.28704753
> 70 -4.28717529
> 80 -4.28739243
> 90 -4.28771080
> 100 -4.28803666
> 110 -4.28853887
> 120 -4.28941450
> 130 -4.28990855
> 140 -4.29054764
> 150 -4.29142411
> 160 -4.29309040
>
> What I notice is that the change in energy values (different between
> successive values) initially start decreasing, but slowly start increasing
> and oscillating but always positive, meaning that the energy was
> continually decreasing. This doesnot help me conclude ecutwfc's convergence
> point.
>
> Now, I tried varying the degauss values and even tried increasing the k
> points, but I still see the same behavior. Can I get some pointers in this
> regard?
>
> Meenakshi Sundaram
> Graduate Student
> Mechanical and Aerospace Engg.
> Cornell
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From d.tiana at bath.ac.uk  Thu Jul  5 22:40:55 2012
From: d.tiana at bath.ac.uk (Davide Tiana)
Date: Thu, 05 Jul 2012 21:40:55 +0100
Subject: [Pw_forum] I can't find the error
In-Reply-To: <mailman.3745.1341519306.9401.pw_forum@pwscf.org>
References: <mailman.3745.1341519306.9401.pw_forum@pwscf.org>
Message-ID: <20120705214055.Horde.kb6CTs1vlIJP9fvX8TYWaRA@webmail.bath.ac.uk>

Dear again,
thanks for helping.

@Duy
> It is usually easier for pwscfers to help you if you post error messages as
> well.

sorry about that, I did not post it since I guess the error is a wrong  
digit somewhere. However:


   
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      from  read_namelists  : error #      5010
       reading namelist system
   
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


>
> BTW, what are the question marks (?) in cosAB... standing for?

well in the original input they are -. Something horrible happened  
open the file with abiword (to copy and paste here). so nothing to  
worry about that.


@Paolo
>
>
> On Jul 5, 2012, at 21:17 , Davide Tiana wrote:
>
>> I can't figure out why this input is wrong
>
> I can't figure out why you do not specify "what" is wrong
>
> P.
> ---

Sorry if I was too cryptic. That is the problem. From my side the  
input should be fine but it push out the error I post above in the  
message. i.e. there is something wrong inside but I am not able to  
find where it is wrong.


From degironc at sissa.it  Thu Jul  5 23:00:44 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 05 Jul 2012 23:00:44 +0200
Subject: [Pw_forum] I can't find the error
In-Reply-To: <20120705214055.Horde.kb6CTs1vlIJP9fvX8TYWaRA@webmail.bath.ac.uk>
References: <mailman.3745.1341519306.9401.pw_forum@pwscf.org>
	<20120705214055.Horde.kb6CTs1vlIJP9fvX8TYWaRA@webmail.bath.ac.uk>
Message-ID: <4FF6007C.1010700@sissa.it>

On 07/05/2012 10:40 PM, Davide Tiana wrote:
>
>> BTW, what are the question marks (?) in cosAB... standing for?
> well in the original input they are -. Something horrible happened
> open the file with abiword (to copy and paste here). so nothing to
> worry about that.
>
so maybe there is some horrible non-printable characters in your input...

why don't you create a new input file taking a working one and typing in 
the data using a simple editor and try again ?

stefano

From ttduyle at gmail.com  Thu Jul  5 23:02:09 2012
From: ttduyle at gmail.com (Duy Le)
Date: Thu, 5 Jul 2012 17:02:09 -0400
Subject: [Pw_forum] I can't find the error
In-Reply-To: <20120705214055.Horde.kb6CTs1vlIJP9fvX8TYWaRA@webmail.bath.ac.uk>
References: <mailman.3745.1341519306.9401.pw_forum@pwscf.org>
	<20120705214055.Horde.kb6CTs1vlIJP9fvX8TYWaRA@webmail.bath.ac.uk>
Message-ID: <CAF-j6z9t1-2vi5qjf697tUM2anorVGSXZTypf0jAeh3ti4in0Q@mail.gmail.com>

On Thu, Jul 5, 2012 at 4:40 PM, Davide Tiana <d.tiana at bath.ac.uk> wrote:

> Dear again,
> thanks for helping.
>
> @Duy
> > It is usually easier for pwscfers to help you if you post error messages
> as
> > well.
>
> sorry about that, I did not post it since I guess the error is a wrong
> digit somewhere. However:
>
>
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       from  read_namelists  : error #      5010
>        reading namelist system
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> So, focus on this section. Adding commas to the last two keywords

>
> >
> > BTW, what are the question marks (?) in cosAB... standing for?
>
> well in the original input they are -. Something horrible happened
> open the file with abiword (to copy and paste here). so nothing to
> worry about that.
>
> Fix it. Until you can copy and paste exactly what you want to this email,
PWscf won't be able to run.

----------------------------------------------------
Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


>
> @Paolo
> >
> >
> > On Jul 5, 2012, at 21:17 , Davide Tiana wrote:
> >
> >> I can't figure out why this input is wrong
> >
> > I can't figure out why you do not specify "what" is wrong
> >
> > P.
> > ---
>
> Sorry if I was too cryptic. That is the problem. From my side the
> input should be fine but it push out the error I post above in the
> message. i.e. there is something wrong inside but I am not able to
> find where it is wrong.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From mm2422 at cornell.edu  Thu Jul  5 23:05:59 2012
From: mm2422 at cornell.edu (MMS)
Date: Thu, 5 Jul 2012 17:05:59 -0400
Subject: [Pw_forum] Convergence issues with Bulk Magnesium
In-Reply-To: <CAB+vMKR5HSAkmQXxp_YxL5Q1vgONqGp0Wf82zAG87zXQSh+PtA@mail.gmail.com>
References: <CAB+vMKR5HSAkmQXxp_YxL5Q1vgONqGp0Wf82zAG87zXQSh+PtA@mail.gmail.com>
Message-ID: <CAB+vMKT0d=QR++uYPKgoPLjoyLH6NtCKbVz4nki9QpgRKfqN_Q@mail.gmail.com>

Dear Giovanni,

Thanks a lot for helping me out. With regard to your suggestions

1. The calculations converge w.r.t nbnds. The energy values for
nbnds=10 and nbnds=40 are identical with ecutwfc=50 and ecutrho=500.
2. With regard to degauss value how should I perform the convergence?
   Should I just increase it from say 0.02Ry to 0.06Ry and study the
energy values?
   While searching the forums I came across this thread
   http://www.democritos.it/pipermail/pw_forum/2008-January/008157.html
   which tells me that I should find a k-point set and a smearing
value that kind of complement each other. So how do I do that?
3. I have a question regarding k point test.
   I always thought that the calculations were performed per k point
and then summed up to find the total integral value.
   So, is it not enough to have a moderate sized k point mesh
initially to test out the convergence of the
   ecutwfc values and then followed by a k point convergence test?

4. Lastly, I find ecutrho every time I update ecutwfc when I had
formed that table.

I once again thank you for helping me out.

Regards

Meenakshi Sundaram
Graduate Student
Mechanical and Aerospace Engg.
Cornell
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From ejwalt at wm.edu  Thu Jul  5 23:06:14 2012
From: ejwalt at wm.edu (Eric J. Walter)
Date: Thu, 05 Jul 2012 17:06:14 -0400
Subject: [Pw_forum] I can't find the error
In-Reply-To: <4FF6007C.1010700@sissa.it>
References: <mailman.3745.1341519306.9401.pw_forum@pwscf.org>
	<20120705214055.Horde.kb6CTs1vlIJP9fvX8TYWaRA@webmail.bath.ac.uk>
	<4FF6007C.1010700@sissa.it>
Message-ID: <4FF601C6.5020008@wm.edu>



cat -vte <file>

works well for finding bad characters.

Eric


On 07/05/2012 05:00 PM, Stefano de Gironcoli wrote:
> On 07/05/2012 10:40 PM, Davide Tiana wrote:
>>> BTW, what are the question marks (?) in cosAB... standing for?
>> well in the original input they are -. Something horrible happened
>> open the file with abiword (to copy and paste here). so nothing to
>> worry about that.
>>
> so maybe there is some horrible non-printable characters in your input...
>
> why don't you create a new input file taking a working one and typing in
> the data using a simple editor and try again ?
>
> stefano
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From lorenzo.paulatto at impmc.upmc.fr  Thu Jul  5 23:14:55 2012
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 5 Jul 2012 23:14:55 +0200
Subject: [Pw_forum] Convergence issues with Bulk Magnesium
In-Reply-To: <CAB+vMKR5HSAkmQXxp_YxL5Q1vgONqGp0Wf82zAG87zXQSh+PtA@mail.gmail.com>
References: <CAB+vMKR5HSAkmQXxp_YxL5Q1vgONqGp0Wf82zAG87zXQSh+PtA@mail.gmail.com>
Message-ID: <CAG+GtJc28i2Gwvz9ZfsOXM73_dV4E8XDsnRR8X=yXHdgS06xpA@mail.gmail.com>

On Thu, Jul 5, 2012 at 9:30 PM, MMS <mm2422 at cornell.edu> wrote:

> Mg 24.305 Mg.pz-n-vbc.UPF
>

This pseudopotential is actually norm.conserving (there is an error in the
web site, but you can check directly in the UPF file yourself). So you do
not need to specify ecutrho.


>
> Now, I tried varying the degauss values and even tried increasing the k
> points, but I still see the same behavior. Can I get some pointers in this
> regard?
>
>
This fact would suggest that the pseudopotential has a ghost state at very
high energy. This is not necessarily a problem, every pseudo do, i.e. no
vbc pseudopotential is equivalent to a real atom up to infinite energy. In
your case the energy is converged at 30 Ry; at 60ry there is some problem.

Try again without ecutrho to see if you can get a clear convergece, if you
do not find clearly a convergence energy I suggest you use another pseudo

-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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From mm2422 at cornell.edu  Thu Jul  5 23:30:50 2012
From: mm2422 at cornell.edu (MMS)
Date: Thu, 5 Jul 2012 17:30:50 -0400
Subject: [Pw_forum] Convergence issues with Bulk Magnesium
In-Reply-To: <CAB+vMKT0d=QR++uYPKgoPLjoyLH6NtCKbVz4nki9QpgRKfqN_Q@mail.gmail.com>
References: <CAB+vMKR5HSAkmQXxp_YxL5Q1vgONqGp0Wf82zAG87zXQSh+PtA@mail.gmail.com>
	<CAB+vMKT0d=QR++uYPKgoPLjoyLH6NtCKbVz4nki9QpgRKfqN_Q@mail.gmail.com>
Message-ID: <CAB+vMKT5kVV0Zo05M5ufQD6eL=xB9_AZ_K_a2XmfDNzcvhi6wg@mail.gmail.com>

Dear Lorenzo,

That helped. Once I removed ecutrho, it converged. You made my day. Thanks
:)

Peace
Meenakshi Sundaram
Graduate Student
Mechanical and Aerospace Engg.
Cornell
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From abmus007 at gmail.com  Fri Jul  6 08:03:30 2012
From: abmus007 at gmail.com (Abolore Musari)
Date: Fri, 6 Jul 2012 07:03:30 +0100
Subject: [Pw_forum] bamd structure of FeS2
Message-ID: <CAOP21kJW6FNCzP3usK3geWwvUu1COqVnzSDxDd-ySBPGCqW=DA@mail.gmail.com>

Dear QE users
Sir I am doing some calculations on FeS2 which is a diamagnetic
semiconductor of expt band gap of 0.9eV and i got this band structure
attached to this mail aand I would like to ask if it is possible for some
band from valence band to cross fermi level for a semiconductor material as
seen in the figure in whjch band at the edges crosses the fermi level and
if it is correct is there any explanation for this.

Thanks

Musari Abolore
Ph.d student
Physics dept
University of Agriculture Nigeria
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From giannozz at democritos.it  Fri Jul  6 09:09:30 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 6 Jul 2012 09:09:30 +0200
Subject: [Pw_forum] bamd structure of FeS2
In-Reply-To: <CAOP21kJW6FNCzP3usK3geWwvUu1COqVnzSDxDd-ySBPGCqW=DA@mail.gmail.com>
References: <CAOP21kJW6FNCzP3usK3geWwvUu1COqVnzSDxDd-ySBPGCqW=DA@mail.gmail.com>
Message-ID: <DB68C654-838E-41E6-B72E-2D807CAD5B9E@democritos.it>


On Jul 6, 2012, at 8:03 , Abolore Musari wrote:

> I would like to ask if it is possible for some band from valence
> band to cross fermi level for a semiconductor material

if a band crosses the Fermi energy, it is not a semiconductor,
by definition.

> is there any explanation for this.


there is a gap in your band strcture. Tthe Fermi energy is not where
you placed it but 1eV or so above, somewhere in the gap

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From manojnarayan86 at gmail.com  Fri Jul  6 09:13:29 2012
From: manojnarayan86 at gmail.com (manoj narayanan)
Date: Fri, 6 Jul 2012 12:43:29 +0530
Subject: [Pw_forum] core level shifting calculation
In-Reply-To: <CAFy9Os=9OsCGG8tgC6nkTZ0RPK+-iGrKbcROREK0Yx2RQVk0xQ@mail.gmail.com>
References: <CAFy9Os=9OsCGG8tgC6nkTZ0RPK+-iGrKbcROREK0Yx2RQVk0xQ@mail.gmail.com>
Message-ID: <CAFy9Os=3G=sp4MxyzGN0F5zEzTg6ZLRPs20S+hhG82ppDt4WEA@mail.gmail.com>

Thank you Prof. *Paolo Giannozzi* for the reply.   So is it ok to use the
Z+1 approximation rather than using core excited pseudo potential ?


Regards

Manoj
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From giannozz at democritos.it  Fri Jul  6 09:25:00 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 6 Jul 2012 09:25:00 +0200
Subject: [Pw_forum] core level shifting calculation
In-Reply-To: <CAFy9Os=3G=sp4MxyzGN0F5zEzTg6ZLRPs20S+hhG82ppDt4WEA@mail.gmail.com>
References: <CAFy9Os=9OsCGG8tgC6nkTZ0RPK+-iGrKbcROREK0Yx2RQVk0xQ@mail.gmail.com>
	<CAFy9Os=3G=sp4MxyzGN0F5zEzTg6ZLRPs20S+hhG82ppDt4WEA@mail.gmail.com>
Message-ID: <7E99F15C-2046-4774-931B-192AB3A8B9B1@democritos.it>


On Jul 6, 2012, at 9:13 , manoj narayanan wrote:

>  So is it ok to use the Z+1 approximation rather
> than using core excited pseudo potential ?

this is about physics, not about software, and the answer
should be found in papers.

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From d.tiana at bath.ac.uk  Fri Jul  6 11:01:36 2012
From: d.tiana at bath.ac.uk (Davide Tiana)
Date: Fri, 06 Jul 2012 10:01:36 +0100
Subject: [Pw_forum] I can't find the error (SOLVED!)
In-Reply-To: <mailman.3752.1341554625.9401.pw_forum@pwscf.org>
References: <mailman.3752.1341554625.9401.pw_forum@pwscf.org>
Message-ID: <20120706100136.Horde.BY4jQc1vlIJP9qlwjmjxMnA@webmail.bath.ac.uk>

> so maybe there is some horrible non-printable characters in your input...
>
> why don't you create a new input file taking a working one and typing in
> the data using a simple editor and try again ?
>
> stefano
>
>
> cat -vte <file>
>
> works well for finding bad characters.
>
> Eric
>

Here we are. That was the problem.

cat -vte opt.in

    cosBC=M-bM-^HM-^R0.073568915,$
    cosAC=M-bM-^HM-^R0.163584241,$
    cosAB=M-bM-^HM-^R0.046461386,$

Originated copy and paste from calculator.

Thanks all of you
Davide


From nazari at iasbs.ac.ir  Fri Jul  6 13:38:10 2012
From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir)
Date: Fri, 6 Jul 2012 16:08:10 +0430
Subject: [Pw_forum] Kohn-Sham orbitals cube file, pp.x, output: 6
In-Reply-To: <CAG+GtJdPPfLPaUnD7bjkT8de6NsC9sp=UP7PTK5bShDDQVuROQ@mail.gmail.com>
References: <7B78F2C8-460B-40AF-988A-5EE4FE1CF02F@gmail.com>
	<CAM2BXVDZ0dYDyiE2Vdgv87JTw04WDcPtORu=7NUZ2aAYaLkoYA@mail.gmail.com>
	<CAOwUK0Dss3XFDCxbW9bL+08Kb=_S28Kn_wdYBCXLVU69a9RSkA@mail.gmail.com>
	<CAGCSmJSs2zqTu5vZ2mbtnJHZcHq+_ek5XKMO_NfSJPRS_80UWw@mail.gmail.com>
	<5ba251587673aa3e6f817806dadee2de.squirrel@mail.iasbs.ac.ir>
	<f676c8fc45abf12cd4a69373dcd1b014.squirrel@mail.iasbs.ac.ir>
	<CAG+GtJdPPfLPaUnD7bjkT8de6NsC9sp=UP7PTK5bShDDQVuROQ@mail.gmail.com>
Message-ID: <cf71510b668fa491d383b40e1e476b31.squirrel@mail.iasbs.ac.ir>



Dear All,
I wish to have a kohn-sham orbitals for different states in
cube format.? In? pp.x if? the output format 6 is chosen
the cube file will be produced but? the density is written in cube
format ( header of output: Cubfile created from PWScf
calculation, Total SCF Density). How can I obtain the kohen-sham orbitals
in cube file format.
Regards
Fariba Nazari
IASBS




> On Fri, Jun 29, 2012 at 11:14 AM,
<nazari at iasbs.ac.ir> wrote: 
> 
>> Dear All, 
>> Would you please let me know if it is possible that the
kohn-Sham 
>> orbitals is written in cube format. I mean I need
the PSI(r) in cube 
>> format?? not density. 
>> regards 
>> Fariba Nazari 
>> IASBS?

> 
> 

From fratesi at mater.unimib.it  Fri Jul  6 14:54:25 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Fri, 06 Jul 2012 14:54:25 +0200
Subject: [Pw_forum] Kohn-Sham orbitals cube file, pp.x, output: 6
In-Reply-To: <cf71510b668fa491d383b40e1e476b31.squirrel@mail.iasbs.ac.ir>
References: <7B78F2C8-460B-40AF-988A-5EE4FE1CF02F@gmail.com>
	<CAM2BXVDZ0dYDyiE2Vdgv87JTw04WDcPtORu=7NUZ2aAYaLkoYA@mail.gmail.com>
	<CAOwUK0Dss3XFDCxbW9bL+08Kb=_S28Kn_wdYBCXLVU69a9RSkA@mail.gmail.com>
	<CAGCSmJSs2zqTu5vZ2mbtnJHZcHq+_ek5XKMO_NfSJPRS_80UWw@mail.gmail.com>
	<5ba251587673aa3e6f817806dadee2de.squirrel@mail.iasbs.ac.ir>
	<f676c8fc45abf12cd4a69373dcd1b014.squirrel@mail.iasbs.ac.ir>
	<CAG+GtJdPPfLPaUnD7bjkT8de6NsC9sp=UP7PTK5bShDDQVuROQ@mail.gmail.com>
	<cf71510b668fa491d383b40e1e476b31.squirrel@mail.iasbs.ac.ir>
Message-ID: <4FF6E001.1030602@mater.unimib.it>

Have you specified plot_num=7?

On 07/06/2012 01:38 PM, nazari at iasbs.ac.ir wrote:
> Dear All,
> I wish to have a kohn-sham orbitals for different states in cube
> format.  In  pp.x if  the output format 6 is chosen the cube file will
> be produced but  the density is written in cube format ( header of
> output: Cubfile created from PWScf calculation, Total SCF Density). How
> can I obtain the kohen-sham orbitals in cube file format.
> Regards
> Fariba Nazari
> IASBS
>
>
>
>
>  > On Fri, Jun 29, 2012 at 11:14 AM, <nazari at iasbs.ac.ir> wrote:
>  >
>  >> Dear All,
>  >> Would you please let me know if it is possible that the kohn-Sham
>  >> orbitals is written in cube format. I mean I need the PSI(r) in cube
>  >> format   not density.
>  >> regards
>  >> Fariba Nazari
>  >> IASBS
>  >
>  >
>  From INPUT_PP.txt:
>  > +--------------------------------------------------------------------
>  > Variable: output_format
>  >
>  > Type: INTEGER
>  > Description: (ignored on 1D plot)
>  > 0 format suitable for gnuplot (1D)
>  > 1 format suitable for contour.x (2D)
>  > 2 format suitable for plotrho (2D)
>  > 3 format suitable for XCRYSDEN (2D or user-supplied
>  > 3D
>  > region)
>  > 4 format suitable for gOpenMol (3D)
>  > (formatted: convert to unformatted *.plt)
>  > 5 format suitable for XCRYSDEN (3D, using entire FFT
>  > grid)
>  > 6 format as gaussian cube file (3D)
>  > (can be read by many programs)
>  > +--------------------------------------------------------------------
>  >
>  >
>  > --
>  > Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
>  > phone: +33 (0)1 44275 084 / skype: paulatz
>  > www: http://www-int.impmc.upmc.fr/~paulatto/
>  > mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris
> C?dex 05
>  >
>  > --
>  > This message has been scanned for viruses and
>  > dangerous content by MailScanner, and is
>  > believed to be clean.
>  >
>  > _______________________________________________
>  > Pw_forum mailing list
>  > Pw_forum at pwscf.org
>  > http://www.democritos.it/mailman/listinfo/pw_forum
>  >
>
> --
> This message has been scanned for viruses and
> dangerous content by *MailScanner* <http://www.mailscanner.info/>, and is
> believed to be clean.
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy

From nazari at iasbs.ac.ir  Fri Jul  6 15:12:12 2012
From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir)
Date: Fri, 6 Jul 2012 17:42:12 +0430
Subject: [Pw_forum] Kohn-Sham orbitals cube file, pp.x, output: 6
In-Reply-To: <4FF6E001.1030602@mater.unimib.it>
References: <7B78F2C8-460B-40AF-988A-5EE4FE1CF02F@gmail.com>
	<CAM2BXVDZ0dYDyiE2Vdgv87JTw04WDcPtORu=7NUZ2aAYaLkoYA@mail.gmail.com>
	<CAOwUK0Dss3XFDCxbW9bL+08Kb=_S28Kn_wdYBCXLVU69a9RSkA@mail.gmail.com>
	<CAGCSmJSs2zqTu5vZ2mbtnJHZcHq+_ek5XKMO_NfSJPRS_80UWw@mail.gmail.com>
	<5ba251587673aa3e6f817806dadee2de.squirrel@mail.iasbs.ac.ir>
	<f676c8fc45abf12cd4a69373dcd1b014.squirrel@mail.iasbs.ac.ir>
	<CAG+GtJdPPfLPaUnD7bjkT8de6NsC9sp=UP7PTK5bShDDQVuROQ@mail.gmail.com>
	<cf71510b668fa491d383b40e1e476b31.squirrel@mail.iasbs.ac.ir>
	<4FF6E001.1030602@mater.unimib.it>
Message-ID: <65e75df7030a50331e381e79fbeb55fb.squirrel@mail.iasbs.ac.ir>



?No, You mean in this case the kohen-sham orbitals is wriiten in cube
file??
?If I am right? how can I distinguish the
kohen-sham orbital for different state?
?thank you


> Have you specified plot_num=7? 
> 
> On
07/06/2012 01:38 PM, nazari at iasbs.ac.ir wrote: 
>> Dear All,

>> I wish to have a kohn-sham orbitals for different states in
cube 
>> format. In pp.x if the output format 6 is chosen the
cube file will 
>> be produced but the density is written in
cube format ( header of 
>> output: Cubfile created from PWScf
calculation, Total SCF Density). How 
>> can I obtain the
kohen-sham orbitals in cube file format. 
>> Regards 
>> Fariba Nazari 
>> IASBS 
>> 
>> 
>> 
>> 
>> > On Fri, Jun
29, 2012 at 11:14 AM, <nazari at iasbs.ac.ir> wrote: 
>>
> 
>> >> Dear All, 
>> >> Would you
please let me know if it is possible that the kohn-Sham 
>>
>> orbitals is written in cube format. I mean I need the PSI(r) in
cube 
>> >> format not density. 
>> >>
regards 
>> >> Fariba Nazari 
>> >>
IASBS 
>> > 
>> > 
>> 
From
INPUT_PP.txt: 
>> >
+-------------------------------------------------------------------- 
>> > Variable: output_format 
>> > 
>>
> Type: INTEGER 
>> > Description: (ignored on 1D plot)

>> > 0 format suitable for gnuplot (1D) 
>> >
1 format suitable for contour.x (2D) 
>> > 2 format suitable
for plotrho (2D) 
>> > 3 format suitable for XCRYSDEN (2D or
user-supplied 
>> > 3D 
>> > region) 
>> > 4 format suitable for gOpenMol (3D) 
>> >
(formatted: convert to unformatted *.plt) 
>> > 5 format
suitable for XCRYSDEN (3D, using entire FFT 
>> > grid) 
>> > 6 format as gaussian cube file (3D) 
>> >
(can be read by many programs) 
>> >
+-------------------------------------------------------------------- 
>> > 
>> > 
>> > -- 
>>
> Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 
>> > phone: +33 (0)1 44275 084 / skype: paulatz 
>>
> www: http://www-int.impmc.upmc.fr/~paulatto/ 
>> >
mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252
Paris 
>> C?dex 05 
>> > 
>>
> -- 
>> > This message has been scanned for viruses and

>> > dangerous content by MailScanner, and is 
>> > believed to be clean. 
>> > 
>>
> _______________________________________________ 
>> >
Pw_forum mailing list 
>> > Pw_forum at pwscf.org 
>> > http://www.democritos.it/mailman/listinfo/pw_forum 
>> > 
>> 
>> -- 
>> This
message has been scanned for viruses and 
>> dangerous content
by *MailScanner* <http://www.mailscanner.info/>, and 
>>
is 
>> believed to be clean. 
>> 
>> 
>> _______________________________________________ 
>>
Pw_forum mailing list 
>> Pw_forum at pwscf.org 
>>
http://www.democritos.it/mailman/listinfo/pw_forum 
>> 
> 
> -- 
> Guido Fratesi 
> 
>
Dipartimento di Scienza dei Materiali 
> Universita` degli Studi
di Milano-Bicocca 
> via Cozzi 53, 20125 Milano, Italy 
>
_______________________________________________ 
> Pw_forum
mailing list 
> Pw_forum at pwscf.org 
>
http://www.democritos.it/mailman/listinfo/pw_forum 
> 
>
-- 
> This message has been scanned for viruses and 
>
dangerous content by MailScanner, and is 
> believed to be clean.

> 
> 


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

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From giannozz at democritos.it  Fri Jul  6 15:17:51 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 6 Jul 2012 15:17:51 +0200
Subject: [Pw_forum] Kohn-Sham orbitals cube file, pp.x, output: 6
In-Reply-To: <65e75df7030a50331e381e79fbeb55fb.squirrel@mail.iasbs.ac.ir>
References: <7B78F2C8-460B-40AF-988A-5EE4FE1CF02F@gmail.com>
	<CAM2BXVDZ0dYDyiE2Vdgv87JTw04WDcPtORu=7NUZ2aAYaLkoYA@mail.gmail.com>
	<CAOwUK0Dss3XFDCxbW9bL+08Kb=_S28Kn_wdYBCXLVU69a9RSkA@mail.gmail.com>
	<CAGCSmJSs2zqTu5vZ2mbtnJHZcHq+_ek5XKMO_NfSJPRS_80UWw@mail.gmail.com>
	<5ba251587673aa3e6f817806dadee2de.squirrel@mail.iasbs.ac.ir>
	<f676c8fc45abf12cd4a69373dcd1b014.squirrel@mail.iasbs.ac.ir>
	<CAG+GtJdPPfLPaUnD7bjkT8de6NsC9sp=UP7PTK5bShDDQVuROQ@mail.gmail.com>
	<cf71510b668fa491d383b40e1e476b31.squirrel@mail.iasbs.ac.ir>
	<4FF6E001.1030602@mater.unimib.it>
	<65e75df7030a50331e381e79fbeb55fb.squirrel@mail.iasbs.ac.ir>
Message-ID: <87329A85-A52D-46EC-A253-DB7352596DBC@democritos.it>


On Jul 6, 2012, at 15:12 , nazari at iasbs.ac.ir wrote:

>  how can I distinguish the kohn-sham orbital for different state?

you choose which one you want to plot (one at the time), using
(documented) input variables

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From gkucukdalyan at gmail.com  Fri Jul  6 18:42:23 2012
From: gkucukdalyan at gmail.com (Gulcin Kucukdalyan)
Date: Fri, 6 Jul 2012 12:42:23 -0400
Subject: [Pw_forum] Charge Density of the Graphene-Lithium System
Message-ID: <CAOwUK0BbefkXzwtcfP106gFa3mEBQqOUtcW9MKjGNMRkJJZH9Q@mail.gmail.com>

Hi All,

I am trying to calculate the charge density of the graphene -lithium system
by showing the negative and positive regions on it. When i uploaded the
below input file to Xcrysden i cannnot see  either  the negative and
positive regions  nor  the charge flow on 3D Xccrysden figure. How should i
modify my file to do so?

Thansk in advance,

Gulcin

# self-consistent calculation
    cat > gli.scf.in << EOF
 &control
    calculation = 'scf'
    restart_mode='from_scratch',
    prefix='gli',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
 /
 &system
    ibrav=  4, celldm(1) =8.0777, celldm(3)=0.83305, nat=  7, ntyp= 2,
    ecutwfc =60.0,
    ecutrho = 500.0
 occupations='smearing', smearing='methfessel-paxton', degauss=0.02
 /
 &electrons
    mixing_mode = 'plain'
    mixing_beta = 0.7
    conv_thr =  1.0d-7
 /
ATOMIC_SPECIES
 C   12.0107  C.pz-rrkjus.UPF
 Li  6.9142   Li.pz-n-vbc.UPF
ATOMIC_POSITIONS
C       -0.000169177  -0.000292351   0.000000000
C        0.333413183  -0.000292351   0.000000000
C        0.500204479   0.288597992   0.000000000
C        0.333413183   0.577488334   0.000000000
C       -0.000169177   0.577488334   0.000000000
C       -0.166960373   0.288597992   0.000000000
Li       0.166621953   0.288597992   0.416524683
K_POINTS AUTOMATIC
5 5 6 0 0 0
EOF
    $ECHO "  running the scf calculation for Gr-Li...\c"
    $PW_COMMAND < gli.scf.in > gli.scf.out
    check_failure $?
    $ECHO " done"

# post-processing for charge density
cat > gli.pp.in << EOF
   &inputpp
   prefix  = 'gli'
   outdir = '$TMP_DIR/'
   filplot = 'gli.pp'
   plot_num= 7
   kpoint = 1
   kband = 14
   spin_component = 0

/

 &plot
    nfile = 1
    filepp(1) = 'gli.pp'
    weight(1) = 1.0
    iflag = 3
    output_format = 5
    fileout = 'gli.xsf'
    /
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From tkaloni at gmail.com  Fri Jul  6 18:53:50 2012
From: tkaloni at gmail.com (Thaneshwor Kaloni)
Date: Fri, 6 Jul 2012 19:53:50 +0300
Subject: [Pw_forum] Charge Density of the Graphene-Lithium System
Message-ID: <CABvS7QJfGwW_Rn_4i-D+pdwc7QrjasnC+dcRcFdeYS8dzFovaQ@mail.gmail.com>

Dear Gulcin,

Please run three scf in three different out directory like as,
1) graphene+Li
2)graphene
3)Li

Then run three post processing by pp.x
1) graphene+Li
2)graphene
3)Li

Then, run a final post processing by pp.x
The final input looking  like one pasted below,

 &inputpp
/
&plot
nfile=3
filepp(1)='all.charge'
filepp(2)='Li.charge'
filepp(3)='graphene.charge'
weight(1)=1
weight(2)=-1
weight(3)=-1
iflag=3
output_format=5
fileout='chden.xsf'
/

Finally, plot chden.xsf file.
I hope it will help you.

Kaloni

KAUST, KSA



Message: 6
Date: Fri, 6 Jul 2012 12:42:23 -0400
From: Gulcin Kucukdalyan <gkucukdalyan at gmail.com>
Subject: [Pw_forum] Charge Density of the Graphene-Lithium System
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
        <CAOwUK0BbefkXzwtcfP106gFa3mEBQqOUtcW9MKjGNMRkJJZH9Q at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi All,

I am trying to calculate the charge density of the graphene -lithium system
by showing the negative and positive regions on it. When i uploaded the
below input file to Xcrysden i cannnot see  either  the negative and
positive regions  nor  the charge flow on 3D Xccrysden figure. How should i
modify my file to do so?

Thansk in advance,

Gulcin

# self-consistent calculation
    cat > gli.scf.in << EOF
 &control
    calculation = 'scf'
    restart_mode='from_scratch',
    prefix='gli',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
 /
 &system
    ibrav=  4, celldm(1) =8.0777, celldm(3)=0.83305, nat=  7, ntyp= 2,
    ecutwfc =60.0,
    ecutrho = 500.0
 occupations='smearing', smearing='methfessel-paxton', degauss=0.02
 /
 &electrons
    mixing_mode = 'plain'
    mixing_beta = 0.7
    conv_thr =  1.0d-7
 /
ATOMIC_SPECIES
 C   12.0107  C.pz-rrkjus.UPF
 Li  6.9142   Li.pz-n-vbc.UPF
ATOMIC_POSITIONS
C       -0.000169177  -0.000292351   0.000000000
C        0.333413183  -0.000292351   0.000000000
C        0.500204479   0.288597992   0.000000000
C        0.333413183   0.577488334   0.000000000
C       -0.000169177   0.577488334   0.000000000
C       -0.166960373   0.288597992   0.000000000
Li       0.166621953   0.288597992   0.416524683
K_POINTS AUTOMATIC
5 5 6 0 0 0
EOF
    $ECHO "  running the scf calculation for Gr-Li...\c"
    $PW_COMMAND < gli.scf.in > gli.scf.out
    check_failure $?
    $ECHO " done"

# post-processing for charge density
cat > gli.pp.in << EOF
   &inputpp
   prefix  = 'gli'
   outdir = '$TMP_DIR/'
   filplot = 'gli.pp'
   plot_num= 7
   kpoint = 1
   kband = 14
   spin_component = 0

/

 &plot
    nfile = 1
    filepp(1) = 'gli.pp'
    weight(1) = 1.0
    iflag = 3
    output_format = 5
    fileout = 'gli.xsf'
    /
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From baroni at sissa.it  Fri Jul  6 21:42:49 2012
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 6 Jul 2012 21:42:49 +0200
Subject: [Pw_forum] core level shifting calculation
In-Reply-To: <7E99F15C-2046-4774-931B-192AB3A8B9B1@democritos.it>
References: <CAFy9Os=9OsCGG8tgC6nkTZ0RPK+-iGrKbcROREK0Yx2RQVk0xQ@mail.gmail.com>
	<CAFy9Os=3G=sp4MxyzGN0F5zEzTg6ZLRPs20S+hhG82ppDt4WEA@mail.gmail.com>
	<7E99F15C-2046-4774-931B-192AB3A8B9B1@democritos.it>
Message-ID: <8571BBCC-2908-4EEB-B14F-B12080BC303B@sissa.it>


On Jul 6, 2012, at 9:25 AM, Paolo Giannozzi wrote:

> 
> On Jul 6, 2012, at 9:13 , manoj narayanan wrote:
> 
>> So is it ok to use the Z+1 approximation rather
>> than using core excited pseudo potential ?
> 
> this is about physics, not about software, and the answer
> should be found in papers.

... or, even better, by direct experience
SB


---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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From ytaghipour at aeoi.org.ir  Sat Jul  7 15:54:08 2012
From: ytaghipour at aeoi.org.ir (Yavar Taghipour Azar)
Date: Sat, 07 Jul 2012 18:24:08 +0430
Subject: [Pw_forum] HOMO, LUMO isosurfaces.  NCPP or USPP,
	which is more accurate?
Message-ID: <WC20120707135408.030532@aeoi.org.ir>


 
Dear QE users.
 
 
I want to plot HOMO, LUMO isosurfaces. what is the physical origin of 
difference between results from choosing USPP with NCPP? 
 Thanks in advance.
 
 
-------------------------------------------
Yavar Taghipour Azar
PhD Student
Physics Group, AEOI
Tehran-Iran
 
Email: ytaghipour at aeoi.org.ir
Phone: +98 (0) 21 82064556
-----------------------------------------------------------
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From ytaghipour at aeoi.org.ir  Sat Jul  7 15:52:36 2012
From: ytaghipour at aeoi.org.ir (Yavar Taghipour Azar)
Date: Sat, 07 Jul 2012 18:22:36 +0430
Subject: [Pw_forum] HOMO,LUMO isosurface, USPP  or NCPP?
Message-ID: <WC20120707135236.320531@aeoi.org.ir>


 
Dear QE users.
 
 
I want to plot HOMO, LUMO isosurfaces. what is the physical origin of 
difference between results from choosing USPP with NCPP? 
 Thanks in advance.
 
 
-------------------------------------------
Yavar Taghipour Azar
PhD Student
Physics Group, AEOI
Tehran-Iran
 
Email: ytaghipour at aeoi.org.ir
Phone: +98 (0) 21 82064556
-----------------------------------------------------------
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From degironc at sissa.it  Sun Jul  8 11:40:04 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sun, 08 Jul 2012 11:40:04 +0200
Subject: [Pw_forum] Problems in Bands of Graphene Nanoribbon
In-Reply-To: <tencent_359138802162644611A8C827@qq.com>
References: <tencent_359138802162644611A8C827@qq.com>
Message-ID: <4FF95574.2070906@sissa.it>

Dear Zhida Song

       I'm putting the Pw_forum mailing list in cc as that would be a 
more appropriate address where to submit queries about PWscf. Please 
sign your future posts with your affiliation.

        coming to your question.... think what is the difference between 
a localized basis set code and plane wave one ?

        what would be the results of an empty cell by flpo ? empty !
        what would be the result of a pw code ? the 3-D free electron 
band structure projected on the z axis..
        which one is correct ?

        so what is missing in your friend's band structure that Pwscf 
correctly gives ?

        hope this helps, best,

   stefano
-
Stefano de Gironcoli - SISSA and DEMOCRITOS

On 07/08/2012 11:24 AM, ???? wrote:
> Hi!
>    I'm trying to calculate the quantum conductance of quasi one dimension structure with Wannier90 and PWscf.
>   But the one dimension band structure of suppercell is weird: bands with high energy seem very "crowded".
>   I meet this problem when calculating Al nanowire and graphene nanoribbon. It seems a computation error as
>   energy seems to be limitted in a small range.
>   I have raised the value of cutoff and distance between nanoribbons in directions perpendicular to transport,
>   but results changed little.
>   My friend plots the bands of graphene nanoribbon with fplo, which can be a reference I think.
>    
>   The input files and bands are in attachment.
>    
>   Thank you very much!
>    
>   Zhida Song

From ptao10b at imr.ac.cn  Mon Jul  9 03:09:05 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Mon, 9 Jul 2012 09:09:05 +0800 (GMT+08:00)
Subject: [Pw_forum] q not allowed when using q2r.x to calculate a2F
Message-ID: <2db51a.4f12.138694858c8.Coremail.ptao10b@imr.ac.cn>

Dear all,


I happened to meet a problem during the e-ph constant calculation. 
When I apply the q2r.x, the calculation of ordinary phonon force constant 
matrix seems OK, but the following step of a2F calculation shows an error
as follows:


   q-space grid ok, #points =  100
 
   fft-check warning: sum of imaginary terms = .1593535E-07


   Preparing gamma for a2F
 
 
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      from init : error #         1
      q not allowed
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


What reason causes this error? Any advice I would be very grateful. 


Best regards,
Plato Tao




--
-------------------------------------------------------------------
PH.D. candidate Peng Tao
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------


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From eariel99 at gmail.com  Mon Jul  9 09:44:20 2012
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Mon, 9 Jul 2012 09:44:20 +0200
Subject: [Pw_forum] HOMO,LUMO isosurface, USPP or NCPP?
Message-ID: <CAM5Vcw_0Ky8aC8OcS4piakuHHux8h1cNnqs3JB1SMaxYbbEwQQ@mail.gmail.com>

 Dear Yavar

USPP and NCPP are mathematical methods to approximate the solution of the
same physical problem. Hence, there must be no physically different
results, unless one of the pseudopotentials is faulty. Both types of
pseudopotentials have cutoff radii, which are larger for NCPP than for
USPP. The wavefunctions computed with any pseudopotential should be equal
to the all-electron wavefunctions in the spatial region outside the spheres
centered at each atom with spheres radii equal to the cutoff radii of the
corresponding pseudopotential. Inside any sphere, the wavefunctions are
different and are meaningless. To have the correct wavefunctions inside the
spheres you have any of the following options a) all-electron calculations
(with a different code,e.g. ADF, Gaussian, LMTO, etc), b) use a PP with a
smaller cutoff radius (and larger ecutrho and ecutwfc), c) use PAW
(projector augmented wave).

sincerely yours


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
28049 Madrid, Spain
Phone: +34 91 497 6706



 Dear QE users.
>
>
> I want to plot HOMO, LUMO isosurfaces. what is the physical origin
> of difference between results from choosing USPP with NCPP?
>  Thanks in advance.
>
>
> -------------------------------------------
> Yavar Taghipour Azar
> PhD Student
> Physics Group, AEOI
> Tehran-Iran
>
> Email: ytaghipour at aeoi.org.ir
> Phone: +98 (0) 21 82064556
> -----------------------------------------------------------
>
>
>
>
>
--
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From ramzialaya at hotmail.fr  Mon Jul  9 12:50:51 2012
From: ramzialaya at hotmail.fr (ramzi alaya)
Date: Mon, 9 Jul 2012 11:50:51 +0100
Subject: [Pw_forum] K-points
Message-ID: <BAY151-W130871F45D0DE9021E0B5FA3D30@phx.gbl>


Dear all;
I'm going to study the structural propertie of AlAs in the two structures ZB and wurtzite and I have a question about the K-point.
 Is what I use the same number of K points  for this two structures?


******************************************************************************************************************************************************************************
Ramzi AlayaE-mail : ramzialaya at hotmail.fr
Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie
Unit? de Recherche sur les H?t?ro-Epitaxies et Applications
 		 	   		  
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From anjalisinghromi at gmail.com  Mon Jul  9 13:53:29 2012
From: anjalisinghromi at gmail.com (Anjali Singh)
Date: Mon, 9 Jul 2012 17:23:29 +0530
Subject: [Pw_forum] (no subject)
Message-ID: <CAOUaTpQe_YbwCtgQAVs1WkaAY5Oc3iT0Rk47XxOYmU=R6NDzdg@mail.gmail.com>

I am doing phonon calculation for Boron Nitrite system with 96 atom
every time i am getting error which says

     Self-consistent Calculation

     Pert. #  1: Fermi energy shift (Ry) = NaN            NaN

      iter #   1 total cpu time : 11235.6 secs   av.it.:   3.6
      thresh= 0.100E-01 alpha_mix =  0.100 |ddv_scf|^2 =  NaN
     kpoint   1 ibnd 193 solve_linter: root not converged  NaN
     kpoint   2 ibnd 193 solve_linter: root not converged  NaN
     kpoint   3 ibnd 193 solve_linter: root not converged  NaN
     kpoint   4 ibnd 193 solve_linter: root not converged  NaN
     kpoint   5 ibnd 193 solve_linter: root not converged  NaN
     kpoint   6 ibnd 193 solve_linter: root not converged  NaN
     kpoint   7 ibnd 193 solve_linter: root not converged  NaN

     Pert. #  1: Fermi energy shift (Ry) = NaN            NaN

      iter #   2 total cpu time : 17553.7 secs   av.it.: 200.0
      thresh= 0.100E-01 alpha_mix =  0.100 |ddv_scf|^2 =  NaN
     kpoint   1 ibnd 193 solve_linter: root not converged  NaN


can somebody help me
-- 
With Thanks and Regards
Anjali Singh
Material Theory Group
Theoretical Science Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur,Bangalore 560 064
India
email id : anjalisinghromi at gmail.com
phone no:+91-89703-58107
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From akohlmey at gmail.com  Mon Jul  9 13:57:03 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Mon, 9 Jul 2012 13:57:03 +0200
Subject: [Pw_forum] (no subject)
In-Reply-To: <CAOUaTpQe_YbwCtgQAVs1WkaAY5Oc3iT0Rk47XxOYmU=R6NDzdg@mail.gmail.com>
References: <CAOUaTpQe_YbwCtgQAVs1WkaAY5Oc3iT0Rk47XxOYmU=R6NDzdg@mail.gmail.com>
Message-ID: <CADTmJ6Hx4LKVZp1LSSQcvpFv-S10fQhpngdoC20BQqpsEgmcrQ@mail.gmail.com>

On Mon, Jul 9, 2012 at 1:53 PM, Anjali Singh <anjalisinghromi at gmail.com> wrote:
> I am doing phonon calculation for Boron Nitrite system with 96 atom
> every time i am getting error which says
>
>      Self-consistent Calculation
>
>      Pert. #  1: Fermi energy shift (Ry) = NaN            NaN

the NaN is a "very bad sign (tm)".

there is likely something fundamentally wrong
with your input or the data it is pointing to.

have you tried running the same kind of calculation
with a simpler/smaller system?

axel.



>       iter #   1 total cpu time : 11235.6 secs   av.it.:   3.6
>       thresh= 0.100E-01 alpha_mix =  0.100 |ddv_scf|^2 =  NaN
>      kpoint   1 ibnd 193 solve_linter: root not converged  NaN
>      kpoint   2 ibnd 193 solve_linter: root not converged  NaN
>      kpoint   3 ibnd 193 solve_linter: root not converged  NaN
>      kpoint   4 ibnd 193 solve_linter: root not converged  NaN
>      kpoint   5 ibnd 193 solve_linter: root not converged  NaN
>      kpoint   6 ibnd 193 solve_linter: root not converged  NaN
>      kpoint   7 ibnd 193 solve_linter: root not converged  NaN
>
>      Pert. #  1: Fermi energy shift (Ry) = NaN            NaN
>
>       iter #   2 total cpu time : 17553.7 secs   av.it.: 200.0
>       thresh= 0.100E-01 alpha_mix =  0.100 |ddv_scf|^2 =  NaN
>      kpoint   1 ibnd 193 solve_linter: root not converged  NaN
>
>
> can somebody help me
> --
> With Thanks and Regards
> Anjali Singh
> Material Theory Group
> Theoretical Science Unit
> Jawaharlal Nehru Centre for Advanced Scientific Research
> Jakkur,Bangalore 560 064
> India
> email id : anjalisinghromi at gmail.com
> phone no:+91-89703-58107
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

From negarastani at gmail.com  Mon Jul  9 14:18:31 2012
From: negarastani at gmail.com (Negar Ashari Astani)
Date: Mon, 9 Jul 2012 14:18:31 +0200
Subject: [Pw_forum] Old problem with cppp.x
Message-ID: <CAJqU8JA3kvyd9jA_VKC=z7BuWFuXYvrcfPYVPbEworKyQN79Ng@mail.gmail.com>

Hello everyone,

I'm confronting a probably stupid problem with cppp.x! I saw this problem
being reported two times in the forum:

http://www.democritos.it/pipermail/pw_forum/2011-February/019298.html

http://www.democritos.it/pipermail/pw_forum/2008-May/009020.html

Having read those, I'm still getting the following error:

Cannot open file ....espresso/out/cp_51.save/data-file.xml

I checked the corresponding address, and the files are there!
and I also renamed the save directory and files to match the default cp_51
and .....


This is my input file for cppp.x:


&INPUTPP
!  prefix=Anatase,
   fileout=out,
   output=xsf,
   outdir=..mypath../espresso/out,
   wfcdir=..mypath../espresso/out,
   lcharge=.TRUE.,
   lforces=.TRUE.,
   ldynamics=.TRUE.,
   lpdb=.TRUE.,
   lrotation,
   ns1, ns2, ns3,
   np1, np2, np3,
   nframes=50,
!   ndr=90,
!   ndw=91,
   atomic_number(1) 22
   atomic_number(2) 8,
   charge_density,
   state= KS_1,
   lbinary=.TRUE.
/

Although I'm using Q.Espresso.5, I tried to replace fpmdpp.f90 with the
file provided by Paolo in the second link!
That didn't work either!

Many thanks,
Nash
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From gabriele.sclauzero at epfl.ch  Mon Jul  9 14:47:07 2012
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Mon, 9 Jul 2012 14:47:07 +0200
Subject: [Pw_forum] Old problem with cppp.x
In-Reply-To: <CAJqU8JA3kvyd9jA_VKC=z7BuWFuXYvrcfPYVPbEworKyQN79Ng@mail.gmail.com>
References: <CAJqU8JA3kvyd9jA_VKC=z7BuWFuXYvrcfPYVPbEworKyQN79Ng@mail.gmail.com>
Message-ID: <31D44899-A5DF-4D6C-A44B-9A00E607E207@epfl.ch>

Hello,

> Hello everyone,
> 
> I'm confronting a probably stupid problem with cppp.x! I saw this problem being reported two times in the forum:
> 
> http://www.democritos.it/pipermail/pw_forum/2011-February/019298.html
> 
> http://www.democritos.it/pipermail/pw_forum/2008-May/009020.html
> 

I think the second link here above is not related to your error message.

> Having read those, I'm still getting the following error:
> 
> Cannot open file ....espresso/out/cp_51.save/data-file.xml
> 
> I checked the corresponding address, and the files are there!
> and I also renamed the save directory and files to match the default cp_51 and .....
> 
> 
> This is my input file for cppp.x:
> 
> 
> &INPUTPP
> !  prefix=Anatase,
>    fileout=out,
>    output=xsf,
>    outdir=..mypath../espresso/out,

outdir should be a fortran string, that is to say that you have to enclose the path within quotation marks ( " or ' ).

>    wfcdir=..mypath../espresso/out,

This variable is not in the namelist, so you should get another error message from the code when the input is read.
Is this really the input file you used?

>    lrotation,
>    ns1, ns2, ns3,
>    np1, np2, np3,

Also these three lines above (and many others below) would make the code complain. Inside a namelist you have to stick to the list-directed syntax of F90, i.e.
variable = value,
where variable is one of those listed here:
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_CPPP.html


HTH


GS


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne







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From sohailphysics at yahoo.co.in  Mon Jul  9 16:10:23 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Mon, 9 Jul 2012 22:10:23 +0800 (SGT)
Subject: [Pw_forum] Error #17 in Convergence test of MoS2
Message-ID: <1341843023.27106.YahooMailClassic@web192204.mail.sg3.yahoo.com>

I am trying to check the convergence test of the total energy of the system as a function of cut off energy for MoS2 as first step in QE calculation

My input file is attached, i am getting error # 17
I am new to QE,
Any help will be highly appreciated

This program is part of the open-source Quantum ESPRESSO suite
???? for quantum simulation of materials; please acknowledge
???????? "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
????????? URL http://www.quantum-espresso.org", 
???? in publications or presentations arising from this work. More details at
???? http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

???? Current dimensions of program PWSCF are:
???? Max number of different atomic species (ntypx) = 10
???? Max number of k-points (npk) =? 40000
???? Max angular momentum in pseudopotentials (lmaxx) =? 3
???? Waiting for input...

?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
???? from? read_namelists? : error #??????? 17
????? reading namelist system 
?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

???? stopping ...

&control
??? calculation='scf',
??? restart_mode='from_scratch',
??? prefix='MoS2',
??? pseudo_dir = '/home/sohail/espresso-4.2.1/pseudo/',
??? outdir='./OUT'
?/
?&system
??? ibrav = 4, celldm(1) = 3.16, celldm(3) = 3.89, nat=? 6, ntyp= 2,
??? ecutwfc = $i,
??? ecutrho = 500,
??? nbnd = 10,
??? occupations='smearing', smearing=' gaussian', degauss=0.001,
??? nspin=2,
??? starting_magnetization(1)=0.5d0,
/
&electrons
??? mixing_beta = 0.3
??? conv_thr =? 1.0d-9
?/
ATOMIC_SPECIES 
Mo?? 95.96?? Mo.pw91-n-van.UPF
S??? 32.06?? S.pw91-van_ak.UPF
ATOMIC_POSITIONS {crystal}
Mo? 0.33333333? 0.66666667? 0.25000000
Mo? 0.66666667? 0.33333333? 0.75000000
S?? 0.33333333? 0.66666667? 0.62000000
S?? 0.66666667? 0.33333333? 0.12000000
S?? 0.66666667? 0.33333333 -0.62000000
S?? 0.33333333? 0.66666667 -0.12000000
K_POINTS AUTOMATIC
4 4 4 1 1 1

Thanks
Sohail
KKU
Saudi Arabia

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From giannozz at democritos.it  Mon Jul  9 17:52:58 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 9 Jul 2012 17:52:58 +0200
Subject: [Pw_forum] Error #17 in Convergence test of MoS2
In-Reply-To: <1341843023.27106.YahooMailClassic@web192204.mail.sg3.yahoo.com>
References: <1341843023.27106.YahooMailClassic@web192204.mail.sg3.yahoo.com>
Message-ID: <7EF66725-4954-4B45-9E3B-DCED429DF4F2@democritos.it>


On Jul 9, 2012, at 16:10 , Sohail Ahmad wrote:

>       reading namelist system

this is the error. Check whether $i assumes a proper value here:

>  &system
>     ibrav = 4, celldm(1) = 3.16, celldm(3) = 3.89, nat=  6, ntyp= 2,
>     ecutwfc = $i,
>     ecutrho = 500,
>     nbnd = 10,
>     occupations='smearing', smearing=' gaussian', degauss=0.001,
>     nspin=2,
>     starting_magnetization(1)=0.5d0,
> /

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From negarastani at gmail.com  Mon Jul  9 18:01:32 2012
From: negarastani at gmail.com (Negar Ashari Astani)
Date: Mon, 9 Jul 2012 18:01:32 +0200
Subject: [Pw_forum] Old problem with cppp.x
In-Reply-To: <CAJqU8JA3kvyd9jA_VKC=z7BuWFuXYvrcfPYVPbEworKyQN79Ng@mail.gmail.com>
References: <CAJqU8JA3kvyd9jA_VKC=z7BuWFuXYvrcfPYVPbEworKyQN79Ng@mail.gmail.com>
Message-ID: <CAJqU8JBX2xyxCR5Z5yYEMKnZOYFssO1mCnTueO4fuj02x4f67A@mail.gmail.com>

Dear Gabriele,

Thanks for your reply, I should have been more thoughtful about the
quotations!
I'll put my actual input here:

&INPUTPP
!  prefix = 'Anatase',
  fileout ='out',
   output = 'xsf',
   outdir = '/scratch/negar/espresso/out/',
   lcharge=.TRUE.,
   lforces=.TRUE.,
   ldynamics =.False.,
   lpdb=.TRUE.,
   lrotation = .False.,
!   ns1, ns2, ns3,
!   np1, np2, np3,
!   nframes=50,
   ndr=50,
!   ndw=91,
   atomic_number(1)=22
   atomic_number(2)=8,
!   charge_density= 'full',
   state= 'KS_1',
   lbinary=.TRUE.
/

I'm still getting the same error! and what surprises me is that I have set
the ndr value equal to 50 in both my cp.in and cppp.in and the program is
still looking for cp_51.save! which doesn't exist! (Even if I change the
folder name to 50 manually, that wouldn't change anything!)

Many thanks,
Nash



On Mon, Jul 9, 2012 at 2:18 PM, Negar Ashari Astani
<negarastani at gmail.com>wrote:

>
> Hello everyone,
>
> I'm confronting a probably stupid problem with cppp.x! I saw this problem
> being reported two times in the forum:
>
> http://www.democritos.it/pipermail/pw_forum/2011-February/019298.html
>
> http://www.democritos.it/pipermail/pw_forum/2008-May/009020.html
>
> Having read those, I'm still getting the following error:
>
> Cannot open file ....espresso/out/cp_51.save/data-file.xml
>
> I checked the corresponding address, and the files are there!
> and I also renamed the save directory and files to match the default cp_51
> and .....
>
>
> This is my input file for cppp.x:
>
>
> &INPUTPP
> !  prefix=Anatase,
>    fileout=out,
>    output=xsf,
>    outdir=..mypath../espresso/out,
>    wfcdir=..mypath../espresso/out,
>    lcharge=.TRUE.,
>    lforces=.TRUE.,
>    ldynamics=.TRUE.,
>    lpdb=.TRUE.,
>    lrotation,
>    ns1, ns2, ns3,
>    np1, np2, np3,
>    nframes=50,
> !   ndr=90,
> !   ndw=91,
>    atomic_number(1) 22
>    atomic_number(2) 8,
>    charge_density,
>    state= KS_1,
>    lbinary=.TRUE.
> /
>
> Although I'm using Q.Espresso.5, I tried to replace fpmdpp.f90 with the
> file provided by Paolo in the second link!
> That didn't work either!
>
> Many thanks,
> Nash
>
>
>


-- 
Negar Ashari Astani
PhD student
Laboratory of Computational Biochemistry and Chemistry (LCBC)
Swiss Federal Institute of Technology (EPFL)
BCH 4118 (Bat. BCH)
CH-1015 Lausanne
Phone: +41 (0)21 693 03 26
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From gabriele.sclauzero at epfl.ch  Mon Jul  9 18:59:48 2012
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Mon, 9 Jul 2012 18:59:48 +0200
Subject: [Pw_forum] Old problem with cppp.x
In-Reply-To: <CAJqU8JBX2xyxCR5Z5yYEMKnZOYFssO1mCnTueO4fuj02x4f67A@mail.gmail.com>
References: <CAJqU8JA3kvyd9jA_VKC=z7BuWFuXYvrcfPYVPbEworKyQN79Ng@mail.gmail.com>
	<CAJqU8JBX2xyxCR5Z5yYEMKnZOYFssO1mCnTueO4fuj02x4f67A@mail.gmail.com>
Message-ID: <AD6B1035-A4F8-4776-8B47-3C1DE2474091@epfl.ch>

Dear Negar,

    hard to say what is happening if you don't provide more details (serial or parallel version, distributed or global scratch, which compiler, cp input, how you run the commands, etc....).
Why have you the prefix commented out in the input? What is the actual restart directory that you want to read?
The default prefix is 'cp', so that the code should search for cp_50.save. Have you got that file in outdir?
If the code searches for cp_51.save then your input might not have been read correctly, since 51 is the default ndr.
Are you sure that you haven't got some spurious characters in your input (this may happen if you convert from Win to Linux or copy paste from some text editors).
Have you tried with some other (small) test system, on another machine, etc.?
If you tried everything correcly and still get stuck you may submit a small input file (both for cp and cppp) that can be run fast and shows the problem.

Regards,

GS

Il giorno 09/lug/2012, alle ore 18.01, Negar Ashari Astani ha scritto:
> Dear Gabriele,
> 
> Thanks for your reply, I should have been more thoughtful about the quotations!
> I'll put my actual input here:
> 
> &INPUTPP
> !  prefix = 'Anatase',
>   fileout ='out',
>    output = 'xsf',
>    outdir = '/scratch/negar/espresso/out/',
>    lcharge=.TRUE.,
>    lforces=.TRUE.,
>    ldynamics =.False.,
>    lpdb=.TRUE.,
>    lrotation = .False.,
> !   ns1, ns2, ns3,
> !   np1, np2, np3,
> !   nframes=50,
>    ndr=50,
> !   ndw=91,
>    atomic_number(1)=22
>    atomic_number(2)=8,
> !   charge_density= 'full',
>    state= 'KS_1',
>    lbinary=.TRUE.
> /
> 
> I'm still getting the same error! and what surprises me is that I have set the ndr value equal to 50 in both my cp.in and cppp.in and the program is still looking for cp_51.save! which doesn't exist! (Even if I change the folder name to 50 manually, that wouldn't change anything!)
> 
> Many thanks,
> Nash
> 


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne







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From Trinh.Vo at jpl.nasa.gov  Mon Jul  9 23:43:32 2012
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Mon, 9 Jul 2012 21:43:32 +0000
Subject: [Pw_forum] Memory (RAM)
Message-ID: <CC209E94.AC26%Trinh.Vo@jpl.nasa.gov>

Dear All,

I am running very large job (nscf calculation 15x15x15) using QE version 4.3.2.   The job keeps being crashed due to memory problem (out of memory, RAM).  Is there a way that I can estimate how much memory   (RAM) required for running a nscf calculation?

Thank you very much,

Trinh Vo

JPL/CalcTech
High Capability Computing and Modeling Group


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From ptao10b at imr.ac.cn  Tue Jul 10 03:33:43 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Tue, 10 Jul 2012 09:33:43 +0800 (GMT+08:00)
Subject: [Pw_forum] GRID example of e-ph
Message-ID: <1186790.7d33.1386e8543b8.Coremail.ptao10b@imr.ac.cn>

Dear all,


As we know, the phonon calculation is quite slow and unexpected errors might occur at any time. 
Thanks to the GRID example, split runs is available. However, no example is provided to split
the e-ph calculation. So, dear professors, could you show me a method to realize it?

Sincerely yours
Plato Tao

--
-------------------------------------------------------------------
PH.D. candidate Peng Tao
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------


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From konda.physics at gmail.com  Tue Jul 10 05:53:38 2012
From: konda.physics at gmail.com (Kondaiah Samudrala)
Date: Tue, 10 Jul 2012 09:23:38 +0530
Subject: [Pw_forum] regarding phonon dispersion
Message-ID: <CAKjMXpbvO5dmDtSfbfjGm9SsJL-_1G0K8Miyy7TiNcm=RHwL9g@mail.gmail.com>

Dear all,

I am running phonon dispersion for YSn3, which is crystallizes in cubic
structure. While running the programme i dont have any imaginary
frequencies in my o/p file (ph.out). But using plotband.x tool  for
plotting dispersion,  my final plot got negative axis exactly starting from
the value of Fermi energy. Below i am sending the plotband.x details

Reading   12 bands at    101 k-points
Range:    0.0000  133.5007eV  Emin, Emax > 0 140
high-symmetry point:  0.0000 0.0000 0.0000   x coordinate   0.0000
high-symmetry point:  0.5000 0.0000 0.0000   x coordinate   0.5000
high-symmetry point:  0.5000 0.5000 0.0000   x coordinate   1.0000
high-symmetry point:  0.0000 0.0000 0.0000   x coordinate   1.7071
high-symmetry point:  0.5000 0.5000 0.5000   x coordinate   2.5731
high-symmetry point:  0.5000-0.5000 0.5000   x coordinate   3.5731
high-symmetry point:  0.0000 0.0000 0.5000   x coordinate   4.2802
output file (xmgr) > YSn3.xmgr
bands in xmgr format written to file
YSn3.xmgr

output file (ps) > YSn3.ps
Efermi > 13.2559
deltaE, reference E (for tics) 30, 13.2559
bands in PostScript format written to file YSn3.ps  .

Is there any error in my calculation or any bug in plotband.x. Because the
same o/p YSn3.xmgr from this plotband.x shows nicely with xmgrce shows.

please help me  in this. Thanks in advance

S.Appalakondaiah
Research scholar
University of Hyderabad
Hyderabad
India
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From pchen at ion.chem.utk.edu  Tue Jul 10 05:54:07 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Mon, 9 Jul 2012 23:54:07 -0400
Subject: [Pw_forum] U calculation in LDA+U
Message-ID: <CAP_5U0cVAHQYUfpX_t_13ws=cqzwVKE+232zx_Tf0yRorcmZgQ@mail.gmail.com>

Dear All,

In the calculation of U, how can we determine the equivalence of the ions,
by site symmetry or space group symmetry?
E.g  ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run
calculation on perturbing B(1) and B(2) ions or  just a B ion?

 In order to find U in B  ions, I tried to run calculation with perturbing
just on B, and r.x gave some errors that it needs to read more data.
So I guess it needs the perturbed data from other atoms. Shall I use the
procedures listed below?
1. run scf calculation with Hubbard_U(i)= 1.d-20
2. run scf with perturbing on an A ion
3.   run scf with perturbing on a B(1) ion
4.   run scf with perturbing on a B(2) ion
5.   run scf with perturbing on an O ion




-- 
  Best Regards.
        Peng
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From chenjianyong0223 at 126.com  Tue Jul 10 06:08:34 2012
From: chenjianyong0223 at 126.com (=?GBK?B?s8K9qNPC?=)
Date: Tue, 10 Jul 2012 12:08:34 +0800 (CST)
Subject: [Pw_forum] confused  by  electron-phonon  coupling   recover
Message-ID: <319fe5c2.1bff5.1386f13092e.Coremail.chenjianyong0223@126.com>

Dear  all?
      Sorry  for  interruption .I am  confused  for  two months by the  recover problem of  Aluminum   electron phonon coupling calculation .
       As  we  all   know,the most time-consuming part of the calculation is  the  running   of   ph.x   program.  Ph.x  can  not  complet  all the  q  vetors   in one  job  time due to the jobtime limit of our machine .What I can do is to submit   job  for the second time with "recover=.true." setted in  ph.in   file (the input file for ph.x grogram)  .then  go on  the calculation of q2r.x and  matdyn.x  .It is obvious that  the result is not  rational  because both  e-p coupling strength and  Eliashberg  function is ZERO.
       The  attachment is all  my input file for  e-p  calculation .
       It  will be very   gratefull  if you will be kind enough  to give me  some hints  ,I  am  dying ,help  me ,please
 
       best  regards !!
 
                                                                                                                                  Jianyong  Chen
                                                                                                   institue of physics  Chines academy of  science 

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From lorenzo.paulatto at impmc.upmc.fr  Tue Jul 10 08:39:04 2012
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Tue, 10 Jul 2012 08:39:04 +0200
Subject: [Pw_forum] regarding phonon dispersion
In-Reply-To: <CAKjMXpbvO5dmDtSfbfjGm9SsJL-_1G0K8Miyy7TiNcm=RHwL9g@mail.gmail.com>
References: <CAKjMXpbvO5dmDtSfbfjGm9SsJL-_1G0K8Miyy7TiNcm=RHwL9g@mail.gmail.com>
Message-ID: <CAG+GtJev+zvzkUb2Z=kWXN7CbFd25x6ZVXCwpMkZ0NeVUkZLHg@mail.gmail.com>

On Tue, Jul 10, 2012 at 5:53 AM, Kondaiah Samudrala <konda.physics at gmail.com
> wrote:

> Dear all,
>
> I am running phonon dispersion for YSn3, which is crystallizes in cubic
> structure. While running the programme i dont have any imaginary
> frequencies in my o/p file (ph.out). But using plotband.x tool  for
> plotting dispersion,  my final plot got negative axis exactly starting from
> the value of Fermi energy. Below i am sending the plotband.x details
>
>
Dear Kondaiah,
plotband.x was written to plot electronic bands, hence it sets the energy
zero at the "Fermu energy" level specified in input. When using it to plot
phonon bands, just set Efermi to zero.

bests
-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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From degironc at sissa.it  Tue Jul 10 08:45:18 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 10 Jul 2012 08:45:18 +0200
Subject: [Pw_forum] U calculation in LDA+U
In-Reply-To: <CAP_5U0cVAHQYUfpX_t_13ws=cqzwVKE+232zx_Tf0yRorcmZgQ@mail.gmail.com>
References: <CAP_5U0cVAHQYUfpX_t_13ws=cqzwVKE+232zx_Tf0yRorcmZgQ@mail.gmail.com>
Message-ID: <4FFBCF7E.8030903@sissa.it>

I don't know the details of r.x code but I think that, physically, what 
matters is the two atoms are crystallographically equivalent or not 
.therefore I think space group symmetry is the relevant one.

stefano

On 07/10/2012 05:54 AM, Peng Chen wrote:
> Dear All,
>
> In the calculation of U, how can we determine the equivalence of the ions,
> by site symmetry or space group symmetry?
> E.g  ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run
> calculation on perturbing B(1) and B(2) ions or  just a B ion?
>
>   In order to find U in B  ions, I tried to run calculation with perturbing
> just on B, and r.x gave some errors that it needs to read more data.
> So I guess it needs the perturbed data from other atoms. Shall I use the
> procedures listed below?
> 1. run scf calculation with Hubbard_U(i)= 1.d-20
> 2. run scf with perturbing on an A ion
> 3.   run scf with perturbing on a B(1) ion
> 4.   run scf with perturbing on a B(2) ion
> 5.   run scf with perturbing on an O ion
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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From ytaghipour at aeoi.org.ir  Tue Jul 10 08:53:55 2012
From: ytaghipour at aeoi.org.ir (Yavar Taghipour Azar)
Date: Tue, 10 Jul 2012 11:23:55 +0430
Subject: [Pw_forum] HOMO,LUMO isosurface, USPP or NCPP?
In-Reply-To: <CAM5Vcw_0Ky8aC8OcS4piakuHHux8h1cNnqs3JB1SMaxYbbEwQQ@mail.gmail.com>
References: <CAM5Vcw_0Ky8aC8OcS4piakuHHux8h1cNnqs3JB1SMaxYbbEwQQ@mail.gmail.com>
Message-ID: <WC20120710065355.720023@aeoi.org.ir>



-----Original Message-----
From: Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>
To: pw_forum at pwscf.org
Date: Mon, 9 Jul 2012 09:44:20 +0200
Subject: Re: [Pw_forum] HOMO,LUMO isosurface, USPP or NCPP?

>  Dear Yavar
> 
> USPP and NCPP are mathematical methods to approximate the solution of
> the
> same physical problem. Hence, there must be no physically different
> results, unless one of the pseudopotentials is faulty. Both types of
> pseudopotentials have cutoff radii, which are larger for NCPP than for
> USPP. The wavefunctions computed with any pseudopotential should be
> equal
> to the all-electron wavefunctions in the spatial region outside the
> spheres
> centered at each atom with spheres radii equal to the cutoff radii of
> the
> corresponding pseudopotential. Inside any sphere, the wavefunctions are
> different and are meaningless. To have the correct wavefunctions inside
> the
> spheres you have any of the following options a) all-electron
> calculations
> (with a different code,e.g. ADF, Gaussian, LMTO, etc), b) use a PP with
> a
> smaller cutoff radius (and larger ecutrho and ecutwfc), c) use PAW
> (projector augmented wave).
> 
> sincerely yours
> 
> 
> Eduardo Menendez Proupin
> Departamento de Qu?mica Fisica Aplicada
> Facultad de Ciencias
> Universidad Aut?noma de Madrid
> 28049 Madrid, Spain
> Phone: +34 91 497 6706
> 
> 
> 
>  Dear QE users.
> >
> >
> > I want to plot HOMO, LUMO isosurfaces. what is the physical origin
> > of difference between results from choosing USPP with NCPP?
> >  Thanks in advance.
> >
> >
> > -------------------------------------------
> > Yavar Taghipour Azar
> > PhD Student
> > Physics Group, AEOI
> > Tehran-Iran
> >
> > Email: ytaghipour at aeoi.org.ir
> > Phone: +98 (0) 21 82064556
> > -----------------------------------------------------------
> >
> >
> >
> >
> >
> --
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From ytaghipour at aeoi.org.ir  Tue Jul 10 09:01:44 2012
From: ytaghipour at aeoi.org.ir (Yavar Taghipour Azar)
Date: Tue, 10 Jul 2012 11:31:44 +0430
Subject: [Pw_forum] HOMO,LUMO isosurface, USPP or NCPP?
In-Reply-To: <CAM5Vcw_0Ky8aC8OcS4piakuHHux8h1cNnqs3JB1SMaxYbbEwQQ@mail.gmail.com>
References: <CAM5Vcw_0Ky8aC8OcS4piakuHHux8h1cNnqs3JB1SMaxYbbEwQQ@mail.gmail.com>
Message-ID: <WC20120710070144.250025@aeoi.org.ir>


Dear Eduardo,

thanks for your consideration on my problem,

Bests.

Yavar


-----Original Message-----
From: Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>
To: pw_forum at pwscf.org
Date: Mon, 9 Jul 2012 09:44:20 +0200
Subject: Re: [Pw_forum] HOMO,LUMO isosurface, USPP or NCPP?

Dear Yavar

USPP and NCPP are mathematical methods to approximate the solution of the 
same physical problem. Hence, there must be no physically different results, 
unless one of the pseudopotentials is faulty. Both types of pseudopotentials 
have cutoff radii, which are larger for NCPP than for USPP. The 
wavefunctions computed with any pseudopotential should be equal to the 
all-electron wavefunctions in the spatial region outside the spheres 
centered at each atom with spheres radii equal to the cutoff radii of the 
corresponding pseudopotential. Inside any sphere, the wavefunctions are 
different and are meaningless. To have the correct wavefunctions inside the 
spheres you have any of the following options a) all-electron calculations 
(with a different code,e.g. ADF, Gaussian, LMTO, etc), b) use a PP with a 
smaller cutoff radius (and larger ecutrho and ecutwfc), c) use PAW 
(projector augmented wave). 

sincerely yours





Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
28049 Madrid, Spain

Phone: +34 91 497 6706




Dear QE users.
 
 
I want to plot HOMO, LUMO isosurfaces. what is the physical origin of 
difference between results from choosing USPP with NCPP?
 Thanks in advance.
 
 
-------------------------------------------
Yavar Taghipour Azar
PhD Student
Physics Group, AEOI
Tehran-Iran
 
Email: ytaghipour at aeoi.org.ir
Phone: +98 (0) 21 82064556
-----------------------------------------------------------


 



-- 
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From dalcorso at sissa.it  Tue Jul 10 11:06:16 2012
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Tue, 10 Jul 2012 11:06:16 +0200
Subject: [Pw_forum] GRID example of e-ph
In-Reply-To: <1186790.7d33.1386e8543b8.Coremail.ptao10b@imr.ac.cn>
References: <1186790.7d33.1386e8543b8.Coremail.ptao10b@imr.ac.cn>
Message-ID: <1341911176.9891.4.camel@ulisse.cm.sissa.it>


On Tue, 2012-07-10 at 09:33 +0800, Peng Tao wrote:
> Dear all,
> 
> 
> As we know, the phonon calculation is quite slow and unexpected errors
> might occur at any time. 
> Thanks to the GRID example, split runs is available. However, no
> example is provided to split
> the e-ph calculation. So, dear professors, could you show me a method
> to realize it?
> 

PHonon/examples/GRID_example/run_example_2 

in QE 5.0. 

HTH

Andrea


> Sincerely yours
> Plato Tao
> 
> --
> -------------------------------------------------------------------
> PH.D. candidate Peng Tao 
> Magnetism and Magnetic Materials Division
> National Laboratory for Material Science
> Institute of Metal Research, Chinese Academy of Sciences
> Phone  +86-024-83978751
> -------------------------------------------------------------------
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Bonomea 265              Fax. 0039-040-3787249
I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it



From sohailphysics at yahoo.co.in  Tue Jul 10 11:09:37 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Tue, 10 Jul 2012 17:09:37 +0800 (SGT)
Subject: [Pw_forum] Error #19  MoS2 ecutoff convergence test
Message-ID: <1341911377.34524.YahooMailClassic@web192203.mail.sg3.yahoo.com>

Dear QE users

I am unable to understand the reason behind error #19
Kindly help


----
http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

???? Current dimensions of program PWSCF are:
???? Max number of different atomic species (ntypx) = 10
???? Max number of k-points (npk) =? 40000
???? Max angular momentum in pseudopotentials (lmaxx) =? 3
???? Waiting for input...

?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
???? from? read_namelists? : error #??????? 19
????? reading namelist system
?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

???? stopping ...
-------------------------------
#!/bin/sh

for i in 30 35 40 45 50 55 60 65
do

#j=$[$i*8]
echo " calculation ecutoff $i is running "

cat >> MoS2$i.in << EOF
?&control
? calculation = 'scf',
? restart_mode = 'from_scratch',
? prefix = 'MoS2',
? pseudo_dir = '/home/sohail/espresso-4.2.1/pseudo',
? outdir = './OUT'
?/
?&system
? ibrav = 4, celldm(1) = 5.9715031, celldm(3) = 3.89, nat = 6, ntyp = 2,
? ecutwfc = $i,
? ecutrho = 300,
? nband = 10,
? occupations = 'smearing', smearing = 'gaussian', degauss= 0.001,
? nspin = 2,
? starting_magnetization(1) = 0.5d0,
?/
?&electrons
? mixing_beta = 0.3,
? conv_thr = 1.0d-9,
?/
ATOMIC_SPECIES
Mo? 95.96? Mo.pbe-paw-nh.UPF
S?? 32.06? S.pbe-van_bm.UPF
ATOMIC_POSITIONS {crystal}
Mo? 0.33333333? 0.66666667? 0.25000000
Mo? 0.66666667? 0.33333333? 0.75000000
S?? 0.33333333? 0.66666667? 0.62000000
S?? 0.66666667? 0.33333333? 0.12000000
S?? 0.66666667? 0.33333333 -0.62000000
S?? 0.33333333? 0.66666667 -0.12000000
K_POINTS AUTOMATIC
4 4 4 1 1 1
EOF
pw.x < MoS2$i.in> MoS2$i.out

rm -rf OUT/*

done
---------------------------------------------------
Sohail Ahmad
King Khalid University
Saudi Arabia

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From lorenzo.paulatto at impmc.upmc.fr  Tue Jul 10 11:23:21 2012
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Tue, 10 Jul 2012 11:23:21 +0200
Subject: [Pw_forum] Error #19 MoS2 ecutoff convergence test
In-Reply-To: <1341911377.34524.YahooMailClassic@web192203.mail.sg3.yahoo.com>
References: <1341911377.34524.YahooMailClassic@web192203.mail.sg3.yahoo.com>
Message-ID: <CAG+GtJd9j4eo7ED=hPVDmMzofE9fR-mCp8_7eZvTfwRUme2UFQ@mail.gmail.com>

On Tue, Jul 10, 2012 at 11:09 AM, Sohail Ahmad <sohailphysics at yahoo.co.in>wrote:

>   nband = 10,
>
>
This should be
  nbnd = 10,

best regards


-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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From giannozz at democritos.it  Tue Jul 10 11:50:08 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 10 Jul 2012 11:50:08 +0200
Subject: [Pw_forum] Memory (RAM)
In-Reply-To: <CC209E94.AC26%Trinh.Vo@jpl.nasa.gov>
References: <CC209E94.AC26%Trinh.Vo@jpl.nasa.gov>
Message-ID: <150B8A98-5EEB-49AE-AB05-EC5163B7F9A5@democritos.it>


On Jul 9, 2012, at 23:43 , Vo, Trinh (388C) wrote:

> I am running very large job (nscf calculation 15x15x15) using QE  
> version 4.3.2.
> The job keeps being crashed due to memory problem (out of memory,  
> RAM).
> Is there a way that I can estimate how much memory   (RAM) required  
> for running
> a nscf calculation?

some explanations here:
   http://www.quantum-espresso.org/wp-content/uploads/Doc/ 
pw_user_guide/node13.html
Note that a large number of k-points does not imply a large RAM, but  
a large number
of bands does.

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From flux_ray12 at 163.com  Tue Jul 10 11:54:30 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Tue, 10 Jul 2012 17:54:30 +0800 (CST)
Subject: [Pw_forum] Error #19  MoS2 ecutoff convergence test
In-Reply-To: <1341911377.34524.YahooMailClassic@web192203.mail.sg3.yahoo.com>
References: <1341911377.34524.YahooMailClassic@web192203.mail.sg3.yahoo.com>
Message-ID: <2e265885.1de5b.138704fbde3.Coremail.flux_ray12@163.com>

Well, the error actually is very small, please check carefully next time, since this must only due to your own careless~
in &system, to define the number of band, we use the parameter "nbnd" instead of "nband"......


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-07-10 17:09:37,"Sohail Ahmad" <sohailphysics at yahoo.co.in> wrote:

| Dear QE users

I am unable to understand the reason behind error #19
Kindly help


----
http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from  read_namelists  : error #        19
      reading namelist system
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
-------------------------------
#!/bin/sh

for i in 30 35 40 45 50 55 60 65
do

#j=$[$i*8]
echo " calculation ecutoff $i is running "

cat >> MoS2$i.in << EOF
 &control
  calculation = 'scf',
  restart_mode = 'from_scratch',
  prefix = 'MoS2',
  pseudo_dir = '/home/sohail/espresso-4.2.1/pseudo',
  outdir = './OUT'
 /
 &system
  ibrav = 4, celldm(1) = 5.9715031, celldm(3) = 3.89, nat = 6, ntyp = 2,
  ecutwfc = $i,
  ecutrho = 300,
  nband = 10,
  occupations = 'smearing', smearing = 'gaussian', degauss= 0.001,
  nspin = 2,
  starting_magnetization(1) = 0.5d0,
 /
 &electrons
  mixing_beta = 0.3,
  conv_thr = 1.0d-9,
 /
ATOMIC_SPECIES
Mo  95.96  Mo.pbe-paw-nh.UPF
S   32.06  S.pbe-van_bm.UPF
ATOMIC_POSITIONS {crystal}
Mo  0.33333333  0.66666667  0.25000000
Mo  0.66666667  0.33333333  0.75000000
S   0.33333333  0.66666667  0.62000000
S   0.66666667  0.33333333  0.12000000
S   0.66666667  0.33333333 -0.62000000
S   0.33333333  0.66666667 -0.12000000
K_POINTS AUTOMATIC
4 4 4 1 1 1
EOF
pw.x < MoS2$i.in> MoS2$i.out

rm -rf OUT/*

done
---------------------------------------------------
Sohail Ahmad
King Khalid University
Saudi Arabia

|
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From giuseppe.mattioli at ism.cnr.it  Tue Jul 10 12:46:31 2012
From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli)
Date: Tue, 10 Jul 2012 12:46:31 +0200
Subject: [Pw_forum] segfault in projwfc calculation
In-Reply-To: <4FFBCF7E.8030903@sissa.it>
References: <CAP_5U0cVAHQYUfpX_t_13ws=cqzwVKE+232zx_Tf0yRorcmZgQ@mail.gmail.com>
	<4FFBCF7E.8030903@sissa.it>
Message-ID: <201207101246.31547.giuseppe.mattioli@ism.cnr.it>


Dear all
I'm trying to perform some post-processing calculations with QE 5.0 compiled against
gfortran 4.4.4 and mkl on a parallel machine. pw.x calculations are OK, as well as dos.x and pp.x 
ones. projwfc.x calculations stop instead without complaining and I found this system error

mpirun noticed that process rank 2 with PID 12250 on node compute-1-1 exited on signal 11 
(Segmentation fault).

You may perform yourself the calculations, if you want; it's a simple water molecule in a small box  
(O and H can be found in the pseudo library). Any suggestion will be appreciated...

Giuseppe


export MACHINE_FILE=`pwd`/Machine
export NP=8
export ESPRESSO=/home/mattioligi/5.0-gcc4.4/bin
export PARA_PREFIX="mpirun -machinefile $MACHINE_FILE -np $NP"
export PARA_POSTFIX=
export OMP_NUM_THREADS=1

export FILE="h2o-test"
export INPFILE=$FILE-1.inp
export OUTFILE=$FILE-1.out
echo " $FILE"
echo " $INPFILE"
echo " $OUTFILE"

cat > $INPFILE << EOF
 &control
    calculation = 'relax'
    restart_mode='restart',
    prefix='$FILE',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/',
 /
 &system
    ibrav=1, celldm(1)=10.00000,
    nat=3, ntyp=2,
    ecutwfc=30.0,
    ecutrho=180.0,
    nspin=1,
 /
 &electrons
    mixing_mode='plain'
    mixing_beta=0.3
    conv_thr=1.0d-6
    electron_maxstep=200
 /
 &ions
    ion_dynamics='bfgs'
 /
ATOMIC_SPECIES
O    15.999    O_pbe.van.UPF
H     1.008    H_pbe.van.UPF
ATOMIC_POSITIONS {angstrom}
O        2.000000000   2.000000000   1.807818969    0   0   1
H        2.000000000   2.775615577   1.200000000    0   1   0
H        2.000000000   1.224385277   1.200000000    0   1   0
K_POINTS {gamma}
EOF
$PARA_PREFIX $ESPRESSO/pw.x -ndiag 4 $PARA_POSTFIX < $INPFILE >> $OUTFILE

export FILEA="$FILE"
export INPFILE=$FILEA-dos.inp
export OUTFILE=$FILEA-dos.out
echo " $FILEA"
echo " $INPFILE"
echo " $OUTFILE"
cat > $INPFILE << EOF
 &dos
    prefix  = '$FILEA'
    outdir = '$TMP_DIR/'
    fildos='$FILEA.dos'
 /
EOF
$PARA_PREFIX $ESPRESSO/dos.x $PARA_POSTFIX < $INPFILE >> $OUTFILE

export INPFILE=$FILEA-pdos.inp
export OUTFILE=$FILEA-pdos.out
echo " $INPFILE"
echo " $OUTFILE"

cat > $INPFILE << EOF
 &projwfc
    prefix  = '$FILEA'
    outdir = '$TMP_DIR/'
    filproj='$FILEA.proj'
    filpdos='$FILEA.pdos'
 /
EOF
$PARA_PREFIX $ESPRESSO/projwfc.x $PARA_POSTFIX < $INPFILE >> $OUTFILE

This is the standard output of the projwfc calculation

     Program PROJWFC v.5.0      starts on 10Jul2012 at 12:20: 1

     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org",
     in publications or presentations arising from this work. More details at
     http://www.quantum-espresso.org/quote.php

     Parallel version (MPI), running on     8 processors
     R & G space division:  proc/pool =    8

   Info: using nr1, nr2, nr3 values from input

   Info: using nr1s, nr2s, nr3s values from input

     IMPORTANT: XC functional enforced from input :
     Exchange-correlation      =  SLA  PW   PBE  PBE ( 1 4 3 4 0)
     EXX-fraction              =        0.00
     Any further DFT definition will be discarded
     Please, verify this is what you really want


     Parallelization info
     --------------------
     sticks:   dense  smooth     PW     G-vecs:    dense   smooth      PW
     Min         178     118     30                 5078     2754     346
     Max         180     120     31                 5084     2773     350
     Sum        1433     949    241                40651    22119    2777
     Tot         717     475    121


     negative rho (up, down):  0.186E-02 0.000E+00

     Gaussian broadening (default values): ngauss,degauss=   0    0.000735


     Calling pprojwave ....
     gamma-point specific algorithms are used

  Problem Sizes
  natomwfc =            6
  nbnd     =            4
  nkstot   =            1
  npwx     =          175
  nkb      =           10


-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

   Giuseppe Mattioli                            
   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
   v. Salaria Km 29,300 - C.P. 10                
   I 00015 - Monterotondo Stazione (RM)          
   Tel + 39 06 90672836 - Fax +39 06 90672316    
   E-mail: <giuseppe.mattioli at ism.cnr.it>

From negarastani at gmail.com  Tue Jul 10 14:35:46 2012
From: negarastani at gmail.com (Negar Ashari Astani)
Date: Tue, 10 Jul 2012 14:35:46 +0200
Subject: [Pw_forum] Old problem with cppp.x
In-Reply-To: <CAJqU8JBX2xyxCR5Z5yYEMKnZOYFssO1mCnTueO4fuj02x4f67A@mail.gmail.com>
References: <CAJqU8JA3kvyd9jA_VKC=z7BuWFuXYvrcfPYVPbEworKyQN79Ng@mail.gmail.com>
	<CAJqU8JBX2xyxCR5Z5yYEMKnZOYFssO1mCnTueO4fuj02x4f67A@mail.gmail.com>
Message-ID: <CAJqU8JAfhN1XwPNDH-sEp5YOU_j_QN8GtDQnr21QaucpPb75+A@mail.gmail.com>

Problem solved!
My mistake!
I was using the same parallel running script that I use for cp.x to run
cppp.x! Just don't run it with mpirun!!!!!
It's serial!

Thanks a lot,
Negar

On Mon, Jul 9, 2012 at 6:01 PM, Negar Ashari Astani
<negarastani at gmail.com>wrote:

> Dear Gabriele,
>
> Thanks for your reply, I should have been more thoughtful about the
> quotations!
> I'll put my actual input here:
>
> &INPUTPP
> !  prefix = 'Anatase',
>   fileout ='out',
>    output = 'xsf',
>    outdir = '/scratch/negar/espresso/out/',
>    lcharge=.TRUE.,
>    lforces=.TRUE.,
>    ldynamics =.False.,
>    lpdb=.TRUE.,
>    lrotation = .False.,
> !   ns1, ns2, ns3,
> !   np1, np2, np3,
> !   nframes=50,
>    ndr=50,
> !   ndw=91,
>    atomic_number(1)=22
>    atomic_number(2)=8,
> !   charge_density= 'full',
>    state= 'KS_1',
>    lbinary=.TRUE.
> /
>
> I'm still getting the same error! and what surprises me is that I have set
> the ndr value equal to 50 in both my cp.in and cppp.in and the program is
> still looking for cp_51.save! which doesn't exist! (Even if I change the
> folder name to 50 manually, that wouldn't change anything!)
>
> Many thanks,
> Nash
>
>
>
>
> On Mon, Jul 9, 2012 at 2:18 PM, Negar Ashari Astani <negarastani at gmail.com
> > wrote:
>
>>
>> Hello everyone,
>>
>> I'm confronting a probably stupid problem with cppp.x! I saw this problem
>> being reported two times in the forum:
>>
>> http://www.democritos.it/pipermail/pw_forum/2011-February/019298.html
>>
>> http://www.democritos.it/pipermail/pw_forum/2008-May/009020.html
>>
>> Having read those, I'm still getting the following error:
>>
>> Cannot open file ....espresso/out/cp_51.save/data-file.xml
>>
>> I checked the corresponding address, and the files are there!
>> and I also renamed the save directory and files to match the default
>> cp_51 and .....
>>
>>
>> This is my input file for cppp.x:
>>
>>
>> &INPUTPP
>> !  prefix=Anatase,
>>    fileout=out,
>>    output=xsf,
>>    outdir=..mypath../espresso/out,
>>    wfcdir=..mypath../espresso/out,
>>    lcharge=.TRUE.,
>>    lforces=.TRUE.,
>>    ldynamics=.TRUE.,
>>    lpdb=.TRUE.,
>>    lrotation,
>>    ns1, ns2, ns3,
>>    np1, np2, np3,
>>    nframes=50,
>> !   ndr=90,
>> !   ndw=91,
>>    atomic_number(1) 22
>>    atomic_number(2) 8,
>>    charge_density,
>>    state= KS_1,
>>    lbinary=.TRUE.
>> /
>>
>> Although I'm using Q.Espresso.5, I tried to replace fpmdpp.f90 with the
>> file provided by Paolo in the second link!
>> That didn't work either!
>>
>> Many thanks,
>> Nash
>>
>>
>>
>
>
>
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From himm0013 at umn.edu  Tue Jul 10 15:37:16 2012
From: himm0013 at umn.edu (Burak Himmetoglu)
Date: Tue, 10 Jul 2012 08:37:16 -0500
Subject: [Pw_forum] U calculation in LDA+U
In-Reply-To: <4FFBCF7E.8030903@sissa.it>
References: <CAP_5U0cVAHQYUfpX_t_13ws=cqzwVKE+232zx_Tf0yRorcmZgQ@mail.gmail.com>
	<4FFBCF7E.8030903@sissa.it>
Message-ID: <CAH55yVSPM_M8K=mG8A3fqY5Wb+Sve9xBLH6wBMhXav1KZvEU1g@mail.gmail.com>

Hi Peng,

r.x assigns the values of the response matrices only by considering the
distance between atoms and whether they have the same spin and type or not.
This information has to be given by the user in the positions file
"filepos" read by &input_mat. If B(1) and B(2) are different types
(e.g. crystallographically) you should perturb them separately, as you
outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type
2 is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x

Best regards,

Burak

On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli <degironc at sissa.it>wrote:

>  I don't know the details of r.x code but I think that, physically, what
> matters is the two atoms are crystallographically equivalent or not
> .therefore I think space group symmetry is the relevant one.
>
> stefano
>
>
> On 07/10/2012 05:54 AM, Peng Chen wrote:
>
> Dear All,
>
> In the calculation of U, how can we determine the equivalence of the ions,
> by site symmetry or space group symmetry?
> E.g  ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run
> calculation on perturbing B(1) and B(2) ions or  just a B ion?
>
>  In order to find U in B  ions, I tried to run calculation with perturbing
> just on B, and r.x gave some errors that it needs to read more data.
> So I guess it needs the perturbed data from other atoms. Shall I use the
> procedures listed below?
> 1. run scf calculation with Hubbard_U(i)= 1.d-20
> 2. run scf with perturbing on an A ion
> 3.   run scf with perturbing on a B(1) ion
> 4.   run scf with perturbing on a B(2) ion
> 5.   run scf with perturbing on an O ion
>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From giannozz at democritos.it  Tue Jul 10 15:54:13 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 10 Jul 2012 15:54:13 +0200
Subject: [Pw_forum] segfault in projwfc calculation
In-Reply-To: <201207101246.31547.giuseppe.mattioli@ism.cnr.it>
References: <CAP_5U0cVAHQYUfpX_t_13ws=cqzwVKE+232zx_Tf0yRorcmZgQ@mail.gmail.com>
	<4FFBCF7E.8030903@sissa.it>
	<201207101246.31547.giuseppe.mattioli@ism.cnr.it>
Message-ID: <7DEBB80B-51FE-47BB-BF98-CE64C31BFB14@democritos.it>


On Jul 10, 2012, at 12:46 , Giuseppe Mattioli wrote:

> mpirun noticed that process rank 2 with PID 12250 on node compute-1-1
> exited on signal 11 (Segmentation fault).


it works for me both in serial and in parallel execution. It is likely a
compiler or library problem. There is little that can be done in cases
like this

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From pchen at ion.chem.utk.edu  Tue Jul 10 16:06:16 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Tue, 10 Jul 2012 10:06:16 -0400
Subject: [Pw_forum] U calculation in LDA+U
In-Reply-To: <CAH55yVSPM_M8K=mG8A3fqY5Wb+Sve9xBLH6wBMhXav1KZvEU1g@mail.gmail.com>
References: <CAP_5U0cVAHQYUfpX_t_13ws=cqzwVKE+232zx_Tf0yRorcmZgQ@mail.gmail.com>
	<4FFBCF7E.8030903@sissa.it>
	<CAH55yVSPM_M8K=mG8A3fqY5Wb+Sve9xBLH6wBMhXav1KZvEU1g@mail.gmail.com>
Message-ID: <CAP_5U0c5QOBTztTGQvaQibVQ8u9SYZcuU_uiU+c36J-eX+kqLg@mail.gmail.com>

Thanks  stefano and Burak.

If space group matters, then the 3 types will be A, B and O.

On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu <himm0013 at umn.edu> wrote:

> Hi Peng,
>
> r.x assigns the values of the response matrices only by considering the
> distance between atoms and whether they have the same spin and type or not.
> This information has to be given by the user in the positions file
> "filepos" read by &input_mat. If B(1) and B(2) are different types
> (e.g. crystallographically) you should perturb them separately, as you
> outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type
> 2 is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x
>
> Best regards,
>
> Burak
>
>
> On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli <degironc at sissa.it>wrote:
>
>>  I don't know the details of r.x code but I think that, physically, what
>> matters is the two atoms are crystallographically equivalent or not
>> .therefore I think space group symmetry is the relevant one.
>>
>> stefano
>>
>>
>> On 07/10/2012 05:54 AM, Peng Chen wrote:
>>
>> Dear All,
>>
>> In the calculation of U, how can we determine the equivalence of the ions,
>> by site symmetry or space group symmetry?
>> E.g  ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run
>> calculation on perturbing B(1) and B(2) ions or  just a B ion?
>>
>>  In order to find U in B  ions, I tried to run calculation with perturbing
>> just on B, and r.x gave some errors that it needs to read more data.
>> So I guess it needs the perturbed data from other atoms. Shall I use the
>> procedures listed below?
>> 1. run scf calculation with Hubbard_U(i)= 1.d-20
>> 2. run scf with perturbing on an A ion
>> 3.   run scf with perturbing on a B(1) ion
>> 4.   run scf with perturbing on a B(2) ion
>> 5.   run scf with perturbing on an O ion
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
  Best Regards.
        Peng
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From torstein.fjermestad at kjemi.uio.no  Tue Jul 10 16:44:56 2012
From: torstein.fjermestad at kjemi.uio.no (Torstein Fjermestad)
Date: Tue, 10 Jul 2012 16:44:56 +0200
Subject: [Pw_forum] Calculation of Gibbs free energies
Message-ID: <9ab5bb3130dbbdad6da9232ea8e9585c@ulrik.uio.no>

 Dear all,

 In one of my projects I would need to compute the Gibbs free energies 
 of structures along a reaction path. After looking through the QE 
 webpage, the pw_forum, and the documentation in the quantum espresso 
 installation directory I think I understand the general procedure:

 1. one calculates the phonons
 2. one computes the interatomic Force Constants with the q2r.x program
 3. one uses the matdyn.x to produce input for the F_QHA.x program
 4. with the F_QHA.x program one can compute the Gibbs free energy and 
 other thermodynamical properties.

 (please correct me if I have misunderstood this general procedure)

 The problem is that I have so far only managed to complete step 1, to 
 compute the phonons. I am currently doing test calculations on a water 
 molecule and this is the input file of the phonon calculation:

 phonons of H2O in super cell at Gamma
  &inputph
   outdir='./',
   prefix='h2o',
   amass(1)=1.01,
   amass(2)=16.01,
   fildyn='h2o.dynG',
   trans= .true.
  /
 0.0 0.0 0.0

 I then try to run the q2r.x calculation with the following input:

 test of q2r calculation
 &input
   fildyn='h2o.dynG',
   flfrc='h2o-output-q2r.fc',
   zasr='no'

 This calculation crashes presumably because it expects a file called 
 h2o.dynG0. But from where do I get this file? As far as I can see the 
 phonon calculation only produces the file h2o.dynG, not a h2o.dynG0 
 file.

 I am completely lost at the moment so I would appreciate if anyone 
 could help me with carrying out the q2r calculation correctly.
 
 Thank you very much in advance,

 Yours sincerely,

 Torstein Fjermestad,
 University of Oslo,
 Norway










 

From pchen at ion.chem.utk.edu  Tue Jul 10 17:03:43 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Tue, 10 Jul 2012 11:03:43 -0400
Subject: [Pw_forum] U calculation in LDA+U
In-Reply-To: <CAH55yVSPM_M8K=mG8A3fqY5Wb+Sve9xBLH6wBMhXav1KZvEU1g@mail.gmail.com>
References: <CAP_5U0cVAHQYUfpX_t_13ws=cqzwVKE+232zx_Tf0yRorcmZgQ@mail.gmail.com>
	<4FFBCF7E.8030903@sissa.it>
	<CAH55yVSPM_M8K=mG8A3fqY5Wb+Sve9xBLH6wBMhXav1KZvEU1g@mail.gmail.com>
Message-ID: <CAP_5U0fcpJHcvqd6iGeSdG+FRE2zDeSB1x8vpG=Crhv712V+qA@mail.gmail.com>

When O is perturbed in the case of NiO in tutorial, it is re-positioned and
there are 2 different kinds of O (first with 1 atom, the second with 7
atoms).  Then the kind with only one O is perturbed. In the tutorial, it
reads "This is done to preserve the largest possible number of symmetries".
 Is this process necessary? Can we just run computation without
re-position? In that case, there is only one kind of O with 8 atoms.

In the position file "filepos", the scale of cell length is always 10, even
if the scale is 7.9 in NiO and 5.42 in Fe. Shall we always use 10 in
position file no matter what the real scale is?

On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu <himm0013 at umn.edu> wrote:

> Hi Peng,
>
> r.x assigns the values of the response matrices only by considering the
> distance between atoms and whether they have the same spin and type or not.
> This information has to be given by the user in the positions file
> "filepos" read by &input_mat. If B(1) and B(2) are different types
> (e.g. crystallographically) you should perturb them separately, as you
> outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type
> 2 is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x
>
> Best regards,
>
> Burak
>
>
> On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli <degironc at sissa.it>wrote:
>
>>  I don't know the details of r.x code but I think that, physically, what
>> matters is the two atoms are crystallographically equivalent or not
>> .therefore I think space group symmetry is the relevant one.
>>
>> stefano
>>
>>
>> On 07/10/2012 05:54 AM, Peng Chen wrote:
>>
>> Dear All,
>>
>> In the calculation of U, how can we determine the equivalence of the ions,
>> by site symmetry or space group symmetry?
>> E.g  ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run
>> calculation on perturbing B(1) and B(2) ions or  just a B ion?
>>
>>  In order to find U in B  ions, I tried to run calculation with perturbing
>> just on B, and r.x gave some errors that it needs to read more data.
>> So I guess it needs the perturbed data from other atoms. Shall I use the
>> procedures listed below?
>> 1. run scf calculation with Hubbard_U(i)= 1.d-20
>> 2. run scf with perturbing on an A ion
>> 3.   run scf with perturbing on a B(1) ion
>> 4.   run scf with perturbing on a B(2) ion
>> 5.   run scf with perturbing on an O ion
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
  Best Regards.
        Peng
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From giannozz at democritos.it  Tue Jul 10 17:11:15 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 10 Jul 2012 17:11:15 +0200
Subject: [Pw_forum] Calculation of Gibbs free energies
In-Reply-To: <9ab5bb3130dbbdad6da9232ea8e9585c@ulrik.uio.no>
References: <9ab5bb3130dbbdad6da9232ea8e9585c@ulrik.uio.no>
Message-ID: <A36B4B39-661A-4C13-88EA-0975B6F20EB2@democritos.it>


On Jul 10, 2012, at 16:44 , Torstein Fjermestad wrote:

> this is the input file of the phonon calculation:

this is the input file for a SINGLE phonon calculation. You need
to specify "disp=.true." and a wave-vector grid to get the phonon
dispersions needed to calculate interatomic force constants

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From himm0013 at umn.edu  Tue Jul 10 17:11:45 2012
From: himm0013 at umn.edu (Burak Himmetoglu)
Date: Tue, 10 Jul 2012 10:11:45 -0500
Subject: [Pw_forum] U calculation in LDA+U
In-Reply-To: <CAP_5U0fcpJHcvqd6iGeSdG+FRE2zDeSB1x8vpG=Crhv712V+qA@mail.gmail.com>
References: <CAP_5U0cVAHQYUfpX_t_13ws=cqzwVKE+232zx_Tf0yRorcmZgQ@mail.gmail.com>
	<4FFBCF7E.8030903@sissa.it>
	<CAH55yVSPM_M8K=mG8A3fqY5Wb+Sve9xBLH6wBMhXav1KZvEU1g@mail.gmail.com>
	<CAP_5U0fcpJHcvqd6iGeSdG+FRE2zDeSB1x8vpG=Crhv712V+qA@mail.gmail.com>
Message-ID: <CAH55yVT92Rhpasrjv=By8V+fcbg60tQHrjCO3qfmYvsgo+1Arw@mail.gmail.com>

Hi Peng,

In my experience, the process of shifting the O atom to the origin is
recommended since it produces more stable results numerically, especially
in the second part of r.x where the program extrapolates to larger
supercells using the results from the starting supercell you have used.
However, if the crystal has already very  small number of symmetries, then
you should be able to avoid this shifting.

The first three entries in filepos are the lattice vectors in units of alat
(like the CELL_PARAMETERS when ibrav=0). The unit cell is expanded by a
factor of 10 in the tutorial. The length scale in filepos is not necessary.
That file is used only to compare the distances between pairs of atoms and
the scale does not really matter. It is generally better to scale up only
for numerical stability reasons.

Best regards,

Burak

On Tue, Jul 10, 2012 at 10:03 AM, Peng Chen <pchen at ion.chem.utk.edu> wrote:

> When O is perturbed in the case of NiO in tutorial, it
> is re-positioned and there are 2 different kinds of O (first with 1 atom,
> the second with 7 atoms).  Then the kind with only one O is perturbed. In
> the tutorial, it reads "This is done to preserve the largest possible
> number of symmetries".  Is this process necessary? Can we just run
> computation without re-position? In that case, there is only one kind of O
> with 8 atoms.
>
> In the position file "filepos", the scale of cell length is always 10,
> even if the scale is 7.9 in NiO and 5.42 in Fe. Shall we always use 10 in
> position file no matter what the real scale is?
>
> On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu <himm0013 at umn.edu>wrote:
>
>> Hi Peng,
>>
>> r.x assigns the values of the response matrices only by considering the
>> distance between atoms and whether they have the same spin and type or not.
>> This information has to be given by the user in the positions file
>> "filepos" read by &input_mat. If B(1) and B(2) are different types
>> (e.g. crystallographically) you should perturb them separately, as you
>> outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type
>> 2 is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x
>>
>> Best regards,
>>
>> Burak
>>
>>
>> On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli <degironc at sissa.it>wrote:
>>
>>>  I don't know the details of r.x code but I think that, physically,
>>> what matters is the two atoms are crystallographically equivalent or not
>>> .therefore I think space group symmetry is the relevant one.
>>>
>>> stefano
>>>
>>>
>>> On 07/10/2012 05:54 AM, Peng Chen wrote:
>>>
>>> Dear All,
>>>
>>> In the calculation of U, how can we determine the equivalence of the ions,
>>> by site symmetry or space group symmetry?
>>> E.g  ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run
>>> calculation on perturbing B(1) and B(2) ions or  just a B ion?
>>>
>>>  In order to find U in B  ions, I tried to run calculation with perturbing
>>> just on B, and r.x gave some errors that it needs to read more data.
>>> So I guess it needs the perturbed data from other atoms. Shall I use the
>>> procedures listed below?
>>> 1. run scf calculation with Hubbard_U(i)= 1.d-20
>>> 2. run scf with perturbing on an A ion
>>> 3.   run scf with perturbing on a B(1) ion
>>> 4.   run scf with perturbing on a B(2) ion
>>> 5.   run scf with perturbing on an O ion
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
>   Best Regards.
>         Peng
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From lorenzo.paulatto at impmc.upmc.fr  Tue Jul 10 17:17:57 2012
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Tue, 10 Jul 2012 17:17:57 +0200
Subject: [Pw_forum] Calculation of Gibbs free energies
In-Reply-To: <9ab5bb3130dbbdad6da9232ea8e9585c@ulrik.uio.no>
References: <9ab5bb3130dbbdad6da9232ea8e9585c@ulrik.uio.no>
Message-ID: <CAG+GtJdV-FYqkXsPj9O65oQrgaHb1tKLJOdtgi-OhLzXine7iA@mail.gmail.com>

On Tue, Jul 10, 2012 at 4:44 PM, Torstein Fjermestad <
torstein.fjermestad at kjemi.uio.no> wrote:

>  The problem is that I have so far only managed to complete step 1, to
>  compute the phonons. I am currently doing test calculations on a water
>  molecule and this is the input file of the phonon calculation:
>
> ...

 This calculation crashes presumably because it expects a file called
>  h2o.dynG0. But from where do I get this file? As far as I can see the
>  phonon calculation only produces the file h2o.dynG, not a h2o.dynG0
>  file.
>
>
 Dear Torstein,
the problem in your case is that q2r.x expects to find a phonon
*dispersion* calculation, i.e. the phonon computed over a regular grid of
q-points n reciprocal space. On the other hand, you only computed the
phonons at Gamma. It is true that Gamma is just a 1x1x1 grid, and if you
are sure it is enough to describe your system you can manage to convince
q2r to use it. You need to do the following:
1. move h2o.dynG to h2o.dynG1
2. create a file called h2o.dynG0 which this inside:
 1 1 1
 1
 0.0 0.0 0.0
3. try again with q2r.x

Alternatively, you can just repeat the phonon calculation with ldisp =
.true.; if you want your grid to be just the Gamma point you specify nq1=1,
nq2=1, nq3=1.

I stress that a single-point sampling may not be enough to describe
accurately the properties of your system (unless the supercell is very
large) but this you need to check for yourself.

good work


-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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From pchen at ion.chem.utk.edu  Tue Jul 10 17:25:43 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Tue, 10 Jul 2012 11:25:43 -0400
Subject: [Pw_forum] U calculation in LDA+U
In-Reply-To: <CAH55yVT92Rhpasrjv=By8V+fcbg60tQHrjCO3qfmYvsgo+1Arw@mail.gmail.com>
References: <CAP_5U0cVAHQYUfpX_t_13ws=cqzwVKE+232zx_Tf0yRorcmZgQ@mail.gmail.com>
	<4FFBCF7E.8030903@sissa.it>
	<CAH55yVSPM_M8K=mG8A3fqY5Wb+Sve9xBLH6wBMhXav1KZvEU1g@mail.gmail.com>
	<CAP_5U0fcpJHcvqd6iGeSdG+FRE2zDeSB1x8vpG=Crhv712V+qA@mail.gmail.com>
	<CAH55yVT92Rhpasrjv=By8V+fcbg60tQHrjCO3qfmYvsgo+1Arw@mail.gmail.com>
Message-ID: <CAP_5U0d30xmi4W92zxDHTNZAviY-cxFTuBmV3Jqd9R2nzuy5og@mail.gmail.com>

Thanks Burak. I appreciate your suggestions and I will try.

On Tue, Jul 10, 2012 at 11:11 AM, Burak Himmetoglu <himm0013 at umn.edu> wrote:

> Hi Peng,
>
> In my experience, the process of shifting the O atom to the origin is
> recommended since it produces more stable results numerically, especially
> in the second part of r.x where the program extrapolates to larger
> supercells using the results from the starting supercell you have used.
> However, if the crystal has already very  small number of symmetries, then
> you should be able to avoid this shifting.
>
> The first three entries in filepos are the lattice vectors in units of
> alat (like the CELL_PARAMETERS when ibrav=0). The unit cell is expanded by
> a factor of 10 in the tutorial. The length scale in filepos is not
> necessary. That file is used only to compare the distances between pairs of
> atoms and the scale does not really matter. It is generally better to scale
> up only for numerical stability reasons.
>
> Best regards,
>
> Burak
>
> On Tue, Jul 10, 2012 at 10:03 AM, Peng Chen <pchen at ion.chem.utk.edu>wrote:
>
>> When O is perturbed in the case of NiO in tutorial, it
>> is re-positioned and there are 2 different kinds of O (first with 1 atom,
>> the second with 7 atoms).  Then the kind with only one O is perturbed. In
>> the tutorial, it reads "This is done to preserve the largest possible
>> number of symmetries".  Is this process necessary? Can we just run
>> computation without re-position? In that case, there is only one kind of O
>> with 8 atoms.
>>
>> In the position file "filepos", the scale of cell length is always 10,
>> even if the scale is 7.9 in NiO and 5.42 in Fe. Shall we always use 10 in
>> position file no matter what the real scale is?
>>
>> On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu <himm0013 at umn.edu>wrote:
>>
>>> Hi Peng,
>>>
>>> r.x assigns the values of the response matrices only by considering the
>>> distance between atoms and whether they have the same spin and type or not.
>>> This information has to be given by the user in the positions file
>>> "filepos" read by &input_mat. If B(1) and B(2) are different types
>>> (e.g. crystallographically) you should perturb them separately, as you
>>> outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type
>>> 2 is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x
>>>
>>> Best regards,
>>>
>>> Burak
>>>
>>>
>>> On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli <degironc at sissa.it
>>> > wrote:
>>>
>>>>  I don't know the details of r.x code but I think that, physically,
>>>> what matters is the two atoms are crystallographically equivalent or not
>>>> .therefore I think space group symmetry is the relevant one.
>>>>
>>>> stefano
>>>>
>>>>
>>>> On 07/10/2012 05:54 AM, Peng Chen wrote:
>>>>
>>>> Dear All,
>>>>
>>>> In the calculation of U, how can we determine the equivalence of the ions,
>>>> by site symmetry or space group symmetry?
>>>> E.g  ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run
>>>> calculation on perturbing B(1) and B(2) ions or  just a B ion?
>>>>
>>>>  In order to find U in B  ions, I tried to run calculation with perturbing
>>>> just on B, and r.x gave some errors that it needs to read more data.
>>>> So I guess it needs the perturbed data from other atoms. Shall I use the
>>>> procedures listed below?
>>>> 1. run scf calculation with Hubbard_U(i)= 1.d-20
>>>> 2. run scf with perturbing on an A ion
>>>> 3.   run scf with perturbing on a B(1) ion
>>>> 4.   run scf with perturbing on a B(2) ion
>>>> 5.   run scf with perturbing on an O ion
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Pw_forum mailing list
>>>> Pw_forum at pwscf.org
>>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>
>>
>> --
>>   Best Regards.
>>         Peng
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
  Best Regards.
        Peng
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From matteo at umn.edu  Tue Jul 10 17:15:55 2012
From: matteo at umn.edu (Matteo Cococcioni)
Date: Tue, 10 Jul 2012 10:15:55 -0500
Subject: [Pw_forum] U calculation in LDA+U
In-Reply-To: <CAP_5U0fcpJHcvqd6iGeSdG+FRE2zDeSB1x8vpG=Crhv712V+qA@mail.gmail.com>
References: <CAP_5U0cVAHQYUfpX_t_13ws=cqzwVKE+232zx_Tf0yRorcmZgQ@mail.gmail.com>
	<4FFBCF7E.8030903@sissa.it>
	<CAH55yVSPM_M8K=mG8A3fqY5Wb+Sve9xBLH6wBMhXav1KZvEU1g@mail.gmail.com>
	<CAP_5U0fcpJHcvqd6iGeSdG+FRE2zDeSB1x8vpG=Crhv712V+qA@mail.gmail.com>
Message-ID: <CAMZASgG3MP1MQ3mKi5W5m1MigE-dbboZ+95-EXK4=gfYG+poAQ@mail.gmail.com>

Dear Peng,

let me add one word to Burak's.
you need to distinguish two O kinds anyway, whether you shift the
atomic position or not. if you don't do that you will be perturbing
all the oxygen atoms at the same time.
The necessity to have the perturbed atom described as of a different
type (although with the same pseudopotential) is what makes it
convenient (most of the time) to place it at the origin of the unit
cell.

best,

Matteo



On Tue, Jul 10, 2012 at 10:03 AM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
> When O is perturbed in the case of NiO in tutorial, it is?re-positioned?and
> there are 2 different kinds of O (first with 1 atom, the second with 7
> atoms).??Then the kind with only one O is perturbed. In the tutorial, it
> reads "This is done to preserve the largest possible number of symmetries".
> ?Is this process necessary? Can we just run computation without re-position?
> In that case, there is only one kind of O with 8 atoms.
>
> In the position file "filepos", the scale of cell length is always 10, even
> if the scale is 7.9 in NiO and 5.42 in Fe. Shall we always use 10 in
> position file no matter what the real scale is?
>
> On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu <himm0013 at umn.edu> wrote:
>>
>> Hi Peng,
>>
>> r.x assigns the values of the response matrices only by considering the
>> distance between atoms and whether they have the same spin and type or not.
>> This information has to be given by the user in the positions file "filepos"
>> read by &input_mat.?If B(1) and B(2) are different types
>> (e.g.?crystallographically)?you should perturb them?separately, as you
>> outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type 2
>> is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x
>>
>> Best regards,
>>
>> Burak
>>
>>
>> On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli <degironc at sissa.it>
>> wrote:
>>>
>>> I don't know the details of r.x code but I think that, physically, what
>>> matters is the two atoms are crystallographically equivalent or not
>>> .therefore I think space group symmetry is the relevant one.
>>>
>>> stefano
>>>
>>>
>>> On 07/10/2012 05:54 AM, Peng Chen wrote:
>>>
>>> Dear All,
>>>
>>> In the calculation of U, how can we determine the equivalence of the
>>> ions,
>>> by site symmetry or space group symmetry?
>>> E.g  ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we
>>> run
>>> calculation on perturbing B(1) and B(2) ions or  just a B ion?
>>>
>>>  In order to find U in B  ions, I tried to run calculation with
>>> perturbing
>>> just on B, and r.x gave some errors that it needs to read more data.
>>> So I guess it needs the perturbed data from other atoms. Shall I use the
>>> procedures listed below?
>>> 1. run scf calculation with Hubbard_U(i)= 1.d-20
>>> 2. run scf with perturbing on an A ion
>>> 3.   run scf with perturbing on a B(1) ion
>>> 4.   run scf with perturbing on a B(2) ion
>>> 5.   run scf with perturbing on an O ion
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
> --
> ? Best Regards.
> ? ? ? ? Peng
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056 ? ?Fax +1 612 626 7246

From davemeel at yahoo.com  Tue Jul 10 17:50:06 2012
From: davemeel at yahoo.com (David Miller)
Date: Tue, 10 Jul 2012 08:50:06 -0700 (PDT)
Subject: [Pw_forum] phonon eigenvector units
Message-ID: <1341935406.70896.YahooMailNeo@web121101.mail.ne1.yahoo.com>

Hello,

I have performed a phonon calculation using ph.x. During the scf calculation (prior to using ph.x), the ATOMIC_POSITIONS is in Bohr units. I am also using ibrav = 0 and an orthorhombic crystal system. After ph.x, I have used dynmat.x to apply asymmetric sum rule and ?get the new phonon eigenvalues and eigenvectors. The output of dynmat.x has the following format:?


? ? ?omega(12) = ? ? ? 1.305968 [THz] = ? ? ?43.562397 [cm-1]
?( -0.052340 ? 0.000000 ? ?-0.021008 ? 0.000000 ? ? 0.002346 ? 0.000000 ? )
?( -0.003841 ? 0.000000 ? ?-0.009204 ? 0.000000 ? ? 0.053835 ? 0.000000 ? )
?( ?0.014655 ? 0.000000 ? ?-0.015822 ? 0.000000 ? ? 0.085998 ? 0.000000 ? )
?( -0.013791 ? 0.000000 ? ?-0.035434 ? 0.000000 ? ? 0.066956 ? 0.000000 ? )

While the units of omega is evident, the unit of eigenvectors is not clear. I wonder what is the unit of eigenvectors ?

The atomic position have the following units:
ATOMIC_POSITIONS { alat | bohr | crystal | angstrom }

Do the phonon eigenvectors have the same units as atomic positions or they have one particular unit always ? If it is one particular unit then what it is ? I noticed that the dynamical matrix is written in cartesian axes (I assume it means ?in the units of alat).?

Thanks,

David
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From pchen at ion.chem.utk.edu  Tue Jul 10 18:15:18 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Tue, 10 Jul 2012 12:15:18 -0400
Subject: [Pw_forum] U calculation in LDA+U
In-Reply-To: <CAMZASgG3MP1MQ3mKi5W5m1MigE-dbboZ+95-EXK4=gfYG+poAQ@mail.gmail.com>
References: <CAP_5U0cVAHQYUfpX_t_13ws=cqzwVKE+232zx_Tf0yRorcmZgQ@mail.gmail.com>
	<4FFBCF7E.8030903@sissa.it>
	<CAH55yVSPM_M8K=mG8A3fqY5Wb+Sve9xBLH6wBMhXav1KZvEU1g@mail.gmail.com>
	<CAP_5U0fcpJHcvqd6iGeSdG+FRE2zDeSB1x8vpG=Crhv712V+qA@mail.gmail.com>
	<CAMZASgG3MP1MQ3mKi5W5m1MigE-dbboZ+95-EXK4=gfYG+poAQ@mail.gmail.com>
Message-ID: <CAP_5U0c96OEDpwVbBgR77Xj1A8_NejN7r6pC2og9s30E4Q7qLQ@mail.gmail.com>

Thanks Dr. Matteo. That is helpful.

On Tue, Jul 10, 2012 at 11:15 AM, Matteo Cococcioni <matteo at umn.edu> wrote:

> Dear Peng,
>
> let me add one word to Burak's.
> you need to distinguish two O kinds anyway, whether you shift the
> atomic position or not. if you don't do that you will be perturbing
> all the oxygen atoms at the same time.
> The necessity to have the perturbed atom described as of a different
> type (although with the same pseudopotential) is what makes it
> convenient (most of the time) to place it at the origin of the unit
> cell.
>
> best,
>
> Matteo
>
>
>
> On Tue, Jul 10, 2012 at 10:03 AM, Peng Chen <pchen at ion.chem.utk.edu>
> wrote:
> > When O is perturbed in the case of NiO in tutorial, it
> is re-positioned and
> > there are 2 different kinds of O (first with 1 atom, the second with 7
> > atoms).  Then the kind with only one O is perturbed. In the tutorial, it
> > reads "This is done to preserve the largest possible number of
> symmetries".
> >  Is this process necessary? Can we just run computation without
> re-position?
> > In that case, there is only one kind of O with 8 atoms.
> >
> > In the position file "filepos", the scale of cell length is always 10,
> even
> > if the scale is 7.9 in NiO and 5.42 in Fe. Shall we always use 10 in
> > position file no matter what the real scale is?
> >
> > On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu <himm0013 at umn.edu>
> wrote:
> >>
> >> Hi Peng,
> >>
> >> r.x assigns the values of the response matrices only by considering the
> >> distance between atoms and whether they have the same spin and type or
> not.
> >> This information has to be given by the user in the positions file
> "filepos"
> >> read by &input_mat. If B(1) and B(2) are different types
> >> (e.g. crystallographically) you should perturb them separately, as you
> >> outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1),
> type 2
> >> is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x
> >>
> >> Best regards,
> >>
> >> Burak
> >>
> >>
> >> On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli <
> degironc at sissa.it>
> >> wrote:
> >>>
> >>> I don't know the details of r.x code but I think that, physically, what
> >>> matters is the two atoms are crystallographically equivalent or not
> >>> .therefore I think space group symmetry is the relevant one.
> >>>
> >>> stefano
> >>>
> >>>
> >>> On 07/10/2012 05:54 AM, Peng Chen wrote:
> >>>
> >>> Dear All,
> >>>
> >>> In the calculation of U, how can we determine the equivalence of the
> >>> ions,
> >>> by site symmetry or space group symmetry?
> >>> E.g  ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we
> >>> run
> >>> calculation on perturbing B(1) and B(2) ions or  just a B ion?
> >>>
> >>>  In order to find U in B  ions, I tried to run calculation with
> >>> perturbing
> >>> just on B, and r.x gave some errors that it needs to read more data.
> >>> So I guess it needs the perturbed data from other atoms. Shall I use
> the
> >>> procedures listed below?
> >>> 1. run scf calculation with Hubbard_U(i)= 1.d-20
> >>> 2. run scf with perturbing on an A ion
> >>> 3.   run scf with perturbing on a B(1) ion
> >>> 4.   run scf with perturbing on a B(2) ion
> >>> 5.   run scf with perturbing on an O ion
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> Pw_forum mailing list
> >>> Pw_forum at pwscf.org
> >>> http://www.democritos.it/mailman/listinfo/pw_forum
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> Pw_forum mailing list
> >>> Pw_forum at pwscf.org
> >>> http://www.democritos.it/mailman/listinfo/pw_forum
> >>>
> >>
> >>
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >>
> >
> >
> >
> > --
> >   Best Regards.
> >         Peng
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Matteo Cococcioni
> Department of Chemical Engineering and Materials Science,
> University of Minnesota
> 421 Washington Av. SE
> Minneapolis, MN 55455
> Tel. +1 612 624 9056    Fax +1 612 626 7246
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
  Best Regards.
        Peng
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From jptrinastic at phys.ufl.edu  Tue Jul 10 17:18:17 2012
From: jptrinastic at phys.ufl.edu (Jonathan Trinastic)
Date: Tue, 10 Jul 2012 11:18:17 -0400
Subject: [Pw_forum] pwcond transmission tran_file
Message-ID: <4FFC47B9.1010007@phys.ufl.edu>

Hi all,

This question should probably be directed to Alexander Smogunov, as it 
is about the pwcond code.  I'm currently doing some transport 
calculations with FeCo / MgO systems - I'm getting expected results 
using a 4 layer MgO, however, I want to compare to larger barrier 
widths, but the total transmissions given in the tran_file are small, 
and I require more than the seven decimal limit for the minority channel 
transmissions results.

Can you tell me where in the code I can extend the output for the 
tran_file so I can see results to greater than seven decimal places?

Thanks,
Jonathan

-- 
Jonathan Trinastic, M.S.
Graduate Student
Department of Physics
University of Florida


From asmogunov at gmail.com  Tue Jul 10 20:51:48 2012
From: asmogunov at gmail.com (Alex Smogunov)
Date: Tue, 10 Jul 2012 20:51:48 +0200
Subject: [Pw_forum] pwcond transmission tran_file
In-Reply-To: <4FFC47B9.1010007@phys.ufl.edu>
References: <4FFC47B9.1010007@phys.ufl.edu>
Message-ID: <CAHuemf_BZcn0szNPS8HSEaWP9Sj1UKYWxXxQqiGV5htBbnXrZg@mail.gmail.com>

Dear  Jonathan
It is in summary_tran.f90
regards,
Alexander

2012/7/10 Jonathan Trinastic <jptrinastic at phys.ufl.edu>

> Hi all,
>
> This question should probably be directed to Alexander Smogunov, as it
> is about the pwcond code.  I'm currently doing some transport
> calculations with FeCo / MgO systems - I'm getting expected results
> using a 4 layer MgO, however, I want to compare to larger barrier
> widths, but the total transmissions given in the tran_file are small,
> and I require more than the seven decimal limit for the minority channel
> transmissions results.
>
> Can you tell me where in the code I can extend the output for the
> tran_file so I can see results to greater than seven decimal places?
>
> Thanks,
> Jonathan
>
> --
> Jonathan Trinastic, M.S.
> Graduate Student
> Department of Physics
> University of Florida
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From ptao10b at imr.ac.cn  Wed Jul 11 02:31:04 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Wed, 11 Jul 2012 08:31:04 +0800 (GMT+08:00)
Subject: [Pw_forum] GRID example of e-ph
In-Reply-To: <1341911176.9891.4.camel@ulisse.cm.sissa.it>
References: <1341911176.9891.4.camel@ulisse.cm.sissa.it>
	<1186790.7d33.1386e8543b8.Coremail.ptao10b@imr.ac.cn>
Message-ID: <1091c15.b17b.1387372434b.Coremail.ptao10b@imr.ac.cn>

OK. Thank you very much. What a pity that my QE version is 4.3.2. I'll update it soon.

Yours,
Plato

> -----Original Messages-----
> From: "Andrea Dal Corso" <dalcorso at sissa.it>
> Sent Time: Tuesday, July 10, 2012
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Cc: 
> Subject: Re: [Pw_forum] GRID example of e-ph
> 
> 
> On Tue, 2012-07-10 at 09:33 +0800, Peng Tao wrote:
> > Dear all,
> > 
> > 
> > As we know, the phonon calculation is quite slow and unexpected errors
> > might occur at any time. 
> > Thanks to the GRID example, split runs is available. However, no
> > example is provided to split
> > the e-ph calculation. So, dear professors, could you show me a method
> > to realize it?
> > 
> 
> PHonon/examples/GRID_example/run_example_2 
> 
> in QE 5.0. 
> 
> HTH
> 
> Andrea
> 
> 
> > Sincerely yours
> > Plato Tao
> > 
> > --
> > -------------------------------------------------------------------
> > PH.D. candidate Peng Tao 
> > Magnetism and Magnetic Materials Division
> > National Laboratory for Material Science
> > Institute of Metal Research, Chinese Academy of Sciences
> > Phone  +86-024-83978751
> > -------------------------------------------------------------------
> > 
> > 
> > 
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> -- 
> Andrea Dal Corso                    Tel. 0039-040-3787428
> SISSA, Via Bonomea 265              Fax. 0039-040-3787249
> I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------





From renpj at dicp.ac.cn  Wed Jul 11 03:46:28 2012
From: renpj at dicp.ac.cn (renpj at dicp.ac.cn)
Date: Wed, 11 Jul 2012 09:46:28 +0800
Subject: [Pw_forum] How to calculate NMR for negative charged system?
Message-ID: <dfd47a72e735438aca942dfea591a99b.squirrel@webmail.dicp.ac.cn>

Dear all,

I want to calculate NMR of fullerene with 2 negative charge. The first
step scf calculation can not converged only if smearing is used. But for
NMR calculation, smearing is forbidden. Does anyone know how to solve this
problem?

I have tried that first do a scf calcultion with smearing, then do nscf
calculation without smearing. At last do NMR calculation. But the result
is so wrong!

Thanks.

PJ Ren

Dalian Institution of Chemical Physics, Chinese Academy of Science.


From spiga.filippo at gmail.com  Wed Jul 11 08:00:30 2012
From: spiga.filippo at gmail.com (Filippo Spiga)
Date: Wed, 11 Jul 2012 14:00:30 +0800
Subject: [Pw_forum] "espresso-4.3.2-GPU.tar.gz" and
	"espresso-5.0-GPU.tar.gz" available on QE-FORGE
Message-ID: <214A90F3-9737-4D80-9F52-22B9924251F7@gmail.com>

Dear QE users,

the GPU implementation is going forward but recently we have been working to close some gaps in the current release before push in other new things. We improved the support to GNU compilers, new PGI 12.x and CRAY systems. We (try to) improved the documentation (see README.GPU) and we disabled all the experimental features not properly tested.

Now you can find  two packages available for download QE-FORGE[1]:
- espresso-4.3.2-GPU.tar.gz (GPU-accelerated PWscf and NEB, both compatible with the CPU-only Quantum ESPRESSO 4.3.2)
- espresso-5.0-GPU.tar.gz (GPU-accelerated PWscf and NEB, both compatible with CPU-only Quantum ESPRESSO 5.0)

My suggestion is to switch and start using Quantum ESPRESSO 5.0  (-:

I want to sponsor the fact that a specific mailing-list exists for the GPU-accelerated version: q-e-gpgpu at qe-forge.org 
For any issue, error, bug, problem, advice? write directly there! 

There is also a Facebook page[2] and a Linkedin[3] group related to QE. Everybody is welcome!

Enjoy.
F.

[1] http://qe-forge.org/frs/shownotes.php?release_id=119
[2] https://www.facebook.com/QuantumESPRESSO
[3] http://www.linkedin.com/company/2148003?trk=tyah

-- 
Mr. Filippo SPIGA (???), HPC and GPU Technologist <spiga.filippo_at_gmail.com>
website: http://filippospiga.me  ~  skype: filippo.spiga

?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert

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From giannozz at democritos.it  Wed Jul 11 08:28:52 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 11 Jul 2012 08:28:52 +0200
Subject: [Pw_forum] GRID example of e-ph
In-Reply-To: <1091c15.b17b.1387372434b.Coremail.ptao10b@imr.ac.cn>
References: <1341911176.9891.4.camel@ulisse.cm.sissa.it>
	<1186790.7d33.1386e8543b8.Coremail.ptao10b@imr.ac.cn>
	<1091c15.b17b.1387372434b.Coremail.ptao10b@imr.ac.cn>
Message-ID: <2ECE0A26-7455-461B-BDD0-4F08B320B53A@democritos.it>


On Jul 11, 2012, at 2:31 , Peng Tao wrote:

> OK. Thank you very much. What a pity that my QE version is 4.3.2.  
> I'll update it soon.

this is a good idea anyway, but note that the GRID example is present  
in the 4.3.2
version as well, in examples/GRID_example. Also note that there is no  
guarantee
that it works for the electron-phonon calculation

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From ptao10b at imr.ac.cn  Wed Jul 11 08:33:29 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Wed, 11 Jul 2012 14:33:29 +0800 (GMT+08:00)
Subject: [Pw_forum] q not allowed in example07
Message-ID: <71238d.c6c5.13874be10de.Coremail.ptao10b@imr.ac.cn>

Dear all,


It seems very strange that when I run the example07: The error of  "q not allowed" 
occurs when the command q2r.x is executed. I use the identical parameters as the 
example and do not change anything except the out_dir and pp_dir.


Here are my input and output files:
--------------------------------------------------------------------------------------------------
al.scf.fit.in
 &control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='al',
    wf_collect=.true.
    pseudo_dir = '/home/soft/q-e-scm-2009-07-04/espresso/pseudo/',
    outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/'
 /
 &system
    ibrav=  2, celldm(1) =7.5, nat= 1, ntyp= 1,
    ecutwfc =15.0,
    occupations='smearing', smearing='methfessel-paxton', degauss=0.05,
    la2F = .true.,
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Al  26.98 Al.pz-vbc.UPF
ATOMIC_POSITIONS
 Al 0.00 0.00 0.00
K_POINTS {automatic}
 16 16 16  0 0 0
------------------------------------------------------------------------------------------------
al.scf.in
 &control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='al',
    wf_collect=.true.
    pseudo_dir = '/home/soft/q-e-scm-2009-07-04/espresso/pseudo/',
    outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/'
 /
 &system
    ibrav=  2, celldm(1) =7.5, nat= 1, ntyp= 1,
    ecutwfc =15.0,
    occupations='smearing', smearing='methfessel-paxton', degauss=0.05
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Al  26.98 Al.pz-vbc.UPF
ATOMIC_POSITIONS
 Al 0.00 0.00 0.00
K_POINTS {automatic}
 8 8 8  0 0 0
--------------------------------------------------------------------------------------------
al.elph.in
Electron-phonon coefficients for Al
 &inputph
  tr2_ph=1.0d-10,
  prefix='al',
  fildvscf='aldv',
  amass(1)=26.98,
  outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/',
  fildyn='al.dyn',
  elph=.true.,
  trans=.true.,
  ldisp=.true.
  nq1=4, nq2=4, nq3=4
 /
---------------------------------------------------------------------------------------------
q2r.in
 &input
  zasr='simple',  fildyn='al.dyn', flfrc='Al444.fc', la2F=.true.
 /
---------------------------------------------------------------------------------------------
q2r.out
............................
  reading force constants from file al.dyn8
  nqs=            6
 q=  -0.50000000 -1.00000000  0.00000000
 q=   0.00000000  1.00000000  0.50000000
 q=   0.00000000 -1.00000000 -0.50000000
 q=   0.50000000  1.00000000  0.00000000
 q=  -1.00000000 -0.50000000  0.00000000
 q=   0.00000000 -0.50000000 -1.00000000


      q-space grid ok, #points =   64


      fft-check success (sum of imaginary terms < 10^-12)
 
   Preparing gamma for a2F 
 


 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from init : error #         1
     q not allowed
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


     stopping ...


Thanks in advance!


Warmest regards,
Peng Tao



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------


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From raincoatrun at gmail.com  Wed Jul 11 08:55:04 2012
From: raincoatrun at gmail.com (=?UTF-8?B?5pu55rW35YWD?=)
Date: Wed, 11 Jul 2012 14:55:04 +0800
Subject: [Pw_forum] Calculate the electron-phonon interaction matrix element
 for specific k point
Message-ID: <CAHp7=yaSSsEhh_SuP7X27rxnobkiU7gVFt5a=R67eotNagDaCQ@mail.gmail.com>

Dear all?
Now I'm using QE to calculate the e-ph coupling in graphene. I want to
calculate the e-ph interaction matrix elements for specific k at the Dirac
Point as a function of phonon wave vector q. Can I set the k point in QE
e-ph calculation to realize this ?

Thanks for your help.

Cao Haiyuan


PhD Candidate Haiyuan Cao
Department of Physics, Fudan University, China
Email: raincoatrun at gmail.com
Phone?+86 21 65643523
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From 1009ukumar at gmail.com  Wed Jul 11 09:23:00 2012
From: 1009ukumar at gmail.com (Sonu Kumar)
Date: Wed, 11 Jul 2012 12:53:00 +0530
Subject: [Pw_forum] negative dr2
Message-ID: <CAHePdfDZapTRmHmFJbeT4OJQ-BtTSYZ32EWprvXNdeT58FbBNQ@mail.gmail.com>

Dear all QE users and developers,

While using PAW pseudopotential, i got the error "NEGATIVE dr2".

Commenting out the line (used to check the error in energy in scf cycle )
as suggested in
http://www.democritos.it/pipermail/pw_forum/2011-July/021150.html, i got
the convergence.

Is it a trustworthy/robust solution to avoid the error ?
or do i have to generate new PAW potential to correctly represent the core
region density?

With Regards,
sonu

==========================================
Sonu Kumar
Phd Student,Physics Department
Indian Institute of Technology ,Delhi-110016, India
web:-http://www.iitd.ac.in/
==========================================
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From giannozz at democritos.it  Wed Jul 11 10:14:49 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 11 Jul 2012 10:14:49 +0200
Subject: [Pw_forum] q not allowed in example07
In-Reply-To: <71238d.c6c5.13874be10de.Coremail.ptao10b@imr.ac.cn>
References: <71238d.c6c5.13874be10de.Coremail.ptao10b@imr.ac.cn>
Message-ID: <1BBCAE0A-E16C-4B25-9489-70619C05042F@democritos.it>


On Jul 11, 2012, at 8:33 , Peng Tao wrote:

> I use the identical parameters as the example and do not change  
> anything
> except the out_dir and pp_dir.

not true: this

>     wf_collect=.true.

is not in the example. And you haven't explained
- which version of the code you are talking about
- if you are running in serial or in parallel, and how in the latter  
case
- whether the unmodified example works

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Wed Jul 11 10:37:21 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 11 Jul 2012 10:37:21 +0200
Subject: [Pw_forum] phonon eigenvector units
In-Reply-To: <1341935406.70896.YahooMailNeo@web121101.mail.ne1.yahoo.com>
References: <1341935406.70896.YahooMailNeo@web121101.mail.ne1.yahoo.com>
Message-ID: <35A8721F-209A-49A9-BFCF-4F0E524A6B45@democritos.it>


On Jul 10, 2012, at 17:50 , David Miller wrote:

> I wonder what is the unit of eigenvectors ?

adimensional: they are normalized to 1

> I noticed that the dynamical matrix is written in cartesian axes
> (I assume it means  in the units of alat)

no, it means "in cartesian axis", i.e. wrt displacements along x,y,z
>


P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From degliesposti at bo.imm.cnr.it  Wed Jul 11 11:39:10 2012
From: degliesposti at bo.imm.cnr.it (Cristian Degli Esposti Boschi)
Date: Wed, 11 Jul 2012 11:39:10 +0200
Subject: [Pw_forum] little 'bug' in bands_FS
Message-ID: <4FFD49BE.3000507@bo.imm.cnr.it>

Dear developers,

I have just noticed a little 'bug' in the code bands_FS for Fermi 
surfaces visualisation, in the sense that it was probably written
and tested to read correctly the usual (text) file coming out from 
previous bands/nscf calculations with pw.x.

But if the bands/nscf calculation is performed with the option of *high
verbosity*, then in the output file there appear occupation numbers
just after the list of Kohn-Sham energies for a given wavevector
and the number of desired bands.

As a result in this case (i.e. high verbosity) the file is not read
correctly from bands_FS.x and one gets a read error.

I guess that the solution would be either (i) to rembember to exclude 
verbose output in the preliminar bands/nscf calculation or (ii) add a 
little control within bands_FS in order to skip the occupation numbers 
lines while reading the energies from the file.

Thanks for your time
-- 
Cristian Degli Esposti Boschi
CNR-IMM, Sezione di Bologna,
via Gobetti, 101, 40129, Bologna, Italia
tel. ++39 051 6399152, fax ++39 051 6399216
email: degliesposti -AT- bo.imm.cnr.it
web:   www.bo.imm.cnr.it/site/staff/personal_pages/degliesposti/

From flux_ray12 at 163.com  Wed Jul 11 11:54:42 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Wed, 11 Jul 2012 17:54:42 +0800 (CST)
Subject: [Pw_forum] Calculation of Gibbs free energies
In-Reply-To: <9ab5bb3130dbbdad6da9232ea8e9585c@ulrik.uio.no>
References: <9ab5bb3130dbbdad6da9232ea8e9585c@ulrik.uio.no>
Message-ID: <29607723.dee4.1387576487b.Coremail.flux_ray12@163.com>

According to my experience, the general process is right, but, this general process is normally working for crystal rather than amorphous, liquid and gas. Since the contribution from vibration is not that much in those matter, for example, transition contributes much more in gas phase. Therefore, Monte Carlo or Molecular Dynamic could be better choice in these cases.
Technically, in your calculation, H2O molecule may exist in a box, therefore only the Gamma phonon calculation is meaningful. Since q2r means fitting the finite samplings of dynamic matrics to infinite interatomic force constants, only one point is not that reliable to find good aproach of IFCs. Actually, since vibrational free energy is defined with the term of hv, you can derectly obtain Fvib from your first step.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 



At 2012-07-10 22:44:56,"Torstein Fjermestad" <torstein.fjermestad at kjemi.uio.no> wrote:
> Dear all,
>
> In one of my projects I would need to compute the Gibbs free energies 
> of structures along a reaction path. After looking through the QE 
> webpage, the pw_forum, and the documentation in the quantum espresso 
> installation directory I think I understand the general procedure:
>
> 1. one calculates the phonons
> 2. one computes the interatomic Force Constants with the q2r.x program
> 3. one uses the matdyn.x to produce input for the F_QHA.x program
> 4. with the F_QHA.x program one can compute the Gibbs free energy and 
> other thermodynamical properties.
>
> (please correct me if I have misunderstood this general procedure)
>
> The problem is that I have so far only managed to complete step 1, to 
> compute the phonons. I am currently doing test calculations on a water 
> molecule and this is the input file of the phonon calculation:
>
> phonons of H2O in super cell at Gamma
>  &inputph
>   outdir='./',
>   prefix='h2o',
>   amass(1)=1.01,
>   amass(2)=16.01,
>   fildyn='h2o.dynG',
>   trans= .true.
>  /
> 0.0 0.0 0.0
>
> I then try to run the q2r.x calculation with the following input:
>
> test of q2r calculation
> &input
>   fildyn='h2o.dynG',
>   flfrc='h2o-output-q2r.fc',
>   zasr='no'
>
> This calculation crashes presumably because it expects a file called 
> h2o.dynG0. But from where do I get this file? As far as I can see the 
> phonon calculation only produces the file h2o.dynG, not a h2o.dynG0 
> file.
>
> I am completely lost at the moment so I would appreciate if anyone 
> could help me with carrying out the q2r calculation correctly.
> 
> Thank you very much in advance,
>
> Yours sincerely,
>
> Torstein Fjermestad,
> University of Oslo,
> Norway
>
>
>
>
>
>
>
>
>
>
> 
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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From bfazi90 at gmail.com  Wed Jul 11 12:01:41 2012
From: bfazi90 at gmail.com (bf azi)
Date: Wed, 11 Jul 2012 14:31:41 +0430
Subject: [Pw_forum] (no subject)
Message-ID: <CAC+sowLdSBxpbRLig-8=dR7EgDchGrsXYtAWJZm=jq-L1nKPRA@mail.gmail.com>

Dear all

I have problem in Landauer Formula and my problem is:

What is meaning of channels in "Landauer Formula" and Why
"Transmission" is unit?

thanks a lot

Bani Adam
Faculty of Science
Egypt

From ptao10b at imr.ac.cn  Wed Jul 11 13:50:34 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Wed, 11 Jul 2012 19:50:34 +0800 (GMT+08:00)
Subject: [Pw_forum] q not allowed in example07
In-Reply-To: <1BBCAE0A-E16C-4B25-9489-70619C05042F@democritos.it>
References: <1BBCAE0A-E16C-4B25-9489-70619C05042F@democritos.it>
	<71238d.c6c5.13874be10de.Coremail.ptao10b@imr.ac.cn>
Message-ID: <59180f.d50f.13875e05b1e.Coremail.ptao10b@imr.ac.cn>

Thank you for your reply!

My QE version is 4.3.2. "wf_collect=.true." is just set to run parallel, and I keep other parameters unchanged.
And I find that the error always exists in both serial and parallel cases. The error did not happen when I tried to
calculate the example07 for the first time about one year ago.

Right now I copy the file of run_example, and run the example in serial. Unfortunately the same error occurs again:

 Preparing gamma for a2F
 
 
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      from init : error #         1
      q not allowed
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      stopping ...

And my input files copied from example(keeping everything unchanged except ppdir and outdir):
------------------------------------------------------------------
al.scf.fit.in
------------------------------------------------------------------
 &control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='al',
    pseudo_dir = '/home/soft/q-e-scm-2009-07-04/espresso/pseudo/',
    outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/'
 /
 &system
    ibrav=  2, celldm(1) =7.5, nat= 1, ntyp= 1,
    ecutwfc =15.0,
    occupations='smearing', smearing='methfessel-paxton', degauss=0.05,
    la2F = .true.,
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Al  26.98 Al.pz-vbc.UPF
ATOMIC_POSITIONS
 Al 0.00 0.00 0.00
K_POINTS {automatic}
 16 16 16  0 0 0
----------------------------------------------------------------------------
al.scf.in
 &control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='al',
    pseudo_dir = '/home/soft/q-e-scm-2009-07-04/espresso/pseudo/',
    outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/'
 /
 &system
    ibrav=  2, celldm(1) =7.5, nat= 1, ntyp= 1,
    ecutwfc =15.0,
    occupations='smearing', smearing='methfessel-paxton', degauss=0.05
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Al  26.98 Al.pz-vbc.UPF
ATOMIC_POSITIONS
 Al 0.00 0.00 0.00
K_POINTS {automatic}
 8 8 8  0 0 0
----------------------------------------------------------------------------
al.elph.in
---------------------------------------------------------------------------
Electron-phonon coefficients for Al
 &inputph
  tr2_ph=1.0d-10,
  prefix='al',
  fildvscf='aldv',
  amass(1)=26.98,
  outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/',
  fildyn='al.dyn',
  elph=.true.,
  trans=.true.,
  ldisp=.true.
  nq1=4, nq2=4, nq3=4
 /
----------------------------------------------------------------------------
q2r.in
----------------------------------------------------------------------------
&input
  zasr='simple',  fildyn='al.dyn', flfrc='Al444.fc', la2F=.true.
 /

------------------------------------------------------------------------------
Please help me! Thanks in advance.

Warmest regards,
Peng Tao










-------------------------------------------------------------------------------
> -----Original Messages-----
> From: "Paolo Giannozzi" <giannozz at democritos.it>
> Sent Time: Wednesday, July 11, 2012
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Cc: 
> Subject: Re: [Pw_forum] q not allowed in example07
> 
> 
> On Jul 11, 2012, at 8:33 , Peng Tao wrote:
> 
> > I use the identical parameters as the example and do not change  
> > anything
> > except the out_dir and pp_dir.
> 
> not true: this
> 
> >     wf_collect=.true.
> 
> is not in the example. And you haven't explained
> - which version of the code you are talking about
> - if you are running in serial or in parallel, and how in the latter  
> case
> - whether the unmodified example works
> 
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------





From giannozz at democritos.it  Wed Jul 11 14:07:28 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 11 Jul 2012 14:07:28 +0200
Subject: [Pw_forum] little 'bug' in bands_FS
In-Reply-To: <4FFD49BE.3000507@bo.imm.cnr.it>
References: <4FFD49BE.3000507@bo.imm.cnr.it>
Message-ID: <65EF1AEC-F856-40AE-95AC-83D30FB3C5D2@democritos.it>


On Jul 11, 2012, at 11:39 , Cristian Degli Esposti Boschi wrote:

> I guess that the solution would be either (i) to rembember to exclude
> verbose output in the preliminar bands/nscf calculation or (ii) add a
> little control within bands_FS in order to skip the occupation numbers
> lines while reading the energies from the file.

thank you. The best solution is yet another: bands_FS should read
the data file, not the output files that changes more often than not.
Any volunteers?

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Wed Jul 11 14:49:11 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 11 Jul 2012 14:49:11 +0200
Subject: [Pw_forum] q not allowed in example07
In-Reply-To: <59180f.d50f.13875e05b1e.Coremail.ptao10b@imr.ac.cn>
References: <1BBCAE0A-E16C-4B25-9489-70619C05042F@democritos.it>
	<71238d.c6c5.13874be10de.Coremail.ptao10b@imr.ac.cn>
	<59180f.d50f.13875e05b1e.Coremail.ptao10b@imr.ac.cn>
Message-ID: <64C90DDE-4848-44BE-81B3-7ED8658FA736@democritos.it>


On Jul 11, 2012, at 13:50 , Peng Tao wrote:

> The error did not happen when I tried to calculate the example07  
> for the first time
> about one year ago.

and if you try now? without changing anything in example07?

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From raincoatrun at gmail.com  Wed Jul 11 17:02:38 2012
From: raincoatrun at gmail.com (=?UTF-8?B?5pu55rW35YWD?=)
Date: Wed, 11 Jul 2012 23:02:38 +0800
Subject: [Pw_forum] Calculate the electron-phonon interaction matrix element
 for specific k point
In-Reply-To: <CAHp7=yaSSsEhh_SuP7X27rxnobkiU7gVFt5a=R67eotNagDaCQ@mail.gmail.com>
References: <CAHp7=yaSSsEhh_SuP7X27rxnobkiU7gVFt5a=R67eotNagDaCQ@mail.gmail.com>
Message-ID: <CAHp7=ya5VAjFv6AmD7p4SM_gWdqvLDE-4B4hEUbeL-a+0qRqkg@mail.gmail.com>

Dear all?
Now I'm using QE to calculate the e-ph coupling in graphene. I want to
calculate the e-ph interaction matrix elements for specific k at the Dirac
Point as a function of phonon wave vector q. Can I set the k point in QE
e-ph calculation to realize this ?

Thanks for your help.

Cao Haiyuan


PhD Candidate Haiyuan Cao
Department of Physics, Fudan University, China
Email: raincoatrun at gmail.com
Phone?+86 21 65643523
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From pandey.bramha at gmail.com  Wed Jul 11 18:19:33 2012
From: pandey.bramha at gmail.com (bramha pandey)
Date: Wed, 11 Jul 2012 21:49:33 +0530
Subject: [Pw_forum] Plotting Band Structure by using Xmgrace
In-Reply-To: <9D4FE2FD-F16E-47F2-A6A6-58755245E1A1@gmail.com>
References: <9D4FE2FD-F16E-47F2-A6A6-58755245E1A1@gmail.com>
Message-ID: <CAC2dNGGFfNw-sJesVdL8njoU3WtCX5CXUsbV50QoZa4aoe0zcA@mail.gmail.com>

On Fri, Jun 15, 2012 at 9:00 AM, Gulcin Tetiker <gkucukdalyan at gmail.com>wrote:

> Hi All,
>
> I am trying to plot the band structure by using xmgrace and could not
> figure out how to draw a horizontal fermi energy line, and also i would
> like to label c axis by using high-symmetry points.


gnuplot would be the better option.


> Could someone please help me?
>
> Gulcin
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Thanks and Regards
Bramha Prasad Pandey
Ph.D Student Indian School of Mines(ISM)
Dhanbad, INDIA.
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From ptao10b at imr.ac.cn  Thu Jul 12 01:48:45 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Thu, 12 Jul 2012 07:48:45 +0800 (GMT+08:00)
Subject: [Pw_forum] q not allowed in example07
In-Reply-To: <59180f.d50f.13875e05b1e.Coremail.ptao10b@imr.ac.cn>
References: <59180f.d50f.13875e05b1e.Coremail.ptao10b@imr.ac.cn>
	<1BBCAE0A-E16C-4B25-9489-70619C05042F@democritos.it>
	<71238d.c6c5.13874be10de.Coremail.ptao10b@imr.ac.cn>
Message-ID: <1a280e1.ca66.1387871e072.Coremail.ptao10b@imr.ac.cn>

Yes,I have tried for several times yesterday (The words "right now" I've chosen), copied the file of run_example with nothing changed.


> -----Original Messages-----
> From: "Peng Tao" <ptao10b at imr.ac.cn>
> Sent Time: Wednesday, July 11, 2012
> To: giannozz at democritos.it, "PWSCF Forum" <pw_forum at pwscf.org>
> Cc: 
> Subject: Re: [Pw_forum] q not allowed in example07
> 
> Thank you for your reply!
> 
> My QE version is 4.3.2. "wf_collect=.true." is just set to run parallel, and I keep other parameters unchanged.
> And I find that the error always exists in both serial and parallel cases. The error did not happen when I tried to
> calculate the example07 for the first time about one year ago.
> 
> Right now I copy the file of run_example, and run the example in serial. Unfortunately the same error occurs again:
> 
>  Preparing gamma for a2F
>  
>  
>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       from init : error #         1
>       q not allowed
>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       stopping ...
> 
> And my input files copied from example(keeping everything unchanged except ppdir and outdir):
> ------------------------------------------------------------------
> al.scf.fit.in
> ------------------------------------------------------------------
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     prefix='al',
>     pseudo_dir = '/home/soft/q-e-scm-2009-07-04/espresso/pseudo/',
>     outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/'
>  /
>  &system
>     ibrav=  2, celldm(1) =7.5, nat= 1, ntyp= 1,
>     ecutwfc =15.0,
>     occupations='smearing', smearing='methfessel-paxton', degauss=0.05,
>     la2F = .true.,
>  /
>  &electrons
>     conv_thr =  1.0d-8
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Al  26.98 Al.pz-vbc.UPF
> ATOMIC_POSITIONS
>  Al 0.00 0.00 0.00
> K_POINTS {automatic}
>  16 16 16  0 0 0
> ----------------------------------------------------------------------------
> al.scf.in
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     prefix='al',
>     pseudo_dir = '/home/soft/q-e-scm-2009-07-04/espresso/pseudo/',
>     outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/'
>  /
>  &system
>     ibrav=  2, celldm(1) =7.5, nat= 1, ntyp= 1,
>     ecutwfc =15.0,
>     occupations='smearing', smearing='methfessel-paxton', degauss=0.05
>  /
>  &electrons
>     conv_thr =  1.0d-8
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Al  26.98 Al.pz-vbc.UPF
> ATOMIC_POSITIONS
>  Al 0.00 0.00 0.00
> K_POINTS {automatic}
>  8 8 8  0 0 0
> ----------------------------------------------------------------------------
> al.elph.in
> ---------------------------------------------------------------------------
> Electron-phonon coefficients for Al
>  &inputph
>   tr2_ph=1.0d-10,
>   prefix='al',
>   fildvscf='aldv',
>   amass(1)=26.98,
>   outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/',
>   fildyn='al.dyn',
>   elph=.true.,
>   trans=.true.,
>   ldisp=.true.
>   nq1=4, nq2=4, nq3=4
>  /
> ----------------------------------------------------------------------------
> q2r.in
> ----------------------------------------------------------------------------
> &input
>   zasr='simple',  fildyn='al.dyn', flfrc='Al444.fc', la2F=.true.
>  /
> 
> ------------------------------------------------------------------------------
> Please help me! Thanks in advance.
> 
> Warmest regards,
> Peng Tao
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> -------------------------------------------------------------------------------
> > -----Original Messages-----
> > From: "Paolo Giannozzi" <giannozz at democritos.it>
> > Sent Time: Wednesday, July 11, 2012
> > To: "PWSCF Forum" <pw_forum at pwscf.org>
> > Cc: 
> > Subject: Re: [Pw_forum] q not allowed in example07
> > 
> > 
> > On Jul 11, 2012, at 8:33 , Peng Tao wrote:
> > 
> > > I use the identical parameters as the example and do not change  
> > > anything
> > > except the out_dir and pp_dir.
> > 
> > not true: this
> > 
> > >     wf_collect=.true.
> > 
> > is not in the example. And you haven't explained
> > - which version of the code you are talking about
> > - if you are running in serial or in parallel, and how in the latter  
> > case
> > - whether the unmodified example works
> > 
> > P.
> > ---
> > Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > Phone +39-0432-558216, fax +39-0432-558222
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> --
> -------------------------------------------------------------------
> PH.D. candidate Peng Tao 
> Magnetism and Magnetic Materials Division
> National Laboratory for Material Science
> Institute of Metal Research, Chinese Academy of Sciences
> Phone  +86-024-83978751
> -------------------------------------------------------------------
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------



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From prasenjit.jnc at gmail.com  Thu Jul 12 04:01:23 2012
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Thu, 12 Jul 2012 07:31:23 +0530
Subject: [Pw_forum] GIPAW for metallic system
Message-ID: <CAN3VX3K-2hk2WM4cLZzvpSyR22uvFzSKuO7DwCk+0yFX0ZeK_Q@mail.gmail.com>

Dear all,

Has GIPAW been included for calculations using smearing?  Some early posts
says that it has not been done.

I want to calculate the nmr spectra of a system which is magnetic and for
that I need to use smearing.

So I was wondering whether in the latest version of QE, GIPAW with
occupations smearing has been implemented or not.

With regards,

Prasenjit

-- 
PRASENJIT GHOSH,
IISER Pune,
First floor, Central Tower, Sai Trinity Building
Garware Circle, Sutarwadi, Pashan
Pune, Maharashtra 411021, India

Phone: +91 (20) 2590 8203
Fax: +91 (20) 2589 9790
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From sxu2 at ncsu.edu  Thu Jul 12 04:46:41 2012
From: sxu2 at ncsu.edu (shu xu)
Date: Wed, 11 Jul 2012 21:46:41 -0500
Subject: [Pw_forum] Plotting Band Structure by using Xmgrace
In-Reply-To: <CAC2dNGGFfNw-sJesVdL8njoU3WtCX5CXUsbV50QoZa4aoe0zcA@mail.gmail.com>
References: <9D4FE2FD-F16E-47F2-A6A6-58755245E1A1@gmail.com>
	<CAC2dNGGFfNw-sJesVdL8njoU3WtCX5CXUsbV50QoZa4aoe0zcA@mail.gmail.com>
Message-ID: <CAKfkky=bUN=_cD63=M07D0C-EBoT5urgV7AeOMuwabLae_Uq3Q@mail.gmail.com>

creat another file with the coordinates of the Fermi line. Then import both
the bands.xmgr and Fermi.data file.

On Wed, Jul 11, 2012 at 11:19 AM, bramha pandey <pandey.bramha at gmail.com>wrote:

>
>
> On Fri, Jun 15, 2012 at 9:00 AM, Gulcin Tetiker <gkucukdalyan at gmail.com>wrote:
>
>> Hi All,
>>
>> I am trying to plot the band structure by using xmgrace and could not
>> figure out how to draw a horizontal fermi energy line, and also i would
>> like to label c axis by using high-symmetry points.
>
>
> gnuplot would be the better option.
>
>
>> Could someone please help me?
>>
>> Gulcin
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Thanks and Regards
> Bramha Prasad Pandey
> Ph.D Student Indian School of Mines(ISM)
> Dhanbad, INDIA.
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From raincoatrun at gmail.com  Thu Jul 12 05:57:01 2012
From: raincoatrun at gmail.com (=?UTF-8?B?5pu55rW35YWD?=)
Date: Thu, 12 Jul 2012 11:57:01 +0800
Subject: [Pw_forum] Calculate the electron-phonon interaction matrix element
 for specific k point
In-Reply-To: <CAHp7=yaSSsEhh_SuP7X27rxnobkiU7gVFt5a=R67eotNagDaCQ@mail.gmail.com>
References: <CAHp7=yaSSsEhh_SuP7X27rxnobkiU7gVFt5a=R67eotNagDaCQ@mail.gmail.com>
Message-ID: <CAHp7=yaJkxJ2OBTzb-ndVYbYJenAG8-wf5RHvz_E21qVvTAWnA@mail.gmail.com>

Dear all?
Now I'm using QE to calculate the e-ph coupling in graphene. I want to
calculate the e-ph interaction matrix elements for specific k at the Dirac
Point as a function of phonon wave vector q. Can I set the k point in QE
e-ph calculation to realize this ?

Thanks for your help.

Cao Haiyuan


PhD Candidate Haiyuan Cao
Department of Physics, Fudan University, China
Email: raincoatrun at gmail.com
Phone?+86 21 65643523
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From davide.ceresoli at istm.cnr.it  Thu Jul 12 09:19:46 2012
From: davide.ceresoli at istm.cnr.it (Davide Ceresoli)
Date: Thu, 12 Jul 2012 09:19:46 +0200
Subject: [Pw_forum] GIPAW for metallic system
In-Reply-To: <CAN3VX3K-2hk2WM4cLZzvpSyR22uvFzSKuO7DwCk+0yFX0ZeK_Q@mail.gmail.com>
References: <CAN3VX3K-2hk2WM4cLZzvpSyR22uvFzSKuO7DwCk+0yFX0ZeK_Q@mail.gmail.com>
Message-ID: <4FFE7A92.4080409@istm.cnr.it>

Dear Prasenjit,
     it's not implemented yet.

Davide


On 07/12/2012 04:01 AM, Prasenjit Ghosh wrote:
> Dear all,
>
> Has GIPAW been included for calculations using smearing?  Some early posts says
> that it has not been done.
>
> I want to calculate the nmr spectra of a system which is magnetic and for that I
> need to use smearing.
>
> So I was wondering whether in the latest version of QE, GIPAW with occupations
> smearing has been implemented or not.
>
> With regards,
>
> Prasenjit
>
> --
> PRASENJIT GHOSH,
> IISER Pune,
> First floor, Central Tower, Sai Trinity Building
> Garware Circle, Sutarwadi, Pashan
> Pune, Maharashtra 411021, India
>
> Phone: +91 (20) 2590 8203
> Fax: +91 (20) 2589 9790


From pourazar2012 at gmail.com  Thu Jul 12 10:52:14 2012
From: pourazar2012 at gmail.com (yavar pour azar)
Date: Thu, 12 Jul 2012 13:22:14 +0430
Subject: [Pw_forum] where I can find BLYP USPP for Ru?
Message-ID: <CAFgXaNjLU7Tj=pega9XqiqpMSd2ev28CHvaJ1viE+-jEpVHd2w@mail.gmail.com>

Dear QE users,

I want to use US.PP, generated by blyp functional for Ru.

But according to "Notes on pseudopotential generation" by prf. Giannozzi,
this functionals are not allowed in atomic code.

anyone can help me to find or generate such pseudopotential for Ru arom?


thanks in advance.



Y.  Taghipour Azar
PhD students
Physics Group, AEOI, Tehran, Iran
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From flux_ray12 at 163.com  Thu Jul 12 11:26:30 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 12 Jul 2012 17:26:30 +0800 (CST)
Subject: [Pw_forum] where I can find BLYP USPP for Ru?
In-Reply-To: <CAFgXaNjLU7Tj=pega9XqiqpMSd2ev28CHvaJ1viE+-jEpVHd2w@mail.gmail.com>
References: <CAFgXaNjLU7Tj=pega9XqiqpMSd2ev28CHvaJ1viE+-jEpVHd2w@mail.gmail.com>
Message-ID: <1905451c.1dc18.1387a82d29a.Coremail.flux_ray12@163.com>

Really? I remember that one can simply set dft='blyp' in &input namelist of ld1.x......


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-07-12 16:52:14,"yavar pour azar" <pourazar2012 at gmail.com> wrote:
Dear QE users,

I want to use US.PP, generated by blyp functional for Ru.

But according to "Notes on pseudopotential generation" by prf. Giannozzi, this functionals are not allowed in atomic code.

anyone can help me to find or generate such pseudopotential for Ru arom?


thanks in advance.



Y.  Taghipour Azar
PhD students
Physics Group, AEOI, Tehran, Iran

 
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From giannozz at democritos.it  Thu Jul 12 11:27:54 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 12 Jul 2012 11:27:54 +0200
Subject: [Pw_forum] where I can find BLYP USPP for Ru?
In-Reply-To: <CAFgXaNjLU7Tj=pega9XqiqpMSd2ev28CHvaJ1viE+-jEpVHd2w@mail.gmail.com>
References: <CAFgXaNjLU7Tj=pega9XqiqpMSd2ev28CHvaJ1viE+-jEpVHd2w@mail.gmail.com>
Message-ID: <CD0DC29C-6246-490C-BF6C-F8F1465DB75C@democritos.it>


On Jul 12, 2012, at 10:52 , yavar pour azar wrote:

> I want to use US.PP, generated by blyp functional for Ru.
> But according to "Notes on pseudopotential generation" by
> prf. Giannozzi, this functionals are not allowed in atomic code.

not sure what version of my notes you are referring to. In any case,
this is not (or no longer) true.

> anyone can help me to find or generate such pseudopotential for Ru  
> arom?

standard answer apply: go to the QE web site, under "Pseudopotentials".
You can find a lot of pointers there

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From pourazar2012 at gmail.com  Thu Jul 12 11:44:07 2012
From: pourazar2012 at gmail.com (yavar pour azar)
Date: Thu, 12 Jul 2012 14:14:07 +0430
Subject: [Pw_forum] "Reciprocity of Supercells & BZ Sampling",
 If I choose gamma point for supercell, will I lose some information?
Message-ID: <CAFgXaNiSsftvxcr4LFemJ7jBD+vvZtBRriv=Zym7pczF7+HP=g@mail.gmail.com>

Dear QE users,

I have a conceptual problem with k-point sampling in supercells.

Suppose we have a simple cubic unit cell for the bulk, which it's
electronic structure, total energy and etc... is calculated by n*n*n BZ
Sampling.
for example I can see band width and band curvature along k axis, and i
will have max and min points for every band in different k_points such
gamma, X, L,......

Now, if we want to make a n*n*n supercell from this unit cell, it is the
known fact that just gamma point calculations is enough.

Anyone can see following sentences in most QE tutorials;
"Increase supercell in real space by a factor N along a ; EXACTLY same
results obtained by reducing  divisions in k mesh (in the new smaller BZ)
by factor N"

This is the problem that I cant understand : when we substitute the unit
cell by n*n*n  supercell ( k=0), the calculated bands with new sampling has
no curvature and extension along k axis, because we have just a K point.
Total Energy, probably is same as former unit cell (by integer factor), but
if we will lose information about other aspects of electronic structure by
this sampling?

I would appreciate it if anyone can help me to understand this, or refer me
to a source.


PS:  suppose supercell sustained no relaxation or similar changes, and we
have just the two different scales from one infinite, periodic lattice.




Thanks in advance.

Yavar Taghipour Azar
PhD student
Physics Group, AEOI, Tehran, Iran
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From pourazar2012 at gmail.com  Thu Jul 12 12:12:11 2012
From: pourazar2012 at gmail.com (yavar pour azar)
Date: Thu, 12 Jul 2012 14:42:11 +0430
Subject: [Pw_forum] where I can find BLYP USPP for Ru?
In-Reply-To: <CD0DC29C-6246-490C-BF6C-F8F1465DB75C@democritos.it>
References: <CAFgXaNjLU7Tj=pega9XqiqpMSd2ev28CHvaJ1viE+-jEpVHd2w@mail.gmail.com>
	<CD0DC29C-6246-490C-BF6C-F8F1465DB75C@democritos.it>
Message-ID: <CAFgXaNiLA5X5UxYvw+DOjQ2mQuMnBDjFXdTvdmQFxE0UJ3YT-Q@mail.gmail.com>

Dear Prof. Giannozzi

I am so sorry for bad explanation of my problem. I mistook blyp for b3lyp (
"hybrid functionals")

thanks for your consideration and your time.

Bests.







On Thu, Jul 12, 2012 at 1:57 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Jul 12, 2012, at 10:52 , yavar pour azar wrote:
>
> > I want to use US.PP, generated by blyp functional for Ru.
> > But according to "Notes on pseudopotential generation" by
> > prf. Giannozzi, this functionals are not allowed in atomic code.
>
> not sure what version of my notes you are referring to. In any case,
> this is not (or no longer) true.
>
> > anyone can help me to find or generate such pseudopotential for Ru
> > arom?
>
> standard answer apply: go to the QE web site, under "Pseudopotentials".
> You can find a lot of pointers there
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From giuseppe.mattioli at ism.cnr.it  Thu Jul 12 13:34:37 2012
From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli)
Date: Thu, 12 Jul 2012 13:34:37 +0200
Subject: [Pw_forum] where I can find BLYP USPP for Ru?
In-Reply-To: <CAFgXaNiLA5X5UxYvw+DOjQ2mQuMnBDjFXdTvdmQFxE0UJ3YT-Q@mail.gmail.com>
References: <CAFgXaNjLU7Tj=pega9XqiqpMSd2ev28CHvaJ1viE+-jEpVHd2w@mail.gmail.com>
	<CD0DC29C-6246-490C-BF6C-F8F1465DB75C@democritos.it>
	<CAFgXaNiLA5X5UxYvw+DOjQ2mQuMnBDjFXdTvdmQFxE0UJ3YT-Q@mail.gmail.com>
Message-ID: <201207121334.38022.giuseppe.mattioli@ism.cnr.it>


Again, this has been asked half a million of times... No code (I suppose it is still true) is able 
to generate pseudopotentials by using hybrid functionals. Use a BLYP PP for your B3LYP calculations. 

Giuseppe


On Thursday 12 July 2012 12:12:11 yavar pour azar wrote:
> Dear Prof. Giannozzi
> 
> I am so sorry for bad explanation of my problem. I mistook blyp for b3lyp (
> "hybrid functionals")
> 
> thanks for your consideration and your time.
> 
> Bests.
> 
> On Thu, Jul 12, 2012 at 1:57 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:
> > On Jul 12, 2012, at 10:52 , yavar pour azar wrote:
> > > I want to use US.PP, generated by blyp functional for Ru.
> > > But according to "Notes on pseudopotential generation" by
> > > prf. Giannozzi, this functionals are not allowed in atomic code.
> > 
> > not sure what version of my notes you are referring to. In any case,
> > this is not (or no longer) true.
> > 
> > > anyone can help me to find or generate such pseudopotential for Ru
> > > arom?
> > 
> > standard answer apply: go to the QE web site, under "Pseudopotentials".
> > You can find a lot of pointers there
> > 
> > P.
> > ---
> > Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > Phone +39-0432-558216, fax +39-0432-558222
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum

-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

   Giuseppe Mattioli                            
   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
   v. Salaria Km 29,300 - C.P. 10                
   I 00015 - Monterotondo Stazione (RM)          
   Tel + 39 06 90672836 - Fax +39 06 90672316    
   E-mail: <giuseppe.mattioli at ism.cnr.it>

From anjalisinghromi at gmail.com  Thu Jul 12 14:21:53 2012
From: anjalisinghromi at gmail.com (Anjali Singh)
Date: Thu, 12 Jul 2012 17:51:53 +0530
Subject: [Pw_forum] phonon calculation at gamma point
Message-ID: <CAOUaTpRQcAsKSKs3m0enXurXh-37Zof9xZqCMtt0pr6ejZeA=w@mail.gmail.com>

Still my problem is not solved.I am doing phonon calculation at gamma point
for system of 96 atom for boron nitride.
my input file is

at gamma point
&inputph
  tr2_ph=1.0d-10,
  alpha_mix(1)=0.1,
  nmix_ph=2,
  prefix='BNR96',
  epsil=.false.,
  amass(1)=10.81,
  amass(2)=14.0,
  outdir='./tmp',
  fildyn='bn.dynG',
 /
0.0 0.0 0.0

and the error which I am getting in output file is

Self-consistent Calculation

     Pert. #  1: Fermi energy shift (Ry) = NaN            NaN

      iter #   1 total cpu time : 12036.5 secs   av.it.:   3.6
      thresh= 0.100E-01 alpha_mix =  0.100 |ddv_scf|^2 =  NaN

it would be good if somebody can help me.

-- 
With Thanks and Regards
Anjali Singh
Material Theory Group
Theoretical Science Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur,Bangalore 560 064
India
email id : anjalisinghromi at gmail.com
phone no:+91-89703-58107
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From ptao10b at imr.ac.cn  Thu Jul 12 14:49:53 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Thu, 12 Jul 2012 20:49:53 +0800 (GMT+08:00)
Subject: [Pw_forum] q not allowed in example07
In-Reply-To: <1a280e1.ca66.1387871e072.Coremail.ptao10b@imr.ac.cn>
References: <1a280e1.ca66.1387871e072.Coremail.ptao10b@imr.ac.cn>
	<59180f.d50f.13875e05b1e.Coremail.ptao10b@imr.ac.cn>
	<1BBCAE0A-E16C-4B25-9489-70619C05042F@democritos.it>
	<71238d.c6c5.13874be10de.Coremail.ptao10b@imr.ac.cn>
Message-ID: <1facabd.fc90.1387b3d08a3.Coremail.ptao10b@imr.ac.cn>

I'm sure there is something wrong I've never been aware. I copied everything in the file of run_example today, and what a pity it still cannot run. I am so frustrated. Please help me!

Peng Tao
-----Original Messages-----
From: "Peng Tao" <ptao10b at imr.ac.cn>
Sent Time: Thursday, July 12, 2012
To: "PWSCF Forum" <pw_forum at pwscf.org>, giannozz at democritos.it
Cc:
Subject: Re: [Pw_forum] q not allowed in example07-----Original Messages-----From: "Paolo Giannozzi" <giannozz at democritos.it>Sent Time: Wednesday, July 11, 2012To: "PWSCF Forum" <pw_forum at pwscf.org>Cc: Subject: Re: [Pw_forum] q not allowed in example07On Jul 11, 2012, at 13:50 , Peng Tao wrote:
> The error did not happen when I tried to calculate the example07  > for the first time> about one year ago.
and if you try now? without changing anything in example07?
Yes,I have tried for several times yesterday (The words "right now" I've chosen), copied the file of run_example with nothing changed.


> -----Original Messages-----
> From: "Peng Tao" <ptao10b at imr.ac.cn>
> Sent Time: Wednesday, July 11, 2012
> To: giannozz at democritos.it, "PWSCF Forum" <pw_forum at pwscf.org>
> Cc: 
> Subject: Re: [Pw_forum] q not allowed in example07
> 
> Thank you for your reply!
> 
> My QE version is 4.3.2. "wf_collect=.true." is just set to run parallel, and I keep other parameters unchanged.
> And I find that the error always exists in both serial and parallel cases. The error did not happen when I tried to
> calculate the example07 for the first time about one year ago.
> 
> Right now I copy the file of run_example, and run the example in serial. Unfortunately the same error occurs again:
> 
>  Preparing gamma for a2F
>  
>  
>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       from init : error #         1
>       q not allowed
>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       stopping ...
> 
> And my input files copied from example(keeping everything unchanged except ppdir and outdir):
> ------------------------------------------------------------------
> al.scf.fit.in
> ------------------------------------------------------------------
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     prefix='al',
>     pseudo_dir = '/home/soft/q-e-scm-2009-07-04/espresso/pseudo/',
>     outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/'
>  /
>  &system
>     ibrav=  2, celldm(1) =7.5, nat= 1, ntyp= 1,
>     ecutwfc =15.0,
>     occupations='smearing', smearing='methfessel-paxton', degauss=0.05,
>     la2F = .true.,
>  /
>  &electrons
>     conv_thr =  1.0d-8
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Al  26.98 Al.pz-vbc.UPF
> ATOMIC_POSITIONS
>  Al 0.00 0.00 0.00
> K_POINTS {automatic}
>  16 16 16  0 0 0
> ----------------------------------------------------------------------------
> al.scf.in
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     prefix='al',
>     pseudo_dir = '/home/soft/q-e-scm-2009-07-04/espresso/pseudo/',
>     outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/'
>  /
>  &system
>     ibrav=  2, celldm(1) =7.5, nat= 1, ntyp= 1,
>     ecutwfc =15.0,
>     occupations='smearing', smearing='methfessel-paxton', degauss=0.05
>  /
>  &electrons
>     conv_thr =  1.0d-8
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Al  26.98 Al.pz-vbc.UPF
> ATOMIC_POSITIONS
>  Al 0.00 0.00 0.00
> K_POINTS {automatic}
>  8 8 8  0 0 0
> ----------------------------------------------------------------------------
> al.elph.in
> ---------------------------------------------------------------------------
> Electron-phonon coefficients for Al
>  &inputph
>   tr2_ph=1.0d-10,
>   prefix='al',
>   fildvscf='aldv',
>   amass(1)=26.98,
>   outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/',
>   fildyn='al.dyn',
>   elph=.true.,
>   trans=.true.,
>   ldisp=.true.
>   nq1=4, nq2=4, nq3=4
>  /
> ----------------------------------------------------------------------------
> q2r.in
> ----------------------------------------------------------------------------
> &input
>   zasr='simple',  fildyn='al.dyn', flfrc='Al444.fc', la2F=.true.
>  /
> 
> ------------------------------------------------------------------------------
> Please help me! Thanks in advance.
> 
> Warmest regards,
> Peng Tao
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> -------------------------------------------------------------------------------
> > -----Original Messages-----
> > From: "Paolo Giannozzi" <giannozz at democritos.it>
> > Sent Time: Wednesday, July 11, 2012
> > To: "PWSCF Forum" <pw_forum at pwscf.org>
> > Cc: 
> > Subject: Re: [Pw_forum] q not allowed in example07
> > 
> > 
> > On Jul 11, 2012, at 8:33 , Peng Tao wrote:
> > 
> > > I use the identical parameters as the example and do not change  
> > > anything
> > > except the out_dir and pp_dir.
> > 
> > not true: this
> > 
> > >     wf_collect=.true.
> > 
> > is not in the example. And you haven't explained
> > - which version of the code you are talking about
> > - if you are running in serial or in parallel, and how in the latter  
> > case
> > - whether the unmodified example works
> > 
> > P.
> > ---
> > Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > Phone +39-0432-558216, fax +39-0432-558222
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> --
> -------------------------------------------------------------------
> PH.D. candidate Peng Tao 
> Magnetism and Magnetic Materials Division
> National Laboratory for Material Science
> Institute of Metal Research, Chinese Academy of Sciences
> Phone  +86-024-83978751
> -------------------------------------------------------------------
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------





--
-------------------------------------------------------------------
PH.D. candidate Peng Tao
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------


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From prasenjit.jnc at gmail.com  Thu Jul 12 14:52:48 2012
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Thu, 12 Jul 2012 18:22:48 +0530
Subject: [Pw_forum] GIPAW for metallic system
In-Reply-To: <4FFE7A92.4080409@istm.cnr.it>
References: <CAN3VX3K-2hk2WM4cLZzvpSyR22uvFzSKuO7DwCk+0yFX0ZeK_Q@mail.gmail.com>
	<4FFE7A92.4080409@istm.cnr.it>
Message-ID: <CAN3VX3Ljnp-+OHh0dqzGs9nrc9s=QHD1rjK903WC5Y37haYHAw@mail.gmail.com>

Dear Davide,

Thanks a lot.

Do you have any suggestion then on how to do nmr calculations for magnetic
systems?
Actually I want to calculate the C nmr of Pd cluster on graphene oxide.
However, the Pd cluster is magnetic.

With regards,

Prasenjit

On 12 July 2012 12:49, Davide Ceresoli <davide.ceresoli at istm.cnr.it> wrote:

> Dear Prasenjit,
>      it's not implemented yet.
>
> Davide
>
>
> On 07/12/2012 04:01 AM, Prasenjit Ghosh wrote:
> > Dear all,
> >
> > Has GIPAW been included for calculations using smearing?  Some early
> posts says
> > that it has not been done.
> >
> > I want to calculate the nmr spectra of a system which is magnetic and
> for that I
> > need to use smearing.
> >
> > So I was wondering whether in the latest version of QE, GIPAW with
> occupations
> > smearing has been implemented or not.
> >
> > With regards,
> >
> > Prasenjit
> >
> > --
> > PRASENJIT GHOSH,
> > IISER Pune,
> > First floor, Central Tower, Sai Trinity Building
> > Garware Circle, Sutarwadi, Pashan
> > Pune, Maharashtra 411021, India
> >
> > Phone: +91 (20) 2590 8203
> > Fax: +91 (20) 2589 9790
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
PRASENJIT GHOSH,
IISER Pune,
First floor, Central Tower, Sai Trinity Building
Garware Circle, Sutarwadi, Pashan
Pune, Maharashtra 411021, India

Phone: +91 (20) 2590 8203
Fax: +91 (20) 2589 9790
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From laura.zhu at mail.utoronto.ca  Thu Jul 12 17:54:10 2012
From: laura.zhu at mail.utoronto.ca (Zhihui Zhu)
Date: Thu, 12 Jul 2012 15:54:10 +0000
Subject: [Pw_forum] supercell contraction and cell_factor parameter
Message-ID: <074D4C2D9374214C96A35794E0E7EAE0384D6772@BY2PRD0310MB389.namprd03.prod.outlook.com>

Dear all,

I'm using QE to calculate the binding energy of H2 molecules on graphene sheet. I'm doing vc-relax calculation, and I set the cell_factor to 3. The c axis of the cell is set to be 35 angstroms. I tried a plenty of other c-axis values, but I noticed from my runs that all my supercell shrank to their halves. I'm not sure if this is related to the cell factor parameter. Can anyone please explain what the cell-factor variable represent?

Best regards,
Laura
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From sohailphysics at yahoo.co.in  Fri Jul 13 07:40:16 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Fri, 13 Jul 2012 13:40:16 +0800 (SGT)
Subject: [Pw_forum] Creating a vacuum and isolating cell of 2layers
Message-ID: <1342158016.98316.YahooMailClassic@web192203.mail.sg3.yahoo.com>

Dear QE users

I wish to isolate 2 layers/4 layers by creating a vacuum of a compound which exists in hexagonal form in bulk.

?i have succesfully run the program for its bulk structure

i dont know how to do that
Can anybody explain in detail as i am new to QE

Thanks

Sohail
KKU
Saudi 

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From flux_ray12 at 163.com  Fri Jul 13 07:52:43 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Fri, 13 Jul 2012 13:52:43 +0800 (CST)
Subject: [Pw_forum] q not allowed in example07
In-Reply-To: <1facabd.fc90.1387b3d08a3.Coremail.ptao10b@imr.ac.cn>
References: <1a280e1.ca66.1387871e072.Coremail.ptao10b@imr.ac.cn>
	<59180f.d50f.13875e05b1e.Coremail.ptao10b@imr.ac.cn>
	<1BBCAE0A-E16C-4B25-9489-70619C05042F@democritos.it>
	<71238d.c6c5.13874be10de.Coremail.ptao10b@imr.ac.cn>
	<1facabd.fc90.1387b3d08a3.Coremail.ptao10b@imr.ac.cn>
Message-ID: <66e0da7.7fab.1387ee575c8.Coremail.flux_ray12@163.com>

I tried PHonon/examples/example03, for the el-ph calculation of FCC-Al, everything shows fine:
  running the scf calculation with dense k-point grid...  done
  running the scf calculation...  done
  running the el-ph calculation...  done
  running q2r...  done
  running matdyn for frequency calculation...  done
  running matdyn for a2F(omega) calculation...  done
  running lambda.x for lambda calculation...  done
I also tried it by QE v4.3.2 half year ago, also no any problem occurred.
"q-point not allowed" is usually given from the non-high-symmetry point in the q-points mesh, such as doing vc-relax instead of scf before phonon calculation. You can verify it in your *.dyn0 file.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-07-12 20:49:53,"Peng Tao" <ptao10b at imr.ac.cn> wrote:
I'm sure there is something wrong I've never been aware. I copied everything in the file of run_example today, and what a pity it still cannot run. I am so frustrated. Please help me!

Peng Tao
-----Original Messages-----
From: "Peng Tao" <ptao10b at imr.ac.cn>
Sent Time: Thursday, July 12, 2012
To: "PWSCF Forum" <pw_forum at pwscf.org>, giannozz at democritos.it
Cc:
Subject: Re: [Pw_forum] q not allowed in example07-----Original Messages-----From: "Paolo Giannozzi" <giannozz at democritos.it>Sent Time: Wednesday, July 11, 2012To: "PWSCF Forum" <pw_forum at pwscf.org>Cc: Subject: Re: [Pw_forum] q not allowed in example07On Jul 11, 2012, at 13:50 , Peng Tao wrote:
> The error did not happen when I tried to calculate the example07  > for the first time> about one year ago.
and if you try now? without changing anything in example07?
Yes,I have tried for several times yesterday (The words "right now" I've chosen), copied the file of run_example with nothing changed.


> -----Original Messages-----
> From: "Peng Tao" <ptao10b at imr.ac.cn>
> Sent Time: Wednesday, July 11, 2012
> To: giannozz at democritos.it, "PWSCF Forum" <pw_forum at pwscf.org>
> Cc: 
> Subject: Re: [Pw_forum] q not allowed in example07
> 
> Thank you for your reply!
> 
> My QE version is 4.3.2. "wf_collect=.true." is just set to run parallel, and I keep other parameters unchanged.
> And I find that the error always exists in both serial and parallel cases. The error did not happen when I tried to
> calculate the example07 for the first time about one year ago.
> 
> Right now I copy the file of run_example, and run the example in serial. Unfortunately the same error occurs again:
> 
>  Preparing gamma for a2F
>  
>  
>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       from init : error #         1
>       q not allowed
>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       stopping ...
> 
> And my input files copied from example(keeping everything unchanged except ppdir and outdir):
> ------------------------------------------------------------------
> al.scf.fit.in
> ------------------------------------------------------------------
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     prefix='al',
>     pseudo_dir = '/home/soft/q-e-scm-2009-07-04/espresso/pseudo/',
>     outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/'
>  /
>  &system
>     ibrav=  2, celldm(1) =7.5, nat= 1, ntyp= 1,
>     ecutwfc =15.0,
>     occupations='smearing', smearing='methfessel-paxton', degauss=0.05,
>     la2F = .true.,
>  /
>  &electrons
>     conv_thr =  1.0d-8
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Al  26.98 Al.pz-vbc.UPF
> ATOMIC_POSITIONS
>  Al 0.00 0.00 0.00
> K_POINTS {automatic}
>  16 16 16  0 0 0
> ----------------------------------------------------------------------------
> al.scf.in
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     prefix='al',
>     pseudo_dir = '/home/soft/q-e-scm-2009-07-04/espresso/pseudo/',
>     outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/'
>  /
>  &system
>     ibrav=  2, celldm(1) =7.5, nat= 1, ntyp= 1,
>     ecutwfc =15.0,
>     occupations='smearing', smearing='methfessel-paxton', degauss=0.05
>  /
>  &electrons
>     conv_thr =  1.0d-8
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Al  26.98 Al.pz-vbc.UPF
> ATOMIC_POSITIONS
>  Al 0.00 0.00 0.00
> K_POINTS {automatic}
>  8 8 8  0 0 0
> ----------------------------------------------------------------------------
> al.elph.in
> ---------------------------------------------------------------------------
> Electron-phonon coefficients for Al
>  &inputph
>   tr2_ph=1.0d-10,
>   prefix='al',
>   fildvscf='aldv',
>   amass(1)=26.98,
>   outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/',
>   fildyn='al.dyn',
>   elph=.true.,
>   trans=.true.,
>   ldisp=.true.
>   nq1=4, nq2=4, nq3=4
>  /
> ----------------------------------------------------------------------------
> q2r.in
> ----------------------------------------------------------------------------
> &input
>   zasr='simple',  fildyn='al.dyn', flfrc='Al444.fc', la2F=.true.
>  /
> 
> ------------------------------------------------------------------------------
> Please help me! Thanks in advance.
> 
> Warmest regards,
> Peng Tao
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> -------------------------------------------------------------------------------
> > -----Original Messages-----
> > From: "Paolo Giannozzi" <giannozz at democritos.it>
> > Sent Time: Wednesday, July 11, 2012
> > To: "PWSCF Forum" <pw_forum at pwscf.org>
> > Cc: 
> > Subject: Re: [Pw_forum] q not allowed in example07
> > 
> > 
> > On Jul 11, 2012, at 8:33 , Peng Tao wrote:
> > 
> > > I use the identical parameters as the example and do not change  
> > > anything
> > > except the out_dir and pp_dir.
> > 
> > not true: this
> > 
> > >     wf_collect=.true.
> > 
> > is not in the example. And you haven't explained
> > - which version of the code you are talking about
> > - if you are running in serial or in parallel, and how in the latter  
> > case
> > - whether the unmodified example works
> > 
> > P.
> > ---
> > Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > Phone +39-0432-558216, fax +39-0432-558222
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> --
> -------------------------------------------------------------------
> PH.D. candidate Peng Tao 
> Magnetism and Magnetic Materials Division
> National Laboratory for Material Science
> Institute of Metal Research, Chinese Academy of Sciences
> Phone  +86-024-83978751
> -------------------------------------------------------------------
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------





--
-------------------------------------------------------------------
PH.D. candidate Peng Tao
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------


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From tkaloni at gmail.com  Fri Jul 13 08:19:43 2012
From: tkaloni at gmail.com (Thaneshwor Kaloni)
Date: Fri, 13 Jul 2012 09:19:43 +0300
Subject: [Pw_forum] Creating a vacuum and isolating cell of 2layers
Message-ID: <CABvS7Q+FhJLfixnphJh7bO2czds=yuwTzNbuD=FSMArhyo8fVQ@mail.gmail.com>

Dear Sohail,

If I understand you point clearly, creating a supercell can be a easy task.
Anyways, you could use Xcrysden to create your structure. I believe you
could
find some useful information in pw_forum arxiv. Without looking any
structure
its hard to comments or reply.
I would suggest you please paste your input file here to get further help!

Kaloni
Dear QE users

I wish to isolate 2 layers/4 layers by creating a vacuum of a compound
which exists in hexagonal form in bulk.

?i have succesfully run the program for its bulk structure

i dont know how to do that
Can anybody explain in detail as i am new to QE

Thanks

Sohail
KKU
Saudi
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From davide.ceresoli at istm.cnr.it  Fri Jul 13 09:31:28 2012
From: davide.ceresoli at istm.cnr.it (Davide Ceresoli)
Date: Fri, 13 Jul 2012 09:31:28 +0200
Subject: [Pw_forum] GIPAW for metallic system
In-Reply-To: <CAN3VX3Ljnp-+OHh0dqzGs9nrc9s=QHD1rjK903WC5Y37haYHAw@mail.gmail.com>
References: <CAN3VX3K-2hk2WM4cLZzvpSyR22uvFzSKuO7DwCk+0yFX0ZeK_Q@mail.gmail.com>
	<4FFE7A92.4080409@istm.cnr.it>
	<CAN3VX3Ljnp-+OHh0dqzGs9nrc9s=QHD1rjK903WC5Y37haYHAw@mail.gmail.com>
Message-ID: <4FFFCED0.3050602@istm.cnr.it>

Dear Prasenjit,
     not easy. Are you using only one k-point? could
you try to restart PW with occupations='fixed' or
occupations='from_input'?

Davide



On 07/12/2012 02:52 PM, Prasenjit Ghosh wrote:
> Dear Davide,
>
> Thanks a lot.
>
> Do you have any suggestion then on how to do nmr calculations for magnetic systems?
> Actually I want to calculate the C nmr of Pd cluster on graphene oxide. However,
> the Pd cluster is magnetic.
>
> With regards,
>
> Prasenjit
>
> On 12 July 2012 12:49, Davide Ceresoli <davide.ceresoli at istm.cnr.it
> <mailto:davide.ceresoli at istm.cnr.it>> wrote:
>
>     Dear Prasenjit,
>           it's not implemented yet.
>
>     Davide
>
>
>     On 07/12/2012 04:01 AM, Prasenjit Ghosh wrote:
>      > Dear all,
>      >
>      > Has GIPAW been included for calculations using smearing?  Some early
>     posts says
>      > that it has not been done.
>      >
>      > I want to calculate the nmr spectra of a system which is magnetic and for
>     that I
>      > need to use smearing.
>      >
>      > So I was wondering whether in the latest version of QE, GIPAW with
>     occupations
>      > smearing has been implemented or not.
>      >
>      > With regards,
>      >
>      > Prasenjit
>      >
>      > --
>      > PRASENJIT GHOSH,
>      > IISER Pune,
>      > First floor, Central Tower, Sai Trinity Building
>      > Garware Circle, Sutarwadi, Pashan
>      > Pune, Maharashtra 411021, India
>      >
>      > Phone: +91 (20) 2590 8203
>      > Fax: +91 (20) 2589 9790
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
> PRASENJIT GHOSH,
> IISER Pune,
> First floor, Central Tower, Sai Trinity Building
> Garware Circle, Sutarwadi, Pashan
> Pune, Maharashtra 411021, India
>
> Phone: +91 (20) 2590 8203
> Fax: +91 (20) 2589 9790


From rameshchitumalla at gmail.com  Fri Jul 13 13:55:05 2012
From: rameshchitumalla at gmail.com (Ramesh Kumar)
Date: Fri, 13 Jul 2012 17:25:05 +0530
Subject: [Pw_forum] Bad data for namelist object mixing_mode
Message-ID: <CAO1fJnvD9RbVoS+imV52=cQFq7nvr0rDTuB1fwSFkpOhRqFq1g@mail.gmail.com>

Dear Users,

When I run 'relax' calculation of TiO2 with  v.4.3.1, it is running
successfully.
The same file, if I run in v.5.0, its giving an error "Bad data for
namelist object mixing_mode" and if I remove the mixing_mode from the input
file, in v.5.0 also it is running successfully. Please some one help me in
this regard. I am giving the input here....

&CONTROL
  calculation = "relax",
  pseudo_dir  = "/opt/espresso-4.3.1/pseudo-hcl",
  title       = "TiO2-supercell-3x1x2 at 25Ry",
  verbosity   = "high",
  outdir      = "/tmp",
  wfcdir      = "/tmp",
  nstep       = 300,
  forc_conv_thr = 1.0D-2,
  restart_mode = "from_scratch",
  disk_io     = "high",
/
 &SYSTEM
  ibrav = 14,
  A = 10.2395,
  B = 11.3526,
  C = 18.8588,
  cosAB = 0,
  cosAC = 0,
  cosBC = 0,
  nat = 72,
  ntyp = 2,
  ecutwfc = 25,
 /
 &ELECTRONS
  electron_maxstep = 500,
  diago_david_ndim = 6,
  mixing_beta = 0.1,
  mixing_mode = local-TF,
/
 &IONS
  ion_dynamics = 'bfgs',
/
ATOMIC_SPECIES
  O    16.000 O.pw91-van_ak.UPF
  Ti   47.862 Ti.pw91-nsp-van.UPF
ATOMIC_POSITIONS angstrom
Ti       7.802601390   0.000000000   0.731726700
Ti       7.802601390   3.784200000   0.731726700
Ti       7.802601390   7.568400000   0.731726700
Ti       9.189153004  -0.006515422   4.448918595
Ti       9.189954718   3.775789308   4.449899070
-
-
-
O        0.824867440  -0.004475915   3.563076597
O        0.824908130   3.791766218   3.563292452
O        0.824597987   7.563798394   3.561725593
K_POINTS automatic
  1 1 1   0 0 0


Thank you in advance.


-
*With Best Regards:

*
*CH. Ramesh Kumar
Ph.D Student,
Computational Chemistry Lab,
Indian Institute of Chemical Technology(IICT),*
*Tarnaka, **
Hyderabad.
*
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From flux_ray12 at 163.com  Fri Jul 13 14:04:37 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Fri, 13 Jul 2012 20:04:37 +0800 (CST)
Subject: [Pw_forum] Bad data for namelist object mixing_mode
In-Reply-To: <CAO1fJnvD9RbVoS+imV52=cQFq7nvr0rDTuB1fwSFkpOhRqFq1g@mail.gmail.com>
References: <CAO1fJnvD9RbVoS+imV52=cQFq7nvr0rDTuB1fwSFkpOhRqFq1g@mail.gmail.com>
Message-ID: <1f822f40.e92a.1388039f32f.Coremail.flux_ray12@163.com>

how about writing it as:
mixing_mode = 'local-TF' ,
?

--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-07-13 19:55:05,"Ramesh Kumar" <rameshchitumalla at gmail.com> wrote:

Dear Users,


When I run 'relax' calculation of TiO2 with  v.4.3.1, it is running successfully.
The same file, if I run in v.5.0, its giving an error "Bad data for namelist object mixing_mode" and if I remove the mixing_mode from the input file, in v.5.0 also it is running successfully. Please some one help me in this regard. I am giving the input here.... 


&CONTROL
  calculation = "relax",
  pseudo_dir  = "/opt/espresso-4.3.1/pseudo-hcl",
  title       = "TiO2-supercell-3x1x2 at 25Ry",
  verbosity   = "high",
  outdir      = "/tmp",
  wfcdir      = "/tmp",
  nstep       = 300,
  forc_conv_thr = 1.0D-2,
  restart_mode = "from_scratch",
  disk_io     = "high",
/
 &SYSTEM
  ibrav = 14,
  A = 10.2395,
  B = 11.3526,
  C = 18.8588,
  cosAB = 0,
  cosAC = 0,
  cosBC = 0,  
  nat = 72,
  ntyp = 2,
  ecutwfc = 25,
 /
 &ELECTRONS
  electron_maxstep = 500,
  diago_david_ndim = 6, 
  mixing_beta = 0.1,
  mixing_mode = local-TF,
/
 &IONS
  ion_dynamics = 'bfgs',
/
ATOMIC_SPECIES
  O    16.000 O.pw91-van_ak.UPF   
  Ti   47.862 Ti.pw91-nsp-van.UPF
ATOMIC_POSITIONS angstrom 
Ti       7.802601390   0.000000000   0.731726700   
Ti       7.802601390   3.784200000   0.731726700   
Ti       7.802601390   7.568400000   0.731726700   
Ti       9.189153004  -0.006515422   4.448918595
Ti       9.189954718   3.775789308   4.449899070
-
-
-
O        0.824867440  -0.004475915   3.563076597
O        0.824908130   3.791766218   3.563292452
O        0.824597987   7.563798394   3.561725593
K_POINTS automatic                               
  1 1 1   0 0 0   




Thank you in advance.




-
With Best Regards:


CH. Ramesh Kumar
Ph.D Student,
Computational Chemistry Lab,
Indian Institute of Chemical Technology(IICT),
Tarnaka, 
Hyderabad.

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From rameshchitumalla at gmail.com  Fri Jul 13 14:29:09 2012
From: rameshchitumalla at gmail.com (Ramesh Kumar)
Date: Fri, 13 Jul 2012 17:59:09 +0530
Subject: [Pw_forum] Bad data for namelist object mixing_mode
In-Reply-To: <CAO1fJnvD9RbVoS+imV52=cQFq7nvr0rDTuB1fwSFkpOhRqFq1g@mail.gmail.com>
References: <CAO1fJnvD9RbVoS+imV52=cQFq7nvr0rDTuB1fwSFkpOhRqFq1g@mail.gmail.com>
Message-ID: <CAO1fJnsBHmcY4ztSR6jJDqB2F5gAP21+bcm-4CUZ7L=gQhYAmg@mail.gmail.com>

Dear GAO Zhe,

Thank you for the reply, Its working fine now.




how about writing it as:
mixing_mode = 'local-TF' ,
?

--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea


On Fri, Jul 13, 2012 at 5:25 PM, Ramesh Kumar <rameshchitumalla at gmail.com>wrote:

> Dear Users,
>
> When I run 'relax' calculation of TiO2 with  v.4.3.1, it is running
> successfully.
> The same file, if I run in v.5.0, its giving an error "Bad data for
> namelist object mixing_mode" and if I remove the mixing_mode from the input
> file, in v.5.0 also it is running successfully. Please some one help me in
> this regard. I am giving the input here....
>
> -
> *With Best Regards:
>
> *
> *CH. Ramesh Kumar
> Ph.D Student,
> Computational Chemistry Lab,
> Indian Institute of Chemical Technology(IICT),*
> *Tarnaka, **
> Hyderabad.
> *
>
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From li.chengyang at wmich.edu  Fri Jul 13 23:24:02 2012
From: li.chengyang at wmich.edu (Chengyang Li)
Date: Fri, 13 Jul 2012 17:24:02 -0400 (EDT)
Subject: [Pw_forum] question about compiling espresso-4.3.2-GPU
In-Reply-To: <1335342013.775902.1342214255682.JavaMail.root@wmu-mailstore05>
Message-ID: <281000915.775953.1342214642243.JavaMail.root@wmu-mailstore05>

Dear Users

I download espresso-4.3.2-GPU and ask the cluster administrator to install it for parallel calculation. However when we compiled the software, some errors happened.It seems like there are some problems with FORTRAN. Does anyone have any idea about this? Thank you.


The command run is "make pw" for the "basic code for scf, structure
optimization, MD".  The version of gfortran is :

     # mpif90 --version
GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
Copyright (C) 2007 Free Software Foundation, Inc.

The version of related software:

        espresso-4.3.2-GPU
        lapack-3.2
        fftw3-3.3.2

Configure command for Quantum Espresso is:

  ./configure --enable-phigemm --prefix=/opt/qe432 --enable-parallel
--enable-cuda --with-cuda-dir=/opt/cuda --with-gpu-arch=13 --enable-openmp
--with-internal-blas --with-internal-lapack
FFT_LIBS=/usr/local/fftw332/lib/libfftw3_mpi.a

Cuda version is nvcc --version:

nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2011 NVIDIA Corporation
Built on Thu_Jan_12_14:41:45_PST_2012
Cuda compilation tools, release 4.1, V0.2.1221



Chengyang Li

Department of Physics
WMU
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From pourazar2012 at gmail.com  Sat Jul 14 07:03:00 2012
From: pourazar2012 at gmail.com (yavar pour azar)
Date: Sat, 14 Jul 2012 09:33:00 +0430
Subject: [Pw_forum] Fwd: "Reciprocity of Supercells & BZ Sampling",
 If I choose gamma point for supercell, will I lose some information?
In-Reply-To: <CAFgXaNiSsftvxcr4LFemJ7jBD+vvZtBRriv=Zym7pczF7+HP=g@mail.gmail.com>
References: <CAFgXaNiSsftvxcr4LFemJ7jBD+vvZtBRriv=Zym7pczF7+HP=g@mail.gmail.com>
Message-ID: <CAFgXaNhnKQFRs=LN0OraN7z4GWCD5aVKSzComSpXmjK=C674tg@mail.gmail.com>

---------- Forwarded message ----------
From: yavar pour azar <pourazar2012 at gmail.com>
Date: Thu, Jul 12, 2012 at 2:14 PM
Subject: "Reciprocity of Supercells & BZ Sampling", If I choose gamma point
for supercell, will I lose some information?
To: pw_forum at pwscf.org


Dear QE users,

I have a conceptual problem with k-point sampling in supercells.

Suppose we have a simple cubic unit cell for the bulk, which it's
electronic structure, total energy and etc... is calculated by n*n*n BZ
Sampling.
for example I can see band width and band curvature along k axis, and i
will have max and min points for every band in different k_points such
gamma, X, L,......

Now, if we want to make a n*n*n supercell from this unit cell, it is the
known fact that just gamma point calculations is enough.

Anyone can see following sentences in most QE tutorials;
"Increase supercell in real space by a factor N along a ; EXACTLY same
results obtained by reducing  divisions in k mesh (in the new smaller BZ)
by factor N"

This is the problem that I cant understand : when we substitute the unit
cell by n*n*n  supercell ( k=0), the calculated bands with new sampling has
no curvature and extension along k axis, because we have just a K point.
Total Energy, probably is same as former unit cell (by integer factor), but
if we will lose information about other aspects of electronic structure by
this sampling?

I would appreciate it if anyone can help me to understand this, or refer me
to a source.


PS:  suppose supercell sustained no relaxation or similar changes, and we
have just the two different scales from one infinite, periodic lattice.




Thanks in advance.

Yavar Taghipour Azar
PhD student
Physics Group, AEOI, Tehran, Iran
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From swetarekharam at gmail.com  Sat Jul 14 07:12:52 2012
From: swetarekharam at gmail.com (Swetarekha Ram)
Date: Sat, 14 Jul 2012 10:42:52 +0530
Subject: [Pw_forum] reg: Tc calculation
Message-ID: <CAFsnUVZUzBbB-0dx9GbQb3zEy9DrWZOqwUyDbR9-EFMZ4BC=Eg@mail.gmail.com>

Dear users,

 I want to calculate the Tc for cubic system.

For that I have done  all the calculation till lamda.out

But my doubt is
In the lamda.out file we have lamda, omega and Tc values for the degauss
value starting from 0.05 to 0.5.

So, which value we have to consider for our system.

The value corresponding to the degauss value, which we have used in our
calculation or something else.
Suppose I have used the degauss value in the scf calculation is 0.04, then
from the lamda.out I should take the lamda, omega and Tc value for the
degauss 0.04 or what should I do.

I am confused in this point.
Can any one give suggestion to come out from this problem.

-- 
Swetarekha Ram,
Research Scholar,
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From pourazar2012 at gmail.com  Sat Jul 14 07:34:31 2012
From: pourazar2012 at gmail.com (yavar pour azar)
Date: Sat, 14 Jul 2012 10:04:31 +0430
Subject: [Pw_forum] Reciprocity of Supercells & BZ Sampling
Message-ID: <CAFgXaNiphjWkeOMTRZXUmC0xQBo1tuLN89-feToTtZkOFZpDQw@mail.gmail.com>

Dear QE users,

I have a conceptual problem with k-point sampling in supercells.

Suppose we have a simple cubic unit cell for the bulk, which it's
electronic structure, total energy and etc... is calculated by n*n*n BZ
Sampling.
for example I can see band width and band curvature along k axis, and i
will have max and min points for every band in different k_points such
gamma, X, L,......

Now, if we want to make a n*n*n supercell from this unit cell, it is the
known fact that just gamma point calculations is enough.

Anyone can see following sentences in most QE tutorials;
"Increase supercell in real space by a factor N along a ; EXACTLY same
results obtained by reducing  divisions in k mesh (in the new smaller BZ)
by factor N"

This is the problem that I cant understand : when we substitute the unit
cell by n*n*n  supercell ( k=0), the calculated bands with new sampling has
no curvature and extension along k axis, because we have just a K point.
Total Energy, probably is same as former unit cell (by integer factor), but
if we will lose information about other aspects of electronic structure by
this sampling?

I would appreciate it if anyone can help me to understand this, or refer me
to a source.


PS:  suppose supercell sustained no relaxation or similar changes, and we
have just the two different scales from one infinite, periodic lattice.



Thanks in advance.

Yavar Taghipour Azar
PhD student
Physics Group, AEOI, Tehran, Iran
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From pourazar2012 at gmail.com  Sat Jul 14 09:20:22 2012
From: pourazar2012 at gmail.com (yavar pour azar)
Date: Sat, 14 Jul 2012 11:50:22 +0430
Subject: [Pw_forum] i can not see my email
Message-ID: <CAFgXaNgArV2FJeW_fFRdnskmG9gQj3BxpGMjNBeCyE522eyeHg@mail.gmail.com>

Dear QE users,

I receive acknowledgment message but  I can not see my own email yet.
anyone can help me?

thanks in advance

Y. Taghipour
physics group, AEOI.Tehran. Iran
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From akohlmey at gmail.com  Sat Jul 14 12:13:57 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Sat, 14 Jul 2012 12:13:57 +0200
Subject: [Pw_forum] i can not see my email
In-Reply-To: <CAFgXaNgArV2FJeW_fFRdnskmG9gQj3BxpGMjNBeCyE522eyeHg@mail.gmail.com>
References: <CAFgXaNgArV2FJeW_fFRdnskmG9gQj3BxpGMjNBeCyE522eyeHg@mail.gmail.com>
Message-ID: <CADTmJ6HQ4u1n8=ewVf-L2S+EG1GP3UkdVnzRthQGtigpsf-=7Q@mail.gmail.com>

On Sat, Jul 14, 2012 at 9:20 AM, yavar pour azar <pourazar2012 at gmail.com> wrote:
> Dear QE users,
>
> I receive acknowledgment message but  I can not see my own email yet.
> anyone can help me?

no need to help. you are using gmail and gmail
recognizes e-mails that you sent yourself and
thus they won't show again when they get distributed
from the mailing list.

axel.

>
> thanks in advance
>
> Y. Taghipour
> physics group, AEOI.Tehran. Iran
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

From pourazar2012 at gmail.com  Sat Jul 14 12:23:42 2012
From: pourazar2012 at gmail.com (yavar pour azar)
Date: Sat, 14 Jul 2012 14:53:42 +0430
Subject: [Pw_forum] i can not see my email
In-Reply-To: <CADTmJ6HQ4u1n8=ewVf-L2S+EG1GP3UkdVnzRthQGtigpsf-=7Q@mail.gmail.com>
References: <CAFgXaNgArV2FJeW_fFRdnskmG9gQj3BxpGMjNBeCyE522eyeHg@mail.gmail.com>
	<CADTmJ6HQ4u1n8=ewVf-L2S+EG1GP3UkdVnzRthQGtigpsf-=7Q@mail.gmail.com>
Message-ID: <CAFgXaNgV2N_-XpyNVZzXK14xwwxJu0OfqR-23w47YM+=EjdPGg@mail.gmail.com>

Dear Axel,

thanks for your time and consideration.

bests.

On Sat, Jul 14, 2012 at 2:43 PM, Axel Kohlmeyer <akohlmey at gmail.com> wrote:

> On Sat, Jul 14, 2012 at 9:20 AM, yavar pour azar <pourazar2012 at gmail.com>
> wrote:
> > Dear QE users,
> >
> > I receive acknowledgment message but  I can not see my own email yet.
> > anyone can help me?
>
> no need to help. you are using gmail and gmail
> recognizes e-mails that you sent yourself and
> thus they won't show again when they get distributed
> from the mailing list.
>
> axel.
>
> >
> > thanks in advance
> >
> > Y. Taghipour
> > physics group, AEOI.Tehran. Iran
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From pourazar2012 at gmail.com  Sat Jul 14 13:37:45 2012
From: pourazar2012 at gmail.com (yavar pour azar)
Date: Sat, 14 Jul 2012 16:07:45 +0430
Subject: [Pw_forum] relax or vc-relax for supercell?
Message-ID: <CAFgXaNg2ym0_xxbE7MYv+8+fDAKCgszZ2Pk5eAJwzAo8a8ic8g@mail.gmail.com>

Dear QE users,

I want to  build * *the supercell.
primarily, I do vc-relax calculation on the bulk structure. (until force
and pressure ~0)
in the next step, I build the supercell by bulk ideal atomic positions,
and finally I should use relaxation.
in this level,  the vc-relax is necessary or just the relax?

when I used only the relax'  option, after relaxation of  supercell
pressure was about 10Kbar, is this means that I should use vc-relax.

If this is true, what is physical interpretation of changes in lattice
parameters? this means outermost layer's cell differ from interior ones?


thanks in advance.

Yavar  Taghipour
PhD student

Physics Group.AEOI. Tehran. Iran
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From spiga.filippo at gmail.com  Sat Jul 14 16:41:42 2012
From: spiga.filippo at gmail.com (Filippo Spiga)
Date: Sat, 14 Jul 2012 22:41:42 +0800
Subject: [Pw_forum] question about compiling espresso-4.3.2-GPU
In-Reply-To: <281000915.775953.1342214642243.JavaMail.root@wmu-mailstore05>
References: <281000915.775953.1342214642243.JavaMail.root@wmu-mailstore05>
Message-ID: <D06A796E-8841-4187-97F7-9EDEFABD8A4D@gmail.com>

Dear Chengyang Li,

the problem that I can see is the GFORTRAN version. GFORTRAN 4.1 does not have iso_c_binding extensions (as far as I know, I will double-check this). So you need a newer version of GCC/GFORTRAN and I suggest you the GCC 4.4. There is no way to workaround this issue, you should upgrade your GNU compilers. However, think about to compile the code using Intel compiler (if available).  Moreover I do not understand why you want to link FFTW in that way (especially the library with MPI support). If OpenMP is enable, leave the code to use its internal FFTW library. 

I see you want to target GPU with (only) compute capability 1.3. What kind of GPU system do you have?

There is a specific ML for the GPU stuff. I monitor constantly that one instead of this general one that is more related to the entire QE. The address is  q-e-gpgpu at qe-forge.org and you can subscribe directly here: http://qe-forge.org/mailman/listinfo/q-e-gpgpu

Regards,
Filippo


On Jul 14, 2012, at 5:24 AM, Chengyang Li wrote:
> Dear Users
> 
> I download espresso-4.3.2-GPU and ask the cluster administrator to install it for parallel calculation. However when we compiled the software, some errors happened.It seems like there are some problems with FORTRAN. Does anyone have any idea about this? Thank you.
> 
> 
> The command run is "make pw" for the "basic code for scf, structure
> optimization, MD".  The version of gfortran is :
> 
>     # mpif90 --version
> GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
> Copyright (C) 2007 Free Software Foundation, Inc.
> 
> The version of related software:
> 
>        espresso-4.3.2-GPU
>        lapack-3.2
>        fftw3-3.3.2
> 
> Configure command for Quantum Espresso is:
> 
>  ./configure --enable-phigemm --prefix=/opt/qe432 --enable-parallel
> --enable-cuda --with-cuda-dir=/opt/cuda --with-gpu-arch=13 --enable-openmp
> --with-internal-blas --with-internal-lapack
> FFT_LIBS=/usr/local/fftw332/lib/libfftw3_mpi.a
> 
> Cuda version is nvcc --version:
> 
> nvcc: NVIDIA (R) Cuda compiler driver
> Copyright (c) 2005-2011 NVIDIA Corporation
> Built on Thu_Jan_12_14:41:45_PST_2012
> Cuda compilation tools, release 4.1, V0.2.1221
> 
> 
> 
> Chengyang Li
> 
> Department of Physics
> WMU
> <gfort.err>_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
Mr. Filippo SPIGA (???), HPC and GPU Technologist <spiga.filippo_at_gmail.com>
website: http://filippospiga.me  ~  skype: filippo.spiga

?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert

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From 809997648 at qq.com  Sun Jul 15 05:08:35 2012
From: 809997648 at qq.com (=?gb18030?B?wdm358WqtdE=?=)
Date: Sun, 15 Jul 2012 11:08:35 +0800
Subject: [Pw_forum] A question about efield
Message-ID: <tencent_1168DEC03CE5062C6B2CBE4E@qq.com>

Dear all
  
 I have a question about the use of an external sawlike potential in PWscf.
 The discription of parameter "eamp" says "the change of slope of this
potential must be located in the empty region". 
  
 This means the two points emaxpos and emaxpos+epreg must be located
 in vacuum or the region from emaxpos to emaxpos+epreg must be located
 in vacuum?
  
 Thank you.
  
 Zhida Song
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From spiga.filippo at gmail.com  Sun Jul 15 07:17:17 2012
From: spiga.filippo at gmail.com (Filippo Spiga)
Date: Sun, 15 Jul 2012 13:17:17 +0800
Subject: [Pw_forum] question about compiling espresso-4.3.2-GPU
In-Reply-To: <D06A796E-8841-4187-97F7-9EDEFABD8A4D@gmail.com>
References: <281000915.775953.1342214642243.JavaMail.root@wmu-mailstore05>
	<D06A796E-8841-4187-97F7-9EDEFABD8A4D@gmail.com>
Message-ID: <ECDDBE30-420C-4AA4-9A37-79CF86E1F9F3@gmail.com>

Dear Chengyang Li,

I thought a bit  and there is a way to workaround the ISO_C_BINDING dependency. The ISO_C_BINDING dependency is mainly related to pinned memory allocations. Most of the time I suggest to do not turn on pinned allocations because, despite better data transfer between GPU and CPU,  the overall calculation usually slow down.

So, I managed to remove all the ISO_C_BINDING dependencies in the code where __CUDA_PINNED is not defined. This workaround also exclude  MAGMA because in order to efficiently use it some data structure has to be pinned (so the code need ISO_C_BINDING so you need to upgrade GFORTRAN). Since you are using GPU with compute capability 1.3, in the README.GPU I already suggested to disable MAGMA on cc1.3.

I rebuild the package for you (build8_alpha). The new code is here:
http://www.fislab.disco.unimib.it/~filippo/qe-builds/espresso-5.0-GPU-build8_alpha.tar.gz

Please You can try to compile this build in this way
$ ./configure --enable-phigemm --disable-magma --prefix=/opt/qe432 --enable-parallel --enable-cuda --with-cuda-dir=/opt/cuda --with-gpu-arch=13 --enable-openmp

I did a test on a workstation and it failed. It failed because GFORTRAN 4.1 is not able to compile a file called sum_band.f90 (standard CPU code, no GPU code inside it). This is the version:
$ gfortran -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --disable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-50)


I suggest you to upgrade GCC/GFORTRAn to 4.4 (not  version 4.5 because GNU 4.5 are not compatible with CUDA 4.0 or 4.1). Since you do not have Intel MKL library, instead of using the internal BLAS/LAPACK you can use GotoBLAS. The compilation of GotoBLAS is very easy and it supports multi-threading (by define GOTO_NUM_THREADS=XXX). Moreover phiGEMM and MAGMA are compatible with it. You can find the source code here:
http://www.fislab.disco.unimib.it/~filippo/qe-builds/GotoBLAS2-1.13.tar.gz
or here:
http://www.tacc.utexas.edu/tacc-projects/gotoblas2/

Hope this help. I look forward to receiving a feedback from you.

Cheers
F

On Jul 14, 2012, at 10:41 PM, Filippo Spiga wrote:
> Dear Chengyang Li,
> 
> the problem that I can see is the GFORTRAN version. GFORTRAN 4.1 does not have iso_c_binding extensions (as far as I know, I will double-check this). So you need a newer version of GCC/GFORTRAN and I suggest you the GCC 4.4. There is no way to workaround this issue, you should upgrade your GNU compilers. However, think about to compile the code using Intel compiler (if available).  Moreover I do not understand why you want to link FFTW in that way (especially the library with MPI support). If OpenMP is enable, leave the code to use its internal FFTW library. 
> 
> I see you want to target GPU with (only) compute capability 1.3. What kind of GPU system do you have?
> 
> There is a specific ML for the GPU stuff. I monitor constantly that one instead of this general one that is more related to the entire QE. The address is  q-e-gpgpu at qe-forge.org and you can subscribe directly here: http://qe-forge.org/mailman/listinfo/q-e-gpgpu
> 
> Regards,
> Filippo

-- 
Mr. Filippo SPIGA (???), HPC and GPU Technologist <spiga.filippo_at_gmail.com>
website: http://filippospiga.me  ~  skype: filippo.spiga

?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert

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From arebol2 at uic.edu  Sun Jul 15 22:27:17 2012
From: arebol2 at uic.edu (=?iso-8859-1?Q?=22Alejandro_R=E9bola=22?=)
Date: Sun, 15 Jul 2012 15:27:17 -0500
Subject: [Pw_forum] q not allowed when running q2r.x
Message-ID: <815f68742c7807669ce149e0dadac09b.squirrel@webmail.uic.edu>

Dear all,

I'm trying to calculate the phonon dispersion for STO. I ran successfully
the ph.x code for a grid of q points. Then I'm trying to get the force
constants in real space by using the q2r.x code, but I keep getting the
following error:

from init : error #         1
     q not allowed

First I thought it was due to some problem with the recovery mode, my
calculation had been interrupted and then resumed, but then I ran a full
calculation, and I got the same error when running q2r.x. I'm using the
4.3.2 version.
The phonon input card I'm using is:

phonons of STO
 &inputph
  tr2_ph=1.0d-14,
  ldisp=.true.,
  nq1=4, nq2=4, nq3=4
  amass(1)=87.62,
  amass(2)=47.867,
  amass(3)=15.9994,
  epsil=.true.
  prefix='sto',
  fildyn='sto.dyn',
 /

This runs successfully.
The input for the q2r.x code is simply:

&input
   fildyn='sto.dyn', zasr='simple', flfrc='sto.fc'
 /

and then I get the "q not allowed" message.

Does anybody know what the problem could be?

Thank you in advance,

Alejandro




From ptao10b at imr.ac.cn  Mon Jul 16 02:13:29 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Mon, 16 Jul 2012 08:13:29 +0800 (GMT+08:00)
Subject: [Pw_forum] q not allowed when running q2r.x
In-Reply-To: <815f68742c7807669ce149e0dadac09b.squirrel@webmail.uic.edu>
References: <815f68742c7807669ce149e0dadac09b.squirrel@webmail.uic.edu>
Message-ID: <1a076f.14ad5.1388d21f72d.Coremail.ptao10b@imr.ac.cn>

We meet the same problem. Could anyone give some advice?


> -----Original Messages-----
> From: "\"Alejandro R?bola\"" <arebol2 at uic.edu>
> Sent Time: Monday, July 16, 2012
> To: pw_forum at pwscf.org
> Cc: 
> Subject: [Pw_forum] q not allowed when running q2r.x
> 
> Dear all,
> 
> I'm trying to calculate the phonon dispersion for STO. I ran successfully
> the ph.x code for a grid of q points. Then I'm trying to get the force
> constants in real space by using the q2r.x code, but I keep getting the
> following error:
> 
> from init : error #         1
>      q not allowed
> 
> First I thought it was due to some problem with the recovery mode, my
> calculation had been interrupted and then resumed, but then I ran a full
> calculation, and I got the same error when running q2r.x. I'm using the
> 4.3.2 version.
> The phonon input card I'm using is:
> 
> phonons of STO
>  &inputph
>   tr2_ph=1.0d-14,
>   ldisp=.true.,
>   nq1=4, nq2=4, nq3=4
>   amass(1)=87.62,
>   amass(2)=47.867,
>   amass(3)=15.9994,
>   epsil=.true.
>   prefix='sto',
>   fildyn='sto.dyn',
>  /
> 
> This runs successfully.
> The input for the q2r.x code is simply:
> 
> &input
>    fildyn='sto.dyn', zasr='simple', flfrc='sto.fc'
>  /
> 
> and then I get the "q not allowed" message.
> 
> Does anybody know what the problem could be?
> 
> Thank you in advance,
> 
> Alejandro
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------



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From ptao10b at imr.ac.cn  Mon Jul 16 02:17:54 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Mon, 16 Jul 2012 08:17:54 +0800 (GMT+08:00)
Subject: [Pw_forum] q not allowed in example07
In-Reply-To: <66e0da7.7fab.1387ee575c8.Coremail.flux_ray12@163.com>
References: <66e0da7.7fab.1387ee575c8.Coremail.flux_ray12@163.com>
	<1a280e1.ca66.1387871e072.Coremail.ptao10b@imr.ac.cn>
	<59180f.d50f.13875e05b1e.Coremail.ptao10b@imr.ac.cn>
	<1BBCAE0A-E16C-4B25-9489-70619C05042F@democritos.it>
	<71238d.c6c5.13874be10de.Coremail.ptao10b@imr.ac.cn>
	<1facabd.fc90.1387b3d08a3.Coremail.ptao10b@imr.ac.cn>
Message-ID: <419ee8.14b0a.1388d260019.Coremail.ptao10b@imr.ac.cn>

My mentor said perhaps the damage of evironmental parameters caused this problem.


-----Original Messages-----
From: "GAO Zhe" <flux_ray12 at 163.com>
Sent Time: Friday, July 13, 2012
To: "PWSCF Forum" <pw_forum at pwscf.org>
Cc:
Subject: Re: [Pw_forum] q not allowed in example07


I tried PHonon/examples/example03, for the el-ph calculation of FCC-Al, everything shows fine:
  running the scf calculation with dense k-point grid...  done
  running the scf calculation...  done
  running the el-ph calculation...  done
  running q2r...  done
  running matdyn for frequency calculation...  done
  running matdyn for a2F(omega) calculation...  done
  running lambda.x for lambda calculation...  done
I also tried it by QE v4.3.2 half year ago, also no any problem occurred.
"q-point not allowed" is usually given from the non-high-symmetry point in the q-points mesh, such as doing vc-relax instead of scf before phonon calculation. You can verify it in your *.dyn0 file.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-07-12 20:49:53,"Peng Tao" <ptao10b at imr.ac.cn> wrote:
I'm sure there is something wrong I've never been aware. I copied everything in the file of run_example today, and what a pity it still cannot run. I am so frustrated. Please help me!

Peng Tao
-----Original Messages-----
From: "Peng Tao" <ptao10b at imr.ac.cn>
Sent Time: Thursday, July 12, 2012
To: "PWSCF Forum" <pw_forum at pwscf.org>, giannozz at democritos.it
Cc:
Subject: Re: [Pw_forum] q not allowed in example07-----Original Messages-----From: "Paolo Giannozzi" <giannozz at democritos.it>Sent Time: Wednesday, July 11, 2012To: "PWSCF Forum" <pw_forum at pwscf.org>Cc: Subject: Re: [Pw_forum] q not allowed in example07On Jul 11, 2012, at 13:50 , Peng Tao wrote:
> The error did not happen when I tried to calculate the example07  > for the first time> about one year ago.
and if you try now? without changing anything in example07?
Yes,I have tried for several times yesterday (The words "right now" I've chosen), copied the file of run_example with nothing changed.


> -----Original Messages-----
> From: "Peng Tao" <ptao10b at imr.ac.cn>
> Sent Time: Wednesday, July 11, 2012
> To: giannozz at democritos.it, "PWSCF Forum" <pw_forum at pwscf.org>
> Cc: 
> Subject: Re: [Pw_forum] q not allowed in example07
> 
> Thank you for your reply!
> 
> My QE version is 4.3.2. "wf_collect=.true." is just set to run parallel, and I keep other parameters unchanged.
> And I find that the error always exists in both serial and parallel cases. The error did not happen when I tried to
> calculate the example07 for the first time about one year ago.
> 
> Right now I copy the file of run_example, and run the example in serial. Unfortunately the same error occurs again:
> 
>  Preparing gamma for a2F
>  
>  
>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       from init : error #         1
>       q not allowed
>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       stopping ...
> 
> And my input files copied from example(keeping everything unchanged except ppdir and outdir):
> ------------------------------------------------------------------
> al.scf.fit.in
> ------------------------------------------------------------------
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     prefix='al',
>     pseudo_dir = '/home/soft/q-e-scm-2009-07-04/espresso/pseudo/',
>     outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/'
>  /
>  &system
>     ibrav=  2, celldm(1) =7.5, nat= 1, ntyp= 1,
>     ecutwfc =15.0,
>     occupations='smearing', smearing='methfessel-paxton', degauss=0.05,
>     la2F = .true.,
>  /
>  &electrons
>     conv_thr =  1.0d-8
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Al  26.98 Al.pz-vbc.UPF
> ATOMIC_POSITIONS
>  Al 0.00 0.00 0.00
> K_POINTS {automatic}
>  16 16 16  0 0 0
> ----------------------------------------------------------------------------
> al.scf.in
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     prefix='al',
>     pseudo_dir = '/home/soft/q-e-scm-2009-07-04/espresso/pseudo/',
>     outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/'
>  /
>  &system
>     ibrav=  2, celldm(1) =7.5, nat= 1, ntyp= 1,
>     ecutwfc =15.0,
>     occupations='smearing', smearing='methfessel-paxton', degauss=0.05
>  /
>  &electrons
>     conv_thr =  1.0d-8
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Al  26.98 Al.pz-vbc.UPF
> ATOMIC_POSITIONS
>  Al 0.00 0.00 0.00
> K_POINTS {automatic}
>  8 8 8  0 0 0
> ----------------------------------------------------------------------------
> al.elph.in
> ---------------------------------------------------------------------------
> Electron-phonon coefficients for Al
>  &inputph
>   tr2_ph=1.0d-10,
>   prefix='al',
>   fildvscf='aldv',
>   amass(1)=26.98,
>   outdir='/home/taopeng/Documents/pwscf/examples/example07/trat/',
>   fildyn='al.dyn',
>   elph=.true.,
>   trans=.true.,
>   ldisp=.true.
>   nq1=4, nq2=4, nq3=4
>  /
> ----------------------------------------------------------------------------
> q2r.in
> ----------------------------------------------------------------------------
> &input
>   zasr='simple',  fildyn='al.dyn', flfrc='Al444.fc', la2F=.true.
>  /
> 
> ------------------------------------------------------------------------------
> Please help me! Thanks in advance.
> 
> Warmest regards,
> Peng Tao
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> -------------------------------------------------------------------------------
> > -----Original Messages-----
> > From: "Paolo Giannozzi" <giannozz at democritos.it>
> > Sent Time: Wednesday, July 11, 2012
> > To: "PWSCF Forum" <pw_forum at pwscf.org>
> > Cc: 
> > Subject: Re: [Pw_forum] q not allowed in example07
> > 
> > 
> > On Jul 11, 2012, at 8:33 , Peng Tao wrote:
> > 
> > > I use the identical parameters as the example and do not change  
> > > anything
> > > except the out_dir and pp_dir.
> > 
> > not true: this
> > 
> > >     wf_collect=.true.
> > 
> > is not in the example. And you haven't explained
> > - which version of the code you are talking about
> > - if you are running in serial or in parallel, and how in the latter  
> > case
> > - whether the unmodified example works
> > 
> > P.
> > ---
> > Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > Phone +39-0432-558216, fax +39-0432-558222
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> --
> -------------------------------------------------------------------
> PH.D. candidate Peng Tao 
> Magnetism and Magnetic Materials Division
> National Laboratory for Material Science
> Institute of Metal Research, Chinese Academy of Sciences
> Phone  +86-024-83978751
> -------------------------------------------------------------------
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------





--
-------------------------------------------------------------------
PH.D. candidate Peng Tao
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------







--
-------------------------------------------------------------------
PH.D. candidate Peng Tao
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------


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From prasenjit.jnc at gmail.com  Mon Jul 16 05:20:52 2012
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Mon, 16 Jul 2012 08:50:52 +0530
Subject: [Pw_forum] GIPAW for metallic system
In-Reply-To: <4FFFCED0.3050602@istm.cnr.it>
References: <CAN3VX3K-2hk2WM4cLZzvpSyR22uvFzSKuO7DwCk+0yFX0ZeK_Q@mail.gmail.com>
	<4FFE7A92.4080409@istm.cnr.it>
	<CAN3VX3Ljnp-+OHh0dqzGs9nrc9s=QHD1rjK903WC5Y37haYHAw@mail.gmail.com>
	<4FFFCED0.3050602@istm.cnr.it>
Message-ID: <CAN3VX3L6sq7hC3t_zzWGaFYm8pcTHLGHDFbvdU3H2BJc+Y=x=A@mail.gmail.com>

Thanks Davide.

Let me try out your suggestion.

With regards,

Prasenjit

On 13 July 2012 13:01, Davide Ceresoli <davide.ceresoli at istm.cnr.it> wrote:

> Dear Prasenjit,
>      not easy. Are you using only one k-point? could
> you try to restart PW with occupations='fixed' or
> occupations='from_input'?
>
> Davide
>
>
>
> On 07/12/2012 02:52 PM, Prasenjit Ghosh wrote:
> > Dear Davide,
> >
> > Thanks a lot.
> >
> > Do you have any suggestion then on how to do nmr calculations for
> magnetic systems?
> > Actually I want to calculate the C nmr of Pd cluster on graphene oxide.
> However,
> > the Pd cluster is magnetic.
> >
> > With regards,
> >
> > Prasenjit
> >
> > On 12 July 2012 12:49, Davide Ceresoli <davide.ceresoli at istm.cnr.it
> > <mailto:davide.ceresoli at istm.cnr.it>> wrote:
> >
> >     Dear Prasenjit,
> >           it's not implemented yet.
> >
> >     Davide
> >
> >
> >     On 07/12/2012 04:01 AM, Prasenjit Ghosh wrote:
> >      > Dear all,
> >      >
> >      > Has GIPAW been included for calculations using smearing?  Some
> early
> >     posts says
> >      > that it has not been done.
> >      >
> >      > I want to calculate the nmr spectra of a system which is magnetic
> and for
> >     that I
> >      > need to use smearing.
> >      >
> >      > So I was wondering whether in the latest version of QE, GIPAW with
> >     occupations
> >      > smearing has been implemented or not.
> >      >
> >      > With regards,
> >      >
> >      > Prasenjit
> >      >
> >      > --
> >      > PRASENJIT GHOSH,
> >      > IISER Pune,
> >      > First floor, Central Tower, Sai Trinity Building
> >      > Garware Circle, Sutarwadi, Pashan
> >      > Pune, Maharashtra 411021, India
> >      >
> >      > Phone: +91 (20) 2590 8203
> >      > Fax: +91 (20) 2589 9790
> >
> >     _______________________________________________
> >     Pw_forum mailing list
> >     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >     http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> > PRASENJIT GHOSH,
> > IISER Pune,
> > First floor, Central Tower, Sai Trinity Building
> > Garware Circle, Sutarwadi, Pashan
> > Pune, Maharashtra 411021, India
> >
> > Phone: +91 (20) 2590 8203
> > Fax: +91 (20) 2589 9790
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
PRASENJIT GHOSH,
IISER Pune,
First floor, Central Tower, Sai Trinity Building
Garware Circle, Sutarwadi, Pashan
Pune, Maharashtra 411021, India

Phone: +91 (20) 2590 8203
Fax: +91 (20) 2589 9790
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From sohailphysics at yahoo.co.in  Mon Jul 16 07:47:45 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Mon, 16 Jul 2012 13:47:45 +0800 (SGT)
Subject: [Pw_forum] ecutwfc
Message-ID: <1342417665.50599.YahooMailClassic@web192203.mail.sg3.yahoo.com>

Dear Users,
In QE, the usual first step is testing PP and ecutwfc
I did it the same for bulk structure of a compound and followed further calculations

?May i consider the same value of ecutoff for mono or bilayers of the same compound as i am considering the same pseudo potential

This testing is required for pp or for structure

Sohail
KKU
Saudi
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From ptao10b at imr.ac.cn  Mon Jul 16 08:43:05 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Mon, 16 Jul 2012 14:43:05 +0800 (GMT+08:00)
Subject: [Pw_forum] q not allowed when running q2r.x
In-Reply-To: <815f68742c7807669ce149e0dadac09b.squirrel@webmail.uic.edu>
References: <815f68742c7807669ce149e0dadac09b.squirrel@webmail.uic.edu>
Message-ID: <75b34.15ebb.1388e86a551.Coremail.ptao10b@imr.ac.cn>

Where is the "elph=.true." ? No elph means no q in la2F run.


> -----Original Messages-----
> From: "\"Alejandro R?bola\"" <arebol2 at uic.edu>
> Sent Time: Monday, July 16, 2012
> To: pw_forum at pwscf.org
> Cc: 
> Subject: [Pw_forum] q not allowed when running q2r.x
> 
> Dear all,
> 
> I'm trying to calculate the phonon dispersion for STO. I ran successfully
> the ph.x code for a grid of q points. Then I'm trying to get the force
> constants in real space by using the q2r.x code, but I keep getting the
> following error:
> 
> from init : error #         1
>      q not allowed
> 
> First I thought it was due to some problem with the recovery mode, my
> calculation had been interrupted and then resumed, but then I ran a full
> calculation, and I got the same error when running q2r.x. I'm using the
> 4.3.2 version.
> The phonon input card I'm using is:
> 
> phonons of STO
>  &inputph
>   tr2_ph=1.0d-14,
>   ldisp=.true.,
>   nq1=4, nq2=4, nq3=4
>   amass(1)=87.62,
>   amass(2)=47.867,
>   amass(3)=15.9994,
>   epsil=.true.
>   prefix='sto',
>   fildyn='sto.dyn',
>  /
> 
> This runs successfully.
> The input for the q2r.x code is simply:
> 
> &input
>    fildyn='sto.dyn', zasr='simple', flfrc='sto.fc'
>  /
> 
> and then I get the "q not allowed" message.
> 
> Does anybody know what the problem could be?
> 
> Thank you in advance,
> 
> Alejandro
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------



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From ptao10b at imr.ac.cn  Mon Jul 16 08:47:48 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Mon, 16 Jul 2012 14:47:48 +0800 (GMT+08:00)
Subject: [Pw_forum] q not allowed when running q2r.x
In-Reply-To: <75b34.15ebb.1388e86a551.Coremail.ptao10b@imr.ac.cn>
References: <75b34.15ebb.1388e86a551.Coremail.ptao10b@imr.ac.cn>
	<815f68742c7807669ce149e0dadac09b.squirrel@webmail.uic.edu>
Message-ID: <5279af.15ef9.1388e8af99b.Coremail.ptao10b@imr.ac.cn>

Sorry, I assumed you are trying to calculate elph.


-----Original Messages-----
From: "Peng Tao" <ptao10b at imr.ac.cn>
Sent Time: Monday, July 16, 2012
To: "PWSCF Forum" <pw_forum at pwscf.org>
Cc:
Subject: Re: [Pw_forum] q not allowed when running q2r.x

Where is the "elph=.true." ? No elph means no q in la2F run.


> -----Original Messages-----
> From: "\"Alejandro R?bola\"" <arebol2 at uic.edu>
> Sent Time: Monday, July 16, 2012
> To: pw_forum at pwscf.org
> Cc: 
> Subject: [Pw_forum] q not allowed when running q2r.x
> 
> Dear all,
> 
> I'm trying to calculate the phonon dispersion for STO. I ran successfully
> the ph.x code for a grid of q points. Then I'm trying to get the force
> constants in real space by using the q2r.x code, but I keep getting the
> following error:
> 
> from init : error #         1
>      q not allowed
> 
> First I thought it was due to some problem with the recovery mode, my
> calculation had been interrupted and then resumed, but then I ran a full
> calculation, and I got the same error when running q2r.x. I'm using the
> 4.3.2 version.
> The phonon input card I'm using is:
> 
> phonons of STO
>  &inputph
>   tr2_ph=1.0d-14,
>   ldisp=.true.,
>   nq1=4, nq2=4, nq3=4
>   amass(1)=87.62,
>   amass(2)=47.867,
>   amass(3)=15.9994,
>   epsil=.true.
>   prefix='sto',
>   fildyn='sto.dyn',
>  /
> 
> This runs successfully.
> The input for the q2r.x code is simply:
> 
> &input
>    fildyn='sto.dyn', zasr='simple', flfrc='sto.fc'
>  /
> 
> and then I get the "q not allowed" message.
> 
> Does anybody know what the problem could be?
> 
> Thank you in advance,
> 
> Alejandro
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------





--
-------------------------------------------------------------------
PH.D. candidate Peng Tao
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------


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From subacalvince at gmail.com  Mon Jul 16 15:29:38 2012
From: subacalvince at gmail.com (Nyaruanda Calvince)
Date: Mon, 16 Jul 2012 16:29:38 +0300
Subject: [Pw_forum] help
Message-ID: <CA+SHJWTOudYZfa9YKnwXxoc2xeM3nSGM70hnr3SP9CozeGanxA@mail.gmail.com>

am a new user .
am running mpirun -np 2 pw.x < Si.band.in > Si.band.out calculation. The
following is my output:

     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org",
     in publications or presentations arising from this work. More details
at
     http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

     Parallel version (MPI), running on     2 processors
     R & G space division:  proc/pool =    2

     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...
     Reading input from stdin

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from card_kpoints : error #         1
      error while reading automatic k points
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

Additionally, from my command line the following error messages appear
after the above run command.
may you help me please.
Regards
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From giovanni.cantele at spin.cnr.it  Mon Jul 16 15:35:04 2012
From: giovanni.cantele at spin.cnr.it (Giovanni Cantele)
Date: Mon, 16 Jul 2012 15:35:04 +0200
Subject: [Pw_forum] help
In-Reply-To: <CA+SHJWTOudYZfa9YKnwXxoc2xeM3nSGM70hnr3SP9CozeGanxA@mail.gmail.com>
References: <CA+SHJWTOudYZfa9YKnwXxoc2xeM3nSGM70hnr3SP9CozeGanxA@mail.gmail.com>
Message-ID: <0FE69C4B-D38E-429F-99E9-5ECBC61A7700@spin.cnr.it>


On Jul 16, 2012, at 3:29 PM, Nyaruanda Calvince wrote:

> am a new user .
> am running mpirun -np 2 pw.x < Si.band.in > Si.band.out calculation. The following is my output:
> 
>      This program is part of the open-source Quantum ESPRESSO suite
>      for quantum simulation of materials; please cite
>          "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>           URL http://www.quantum-espresso.org",
>      in publications or presentations arising from this work. More details at
>      http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
> 
>      Parallel version (MPI), running on     2 processors
>      R & G space division:  proc/pool =    2
> 
>      Current dimensions of program PWSCF are:
>      Max number of different atomic species (ntypx) = 10
>      Max number of k-points (npk) =  40000
>      Max angular momentum in pseudopotentials (lmaxx) =  3
>      Waiting for input...
>      Reading input from stdin
> 
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from card_kpoints : error #         1
>       error while reading automatic k points
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
>      stopping ...
> 
> Additionally, from my command line the following error messages appear after the above run command.
> may you help me please. 
> Regards
> _______________________________________________


You have incorrectly specified the k-point grid in the card K_POINTS, but it is difficult to say why, if you don't provide the input as well.

Giovanni




--

**** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it

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From flux_ray12 at 163.com  Mon Jul 16 15:35:12 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Mon, 16 Jul 2012 21:35:12 +0800 (CST)
Subject: [Pw_forum] help
In-Reply-To: <CA+SHJWTOudYZfa9YKnwXxoc2xeM3nSGM70hnr3SP9CozeGanxA@mail.gmail.com>
References: <CA+SHJWTOudYZfa9YKnwXxoc2xeM3nSGM70hnr3SP9CozeGanxA@mail.gmail.com>
Message-ID: <43a1ac02.1abb7.1388ffff2c6.Coremail.flux_ray12@163.com>

That means the parameter or format for the card K_POINTS {automatic} is wrong in your Si.band.in.
Please provide your input file, no person can point out the exact error due to the lack of information.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-07-16 21:29:38,"Nyaruanda Calvince" <subacalvince at gmail.com> wrote:

am a new user .
am running mpirun -np 2 pw.x < Si.band.in > Si.band.out calculation. The following is my output:


     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org",
     in publications or presentations arising from this work. More details at
     http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO


     Parallel version (MPI), running on     2 processors
     R & G space division:  proc/pool =    2


     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...
     Reading input from stdin


 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from card_kpoints : error #         1
      error while reading automatic k points
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


     stopping ...


Additionally, from my command line the following error messages appear after the above run command.
may you help me please. 
Regards
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From jdeslip at gmail.com  Mon Jul 16 17:14:27 2012
From: jdeslip at gmail.com (Jack Deslippe)
Date: Mon, 16 Jul 2012 08:14:27 -0700
Subject: [Pw_forum] ntg with Hybrid Calculations
Message-ID: <CAO9Dko=sUpSaPSaCNg2rv83ef6482PRp-qP9h3R_BJ5HiS70nA@mail.gmail.com>

Hi All,

Sorry if this has been asked before etc... I searched around but failed to
find a comment about this.

Is -ntg expected to work with hybrid functionals? It appears that when I
try, it successfully completes the the local xc iterations, but when it
starts on the hybrid calculation (with Quantum ESPRESSO 5.0.0), I see:

     task #         1
     from  tg_cfft  : error #         2
      inconsistent size

I'm running with 48 cores and "-ntg 2"

Below is the input file:

------------------

&control
prefix = 'silicon'
calculation = 'scf'
restart_mode = 'from_scratch'
wf_collect = .false.
disk_io = 'none'
tstress = .true.
tprnfor = .true.
outdir = './'
wfcdir = './'
pseudo_dir = './'
/
&system
ibrav = 0
celldm(1) = 10.2612
nat = 54
ntyp = 1
nbnd = 108
ecutwfc = 30
input_dft = 'hse'
/
&electrons
electron_maxstep = 100
conv_thr = 1.0d-10
mixing_mode = 'plain'
mixing_beta = 0.7
mixing_ndim = 8
diagonalization = 'david'
diago_david_ndim = 4
diago_full_acc = .true.
/
CELL_PARAMETERS
0.0 1.5 1.5
1.5 0.0 1.5
1.5 1.5 0.0
ATOMIC_SPECIES
Si  28.086  Si.UPF
ATOMIC_POSITIONS crystal
Si 0.0 0.0 0.0
Si 0.0833333333333 0.0833333333333 0.0833333333333
Si 0.0 0.0 0.333333333333
Si 0.0833333333333 0.0833333333333 0.416666666667
Si 0.0 0.0 0.666666666667
Si 0.0833333333333 0.0833333333333 0.75
Si 0.0 0.333333333333 0.0
Si 0.0833333333333 0.416666666667 0.0833333333333
Si 0.0 0.333333333333 0.333333333333
Si 0.0833333333333 0.416666666667 0.416666666667
Si 0.0 0.333333333333 0.666666666667
Si 0.0833333333333 0.416666666667 0.75
Si 0.0 0.666666666667 0.0
Si 0.0833333333333 0.75 0.0833333333333
Si 0.0 0.666666666667 0.333333333333
Si 0.0833333333333 0.75 0.416666666667
Si 0.0 0.666666666667 0.666666666667
Si 0.0833333333333 0.75 0.75
Si 0.333333333333 0.0 0.0
Si 0.416666666667 0.0833333333333 0.0833333333333
Si 0.333333333333 0.0 0.333333333333
Si 0.416666666667 0.0833333333333 0.416666666667
Si 0.333333333333 0.0 0.666666666667
Si 0.416666666667 0.0833333333333 0.75
Si 0.333333333333 0.333333333333 0.0
Si 0.416666666667 0.416666666667 0.0833333333333
Si 0.333333333333 0.333333333333 0.333333333333
Si 0.416666666667 0.416666666667 0.416666666667
Si 0.333333333333 0.333333333333 0.666666666667
Si 0.416666666667 0.416666666667 0.75
Si 0.333333333333 0.666666666667 0.0
Si 0.416666666667 0.75 0.0833333333333
Si 0.333333333333 0.666666666667 0.333333333333
Si 0.416666666667 0.75 0.416666666667
Si 0.333333333333 0.666666666667 0.666666666667
Si 0.416666666667 0.75 0.75
Si 0.666666666667 0.0 0.0
Si 0.75 0.0833333333333 0.0833333333333
Si 0.666666666667 0.0 0.333333333333
Si 0.75 0.0833333333333 0.416666666667
Si 0.666666666667 0.0 0.666666666667
Si 0.75 0.0833333333333 0.75
Si 0.666666666667 0.333333333333 0.0
Si 0.75 0.416666666667 0.0833333333333
Si 0.666666666667 0.333333333333 0.333333333333
Si 0.75 0.416666666667 0.416666666667
Si 0.666666666667 0.333333333333 0.666666666667
Si 0.75 0.416666666667 0.75
Si 0.666666666667 0.666666666667 0.0
Si 0.75 0.75 0.0833333333333
Si 0.666666666667 0.666666666667 0.333333333333
Si 0.75 0.75 0.416666666667
Si 0.666666666667 0.666666666667 0.666666666667
Si 0.75 0.75 0.75
K_POINTS automatic
1 1 1 1 1 1
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From koushik at jncasr.ac.in  Mon Jul 16 18:30:56 2012
From: koushik at jncasr.ac.in (Koushik Pal)
Date: Mon, 16 Jul 2012 22:00:56 +0530
Subject: [Pw_forum] Problem with visualizing wave function with appropriate
 sign (using "lsign") in a spin-orbit calculation
Message-ID: <CAMhFyZoxZyH-Lc08ZpvP0ego3enrZd_aT9ED+0AS9Qe+Z_KbMg@mail.gmail.com>

Dear sir,
 I am doing a *spin-orbit calculation* and I want to visualize the
wavefunction for a particular band with appropriate sign in it. I used the
'lisgn' variable with kpoint=1 (as in the scf.out file Gamma point is the
first point in the kpoint list) in the input file of pp.x, . After running
the pp.x, the program stops with an error "*from local_dos : error #
1       not available*". I searched the forum and got something on the same
issue but it did not help me. Can somebody please help me how to include
the sign of the wavefunction?  Here is my pp.in file

&inputpp
    prefix  = 'abc'
    outdir = 'tmp'
    filplot = 'gamma-density.dat'
    plot_num= 7
    kpoint=1
    kband=32
    lsign=.true.
 /
 &plot
    nfile = 1
    weight(1) = 1.0
    iflag = 3
    output_format = 3
    fileout = 'gamma-density1.xsf'
    nx=50,ny=50,nz=50

Thanks in advance.
=============
Koushik
Graduate student
JNCASR
Bangalore, India
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From dalcorso at sissa.it  Mon Jul 16 18:46:31 2012
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Mon, 16 Jul 2012 18:46:31 +0200
Subject: [Pw_forum] Problem with visualizing wave function
	with	appropriate sign (using "lsign") in a spin-orbit calculation
In-Reply-To: <CAMhFyZoxZyH-Lc08ZpvP0ego3enrZd_aT9ED+0AS9Qe+Z_KbMg@mail.gmail.com>
References: <CAMhFyZoxZyH-Lc08ZpvP0ego3enrZd_aT9ED+0AS9Qe+Z_KbMg@mail.gmail.com>
Message-ID: <1342457191.3808.21.camel@ulisse.cm.sissa.it>

This is a tricky question. At the moment in QE spinor wavefunctions that
are needed for spin-orbit are complex even at gamma. Therefore you
cannot extract the sign. That's the reason why this option is not
available and why there is not the gamma-only version of PW with
spinors.
Maybe somebody else has better ideas than me on how this point.

HTH,

Andrea


On Mon, 2012-07-16 at 22:00 +0530, Koushik Pal wrote:
> Dear sir,
>  I am doing a spin-orbit calculation and I want to visualize the
> wavefunction for a particular band with appropriate sign in it. I used
> the 'lisgn' variable with kpoint=1 (as in the scf.out file Gamma point
> is the first point in the kpoint list) in the input file of pp.x, .
> After running the pp.x, the program stops with an error "from
> local_dos : error #      1       not available". I searched the forum
> and got something on the same issue but it did not help me. Can
> somebody please help me how to include the sign of the wavefunction?
> Here is my pp.in file
> 
> &inputpp
>     prefix  = 'abc'
>     outdir = 'tmp'
>     filplot = 'gamma-density.dat'
>     plot_num= 7
>     kpoint=1
>     kband=32
>     lsign=.true.
>  /
>  &plot
>     nfile = 1
>     weight(1) = 1.0
>     iflag = 3
>     output_format = 3
>     fileout = 'gamma-density1.xsf'
>     nx=50,ny=50,nz=50
> 
> Thanks in advance.
> =============
> Koushik
> Graduate student
> JNCASR
> Bangalore, India
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Bonomea 265              Fax. 0039-040-3787249
I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it



From nicvok at freenet.de  Mon Jul 16 22:18:59 2012
From: nicvok at freenet.de (Nicki Frank Hinsche)
Date: Mon, 16 Jul 2012 22:18:59 +0200
Subject: [Pw_forum] Change Fermi energy in e-ph calculation
Message-ID: <404A370F-C9E9-4F08-9000-FFDBF6FA431A@freenet.de>

Dear all,

is there a possibility to adapt the Fermi energy (obtained by scf) to  
a different value for the
calculation of the Eliashberg function without hardcoding "efermig" in  
elph.f90?
The information on Ef is stored in the binary file "fildvscf",  
therefore cannot be easily manipulated.

The reason for my inquiry is, that I want to enable to calculate the  
Eliashberg function for a "doped"
semiconductor in a sense of rigid band shift. As Ef lies in or at the  
band gap for an undoped semiconductor,
the calculation of the Eliashberg function would make no sense there.

thanks a lot in advance,

Nicki

-------------------------------------------------------------
Nicki Frank Hinsche, Dipl. Phys.
Institute of physics - Theoretical physics,
Martin-Luther-University Halle-Wittenberg,
Von-Seckendorff-Platz 1, Room 0.20
D-06120 Halle/Saale, Germany
Tel.: ++49 345 5525434
-------------------------------------------------------------
Fellow of the International Max Planck Re-
search School-MPI for Microstructure Physics
-------------------------------------------------------------
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From giannozz at democritos.it  Mon Jul 16 22:58:50 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 16 Jul 2012 22:58:50 +0200
Subject: [Pw_forum] q not allowed when running q2r.x
In-Reply-To: <815f68742c7807669ce149e0dadac09b.squirrel@webmail.uic.edu>
References: <815f68742c7807669ce149e0dadac09b.squirrel@webmail.uic.edu>
Message-ID: <EC9112FD-25FC-41B4-A3A9-F89F14558801@democritos.it>


On Jul 15, 2012, at 22:27 , Alejandro R?bola wrote:

> Does anybody know what the problem could be?

in order to know, one needs the data to reproduce
the problem, provided it can be done on a small
machine in a reasonably short amount of time

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From mahdi_fn109 at yahoo.com  Tue Jul 17 10:51:26 2012
From: mahdi_fn109 at yahoo.com (Mahdi Faghih nasiri)
Date: Tue, 17 Jul 2012 01:51:26 -0700 (PDT)
Subject: [Pw_forum] Problem on compiling espresso-4.3.2
Message-ID: <1342515086.25072.YahooMailNeo@web43143.mail.sp1.yahoo.com>

Dear all,
?When I tried to compile espresso-4.3.2 with composer_xe_2011_sp1.6.233, the error "cannot find -lmkl_em64t_nothread" came out.
i use this command for installing QE from link below:
http://www.democritos.it/pipermail/pw_forum/2011-February/019440.html

./configure BLAS_LIBS="-L/tmp/espresso-4.3.2/install -L/opt/intel/mkl/lib/intel64 -lmkl_em64t_nothread" LAPACK_LIBS="-L/tmp/espresso-4.3.2/install -L/opt/intel/mkl/lib/intel64"
make all

i think mkl library changed in this version.
Please help me to resolve it, thank you in advance!


?
Mahdi Faghih nasiri
MSC,
Guilan University,
Rasht, Iran.
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From giovanni.cantele at spin.cnr.it  Tue Jul 17 11:02:43 2012
From: giovanni.cantele at spin.cnr.it (Giovanni Cantele)
Date: Tue, 17 Jul 2012 11:02:43 +0200
Subject: [Pw_forum] Problem on compiling espresso-4.3.2
In-Reply-To: <1342515086.25072.YahooMailNeo@web43143.mail.sp1.yahoo.com>
References: <1342515086.25072.YahooMailNeo@web43143.mail.sp1.yahoo.com>
Message-ID: <939DD828-8A53-4EEB-9124-06032BFEFD9C@spin.cnr.it>


On Jul 17, 2012, at 10:51 AM, Mahdi Faghih nasiri wrote:

> Dear all,
>  When I tried to compile espresso-4.3.2 with composer_xe_2011_sp1.6.233, the error "cannot find -lmkl_em64t_nothread" came out.
> i use this command for installing QE from link below:
> http://www.democritos.it/pipermail/pw_forum/2011-February/019440.html
> 
> ./configure BLAS_LIBS="-L/tmp/espresso-4.3.2/install -L/opt/intel/mkl/lib/intel64 -lmkl_em64t_nothread" LAPACK_LIBS="-L/tmp/espresso-4.3.2/install -L/opt/intel/mkl/lib/intel64"
> make all
> 
> i think mkl library changed in this version.
> Please help me to resolve it, thank you in advance!
> 
>  
> Mahdi Faghih nasiri
> MSC,
> Guilan University,
> Rasht, Iran.


try either of the following:
1) modify your make.sys according to the following lines:
LDFLAGS        = -static-intel -Wl,--start-group /opt/intel/mkl/lib/intel64//libmkl_intel_lp64.a /opt/intel/mkl/lib/intel64//libmkl_sequential.a /opt/intel/mkl/lib/intel64//libmkl_core.a -Wl,--end-group -lpthread -lm
BLAS_LIBS      =   -lmkl_intel_lp64  -lmkl_sequential -lmkl_core
LAPACK_LIBS    =

2) run the configure script using:
./configure LDFLAGS="-Wl,--start-group ${MKL_PATH}/libmkl_intel_lp64.a ${MKL_PATH}/libmkl_sequential.a ${MKL_PATH}/libmkl_core.a -Wl,--end-group -lpthread -lm"
where MKL_PATH=/opt/intel/mkl/lib/intel64

Anyhow, you can also refer to the following link:
http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/
where, by selecting the INTEL compiler/mkl version you use and your platform, the correct way of linking to mkl
is shown.

Giocanni


--

**** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it

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From giovanni.cantele at spin.cnr.it  Tue Jul 17 11:05:46 2012
From: giovanni.cantele at spin.cnr.it (Giovanni Cantele)
Date: Tue, 17 Jul 2012 11:05:46 +0200
Subject: [Pw_forum] Reciprocity of Supercells & BZ Sampling
In-Reply-To: <CAFgXaNiphjWkeOMTRZXUmC0xQBo1tuLN89-feToTtZkOFZpDQw@mail.gmail.com>
References: <CAFgXaNiphjWkeOMTRZXUmC0xQBo1tuLN89-feToTtZkOFZpDQw@mail.gmail.com>
Message-ID: <B1BD2EEB-63F2-473E-8C84-C28F94F94E83@spin.cnr.it>


On Jul 14, 2012, at 7:34 AM, yavar pour azar wrote:

> Dear QE users,
> 
> I have a conceptual problem with k-point sampling in supercells.
> 
> Suppose we have a simple cubic unit cell for the bulk, which it's electronic structure, total energy and etc... is calculated by n*n*n BZ Sampling.
> for example I can see band width and band curvature along k axis, and i will have max and min points for every band in different k_points such gamma, X, L,......
> 
> Now, if we want to make a n*n*n supercell from this unit cell, it is the  known fact that just gamma point calculations is enough.
> 
> Anyone can see following sentences in most QE tutorials; 
> "Increase supercell in real space by a factor N along a ; EXACTLY same results obtained by reducing  divisions in k mesh (in the new smaller BZ) by factor N"
> 
> This is the problem that I cant understand : when we substitute the unit cell by n*n*n  supercell ( k=0), the calculated bands with new sampling has no curvature and extension along k axis, because we have just a K point. Total Energy, probably is same as former unit cell (by integer factor), but if we will lose information about other aspects of electronic structure by this sampling?
> I would appreciate it if anyone can help me to understand this, or refer me to a source.
> 
> 
> 
> PS:  suppose supercell sustained no relaxation or similar changes, and we have just the two different scales from one infinite, periodic lattice.
> 
> 
> 
> Thanks in advance.
> 
> Yavar Taghipour Azar 
> PhD student
> Physics Group, AEOI, Tehran, Iran _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


If you build your supercell correctly, of course no information will be lost. 
Reverting to the example you did --namely, the same cubic structure simulated by using either a 1x1x1 unit cell with an NxNxN sampling
or an NxNxN supercell with a 1x1x1 sampling of the BZ-- you should consider that the band structure you plot in both cases is along a path
in the BZ that has NOTHING to do, in principle, with the sampling of the BZ itself.

The BZ sampling controls the convergence of the calculated properties (the ground-state charge density, for example) with respect to the BZ
integration.
The path along the BZ you use for band structure calculations is instead just a collection of k-points inside the BZ which you choose in order
to plot the band structure of a system. Of course, for the NxNxN supercell you expect to get a number of bands which is NxNxN times that
of the 1x1x1 calculation: this is the so called band structure folding. That means that your band structure, even though apparently
different, is just the same but described within a BZ which is NxNxN times smaller than for the 1x1x1 unit cell.
In conclusion, even for the NxNxN supercell, if you select a path in the BZ, you'll find the same electronic bands, gaps, curvature, even though
described within a different BZ.

Giovanni

--

**** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it

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From giovanni.cantele at spin.cnr.it  Tue Jul 17 11:24:41 2012
From: giovanni.cantele at spin.cnr.it (Giovanni Cantele)
Date: Tue, 17 Jul 2012 11:24:41 +0200
Subject: [Pw_forum] Problem on compiling espresso-4.3.2
In-Reply-To: <1342516794.81517.YahooMailNeo@web43136.mail.sp1.yahoo.com>
References: <1342515086.25072.YahooMailNeo@web43143.mail.sp1.yahoo.com>
	<939DD828-8A53-4EEB-9124-06032BFEFD9C@spin.cnr.it>
	<1342516794.81517.YahooMailNeo@web43136.mail.sp1.yahoo.com>
Message-ID: <9D69BA58-5C42-4058-A148-71F3A3210B6F@spin.cnr.it>

ok, the config.log contains the answer, but I guess you didn't
export MKL_PATH=/opt/intel/mkl/lib/intel64/
which is not mandatory, but if you don't do it, you cannot use the variable ${MKL_PATH} but you must specify
for example /opt/intel/mkl/lib/intel64/libmkl_intel_lp64.a, etc.

Giovanni


On Jul 17, 2012, at 11:19 AM, Mahdi Faghih nasiri wrote:

> Thank you.
> I've edit the make.sys, But the following occurs:
> 
> 
> 
> linux-0zne:~/Desktop/pwscf/espresso-4.3.2 # ./configure LDFLAGS="-Wl,--start-group ${MKL_PATH}/libmkl_intel_lp64.a ${MKL_PATH}/libmkl_sequential.a ${MKL_PATH}/libmkl_core.a -Wl,--end-group -lpthread -lm"checking build system type... x86_64-unknown-linux-gnu
> checking architecture... x86_64
> checking for ifort... ifort
> configure: WARNING: In the future, Autoconf will not detect cross-tools
> whose name does not start with the host triplet.  If you think this
> configuration is useful to you, please write to autoconf at gnu.org.
> checking for Fortran compiler default output file name... 
> configure: error: Fortran compiler cannot create executables
> See `config.log' for more details.
> 
> 
>  
> Mahdi Faghih nasiri
> MSC,
> Guilan University,
> Rasht, Iran.
> From: Giovanni Cantele <giovanni.cantele at spin.cnr.it>
> To: Mahdi Faghih nasiri <mahdi_fn109 at yahoo.com>; PWSCF Forum <pw_forum at pwscf.org> 
> Sent: Tuesday, July 17, 2012 1:32 PM
> Subject: Re: [Pw_forum] Problem on compiling espresso-4.3.2
> 
> 
> On Jul 17, 2012, at 10:51 AM, Mahdi Faghih nasiri wrote:
> 
>> Dear all,
>>  When I tried to compile espresso-4.3.2 with composer_xe_2011_sp1.6.233, the error "cannot find -lmkl_em64t_nothread" came out.
>> i use this command for installing QE from link below:
>> http://www.democritos.it/pipermail/pw_forum/2011-February/019440.html
>> 
>> ./configure BLAS_LIBS="-L/tmp/espresso-4.3.2/install -L/opt/intel/mkl/lib/intel64 -lmkl_em64t_nothread" LAPACK_LIBS="-L/tmp/espresso-4.3.2/install -L/opt/intel/mkl/lib/intel64"
>> make all
>> 
>> i think mkl library changed in this version.
>> Please help me to resolve it, thank you in advance!
>> 
>>  
>> Mahdi Faghih nasiri
>> MSC,
>> Guilan University,
>> Rasht, Iran.
> 
> 
> try either of the following:
> 1) modify your make.sys according to the following lines:
> LDFLAGS        = -static-intel -Wl,--start-group /opt/intel/mkl/lib/intel64//libmkl_intel_lp64.a /opt/intel/mkl/lib/intel64//libmkl_sequential.a /opt/intel/mkl/lib/intel64//libmkl_core.a -Wl,--end-group -lpthread -lm
> BLAS_LIBS      =   -lmkl_intel_lp64  -lmkl_sequential -lmkl_core
> LAPACK_LIBS    =
> 
> 2) run the configure script using:
> ./configure LDFLAGS="-Wl,--start-group ${MKL_PATH}/libmkl_intel_lp64.a ${MKL_PATH}/libmkl_sequential.a ${MKL_PATH}/libmkl_core.a -Wl,--end-group -lpthread -lm"
> where MKL_PATH=/opt/intel/mkl/lib/intel64
> 
> Anyhow, you can also refer to the following link:
> http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/
> where, by selecting the INTEL compiler/mkl version you use and your platform, the correct way of linking to mkl
> is shown.
> 
> Giocanni
> 
> 
> --
> 
> **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it
> 
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Scienze Fisiche
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> Phone: +39 081 676910
> Skype contact: giocan74
> 
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>                      http://www.nanomat.unina.it
> 
> 
> 




--

**** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it

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From konda.physics at gmail.com  Tue Jul 17 12:04:19 2012
From: konda.physics at gmail.com (Kondaiah Samudrala)
Date: Tue, 17 Jul 2012 15:34:19 +0530
Subject: [Pw_forum] Regarding QHA calculations
Message-ID: <CAKjMXpboYYMOJCtpBH-Q3c80RY=i5Nr2-Nkj_09tWA0f1doJkg@mail.gmail.com>

Dear all,

I completed successfully phonon dispersion calculations for cubic  (ibrav=
1) compound without any imaginary frequencies. When i am trying QHA
approximation .. i got below error

#   T         E_internal        F_vibration          Specific heat
(C_v)       Entropy
############################################################################################################
    0.00               NaN               NaN
NaN                   NaN
    5.00      0.0049960582               NaN
0.0670241577                   NaN
   10.00      0.0050013101               NaN
0.3147779147                   NaN
   15.00      0.0050196360               NaN
0.8999194212                   NaN
   20.00      0.0050613782               NaN
1.7727713167                   NaN
   25.00      0.0051333709               NaN
2.7850724371                   NaN
   30.00      0.0052378692               NaN
3.8091143892                   NaN
   35.00      0.0053739475               NaN
4.7713131374                   NaN
   40.00      0.0055390448               NaN
5.6388435196                   NaN
   45.00      0.0057299757               NaN
6.4027181221                   NaN
   50.00      0.0059434901               NaN
7.0663660164                   NaN
   55.00      0.0061765495               NaN
7.6388978030                   NaN

  Is theer any error in my calculations???

with regards
S.Appalakondaiah
UOH
Hyd
India
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From giannozz at democritos.it  Tue Jul 17 12:15:51 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 17 Jul 2012 12:15:51 +0200
Subject: [Pw_forum] Regarding QHA calculations
In-Reply-To: <CAKjMXpboYYMOJCtpBH-Q3c80RY=i5Nr2-Nkj_09tWA0f1doJkg@mail.gmail.com>
References: <CAKjMXpboYYMOJCtpBH-Q3c80RY=i5Nr2-Nkj_09tWA0f1doJkg@mail.gmail.com>
Message-ID: <1342520151.15684.11.camel@fe12lx.fisica.uniud.it>

At T=0, the code performs a division by zero. Start from T > 0.

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From pourazar2012 at gmail.com  Tue Jul 17 13:52:04 2012
From: pourazar2012 at gmail.com (yavar pour azar)
Date: Tue, 17 Jul 2012 16:22:04 +0430
Subject: [Pw_forum] Reciprocity of Supercells & BZ Sampling
In-Reply-To: <B1BD2EEB-63F2-473E-8C84-C28F94F94E83@spin.cnr.it>
References: <CAFgXaNiphjWkeOMTRZXUmC0xQBo1tuLN89-feToTtZkOFZpDQw@mail.gmail.com>
	<B1BD2EEB-63F2-473E-8C84-C28F94F94E83@spin.cnr.it>
Message-ID: <CAFgXaNggi3MpQGH0gou10COK2v9PsK4dM6iASa0B9+SnNCNcnA@mail.gmail.com>

Dear Professor Cantele.

Thanks for your time,consideration and detailed description.

Best regards.

Yavar



On Tue, Jul 17, 2012 at 1:35 PM, Giovanni Cantele <
giovanni.cantele at spin.cnr.it> wrote:

>
> On Jul 14, 2012, at 7:34 AM, yavar pour azar wrote:
>
> Dear QE users,
>
> I have a conceptual problem with k-point sampling in supercells.
>
> Suppose we have a simple cubic unit cell for the bulk, which it's
> electronic structure, total energy and etc... is calculated by n*n*n BZ
> Sampling.
> for example I can see band width and band curvature along k axis, and i
> will have max and min points for every band in different k_points such
> gamma, X, L,......
>
> Now, if we want to make a n*n*n supercell from this unit cell, it is the
> known fact that just gamma point calculations is enough.
>
> Anyone can see following sentences in most QE tutorials;
> "Increase supercell in real space by a factor N along a ; EXACTLY same
> results obtained by reducing  divisions in k mesh (in the new smaller BZ)
> by factor N"
>
> This is the problem that I cant understand : when we substitute the unit
> cell by n*n*n  supercell ( k=0), the calculated bands with new sampling has
> no curvature and extension along k axis, because we have just a K point.
> Total Energy, probably is same as former unit cell (by integer factor), but
> if we will lose information about other aspects of electronic structure by
> this sampling?
>
> I would appreciate it if anyone can help me to understand this, or refer
> me to a source.
>
>
> PS:  suppose supercell sustained no relaxation or similar changes, and we
> have just the two different scales from one infinite, periodic lattice.
>
>
>
> Thanks in advance.
>
> Yavar Taghipour Azar
> PhD student
> Physics Group, AEOI, Tehran, Iran
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> If you build your supercell correctly, of course no information will be
> lost.
> Reverting to the example you did --namely, the same cubic structure
> simulated by using either a 1x1x1 unit cell with an NxNxN sampling
> or an NxNxN supercell with a 1x1x1 sampling of the BZ-- you should
> consider that the band structure you plot in both cases is along a path
> in the BZ that has NOTHING to do, in principle, with the sampling of the
> BZ itself.
>
> The BZ sampling controls the convergence of the calculated properties (the
> ground-state charge density, for example) with respect to the BZ
> integration.
> The path along the BZ you use for band structure calculations is instead
> just a collection of k-points inside the BZ which you choose in order
> to plot the band structure of a system. Of course, for the NxNxN supercell
> you expect to get a number of bands which is NxNxN times that
> of the 1x1x1 calculation: this is the so called band structure folding.
> That means that your band structure, even though apparently
> different, is just the same but described within a BZ which is NxNxN times
> smaller than for the 1x1x1 unit cell.
> In conclusion, even for the NxNxN supercell, if you select a path in the
> BZ, you'll find the same electronic bands, gaps, curvature, even though
> described within a different BZ.
>
> Giovanni
>
> --
>
> **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Scienze Fisiche
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>                      http://www.nanomat.unina.it
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From thomas.gruber at physik.tu-freiberg.de  Tue Jul 17 13:52:50 2012
From: thomas.gruber at physik.tu-freiberg.de (Thomas Gruber)
Date: Tue, 17 Jul 2012 13:52:50 +0200
Subject: [Pw_forum] Why does Ewald sum calculation need so much RAM
Message-ID: <50055212.80102@physik.tu-freiberg.de>

Dear all,

I am doing phonon calculations with PAW pseudopotentials for systems 
with metallic character and wondering/have problems with the small RAM 
from the cluster. Example 1:  A system with 36 atoms (fcc) a have done 2 
scf calculation with an k-grid of 6x6x6 with occupation="tetrahedra" and 
"smearing" (generatet k points=12). For the phonon dispersion the 
symmetry get reduced and the

-- 
Thomas Gruber
Institut f?r Theoretische Physik
TU Bergakademie Freiberg
Leipziger Str. 23, 09599 Freiberg, Germany
Tel: +49 (0)3731 392006
Email: thomas.gruber at physik.tu-freiberg.de


From koushik at jncasr.ac.in  Tue Jul 17 15:16:40 2012
From: koushik at jncasr.ac.in (Koushik Pal)
Date: Tue, 17 Jul 2012 18:46:40 +0530
Subject: [Pw_forum] anomaly in phonon frequencies as obtained using DFPT
 (ph.x) in a spin-orbit calculation
Message-ID: <CAMhFyZpePHsw3Zh9OXmwVCgjfbSuNoZW6r-VZOsKg4Gy2JkZzQ@mail.gmail.com>

Dear sir,
  I calculated the phonon frequencies of a system using both the frozen
phonon method as well as DFPT (ph.x) in *fully relativistic regime
(spin-orbit interaction)* using QE verson 4.3. According to group theory
the 12 optical modes of the system are 2A1g + 2Eg + 2A2u +2Eu. I got
accurate results for the frequncies in the frozen phonon method (means, the
frequencies obeyed the symmetry rule as predicted by the group theory. Also
I visualized the eigenmodes which also agree well), but in the DFPT (linear
response theory), the obtained frequencies and eigenmodes do not obey the
above symmetry principles as predicted by group theory (though the
frequencies are near the frequencies as obtained in frozen-phonon method) .
It seems that the degeneracies in the frequencies are broken in DFPT. What
is the reason behind that? Please help. Please give references with
mathematical details (if available).

Thanks in advance.

=============
Koushik
Grad. student
Chemistry and Physics of Materials Unit
JNCASR
Bangalore , India
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From giannozz at democritos.it  Tue Jul 17 15:53:56 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 17 Jul 2012 15:53:56 +0200
Subject: [Pw_forum] Why does Ewald sum calculation need so much RAM
In-Reply-To: <50055212.80102@physik.tu-freiberg.de>
References: <50055212.80102@physik.tu-freiberg.de>
Message-ID: <1342533236.16360.11.camel@fe12lx.fisica.uniud.it>

On Tue, 2012-07-17 at 13:52 +0200, Thomas Gruber wrote:

> I am doing phonon calculations with PAW pseudopotentials for systems 
> with metallic character and wondering/have problems with the small RAM 
> from the cluster. Example 1:  A system with 36 atoms (fcc) a have done 2 
> scf calculation with an k-grid of 6x6x6 with occupation="tetrahedra" and 
> "smearing" (generatet k points=12). For the phonon dispersion the 
> symmetry get reduced and the

and the ... ?
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From dalcorso at sissa.it  Tue Jul 17 15:54:12 2012
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Tue, 17 Jul 2012 15:54:12 +0200
Subject: [Pw_forum] anomaly in phonon frequencies as obtained using	DFPT
	(ph.x) in a spin-orbit calculation
In-Reply-To: <CAMhFyZpePHsw3Zh9OXmwVCgjfbSuNoZW6r-VZOsKg4Gy2JkZzQ@mail.gmail.com>
References: <CAMhFyZpePHsw3Zh9OXmwVCgjfbSuNoZW6r-VZOsKg4Gy2JkZzQ@mail.gmail.com>
Message-ID: <1342533252.4490.15.camel@ulisse.cm.sissa.it>

Can you give more information? Which system is it? Does the scalar
relativistic phonon calculation have the correct symmetry?

A.

On Tue, 2012-07-17 at 18:46 +0530, Koushik Pal wrote:
> Dear sir,
>   I calculated the phonon frequencies of a system using both the
> frozen phonon method as well as DFPT (ph.x) in fully relativistic
> regime (spin-orbit interaction) using QE verson 4.3. According to
> group theory the 12 optical modes of the system are 2A1g + 2Eg + 2A2u
> +2Eu. I got accurate results for the frequncies in the frozen phonon
> method (means, the frequencies obeyed the symmetry rule as predicted
> by the group theory. Also I visualized the eigenmodes which also agree
> well), but in the DFPT (linear response theory), the obtained
> frequencies and eigenmodes do not obey the above symmetry principles
> as predicted by group theory (though the frequencies are near the
> frequencies as obtained in frozen-phonon method) . It seems that the
> degeneracies in the frequencies are broken in DFPT. What is the reason
> behind that? Please help. Please give references with mathematical
> details (if available).
> 
> Thanks in advance.
> 
> =============
> Koushik
> Grad. student
> Chemistry and Physics of Materials Unit
> JNCASR
> Bangalore , India
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Bonomea 265              Fax. 0039-040-3787249
I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it



From giannozz at democritos.it  Tue Jul 17 15:59:56 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 17 Jul 2012 15:59:56 +0200
Subject: [Pw_forum] Change Fermi energy in e-ph calculation
In-Reply-To: <404A370F-C9E9-4F08-9000-FFDBF6FA431A@freenet.de>
References: <404A370F-C9E9-4F08-9000-FFDBF6FA431A@freenet.de>
Message-ID: <1342533596.16360.16.camel@fe12lx.fisica.uniud.it>

On Mon, 2012-07-16 at 22:18 +0200, Nicki Frank Hinsche wrote:

> The information on Ef is stored in the binary file "fildvscf",
> therefore cannot be easily manipulated. 

it is also present in "data-file.xml", in readable form, but I don't
know if it is the one that is used by the phonon code or if it is
recalculated

P.

-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From konda.physics at gmail.com  Tue Jul 17 16:54:31 2012
From: konda.physics at gmail.com (Kondaiah Samudrala)
Date: Tue, 17 Jul 2012 20:24:31 +0530
Subject: [Pw_forum] Pw_forum Digest, Vol 61, Issue 49
In-Reply-To: <mailman.4013.1342533263.9401.pw_forum@pwscf.org>
References: <mailman.4013.1342533263.9401.pw_forum@pwscf.org>
Message-ID: <CAKjMXpampzcgqrVMZHs8EdRsWvk7ZbrHbJBygFhNSiShmFLOBQ@mail.gmail.com>

Thank you sir, i tried from 100K
 But my problem is still not solved.

  100.00      0.0088104354               NaN
10.2931041201                   NaN
  105.00      0.0091386637               NaN
10.4342538793                   NaN
  110.00      0.0094711026               NaN
10.5594404965                   NaN
  115.00      0.0098072828               NaN
10.6708830330                   NaN
  120.00      0.0101467994               NaN
10.7704462241                   NaN
  125.00      0.0104893018               NaN
10.8597023137                   NaN
  130.00      0.0108344853               NaN
10.9399816499                   NaN
  135.00      0.0111820840               NaN
11.0124140277                   NaN
  140.00      0.0115318651               NaN
11.0779624771                   NaN
  145.00      0.0118836238               NaN
11.1374509121                   NaN
  150.00      0.0122371799               NaN
11.1915868004                   NaN
  155.00      0.0125923738               NaN
11.2409797990                   NaN
  160.00      0.0129490636               NaN
11.2861571157                   NaN
  165.00      0.0133071235               NaN
11.3275762129                   NaN
  170.00      0.0136664408               NaN
11.3656353467                   NaN
  175.00      0.0140269147               NaN
11.4006823396                   NaN
  180.00      0.0143884549               NaN
11.4330219083                   NaN
  185.00      0.0147509798               NaN
11.4629218040                   NaN
  190.00      0.0151144161               NaN
11.4906179758                   NaN

Pls help me in this

with regards
S.Appalakondaiah
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From thomas.gruber at physik.tu-freiberg.de  Tue Jul 17 16:57:38 2012
From: thomas.gruber at physik.tu-freiberg.de (Thomas Gruber)
Date: Tue, 17 Jul 2012 16:57:38 +0200
Subject: [Pw_forum] Why does Ewald sum calculation need so much RAM
In-Reply-To: <mailman.4013.1342533263.9401.pw_forum@pwscf.org>
References: <mailman.4013.1342533263.9401.pw_forum@pwscf.org>
Message-ID: <50057D62.10807@physik.tu-freiberg.de>

sorry for the half mail. I came accidentally on the send instead of the 
save button. I stopped writing the mail because I did some more tests.
I was wondering why the required RAM for the same phonon calculation 
increase by a few times, where in one calculation the scf calculation 
was done with the keyword occupation="tetrahedra" and the other one with 
"smearing". I find out that the change was in using "-npool 12" when 
calling the mpirun. I wanted to use it to save cpu time, but then i get 
over the limit of my available RAM.
For example the the RAM usage of a band structure calculation increases 
from 114MB per core to 800MB per core (12 cores) by changing "-npool 1" 
to "-npool 12". Can this factor be estimated and is this one the same 
during the Ewald sum calculation of a phonon calculation? The Ewald sum 
calculation seems to be the part of the phonon calculation with the 
highest demand on RAM. For my phonon calculation at the gamma point of a 
system with 154 atoms (PAW pseudopotentials, orthorombic, kgrid:5x2x3, 
12 generated k-points) and "-npool 8" it needs over 250 GB RAM with 32 
cores (on one node). Is this realistic? Probably there is no keyword to 
set the maximum amount of available RAM in the input file or a way to 
estimate the RAM usage during the Ewald sum calculation.
For small systems this Ewald sum calculation is no big deal, but for 
this big system the scale up is pretty poor. With 16 cores it takes "3d 
6h" and on 32 cores it takes "2d 16h" and I have only 5 days on that 
cluster for one job. To calculate at least on representation I need 32 
cores for one job.
My problem is now that I have to use 32 cores per job, split into each 
representations (451) and use "-npool 1" to get these jobs running and 
it calculates the Ewald sum in each job, which actually should be 
calculated only once per q point. So 2/3 of my cpu time is consumed to 
calculate the Ewald sum 451 times instead of once. I have already over 1 
million CPUh and not even half of it is calculated. Is there a way to 
save cpu time?

Thanks in advance.

-- 
Thomas Gruber
Institut f?r Theoretische Physik
TU Bergakademie Freiberg
Leipziger Str. 23, 09599 Freiberg, Germany
Tel: +49 (0)3731 392006
Email: thomas.gruber at physik.tu-freiberg.de


From giannozz at democritos.it  Tue Jul 17 18:05:46 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 17 Jul 2012 18:05:46 +0200
Subject: [Pw_forum] Why does Ewald sum calculation need so much RAM
In-Reply-To: <50057D62.10807@physik.tu-freiberg.de>
References: <mailman.4013.1342533263.9401.pw_forum@pwscf.org>
	<50057D62.10807@physik.tu-freiberg.de>
Message-ID: <1342541146.16360.64.camel@fe12lx.fisica.uniud.it>

On Tue, 2012-07-17 at 16:57 +0200, Thomas Gruber wrote:

> For example the the RAM usage of a band structure calculation
> increases from 114MB per core to 800MB per core (12 cores) by 
> changing "-npool 1" to "-npool 12". 

k-point parallelization (aka pools) does not distribute memory, 
so each processors has a complete copy of (almost) all arrays.
Plane-wave parallelization instead distributes most memory (but 
not all). Other parallelization levels, not always present, 
distribute more computation and more arrays. With larger and
more complex calculations becoming available, more computation
and more arrays that used to be considered as irrelevant become
bottlenecks and need to be distributed as well. 

> The Ewald sum calculation seems to be the part of the phonon
> calculation with the highest demand on RAM [...] For small 
> systems this Ewald sum calculation is no big deal, but for this 
> big system the scale up is pretty poor. With 16 cores it takes "3d 6h"

are we talking about RAM, or about CPU, or both, and in which subroutine
exactly? I am quite sure that the Ewald term used to be rather
insignificant on both counts, at least for systems of tens of atoms
(e.g. C60). 

> My problem is now that I have to use 32 cores per job, split into each 
> representations (451) and use "-npool 1" to get these jobs running and 
> it calculates the Ewald sum in each job, which actually should be 
> calculated only once per q point. So 2/3 of my cpu time is consumed to 
> calculate the Ewald sum 451 times instead of once.

it was done in this way because the Ewald part has never been a
serious problem for anybody until now.

>  I have already over 1 
> million CPUh and not even half of it is calculated. Is there a way to 
> save cpu time?

sure there is, but you need to locate exactly where too much cpu time is
spent and where too much RAM is required. Then, we can discuss about
possible solutions. 

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From giannozz at democritos.it  Tue Jul 17 18:21:09 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 17 Jul 2012 18:21:09 +0200
Subject: [Pw_forum] supercell contraction and cell_factor parameter
In-Reply-To: <074D4C2D9374214C96A35794E0E7EAE0384D6772@BY2PRD0310MB389.namprd03.prod.outlook.com>
References: <074D4C2D9374214C96A35794E0E7EAE0384D6772@BY2PRD0310MB389.namprd03.prod.outlook.com>
Message-ID: <1342542069.16360.80.camel@fe12lx.fisica.uniud.it>

On Thu, 2012-07-12 at 15:54 +0000, Zhihui Zhu wrote:

> Can anyone please explain what the cell-factor variable represent?

it represent a not-so-smart solution to a purely technical problem.
the code computes interpolation tables in reciprocal space at the
beginning of the calculation. During a variable-cell optimization,
if the cell contracts in real space, it expands in reciprocal space.
Interpolation tables extend up to cell_factor*q_max, where q_max
is what is needed at the beginning of the calculation. It does not
affect in any way the results.

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From konda.physics at gmail.com  Tue Jul 17 20:01:01 2012
From: konda.physics at gmail.com (Kondaiah Samudrala)
Date: Tue, 17 Jul 2012 23:31:01 +0530
Subject: [Pw_forum] Regarding QHA
Message-ID: <CAKjMXpY5dZ4ZhDaJWq9CW=-8uEFbDCWYz_=n-XmY-Bng6txjEg@mail.gmail.com>

Thank you sir, i tried from 100K
 But my problem is still not solved.

  100.00      0.0088104354               NaN
10.2931041201
  NaN
  105.00      0.0091386637               NaN
10.4342538793                   NaN
  110.00      0.0094711026               NaN
10.5594404965                   NaN
  115.00      0.0098072828               NaN
10.6708830330                   NaN
  120.00      0.0101467994               NaN
10.7704462241                   NaN
  125.00      0.0104893018               NaN
10.8597023137                   NaN
  130.00      0.0108344853               NaN
10.9399816499                   NaN
  135.00      0.0111820840               NaN
11.0124140277                   NaN
  140.00      0.0115318651               NaN
11.0779624771                   NaN
  145.00      0.0118836238               NaN
11.1374509121                   NaN
  150.00      0.0122371799               NaN
11.1915868004                   NaN
  155.00      0.0125923738               NaN          11.2409797990
NaN
  160.00      0.0129490636               NaN
11.2861571157                   NaN
  165.00      0.0133071235               NaN
11.3275762129                   NaN
  170.00      0.0136664408               NaN
11.3656353467                   NaN
  175.00      0.0140269147               NaN
11.4006823396                   NaN
  180.00      0.0143884549               NaN
11.4330219083                   NaN
  185.00      0.0147509798               NaN
11.4629218040                   NaN
  190.00      0.0151144161               NaN
11.4906179758                   NaN

Pls help me in this

with regards
S.Appalakondaiah
Research Scholar
HCU
INDIA
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From flima at if.usp.br  Wed Jul 18 01:45:18 2012
From: flima at if.usp.br (Filipe Camargo Dalmatti Alves Lima)
Date: Tue, 17 Jul 2012 20:45:18 -0300
Subject: [Pw_forum] A question about the Ph.x code.
In-Reply-To: <CAGLNc7DOGXk6tKQx_ZWYcg3OYH0kn+FSj2sgALmuxe_OOnbk1A@mail.gmail.com>
References: <CAGLNc7DOGXk6tKQx_ZWYcg3OYH0kn+FSj2sgALmuxe_OOnbk1A@mail.gmail.com>
Message-ID: <CAGLNc7DKDLxo7m=UHPmedgBCHEfgMsEsWRH5bfiCTM2QwBk7wg@mail.gmail.com>

Dear QE users,

I am having a problem regarding the ph.x /dynmat codes,

I am investigating an oxide cluster containing metal ions using a
supercell approach (at least 6A of vaccum in all directions).
I couldn't converge the system without the "smearing" option (which is
normally used to treat metal systems) even though my system has a gap.
Due to the supercell approach, I have chosen only gamma k-point.

When I submit the ph.x, it finishes without any error or warning message.
However, when I calculate the dynmat to extract the results, it
doesn't show me the IR activity

I have attached below a part of the dynmat result.

Do you know any hints am I doing wrongly? I am using the QE version
5.0, US-PP and PBE Exc.

Thank you for your attention,
This is my first time investigating IR properties.
(I studied the examples within the QE folder and the tutorials in the
QE website. )

Best regards,
________________________________________
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics
Department, Nanomol Group, Brazil.

########################################################

    ...Force constants read
     ...epsilon and Z* not read (not found on file)
     A direction for q was not specified:TO-LO splitting will be absent
     Max |d(i,j)-d*(j,i)| =  0.058265
     Max |d(i,j)-d*(j,i)|/|d(i,j)|: 189.4604%

     Polarizability (A^3 units)
     multiply by 1.000000 for Clausius-Mossotti correction
         0.000000    0.000000    0.000000
         0.000000    0.000000    0.000000
         0.000000    0.000000    0.000000

     IR activities are in (D/A)^2/amu units

# mode   [cm-1]    [THz]      IR
    1   -214.16   -6.4202    0.0000
    2   -177.79   -5.3300    0.0000
    3   -148.87   -4.4631    0.0000
    4   -123.72   -3.7090    0.0000
    5   -110.65   -3.3173    0.0000
    6    -94.07   -2.8201    0.0000
    7    -88.21   -2.6445    0.0000
    8    -84.06   -2.5200    0.0000
    9    -76.63   -2.2974    0.0000
   10    -75.77   -2.2717    0.0000
   11    -68.21   -2.0449    0.0000
    ...
################## my ph.x input #################

 &inputph
  tr2_ph=1.0d-14,
  prefix='NbO_opt',
  amass(1)=15.99,
  amass(2)=92.92,
  epsil=.false.,
  trans=.true.,
  fildyn='NbO_opt.dyn',
  niter_ph=100,
  recover=.true.,
 /
 0.0 0.0 0.0

From bamideleibrahim at yahoo.com  Wed Jul 18 07:30:15 2012
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Tue, 17 Jul 2012 22:30:15 -0700 (PDT)
Subject: [Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*)
	failed".
Message-ID: <1342589415.45781.YahooMailNeo@web39406.mail.mud.yahoo.com>

Dear all,
? I am running scf calculation? and relax with the input file below: 

&control
? calculation = 'relax',
? prefix='MgSe'
? pseudo_dir='/home/adetunji/espresso-4.3/pslibrary.0.2.5/pz/PSEUDOPOTENTIALS',
? outdir='./',
/
&system
? ibrav=0,
? nat=8, 
? celldm(1)= 11.32, 
? ntyp=2, 
? ecutwfc = 50.0,
/
&electrons
?mixing_beta = 0.9
?conv_thr = 1.0d-9
/
&ions
ion_dynamics ='bfgs'
/
ATOMIC_SPECIES
Mg 24.305? Mg.pz-n-kjpaw.UPF
Se 78.963? Se.pz-n-kjpaw.UPF
CELL_PARAMETERS 
?? 0.000 0.49 0.49
?? 0.49? 0.000 0.49 
?? 0.49 0.49 0.000

ATOMIC_POSITIONS
Mg 0.00000000? 0.00000000?? 0.00000000
Mg 0.00000000? 0.50000000?? 0.50000000
Mg 0.50000000? 0.00000000?? 0.50000000
Mg 0.50000000? 0.50000000?? 0.00000000
Se 0.25000000? 0.25000000?? 0.25000000
Se 0.75000000? 0.75000000?? 0.25000000
Se 0.75000000? 0.25000000?? 0.75000000
Se 0.25000000? 0.75000000?? 0.75000000

K_POINTS (automatic)
6 6 6? 1 1 1

In both cases, it crashes and produces this error:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
???? from cdiaghg : error #??????? 42
???? diagonalization (ZHEGV*) failed
?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Can anybody in the house tell me what i have done wrong.
????????????????????????????????????????????????????? 


Adetunji Bamidele Ibrahim(PhD Student)
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.
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From zafartariq2003 at yahoo.com  Wed Jul 18 08:05:29 2012
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Tue, 17 Jul 2012 23:05:29 -0700 (PDT)
Subject: [Pw_forum] Re : Regarding QHA
In-Reply-To: <mailman.4033.1342589419.9401.pw_forum@pwscf.org>
Message-ID: <1342591529.78114.YahooMailClassic@web121402.mail.ne1.yahoo.com>

Dear Kondaiah Samudrala
your problem is due to some negative frequency. So change ( tr2_ph = 1.0d-10 ) to some other value i.e -10 to -14 and rerun ph.x and then try QHA. Hope your problem will resolve. 
Best of Luck

Muhammad Zafar

PhD Scholar

Department of Physics

The Islamia University of Bahawalpur,Pakistan

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From abmus007 at gmail.com  Wed Jul 18 08:29:43 2012
From: abmus007 at gmail.com (Abolore Musari)
Date: Wed, 18 Jul 2012 07:29:43 +0100
Subject: [Pw_forum] Band structure of Diamagnetic system
Message-ID: <CAOP21kLZiA_3tZxFGxFHD=tnSzkFXhMeWcCd7vS0sE0ZckrtMw@mail.gmail.com>

Dear QE users,
Sir I want to ask that when calculating the band structure for a
diamagnetic system for example FeS2. Is it  necessary to include a
'starting_magnetization="$value", for Fe atom in the system namelist as its
been done for ferromagnetic and anti-ferromagnetic systems and if YES what
is likely to be appropriate value for the starting_magnetization for the Fe
atom in the diamagnetic system.

thanks

Musari Abolore
ph.d student
UNAAB Nigeria
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From sohailphysics at yahoo.co.in  Wed Jul 18 10:23:38 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Wed, 18 Jul 2012 16:23:38 +0800 (SGT)
Subject: [Pw_forum] nscf calculation
Message-ID: <1342599818.42956.YahooMailClassic@web192205.mail.sg3.yahoo.com>

i am trying to run nscf calculation

it runs? but give message

I have run scf calculation and plotted band structure? and charge density
after that i copied the same scf into nscf and modified
calculation = nscf
occupations = tetrahedra
4 4 4 to now 12 12 12

should i take it or no,?? restart_mode = 'from_scratch',
?input file attached

----
?Max angular momentum in pseudopotentials (lmaxx) =? 3
???? Waiting for input...

???? Atomic positions and unit cell read from directory:
???? ./OUT/MoSb.save/
???? Nothing found: using input atomic positions and unit cell
--------------
&control
? calculation = 'nscf',
? restart_mode = 'from_scratch',
? prefix = 'MoSb',
? pseudo_dir = '/home/sandeep/espresso-4.2.1/pseudo',
? outdir = './OUT',
?/
?&system
? ibrav = 4, celldm(1) = 6.0281946, celldm(3) = 3.89, nat = 6, ntyp = 2,
? ecutwfc = 70,
? ecutrho = 300,
? nbnd = 20,
? occupations = 'tetrahedra',
? nspin = 2,
? starting_magnetization(1) = 0.5d0,
?/
?&electrons
? mixing_beta = 0.3,
? conv_thr = 1.0d-9,
?/
ATOMIC_SPECIES
Mo? 95.96? Mo.pw91-n-van.UPF
S?? 32.06? S.pw91-van_ak.UPF
ATOMIC_POSITIONS {crystal}
Mo? 0.33333333? 0.66666667? 0.25000000
Mo? 0.66666667? 0.33333333? 0.75000000
S?? 0.33333333? 0.66666667? 0.62000000
S?? 0.66666667? 0.33333333? 0.12000000
S?? 0.66666667? 0.33333333 -0.62000000
S?? 0.33333333? 0.66666667 -0.12000000
K_POINTS AUTOMATIC
12 12 12 1 1 1
---

Sohail
kku
Saudi Arabia
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From flux_ray12 at 163.com  Wed Jul 18 10:30:49 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Wed, 18 Jul 2012 16:30:49 +0800 (CST)
Subject: [Pw_forum] scf calculation crashed for "diagonalization
 (ZHEGV*) failed".
In-Reply-To: <1342589415.45781.YahooMailNeo@web39406.mail.mud.yahoo.com>
References: <1342589415.45781.YahooMailNeo@web39406.mail.mud.yahoo.com>
Message-ID: <213fd7ef.1e618.13899360149.Coremail.flux_ray12@163.com>

If there is no model/structure problem, then you can try to set diagonalization='cg' in &electrons namelist, although this method will decrease the calculation speed due to the poor parallel performance.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-07-18 13:30:15,"bamidele ibrahim" <bamideleibrahim at yahoo.com> wrote:

Dear all,
  I am running scf calculation  and relax with the input file below:

&control
  calculation = 'relax',
  prefix='MgSe'
  pseudo_dir='/home/adetunji/espresso-4.3/pslibrary.0.2.5/pz/PSEUDOPOTENTIALS',
  outdir='./',
/
&system
  ibrav=0,
  nat=8,
  celldm(1)= 11.32,
  ntyp=2,
  ecutwfc = 50.0,
/
&electrons
 mixing_beta = 0.9
 conv_thr = 1.0d-9
/
&ions
ion_dynamics ='bfgs'
/
ATOMIC_SPECIES
Mg 24.305  Mg.pz-n-kjpaw.UPF
Se 78.963  Se.pz-n-kjpaw.UPF
CELL_PARAMETERS
   0.000 0.49 0.49
   0.49  0.000 0.49
   0.49 0.49 0.000

ATOMIC_POSITIONS
Mg 0.00000000  0.00000000   0.00000000
Mg 0.00000000  0.50000000   0.50000000
Mg 0.50000000  0.00000000   0.50000000
Mg 0.50000000  0.50000000   0.00000000
Se 0.25000000  0.25000000   0.25000000
Se 0.75000000  0.75000000   0.25000000
Se 0.75000000  0.25000000   0.75000000
Se 0.25000000  0.75000000   0.75000000

K_POINTS (automatic)
6 6 6  1 1 1

In both cases, it crashes and produces this error:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from cdiaghg : error #        42
     diagonalization (ZHEGV*) failed
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Can anybody in the house tell me what i have done wrong.
                                                     


Adetunji Bamidele Ibrahim(PhD Student)
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.
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From bamideleibrahim at yahoo.com  Wed Jul 18 10:38:40 2012
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Wed, 18 Jul 2012 01:38:40 -0700 (PDT)
Subject: [Pw_forum] Clarification on how to compute elastic constants
Message-ID: <1342600720.13495.YahooMailNeo@web39402.mail.mud.yahoo.com>

?Dear all,
Please, i need some clarification on the following? issues on how to calculate elastic constants, 
1. When performing the calculation, is it correct to set 'calculation=scf' or 'relax'? For either of the two cases, can? anybody in the house give me an explanation on it.
2. since we need to set ibrav=0, and define explicitly the primitive vectors for any crystal we are dealing with then, is it necessary to define all the atoms in the primitive cell of the crystal explicitly?? for example ZnSe which has 8 atomic positions if ibrav=0 and this in the cubic B3 phase. 
3. Do i need to use cell dynamics or ion dynamics for the optimization of the cell?

I will be delighted if anybody can give me an explanation on this issue.

Thanks

?
Adetunji Bamidele Ibrahim(PhD Student)
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.
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From bamideleibrahim at yahoo.com  Wed Jul 18 10:41:23 2012
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Wed, 18 Jul 2012 01:41:23 -0700 (PDT)
Subject: [Pw_forum] scf calculation crashed for "diagonalization
	(ZHEGV*) failed".
In-Reply-To: <213fd7ef.1e618.13899360149.Coremail.flux_ray12@163.com>
References: <1342589415.45781.YahooMailNeo@web39406.mail.mud.yahoo.com>
	<213fd7ef.1e618.13899360149.Coremail.flux_ray12@163.com>
Message-ID: <1342600883.74010.YahooMailNeo@web39405.mail.mud.yahoo.com>

Dear GAO,
? Thanks for the explanation, i have tried it , it produced the same result.

?
Adetunji Bamidele Ibrahim(PhD Student)
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.


________________________________
 From: GAO Zhe <flux_ray12 at 163.com>
To: PWSCF Forum <pw_forum at pwscf.org> 
Sent: Wednesday, July 18, 2012 10:30 AM
Subject: Re: [Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed".
 

If there is no model/structure problem, then you can try to set diagonalization='cg' in&electrons namelist, although this method will decrease the calculation speed due to the poor parallel performance.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
?
At 2012-07-18 13:30:15,"bamidele?ibrahim"?<bamideleibrahim at yahoo.com> wrote:

Dear all,
>? I am running scf calculation? and relax with the input file below: 
>&control
>? calculation = 'relax',
>? prefix='MgSe'
>? pseudo_dir='/home/adetunji/espresso-4.3/pslibrary.0.2.5/pz/PSEUDOPOTENTIALS',
>? outdir='./',
>/
>&system
>? ibrav=0,
>? nat=8, 
>? celldm(1)= 11.32, 
>? ntyp=2, 
>? ecutwfc = 50.0,
>/
>&electrons
>?mixing_beta = 0.9
>?conv_thr = 1.0d-9
>/
>&ions
>ion_dynamics ='bfgs'
>/
>ATOMIC_SPECIES
>Mg 24.305? Mg.pz-n-kjpaw.UPF
>Se 78.963? Se.pz-n-kjpaw.UPF
>CELL_PARAMETERS 
>?? 0.000 0.49 0.49
>?? 0.49? 0.000 0.49 
>?? 0.49 0.49 0.000
>
>ATOMIC_POSITIONS
>Mg 0.00000000?
 0.00000000?? 0.00000000
>Mg 0.00000000? 0.50000000?? 0.50000000
>Mg 0.50000000? 0.00000000?? 0.50000000
>Mg 0.50000000? 0.50000000?? 0.00000000
>Se 0.25000000? 0.25000000?? 0.25000000
>Se 0.75000000? 0.75000000?? 0.25000000
>Se 0.75000000? 0.25000000?? 0.75000000
>Se 0.25000000? 0.75000000?? 0.75000000
>
>K_POINTS (automatic)
>6 6 6? 1 1 1
>
>In both cases, it crashes and produces this error:
>
>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>???? from cdiaghg : error #??????? 42
>???? diagonalization (ZHEGV*) failed
>?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>Can anybody in the house tell me what i have done
 wrong.
>????????????????????????????????????????????????????? 
>
>
>Adetunji Bamidele Ibrahim(PhD Student)
>Department of physics,University of Agriculture,
>Abeokuta, Ogun State,Nigeria.


_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From flux_ray12 at 163.com  Wed Jul 18 11:16:17 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Wed, 18 Jul 2012 17:16:17 +0800 (CST)
Subject: [Pw_forum] scf calculation crashed for "diagonalization
 (ZHEGV*) failed".
In-Reply-To: <1342600883.74010.YahooMailNeo@web39405.mail.mud.yahoo.com>
References: <1342589415.45781.YahooMailNeo@web39406.mail.mud.yahoo.com>
	<213fd7ef.1e618.13899360149.Coremail.flux_ray12@163.com>
	<1342600883.74010.YahooMailNeo@web39405.mail.mud.yahoo.com>
Message-ID: <26d57252.1f6f9.138995fa2ad.Coremail.flux_ray12@163.com>

By the way, do you want to calculate the FCC structure (diamond structure)? If so, your model/structure is definitely wrong~
For FCC, the primitive cell contains two atoms, one at (0,0,0), another at (1/4,1/4,1/4), and the cell vectors should be as you used.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-07-18 16:41:23,"bamidele ibrahim" <bamideleibrahim at yahoo.com> wrote:

Dear GAO,
  Thanks for the explanation, i have tried it , it produced the same result.

 
Adetunji Bamidele Ibrahim(PhD Student)
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.


From: GAO Zhe <flux_ray12 at 163.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Wednesday, July 18, 2012 10:30 AM
Subject: Re: [Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed".



If there is no model/structure problem, then you can try to set diagonalization='cg' in &electrons namelist, although this method will decrease the calculation speed due to the poor parallel performance.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-07-18 13:30:15,"bamidele ibrahim" <bamideleibrahim at yahoo.com> wrote:

Dear all,
  I am running scf calculation  and relax with the input file below:

&control
  calculation = 'relax',
  prefix='MgSe'
  pseudo_dir='/home/adetunji/espresso-4.3/pslibrary.0.2.5/pz/PSEUDOPOTENTIALS',
  outdir='./',
/
&system
  ibrav=0,
  nat=8,
  celldm(1)= 11.32,
  ntyp=2,
  ecutwfc = 50.0,
/
&electrons
 mixing_beta = 0.9
 conv_thr = 1.0d-9
/
&ions
ion_dynamics ='bfgs'
/
ATOMIC_SPECIES
Mg 24.305  Mg.pz-n-kjpaw.UPF
Se 78.963  Se.pz-n-kjpaw.UPF
CELL_PARAMETERS
   0.000 0.49 0.49
   0.49  0.000 0.49
   0.49 0.49 0.000

ATOMIC_POSITIONS
Mg 0.00000000  0.00000000   0.00000000
Mg 0.00000000  0.50000000   0.50000000
Mg 0.50000000  0.00000000   0.50000000
Mg 0.50000000  0.50000000   0.00000000
Se 0.25000000  0.25000000   0.25000000
Se 0.75000000  0.75000000   0.25000000
Se 0.75000000  0.25000000   0.75000000
Se 0.25000000  0.75000000   0.75000000

K_POINTS (automatic)
6 6 6  1 1 1

In both cases, it crashes and produces this error:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from cdiaghg : error #        42
     diagonalization (ZHEGV*) failed
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Can anybody in the house tell me what i have done wrong.
                                                     


Adetunji Bamidele Ibrahim(PhD Student)
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.




_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


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From caperott at ucs.br  Wed Jul 18 13:42:10 2012
From: caperott at ucs.br (Claudio Perottoni)
Date: Wed, 18 Jul 2012 08:42:10 -0300
Subject: [Pw_forum] A question about the Ph.x code.
In-Reply-To: <CAGLNc7DKDLxo7m=UHPmedgBCHEfgMsEsWRH5bfiCTM2QwBk7wg@mail.gmail.com>
References: <CAGLNc7DOGXk6tKQx_ZWYcg3OYH0kn+FSj2sgALmuxe_OOnbk1A@mail.gmail.com>
	<CAGLNc7DKDLxo7m=UHPmedgBCHEfgMsEsWRH5bfiCTM2QwBk7wg@mail.gmail.com>
Message-ID: <5006A112.5060308@ucs.br>

Dear Filipe,

Try setting  epsil=.true. in your input file.

Regards,

Claudio


On 17-Jul-12 20:45, Filipe Camargo Dalmatti Alves Lima wrote:
> Dear QE users,
>
> I am having a problem regarding the ph.x /dynmat codes,
>
> I am investigating an oxide cluster containing metal ions using a
> supercell approach (at least 6A of vaccum in all directions).
> I couldn't converge the system without the "smearing" option (which is
> normally used to treat metal systems) even though my system has a gap.
> Due to the supercell approach, I have chosen only gamma k-point.
>
> When I submit the ph.x, it finishes without any error or warning message.
> However, when I calculate the dynmat to extract the results, it
> doesn't show me the IR activity
>
> I have attached below a part of the dynmat result.
>
> Do you know any hints am I doing wrongly? I am using the QE version
> 5.0, US-PP and PBE Exc.
>
> Thank you for your attention,
> This is my first time investigating IR properties.
> (I studied the examples within the QE folder and the tutorials in the
> QE website. )
>
> Best regards,
> ________________________________________
> Filipe Camargo Dalmatti Alves Lima
> PhD Student
> University of S?o Paulo, Physics Institute, Materials Physics
> Department, Nanomol Group, Brazil.
>
> ########################################################
>
>      ...Force constants read
>       ...epsilon and Z* not read (not found on file)
>       A direction for q was not specified:TO-LO splitting will be absent
>       Max |d(i,j)-d*(j,i)| =  0.058265
>       Max |d(i,j)-d*(j,i)|/|d(i,j)|: 189.4604%
>
>       Polarizability (A^3 units)
>       multiply by 1.000000 for Clausius-Mossotti correction
>           0.000000    0.000000    0.000000
>           0.000000    0.000000    0.000000
>           0.000000    0.000000    0.000000
>
>       IR activities are in (D/A)^2/amu units
>
> # mode   [cm-1]    [THz]      IR
>      1   -214.16   -6.4202    0.0000
>      2   -177.79   -5.3300    0.0000
>      3   -148.87   -4.4631    0.0000
>      4   -123.72   -3.7090    0.0000
>      5   -110.65   -3.3173    0.0000
>      6    -94.07   -2.8201    0.0000
>      7    -88.21   -2.6445    0.0000
>      8    -84.06   -2.5200    0.0000
>      9    -76.63   -2.2974    0.0000
>     10    -75.77   -2.2717    0.0000
>     11    -68.21   -2.0449    0.0000
>      ...
> ################## my ph.x input #################
>
>   &inputph
>    tr2_ph=1.0d-14,
>    prefix='NbO_opt',
>    amass(1)=15.99,
>    amass(2)=92.92,
>    epsil=.false.,
>    trans=.true.,
>    fildyn='NbO_opt.dyn',
>    niter_ph=100,
>    recover=.true.,
>   /
>   0.0 0.0 0.0
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
******************************************************************
Dr. Cl?udio A. Perottoni

Universidade de Caxias do Sul
Centro de Ci?ncias Exatas e Tecnologia
Rua Francisco Get?lio Vargas, 1130
95070-560 Caxias do Sul - RS - Brazil
Phone: +55 54 3218 2607
http://www.ucs.br/ccet/defq/caperott/
******************************************************************




From degironc at sissa.it  Wed Jul 18 15:15:07 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 18 Jul 2012 15:15:07 +0200
Subject: [Pw_forum] Clarification on how to compute elastic constants
In-Reply-To: <1342600720.13495.YahooMailNeo@web39402.mail.mud.yahoo.com>
References: <1342600720.13495.YahooMailNeo@web39402.mail.mud.yahoo.com>
Message-ID: <20120718151507.Horde.uxG2Eh8V4mxQBrbblb7hOZA@webmail.sissa.it>

Dear Ibrahim

     1. in order to calculate the elastic constants you need to start  
from the equilibrium geometry (fully relaxed, both with respect to  
internal degrees of freedom and w.r.t the cell shape) and apply a  
deformation of the cell (say +/- 0.5 or 1.0 %,... you should check  
that you are in the linear regime) and then keeping fixed the cell  
shape relax the internal coordinates. Considering a large enough  
number of independent deformations you should be able to extract the  
elastic constants from the stress-strain relationship.You need to  
perform the internal relaxation because the cell deformation and the  
internal degrees of freedom are in general coupled.

     2. The input of pwscf must contain explicitly all the atoms  
present in the unit cell defined by the fundamental lattice vectors of  
your unit cell. If you use ibrav=0, these are the ones you define in  
the CELL_PARAMETERS card...
      as for the example of ZnSe it contains 8 atoms if your unit cell  
is the simple cubic one but only 2 if the fcc fundamental lattice  
vectors are considered.

      3. As for the full structural optimization... vc-relax should  
work well (check carefully that stress calculation in converged).  For  
simple systems, such as SC, FCC, or BCC, a lattice parameter scan + an  
Equation of State fit (ev.x) should also work fine.

      hope this helps,

stefano


Quoting bamidele ibrahim <bamideleibrahim at yahoo.com>:
> ?Dear all,
> Please, i need some clarification on the following? issues on how to  
> calculate elastic constants,
> 1. When performing the calculation, is it correct to set  
> 'calculation=scf' or 'relax'? For either of the two cases, can?  
> anybody in the house give me an explanation on it.
> 2. since we need to set ibrav=0, and define explicitly the primitive  
> vectors for any crystal we are dealing with then, is it necessary to  
> define all the atoms in the primitive cell of the crystal  
> explicitly?? for example ZnSe which has 8 atomic positions if  
> ibrav=0 and this in the cubic B3 phase.
> 3. Do i need to use cell dynamics or ion dynamics for the  
> optimization of the cell?
>
> I will be delighted if anybody can give me an explanation on this issue.
>
> Thanks
>
> ?
> Adetunji Bamidele Ibrahim(PhD Student)
> Department of physics,University of Agriculture,
> Abeokuta, Ogun State,Nigeria.



From flima at if.usp.br  Wed Jul 18 15:43:24 2012
From: flima at if.usp.br (Filipe Camargo Dalmatti Alves Lima)
Date: Wed, 18 Jul 2012 10:43:24 -0300
Subject: [Pw_forum] A question about the Ph.x code.
In-Reply-To: <5006A112.5060308@ucs.br>
References: <CAGLNc7DOGXk6tKQx_ZWYcg3OYH0kn+FSj2sgALmuxe_OOnbk1A@mail.gmail.com>
	<CAGLNc7DKDLxo7m=UHPmedgBCHEfgMsEsWRH5bfiCTM2QwBk7wg@mail.gmail.com>
	<5006A112.5060308@ucs.br>
Message-ID: <CAGLNc7CuVBc8Jsym9zPDM6ccvDnCoTye2VJ3sUsd6KT5To+c1A@mail.gmail.com>

Dear Claudio,

When I set epsil=.true., I receive this error:

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from phq_readin : error #         1
     no elec. field with metals
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

I think it is happening because I am using typical configuration to
converge metallic systems
(occupations='smearing',    smearing='gaussian',  degauss=0.008,)
Otherwise, I can't achieve the scf convergence.

Best regards,

-- 
_________________________________________
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics
Department, Nanomol Group, Brazil.
Phones:    (11) 3091-6881  (USP)
                (11) 8249-4628 (TIM)



On Wed, Jul 18, 2012 at 8:42 AM, Claudio Perottoni <caperott at ucs.br> wrote:
> Dear Filipe,
>
> Try setting  epsil=.true. in your input file.
>
> Regards,
>
> Claudio
>
>
> On 17-Jul-12 20:45, Filipe Camargo Dalmatti Alves Lima wrote:
>> Dear QE users,
>>
>> I am having a problem regarding the ph.x /dynmat codes,
>>
>> I am investigating an oxide cluster containing metal ions using a
>> supercell approach (at least 6A of vaccum in all directions).
>> I couldn't converge the system without the "smearing" option (which is
>> normally used to treat metal systems) even though my system has a gap.
>> Due to the supercell approach, I have chosen only gamma k-point.
>>
>> When I submit the ph.x, it finishes without any error or warning message.
>> However, when I calculate the dynmat to extract the results, it
>> doesn't show me the IR activity
>>
>> I have attached below a part of the dynmat result.
>>
>> Do you know any hints am I doing wrongly? I am using the QE version
>> 5.0, US-PP and PBE Exc.
>>
>> Thank you for your attention,
>> This is my first time investigating IR properties.
>> (I studied the examples within the QE folder and the tutorials in the
>> QE website. )
>>
>> Best regards,
>> ________________________________________
>> Filipe Camargo Dalmatti Alves Lima
>> PhD Student
>> University of S?o Paulo, Physics Institute, Materials Physics
>> Department, Nanomol Group, Brazil.
>>
>> ########################################################
>>
>>      ...Force constants read
>>       ...epsilon and Z* not read (not found on file)
>>       A direction for q was not specified:TO-LO splitting will be absent
>>       Max |d(i,j)-d*(j,i)| =  0.058265
>>       Max |d(i,j)-d*(j,i)|/|d(i,j)|: 189.4604%
>>
>>       Polarizability (A^3 units)
>>       multiply by 1.000000 for Clausius-Mossotti correction
>>           0.000000    0.000000    0.000000
>>           0.000000    0.000000    0.000000
>>           0.000000    0.000000    0.000000
>>
>>       IR activities are in (D/A)^2/amu units
>>
>> # mode   [cm-1]    [THz]      IR
>>      1   -214.16   -6.4202    0.0000
>>      2   -177.79   -5.3300    0.0000
>>      3   -148.87   -4.4631    0.0000
>>      4   -123.72   -3.7090    0.0000
>>      5   -110.65   -3.3173    0.0000
>>      6    -94.07   -2.8201    0.0000
>>      7    -88.21   -2.6445    0.0000
>>      8    -84.06   -2.5200    0.0000
>>      9    -76.63   -2.2974    0.0000
>>     10    -75.77   -2.2717    0.0000
>>     11    -68.21   -2.0449    0.0000
>>      ...
>> ################## my ph.x input #################
>>
>>   &inputph
>>    tr2_ph=1.0d-14,
>>    prefix='NbO_opt',
>>    amass(1)=15.99,
>>    amass(2)=92.92,
>>    epsil=.false.,
>>    trans=.true.,
>>    fildyn='NbO_opt.dyn',
>>    niter_ph=100,
>>    recover=.true.,
>>   /
>>   0.0 0.0 0.0
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
> --
> ******************************************************************
> Dr. Cl?udio A. Perottoni
>
> Universidade de Caxias do Sul
> Centro de Ci?ncias Exatas e Tecnologia
> Rua Francisco Get?lio Vargas, 1130
> 95070-560 Caxias do Sul - RS - Brazil
> Phone: +55 54 3218 2607
> http://www.ucs.br/ccet/defq/caperott/
> ******************************************************************
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

From giannozz at democritos.it  Wed Jul 18 15:48:31 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Jul 2012 15:48:31 +0200
Subject: [Pw_forum] A question about the Ph.x code.
In-Reply-To: <5006A112.5060308@ucs.br>
References: <CAGLNc7DOGXk6tKQx_ZWYcg3OYH0kn+FSj2sgALmuxe_OOnbk1A@mail.gmail.com>
	<CAGLNc7DKDLxo7m=UHPmedgBCHEfgMsEsWRH5bfiCTM2QwBk7wg@mail.gmail.com>
	<5006A112.5060308@ucs.br>
Message-ID: <D5CEA728-2FF5-468F-8758-03629785974A@democritos.it>


On Jul 18, 2012, at 13:42 , Claudio Perottoni wrote:

> Try setting  epsil=.true. in your input file.

it is not sufficient: the code cannot calculate the dielectric
tensor for what appears to be a metal (even if it isn't).
A simple solution might be to perform a calculation with
fixed occupancies read from input, starting from the
self-consistent charge density, before the phonon
calculation

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Wed Jul 18 15:52:26 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Jul 2012 15:52:26 +0200
Subject: [Pw_forum] Band structure of Diamagnetic system
In-Reply-To: <CAOP21kLZiA_3tZxFGxFHD=tnSzkFXhMeWcCd7vS0sE0ZckrtMw@mail.gmail.com>
References: <CAOP21kLZiA_3tZxFGxFHD=tnSzkFXhMeWcCd7vS0sE0ZckrtMw@mail.gmail.com>
Message-ID: <0E36D414-C97F-4DAB-A4A9-DF082F1816F1@democritos.it>


On Jul 18, 2012, at 8:29 , Abolore Musari wrote:

> Sir I want to ask that when calculating the band structure for a  
> diamagnetic system for example FeS2. Is it  necessary to include a  
> 'starting_magnetization="$value"

if you have the self-consistent charge density and you want to  
calculate bands,
you do not need to specify anything for "starting_magnetization": it  
will be ignored
anyway

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Wed Jul 18 15:55:30 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Jul 2012 15:55:30 +0200
Subject: [Pw_forum] scf calculation crashed for "diagonalization
	(ZHEGV*) failed".
In-Reply-To: <1342589415.45781.YahooMailNeo@web39406.mail.mud.yahoo.com>
References: <1342589415.45781.YahooMailNeo@web39406.mail.mud.yahoo.com>
Message-ID: <FD14F05C-747E-4F8C-9E2E-77856E9C0A22@democritos.it>


On Jul 18, 2012, at 7:30 , bamidele ibrahim wrote:

>      from cdiaghg : error #        42
>      diagonalization (ZHEGV*) failed

you should first of all check your atomic positions: they look
strange to me. This message is very often a consequence
of strange input atomic positions, such as almost overlapping
atoms

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From thomas.gruber at physik.tu-freiberg.de  Wed Jul 18 16:12:06 2012
From: thomas.gruber at physik.tu-freiberg.de (Thomas Gruber)
Date: Wed, 18 Jul 2012 16:12:06 +0200
Subject: [Pw_forum] Why does Ewald sum calculation need so much RAM
In-Reply-To: <mailman.4033.1342589419.9401.pw_forum@pwscf.org>
References: <mailman.4033.1342589419.9401.pw_forum@pwscf.org>
Message-ID: <5006C436.5060801@physik.tu-freiberg.de>


> Message-ID: <1342541146.16360.64.camel at fe12lx.fisica.uniud.it>
> are we talking about RAM, or about CPU, or both, and in which 
> subroutine exactly?
To save CPU time it gets a RAM problem because this is the limiting factor.
> it was done in this way because the Ewald part has never been a 
> serious problem for anybody until now.
It looks like it is in my case.
> sure there is, but you need to locate exactly where too much cpu time 
> is spent and where too much RAM is required. Then, we can discuss 
> about possible solutions. P.
I attached a graphic of the RAM usage for an "-npool 8" calculation and 
added the output file named after the time stamp from the graphic. I 
can't tell you more than it takes almost three days to print the line " 
PHONON       :     2d   18h22m CPU        2d   21h55m WALL" and it uses 
4 times more RAM than in the scf iterations afterward. Unfortunately the 
scaling is not very good:
>   With 16 cores it takes "3d
> 6h" and on 32 cores it takes "2d 16h" and I have only 5 days on that
> cluster for one job.
What is the program doing during this time and can I do it only once and 
give it as input for the other splited phonon calculations?
I tried to use the "-npool" flag, but I can't use it because my RAM is 
to "small" (64GB+, some nodes have more). To save time I like to put 
more representations in one job, but because of this time demanding step 
I get over the time limit of 5 days. So i have to repeat this 
calculations 450 times instead of once.

Thanks in advance.

-- 
Thomas Gruber
Institut f?r Theoretische Physik
TU Bergakademie Freiberg
Leipziger Str. 23, 09599 Freiberg, Germany
Tel: +49 (0)3731 392006
Email:thomas.gruber at physik.tu-freiberg.de

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From laura.zhu at mail.utoronto.ca  Wed Jul 18 16:15:41 2012
From: laura.zhu at mail.utoronto.ca (Zhihui Zhu)
Date: Wed, 18 Jul 2012 14:15:41 +0000
Subject: [Pw_forum] supercell contraction and cell_factor parameter
In-Reply-To: <1342542069.16360.80.camel@fe12lx.fisica.uniud.it>
References: <074D4C2D9374214C96A35794E0E7EAE0384D6772@BY2PRD0310MB389.namprd03.prod.outlook.com>,
	<1342542069.16360.80.camel@fe12lx.fisica.uniud.it>
Message-ID: <074D4C2D9374214C96A35794E0E7EAE03C638592@BY2PRD0310MB389.namprd03.prod.outlook.com>

Thank you for your reply Prof. Giannozzi!
________________________________________
From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] on behalf of Paolo Giannozzi [giannozz at democritos.it]
Sent: July 17, 2012 12:21 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] supercell contraction and cell_factor parameter

On Thu, 2012-07-12 at 15:54 +0000, Zhihui Zhu wrote:

> Can anyone please explain what the cell-factor variable represent?

it represent a not-so-smart solution to a purely technical problem.
the code computes interpolation tables in reciprocal space at the
beginning of the calculation. During a variable-cell optimization,
if the cell contracts in real space, it expands in reciprocal space.
Interpolation tables extend up to cell_factor*q_max, where q_max
is what is needed at the beginning of the calculation. It does not
affect in any way the results.

P.
--
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy


_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum



From sohailphysics at yahoo.co.in  Wed Jul 18 16:41:24 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Wed, 18 Jul 2012 22:41:24 +0800 (SGT)
Subject: [Pw_forum] self consistent calculation
Message-ID: <1342622484.86556.YahooMailClassic@web192202.mail.sg3.yahoo.com>

Dear Users

I? run scf and nscf and calculated band structure and DOS succesfully for Molybdenum Disulphide (valence electron =36) in a 4x4x4 with nbnd =20
but the problem in band structure i couldnot see sufficient no. of bands

Then i tried to repeat the same in 12x12x12 with nbnd=30 but the program failed to run

Should i try for lesser mesh for scf? and do bigger mesh for nscf ????

&control
? calculation = 'scf',
? restart_mode = 'from_scratch',
? prefix = 'MoSb1',
? pseudo_dir = '/home/sandeep/espresso-4.2.1/pseudo',
? outdir = './OUT',
?/
?&system
? ibrav = 4, celldm(1) = 6.0281946, celldm(3) = 3.89, nat = 6, ntyp = 2,
? ecutwfc = 70,
? ecutrho = 300,
? nbnd = 30,
? occupations = 'smearing', smearing = 'gaussian', degauss = 0.001,
? nspin = 2,
? starting_magnetization(1) = 0.1d0,
?/
?&electrons
? mixing_beta = 0.3,
? conv_thr = 1.0d-9,
?/
ATOMIC_SPECIES
Mo? 95.96? Mo.pw91-n-van.UPF
S?? 32.06? S.pw91-van_ak.UPF
ATOMIC_POSITIONS {crystal}
Mo? 0.33333333? 0.66666667? 0.25000000
Mo? 0.66666667? 0.33333333? 0.75000000
S?? 0.33333333? 0.66666667? 0.62000000
S?? 0.66666667? 0.33333333? 0.12000000
S?? 0.66666667? 0.33333333 -0.62000000
S?? 0.33333333? 0.66666667 -0.12000000
K_POINTS AUTOMATIC
12 12 12 1 1 1


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From flima at if.usp.br  Wed Jul 18 17:09:23 2012
From: flima at if.usp.br (Filipe Camargo Dalmatti Alves Lima)
Date: Wed, 18 Jul 2012 12:09:23 -0300
Subject: [Pw_forum] self consistent calculation
In-Reply-To: <1342622484.86556.YahooMailClassic@web192202.mail.sg3.yahoo.com>
References: <1342622484.86556.YahooMailClassic@web192202.mail.sg3.yahoo.com>
Message-ID: <CAGLNc7DrSxp97Ngt2LhssWxjv4EHRvN55WDk44bE0cfdprP3+Q@mail.gmail.com>

Dear Ahmad,

The option nbnd is related to the number of electrons that you have in your
system.
You may increase this number without increase the number of k-points.
Usually you should request nbnd equal the number of valence electrons
divided by 2 (plus more bands if you want unoccupied states, I would
suggest add +4 bands at least).

Best regards,

-- 
_________________________________________
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:    (11) 3091-6881  (USP)
                (11) 8249-4628 (TIM)



On Wed, Jul 18, 2012 at 11:41 AM, Sohail Ahmad <sohailphysics at yahoo.co.in>wrote:

> Dear Users
>
> I  run scf and nscf and calculated band structure and DOS succesfully for
> Molybdenum Disulphide (valence electron =36) in a 4x4x4 with nbnd =20
> but the problem in band structure i couldnot see sufficient no. of bands
>
> Then i tried to repeat the same in 12x12x12 with nbnd=30 but the program
> failed to run
>
> Should i try for lesser mesh for scf  and do bigger mesh for nscf ????
>
> &control
>   calculation = 'scf',
>   restart_mode = 'from_scratch',
>   prefix = 'MoSb1',
>   pseudo_dir = '/home/sandeep/espresso-4.2.1/pseudo',
>   outdir = './OUT',
>  /
>  &system
>   ibrav = 4, celldm(1) = 6.0281946, celldm(3) = 3.89, nat = 6, ntyp = 2,
>   ecutwfc = 70,
>   ecutrho = 300,
>   nbnd = 30,
>   occupations = 'smearing', smearing = 'gaussian', degauss = 0.001,
>   nspin = 2,
>   starting_magnetization(1) = 0.1d0,
>  /
>  &electrons
>   mixing_beta = 0.3,
>   conv_thr = 1.0d-9,
>  /
> ATOMIC_SPECIES
> Mo  95.96  Mo.pw91-n-van.UPF
> S   32.06  S.pw91-van_ak.UPF
> ATOMIC_POSITIONS {crystal}
> Mo  0.33333333  0.66666667  0.25000000
> Mo  0.66666667  0.33333333  0.75000000
> S   0.33333333  0.66666667  0.62000000
> S   0.66666667  0.33333333  0.12000000
> S   0.66666667  0.33333333 -0.62000000
> S   0.33333333  0.66666667 -0.12000000
> K_POINTS AUTOMATIC
> 12 12 12 1 1 1
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From abmus007 at gmail.com  Wed Jul 18 17:41:10 2012
From: abmus007 at gmail.com (Abolore Musari)
Date: Wed, 18 Jul 2012 16:41:10 +0100
Subject: [Pw_forum] Band structure of Diamagnetic system
In-Reply-To: <0E36D414-C97F-4DAB-A4A9-DF082F1816F1@democritos.it>
References: <CAOP21kLZiA_3tZxFGxFHD=tnSzkFXhMeWcCd7vS0sE0ZckrtMw@mail.gmail.com>
	<0E36D414-C97F-4DAB-A4A9-DF082F1816F1@democritos.it>
Message-ID: <CAOP21kLZsuePkERv6tqmdZyyddEuXKpY-GVaHm4nZs6-p-uRzA@mail.gmail.com>

Dear Paulo,
what l meant was in the scf calculation shld i include
starting_magnetization and also in my calculation=bands, shld l also
include starting_magnetization in it for fe atom in the system
namelist for fes2 diamagnetic semiconductor.
thanks

On 7/18/12, Paolo Giannozzi <giannozz at democritos.it> wrote:
>
> On Jul 18, 2012, at 8:29 , Abolore Musari wrote:
>
>> Sir I want to ask that when calculating the band structure for a
>> diamagnetic system for example FeS2. Is it  necessary to include a
>> 'starting_magnetization="$value"
>
> if you have the self-consistent charge density and you want to
> calculate bands,
> you do not need to specify anything for "starting_magnetization": it
> will be ignored
> anyway
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From tkaloni at gmail.com  Wed Jul 18 17:47:41 2012
From: tkaloni at gmail.com (Thaneshwor Kaloni)
Date: Wed, 18 Jul 2012 18:47:41 +0300
Subject: [Pw_forum] self consistent calculation
In-Reply-To: <1342622484.86556.YahooMailClassic@web192202.mail.sg3.yahoo.com>
References: <1342622484.86556.YahooMailClassic@web192202.mail.sg3.yahoo.com>
Message-ID: <CABvS7QJgW8JGLvpZieCRieiJ1Cr_GjY_8=EKJUMHOku5-t=ehQ@mail.gmail.com>

Hi Sohail,

>Then i tried to repeat the same in 12x12x12 with nbnd=30 but the >program
failed to run
where is the problem, you must specify and paste over here.
Just now I ran the your scf in my computer and could not find any
error, scf.out file is absolutely fine.
Please read  the following description for K-points,
Type:           INTEGER
   Default:        for an insulator, nbnd = number of valence bands
                   (nbnd = # of electrons /2);
                   for a metal, 20% more (minimum 4 more)
   Description:    number of electronic states (bands) to be calculated.
                   Note that in spin-polarized calculations the number of
                   k-point, not the number of bands per k-point, is doubled
I doubt your nscf file band structure calculation. Could you please paste
your nscf file for band structure here?

Kaloni
http://cpms.kaust.edu.sa/Pages/People.aspx


On Wed, Jul 18, 2012 at 5:41 PM, Sohail Ahmad <sohailphysics at yahoo.co.in>wrote:

> Dear Users
>
> I  run scf and nscf and calculated band structure and DOS succesfully for
> Molybdenum Disulphide (valence electron =36) in a 4x4x4 with nbnd =20
> but the problem in band structure i couldnot see sufficient no. of bands
>
> Then i tried to repeat the same in 12x12x12 with nbnd=30 but the program
> failed to run
>
> Should i try for lesser mesh for scf  and do bigger mesh for nscf ????
>
> &control
>   calculation = 'scf',
>   restart_mode = 'from_scratch',
>   prefix = 'MoSb1',
>   pseudo_dir = '/home/sandeep/espresso-4.2.1/pseudo',
>   outdir = './OUT',
>  /
>  &system
>   ibrav = 4, celldm(1) = 6.0281946, celldm(3) = 3.89, nat = 6, ntyp = 2,
>   ecutwfc = 70,
>   ecutrho = 300,
>   nbnd = 30,
>   occupations = 'smearing', smearing = 'gaussian', degauss = 0.001,
>   nspin = 2,
>   starting_magnetization(1) = 0.1d0,
>  /
>  &electrons
>   mixing_beta = 0.3,
>   conv_thr = 1.0d-9,
>  /
> ATOMIC_SPECIES
> Mo  95.96  Mo.pw91-n-van.UPF
> S   32.06  S.pw91-van_ak.UPF
> ATOMIC_POSITIONS {crystal}
> Mo  0.33333333  0.66666667  0.25000000
> Mo  0.66666667  0.33333333  0.75000000
> S   0.33333333  0.66666667  0.62000000
> S   0.66666667  0.33333333  0.12000000
> S   0.66666667  0.33333333 -0.62000000
> S   0.33333333  0.66666667 -0.12000000
> K_POINTS AUTOMATIC
> 12 12 12 1 1 1
>
>
>


-- 
Best regards, Kaloni
Web page:
http://sa.linkedin.com/pub/thaneshwor-kaloni/18/955/238
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From giannozz at democritos.it  Wed Jul 18 21:21:47 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Jul 2012 21:21:47 +0200
Subject: [Pw_forum] Why does Ewald sum calculation need so much RAM
In-Reply-To: <5006C436.5060801@physik.tu-freiberg.de>
References: <mailman.4033.1342589419.9401.pw_forum@pwscf.org>
	<5006C436.5060801@physik.tu-freiberg.de>
Message-ID: <9846085D-9A29-4DAD-95DA-F61D10342EE7@democritos.it>

I cannot see any evidence from your files that the Ewald term
is responsible for the large RAM and CPU requirements. A lot
of time is spent in the initialization phase ("phq_init"), mostly
in subroutines "drho" and "dvanqq". These calculates terms
required by the PAW and USPP formalism. The rest of the time
is spent in computing the linear response ("phqscf") by solving
a linear system ("solve_linter"), but again, most of the time is
spent in the calculation of PAW/US specific terms ("addusdbec",
"addusddens").

Some improvement could be achieved with a better chosen
parallelization: the number of "pools" should be a divisor of
the number of k-points (so 8 pools is not a good choice with
12 k-points). Note however that
- some calculations cannot be parallelized over k-points
- some other calculations (especially PAW/USPP specific
   stuff) are not parallelized at all
so there is a limit to what parallelization can achieve here
without some work on the code. The phonon code is not
yet ready to be run on very large systems (hundreds of
atoms), and for USPP and PAW, not even on not-so-large
systems. Promises of better scalability have yet to
materialize.

I also notice a disproportionately large cutoff (70Ry).
One of the advantages of PAW/USPP over Norm
Conserving PP is to allow the usage of a much smaller
cutoff. For a Si-Li system, 70Ry seems to me a lot
(unless you are using all-electron Li: with a 1-el Li,
  you could run with norm-conserving PP at a
smaller cutoff).

About the repeated initialization: this is something that
shouldn't be difficult to fix, as long as you run on the
same machine and can read previously written files.
It requires however some modifications of the code
and some understanding of what is going on. The
PAW/USPP formalism is very complex for phonon
calculations and requires the calculation of a
disproportionate number of terms.

P.

On Jul 18, 2012, at 16:12 , Thomas Gruber wrote:

>
>> Message-ID: <1342541146.16360.64.camel at fe12lx.fisica.uniud.it>
>> are we talking about RAM, or about CPU, or both, and in which  
>> subroutine exactly?
> To save CPU time it gets a RAM problem because this is the limiting  
> factor.
>> it was done in this way because the Ewald part has never been a  
>> serious problem for anybody until now.
> It looks like it is in my case.
>> sure there is, but you need to locate exactly where too much cpu  
>> time is spent and where too much RAM is required. Then, we can  
>> discuss about possible solutions. P.
> I attached a graphic of the RAM usage for an "-npool 8" calculation  
> and added the output file named after the time stamp from the  
> graphic. I can't tell you more than it takes almost three days to  
> print the line " PHONON       :     2d   18h22m CPU        2d    
> 21h55m WALL" and it uses 4 times more RAM than in the scf  
> iterations afterward. Unfortunately the scaling is not very good:
>>   With 16 cores it takes "3d
>> 6h" and on 32 cores it takes "2d 16h" and I have only 5 days on that
>> cluster for one job.
> What is the program doing during this time and can I do it only  
> once and give it as input for the other splited phonon calculations?
> I tried to use the "-npool" flag, but I can't use it because my RAM  
> is to "small" (64GB+, some nodes have more). To save time I like to  
> put more representations in one job, but because of this time  
> demanding step I get over the time limit of 5 days. So i have to  
> repeat this calculations 450 times instead of once.
>
> Thanks in advance.
>
> -- 
> Thomas Gruber
> Institut f?r Theoretische Physik
> TU Bergakademie Freiberg
> Leipziger Str. 23, 09599 Freiberg, Germany
> Tel: +49 (0)3731 392006
> Email:thomas.gruber at physik.tu-freiberg.de
>
> <1.out><10.out><4070.out><5360.out><Li12Si7.0.0.1.1.111.log.png>______ 
> _________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Wed Jul 18 22:32:26 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Jul 2012 22:32:26 +0200
Subject: [Pw_forum] ntg with Hybrid Calculations
In-Reply-To: <CAO9Dko=sUpSaPSaCNg2rv83ef6482PRp-qP9h3R_BJ5HiS70nA@mail.gmail.com>
References: <CAO9Dko=sUpSaPSaCNg2rv83ef6482PRp-qP9h3R_BJ5HiS70nA@mail.gmail.com>
Message-ID: <BD7E449F-AB74-45C9-B3AE-4C159C6B4583@democritos.it>


On Jul 16, 2012, at 17:14 , Jack Deslippe wrote:

> Is -ntg expected to work with hybrid functionals?

no, and I thhink it has never been working. In v.5. you can
use (with care, no warranty, etc etc) a different parallelization
over bands: -nbgrp N

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From pmoreira at ifi.unicamp.br  Wed Jul 18 23:05:13 2012
From: pmoreira at ifi.unicamp.br (Pedro Augusto F. P. Moreira)
Date: Wed, 18 Jul 2012 18:05:13 -0300
Subject: [Pw_forum] Input error?
Message-ID: <50072509.4040108@ifi.unicamp.br>

  Dear all,

  I am trying  to pw.x, but the following error happens:

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      task #         0
      from diropn : error #        10
      error opening /home/pedro/Documentos/espresso-5.0/exec/h2o.wfc1
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

  I imagine that the pw.x should open the wcf1 file. Am I rigth? Can 
anyone say why this error is happening? I managed to run the same 
simulation, but with an isolated molecule. My input follows below.

  Thanks,

  Pedro

-- 
Pedro Moreira

IFGW - Unicamp - Brazil

#########################################################
&control
calculation='relax',
restart_mode='from_scratch',
pseudo_dir='/home/pedro/Documentos/espresso-5.0/pseudo',
outdir='/home/pedro/Documentos/espresso-5.0/exec',
prefix='h2o',
tprnfor = .true.,
nstep = 1,
/
&system
ibrav = 0,
nat = 1080, ntyp = 2,
ecutwfc = 70.0, ecutrho = 850.0,
/
&electrons
electron_maxstep = 500,
/
&ions
/
ATOMIC_SPECIES
H 1.00790 H.blyp-van_ak.UPF
O 15.9994 O.blyp-van_ak.UPF
CELL_PARAMETERS angstrom
22.15 0.000 0.000
0.000 23.02 0.000
0.000 0.000 21.55
K_POINTS crystal
1
0.00000000 0.00000000 0.00000000 1.000000e+00
ATOMIC_POSITIONS angstrom

1080 atoms
######################################################

From ttduyle at gmail.com  Wed Jul 18 23:29:29 2012
From: ttduyle at gmail.com (Duy Le)
Date: Wed, 18 Jul 2012 17:29:29 -0400
Subject: [Pw_forum] Input error?
In-Reply-To: <50072509.4040108@ifi.unicamp.br>
References: <50072509.4040108@ifi.unicamp.br>
Message-ID: <CAF-j6z83BuC67r5skf2q1oyCgei8xYun_TV8oYYyqT3Ri8N2uQ@mail.gmail.com>

On Wed, Jul 18, 2012 at 5:05 PM, Pedro Augusto F. P. Moreira <
pmoreira at ifi.unicamp.br> wrote:

>   Dear all,
>
>   I am trying  to pw.x, but the following error happens:
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       task #         0
>       from diropn : error #        10
>       error opening /home/pedro/Documentos/espresso-5.0/exec/h2o.wfc1
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>   I imagine that the pw.x should open the wcf1 file.


It does not need to open any file since you start your calculation from
scratch

Am I rigth? Can
> anyone say why this error is happening? I managed to run the same
> simulation, but with an isolated molecule. My input follows below.
>
>
Delete outdir or change prefix will help.
----------------------------------------------------
Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


>   Thanks,
>
>   Pedro
>
> --
> Pedro Moreira
>
> IFGW - Unicamp - Brazil
>
> #########################################################
> &control
> calculation='relax',
> restart_mode='from_scratch',
> pseudo_dir='/home/pedro/Documentos/espresso-5.0/pseudo',
> outdir='/home/pedro/Documentos/espresso-5.0/exec',
> prefix='h2o',
> tprnfor = .true.,
> nstep = 1,
> /
> &system
> ibrav = 0,
> nat = 1080, ntyp = 2,
> ecutwfc = 70.0, ecutrho = 850.0,
> /
> &electrons
> electron_maxstep = 500,
> /
> &ions
> /
> ATOMIC_SPECIES
> H 1.00790 H.blyp-van_ak.UPF
> O 15.9994 O.blyp-van_ak.UPF
> CELL_PARAMETERS angstrom
> 22.15 0.000 0.000
> 0.000 23.02 0.000
> 0.000 0.000 21.55
> K_POINTS crystal
> 1
> 0.00000000 0.00000000 0.00000000 1.000000e+00
> ATOMIC_POSITIONS angstrom
>
> 1080 atoms
> ######################################################
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From pmoreira at ifi.unicamp.br  Wed Jul 18 23:33:58 2012
From: pmoreira at ifi.unicamp.br (Pedro Augusto F. P. Moreira)
Date: Wed, 18 Jul 2012 18:33:58 -0300
Subject: [Pw_forum] Input error?
In-Reply-To: <CAF-j6z83BuC67r5skf2q1oyCgei8xYun_TV8oYYyqT3Ri8N2uQ@mail.gmail.com>
References: <50072509.4040108@ifi.unicamp.br>
	<CAF-j6z83BuC67r5skf2q1oyCgei8xYun_TV8oYYyqT3Ri8N2uQ@mail.gmail.com>
Message-ID: <50072BC6.8070703@ifi.unicamp.br>

   Dear Duy Le and all,

  my calculation started from scratch as you can see in my input. Due to 
that, I am confused by this error.

  Does anyone have other guess?

   Pedro
____________________
IFGW - Unicamp - Brazil


Em 18-07-2012 18:29, Duy Le escreveu:
>
>
> On Wed, Jul 18, 2012 at 5:05 PM, Pedro Augusto F. P. Moreira 
> <pmoreira at ifi.unicamp.br <mailto:pmoreira at ifi.unicamp.br>> wrote:
>
>       Dear all,
>
>       I am trying  to pw.x, but the following error happens:
>
>     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>           task #         0
>           from diropn : error #        10
>           error opening /home/pedro/Documentos/espresso-5.0/exec/h2o.wfc1
>     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>       I imagine that the pw.x should open the wcf1 file.
>
> It does not need to open any file since you start your calculation 
> from scratch
>
>     Am I rigth? Can
>     anyone say why this error is happening? I managed to run the same
>     simulation, but with an isolated molecule. My input follows below.
>
>
> Delete outdir or change prefix will help.
> ----------------------------------------------------
> Duy Le
> Postdoctoral Associate
> Department of Physics
> University of Central Florida.
> Website: http://www.physics.ucf.edu/~dle 
> <http://www.physics.ucf.edu/%7Edle>
>
>       Thanks,
>
>       Pedro
>
>     --
>     Pedro Moreira
>
>     IFGW - Unicamp - Brazil
>
>     #########################################################
>     &control
>     calculation='relax',
>     restart_mode='from_scratch',
>     pseudo_dir='/home/pedro/Documentos/espresso-5.0/pseudo',
>     outdir='/home/pedro/Documentos/espresso-5.0/exec',
>     prefix='h2o',
>     tprnfor = .true.,
>     nstep = 1,
>     /
>     &system
>     ibrav = 0,
>     nat = 1080, ntyp = 2,
>     ecutwfc = 70.0, ecutrho = 850.0,
>     /
>     &electrons
>     electron_maxstep = 500,
>     /
>     &ions
>     /
>     ATOMIC_SPECIES
>     H 1.00790 H.blyp-van_ak.UPF
>     O 15.9994 O.blyp-van_ak.UPF
>     CELL_PARAMETERS angstrom
>     22.15 0.000 0.000
>     0.000 23.02 0.000
>     0.000 0.000 21.55
>     K_POINTS crystal
>     1
>     0.00000000 0.00000000 0.00000000 1.000000e+00
>     ATOMIC_POSITIONS angstrom
>
>     1080 atoms
>     ######################################################
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
Pedro Moreira

IFGW - Unicamp - Brazil

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From giannozz at democritos.it  Wed Jul 18 23:34:11 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Jul 2012 23:34:11 +0200
Subject: [Pw_forum] Input error?
In-Reply-To: <50072509.4040108@ifi.unicamp.br>
References: <50072509.4040108@ifi.unicamp.br>
Message-ID: <DC4F8142-2B76-496B-8CF2-6CD4F1703DAE@democritos.it>


On Jul 18, 2012, at 23:05 , Pedro Augusto F. P. Moreira wrote:

> Can anyone say why this error is happening?  [...] My input follows  
> below.
> [...]
> 1080 atoms

if you want to run a 1080-atom job, you should be able you find why an
error is happening

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From suyaqiong1988 at 163.com  Thu Jul 19 03:21:07 2012
From: suyaqiong1988 at 163.com (yqsu)
Date: Thu, 19 Jul 2012 09:21:07 +0800
Subject: [Pw_forum] make[2]: warning: Clock skew detected. Your build may be
	incomplete.
Message-ID: <000001cd654c$c673a540$535aefc0$@com>

Dear, sir:

When I make the Quantum-Espresso, a problem always appeared in the last ,so
I want to know a way to solve. The problem list as fllows:

make[2]: warning:  Clock skew detected.  Your build may be incomplete.

make[2]: Leaving directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT/src'

make[2]: Entering directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT/tools'

make[2]: Warning: File `../../make.sys' has modification time 1.3e+04 s in
the future

test -n "" && ( cd ../.. ; make -w  || exit 1) || :

gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW
-I../../include -I../../iotk/src -I../../Modules -I. -c
tddfpt_calculate_spectrum.f90

gfortran -g -o turbo_spectrum.x \

tddfpt_calculate_spectrum.o ../../Modules/libqemod.a ../../PW/libpw.a
../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a
../../iotk/src/libiotk.a
/export/home1/yqsu/espresso-4.3.2/lapack-3.2/lapack.a
/export/home1/yqsu/espresso-4.3.2/BLAS/blas.a   

( cd ../../bin ; ln -fs ../TDDFPT/tools/turbo_spectrum.x . )

if [ -d ../bin ] ; then  ( cd ../bin ; ln -fs ../tools/turbo_spectrum.x . );
fi

make[2]: warning:  Clock skew detected.  Your build may be incomplete.

make[2]: Leaving directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT/tools'

make[1]: Leaving directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT'

make: warning:  Clock skew detected.  Your build may be incomplete.

Thank you for your suggestion !

Best wishes !

Su Yaqiong

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From flux_ray12 at 163.com  Thu Jul 19 07:15:24 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 19 Jul 2012 13:15:24 +0800 (CST)
Subject: [Pw_forum] Input error?
In-Reply-To: <50072509.4040108@ifi.unicamp.br>
References: <50072509.4040108@ifi.unicamp.br>
Message-ID: <899d0c0.7199.1389da975ac.Coremail.flux_ray12@163.com>

The possibilities I guessed:
1, Do you have authority to access that directory?
2, Do you have enough HDD space for the wavefunction file?
3, How about cleaning the directory /home/.../exec/ and re-running the task?


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 



At 2012-07-19 05:05:13,"Pedro Augusto F. P. Moreira" <pmoreira at ifi.unicamp.br> wrote:
>  Dear all,
>
>  I am trying  to pw.x, but the following error happens:
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      task #         0
>      from diropn : error #        10
>      error opening /home/pedro/Documentos/espresso-5.0/exec/h2o.wfc1
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>  I imagine that the pw.x should open the wcf1 file. Am I rigth? Can 
>anyone say why this error is happening? I managed to run the same 
>simulation, but with an isolated molecule. My input follows below.
>
>  Thanks,
>
>  Pedro
>
>-- 
>Pedro Moreira
>
>IFGW - Unicamp - Brazil
>
>#########################################################
>&control
>calculation='relax',
>restart_mode='from_scratch',
>pseudo_dir='/home/pedro/Documentos/espresso-5.0/pseudo',
>outdir='/home/pedro/Documentos/espresso-5.0/exec',
>prefix='h2o',
>tprnfor = .true.,
>nstep = 1,
>/
>&system
>ibrav = 0,
>nat = 1080, ntyp = 2,
>ecutwfc = 70.0, ecutrho = 850.0,
>/
>&electrons
>electron_maxstep = 500,
>/
>&ions
>/
>ATOMIC_SPECIES
>H 1.00790 H.blyp-van_ak.UPF
>O 15.9994 O.blyp-van_ak.UPF
>CELL_PARAMETERS angstrom
>22.15 0.000 0.000
>0.000 23.02 0.000
>0.000 0.000 21.55
>K_POINTS crystal
>1
>0.00000000 0.00000000 0.00000000 1.000000e+00
>ATOMIC_POSITIONS angstrom
>
>1080 atoms
>######################################################
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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From sohailphysics at yahoo.co.in  Thu Jul 19 07:33:18 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Thu, 19 Jul 2012 13:33:18 +0800 (SGT)
Subject: [Pw_forum] Band Structure and nscf calculation
Message-ID: <1342675998.31647.YahooMailClassic@web192202.mail.sg3.yahoo.com>

Dear
I ran scf for MoS2 in K_Points Automatic 4X4x4 mesh with 20 nband and followed calculation for band Structure
but i observed that sufficient no. of bands are not there;; 
then i perform nscf calculation for DOS which seems to be alright

So i did scf calculation again in K-Points Automatic 12x12x12 with a little increase in nband (keeping it in mind nband = # of VE/2 +20% more in metal)

Now i have few questions

1-- While performing band calculation, how should i take K-points
???? K-POINTS AUTOMATIC
???? 12x12x12 1 1 1
??? or the one which i generated manually (150 Points)
???? 150
???? ---- ---- ---- 1
???? ---- ---- ---- 2
???? like that,,,,,,,,,,,,,,,,,,,,,,,,,,,,,which one is a better option? ????

2. While performing nscf calculation, should i write it or no
??? restart_mode = 'from_scratch',
??? i believe no as it may take longer time and some convergence conflict
??? but i need confirmation
?? 
??? Its mentioned in the user guide, that occupations = tetrahedra for DOS
??? Is it required in every case irrespective of magnetic or non magnetic? ???

3? i think nscf is required only for DOS, So can i perform nscf calculation befor the post ? ? ? ?? processing calculation of band calculation? ?????
? ? This question i am asking because i am using computational facility of some other??? place which is available to me for short time only and i am running short of time

Sohail
KKU
SAUDI 
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From akohlmey at gmail.com  Thu Jul 19 09:10:14 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Thu, 19 Jul 2012 09:10:14 +0200
Subject: [Pw_forum] make[2]: warning: Clock skew detected. Your build
 may be incomplete.
In-Reply-To: <000001cd654c$c673a540$535aefc0$@com>
References: <000001cd654c$c673a540$535aefc0$@com>
Message-ID: <CADTmJ6GD75toCgRJ6idZrC=D87FhoMmAAgi9gAq6n=P4Fm_e4A@mail.gmail.com>

On Thu, Jul 19, 2012 at 3:21 AM, yqsu <suyaqiong1988 at 163.com> wrote:
> Dear, sir:
>
> When I make the Quantum-Espresso, a problem always appeared in the last ,so
> I want to know a way to solve. The problem list as fllows:
>
> make[2]: warning:  Clock skew detected.  Your build may be incomplete.

this warning indicates that the time stamps on the created
files are newer than your current time. this can happen, if
you are compiling on a NFS file system where the clock of
the file server and the compilation host are not synchronized
and the clock on the file server is ahead of the compilation
host. you should talk to you system administrator and
suggest to install/configure NTP software to synchronize
the clocks across the cluster.

cheers,
     axel.


>
> make[2]: Leaving directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT/src'
>
> make[2]: Entering directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT/tools'
>
> make[2]: Warning: File `../../make.sys' has modification time 1.3e+04 s in
> the future
>
> test -n "" && ( cd ../.. ; make -w  || exit 1) || :
>
> gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW
> -I../../include -I../../iotk/src -I../../Modules -I. -c
> tddfpt_calculate_spectrum.f90
>
> gfortran -g -o turbo_spectrum.x \
>
> tddfpt_calculate_spectrum.o ../../Modules/libqemod.a ../../PW/libpw.a
> ../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a
> ../../iotk/src/libiotk.a
> /export/home1/yqsu/espresso-4.3.2/lapack-3.2/lapack.a
> /export/home1/yqsu/espresso-4.3.2/BLAS/blas.a
>
> ( cd ../../bin ; ln -fs ../TDDFPT/tools/turbo_spectrum.x . )
>
> if [ -d ../bin ] ; then  ( cd ../bin ; ln -fs ../tools/turbo_spectrum.x . );
> fi
>
> make[2]: warning:  Clock skew detected.  Your build may be incomplete.
>
> make[2]: Leaving directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT/tools'
>
> make[1]: Leaving directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT'
>
> make: warning:  Clock skew detected.  Your build may be incomplete.
>
> Thank you for your suggestion !
>
> Best wishes !
>
> Su Yaqiong
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

From tkaloni at gmail.com  Thu Jul 19 10:01:36 2012
From: tkaloni at gmail.com (Thaneshwor Kaloni)
Date: Thu, 19 Jul 2012 11:01:36 +0300
Subject: [Pw_forum] Band Structure and nscf calculation
Message-ID: <CABvS7Q+sOm4PuBKpdvj0WN85nvb7xtSAjHvWJ_v_fyBQAPhZ1g@mail.gmail.com>

Hi Sohail ,

Please see carefully the example01 of any  versins of the QE.
This example tells you how to set K-points for band structure
as well as the structure of nscf file. Be sure for band calculation
one has to look for the high symmetric K-points.

Best, Kaloni
http://cpms.kaust.edu.sa/Pages/People.aspx?t=Current

Message: 2
Date: Thu, 19 Jul 2012 13:33:18 +0800 (SGT)
From: Sohail Ahmad <sohailphysics at yahoo.co.in>
Subject: [Pw_forum] Band Structure and nscf calculation
To: Plane Wave <pw_forum at pwscf.org>
Message-ID:
        <1342675998.31647.YahooMailClassic at web192202.mail.sg3.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear
I ran scf for MoS2 in K_Points Automatic 4X4x4 mesh with 20 nband and
followed calculation for band Structure
but i observed that sufficient no. of bands are not there;;
then i perform nscf calculation for DOS which seems to be alright

So i did scf calculation again in K-Points Automatic 12x12x12 with a little
increase in nband (keeping it in mind nband = # of VE/2 +20% more in metal)

Now i have few questions

1-- While performing band calculation, how should i take K-points
???? K-POINTS AUTOMATIC
???? 12x12x12 1 1 1
??? or the one which i generated manually (150 Points)
???? 150
???? ---- ---- ---- 1
???? ---- ---- ---- 2
???? like that,,,,,,,,,,,,,,,,,,,,,,,,,,,,,which one is a better option?
????

2. While performing nscf calculation, should i write it or no
??? restart_mode = 'from_scratch',
??? i believe no as it may take longer time and some convergence conflict
??? but i need confirmation
??
??? Its mentioned in the user guide, that occupations = tetrahedra for DOS
??? Is it required in every case irrespective of magnetic or non magnetic?
???

3? i think nscf is required only for DOS, So can i perform nscf calculation
befor the post ? ? ? ?? processing calculation of band calculation? ?????
? ? This question i am asking because i am using computational facility of
some other??? place which is available to me for short time only and i am
running short of time

Sohail
KKU
SAUDI
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From giannozz at democritos.it  Thu Jul 19 10:04:12 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 19 Jul 2012 10:04:12 +0200
Subject: [Pw_forum] Band structure of Diamagnetic system
In-Reply-To: <CAOP21kLZsuePkERv6tqmdZyyddEuXKpY-GVaHm4nZs6-p-uRzA@mail.gmail.com>
References: <CAOP21kLZiA_3tZxFGxFHD=tnSzkFXhMeWcCd7vS0sE0ZckrtMw@mail.gmail.com>
	<0E36D414-C97F-4DAB-A4A9-DF082F1816F1@democritos.it>
	<CAOP21kLZsuePkERv6tqmdZyyddEuXKpY-GVaHm4nZs6-p-uRzA@mail.gmail.com>
Message-ID: <1342685052.1019.1.camel@fe12lx.fisica.uniud.it>

On Wed, 2012-07-18 at 16:41 +0100, Abolore Musari wrote:

> shld l also include starting_magnetization in it for fe atom
> in the system namelist for fes2 diamagnetic semiconductor.

for diamagnnetic semiconductors, it is sufficient to perform
a calculation without spin polarization

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From henod2001 at yahoo.com  Thu Jul 19 14:36:54 2012
From: henod2001 at yahoo.com (henry odhiambo)
Date: Thu, 19 Jul 2012 05:36:54 -0700 (PDT)
Subject: [Pw_forum] TDDFT with turbo_lanczos.x
Message-ID: <1342701414.41608.YahooMailClassic@web122506.mail.ne1.yahoo.com>

Hello users,
?
I am calculating the absorption spetrum. If?I run the code turbo_lanczos.x after performing the ground state scf, the calculation stops and I get the error message bellow:
?
*********************************************************************************
from orthogonalize:???? error? #?? 1
degauss with gamma point algorithm
*********************************************************************************
?
Could any one help. 
?
Thank you.
?
Henry Otunga
Dept. of Physics
Maseno University
Kenya
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From henod2001 at yahoo.com  Thu Jul 19 14:37:42 2012
From: henod2001 at yahoo.com (henry odhiambo)
Date: Thu, 19 Jul 2012 05:37:42 -0700 (PDT)
Subject: [Pw_forum] TDDFT with turbo_lanczos.x
Message-ID: <1342701462.72564.YahooMailClassic@web122502.mail.ne1.yahoo.com>

Hello users,
?
I am calculating the absorption spetrum. If?I run the code turbo_lanczos.x after performing the ground state scf, the calculation stops and I get the error message bellow:
?
*********************************************************************************
from orthogonalize:???? error? #?? 1
degauss with gamma point algorithm
*********************************************************************************
?
Could any one help. 
?
Thank you.
?
Henry Otunga
Dept. of Physics
Maseno University
Kenya
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From sbinnie at sissa.it  Thu Jul 19 14:52:10 2012
From: sbinnie at sissa.it (Simon Binnie)
Date: Thu, 19 Jul 2012 14:52:10 +0200
Subject: [Pw_forum] TDDFT with turbo_lanczos.x
In-Reply-To: <1342701462.72564.YahooMailClassic@web122502.mail.ne1.yahoo.com>
References: <1342701462.72564.YahooMailClassic@web122502.mail.ne1.yahoo.com>
Message-ID: <op.who108c6b4z88i@mugon.cm.sissa.it>

Hi there,

You are trying to use some form of smearing for the occupation numbers  
when you calculate the ground state wavefunctions. This currently isn't  
supported with turboTDDFT.

Brgrds,

Simon


On Thu, 19 Jul 2012 14:37:42 +0200, henry odhiambo <henod2001 at yahoo.com>  
wrote:

> Hello users,
>  I am calculating the absorption spetrum. If I run the code  
> turbo_lanczos.x after performing the ground state scf, the calculation  
> stops and I get the error message bellow:
>   
> *********************************************************************************
> from orthogonalize:     error  #   1
> degauss with gamma point algorithm
> *********************************************************************************
>  Could any one help.
>  Thank you.
>  Henry Otunga
> Dept. of Physics
> Maseno University
> Kenya


-- 
Simon Binnie | Post Doc, Condensed Matter Sector
Scuola Internazionale di Studi Avanzati (SISSA)
Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it

From abmus007 at gmail.com  Fri Jul 20 06:05:01 2012
From: abmus007 at gmail.com (Abolore Musari)
Date: Fri, 20 Jul 2012 05:05:01 +0100
Subject: [Pw_forum] Band structure of Diamagnetic system
In-Reply-To: <1342685052.1019.1.camel@fe12lx.fisica.uniud.it>
References: <CAOP21kLZiA_3tZxFGxFHD=tnSzkFXhMeWcCd7vS0sE0ZckrtMw@mail.gmail.com>
	<0E36D414-C97F-4DAB-A4A9-DF082F1816F1@democritos.it>
	<CAOP21kLZsuePkERv6tqmdZyyddEuXKpY-GVaHm4nZs6-p-uRzA@mail.gmail.com>
	<1342685052.1019.1.camel@fe12lx.fisica.uniud.it>
Message-ID: <CAOP21kLUpGh186aCA4D-mW-T9pdOb6gYHepT5za+Jw6XDLioPw@mail.gmail.com>

Dear Sir,
thank you so much God Bless

On 7/19/12, Paolo Giannozzi <giannozz at democritos.it> wrote:
> On Wed, 2012-07-18 at 16:41 +0100, Abolore Musari wrote:
>
>> shld l also include starting_magnetization in it for fe atom
>> in the system namelist for fes2 diamagnetic semiconductor.
>
> for diamagnnetic semiconductors, it is sufficient to perform
> a calculation without spin polarization
>
> P.
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From koushik at jncasr.ac.in  Fri Jul 20 07:56:18 2012
From: koushik at jncasr.ac.in (Koushik Pal)
Date: Fri, 20 Jul 2012 11:26:18 +0530
Subject: [Pw_forum] anomaly in phonon frequencies as obtained using DFPT
 (ph.x) in a spin-orbit calculation
Message-ID: <CAMhFyZr-vhz_dwDUDDq5Q=+OA4srkFOewCiB+7OrGaKVxN5a=w@mail.gmail.com>

Dear sir,
The system is Sb2Se3 (SG-166). No, the scalar relativistic phonon
calculation  also does not have correct symmetry. I used PBE-GGA NC  PP .
I have one more question. Why doesn't the pw.x code give pressure on the
system in spin-orbit calculation? Can we get any idea of the actual
pressure of the system from the scalar relativistic/non relativistic
calculation?

On Tue, Jul 17, 2012 at 7:24 PM, <pw_forum-request at pwscf.org> wrote:
Send Pw_forum mailing list submissions to
        pw_forum at pwscf.org

------------------------------

Message: 7
Date: Tue, 17 Jul 2012 15:54:12 +0200
From: Andrea Dal Corso <dalcorso at sissa.it>
Subject: Re: [Pw_forum] anomaly in phonon frequencies as obtained
        using   DFPT    (ph.x) in a spin-orbit calculation
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <1342533252.4490.15.camel at ulisse.cm.sissa.it>
Content-Type: text/plain

Can you give more information? Which system is it? Does the scalar
relativistic phonon calculation have the correct symmetry?

A.

On Tue, 2012-07-17 at 18:46 +0530, Koushik Pal wrote:
> Dear sir,
>   I calculated the phonon frequencies of a system using both the
> frozen phonon method as well as DFPT (ph.x) in fully relativistic
> regime (spin-orbit interaction) using QE verson 4.3. According to
> group theory the 12 optical modes of the system are 2A1g + 2Eg + 2A2u
> +2Eu. I got accurate results for the frequncies in the frozen phonon
> method (means, the frequencies obeyed the symmetry rule as predicted
> by the group theory. Also I visualized the eigenmodes which also agree
> well), but in the DFPT (linear response theory), the obtained
> frequencies and eigenmodes do not obey the above symmetry principles
> as predicted by group theory (though the frequencies are near the
> frequencies as obtained in frozen-phonon method) . It seems that the
> degeneracies in the frequencies are broken in DFPT. What is the reason
> behind that? Please help. Please give references with mathematical
> details (if available).
>
> Thanks in advance.
>
> =============
> Koushik
> Grad. student
> Chemistry and Physics of Materials Unit
> JNCASR
> Bangalore , India
> ______________________________
>
> _________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> --
> Andrea Dal Corso                    Tel. 0039-040-3787428
> SISSA, Via Bonomea 265              Fax. 0039-040-3787249
> I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 61, Issue 49
> ****************************************
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From giannozz at democritos.it  Fri Jul 20 08:49:06 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 20 Jul 2012 08:49:06 +0200
Subject: [Pw_forum] anomaly in phonon frequencies as obtained using DFPT
	(ph.x) in a spin-orbit calculation
In-Reply-To: <CAMhFyZr-vhz_dwDUDDq5Q=+OA4srkFOewCiB+7OrGaKVxN5a=w@mail.gmail.com>
References: <CAMhFyZr-vhz_dwDUDDq5Q=+OA4srkFOewCiB+7OrGaKVxN5a=w@mail.gmail.com>
Message-ID: <520E47E7-3BAB-4839-B63D-3305EB5B9B62@democritos.it>


On Jul 20, 2012, at 7:56 , Koushik Pal wrote:

> The system is Sb2Se3 (SG-166). No, the scalar relativistic phonon  
> calculation
>  also does not have correct symmetry.

what about the symmetry of the self-consistent calculation? If it is  
not what
you expect, please note the following:

http://www.quantum-espresso.org/wp-content/uploads/Doc/pw_user_guide/ 
node19.html#SECTION000600190000000000000

> I have one more question. Why doesn't the pw.x code give pressure  
> on the system
> in spin-orbit calculation?

it does: specify tstress=.true. in &control

P.
> ------------------------------
>
> Message: 7
> Date: Tue, 17 Jul 2012 15:54:12 +0200
> From: Andrea Dal Corso <dalcorso at sissa.it>
> Subject: Re: [Pw_forum] anomaly in phonon frequencies as obtained
>         using   DFPT    (ph.x) in a spin-orbit calculation
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1342533252.4490.15.camel at ulisse.cm.sissa.it>
> Content-Type: text/plain
>
> Can you give more information? Which system is it? Does the scalar
> relativistic phonon calculation have the correct symmetry?
>
> A.
>
> On Tue, 2012-07-17 at 18:46 +0530, Koushik Pal wrote:
> > Dear sir,
> >   I calculated the phonon frequencies of a system using both the
> > frozen phonon method as well as DFPT (ph.x) in fully relativistic
> > regime (spin-orbit interaction) using QE verson 4.3. According to
> > group theory the 12 optical modes of the system are 2A1g + 2Eg +  
> 2A2u
> > +2Eu. I got accurate results for the frequncies in the frozen phonon
> > method (means, the frequencies obeyed the symmetry rule as predicted
> > by the group theory. Also I visualized the eigenmodes which also  
> agree
> > well), but in the DFPT (linear response theory), the obtained
> > frequencies and eigenmodes do not obey the above symmetry principles
> > as predicted by group theory (though the frequencies are near the
> > frequencies as obtained in frozen-phonon method) . It seems that the
> > degeneracies in the frequencies are broken in DFPT. What is the  
> reason
> > behind that? Please help. Please give references with mathematical
> > details (if available).
> >
> > Thanks in advance.
> >
> > =============
> > Koushik
> > Grad. student
> > Chemistry and Physics of Materials Unit
> > JNCASR
> > Bangalore , India
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> --
> Andrea Dal Corso                    Tel. 0039-040-3787428
> SISSA, Via Bonomea 265              Fax. 0039-040-3787249
> I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 61, Issue 49
> ****************************************
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From mayankaditya at gmail.com  Fri Jul 20 10:11:59 2012
From: mayankaditya at gmail.com (mayank gupta)
Date: Fri, 20 Jul 2012 13:41:59 +0530
Subject: [Pw_forum] relaxed structure output
Message-ID: <CAHNEyD-KoGuTREu0zXO4p6m-Y0Wy7uJ+siLF4fKxWLKsOPBwGw@mail.gmail.com>

Dear Users


I want to know is there any routine from which I can get relaxed structure
after relaxations in separate file...like CONTCAR in vasp


Thanks

-- 
--
Mayank

 BARC
MUMBAI, INDIA
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From joshiniharika20 at yahoo.in  Fri Jul 20 10:17:00 2012
From: joshiniharika20 at yahoo.in (Niharika Joshi)
Date: Fri, 20 Jul 2012 16:17:00 +0800 (SGT)
Subject: [Pw_forum] Non collinear calculation
Message-ID: <1342772220.85426.YahooMailNeo@web193902.mail.sg3.yahoo.com>

Hello,
I am trying out a non collinear calculation. 

? ? noncolin = .true.
???? angle1(1)= 45.0
???? angle2(1)= 43.5
???? angle1(2)= 46.5
???? angle2(2)= 44.0
?? Upto atom number 7, atoms are? of type 1 (Ni) and atom number 8 and 9 are of type 2 (C).

Section from the output file:

=============================================================================
???? atom number??? 7 relative position :??? 0.5577? -0.1494?? 4.0103
???? charge :???? 8.122736
???? magnetization :????????? 4.136899??? 3.925771??? 5.703123
???? magnetization/charge:??? 0.509299??? 0.483306??? 0.702118
???? polar coord.: r, theta, phi [deg] :???? 8.065434?? 45.000000?? 43.500000

?==============================================================================

?==============================================================================
???? atom number??? 8 relative position :??? 0.5578? -0.1495?? 4.8532
???? charge :???? 1.622393
???? magnetization :????????? 0.008759??? 0.008312??? 0.012075
???? magnetization/charge:??? 0.005399??? 0.005123??? 0.007443
???? polar coord.: r, theta, phi [deg] :???? 0.017077?? 45.000000?? 43.500000

?==============================================================================

?==============================================================================
???? atom number??? 9 relative position :??? 0.0000?? 0.0000?? 4.8520
???? charge :???? 1.618065
???? magnetization :????????? 0.006774??? 0.006428??? 0.009339
???? magnetization/charge:??? 0.004187??? 0.003973??? 0.005772
???? polar coord.: r, theta, phi [deg] :???? 0.013207?? 45.000000?? 43.500000

?==============================================================================
?
Why? then it is taking same values of angle1 and angle2 for both Ni and C atoms?

Thanking in advance.
? 

-Niharika Joshi
(Project student, IISER, Pune, India)
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From giannozz at democritos.it  Fri Jul 20 11:13:15 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 20 Jul 2012 11:13:15 +0200
Subject: [Pw_forum] relaxed structure output
In-Reply-To: <CAHNEyD-KoGuTREu0zXO4p6m-Y0Wy7uJ+siLF4fKxWLKsOPBwGw@mail.gmail.com>
References: <CAHNEyD-KoGuTREu0zXO4p6m-Y0Wy7uJ+siLF4fKxWLKsOPBwGw@mail.gmail.com>
Message-ID: <1342775595.18212.0.camel@fe12lx.fisica.uniud.it>

On Fri, 2012-07-20 at 13:41 +0530, mayank gupta wrote:

> I want to know is there any routine from which I can get relaxed
> structure after relaxations in separate file...like CONTCAR in vasp

you may try to manipulate routine "output_tau"

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From arebol2 at uic.edu  Fri Jul 20 11:27:07 2012
From: arebol2 at uic.edu (=?iso-8859-1?Q?=22Alejandro_R=E9bola=22?=)
Date: Fri, 20 Jul 2012 04:27:07 -0500
Subject: [Pw_forum] Wrong frequencies on STO phonons
Message-ID: <7ede4216e1f49fa6e8b5cce193fecf56.squirrel@webmail.uic.edu>

Dear Quantum Espresso users,

I'm trying to calculate phonons on cubic SrTiO3 by using ph.x (v.4.3.2). I
relaxed the whole structure (vc-relax) and got reasonable lattice and
internal parameters (experimental 3.905 A, calculated 3.92(PBE)).
Afterwards I performed a scf calculations with this structure and then
used the phonon code. The problem is that I'm obtaining mostly negative
frequencies. I know that cubic STO is unstable, but negative values should
only appear around GAMMA, M and R symmetry points. I've also done this
calculation by using the frozen phonon method and in this case results are
in good agreement with the literature. But the frequencies I got from the
ph.x calculation seem to be completely wrong. I've tried changing
parameters, using a dense k-point grid and a high cutoff, but results are
still wrong. I don't have any clue about what is going wrong, could
anybody help?
I'm copying the input files below. Thank you in advance for your help.
Best,

- Alejandro

The relaxed structure:

 &control
    calculation='scf',
    restart_mode='from_scratch',
    pseudo_dir = '/global/homes/r/rebola/pseudo/',
    outdir='/scratch/scratchdirs/rebola/',
    prefix = 'sto',
 /
 &system
    ibrav=0, celldm(1)=7.46252850, nat=5, ntyp=3,
    ecutwfc=40.0, ecutrho = 400,
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Sr 87.62 Sr.pbe-nsp-van.UPF
 Ti 47.867 Ti.pbe-sp-van_ak.UPF
 O  15.9994 O.pbe-van_gipaw.UPF
CELL_PARAMETERS (alat=  7.46252850)
   0.993935603   0.000000000   0.000000000
   0.000000000   0.993935603   0.000000000
   0.000000000   0.000000000   0.993935603
ATOMIC_POSITIONS (alat)
Sr       0.000000000   0.000000000   0.000000000
Ti       0.496967802   0.496967802   0.496967802
O        0.000000000   0.496967802   0.496967802
O        0.496967802   0.000000000   0.496967802
O        0.496967802   0.496967802   0.000000000
K_POINTS (automatic)
4 4 4 0 0 0

The phonon input file:

phonons of STO
 &inputph
  tr2_ph=1.0d-14,
  ldisp=.true.,
  nq1=2, nq2=2, nq3=2
  amass(1)=87.62,
  amass(2)=47.867,
  amass(3)=15.9994,
  epsil=.true.
  prefix='sto',
  outdir='/scratch/scratchdirs/rebola/',
  fildyn='sto.dyn',
 /
~


From giannozz at democritos.it  Fri Jul 20 13:48:17 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 20 Jul 2012 13:48:17 +0200
Subject: [Pw_forum] Wrong frequencies on STO phonons
In-Reply-To: <7ede4216e1f49fa6e8b5cce193fecf56.squirrel@webmail.uic.edu>
References: <7ede4216e1f49fa6e8b5cce193fecf56.squirrel@webmail.uic.edu>
Message-ID: <1342784897.22438.4.camel@fe12lx.fisica.uniud.it>

On Fri, 2012-07-20 at 04:27 -0500, "Alejandro R?bola" wrote:

> The problem is that I'm obtaining mostly negative frequencies

"mostly"? I see 3 negative frequencies at Gamma, 2 at (0,0,0.0503)

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From chenhanghuipwscf at gmail.com  Fri Jul 20 21:28:20 2012
From: chenhanghuipwscf at gmail.com (Hanghui Chen)
Date: Fri, 20 Jul 2012 15:28:20 -0400
Subject: [Pw_forum] atomic projection in the band structure
Message-ID: <CAOE2MOxc=-bugoNkeikz=tt6dpw_-tsOk-viUgFpBDBqWWHSbw@mail.gmail.com>

To Quantum Espresso developers,
     I have a simple question: we can do atomic projections in the DOS
calculations. Can we also do atomic projections in the band structure
calculations as in the VASP? I know Wannier projection may also do the job
but that requires generation of Wannier functions.
     Thank you.

Hanghui Chen
Department of Physics
Columbia University
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From ptao10b at imr.ac.cn  Sat Jul 21 03:38:17 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Sat, 21 Jul 2012 09:38:17 +0800 (GMT+08:00)
Subject: [Pw_forum] My solution to "q not allowed" in a2F run while using
	q2r.x
Message-ID: <dbc719.80bd.138a72f640e.Coremail.ptao10b@imr.ac.cn>

Dear all professors:

About half a month ago I happened to meet a problem in q2r run: The ordinary phonon q2r was OK, but the subsequent a2F q2r run showed "q not allowed".

I tried to solve it for many times, and in lots of different ways. And I found those phenomenon: 

1. When I restarted my calculation in a new folder(NF), it ran with no error. 

2. And then I copied these new input files to the old folder(OF), and ran e-ph( dense scf - scf - elph - q2r, the whole run) in OF, error appeared again.

3. When I copied all the files in NF to the OF and ran e-ph in OF, no error appeared.

4. I read q2r.f90, and realized It must be the fault of "a2Fq2r.*". So I deleted "a2Fq2r.*" and ran with the old input files in OF, it turned OK.

5. I copied the wrong "a2Fq2r.51" in the OF (I did a backup) to the NF, and ran e-ph in NF, and the error appeared. 

Thus I find as soon as the files "a2Fq2r.*" are generated, they are not likely to update with new elph calculations(the whole e-ph calculation). Or, perhaps, they inherit some results of the first calculation.

That is why I always meet the same error without delete "a2Fq2r.*", no matter how I changed the input files and deleted the tmp folders.

To delete all files and begin with zero is the best choice! And thanks in advance, Mr. giannozz and Mr. Gao.




Yours sincerely,

Peng Tao



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------


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From ptao10b at imr.ac.cn  Sat Jul 21 03:44:01 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Sat, 21 Jul 2012 09:44:01 +0800 (GMT+08:00)
Subject: [Pw_forum] My solution to "q not allowed" in a2F run while
 using q2r.x
In-Reply-To: <dbc719.80bd.138a72f640e.Coremail.ptao10b@imr.ac.cn>
References: <dbc719.80bd.138a72f640e.Coremail.ptao10b@imr.ac.cn>
Message-ID: <1c2a67d.80e0.138a734a57a.Coremail.ptao10b@imr.ac.cn>

I'm very sorry to Mr. Giannozzi. Your name should be written in capital letters, I made a mistake. I just copied your name from the email address.


Yours sincerely,

Peng Tao



-----Original Messages-----
From: "Peng Tao" <ptao10b at imr.ac.cn>
Sent Time: Saturday, July 21, 2012
To: giannozz at democritos.it, flux_ray12 at 163.com, pw_forum <pw_forum at pwscf.org>
Cc:
Subject: [Pw_forum] My solution to "q not allowed" in a2F run while using q2r.x



Dear all professors:

About half a month ago I happened to meet a problem in q2r run: The ordinary phonon q2r was OK, but the subsequent a2F q2r run showed "q not allowed".

I tried to solve it for many times, and in lots of different ways. And I found those phenomenon: 

1. When I restarted my calculation in a new folder(NF), it ran with no error. 

2. And then I copied these new input files to the old folder(OF), and ran e-ph( dense scf - scf - elph - q2r, the whole run) in OF, error appeared again.

3. When I copied all the files in NF to the OF and ran e-ph in OF, no error appeared.

4. I read q2r.f90, and realized It must be the fault of "a2Fq2r.*". So I deleted "a2Fq2r.*" and ran with the old input files in OF, it turned OK.

5. I copied the wrong "a2Fq2r.51" in the OF (I did a backup) to the NF, and ran e-ph in NF, and the error appeared. 

Thus I find as soon as the files "a2Fq2r.*" are generated, they are not likely to update with new elph calculations(the whole e-ph calculation). Or, perhaps, they inherit some results of the first calculation.

That is why I always meet the same error without delete "a2Fq2r.*", no matter how I changed the input files and deleted the tmp folders.

To delete all files and begin with zero is the best choice! And thanks in advance, Mr. giannozz and Mr. Gao.




Yours sincerely,

Peng Tao



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------






--
-------------------------------------------------------------------
PH.D. candidate Peng Tao
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------


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From giannozz at democritos.it  Sat Jul 21 09:32:44 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 21 Jul 2012 09:32:44 +0200
Subject: [Pw_forum] atomic projection in the band structure
In-Reply-To: <CAOE2MOxc=-bugoNkeikz=tt6dpw_-tsOk-viUgFpBDBqWWHSbw@mail.gmail.com>
References: <CAOE2MOxc=-bugoNkeikz=tt6dpw_-tsOk-viUgFpBDBqWWHSbw@mail.gmail.com>
Message-ID: <1B67BD24-7E6F-4A7F-B402-B1C93BBC0077@democritos.it>


On Jul 20, 2012, at 21:28 , Hanghui Chen wrote:

> Can we also do atomic projections in the band structure  
> calculations as in the VASP?

see code "projwfc.x"

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From arebol2 at uic.edu  Sat Jul 21 12:55:30 2012
From: arebol2 at uic.edu (=?iso-8859-1?Q?=22Alejandro_R=E9bola=22?=)
Date: Sat, 21 Jul 2012 05:55:30 -0500
Subject: [Pw_forum] Wrong frequencies on STO phonons
In-Reply-To: <1342784897.22438.4.camel@fe12lx.fisica.uniud.it>
References: <7ede4216e1f49fa6e8b5cce193fecf56.squirrel@webmail.uic.edu>
	<1342784897.22438.4.camel@fe12lx.fisica.uniud.it>
Message-ID: <31a229357d0f27bc3f40c6efe5caaf4b.squirrel@webmail.uic.edu>

Dear Paolo,

I'm running the very same files on NERSC, using espresso 4.3.2 and what
I'm getting is:

     q = (    0.000000000   0.000000000   0.000000000 )

 **************************************************************************
     omega( 1) =       1.870681 [THz] =      62.399610 [cm-1]
     omega( 2) =       1.870681 [THz] =      62.399610 [cm-1]
     omega( 3) =       1.870681 [THz] =      62.399610 [cm-1]
     omega( 4) =       5.059448 [THz] =     168.766153 [cm-1]
     omega( 5) =       5.059448 [THz] =     168.766153 [cm-1]
     omega( 6) =       5.059448 [THz] =     168.766153 [cm-1]
     omega( 7) =      13.443974 [THz] =     448.445682 [cm-1]
     omega( 8) =      13.443974 [THz] =     448.445682 [cm-1]
     omega( 9) =      13.443974 [THz] =     448.445682 [cm-1]
     omega(10) =      15.080555 [THz] =     503.036525 [cm-1]
     omega(11) =      15.080555 [THz] =     503.036525 [cm-1]
     omega(12) =      15.080555 [THz] =     503.036525 [cm-1]
     omega(13) =      24.678193 [THz] =     823.181378 [cm-1]
     omega(14) =      24.678193 [THz] =     823.181378 [cm-1]
     omega(15) =      24.678193 [THz] =     823.181378 [cm-1]
 **************************************************************************

and

  q = (    0.000000000   0.000000000  -0.503050699 )

 **************************************************************************
     omega( 1) =     -24.105192 [THz] =    -804.068008 [cm-1]
     omega( 2) =     -24.105192 [THz] =    -804.068008 [cm-1]
     omega( 3) =     -19.909346 [THz] =    -664.108704 [cm-1]
     omega( 4) =     -19.397058 [THz] =    -647.020510 [cm-1]
     omega( 5) =     -19.397058 [THz] =    -647.020510 [cm-1]
     omega( 6) =     -19.039025 [THz] =    -635.077723 [cm-1]
     omega( 7) =     -19.039025 [THz] =    -635.077723 [cm-1]
     omega( 8) =     -17.793909 [THz] =    -593.544859 [cm-1]
     omega( 9) =     -16.687081 [THz] =    -556.624792 [cm-1]
     omega(10) =       3.226165 [THz] =     107.613980 [cm-1]
     omega(11) =       3.226165 [THz] =     107.613980 [cm-1]
     omega(12) =       6.085719 [THz] =     202.999094 [cm-1]
     omega(13) =      22.949446 [THz] =     765.516222 [cm-1]
     omega(14) =      22.949446 [THz] =     765.516222 [cm-1]
     omega(15) =      26.130802 [THz] =     871.635519 [cm-1]
 **************************************************************************

 q = (    0.000000000  -0.503050699  -0.503050699 )

 **************************************************************************
     omega( 1) =     -23.321490 [THz] =    -777.921187 [cm-1]
     omega( 2) =     -22.376404 [THz] =    -746.396502 [cm-1]
     omega( 3) =     -21.599094 [THz] =    -720.468209 [cm-1]
     omega( 4) =     -19.451780 [THz] =    -648.841548 [cm-1]
     omega( 5) =     -19.451780 [THz] =    -648.841548 [cm-1]
     omega( 6) =     -19.276782 [THz] =    -643.004218 [cm-1]
     omega( 7) =     -19.276782 [THz] =    -643.004218 [cm-1]
     omega( 8) =     -16.339999 [THz] =    -545.043709 [cm-1]
     omega( 9) =     -14.170749 [THz] =    -472.685312 [cm-1]
     omega(10) =       3.166941 [THz] =     105.637772 [cm-1]
     omega(11) =       4.376655 [THz] =     145.989511 [cm-1]
     omega(12) =       4.376655 [THz] =     145.989511 [cm-1]
     omega(13) =      22.999526 [THz] =     767.181612 [cm-1]
     omega(14) =      25.783909 [THz] =     860.058618 [cm-1]
     omega(15) =      25.783909 [THz] =     860.058618 [cm-1]
 **************************************************************************


I'm also getting:

 Dielectric constant in cartesian axis

          (******************       0.000000000       0.000000000 )
          (       0.000000000******************       0.000000000 )
          (       0.000000000       0.000000000****************** )

which looks weird. I have no idea what is going on or why I'm not getting
the same results as you by using the very same files.
Thank you in advance for you help,

Alejandro


On Fri, July 20, 2012 6:48 am, Paolo Giannozzi wrote:
> On Fri, 2012-07-20 at 04:27 -0500, "Alejandro R??bola" wrote:
>
>> The problem is that I'm obtaining mostly negative frequencies
>
> "mostly"? I see 3 negative frequencies at Gamma, 2 at (0,0,0.0503)
>
> P.
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


From pchen at ion.chem.utk.edu  Sat Jul 21 18:20:31 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Sat, 21 Jul 2012 12:20:31 -0400
Subject: [Pw_forum] Relax in primitive cell or conventional cell
Message-ID: <CAP_5U0dji9S41TX+vs+1F2Rz8JmEacGPD7yqRWc75yYAwkt0Mw@mail.gmail.com>

Dear All,

I am trying to optimize the structure based on the experimental crystal
structure using 'relax' task.  Shall I use primitive cell or conventional
unit cell to do relax? The primitive cell job (26 atoms) is done and
conventional cell job (52 atoms) is still in progress. I used the same
parameters for both jobs and it looks like the results will be different.

Another quick question: the calculated energy for primitive cell (26 atoms,
3 types) is converged into 0.001 Ry. Is this energy difference (0.001 Ry)
for 26 atoms? In this case, can we say that total energy is converged
within 0.001/26 Ry/atom?  Some workers wrote in their paper that the energy
is converged within 0.5 eV/atom. It is a little weird expression to me
because there are several different types of atoms.

-- 
  Best Regards.
        Peng
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From yccheng.nju at gmail.com  Sun Jul 22 08:54:56 2012
From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=)
Date: Sun, 22 Jul 2012 09:54:56 +0300
Subject: [Pw_forum] atomic projection in the band structure
In-Reply-To: <1B67BD24-7E6F-4A7F-B402-B1C93BBC0077@democritos.it>
References: <CAOE2MOxc=-bugoNkeikz=tt6dpw_-tsOk-viUgFpBDBqWWHSbw@mail.gmail.com>
	<1B67BD24-7E6F-4A7F-B402-B1C93BBC0077@democritos.it>
Message-ID: <CAAzEAhEtQVvuQW+oqHujT7PO=5Ufwp8uSuc02ef_Y9+zqfJs2A@mail.gmail.com>

!!!===============================
!!!The following is code to get projected band structure by Y. C. Cheng
!!! They should be added into "SUBROUTINE projwave( filproj, lsym,
lgww )" in projwfc.f90 file
!!!
!!!They should added in the first
  CHARACTER(LEN=80) :: myname
  CHARACTER(LEN=8) :: bandnumber
!!!The following should added before lowdin charge calculation
     DO nwfc = 1, natomwfc
     WRITE(myname,1000) &
             nwfc, nlmchi(nwfc)%na, atm(ityp(nlmchi(nwfc)%na)), &
             nlmchi(nwfc)%n, nlmchi(nwfc)%l, nlmchi(nwfc)%m

                  !
     open(12,file=myname, form='formatted', status='unknown')
     WRITE (12,'(A11)',advance='no') "K"
            DO ibnd = 1, nbnd
               WRITE(bandnumber,'(i4)') ibnd
               WRITE( 12, '(A11)',advance='no')  'E'//trim(adjustl(bandnumber))
               WRITE( 12, '(A11)',advance='no')  'R'//trim(adjustl(bandnumber))
            END DO

            DO ik = 1, nkstot
                    WRITE( 12, '(/i11)',advance='no') ik
                    DO ibnd = 1, nbnd
                        WRITE( 12, '(f11.5)',advance='no') et (ibnd,
ik) * rytoev
                        WRITE( 12, '(f11.5)',advance='no') proj (nwfc, ibnd,ik)
                    END DO
            END DO
     close (unit=12,status='keep')
     END DO

!!!=============================

2012/7/21 Paolo Giannozzi <giannozz at democritos.it>:
>
> On Jul 20, 2012, at 21:28 , Hanghui Chen wrote:
>
>> Can we also do atomic projections in the band structure
>> calculations as in the VASP?
>
> see code "projwfc.x"
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



-- 
Y. C. Cheng
Department of Physics
Nanjing University
Nanjing 210093
P. R. China
Tel: 86-25-83592907
Email: yccheng.nju at gmail.com

From giannozz at democritos.it  Sun Jul 22 08:58:47 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 22 Jul 2012 08:58:47 +0200
Subject: [Pw_forum] Wrong frequencies on STO phonons
In-Reply-To: <31a229357d0f27bc3f40c6efe5caaf4b.squirrel@webmail.uic.edu>
References: <7ede4216e1f49fa6e8b5cce193fecf56.squirrel@webmail.uic.edu>
	<1342784897.22438.4.camel@fe12lx.fisica.uniud.it>
	<31a229357d0f27bc3f40c6efe5caaf4b.squirrel@webmail.uic.edu>
Message-ID: <2CB721E0-1105-4C5A-B9B5-60E7B81A772D@democritos.it>


On Jul 21, 2012, at 12:55 , Alejandro R?bola wrote:

> I'm running the very same files on NERSC, using espresso 4.3.2 and  
> what
> I'm getting is:

here is what I get (with smaller thresholds, but it makes no
difference):
http://www.fisica.uniud.it/~giannozz/public/STO.tar.gz

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From henod2001 at yahoo.com  Sun Jul 22 14:14:43 2012
From: henod2001 at yahoo.com (henry odhiambo)
Date: Sun, 22 Jul 2012 05:14:43 -0700 (PDT)
Subject: [Pw_forum] Gamm-point tricks
Message-ID: <1342959283.201.YahooMailClassic@web122502.mail.ne1.yahoo.com>

Dear users,
?
I am doing phonon calculation using the code ph.x
?
However, I get the error message bellow:
?
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
????? from phq_readin : error #???????? 1
????? cannot start from pw.x data file using Gamma-point tricks

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
?
I never experienced this before.
?
Could someone, please, help me identify the problem.
?
Henry Otunga
Dept. of Physics
Maseno University
Kenya

?
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From ttduyle at gmail.com  Sun Jul 22 14:23:06 2012
From: ttduyle at gmail.com (Duy Le)
Date: Sun, 22 Jul 2012 08:23:06 -0400
Subject: [Pw_forum] Gamm-point tricks
In-Reply-To: <1342959283.201.YahooMailClassic@web122502.mail.ne1.yahoo.com>
References: <1342959283.201.YahooMailClassic@web122502.mail.ne1.yahoo.com>
Message-ID: <CAF-j6z-XpAMeu34w=VkTMWNn--1PReeq19LtCU+58ONh3QBjPw@mail.gmail.com>

Someone has asked exactly the same question not long ago. Google it for
more details.
Basically, you can not use Gamma only calculation.
----------------------------------------------------
Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Sun, Jul 22, 2012 at 8:14 AM, henry odhiambo <henod2001 at yahoo.com> wrote:

>  Gamma-point tricks
>
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From pandey.bramha at gmail.com  Sun Jul 22 15:46:07 2012
From: pandey.bramha at gmail.com (bramha pandey)
Date: Sun, 22 Jul 2012 19:16:07 +0530
Subject: [Pw_forum] Gamm-point tricks
In-Reply-To: <1342959283.201.YahooMailClassic@web122502.mail.ne1.yahoo.com>
References: <1342959283.201.YahooMailClassic@web122502.mail.ne1.yahoo.com>
Message-ID: <CAC2dNGEHSbWO_ja9uhJUtKJEaaGcPOUxfZzQy-eF2UEhN+qneQ@mail.gmail.com>

Dear Henry,
you can firstly set k-points automatic in scf input file run, then it will
help i hope so.

On Sun, Jul 22, 2012 at 5:44 PM, henry odhiambo <henod2001 at yahoo.com> wrote:

> Dear users,
>
> I am doing phonon calculation using the code ph.x
>
> However, I get the error message bellow:
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       from phq_readin : error #         1
>       cannot start from pw.x data file using Gamma-point tricks
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> I never experienced this before.
>
> Could someone, please, help me identify the problem.
>
> Henry Otunga
> Dept. of Physics
> Maseno University
> Kenya
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Thanks and Regards
Bramha Prasad Pandey
Ph.D Student Indian School of Mines(ISM)
Dhanbad, INDIA.
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From giuseppe.mattioli at ism.cnr.it  Sun Jul 22 16:16:51 2012
From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli)
Date: Sun, 22 Jul 2012 16:16:51 +0200
Subject: [Pw_forum] Gamm-point tricks
In-Reply-To: <CAC2dNGEHSbWO_ja9uhJUtKJEaaGcPOUxfZzQy-eF2UEhN+qneQ@mail.gmail.com>
References: <1342959283.201.YahooMailClassic@web122502.mail.ne1.yahoo.com>
	<CAC2dNGEHSbWO_ja9uhJUtKJEaaGcPOUxfZzQy-eF2UEhN+qneQ@mail.gmail.com>
Message-ID: <20120722161651.8tkqyhwhz4040840@webmail.sic.rm.cnr.it>




More specifically, if your pw.x calculation has been performed by  
using K_POINTS (gamma), you should perform an additional calculation  
starting from your converged system, and using

K_POINTS (automatic)
1, 1, 1, 0, 0, 0

HTH

Giuseppe

Giuseppe Mattioli
ISM-CNR
Italy

> Dear Henry,
> you can firstly set k-points automatic in scf input file run, then it will
> help i hope so.
>
> On Sun, Jul 22, 2012 at 5:44 PM, henry odhiambo <henod2001 at yahoo.com> wrote:
>
>> Dear users,
>>
>> I am doing phonon calculation using the code ph.x
>>
>> However, I get the error message bellow:
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>       from phq_readin : error #         1
>>       cannot start from pw.x data file using Gamma-point tricks
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> I never experienced this before.
>>
>> Could someone, please, help me identify the problem.
>>
>> Henry Otunga
>> Dept. of Physics
>> Maseno University
>> Kenya
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Thanks and Regards
> Bramha Prasad Pandey
> Ph.D Student Indian School of Mines(ISM)
> Dhanbad, INDIA.
>





From sylviankahane at gmail.com  Sun Jul 22 22:55:15 2012
From: sylviankahane at gmail.com (sylvian)
Date: Sun, 22 Jul 2012 23:55:15 +0300
Subject: [Pw_forum] Etot in cp.x vs pw.x
Message-ID: <000001cd684c$4d194f80$e74bee80$@com>



Hello

 

cp.x is printing an Etot at the end of the run (in my case something like
-47 Ha). Taking its state at the end of the run, i.e. ions positions and
charge density, as an input to pw.x (admittedly with a different
pseudopotential)  I am getting a "total energy" differing by an order of
magnitude (in my case -800 Ry).

 

I guess that these two quantities are supposed to be somehow related, so
what are they representing and why are they so different ? 

 

---------------------------------------------------

Sylvian Kahane 

Nuclear Research Center - Negev

P.O.Box 9001, Beer-Sheva, 84190

Israel

Physics Dept. fax: 972-8656-7878

email:  <mailto:skahane at bgumail.bgu.ac.il> sylviankahane at gmail.com

---------------------------------------------------

 

 

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From degironc at sissa.it  Sun Jul 22 23:05:00 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sun, 22 Jul 2012 23:05:00 +0200
Subject: [Pw_forum] Etot in cp.x vs pw.x
In-Reply-To: <000001cd684c$4d194f80$e74bee80$@com>
References: <000001cd684c$4d194f80$e74bee80$@com>
Message-ID: <500C6AFC.80709@sissa.it>

comparing apples with oranges it's usually not a great idea.
make a sensible comparison and report the result if it still puzzles you.
best,
  stefano

On 07/22/2012 10:55 PM, sylvian wrote:
>
> Hello
>
>   
>
> cp.x is printing an Etot at the end of the run (in my case something like
> -47 Ha). Taking its state at the end of the run, i.e. ions positions and
> charge density, as an input to pw.x (admittedly with a different
> pseudopotential)  I am getting a "total energy" differing by an order of
> magnitude (in my case -800 Ry).
>
>   
> I guess that these two quantities are supposed to be somehow related, so
> what are they representing and why are they so different ?
>
>   
> ---------------------------------------------------
>
> Sylvian Kahane
>
> Nuclear Research Center - Negev
>
> P.O.Box 9001, Beer-Sheva, 84190
>
> Israel
>
> Physics Dept. fax: 972-8656-7878
>
> email:  <mailto:skahane at bgumail.bgu.ac.il> sylviankahane at gmail.com
>
> ---------------------------------------------------
>
>   
>
>   
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From giannozz at democritos.it  Sun Jul 22 23:06:01 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 22 Jul 2012 23:06:01 +0200
Subject: [Pw_forum] Etot in cp.x vs pw.x
In-Reply-To: <000001cd684c$4d194f80$e74bee80$@com>
References: <000001cd684c$4d194f80$e74bee80$@com>
Message-ID: <9800F28E-2C0A-4E35-9ABE-14D6EB3962F5@democritos.it>


On Jul 22, 2012, at 22:55 , sylvian wrote:
> I guess that these two quantities are supposed to be somehow related
>
Etot in PWscf (Ry) = 2*Etot in CP (Ha)
> so what are they representing
>
the DFT total energy
> and why are they so different ?
>
because the defaults for atomic positions differ between
the two code. Esplicitly specify
ATOMIC_POSITIONS bohr (or whatever applies)

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From lorenzo.paulatto at impmc.upmc.fr  Sun Jul 22 23:34:15 2012
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Sun, 22 Jul 2012 23:34:15 +0200
Subject: [Pw_forum] Etot in cp.x vs pw.x
In-Reply-To: <000001cd684c$4d194f80$e74bee80$@com>
References: <000001cd684c$4d194f80$e74bee80$@com>
Message-ID: <CAG+GtJfUnPSOH3JWrRZ7=zW1-j0DPvrcxhk5sXkwBMyTGxvqvQ@mail.gmail.com>

On Sun, Jul 22, 2012 at 10:55 PM, sylvian <sylviankahane at gmail.com> wrote:

> cp.x is printing an Etot at the end of the run (in my case something like
> -47 Ha). Taking its state at the end of the run, i.e. ions positions and
> charge density, as an input to pw.x (admittedly with a different
> pseudopotential)  I am getting a "total energy" differing by an order of
> magnitude (in my case -800 Ry).
>
>
>

Dear Sylvan,
absolute energies have no meaning in general. There can be some more or
less natural choices for a zero energy, but n periodic boundary conditions
and with pseudopotential there is none that really makes sense.

It is also true that with fairly similar pseudopotential you often get
similar (if equally meaningless) "total" energies. You are not specifying
which pp's you're using so I can only guess:
1. the pp used in pw.x has more valence electrons
2. the pp used in pw.x is actually a paw dataset, and you are comparing the
all-electron energy with the valence one

best regards

-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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From lorenzo.paulatto at impmc.upmc.fr  Sun Jul 22 23:42:17 2012
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Sun, 22 Jul 2012 23:42:17 +0200
Subject: [Pw_forum] ecutwfc
In-Reply-To: <1342417665.50599.YahooMailClassic@web192203.mail.sg3.yahoo.com>
References: <1342417665.50599.YahooMailClassic@web192203.mail.sg3.yahoo.com>
Message-ID: <CAG+GtJca-JSeA-FEAtP02P6ZQquP1uG5-5TzxUQmskrFZh-J=g@mail.gmail.com>

On Mon, Jul 16, 2012 at 7:47 AM, Sohail Ahmad <sohailphysics at yahoo.co.in>wrote:

> Dear Users,
> In QE, the usual first step is testing PP and ecutwfc
> I did it the same for bulk structure of a compound and followed further
> calculations
>
>  May i consider the same value of ecutoff for mono or bilayers of the
> same compound as i am considering the same pseudo potential
>
>
>
yes, you can
normally, cutoff only depends on the choice of pseudopotentials

-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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From henod2001 at yahoo.com  Mon Jul 23 12:12:40 2012
From: henod2001 at yahoo.com (henry odhiambo)
Date: Mon, 23 Jul 2012 03:12:40 -0700 (PDT)
Subject: [Pw_forum] Gamma-point tricks
In-Reply-To: <mailman.17.1342990521.1439.pw_forum@pwscf.org>
Message-ID: <1343038360.454.YahooMailClassic@web122506.mail.ne1.yahoo.com>

Thanks alot for responses.
?
Problem was with the k-points card in the input file.
?
Problem solved.

Henry Otunga
Dept Physics
Maseno University
Kenya

--- On Sun, 7/22/12, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> wrote:


From: pw_forum-request at pwscf.org <pw_forum-request at pwscf.org>
Subject: Pw_forum Digest, Vol 61, Issue 61
To: pw_forum at pwscf.org
Date: Sunday, July 22, 2012, 1:55 PM


Send Pw_forum mailing list submissions to
??? pw_forum at pwscf.org

To subscribe or unsubscribe via the World Wide Web, visit
??? http://www.democritos.it/mailman/listinfo/pw_forum
or, via email, send a message with subject or body 'help' to
??? pw_forum-request at pwscf.org

You can reach the person managing the list at
??? pw_forum-owner at pwscf.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Pw_forum digest..."


Today's Topics:

???1. Gamm-point tricks (henry odhiambo)
???2. Re: Gamm-point tricks (Duy Le)
???3. Re: Gamm-point tricks (bramha pandey)
???4. Re: Gamm-point tricks (Giuseppe Mattioli)
???5. Etot in cp.x vs pw.x (sylvian)


----------------------------------------------------------------------

Message: 1
Date: Sun, 22 Jul 2012 05:14:43 -0700 (PDT)
From: henry odhiambo <henod2001 at yahoo.com>
Subject: [Pw_forum] Gamm-point tricks
To: pw_forum at pwscf.org
Message-ID:
??? <1342959283.201.YahooMailClassic at web122502.mail.ne1.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear users,
?
I am doing phonon calculation using the code ph.x
?
However, I get the error message bellow:
?
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
????? from phq_readin : error #???????? 1
????? cannot start from pw.x data file using Gamma-point tricks

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
?
I never experienced this before.
?
Could someone, please, help me identify the problem.
?
Henry Otunga
Dept. of Physics
Maseno University
Kenya

?
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------------------------------

Message: 2
Date: Sun, 22 Jul 2012 08:23:06 -0400
From: Duy Le <ttduyle at gmail.com>
Subject: Re: [Pw_forum] Gamm-point tricks
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
??? <CAF-j6z-XpAMeu34w=VkTMWNn--1PReeq19LtCU+58ONh3QBjPw at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Someone has asked exactly the same question not long ago. Google it for
more details.
Basically, you can not use Gamma only calculation.
----------------------------------------------------
Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Sun, Jul 22, 2012 at 8:14 AM, henry odhiambo <henod2001 at yahoo.com> wrote:

>? Gamma-point tricks
>
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------------------------------

Message: 3
Date: Sun, 22 Jul 2012 19:16:07 +0530
From: bramha pandey <pandey.bramha at gmail.com>
Subject: Re: [Pw_forum] Gamm-point tricks
To: PWSCF Forum <pw_forum at pwscf.org>, henod2001 at yahoo.com
Message-ID:
??? <CAC2dNGEHSbWO_ja9uhJUtKJEaaGcPOUxfZzQy-eF2UEhN+qneQ at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Henry,
you can firstly set k-points automatic in scf input file run, then it will
help i hope so.

On Sun, Jul 22, 2012 at 5:44 PM, henry odhiambo <henod2001 at yahoo.com> wrote:

> Dear users,
>
> I am doing phonon calculation using the code ph.x
>
> However, I get the error message bellow:
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>? ? ???from phq_readin : error #? ? ? ???1
>? ? ???cannot start from pw.x data file using Gamma-point tricks
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> I never experienced this before.
>
> Could someone, please, help me identify the problem.
>
> Henry Otunga
> Dept. of Physics
> Maseno University
> Kenya
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Thanks and Regards
Bramha Prasad Pandey
Ph.D Student Indian School of Mines(ISM)
Dhanbad, INDIA.
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------------------------------

Message: 4
Date: Sun, 22 Jul 2012 16:16:51 +0200
From: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
Subject: Re: [Pw_forum] Gamm-point tricks
To: pw_forum at pwscf.org
Message-ID: <20120722161651.8tkqyhwhz4040840 at webmail.sic.rm.cnr.it>
Content-Type: text/plain;??? charset=ISO-8859-1;??? DelSp="Yes";
??? format="flowed"




More specifically, if your pw.x calculation has been performed by? 
using K_POINTS (gamma), you should perform an additional calculation? 
starting from your converged system, and using

K_POINTS (automatic)
1, 1, 1, 0, 0, 0

HTH

Giuseppe

Giuseppe Mattioli
ISM-CNR
Italy

> Dear Henry,
> you can firstly set k-points automatic in scf input file run, then it will
> help i hope so.
>
> On Sun, Jul 22, 2012 at 5:44 PM, henry odhiambo <henod2001 at yahoo.com> wrote:
>
>> Dear users,
>>
>> I am doing phonon calculation using the code ph.x
>>
>> However, I get the error message bellow:
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>? ? ???from phq_readin : error #? ? ? ???1
>>? ? ???cannot start from pw.x data file using Gamma-point tricks
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> I never experienced this before.
>>
>> Could someone, please, help me identify the problem.
>>
>> Henry Otunga
>> Dept. of Physics
>> Maseno University
>> Kenya
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Thanks and Regards
> Bramha Prasad Pandey
> Ph.D Student Indian School of Mines(ISM)
> Dhanbad, INDIA.
>






------------------------------

Message: 5
Date: Sun, 22 Jul 2012 23:55:15 +0300
From: "sylvian" <sylviankahane at gmail.com>
Subject: [Pw_forum] Etot in cp.x vs pw.x
To: <pw_forum at pwscf.org>
Message-ID: <000001cd684c$4d194f80$e74bee80$@com>
Content-Type: text/plain; charset="us-ascii"



Hello



cp.x is printing an Etot at the end of the run (in my case something like
-47 Ha). Taking its state at the end of the run, i.e. ions positions and
charge density, as an input to pw.x (admittedly with a different
pseudopotential)? I am getting a "total energy" differing by an order of
magnitude (in my case -800 Ry).



I guess that these two quantities are supposed to be somehow related, so
what are they representing and why are they so different ? 



---------------------------------------------------

Sylvian Kahane 

Nuclear Research Center - Negev

P.O.Box 9001, Beer-Sheva, 84190

Israel

Physics Dept. fax: 972-8656-7878

email:? <mailto:skahane at bgumail.bgu.ac.il> sylviankahane at gmail.com

---------------------------------------------------





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------------------------------

_______________________________________________
Pw_forum mailing list
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http://www.democritos.it/mailman/listinfo/pw_forum


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From davide.ceresoli at istm.cnr.it  Mon Jul 23 13:57:18 2012
From: davide.ceresoli at istm.cnr.it (Davide Ceresoli)
Date: Mon, 23 Jul 2012 13:57:18 +0200
Subject: [Pw_forum] Wrong representation in 5.0
Message-ID: <500D3C1E.60301@istm.cnr.it>

Dear all,
     I'm performing a phonon calculation on cubic cell (ibrav=1)
containing 65 atoms (64 + 1 impurity).

With espresso-4.3.2 there are no problems, however, using 5.0, PH
terminates with:

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      Error in routine set_irr_sym (3322):
      wrong representation
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

      stopping ...

PW reports that there are 6 symmetry operations. In short:

       6 Sym. Ops. (no inversion) found
       isym =  1     identity
       isym =  2     120 deg rotation - cart. axis [-1,-1,-1]
       isym =  3     120 deg rotation - cart. axis [1,1,1]
       isym =  4     inv. 180 deg rotation - cart. axis [1,-1,0]
       isym =  5     inv. 180 deg rotation - cart. axis [-1,0,1]
       isym =  6     inv. 180 deg rotation - cart. axis [0,1,-1]

      point group C_3v (3m)
      there are  3 classes
      the character table:

        E     2C3   3s_v
A_1    1.00  1.00  1.00
A_2    1.00  1.00 -1.00
E      2.00 -1.00  0.00

      the symmetry operations in each class:
      E        1
      2C3      2    3
      3s_v     4    5    6

I can supply input coordinates and output files to whoever knows
how to fix this problem with PH in version 5.0.

Best regards,
     Davide

From lorenzo.paulatto at impmc.upmc.fr  Mon Jul 23 14:28:10 2012
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Mon, 23 Jul 2012 14:28:10 +0200
Subject: [Pw_forum] Wrong representation in 5.0
In-Reply-To: <500D3C1E.60301@istm.cnr.it>
References: <500D3C1E.60301@istm.cnr.it>
Message-ID: <CAG+GtJefeTXqycByRQYY2Mc3jKzJ2J18Tff+u7dAssv6NxbmoQ@mail.gmail.com>

On Mon, Jul 23, 2012 at 1:57 PM, Davide Ceresoli <
davide.ceresoli at istm.cnr.it> wrote:

> I can supply input coordinates and output files to whoever knows
> how to fix this problem with PH in version 5.0.
>
>
Hi Davide,
the good news is that with espresso 4.x the calculation would run; the bad
news is that it would produce random garbage.

The error arises because of a newly introduced check which verifies that
the irreducible representations are actually representations. The origin of
the problem is the method used to find the irreducible representations: a
random pseudo-dynamical matrix is generated, than it is symmetrized and
diagonalized. The resulting eigenvectors are used as phonon displacement
patters; if the eigenvalues (pseudo-frequencies) of two patterns are
degenerate, also the real frequencies will be.

The problem is that sometimes a bit of numerical error in the
diagonalization makes two modes appear as not degenerate when they should
be, which in turn causes the irreducible representation to not be a
representation. We could increase the threshold a bit, but then there would
be a higher risk of getting accidental degeneration, causing the irr.reps.
to not be irreducible...

As a temporary workaround you can fiddle a bit with the threshold at line
258 of PH/set_irr.f90 or with how the random matrix in generated in
PH/random_matrix.f90 (i.e. increasing the diagonal component). I would also
ask you to send me the coordinates, to use as a test case, as I'm trying to
find a more reliable way to generate the matrix.

bests

-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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From sylviankahane at gmail.com  Mon Jul 23 18:31:50 2012
From: sylviankahane at gmail.com (sylvian kahane)
Date: Mon, 23 Jul 2012 19:31:50 +0300
Subject: [Pw_forum] Etot in cp.x vs pw.x
Message-ID: <CACrNQccQ9q0tRLmPxQ0ebCYv3w848V2AKWaXwtytpStqaCmymg@mail.gmail.com>

Regarding the response of  Lorenzo Paulatto

You are right on both accounts. The calculations involved 54 atoms of Li.
For the cp.x I used Vanderbild uspp with 1 valence electron
and for the pw.x, a paw calculated with Holzwarth program with all 3
electrons as valence.

When I am looking in the literature Jarlborg (Physica Scripta 37, 795
(1988)) gives -14.84 Ry/atom and this is what I got in my pw calculation
-800/54=-14.81, but  Dacorogna and Cohen (Phys. Rev. B 34, 4996 (1986) gave
-0.617 Ry/atom, which is not close but resembles my result from cp.x
-47*2/54=-1.74 Ry/atom.

Why I am bothered by these values ? I got involved in some EOS calculations
and I am trying to solve what is called as first shock
Hugoniot equation (which takes you from an initial state P1, V1, U1
(pressure, volume, internal energy) to a final state P2, T2, U2 by a shock):

                                 (U2 - U1) = 1/2*(P1+P2)*(V2-V1)   if
I remember correctly

in which you have to put the initial values.  For U I use

                                 U=3/2kT + Etot/N (N=54)

following some papers by one Lenosky (I don't have references right here).
So, if in this equation you use -1.74 Ry or -14.8 Ry it makes a hell of a
difference.

-- 
Sylvian (gmail:  sylviankahane at gmail.com)
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From sbinnie at sissa.it  Mon Jul 23 19:56:56 2012
From: sbinnie at sissa.it (Simon Binnie)
Date: Mon, 23 Jul 2012 19:56:56 +0200
Subject: [Pw_forum] Etot in cp.x vs pw.x
In-Reply-To: <CACrNQccQ9q0tRLmPxQ0ebCYv3w848V2AKWaXwtytpStqaCmymg@mail.gmail.com>
References: <CACrNQccQ9q0tRLmPxQ0ebCYv3w848V2AKWaXwtytpStqaCmymg@mail.gmail.com>
Message-ID: <op.whwus6g6b4z88i@hobbes>

On Mon, 23 Jul 2012 18:31:50 +0200, sylvian kahane  
<sylviankahane at gmail.com> wrote:

>
> When I am looking in the literature Jarlborg (Physica Scripta 37, 795
> (1988)) gives -14.84 Ry/atom and this is what I got in my pw calculation
> -800/54=-14.81, but  Dacorogna and Cohen (Phys. Rev. B 34, 4996 (1986)  
> gave
> -0.617 Ry/atom, which is not close but resembles my result from cp.x
> -47*2/54=-1.74 Ry/atom.

This is because the Jarlborg calculations appear to be all electron so  
match up (roughly) with the PAW calculation and the Cohen calculations use  
a pseudopotential with only one valence electron (so match up roughly with  
your pseudopotential calculation). As has been pointed out though total  
energies produced from pseudopotential calculations are meaningless, you  
have to look at energies differences between calculations using the same  
pseudopotentials. Unless you are using the same pseudo as Cohen et al. you  
shouldn't be looking to reproduce their total energies.

>
> Why I am bothered by these values ? I got involved in some EOS  
> calculations
> and I am trying to solve what is called as first shock
> Hugoniot equation (which takes you from an initial state P1, V1, U1
> (pressure, volume, internal energy) to a final state P2, T2, U2 by a  
> shock):
>
>                                  (U2 - U1) = 1/2*(P1+P2)*(V2-V1)   if
> I remember correctly
>
> in which you have to put the initial values.  For U I use
>
>                                  U=3/2kT + Etot/N (N=54)
>
> following some papers by one Lenosky (I don't have references right  
> here).
> So, if in this equation you use -1.74 Ry or -14.8 Ry it makes a hell of a
> difference.
>

This just means that the Etot1 and Etot2 (for use in U1 and U2) need to be  
calculated using the same pseudopotentials, then assuming that the  
pseudopotentials are a reasonable approximation for your system, U1 - U2  
should be the same across all different sets of pseudos.


Best regards,

Simon


-- 
Simon Binnie | Post Doc, Condensed Matter Sector
Scuola Internazionale di Studi Avanzati (SISSA)
Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it

From arebol2 at uic.edu  Mon Jul 23 20:21:40 2012
From: arebol2 at uic.edu (=?iso-8859-1?Q?=22Alejandro_R=E9bola=22?=)
Date: Mon, 23 Jul 2012 13:21:40 -0500
Subject: [Pw_forum] Wrong frequencies on STO phonons
In-Reply-To: <2CB721E0-1105-4C5A-B9B5-60E7B81A772D@democritos.it>
References: <7ede4216e1f49fa6e8b5cce193fecf56.squirrel@webmail.uic.edu>
	<1342784897.22438.4.camel@fe12lx.fisica.uniud.it>
	<31a229357d0f27bc3f40c6efe5caaf4b.squirrel@webmail.uic.edu>
	<2CB721E0-1105-4C5A-B9B5-60E7B81A772D@democritos.it>
Message-ID: <45ea8cc2b754024c0acd7b6800834e18.squirrel@webmail.uic.edu>

Dear Paolo,

The solution was to use the 5.0 version. I tried many times with the 4.2.1
(default on NERSC for some reason), and also with the 4.3.2 version,
obtaining all the time wrong frequencies and wrong dielectric constants. I
also did the same calculations on a different cluster, where they have the
4.3.2 version, same result. I was using exactly the same input files in
all cases and repeating the whole procedure -recalculating scf step. I
have no idea what could be the problem. But when I redid everything with
the 5.0 version instead, I got same results as you did.
Thank you for your time and help,

Alejandro

On Sun, July 22, 2012 1:58 am, Paolo Giannozzi wrote:
>
> On Jul 21, 2012, at 12:55 , Alejandro R?bola wrote:
>
>> I'm running the very same files on NERSC, using espresso 4.3.2 and
>> what
>> I'm getting is:
>
> here is what I get (with smaller thresholds, but it makes no
> difference):
> http://www.fisica.uniud.it/~giannozz/public/STO.tar.gz
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>



From giannozz at democritos.it  Mon Jul 23 21:19:07 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 23 Jul 2012 21:19:07 +0200
Subject: [Pw_forum] Wrong frequencies on STO phonons
In-Reply-To: <45ea8cc2b754024c0acd7b6800834e18.squirrel@webmail.uic.edu>
References: <7ede4216e1f49fa6e8b5cce193fecf56.squirrel@webmail.uic.edu>
	<1342784897.22438.4.camel@fe12lx.fisica.uniud.it>
	<31a229357d0f27bc3f40c6efe5caaf4b.squirrel@webmail.uic.edu>
	<2CB721E0-1105-4C5A-B9B5-60E7B81A772D@democritos.it>
	<45ea8cc2b754024c0acd7b6800834e18.squirrel@webmail.uic.edu>
Message-ID: <128976C5-E2DC-46C7-B707-C1B8C8152394@democritos.it>


On Jul 23, 2012, at 20:21 , Alejandro R?bola wrote:

> The solution was to use the 5.0 version.

funny: I am not aware of any recently fixed bug in the phonon
calculation. Anyway, thank you for reporting this

Paolo
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From dalcorso at sissa.it  Tue Jul 24 09:19:11 2012
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Tue, 24 Jul 2012 09:19:11 +0200
Subject: [Pw_forum] Wrong frequencies on STO phonons
In-Reply-To: <45ea8cc2b754024c0acd7b6800834e18.squirrel@webmail.uic.edu>
References: <7ede4216e1f49fa6e8b5cce193fecf56.squirrel@webmail.uic.edu>
	<1342784897.22438.4.camel@fe12lx.fisica.uniud.it>
	<31a229357d0f27bc3f40c6efe5caaf4b.squirrel@webmail.uic.edu>
	<2CB721E0-1105-4C5A-B9B5-60E7B81A772D@democritos.it>
	<45ea8cc2b754024c0acd7b6800834e18.squirrel@webmail.uic.edu>
Message-ID: <1343114351.3781.14.camel@ulisse.cm.sissa.it>

What happens if you increase nbnd?

HTH,

Andrea

On Mon, 2012-07-23 at 13:21 -0500, "Alejandro R?bola" wrote:
> Dear Paolo,
> 
> The solution was to use the 5.0 version. I tried many times with the 4.2.1
> (default on NERSC for some reason), and also with the 4.3.2 version,
> obtaining all the time wrong frequencies and wrong dielectric constants. I
> also did the same calculations on a different cluster, where they have the
> 4.3.2 version, same result. I was using exactly the same input files in
> all cases and repeating the whole procedure -recalculating scf step. I
> have no idea what could be the problem. But when I redid everything with
> the 5.0 version instead, I got same results as you did.
> Thank you for your time and help,
> 
> Alejandro
> 
> On Sun, July 22, 2012 1:58 am, Paolo Giannozzi wrote:
> >
> > On Jul 21, 2012, at 12:55 , Alejandro R?bola wrote:
> >
> >> I'm running the very same files on NERSC, using espresso 4.3.2 and
> >> what
> >> I'm getting is:
> >
> > here is what I get (with smaller thresholds, but it makes no
> > difference):
> > http://www.fisica.uniud.it/~giannozz/public/STO.tar.gz
> >
> > P.
> > ---
> > Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > Phone +39-0432-558216, fax +39-0432-558222
> >
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Bonomea 265              Fax. 0039-040-3787249
I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it



From bohdan.andriyevskyy at tu.koszalin.pl  Tue Jul 24 09:09:53 2012
From: bohdan.andriyevskyy at tu.koszalin.pl (Bohdan Andriyevskyy)
Date: Tue, 24 Jul 2012 09:09:53 +0200
Subject: [Pw_forum] Problem with epsilon.x
Message-ID: <500E4A41.9030501@tu.koszalin.pl>

Dear All,
when I try to calculate optical properties of my crystal (cluster) I 
obtain the following CRASH file:

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      task #         0
      from epsilon : error #         1
      ban band number
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The previous pw.x run was successful. The corresponding input files and 
the last output file (epsilon) are attached. Please, advise me how to 
resolve this problem.

Regards,
Bohdan
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From giannozz at democritos.it  Tue Jul 24 10:01:12 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 24 Jul 2012 10:01:12 +0200
Subject: [Pw_forum] Problem with epsilon.x
In-Reply-To: <500E4A41.9030501@tu.koszalin.pl>
References: <500E4A41.9030501@tu.koszalin.pl>
Message-ID: <1343116872.6261.3.camel@fe12lx.fisica.uniud.it>

On Tue, 2012-07-24 at 09:09 +0200, Bohdan Andriyevskyy wrote:

>       ban band number

of course the correct error message is "bad band number".
If you search this error message, you will find a comment 
explaining that you need more bands than valence bands only. 
You have valence bands only: occupations='fixed' (it should 
be 'smearing')

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From avms_t at yahoo.com  Tue Jul 24 11:16:15 2012
From: avms_t at yahoo.com (Avms T)
Date: Tue, 24 Jul 2012 02:16:15 -0700 (PDT)
Subject: [Pw_forum] (no subject)
In-Reply-To: <1343088653.74302.YahooMailNeo@web121104.mail.ne1.yahoo.com>
References: <1343088653.74302.YahooMailNeo@web121104.mail.ne1.yahoo.com>
Message-ID: <1343121375.30472.YahooMailNeo@web162305.mail.bf1.yahoo.com>




?Dear all,
I'm trying to calculate charge density of tio2 anatase.I test??a lot of??two orthogonal vectors ,but none of them is true.I can't discern?two orthogonal vectors for charge density input of anatase tio2.
?I would appreciate if you help me in this regard.
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From fratesi at mater.unimib.it  Tue Jul 24 16:05:23 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Tue, 24 Jul 2012 16:05:23 +0200
Subject: [Pw_forum] atomic projection in the band structure
In-Reply-To: <CAAzEAhEtQVvuQW+oqHujT7PO=5Ufwp8uSuc02ef_Y9+zqfJs2A@mail.gmail.com>
References: <CAOE2MOxc=-bugoNkeikz=tt6dpw_-tsOk-viUgFpBDBqWWHSbw@mail.gmail.com>
	<1B67BD24-7E6F-4A7F-B402-B1C93BBC0077@democritos.it>
	<CAAzEAhEtQVvuQW+oqHujT7PO=5Ufwp8uSuc02ef_Y9+zqfJs2A@mail.gmail.com>
Message-ID: <500EABA3.8090608@mater.unimib.it>

It could be useful to point out that the array of atomic projections 
<n,k|psi_nlm> is always written by projwfc.x to the file 
outdir/atomic_proj.xml
Best,
Guido

On 07/22/2012 08:54 AM, ??? wrote:
> !!!===============================
> !!!The following is code to get projected band structure by Y. C. Cheng
> !!! They should be added into "SUBROUTINE projwave( filproj, lsym,
> lgww )" in projwfc.f90 file
> !!!
> !!!They should added in the first
>    CHARACTER(LEN=80) :: myname
>    CHARACTER(LEN=8) :: bandnumber
> !!!The following should added before lowdin charge calculation
>       DO nwfc = 1, natomwfc
>       WRITE(myname,1000) &
>               nwfc, nlmchi(nwfc)%na, atm(ityp(nlmchi(nwfc)%na)), &
>               nlmchi(nwfc)%n, nlmchi(nwfc)%l, nlmchi(nwfc)%m
>
>                    !
>       open(12,file=myname, form='formatted', status='unknown')
>       WRITE (12,'(A11)',advance='no') "K"
>              DO ibnd = 1, nbnd
>                 WRITE(bandnumber,'(i4)') ibnd
>                 WRITE( 12, '(A11)',advance='no')  'E'//trim(adjustl(bandnumber))
>                 WRITE( 12, '(A11)',advance='no')  'R'//trim(adjustl(bandnumber))
>              END DO
>
>              DO ik = 1, nkstot
>                      WRITE( 12, '(/i11)',advance='no') ik
>                      DO ibnd = 1, nbnd
>                          WRITE( 12, '(f11.5)',advance='no') et (ibnd,
> ik) * rytoev
>                          WRITE( 12, '(f11.5)',advance='no') proj (nwfc, ibnd,ik)
>                      END DO
>              END DO
>       close (unit=12,status='keep')
>       END DO
>
> !!!=============================
>
> 2012/7/21 Paolo Giannozzi <giannozz at democritos.it>:
>>
>> On Jul 20, 2012, at 21:28 , Hanghui Chen wrote:
>>
>>> Can we also do atomic projections in the band structure
>>> calculations as in the VASP?
>>
>> see code "projwfc.x"
>>
>> P.
>> ---
>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy

From chiu at theochem.tu-muenchen.de  Tue Jul 24 16:32:57 2012
From: chiu at theochem.tu-muenchen.de (Cheng-chau Chiu)
Date: Tue, 24 Jul 2012 16:32:57 +0200
Subject: [Pw_forum] dipol correction in slab model calculations
Message-ID: <500EB219.3030909@theochem.tu-muenchen.de>

Dear pw_scf users,
I am performing slab model calculations. I want to take account for the 
fact, that the calculated system is also periodical in the direction 
perpendicular to the suface of the slab, by adding a dipol correction in 
that direction. So is it right, that the i have to set tefield and 
dipfield to .TRUE., of doing so? If so, is it convinient to use the 
default settings for eamp, emaxpos and eopreg?
Another question related to that is, if I am perfoming a "gas phase" 
calcualtion  (single molecule in a 20A*20A*20A unit cell) I might need 
to apply dipole correction in all three directions. How can I do this?  
It seems (as far as I have understood the QE documentation) that I can 
only apply the correction in one direction at a time by setting  
edir=1,2, or 3.
Thank you in advance,

Cheng-chau Chiu, PhD-Student
TU Muenchen

From fratesi at mater.unimib.it  Tue Jul 24 17:04:57 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Tue, 24 Jul 2012 17:04:57 +0200
Subject: [Pw_forum] dipol correction in slab model calculations
In-Reply-To: <500EB219.3030909@theochem.tu-muenchen.de>
References: <500EB219.3030909@theochem.tu-muenchen.de>
Message-ID: <500EB999.1060804@mater.unimib.it>

Dear Cheng-chau,

you might find this post helpful:
http://www.democritos.it/pipermail/pw_forum/2009-August/013827.html

As for the gas phase, if you have a polar molecule you could have its 
dipole along one axis and choose edir accordingly. Also have a look to 
the input parameter "assume_isolated", especially for charged species.

HTH
Guido

On 07/24/2012 04:32 PM, Cheng-chau Chiu wrote:
> Dear pw_scf users,
> I am performing slab model calculations. I want to take account for the
> fact, that the calculated system is also periodical in the direction
> perpendicular to the suface of the slab, by adding a dipol correction in
> that direction. So is it right, that the i have to set tefield and
> dipfield to .TRUE., of doing so? If so, is it convinient to use the
> default settings for eamp, emaxpos and eopreg?
> Another question related to that is, if I am perfoming a "gas phase"
> calcualtion  (single molecule in a 20A*20A*20A unit cell) I might need
> to apply dipole correction in all three directions. How can I do this?
> It seems (as far as I have understood the QE documentation) that I can
> only apply the correction in one direction at a time by setting
> edir=1,2, or 3.
> Thank you in advance,
>
> Cheng-chau Chiu, PhD-Student
> TU Muenchen
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy

From bamideleibrahim at yahoo.com  Tue Jul 24 17:50:57 2012
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Tue, 24 Jul 2012 08:50:57 -0700 (PDT)
Subject: [Pw_forum] error in DGETRF during generation of pseudopotential
Message-ID: <1343145057.64090.YahooMailNeo@web39401.mail.mud.yahoo.com>

Dear all,
? I am trying to generate gipaw pseudopotential for Se. And after some time the program will stop and in the output files it produces this error immediately it enter the NC pseudopotential routine. ? 

########################################## 
from invmat : error # 1
?error in DGETRF
###########################################
? I will be delighted if i can get assistance on how to resolve this. i am not an expert in pseudopotential generation.

Adetunji Bamidele Ibrahim(PhD Student)
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.
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From sylviankahane at gmail.com  Tue Jul 24 19:13:30 2012
From: sylviankahane at gmail.com (sylvian kahane)
Date: Tue, 24 Jul 2012 20:13:30 +0300
Subject: [Pw_forum] RE Problem with epsilon.x
Message-ID: <CACrNQcc=LDHZQo7TNvYqA+UGoHGiCmxx3G7+AL7NYeSp2NC19A@mail.gmail.com>

I think that in the in the input to pw you have to put in some place a
nbnd=xx parameter.
How many bands did you produced in your pw run ?
Probably xx has to be a fairly large number to have some band above the
Fermi surface.

-- 
Sylvian (gmail:  sylviankahane at gmail.com)
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From arebol2 at uic.edu  Tue Jul 24 20:09:13 2012
From: arebol2 at uic.edu (=?iso-8859-1?Q?=22Alejandro_R=E9bola=22?=)
Date: Tue, 24 Jul 2012 13:09:13 -0500
Subject: [Pw_forum] Wrong frequencies on STO phonons
In-Reply-To: <1343114351.3781.14.camel@ulisse.cm.sissa.it>
References: <7ede4216e1f49fa6e8b5cce193fecf56.squirrel@webmail.uic.edu>
	<1342784897.22438.4.camel@fe12lx.fisica.uniud.it>
	<31a229357d0f27bc3f40c6efe5caaf4b.squirrel@webmail.uic.edu>
	<2CB721E0-1105-4C5A-B9B5-60E7B81A772D@democritos.it>
	<45ea8cc2b754024c0acd7b6800834e18.squirrel@webmail.uic.edu>
	<1343114351.3781.14.camel@ulisse.cm.sissa.it>
Message-ID: <9e4f127f61c20e64f3fc0a58d62f3f04.squirrel@webmail.uic.edu>

I'm increasing nbnd, I'll see what happens.
I have another question. Apparently there's a change in the format of the
file containing the force constants (name.fc) in espresso 5.0.0 wrt to
previous versions. In 4.3.2, the name.fc contains the type of the
structure on the second line (e.g. cubic), but this line is absent in
5.0.0. This causes the matdyn.x code to crash. Did anybody else have this
problem?
Thanks,

Alejandro


On Tue, July 24, 2012 2:19 am, Andrea Dal Corso wrote:
> What happens if you increase nbnd?
>
> HTH,
>
> Andrea
>
> On Mon, 2012-07-23 at 13:21 -0500, "Alejandro R??bola" wrote:
>> Dear Paolo,
>>
>> The solution was to use the 5.0 version. I tried many times with the
>> 4.2.1
>> (default on NERSC for some reason), and also with the 4.3.2 version,
>> obtaining all the time wrong frequencies and wrong dielectric constants.
>> I
>> also did the same calculations on a different cluster, where they have
>> the
>> 4.3.2 version, same result. I was using exactly the same input files in
>> all cases and repeating the whole procedure -recalculating scf step. I
>> have no idea what could be the problem. But when I redid everything with
>> the 5.0 version instead, I got same results as you did.
>> Thank you for your time and help,
>>
>> Alejandro
>>
>> On Sun, July 22, 2012 1:58 am, Paolo Giannozzi wrote:
>> >
>> > On Jul 21, 2012, at 12:55 , Alejandro R??bola wrote:
>> >
>> >> I'm running the very same files on NERSC, using espresso 4.3.2 and
>> >> what
>> >> I'm getting is:
>> >
>> > here is what I get (with smaller thresholds, but it makes no
>> > difference):
>> > http://www.fisica.uniud.it/~giannozz/public/STO.tar.gz
>> >
>> > P.
>> > ---
>> > Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> > Phone +39-0432-558216, fax +39-0432-558222
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>> >
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> --
> Andrea Dal Corso                    Tel. 0039-040-3787428
> SISSA, Via Bonomea 265              Fax. 0039-040-3787249
> I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


From giannozz at democritos.it  Tue Jul 24 21:05:43 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 24 Jul 2012 21:05:43 +0200
Subject: [Pw_forum] Wrong frequencies on STO phonons
In-Reply-To: <9e4f127f61c20e64f3fc0a58d62f3f04.squirrel@webmail.uic.edu>
References: <7ede4216e1f49fa6e8b5cce193fecf56.squirrel@webmail.uic.edu>
	<1342784897.22438.4.camel@fe12lx.fisica.uniud.it>
	<31a229357d0f27bc3f40c6efe5caaf4b.squirrel@webmail.uic.edu>
	<2CB721E0-1105-4C5A-B9B5-60E7B81A772D@democritos.it>
	<45ea8cc2b754024c0acd7b6800834e18.squirrel@webmail.uic.edu>
	<1343114351.3781.14.camel@ulisse.cm.sissa.it>
	<9e4f127f61c20e64f3fc0a58d62f3f04.squirrel@webmail.uic.edu>
Message-ID: <6B399AB1-0212-48CB-8B9C-1D1F8E2752E4@democritos.it>


On Jul 24, 2012, at 20:09 , Alejandro R?bola wrote:

> Apparently there's a change in the format of the file containing  
> the force
> constants (name.fc) in espresso 5.0.0 wrt to previous versions. In  
> 4.3.2,
> the name.fc contains the type of the structure on the second line  
> (e.g. cubic),
> but this line is absent in 5.0.0. This causes the matdyn.x code to  
> crash.
> Did anybody else have this problem?

I think it is this one:
http://qe-forge.org/scm/viewvc.php?view=rev&root=q-e&revision=9070

P.

---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From zhanhit at hotmail.com  Wed Jul 25 07:13:25 2012
From: zhanhit at hotmail.com (Franklin Zhan)
Date: Wed, 25 Jul 2012 05:13:25 +0000
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
Message-ID: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>


Dear PWSCF users,
I am trying to calculate HOMO and LUMO levels and plot these isosurfaces for O2 molecule.
I first relaxed the O2 and then did nscf calculation. then I used pp.x to calculate the HOMO and LUMO levels. but I can not find the HOMO or LUMO level in output files.
the code for pp.x is pasted as following:

&inputpp
    prefix= 'O2'
    outdir= '/scratch/zhan0273/PWSCF/O2/tmp'
filplot = 'O2'
plot_num= 7
spin_component=0
kpoint=40
kband=8
/
&plot
nfile = 1
filepp(1) = 'O2'
weight(1) = 1.0
iflag = 3
output_format = 5
fileout = 'O2.orb.xsf'
/

So please give advice. Thank you all in advance!

Best regards,



Franklin Zhan
Ph.D student
School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore.



 		 	   		  
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From flima at if.usp.br  Wed Jul 25 08:43:30 2012
From: flima at if.usp.br (Filipe Camargo Dalmatti Alves Lima)
Date: Wed, 25 Jul 2012 03:43:30 -0300
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>
Message-ID: <CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>

Dear Zhan,

The number of electrons on your system determines the occupied bands and
consequently the HOMO level.

So, What you need to do?

First, check the number of electron that you are using. (If you are using
the O default pseudopotencials it should be 6 valence electrons)
Then, you'll have 12 electrons and 6 bands (each bands is occupied by 2
electrons).

Now check your output file, which is generated using the pw.x code.
The band number 6 represents your HOMO level and the band number 7 is the
LUMO one.

So, now you know your bands. Then you can obtain the wavefunction.

You will need to run the pp.x twice: one for HOMO and another for LUMO.
kband=6 (to plot HOMO)
and
kdand=7 (to plot LUMO)

I hope it will solve your problem,

Best regards,


-- 
_________________________________________
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:    (11) 3091-6881  (USP)
                (11) 8249-4628 (TIM)



On Wed, Jul 25, 2012 at 2:13 AM, Franklin Zhan <zhanhit at hotmail.com> wrote:

>  Dear PWSCF users,
> I am trying to calculate HOMO and LUMO levels and plot these isosurfaces
> for O2 molecule.
> I first relaxed the O2 and then did nscf calculation. then I used pp.x to
> calculate the HOMO and LUMO levels. but I can not find the HOMO or LUMO
> level in output files.
> the code for pp.x is pasted as following:
>
> &inputpp
>     prefix= 'O2'
>     outdir= '/scratch/zhan0273/PWSCF/O2/tmp'
> filplot = 'O2'
> plot_num= 7
> spin_component=0
> ! kpoint=40
> kband=8
> /
> &plot
> nfile = 1
> filepp(1) = 'O2'
> weight(1) = 1.0
> iflag = 3
> output_format = 5
> fileout = 'O2.orb.xsf'
> /
>
> So please give advice. Thank you all in advance!
>
> Best regards,
>
> ------------------------------
> Franklin Zhan
> Ph.D student
> School of Mechanical and Aerospace Engineering,
> Nanyang Technological University, Singapore.
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From mahdi_fn109 at yahoo.com  Wed Jul 25 09:10:57 2012
From: mahdi_fn109 at yahoo.com (Mahdi Faghih nasiri)
Date: Wed, 25 Jul 2012 00:10:57 -0700 (PDT)
Subject: [Pw_forum] Problem on runing espresso-4.3.2
Message-ID: <1343200257.64844.YahooMailNeo@web43141.mail.sp1.yahoo.com>

Dear all,
When I tried to run espresso-4.3.2 with composer_xe_2011_sp1.6.233, the error "error while loading shared libraries: 
/opt/intel/mkl/10.0.4.023/lib/em64t/libmkl_intel_lp64.so: 
cannot open shared object file: No such file or directory" came out.
Please help me to resolve it, thank you in advance!

?
Mahdi Faghih nasiri
MSC,
Guilan University,
Rasht, Iran.
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From giuseppe.mattioli at ism.cnr.it  Wed Jul 25 09:16:43 2012
From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli)
Date: Wed, 25 Jul 2012 09:16:43 +0200
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>
	<CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>
Message-ID: <201207250916.45017.giuseppe.mattioli@ism.cnr.it>


Dear Felipe
You seem not to be a chemist...:-)
The ground state of an O2 molecule is a triplet one, with 7 up valence electrons and 5 down.

Dear Zhan
This morning (morning in Italy, at least) you are lucky. I've done (almost) the same thing 
yesterday...

Once the above is settled, first you should perform a relax calculation with K_POINTS (gamma). You do 
not need a nscf calculation if you use a bit of smearing. Something like

 &control
    calculation = 'relax'
    prefix='$FILE',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/',
 /
 &system
    ibrav=1, celldm(1)=30.000000,
    nat=2, ntyp=1,
    ecutwfc =35.0,
    ecutrho =280.0,
    occupations='smearing', degauss=0.01,
    nspin=2,
    starting_magnetization(1)=0.3,
 /
 &electrons
    mixing_mode='plain'
    mixing_beta=0.3
    conv_thr=1.0d-7
    electron_maxstep=200
 /
 &ions
    ion_dynamics='bfgs'
 /
ATOMIC_SPECIES
O    15.999     O_pbe.van.UPF
ATOMIC_POSITIONS {angstrom}
O        5.000576334   5.029093041   5.029093041
O        5.009423666   5.870906959   5.870906959
K_POINTS {gamma}

will provide a sufficient number of unoccupied orbitals for your purpose.

Then, remember that when you use nspin=2 and K_POINTS {gamma} you are formally using two k points 
(gamma up and gamma down) which are labelled as kpoint=1 and kpoint=2, respectively. In your pw.x 
output you should acknowledge (but you should already know it by molecular orbital theory of 
homonuclear diatomic molecules...) that both the HOMO in the up channel (-9.1985  -9.1983) and the 
LUMO in the down channel (-4.9925  -4.9924) are doubly degenerate. Thus, you must plot the single-
electron orbitals and sum them.

 ------ SPIN UP ------------


          k = 0.0000 0.0000 0.0000 ( 47171 PWs)   bands (ev):

   -34.3196 -21.0375 -17.4698 -17.4697 -14.7359  -9.1985  -9.1983  -0.6483
    -0.1403  -0.0924

 ------ SPIN DOWN ----------


          k = 0.0000 0.0000 0.0000 ( 47171 PWs)   bands (ev):

   -33.1724 -19.2543 -13.7742 -12.6937 -12.6937  -4.9925  -4.9924  -0.5833
    -0.0519  -0.0089

     the Fermi energy is    -8.4505 ev

This is quite easy, supposing that you read carefully the pp.x input guide... But, as I said, you 
won a free ride today...

 &inputpp
    prefix  = '$FILEA'
    outdir = '$TMP_DIR/'
    filplot = '$FILEA-HOMOa.dat'
    plot_num= 7
    kpoint=1
    kband=6
 /

$PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE

 &inputpp
    prefix  = '$FILEA'
    outdir = '$TMP_DIR/'
    filplot = '$FILEA-HOMOb.dat'
    plot_num= 7
    kpoint=1
    kband=7
 /

$PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE


 &inputpp
 /
 &plot
    nfile = 2
    filepp(1) = '$FILEA-HOMOa.dat'
    weight(1) = 1.0
    filepp(2) = '$FILEA-HOMOb.dat'
    weight(2) = 1.0
    iflag = 3
    output_format = 5
    fileout = '$FILEA-HOMO.plot'
    e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0,
    e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
    nx=56, ny=40
 /

$PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE

This will produce a nice .xsf file containing your HOMO orbital, which you can plot with xcrysden. 
You may also obtain a cube file, but I cannot remember the output format.

As for the LUMO, use kpoint=2, and the correct kband numbers and do the same thing.

I hope this really help... (in Italy I would have said: you owe me a cup of coffee...)

Giuseppe


On Wednesday 25 July 2012 08:43:30 Filipe Camargo Dalmatti Alves Lima wrote:
> Dear Zhan,
> 
> The number of electrons on your system determines the occupied bands and
> consequently the HOMO level.
> 
> So, What you need to do?
> 
> First, check the number of electron that you are using. (If you are using
> the O default pseudopotencials it should be 6 valence electrons)
> Then, you'll have 12 electrons and 6 bands (each bands is occupied by 2
> electrons).
> 
> Now check your output file, which is generated using the pw.x code.
> The band number 6 represents your HOMO level and the band number 7 is the
> LUMO one.
> 
> So, now you know your bands. Then you can obtain the wavefunction.
> 
> You will need to run the pp.x twice: one for HOMO and another for LUMO.
> kband=6 (to plot HOMO)
> and
> kdand=7 (to plot LUMO)
> 
> I hope it will solve your problem,
> 
> Best regards,
> 
> >  Dear PWSCF users,
> > 
> > I am trying to calculate HOMO and LUMO levels and plot these isosurfaces
> > for O2 molecule.
> > I first relaxed the O2 and then did nscf calculation. then I used pp.x to
> > calculate the HOMO and LUMO levels. but I can not find the HOMO or LUMO
> > level in output files.
> > the code for pp.x is pasted as following:
> > 
> > &inputpp
> > 
> >     prefix= 'O2'
> >     outdir= '/scratch/zhan0273/PWSCF/O2/tmp'
> > 
> > filplot = 'O2'
> > plot_num= 7
> > spin_component=0
> > ! kpoint=40
> > kband=8
> > /
> > &plot
> > nfile = 1
> > filepp(1) = 'O2'
> > weight(1) = 1.0
> > iflag = 3
> > output_format = 5
> > fileout = 'O2.orb.xsf'
> > /
> > 
> > So please give advice. Thank you all in advance!
> > 
> > Best regards,
> > 
> > ------------------------------
> > Franklin Zhan
> > Ph.D student
> > School of Mechanical and Aerospace Engineering,
> > Nanyang Technological University, Singapore.
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum

-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

   Giuseppe Mattioli                            
   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
   v. Salaria Km 29,300 - C.P. 10                
   I 00015 - Monterotondo Stazione (RM)          
   Tel + 39 06 90672836 - Fax +39 06 90672316    
   E-mail: <giuseppe.mattioli at ism.cnr.it>

From torstein.fjermestad at kjemi.uio.no  Wed Jul 25 10:11:40 2012
From: torstein.fjermestad at kjemi.uio.no (Torstein Fjermestad)
Date: Wed, 25 Jul 2012 10:11:40 +0200
Subject: [Pw_forum] =?utf-8?q?Calculation_of_Gibbs_free_energies?=
In-Reply-To: <29607723.dee4.1387576487b.Coremail.flux_ray12@163.com>
References: <9ab5bb3130dbbdad6da9232ea8e9585c@ulrik.uio.no>
	<29607723.dee4.1387576487b.Coremail.flux_ray12@163.com>
Message-ID: <ae4409a5108eb85a0f6f2b2f2e42bdda@ulrik.uio.no>

 Dear GAO Zhe,

 Thanks for your suggestion. Of cause one can calculate the vibrational 
 free energy directly from the frequencies. I did not think about that. 
 :(

 Regards

 Torstein Fjermestad
 University of Oslo
 Norway


 On Wed, 11 Jul 2012 17:54:42 +0800 (CST), "GAO Zhe" 
 <flux_ray12 at 163.com> wrote:
> According to my experience, the general process is right, but, this
> general process is normally working for crystal rather than 
> amorphous,
> liquid and gas. Since the contribution from vibration is not that 
> much
> in those matter, for example, transition contributes much more in gas
> phase. Therefore, Monte Carlo or Molecular Dynamic could be better
> choice in these cases.
> Technically, in your calculation, H2O molecule may exist in a box,
> therefore only the Gamma phonon calculation is meaningful. Since q2r
> means fitting the finite samplings of dynamic matrics to infinite
> interatomic force constants, only one point is not that reliable to
> find good aproach of IFCs. Actually, since vibrational free energy is
> defined with the term of hv, you can derectly obtain Fvib from your
> first step.
>
> --
> GAO Zhe
> CMC Lab, Materials Science & Engineering Department,
> Seoul National University, South Korea
>




From zhanhit at hotmail.com  Wed Jul 25 10:12:09 2012
From: zhanhit at hotmail.com (Franklin Zhan)
Date: Wed, 25 Jul 2012 08:12:09 +0000
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <201207250916.45017.giuseppe.mattioli@ism.cnr.it>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>,
	<CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>,
	<201207250916.45017.giuseppe.mattioli@ism.cnr.it>
Message-ID: <BAY151-W3542EBDFCE52FD76461DC5A7C30@phx.gbl>


Dear Giuseppe,
Deepest thanks for your advice.
Your suggestion is really helpful and inspiring.
If you are in Singapore, I would like to buy you a cup of coffee,
Cheers~,


Franklin


Franklin Zhan
 
Ph.D student
School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore.





> From: giuseppe.mattioli at ism.cnr.it
> To: pw_forum at pwscf.org
> Date: Wed, 25 Jul 2012 09:16:43 +0200
> Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
> 
> 
> Dear Felipe
> You seem not to be a chemist...:-)
> The ground state of an O2 molecule is a triplet one, with 7 up valence electrons and 5 down.
> 
> Dear Zhan
> This morning (morning in Italy, at least) you are lucky. I've done (almost) the same thing 
> yesterday...
> 
> Once the above is settled, first you should perform a relax calculation with K_POINTS (gamma). You do 
> not need a nscf calculation if you use a bit of smearing. Something like
> 
>  &control
>     calculation = 'relax'
>     prefix='$FILE',
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/',
>  /
>  &system
>     ibrav=1, celldm(1)=30.000000,
>     nat=2, ntyp=1,
>     ecutwfc =35.0,
>     ecutrho =280.0,
>     occupations='smearing', degauss=0.01,
>     nspin=2,
>     starting_magnetization(1)=0.3,
>  /
>  &electrons
>     mixing_mode='plain'
>     mixing_beta=0.3
>     conv_thr=1.0d-7
>     electron_maxstep=200
>  /
>  &ions
>     ion_dynamics='bfgs'
>  /
> ATOMIC_SPECIES
> O    15.999     O_pbe.van.UPF
> ATOMIC_POSITIONS {angstrom}
> O        5.000576334   5.029093041   5.029093041
> O        5.009423666   5.870906959   5.870906959
> K_POINTS {gamma}
> 
> will provide a sufficient number of unoccupied orbitals for your purpose.
> 
> Then, remember that when you use nspin=2 and K_POINTS {gamma} you are formally using two k points 
> (gamma up and gamma down) which are labelled as kpoint=1 and kpoint=2, respectively. In your pw.x 
> output you should acknowledge (but you should already know it by molecular orbital theory of 
> homonuclear diatomic molecules...) that both the HOMO in the up channel (-9.1985  -9.1983) and the 
> LUMO in the down channel (-4.9925  -4.9924) are doubly degenerate. Thus, you must plot the single-
> electron orbitals and sum them.
> 
>  ------ SPIN UP ------------
> 
> 
>           k = 0.0000 0.0000 0.0000 ( 47171 PWs)   bands (ev):
> 
>    -34.3196 -21.0375 -17.4698 -17.4697 -14.7359  -9.1985  -9.1983  -0.6483
>     -0.1403  -0.0924
> 
>  ------ SPIN DOWN ----------
> 
> 
>           k = 0.0000 0.0000 0.0000 ( 47171 PWs)   bands (ev):
> 
>    -33.1724 -19.2543 -13.7742 -12.6937 -12.6937  -4.9925  -4.9924  -0.5833
>     -0.0519  -0.0089
> 
>      the Fermi energy is    -8.4505 ev
> 
> This is quite easy, supposing that you read carefully the pp.x input guide... But, as I said, you 
> won a free ride today...
> 
>  &inputpp
>     prefix  = '$FILEA'
>     outdir = '$TMP_DIR/'
>     filplot = '$FILEA-HOMOa.dat'
>     plot_num= 7
>     kpoint=1
>     kband=6
>  /
> 
> $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
> 
>  &inputpp
>     prefix  = '$FILEA'
>     outdir = '$TMP_DIR/'
>     filplot = '$FILEA-HOMOb.dat'
>     plot_num= 7
>     kpoint=1
>     kband=7
>  /
> 
> $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
> 
> 
>  &inputpp
>  /
>  &plot
>     nfile = 2
>     filepp(1) = '$FILEA-HOMOa.dat'
>     weight(1) = 1.0
>     filepp(2) = '$FILEA-HOMOb.dat'
>     weight(2) = 1.0
>     iflag = 3
>     output_format = 5
>     fileout = '$FILEA-HOMO.plot'
>     e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0,
>     e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
>     nx=56, ny=40
>  /
> 
> $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
> 
> This will produce a nice .xsf file containing your HOMO orbital, which you can plot with xcrysden. 
> You may also obtain a cube file, but I cannot remember the output format.
> 
> As for the LUMO, use kpoint=2, and the correct kband numbers and do the same thing.
> 
> I hope this really help... (in Italy I would have said: you owe me a cup of coffee...)
> 
> Giuseppe
> 
> 
> On Wednesday 25 July 2012 08:43:30 Filipe Camargo Dalmatti Alves Lima wrote:
> > Dear Zhan,
> > 
> > The number of electrons on your system determines the occupied bands and
> > consequently the HOMO level.
> > 
> > So, What you need to do?
> > 
> > First, check the number of electron that you are using. (If you are using
> > the O default pseudopotencials it should be 6 valence electrons)
> > Then, you'll have 12 electrons and 6 bands (each bands is occupied by 2
> > electrons).
> > 
> > Now check your output file, which is generated using the pw.x code.
> > The band number 6 represents your HOMO level and the band number 7 is the
> > LUMO one.
> > 
> > So, now you know your bands. Then you can obtain the wavefunction.
> > 
> > You will need to run the pp.x twice: one for HOMO and another for LUMO.
> > kband=6 (to plot HOMO)
> > and
> > kdand=7 (to plot LUMO)
> > 
> > I hope it will solve your problem,
> > 
> > Best regards,
> > 
> > >  Dear PWSCF users,
> > > 
> > > I am trying to calculate HOMO and LUMO levels and plot these isosurfaces
> > > for O2 molecule.
> > > I first relaxed the O2 and then did nscf calculation. then I used pp.x to
> > > calculate the HOMO and LUMO levels. but I can not find the HOMO or LUMO
> > > level in output files.
> > > the code for pp.x is pasted as following:
> > > 
> > > &inputpp
> > > 
> > >     prefix= 'O2'
> > >     outdir= '/scratch/zhan0273/PWSCF/O2/tmp'
> > > 
> > > filplot = 'O2'
> > > plot_num= 7
> > > spin_component=0
> > > ! kpoint=40
> > > kband=8
> > > /
> > > &plot
> > > nfile = 1
> > > filepp(1) = 'O2'
> > > weight(1) = 1.0
> > > iflag = 3
> > > output_format = 5
> > > fileout = 'O2.orb.xsf'
> > > /
> > > 
> > > So please give advice. Thank you all in advance!
> > > 
> > > Best regards,
> > > 
> > > ------------------------------
> > > Franklin Zhan
> > > Ph.D student
> > > School of Mechanical and Aerospace Engineering,
> > > Nanyang Technological University, Singapore.
> > > 
> > > 
> > > 
> > > 
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> 
> -- 
> ********************************************************
> - Article premier - Les hommes naissent et demeurent
> libres et ?gaux en droits. Les distinctions sociales
> ne peuvent ?tre fond?es que sur l'utilit? commune
> - Article 2 - Le but de toute association politique
> est la conservation des droits naturels et 
> imprescriptibles de l'homme. Ces droits sont la libert?,
> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> ********************************************************
> 
>    Giuseppe Mattioli                            
>    CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
>    v. Salaria Km 29,300 - C.P. 10                
>    I 00015 - Monterotondo Stazione (RM)          
>    Tel + 39 06 90672836 - Fax +39 06 90672316    
>    E-mail: <giuseppe.mattioli at ism.cnr.it>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
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From zhanhit at hotmail.com  Wed Jul 25 10:13:22 2012
From: zhanhit at hotmail.com (Franklin Zhan)
Date: Wed, 25 Jul 2012 08:13:22 +0000
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>,
	<CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>
Message-ID: <BAY151-W23837EF42CCB7B44D6B70A7C30@phx.gbl>






Hi Filipe,
Thanks for you reply which makes me clearer a little bit.
I will try to figure out it.

Best regards,



Franklin Zhan
Ph.D student
School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore.





From: flima at if.usp.br
Date: Wed, 25 Jul 2012 03:43:30 -0300
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface

Dear Zhan,
The number of electrons on your system determines the occupied bands and consequently the HOMO level.
So, What you need to do?
First, check the number of electron that you are using. (If you are using the O default pseudopotencials it should be 6 valence electrons)

Then, you'll have 12 electrons and 6 bands (each bands is occupied by 2 electrons).
Now check your output file, which is generated using the pw.x code.The band number 6 represents your HOMO level and the band number 7 is the LUMO one.


So, now you know your bands. Then you can obtain the wavefunction.
You will need to run the pp.x twice: one for HOMO and another for LUMO.kband=6 (to plot HOMO)

andkdand=7 (to plot LUMO)
I hope it will solve your problem,
Best regards,
-- 
_________________________________________


Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil.
Phones:    (11) 3091-6881  (USP)
                (11) 8249-4628 (TIM)



On Wed, Jul 25, 2012 at 2:13 AM, Franklin Zhan <zhanhit at hotmail.com> wrote:






Dear PWSCF users,
I am trying to calculate HOMO and LUMO levels and plot these isosurfaces for O2 molecule.
I first relaxed the O2 and then did nscf calculation. then I used pp.x to calculate the HOMO and LUMO levels. but I can not find the HOMO or LUMO level in output files.


the code for pp.x is pasted as following:

&inputpp
    prefix= 'O2'
    outdir= '/scratch/zhan0273/PWSCF/O2/tmp'


filplot = 'O2'
plot_num= 7
spin_component=0


!
 kpoint=40
kband=8
/
&plot


nfile = 1
filepp(1) = 'O2'
weight(1) = 1.0


iflag = 3
output_format = 5
fileout = 'O2.orb.xsf'


/

So please give advice. Thank you all in advance!

Best regards,



Franklin Zhan
Ph.D student
School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore.



 		 	   		  



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From torstein.fjermestad at kjemi.uio.no  Wed Jul 25 12:12:08 2012
From: torstein.fjermestad at kjemi.uio.no (Torstein Fjermestad)
Date: Wed, 25 Jul 2012 12:12:08 +0200
Subject: [Pw_forum] parallelization of phonon calculations
Message-ID: <d4b8ba5d12cde2868d21c4da6daee748@ulrik.uio.no>

 Dear all,

 I am planing to do a phonon calculation on a zeolite structure. The 
 unit cell contains 37 atoms, the space group is P1, and the number of 
 irreducible representations is therefore 3*37=111. Naturally I would 
 like to parallelize this calculation as efficiently as possible.

 From the documentation of the Quantum Espresso web page I see that the 
 irreducible representations can be grouped into "images" that can be 
 computed largely independently. The following example is given:

 mpirun -np 64 ph.x -nimage 8 -npool 2 ...

 After a slight modification, I executed the following command line:

 mpirun -np 256 -npernode 8 ph.x -nimage 16 < struct0-phonon.inp > 
 struct0-phonon.out


 The calculation terminates normally, but the result is not what I 
 expected. Almost at the beginning of the output file the following it 
 printed:

      Atomic displacements:
      There are 111 irreducible representations

      Representation     1      1 modes - To be done

      Representation     2      1 modes - To be done

      Representation     3      1 modes - To be done

      Representation     4      1 modes - To be done

      Representation     5      1 modes - To be done

      Representation     6      1 modes - To be done

      Representation     7      1 modes - Not done in this run

      Representation     8      1 modes - Not done in this run

      Representation     9      1 modes - Not done in this run

 -------------------------------------------------------------
 The message "Not done in this run" is printed for Representation 7 to 
 111.

 Towards the end of the output file the frequencies are printed. 
 Frequencies 1 to 6 are slightly negative, frequencies 7 to 105 are 
 virtually zero, and frequencies 106 to 111 are slightly positive.

 The first and last part of the mentioned output section are shown 
 below:


      omega( 1) =      -7.228419 [THz] =    -241.114112 [cm-1]
      omega( 2) =      -7.052563 [THz] =    -235.248188 [cm-1]
      omega( 3) =      -6.661820 [THz] =    -222.214395 [cm-1]
      omega( 4) =      -6.390946 [THz] =    -213.179028 [cm-1]
      omega( 5) =      -6.252886 [THz] =    -208.573825 [cm-1]
      omega( 6) =      -5.895227 [THz] =    -196.643621 [cm-1]
      omega( 7) =      -0.000001 [THz] =      -0.000019 [cm-1]
      omega( 8) =      -0.000001 [THz] =      -0.000018 [cm-1]
      omega( 9) =      -0.000001 [THz] =      -0.000018 [cm-1]
      omega(10) =       0.000000 [THz] =      -0.000017 [cm-1]
      omega(11) =       0.000000 [THz] =      -0.000017 [cm-1]
      omega(12) =       0.000000 [THz] =      -0.000015 [cm-1]


      omega(98) =       0.000000 [THz] =       0.000014 [cm-1]
      omega(99) =       0.000000 [THz] =       0.000014 [cm-1]
      omega(**) =       0.000000 [THz] =       0.000015 [cm-1]
      omega(**) =       0.000000 [THz] =       0.000016 [cm-1]
      omega(**) =       0.000000 [THz] =       0.000016 [cm-1]
      omega(**) =       0.000000 [THz] =       0.000016 [cm-1]
      omega(**) =       0.000000 [THz] =       0.000016 [cm-1]
      omega(**) =       0.000001 [THz] =       0.000017 [cm-1]
      omega(**) =      16.552716 [THz] =     552.139187 [cm-1]
      omega(**) =      16.683450 [THz] =     556.499976 [cm-1]
      omega(**) =      17.480012 [THz] =     583.070434 [cm-1]
      omega(**) =      17.635841 [THz] =     588.268333 [cm-1]
      omega(**) =      17.837822 [THz] =     595.005680 [cm-1]
      omega(**) =      18.630530 [THz] =     621.447600 [cm-1]
  
 **************************************************************************

 I have a feeling that I have severely misunderstood some important 
 concepts. I would therefore appreciate if someone could give an 
 explanation on how to correctly perform a parallel phonon calculation.

 Thank you very much in advance for your help.

 Yours sincerely,

 Torstein Fjermestad
 University of Oslo
 Norway

 



 



 

From zhanhit at hotmail.com  Wed Jul 25 12:20:21 2012
From: zhanhit at hotmail.com (Franklin Zhan)
Date: Wed, 25 Jul 2012 10:20:21 +0000
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <201207250916.45017.giuseppe.mattioli@ism.cnr.it>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>,
	<CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>,
	<201207250916.45017.giuseppe.mattioli@ism.cnr.it>
Message-ID: <BAY151-W15A7B151FB71E39F7EF478A7C30@phx.gbl>





Dear Giuseppe,
I find your reply is really a great job. It helps me a lot.
By digesting this example, some questions arise in my mind, may be there are very naive, but I want to be clear about them.
One question is about the nspin value, since O2 is not a magnetic system, why should a spin be considered, when should a spin component be considered?
Another question is about the kpoint number, for example here, the celldm is very big, K_POINTS(gamma) is accurate enough for scf calculation. however, if we calculate other materials, ZnO, for instance, we  may need to use more k points, such as K_POINTS 3x3x3. Under this circumstance, how should we set the kpoint and kband value in the pp.x file?

I know I am very lucky today.

Best regards,




Franklin  Zhan

Ph.D student
School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore.





> From: giuseppe.mattioli at ism.cnr.it
> To: pw_forum at pwscf.org
> Date: Wed, 25 Jul 2012 09:16:43 +0200
> Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
> 
> 
> Dear Felipe
> You seem not to be a chemist...:-)
> The ground state of an O2 molecule is a triplet one, with 7 up valence electrons and 5 down.
> 
> Dear Zhan
> This morning (morning in Italy, at least) you are lucky. I've done (almost) the same thing 
> yesterday...
> 
> Once the above is settled, first you should perform a relax calculation with K_POINTS (gamma). You do 
> not need a nscf calculation if you use a bit of smearing. Something like
> 
>  &control
>     calculation = 'relax'
>     prefix='$FILE',
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/',
>  /
>  &system
>     ibrav=1, celldm(1)=30.000000,
>     nat=2, ntyp=1,
>     ecutwfc =35.0,
>     ecutrho =280.0,
>     occupations='smearing', degauss=0.01,
>     nspin=2,
>     starting_magnetization(1)=0.3,
>  /
>  &electrons
>     mixing_mode='plain'
>     mixing_beta=0.3
>     conv_thr=1.0d-7
>     electron_maxstep=200
>  /
>  &ions
>     ion_dynamics='bfgs'
>  /
> ATOMIC_SPECIES
> O    15.999     O_pbe.van.UPF
> ATOMIC_POSITIONS {angstrom}
> O        5.000576334   5.029093041   5.029093041
> O        5.009423666   5.870906959   5.870906959
> K_POINTS {gamma}
> 
> will provide a sufficient number of unoccupied orbitals for your purpose.
> 
> Then, remember that when you use nspin=2 and K_POINTS {gamma} you are formally using two k points 
> (gamma up and gamma down) which are labelled as kpoint=1 and kpoint=2, respectively. In your pw.x 
> output you should acknowledge (but you should already know it by molecular orbital theory of 
> homonuclear diatomic molecules...) that both the HOMO in the up channel (-9.1985  -9.1983) and the 
> LUMO in the down channel (-4.9925  -4.9924) are doubly degenerate. Thus, you must plot the single-
> electron orbitals and sum them.
> 
>  ------ SPIN UP ------------
> 
> 
>           k = 0.0000 0.0000 0.0000 ( 47171 PWs)   bands (ev):
> 
>    -34.3196 -21.0375 -17.4698 -17.4697 -14.7359  -9.1985  -9.1983  -0.6483
>     -0.1403  -0.0924
> 
>  ------ SPIN DOWN ----------
> 
> 
>           k = 0.0000 0.0000 0.0000 ( 47171 PWs)   bands (ev):
> 
>    -33.1724 -19.2543 -13.7742 -12.6937 -12.6937  -4.9925  -4.9924  -0.5833
>     -0.0519  -0.0089
> 
>      the Fermi energy is    -8.4505 ev
> 
> This is quite easy, supposing that you read carefully the pp.x input guide... But, as I said, you 
> won a free ride today...
> 
>  &inputpp
>     prefix  = '$FILEA'
>     outdir = '$TMP_DIR/'
>     filplot = '$FILEA-HOMOa.dat'
>     plot_num= 7
>     kpoint=1
>     kband=6
>  /
> 
> $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
> 
>  &inputpp
>     prefix  = '$FILEA'
>     outdir = '$TMP_DIR/'
>     filplot = '$FILEA-HOMOb.dat'
>     plot_num= 7
>     kpoint=1
>     kband=7
>  /
> 
> $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
> 
> 
>  &inputpp
>  /
>  &plot
>     nfile = 2
>     filepp(1) = '$FILEA-HOMOa.dat'
>     weight(1) = 1.0
>     filepp(2) = '$FILEA-HOMOb.dat'
>     weight(2) = 1.0
>     iflag = 3
>     output_format = 5
>     fileout = '$FILEA-HOMO.plot'
>     e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0,
>     e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
>     nx=56, ny=40
>  /
> 
> $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
> 
> This will produce a nice .xsf file containing your HOMO orbital, which you can plot with xcrysden. 
> You may also obtain a cube file, but I cannot remember the output format.
> 
> As for the LUMO, use kpoint=2, and the correct kband numbers and do the same thing.
> 
> I hope this really help... (in Italy I would have said: you owe me a cup of coffee...)
> 
> Giuseppe
> 
> 
> On Wednesday 25 July 2012 08:43:30 Filipe Camargo Dalmatti Alves Lima wrote:
> > Dear Zhan,
> > 
> > The number of electrons on your system determines the occupied bands and
> > consequently the HOMO level.
> > 
> > So, What you need to do?
> > 
> > First, check the number of electron that you are using. (If you are using
> > the O default pseudopotencials it should be 6 valence electrons)
> > Then, you'll have 12 electrons and 6 bands (each bands is occupied by 2
> > electrons).
> > 
> > Now check your output file, which is generated using the pw.x code.
> > The band number 6 represents your HOMO level and the band number 7 is the
> > LUMO one.
> > 
> > So, now you know your bands. Then you can obtain the wavefunction.
> > 
> > You will need to run the pp.x twice: one for HOMO and another for LUMO.
> > kband=6 (to plot HOMO)
> > and
> > kdand=7 (to plot LUMO)
> > 
> > I hope it will solve your problem,
> > 
> > Best regards,
> > 
> > >  Dear PWSCF users,
> > > 
> > > I am trying to calculate HOMO and LUMO levels and plot these isosurfaces
> > > for O2 molecule.
> > > I first relaxed the O2 and then did nscf calculation. then I used pp.x to
> > > calculate the HOMO and LUMO levels. but I can not find the HOMO or LUMO
> > > level in output files.
> > > the code for pp.x is pasted as following:
> > > 
> > > &inputpp
> > > 
> > >     prefix= 'O2'
> > >     outdir= '/scratch/zhan0273/PWSCF/O2/tmp'
> > > 
> > > filplot = 'O2'
> > > plot_num= 7
> > > spin_component=0
> > > ! kpoint=40
> > > kband=8
> > > /
> > > &plot
> > > nfile = 1
> > > filepp(1) = 'O2'
> > > weight(1) = 1.0
> > > iflag = 3
> > > output_format = 5
> > > fileout = 'O2.orb.xsf'
> > > /
> > > 
> > > So please give advice. Thank you all in advance!
> > > 
> > > Best regards,
> > > 
> > > ------------------------------
> > > Franklin Zhan
> > > Ph.D student
> > > School of Mechanical and Aerospace Engineering,
> > > Nanyang Technological University, Singapore.
> > > 
> > > 
> > > 
> > > 
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> 
> -- 
> ********************************************************
> - Article premier - Les hommes naissent et demeurent
> libres et ?gaux en droits. Les distinctions sociales
> ne peuvent ?tre fond?es que sur l'utilit? commune
> - Article 2 - Le but de toute association politique
> est la conservation des droits naturels et 
> imprescriptibles de l'homme. Ces droits sont la libert?,
> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> ********************************************************
> 
>    Giuseppe Mattioli                            
>    CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
>    v. Salaria Km 29,300 - C.P. 10                
>    I 00015 - Monterotondo Stazione (RM)          
>    Tel + 39 06 90672836 - Fax +39 06 90672316    
>    E-mail: <giuseppe.mattioli at ism.cnr.it>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

 		 	   		  
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From giannozz at democritos.it  Wed Jul 25 12:25:51 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 25 Jul 2012 12:25:51 +0200
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <BAY151-W15A7B151FB71E39F7EF478A7C30@phx.gbl>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>,
	<CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>,
	<201207250916.45017.giuseppe.mattioli@ism.cnr.it>
	<BAY151-W15A7B151FB71E39F7EF478A7C30@phx.gbl>
Message-ID: <D6C73391-84D0-4A49-8E48-370714B2FCE9@democritos.it>


On Jul 25, 2012, at 12:20 , Franklin Zhan wrote:

> since O2 is not a magnetic system

I beg your pardon?

> > You seem not to be a chemist...:-)
> > The ground state of an O2 molecule is a triplet one, with 7 up  
> valence electrons and 5 down.

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From nazari at iasbs.ac.ir  Wed Jul 25 12:36:13 2012
From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir)
Date: Wed, 25 Jul 2012 15:06:13 +0430
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <D6C73391-84D0-4A49-8E48-370714B2FCE9@democritos.it>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>,
	<CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>,
	<201207250916.45017.giuseppe.mattioli@ism.cnr.it>
	<BAY151-W15A7B151FB71E39F7EF478A7C30@phx.gbl>
	<D6C73391-84D0-4A49-8E48-370714B2FCE9@democritos.it>
Message-ID: <352df52e7348997ed7ca2996051bd4c6.squirrel@mail.iasbs.ac.ir>



?Experimental results show that the stable ground stat? of
oxygen molecule is triplet(2s+1=3).
> 
> On Jul 25, 2012,
at 12:20 , Franklin Zhan wrote: 
> 
>> since O2 is not
a magnetic system 
> 
> I beg your pardon? 
> 
>> > You seem not to be a chemist...:-) 
>> > The
ground state of an O2 molecule is a triplet one, with 7 up 
>>
valence electrons and 5 down. 
> 
> P. 
> --- 
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, 
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy 
>
Phone +39-0432-558216, fax +39-0432-558222 
> 
> 
> 
> 
>
_______________________________________________ 
> Pw_forum
mailing list 
> Pw_forum at pwscf.org 
>
http://www.democritos.it/mailman/listinfo/pw_forum 
> 
>
-- 
> This message has been scanned for viruses and 
>
dangerous content by MailScanner, and is 
> believed to be clean.

> 
> 


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From zhanhit at hotmail.com  Wed Jul 25 12:41:06 2012
From: zhanhit at hotmail.com (Franklin Zhan)
Date: Wed, 25 Jul 2012 10:41:06 +0000
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <D6C73391-84D0-4A49-8E48-370714B2FCE9@democritos.it>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>, ,
	<CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>,
	, <201207250916.45017.giuseppe.mattioli@ism.cnr.it>,
	<BAY151-W15A7B151FB71E39F7EF478A7C30@phx.gbl>,
	<D6C73391-84D0-4A49-8E48-370714B2FCE9@democritos.it>
Message-ID: <BAY151-W23D0EB2B10B9AC604032DEA7C30@phx.gbl>


Dear Prof. Giannozzi,
It is great to hear from you.
In my mind, only when we are dealing with some magnetic materials calculation, such as Ni, iron, the spin polarization is taken into account. However, O2 molecule is not magnetic material, thus I do not know why we need to take the spin polarization into consideration.



Best regards,




Franklin Zhan
 
Ph.D student
School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore.





> From: giannozz at democritos.it
> Date: Wed, 25 Jul 2012 12:25:51 +0200
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
> 
> 
> On Jul 25, 2012, at 12:20 , Franklin Zhan wrote:
> 
> > since O2 is not a magnetic system
> 
> I beg your pardon?
> 
> > > You seem not to be a chemist...:-)
> > > The ground state of an O2 molecule is a triplet one, with 7 up  
> > valence electrons and 5 down.
> 
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
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From zhanhit at hotmail.com  Wed Jul 25 12:43:48 2012
From: zhanhit at hotmail.com (Franklin Zhan)
Date: Wed, 25 Jul 2012 10:43:48 +0000
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <352df52e7348997ed7ca2996051bd4c6.squirrel@mail.iasbs.ac.ir>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>, ,
	<CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>,
	, <201207250916.45017.giuseppe.mattioli@ism.cnr.it>,
	<BAY151-W15A7B151FB71E39F7EF478A7C30@phx.gbl>,
	<D6C73391-84D0-4A49-8E48-370714B2FCE9@democritos.it>,
	<352df52e7348997ed7ca2996051bd4c6.squirrel@mail.iasbs.ac.ir>
Message-ID: <BAY151-W296B7E71F65B904E7BD149A7C30@phx.gbl>



Thanks for you reply.

Best regards,




Franklin  Zhan
Ph.D student
School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore.





Date: Wed, 25 Jul 2012 15:06:13 +0430
From: nazari at iasbs.ac.ir
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface

 Experimental results show that the stable ground stat  of
oxygen molecule is triplet(2s+1=3).
> 
> On Jul 25, 2012,
at 12:20 , Franklin Zhan wrote: 
> 
>> since O2 is not
a magnetic system 
> 
> I beg your pardon? 
> 
>> > You seem not to be a chemist...:-) 
>> > The
ground state of an O2 molecule is a triplet one, with 7 up 
>>
valence electrons and 5 down. 
> 
> P. 
> --- 
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, 
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy 
>
Phone +39-0432-558216, fax +39-0432-558222 
> 
> 
> 
> 
>
_______________________________________________ 
> Pw_forum
mailing list 
> Pw_forum at pwscf.org 
>
http://www.democritos.it/mailman/listinfo/pw_forum 
> 
>
-- 
> This message has been scanned for viruses and 
>
dangerous content by MailScanner, and is 
> believed to be clean.

> 
> 

-- 

This message has been scanned for viruses and

dangerous content by
MailScanner, and is

believed to be clean.



_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum 		 	   		  
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From giuseppe.mattioli at ism.cnr.it  Wed Jul 25 13:08:45 2012
From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli)
Date: Wed, 25 Jul 2012 13:08:45 +0200
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <BAY151-W23D0EB2B10B9AC604032DEA7C30@phx.gbl>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>
	<D6C73391-84D0-4A49-8E48-370714B2FCE9@democritos.it>
	<BAY151-W23D0EB2B10B9AC604032DEA7C30@phx.gbl>
Message-ID: <201207251308.46688.giuseppe.mattioli@ism.cnr.it>



Dear Franklin
You are making a bit of confusion between ferromagnetic systems (Fe, Ni, Co ,...), and paramagnetic 
systems (O2, among many others). Both kinds of system ARE magnetic, and generally require spin 
polarized calculations. Regarding k-points, molecules have electronic levels flat in the Brillouin 
zone (if you do not know what does such a statement mean and imply, a solid state physics textbook 
may help...). Thus, calculations of molecules do not depends on k-points, as long as the box is 
enough large to minimize the interaction between periodically repeated images of the molecule.
Solids, like ZnO, are (in a quite rough manner of speaking...) characterized by dispersed electronic 
bands instead, and require to check the convergence with respect to the k-point mesh.
HTH (another cup, please, and with cream...:-))


On Wednesday 25 July 2012 12:41:06 Franklin Zhan wrote:
> Dear Prof. Giannozzi,
> It is great to hear from you.
> In my mind, only when we are dealing with some magnetic materials
> calculation, such as Ni, iron, the spin polarization is taken into
> account. However, O2 molecule is not magnetic material, thus I do not know
> why we need to take the spin polarization into consideration.
> 
> 
> 
> Best regards,
> 
> 
> 
> 
> Franklin Zhan
> 
> Ph.D student
> School of Mechanical and Aerospace Engineering,
> Nanyang Technological University, Singapore.
> 
> > From: giannozz at democritos.it
> > Date: Wed, 25 Jul 2012 12:25:51 +0200
> > To: pw_forum at pwscf.org
> > Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
> > 
> > On Jul 25, 2012, at 12:20 , Franklin Zhan wrote:
> > > since O2 is not a magnetic system
> > 
> > I beg your pardon?
> > 
> > > > You seem not to be a chemist...:-)
> > > > The ground state of an O2 molecule is a triplet one, with 7 up
> > > 
> > > valence electrons and 5 down.
> > 
> > P.
> > ---
> > Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > Phone +39-0432-558216, fax +39-0432-558222
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum

-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

   Giuseppe Mattioli                            
   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
   v. Salaria Km 29,300 - C.P. 10                
   I 00015 - Monterotondo Stazione (RM)          
   Tel + 39 06 90672836 - Fax +39 06 90672316    
   E-mail: <giuseppe.mattioli at ism.cnr.it>

From carlo.nervi at unito.it  Wed Jul 25 13:15:01 2012
From: carlo.nervi at unito.it (Carlo Nervi)
Date: Wed, 25 Jul 2012 13:15:01 +0200
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <BAY151-W23D0EB2B10B9AC604032DEA7C30@phx.gbl>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>, ,
	<CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>,
	, <201207250916.45017.giuseppe.mattioli@ism.cnr.it>,
	<BAY151-W15A7B151FB71E39F7EF478A7C30@phx.gbl>,
	<D6C73391-84D0-4A49-8E48-370714B2FCE9@democritos.it>
	<BAY151-W23D0EB2B10B9AC604032DEA7C30@phx.gbl>
Message-ID: <500FD535.4080101@unito.it>

Il 25/07/2012 12.41, Franklin Zhan ha scritto:
> ...However, O2 molecule is not magnetic material, thus I do not
> know why we need to take the spin polarization into consideration.

You have to review some chemistry...
Try to have a look here:

http://www.youtube.com/watch?v=Isd9IEnR4bw

Carlo Nervi

-- 
------------------------------------------------------------
Prof. Carlo Nervi carlo.nervi at unito.it  Tel:+39 0116707507/8
Fax: +39 0116707855      -      Dipartimento di Chimica, via
P. Giuria 7, 10125 Torino, Italy.    http://lem.ch.unito.it/

From giannozz at democritos.it  Wed Jul 25 13:40:39 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 25 Jul 2012 13:40:39 +0200
Subject: [Pw_forum] parallelization of phonon calculations
In-Reply-To: <d4b8ba5d12cde2868d21c4da6daee748@ulrik.uio.no>
References: <d4b8ba5d12cde2868d21c4da6daee748@ulrik.uio.no>
Message-ID: <2A85AE86-7673-4CB6-B90F-A5DDBAB41C92@democritos.it>

Which version of the phonon code have you used? P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From zhanhit at hotmail.com  Wed Jul 25 13:42:01 2012
From: zhanhit at hotmail.com (Franklin Zhan)
Date: Wed, 25 Jul 2012 11:42:01 +0000
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <500FD535.4080101@unito.it>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>, , , ,
	<CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>,
	, , , <201207250916.45017.giuseppe.mattioli@ism.cnr.it>, ,
	<BAY151-W15A7B151FB71E39F7EF478A7C30@phx.gbl>, ,
	<D6C73391-84D0-4A49-8E48-370714B2FCE9@democritos.it>,
	<BAY151-W23D0EB2B10B9AC604032DEA7C30@phx.gbl>,
	<500FD535.4080101@unito.it>
Message-ID: <BAY151-W9CF0576EEAFB3773AEFEFA7C30@phx.gbl>








Many thanks to you guys. I learned a lot today.

Best regards,


Franklin  Zhan

Ph.D student
School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore.





> Date: Wed, 25 Jul 2012 13:15:01 +0200
> From: carlo.nervi at unito.it
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
> 
> Il 25/07/2012 12.41, Franklin Zhan ha scritto:
> > ...However, O2 molecule is not magnetic material, thus I do not
> > know why we need to take the spin polarization into consideration.
> 
> You have to review some chemistry...
> Try to have a look here:
> 
> http://www.youtube.com/watch?v=Isd9IEnR4bw
> 
> Carlo Nervi
> 
> -- 
> ------------------------------------------------------------
> Prof. Carlo Nervi carlo.nervi at unito.it  Tel:+39 0116707507/8
> Fax: +39 0116707855      -      Dipartimento di Chimica, via
> P. Giuria 7, 10125 Torino, Italy.    http://lem.ch.unito.it/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


 		 	   		  
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From giannozz at democritos.it  Wed Jul 25 13:43:46 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 25 Jul 2012 13:43:46 +0200
Subject: [Pw_forum] Problem on runing espresso-4.3.2
In-Reply-To: <1343200257.64844.YahooMailNeo@web43141.mail.sp1.yahoo.com>
References: <1343200257.64844.YahooMailNeo@web43141.mail.sp1.yahoo.com>
Message-ID: <97396F02-4BDF-421C-AD30-E802B223863F@democritos.it>


On Jul 25, 2012, at 9:10 , Mahdi Faghih nasiri wrote:

>  "error while loading shared libraries:
> /opt/intel/mkl/10.0.4.023/lib/em64t/libmkl_intel_lp64.so:
> cannot open shared object file: No such file or directory

You have to set up the correct LD_LIBRARY_PATH or
whatever is needed, on all processors on which the code
is running. Please have a look at the documentation of
MKL libraries

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From torstein.fjermestad at kjemi.uio.no  Wed Jul 25 14:37:03 2012
From: torstein.fjermestad at kjemi.uio.no (Torstein Fjermestad)
Date: Wed, 25 Jul 2012 14:37:03 +0200
Subject: [Pw_forum] =?utf-8?q?parallelization_of_phonon_calculations?=
In-Reply-To: <2A85AE86-7673-4CB6-B90F-A5DDBAB41C92@democritos.it>
References: <d4b8ba5d12cde2868d21c4da6daee748@ulrik.uio.no>
	<2A85AE86-7673-4CB6-B90F-A5DDBAB41C92@democritos.it>
Message-ID: <6aa2c48977e04592d26e814b580a7560@ulrik.uio.no>

 Program PHONON v.4.3.2

 On Wed, 25 Jul 2012 13:40:39 +0200, Paolo Giannozzi 
 <giannozz at democritos.it> wrote:
> Which version of the phonon code have you used? P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From flima at if.usp.br  Wed Jul 25 15:03:20 2012
From: flima at if.usp.br (Filipe Camargo Dalmatti Alves Lima)
Date: Wed, 25 Jul 2012 10:03:20 -0300
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <BAY151-W9CF0576EEAFB3773AEFEFA7C30@phx.gbl>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>
	<CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>
	<201207250916.45017.giuseppe.mattioli@ism.cnr.it>
	<BAY151-W15A7B151FB71E39F7EF478A7C30@phx.gbl>
	<D6C73391-84D0-4A49-8E48-370714B2FCE9@democritos.it>
	<BAY151-W23D0EB2B10B9AC604032DEA7C30@phx.gbl>
	<500FD535.4080101@unito.it>
	<BAY151-W9CF0576EEAFB3773AEFEFA7C30@phx.gbl>
Message-ID: <CAGLNc7BYbGPsOUvbe3FF_ztXkZRz3v+jmhRECNwiXMN3tMh_-A@mail.gmail.com>

Dear Giuseppe,

Your are right, I am a physicist! Also, I completely forgot about the O2
fundamental state.
Thank you for reply and for your correction! :-)

Best regards all,

Filipe

On Wed, Jul 25, 2012 at 8:42 AM, Franklin Zhan <zhanhit at hotmail.com> wrote:

>  Many thanks to you guys. I learned a lot today.
>
>
> Best regards,
>  ------------------------------
> Franklin  Zhan
>
> Ph.D student
> School of Mechanical and Aerospace Engineering,
> Nanyang Technological University, Singapore.
>
>
>
>
>
> > Date: Wed, 25 Jul 2012 13:15:01 +0200
> > From: carlo.nervi at unito.it
>
> > To: pw_forum at pwscf.org
> > Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
> >
> > Il 25/07/2012 12.41, Franklin Zhan ha scritto:
> > > ...However, O2 molecule is not magnetic material, thus I do not
> > > know why we need to take the spin polarization into consideration.
> >
> > You have to review some chemistry...
> > Try to have a look here:
> >
> > http://www.youtube.com/watch?v=Isd9IEnR4bw
> >
> > Carlo Nervi
> >
> > --
> > ------------------------------------------------------------
> > Prof. Carlo Nervi carlo.nervi at unito.it Tel! :+39 0116707507/8
>
> > Fax: +39 0116707855 - Dipartimento di Chimica, via
> > P. Giuria 7, 10125 Torino, Italy. http://lem.ch.unito.it/
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
_________________________________________
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:    (11) 3091-6881  (USP)
                (11) 8249-4628 (TIM)
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From kucukben at sissa.it  Wed Jul 25 16:15:48 2012
From: kucukben at sissa.it (Emine Kucukbenli)
Date: Wed, 25 Jul 2012 16:15:48 +0200
Subject: [Pw_forum] QE installation on standard HPC machines.
Message-ID: <20120725161548.Horde.hUquDB8V4mxQD-_UKT4w-uA@webmail.sissa.it>

Hi all,

I have decided to gather working make.sys files, configurations for  
all the standard HPC machines that are commonly used by the community.

My purpose is to build a reference database for installation  
procedures; organize wrt machine/compiler/version/configure options  
and then share it; to make life easier for all; users, mailing list  
responders and hpc admins.

There is a similar thing in /install directory but it doesnt seem very  
up to date, and i think a division with machine would really be  
helpful for starters.

So I would be glad if you can help me construct this reference database
by sending your make.sys and config.log files which you already have;
and further details if necessary, such as the version, list of loaded  
modules, test status etc.
I would also like to acknowledge the contributors so that people using  
the same machine can have an opportunity to get to know each other.

Ok, some examples from the complete list is going to look like the following:

CINECA_fermi_intel_hybrid_make.sys and CINECA_fermi_intel_hybrid-config.log
CSCS_rosa_pgi_mpionly_make.sys CSCS_rosa_pgi_mpionly_config.log
etc.
just to give an idea.

I have also added my CEA_CURIE make/log files here as an example.(on  
CURIE QEv5.0 work out of the box atm, so it is not that useful but  
still..)

If you have any questions, or if you think this already exists, or is  
unnecessary,or bad for IT security etc, please let me know.

Looking forward to hearing from you!
Thanks!

emine kucukbenli
former phd student, sissa, italy
address change to: postdoc, epfl, switzerland.


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From wparker at anl.gov  Wed Jul 25 16:13:35 2012
From: wparker at anl.gov (William Parker)
Date: Wed, 25 Jul 2012 09:13:35 -0500
Subject: [Pw_forum] parallelization of phonon calculations
In-Reply-To: <6aa2c48977e04592d26e814b580a7560@ulrik.uio.no>
References: <d4b8ba5d12cde2868d21c4da6daee748@ulrik.uio.no>
	<2A85AE86-7673-4CB6-B90F-A5DDBAB41C92@democritos.it>
	<6aa2c48977e04592d26e814b580a7560@ulrik.uio.no>
Message-ID: <DCE2ACA9-3F26-4959-A9F0-7D1BC5D1278C@anl.gov>

Each image will output to its own output file labeled out.i_0 where i runs from 1 to N_image - 1.  The frequencies in these files will be garbage unless all of the representations for a particular q-point are contained in one image.  After you run the image-parallelized run, you must copy the data-file.*.*.xml files (not the data-file.*.xml files) to the _ph0/(prefix).phsave/ directory and run again on one image with recover=.true. in your input file.  This will produce the correct frequencies in the output file and the (prefix).dyn* files.  

--William

On Jul 25, 2012, at 7:37 AM, Torstein Fjermestad wrote:

> Program PHONON v.4.3.2
> 
> On Wed, 25 Jul 2012 13:40:39 +0200, Paolo Giannozzi 
> <giannozz at democritos.it> wrote:
>> Which version of the phonon code have you used? P.
>> ---
>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum




*********************************************************
  William D. Parker                 phone: (630) 252-4834
  Computational Postdoctoral Fellow   fax: (630) 252-4798
  MSD-212, Rm. C-215
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*********************************************************






From bfazi90 at gmail.com  Wed Jul 25 17:00:22 2012
From: bfazi90 at gmail.com (bf azi)
Date: Wed, 25 Jul 2012 19:30:22 +0430
Subject: [Pw_forum] pseudopotential
Message-ID: <CAC+sow+avTqLiyibjD7EMzFGe0-396wzuji4GFBiiVFiOiH0sA@mail.gmail.com>

Dear all

I have a question about pseudopotential in quantum espresso.
Which pseudopotential better for describe "Van der Waals" bonding?

Bani Adam
Faculty of Science
Egypt

From akohlmey at gmail.com  Wed Jul 25 17:12:43 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Wed, 25 Jul 2012 17:12:43 +0200
Subject: [Pw_forum] pseudopotential
In-Reply-To: <CAC+sow+avTqLiyibjD7EMzFGe0-396wzuji4GFBiiVFiOiH0sA@mail.gmail.com>
References: <CAC+sow+avTqLiyibjD7EMzFGe0-396wzuji4GFBiiVFiOiH0sA@mail.gmail.com>
Message-ID: <CADTmJ6GHvJv9xYnDuO5NbDxudVgyGYFXi9wta+tFDK_4+yfckg@mail.gmail.com>

On Wed, Jul 25, 2012 at 5:00 PM, bf azi <bfazi90 at gmail.com> wrote:
> Dear all
>
> I have a question about pseudopotential in quantum espresso.
> Which pseudopotential better for describe "Van der Waals" bonding?

please think about this for a little bit:
- in what range (i.e. distance from the atom core) does a pseudopotential
 modify an (atomic) wavefunction and what is it supposed to be like beyond
 that range?
- in what range, i.e. distance between two atoms, do van der waals
  interactions matter?

if you think this through, you should be able to come up with an
answer to your question by yourself.

cheers,
     axel.
>
> Bani Adam
> Faculty of Science
> Egypt
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



-- 
Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

From zhanhit at hotmail.com  Wed Jul 25 18:12:27 2012
From: zhanhit at hotmail.com (Franklin Zhan)
Date: Wed, 25 Jul 2012 16:12:27 +0000
Subject: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
In-Reply-To: <CAGLNc7BYbGPsOUvbe3FF_ztXkZRz3v+jmhRECNwiXMN3tMh_-A@mail.gmail.com>
References: <BAY151-W61EDDD10491AD0EDDAD238A7C30@phx.gbl>,
	<CAGLNc7AgTL3wzN9Mu6w3F4Yw_0UBg1gTZncCTiqEOoRVPk45vQ@mail.gmail.com>,
	<201207250916.45017.giuseppe.mattioli@ism.cnr.it>,
	<BAY151-W15A7B151FB71E39F7EF478A7C30@phx.gbl>,
	<D6C73391-84D0-4A49-8E48-370714B2FCE9@democritos.it>,
	<BAY151-W23D0EB2B10B9AC604032DEA7C30@phx.gbl>,
	<500FD535.4080101@unito.it>,
	<BAY151-W9CF0576EEAFB3773AEFEFA7C30@phx.gbl>,
	<CAGLNc7BYbGPsOUvbe3FF_ztXkZRz3v+jmhRECNwiXMN3tMh_-A@mail.gmail.com>
Message-ID: <BAY151-W5124B80F189B03C56F6490A7C30@phx.gbl>


Dear All,
I am still not very clear about the kband setting for larger system calculation. 
If I use 3X3X2 supercell to calculate VBM or CBM of ZnO:H(H substitues one O site) and plot their isosurface using Xcrysden, in this system,  electron number(ne) is 643, the k_points is 12, and the nspin value should be 2, so set kband=ne/2+1 and kband=ne/2-1 for pp.x input files? besides, How does kpoint be set for pp.x input file?


Thanks in advance.


Franklin  Zhan
Ph.D student
School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore.




 




From: flima at if.usp.br
Date: Wed, 25 Jul 2012 10:03:20 -0300
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface

Dear Giuseppe,


Your are right, I am a physicist! Also, I completely forgot about the O2 fundamental state.
Thank you for reply and for your correction! :-)


Best regards all,


Filipe


On Wed, Jul 25, 2012 at 8:42 AM, Franklin Zhan <zhanhit at hotmail.com> wrote:





Many thanks to you guys. I learned a lot today.


Best regards,


Franklin  Zhan

Ph.D student
School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore.







> Date: Wed, 25 Jul 2012 13:15:01 +0200
> From: carlo.nervi at unito.it

> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
> 

> Il 25/07/2012 12.41, Franklin Zhan ha scritto:
> > ...However, O2 molecule is not magnetic material, thus I do not
> > know why we need to take the spin polarization into consideration.
> 
> You have to review some chemistry...
> Try to have a look here:
> 
> http://www.youtube.com/watch?v=Isd9IEnR4bw
> 
> Carlo Nervi
> 
> -- 
> ------------------------------------------------------------
> Prof. Carlo Nervi carlo.nervi at unito.it Tel! :+39 0116707507/8

> Fax: +39 0116707855 - Dipartimento di Chimica, via
> P. Giuria 7, 10125 Torino, Italy. http://lem.ch.unito.it/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum




-- 
_________________________________________
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil.
Phones:    (11) 3091-6881  (USP)
                (11) 8249-4628 (TIM)

_______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum 		 	   		  
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From kucukben at sissa.it  Wed Jul 25 18:32:04 2012
From: kucukben at sissa.it (Emine Kucukbenli)
Date: Wed, 25 Jul 2012 18:32:04 +0200
Subject: [Pw_forum] pseudopotential
In-Reply-To: <CADTmJ6GHvJv9xYnDuO5NbDxudVgyGYFXi9wta+tFDK_4+yfckg@mail.gmail.com>
References: <CAC+sow+avTqLiyibjD7EMzFGe0-396wzuji4GFBiiVFiOiH0sA@mail.gmail.com>
	<CADTmJ6GHvJv9xYnDuO5NbDxudVgyGYFXi9wta+tFDK_4+yfckg@mail.gmail.com>
Message-ID: <20120725183204.Horde.Qavrfx8V4mxQEB_EyyXDVrA@webmail.sissa.it>

Perhaps knowing the physics behind it, the OP assumed that  
vdW-relevant distinguishing factor between pseudopotentials is the XC  
functionals they are generated with. In that case the question would  
be legit and the answer I suppose would go like the following:

Choose a flavor of vdW you want to use, then

for input_dft="vdW-DF" use a revPBE pseudo
for input_dft="vdW-DF2" use a revised-PW86 (the last commit on this  
was some 5h ago so i would use w caution.)

instead, input_dft="vdw-df-c09" or "vdw-df2-c09" should both be used  
with pseudos generated with c09x

And follow the modifications to Modules/funct.f90 file with care for  
addition of new vdW flavors :)

ciao
emine


Quoting Axel Kohlmeyer <akohlmey at gmail.com>:

> On Wed, Jul 25, 2012 at 5:00 PM, bf azi <bfazi90 at gmail.com> wrote:
>> Dear all
>>
>> I have a question about pseudopotential in quantum espresso.
>> Which pseudopotential better for describe "Van der Waals" bonding?
>
> please think about this for a little bit:


From giannozz at democritos.it  Wed Jul 25 19:15:32 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 25 Jul 2012 19:15:32 +0200
Subject: [Pw_forum] pseudopotential
In-Reply-To: <20120725183204.Horde.Qavrfx8V4mxQEB_EyyXDVrA@webmail.sissa.it>
References: <CAC+sow+avTqLiyibjD7EMzFGe0-396wzuji4GFBiiVFiOiH0sA@mail.gmail.com>
	<CADTmJ6GHvJv9xYnDuO5NbDxudVgyGYFXi9wta+tFDK_4+yfckg@mail.gmail.com>
	<20120725183204.Horde.Qavrfx8V4mxQEB_EyyXDVrA@webmail.sissa.it>
Message-ID: <5E765208-5C5C-4BA8-AA09-16925F7D3EDD@democritos.it>


On Jul 25, 2012, at 18:32 , Emine Kucukbenli wrote:

> for input_dft="vdW-DF2" use a revised-PW86 (the last commit on this
> was some 5h ago so i would use w caution.)

no need to be so cautious: today's commit was a correction to a comment

> And follow the modifications to Modules/funct.f90 file with care for
> addition of new vdW flavors :)

here:
http://qe-forge.org/scm/viewvc.php/trunk/espresso/Modules/funct.f90? 
root=q-e&view=log

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Wed Jul 25 19:45:32 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 25 Jul 2012 19:45:32 +0200
Subject: [Pw_forum] parallelization of phonon calculations
In-Reply-To: <DCE2ACA9-3F26-4959-A9F0-7D1BC5D1278C@anl.gov>
References: <d4b8ba5d12cde2868d21c4da6daee748@ulrik.uio.no>
	<2A85AE86-7673-4CB6-B90F-A5DDBAB41C92@democritos.it>
	<6aa2c48977e04592d26e814b580a7560@ulrik.uio.no>
	<DCE2ACA9-3F26-4959-A9F0-7D1BC5D1278C@anl.gov>
Message-ID: <4A24A2CA-F7E4-48C3-8972-B012EE644E57@democritos.it>


On Jul 25, 2012, at 16:13 , William Parker wrote:

> Each image will output to its own output file labeled out.i_0 where  
> i runs from 1 to N_image - 1.  The frequencies in these files will  
> be garbage unless all of the representations for a particular q- 
> point are contained in one image.  After you run the image- 
> parallelized run, you must copy the data-file.*.*.xml files (not  
> the data-file.*.xml files) to the _ph0/(prefix).phsave/ directory  
> and run again on one image with recover=.true. in your input file.   
> This will produce the correct frequencies in the output file and  
> the (prefix).dyn* files.

funny: "image" parallelization (the one done with MPI, not with separate
calculations on a grid) should automatically perform the final step of
collecting results.

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From konda.physics at gmail.com  Wed Jul 25 19:49:56 2012
From: konda.physics at gmail.com (Kondaiah Samudrala)
Date: Wed, 25 Jul 2012 23:19:56 +0530
Subject: [Pw_forum] Regarding QHA calculations
Message-ID: <CAKjMXpbQzY8v_OhKAVPXQjzMzQ1OOQnJHeq8_2BQ_Aiq=G0-jg@mail.gmail.com>

Dear all,

As First,  Thank you to all helping me in previous questions. I have some
basic doubts in  extending QHA calculations.

1) Is QHA implementation with pwscf is up to primitive orthorhombic only???
Now i want to calculate QHA properties for body centered orthorhombic
structure.  Recently i have seen several literature for different crystal
structure. please suggest me in that point

2) I want to calculate lattice parameters, bulk modulus w.r.t Temperature ,
Thermal expansion coefficient and Grunessian parameter  using QHA. Is there
any tutorial or basic i/ps for those calculations???
  If possible please explain me for cubic structure.

Thanks in advance

with regards
S.Appalakondaiah
Research scholar
University of Hyderabad
India
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From wparker at anl.gov  Wed Jul 25 19:57:14 2012
From: wparker at anl.gov (William Parker)
Date: Wed, 25 Jul 2012 12:57:14 -0500
Subject: [Pw_forum] parallelization of phonon calculations
In-Reply-To: <4A24A2CA-F7E4-48C3-8972-B012EE644E57@democritos.it>
References: <d4b8ba5d12cde2868d21c4da6daee748@ulrik.uio.no>
	<2A85AE86-7673-4CB6-B90F-A5DDBAB41C92@democritos.it>
	<6aa2c48977e04592d26e814b580a7560@ulrik.uio.no>
	<DCE2ACA9-3F26-4959-A9F0-7D1BC5D1278C@anl.gov>
	<4A24A2CA-F7E4-48C3-8972-B012EE644E57@democritos.it>
Message-ID: <6F618A08-9FF1-4231-9521-8C47AC908AB7@anl.gov>

I agree that it should be automatic, but, in any case I've tried, ph.x doesn't find the other directories.  

--William 

On Jul 25, 2012, at 12:45 PM, Paolo Giannozzi wrote:

> 
> On Jul 25, 2012, at 16:13 , William Parker wrote:
> 
>> Each image will output to its own output file labeled out.i_0 where  
>> i runs from 1 to N_image - 1.  The frequencies in these files will  
>> be garbage unless all of the representations for a particular q- 
>> point are contained in one image.  After you run the image- 
>> parallelized run, you must copy the data-file.*.*.xml files (not  
>> the data-file.*.xml files) to the _ph0/(prefix).phsave/ directory  
>> and run again on one image with recover=.true. in your input file.   
>> This will produce the correct frequencies in the output file and  
>> the (prefix).dyn* files.
> 
> funny: "image" parallelization (the one done with MPI, not with separate
> calculations on a grid) should automatically perform the final step of
> collecting results.
> 
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

*********************************************************
  William D. Parker                 phone: (630) 252-4834
  Computational Postdoctoral Fellow   fax: (630) 252-4798
  MSD-212, Rm. C-215
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*********************************************************






From mayankaditya at gmail.com  Wed Jul 25 20:31:13 2012
From: mayankaditya at gmail.com (mayank)
Date: Thu, 26 Jul 2012 00:01:13 +0530
Subject: [Pw_forum] Force constant fron ionic long range part
Message-ID: <1343241073.3121.3.camel@localhost.localdomain>

Dear All QE Users

I am wandering whether I can get real space force constant contribution
of long range and short range potential seperatly. 

Thanks in advance. 

Mayank


From jin.zhang.pku at gmail.com  Wed Jul 25 21:34:40 2012
From: jin.zhang.pku at gmail.com (Jin Zhang)
Date: Wed, 25 Jul 2012 12:34:40 -0700
Subject: [Pw_forum] Postdoc Position at UCLA Chemistry
Message-ID: <CAFQ68xVN4YOZhTvNzz8+eR+M0inPq2KTqrEpV=K_AYZ0teHayA@mail.gmail.com>

There is an open postdoctoral position at UCLA, in the lab of Prof.
Alexandrova, in the area of theoretical surface chemistry, multi-scale
modeling of surface-liquid interfaces, and catalysis. The work will be done
in close collaboration with experimentalists (spectroscopy, scattering,
surface chemistry, catalysis). Qualifications that are particularly looked
for in the candidates are: strong background in quantum chemistry, good
coding and scripting skills, and knowledge of statistical mechanics.
Experience with PBC PAW-DFT calculations for extended systems is also
desirable. Interested candidates should email their CV and request 2
letters of recommendation to be emailed to ana at chem.ucla.edu. The preferred
starting date is September.
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From bfazi90 at gmail.com  Wed Jul 25 23:06:36 2012
From: bfazi90 at gmail.com (bf azi)
Date: Thu, 26 Jul 2012 01:36:36 +0430
Subject: [Pw_forum] pseudopotential
Message-ID: <CAC+sowL03fjotz=YTby+8C1WYpfKJWt7iQ3r3r7d9-TG5G2hqg@mail.gmail.com>

Can you describe more?
I can not understand What to do for creating vdW pseudopotential?

Thanks a lot

From degironc at sissa.it  Wed Jul 25 23:14:52 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 25 Jul 2012 23:14:52 +0200
Subject: [Pw_forum] pseudopotential
In-Reply-To: <CAC+sowL03fjotz=YTby+8C1WYpfKJWt7iQ3r3r7d9-TG5G2hqg@mail.gmail.com>
References: <CAC+sowL03fjotz=YTby+8C1WYpfKJWt7iQ3r3r7d9-TG5G2hqg@mail.gmail.com>
Message-ID: <501061CC.7050902@sissa.it>

Dear Bani Adam
     maybe it would be more useful if you clarify what is your request 
about pseudopotential and vdW.

     are you referring to the XC functional to be used ? then of course 
one should use a pseudo generated with that XC, or in case this is not 
available with an XC as close as possible to it... and this was the 
meaning of Emine's reply
     or are you asking if some specific typer of pseudo can "by itself" 
give better descriptionof vdW system ?.. then please think about the 
lines suggested by Axel..

    or maybe you are thinking about  something else.. please clarify

    best,
stefano


On 07/25/2012 11:06 PM, bf azi wrote:
> Can you describe more?
> I can not understand What to do for creating vdW pseudopotential?
>
> Thanks a lot
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From swetarekharam at gmail.com  Thu Jul 26 06:41:44 2012
From: swetarekharam at gmail.com (Swetarekha Ram)
Date: Thu, 26 Jul 2012 10:11:44 +0530
Subject: [Pw_forum] reg: pseudopotential
Message-ID: <CAFsnUVaNcKizSxbBQr0nPkFHEbJkFqHqe+ofcdvqTLDTyDH0CQ@mail.gmail.com>

Dear users,

     I need Tl pseudopotential, either PBE UPF or pw91 UPF.

Can any one help me to get this potential.



-- 
Swetarekha Ram,
Research Scholar,
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From mohnish.iitk at gmail.com  Thu Jul 26 07:47:57 2012
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Thu, 26 Jul 2012 11:17:57 +0530
Subject: [Pw_forum] reg: pseudopotential
In-Reply-To: <CAFsnUVaNcKizSxbBQr0nPkFHEbJkFqHqe+ofcdvqTLDTyDH0CQ@mail.gmail.com>
References: <CAFsnUVaNcKizSxbBQr0nPkFHEbJkFqHqe+ofcdvqTLDTyDH0CQ@mail.gmail.com>
Message-ID: <CAMhNW-eNMk1YWXHD_=Vq6pbsbrVbSya7PpGNwJ+npH_f42RHQg@mail.gmail.com>

Did you try browsing the QE website? Any below is the link:
http://www.quantum-espresso.org/?page_id=887&el_id=22&unp_id=&fun_id=&colum_k=

Or you can also download the pslibrary which contain the inputs for ld1
code to generate PPs for different atoms.
http://qe-forge.org/projects/pslibrary

PS: Putting the affiliation is very much appreciated.

On Thu, Jul 26, 2012 at 10:11 AM, Swetarekha Ram <swetarekharam at gmail.com>wrote:

> Dear users,
>
>      I need Tl pseudopotential, either PBE UPF or pw91 UPF.
>
> Can any one help me to get this potential.
>
>
>
> --
> Swetarekha Ram,
> Research Scholar,
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
BTech-Mtech, IIT Kanpur
Senior Project Associate,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
-----------------------------------------------------------------
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From ranber14 at gmail.com  Thu Jul 26 09:39:23 2012
From: ranber14 at gmail.com (Ranber Thakur)
Date: Thu, 26 Jul 2012 09:39:23 +0200
Subject: [Pw_forum] vc-md_NOT-STOP
Message-ID: <CAL9r4=K=iLWRZ6VfFL8ozN=di4KXffex05Nj7UiOWJGWKsfApw@mail.gmail.com>

Hi PW form,

VC-md calculations does not stop after nstep. It keep running forever.
What does this mean? Is there some strange bug? Does anybody has fixed?

Best,
Ranber
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From sohailphysics at yahoo.co.in  Thu Jul 26 13:10:07 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Thu, 26 Jul 2012 19:10:07 +0800 (SGT)
Subject: [Pw_forum] k points weights
Message-ID: <1343301007.14468.YahooMailClassic@web190902.mail.sg3.yahoo.com>

Dear Pw users

In example 01 of version QE-4.2.3
In band.in file k points are given as 
?K_POINTS
?28
?? 0.0 0.0 0.0 1.0
?? 0.0 0.0 0.1 1.0
?? 0.0 0.0 0.2 1.0

while
 in lab exercise2
 day1 (given by Prof Shobhana Narasimhan on july 20, 2009) tutorial held
 in Santa Barbara 
http://media.quantum-espresso.org/santa_barbara_2009_07/
36
?? 0.5 0.5 0.5? 1
?? 0.4 0.4 0.4? 2
?? 0.3 0.3 0.3? 3
?? 0.2 0.2 0.2? 4
?? 0.1 0.1 0.1? 5

Now my question is whether i should write weights or the simply serial no. in band.in file
i believe it should be its weitghs then the question is how to claculate

Sohail Ahmad
King Khalid University
Saudi Arbia
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From akohlmey at gmail.com  Thu Jul 26 13:19:17 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Thu, 26 Jul 2012 13:19:17 +0200
Subject: [Pw_forum] k points weights
In-Reply-To: <1343301007.14468.YahooMailClassic@web190902.mail.sg3.yahoo.com>
References: <1343301007.14468.YahooMailClassic@web190902.mail.sg3.yahoo.com>
Message-ID: <CADTmJ6EPkw3ADQjT+xrk5sc+nugo+p_D7rJczHeQ7qXSHUg+-w@mail.gmail.com>

On Thu, Jul 26, 2012 at 1:10 PM, Sohail Ahmad <sohailphysics at yahoo.co.in> wrote:
>
> Dear Pw users
>
> In example 01 of version QE-4.2.3
> In band.in file k points are given as
>  K_POINTS
>  28
>    0.0 0.0 0.0 1.0
>    0.0 0.0 0.1 1.0
>    0.0 0.0 0.2 1.0
>
> while in lab exercise2 day1 (given by Prof Shobhana Narasimhan on july 20,
> 2009) tutorial held in Santa Barbara
> http://media.quantum-espresso.org/santa_barbara_2009_07/
> 36
>    0.5 0.5 0.5  1
>    0.4 0.4 0.4  2
>    0.3 0.3 0.3  3
>    0.2 0.2 0.2  4
>    0.1 0.1 0.1  5
>
> Now my question is whether i should write weights or the simply serial no.
> in band.in file
> i believe it should be its weitghs then the question is how to claculate

it doesn't matter. for non-selfconsistent
calculations, the weights are ignored.

axel.

>
> Sohail Ahmad
> King Khalid University
> Saudi Arbia
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



--
Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

From chiu at theochem.tu-muenchen.de  Thu Jul 26 13:50:22 2012
From: chiu at theochem.tu-muenchen.de (Cheng-chau Chiu)
Date: Thu, 26 Jul 2012 13:50:22 +0200
Subject: [Pw_forum] read out settings for ld1.x run from UPF-file
Message-ID: <50112EFE.3070202@theochem.tu-muenchen.de>

Dear all,
is there a possibility to read from as .UPF- file what the input was for 
the pseudopotnetial generation using ld1.x?
I am trying to reproduce the PAW for Pt published under 
http://nninc.cnf.cornell.edu/psp_files/Pt.pbe-n-kjpaw.UPF
but i still failing to do so.
I this is the input i was using:

&input
    title='Pt',
      zed=78,
    config='[Xe] 6s1 4f14 5d9 6p0'
    iswitch=3,
    dft='PBE'
    nld=3,
        eminld=-4,
        emaxld=4,
        deld=0.01d0,
        rlderiv=2.65,
 /
 &inputp
   pseudotype=3,
   nlcc=.true.,
     !new_core_ps = .true.
     rcore=1.8
  lloc= -1,
  rcloc=2.4,
  rel=1
  file_pseudopw='Pt.pbe-n-kjpaw-chiu.UPF'
   zval=10
   lpaw=.true.
     lnc2paw=.false.
     which_augfun ='BESSEL'
     rmatch_augfun= 2.3000
   tm = .true.
   file_screen='Pt/ld1.scr'
!nX n  l   occ   nrg   rmin   rcut
 /
6
6S  1 0   1.00    0.00   2.00    2.40
6S  1 0   0.00    2.50   2.00    2.40
6P  2 1   0.00    0.00   2.30    2.50
6P  2 1   0.00    3.50   2.30    2.50
5D  3 2   9.00    0.00   1.80    2.20
5D  3 2   0.00    0.80   1.80    2.20

does any body see any obvious differences between the settings in my 
input an the  UPF file posted  above?
Thank you in advance,

Cheng-chau Chiu
PhD-Student, TU Muenchen, Chemistry Department

 

From giuseppe.mattioli at ism.cnr.it  Thu Jul 26 14:02:08 2012
From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli)
Date: Thu, 26 Jul 2012 14:02:08 +0200
Subject: [Pw_forum] read out settings for ld1.x run from UPF-file
In-Reply-To: <50112EFE.3070202@theochem.tu-muenchen.de>
References: <50112EFE.3070202@theochem.tu-muenchen.de>
Message-ID: <201207261402.09984.giuseppe.mattioli@ism.cnr.it>

Dear Cheng-chau Chiu
You can find the input file below, among many others, here:

http://qe-forge.org/projects/pslibrary

HTH

Giuseppe


cat > Pt.$fct-n-kjpaw.in << EOF
 &input
   title='Pt',
   zed=78.,
   rel=$nrel,
   config='[Xe] 4f14 5d9.0 6s1.0 6p0.0',
   iswitch=3,
   dft='$gfun'
 /
 &inputp
   lpaw=.true.,
   pseudotype=3,
   file_pseudopw='Pt.$fct-n-kjpaw.UPF',
   author='ADC',
   lloc=-2,
   rcloc=2.4,
   which_augfun='PSQ',
   rmatch_augfun=1.0,
   nlcc=.true.,
   new_core_ps=.true.,
   rcore=1.6,
   tm=.true.
 /
6
6S  1  0  1.00  0.00  2.00  2.40  0.0
6S  1  0  0.00  2.50  2.00  2.40  0.0
6P  2  1  0.00  0.00  2.30  2.50  0.0
6P  2  1  0.00  3.50  2.30  2.50  0.0
5D  3  2  9.00  0.00  1.80  2.20  0.0
5D  3  2  0.00  0.80  1.80  2.20  0.0
EOF


On Thursday 26 July 2012 13:50:22 Cheng-chau Chiu wrote:
> Dear all,
> is there a possibility to read from as .UPF- file what the input was for
> the pseudopotnetial generation using ld1.x?
> I am trying to reproduce the PAW for Pt published under
> http://nninc.cnf.cornell.edu/psp_files/Pt.pbe-n-kjpaw.UPF
> but i still failing to do so.
> I this is the input i was using:
> 
> &input
>     title='Pt',
>       zed=78,
>     config='[Xe] 6s1 4f14 5d9 6p0'
>     iswitch=3,
>     dft='PBE'
>     nld=3,
>         eminld=-4,
>         emaxld=4,
>         deld=0.01d0,
>         rlderiv=2.65,
>  /
>  &inputp
>    pseudotype=3,
>    nlcc=.true.,
>      !new_core_ps = .true.
>      rcore=1.8
>   lloc= -1,
>   rcloc=2.4,
>   rel=1
>   file_pseudopw='Pt.pbe-n-kjpaw-chiu.UPF'
>    zval=10
>    lpaw=.true.
>      lnc2paw=.false.
>      which_augfun ='BESSEL'
>      rmatch_augfun= 2.3000
>    tm = .true.
>    file_screen='Pt/ld1.scr'
> !nX n  l   occ   nrg   rmin   rcut
>  /
> 6
> 6S  1 0   1.00    0.00   2.00    2.40
> 6S  1 0   0.00    2.50   2.00    2.40
> 6P  2 1   0.00    0.00   2.30    2.50
> 6P  2 1   0.00    3.50   2.30    2.50
> 5D  3 2   9.00    0.00   1.80    2.20
> 5D  3 2   0.00    0.80   1.80    2.20
> 
> does any body see any obvious differences between the settings in my
> input an the  UPF file posted  above?
> Thank you in advance,
> 
> Cheng-chau Chiu
> PhD-Student, TU Muenchen, Chemistry Department
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

   Giuseppe Mattioli                            
   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
   v. Salaria Km 29,300 - C.P. 10                
   I 00015 - Monterotondo Stazione (RM)          
   Tel + 39 06 90672836 - Fax +39 06 90672316    
   E-mail: <giuseppe.mattioli at ism.cnr.it>

From bfazi90 at gmail.com  Thu Jul 26 14:12:44 2012
From: bfazi90 at gmail.com (bf azi)
Date: Thu, 26 Jul 2012 16:42:44 +0430
Subject: [Pw_forum] pseudopotential
Message-ID: <CAC+sowLTfCVK2skJwaymkB-UgtPy1AYSKK8QuKjOhrXiA=CFZw@mail.gmail.com>

In my system london interaction played important role and I perform
suggestion of Emine Kucukbenli (for input_dft="vdW-DF2" use a
revised-PW86), next question is:

Is necessary for london=.True.?

and in ATOMIC_SPECIES , Which kind of pseudopotential better for revised-PW86?

From akohlmey at gmail.com  Thu Jul 26 14:19:00 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Thu, 26 Jul 2012 14:19:00 +0200
Subject: [Pw_forum] pseudopotential
In-Reply-To: <CAC+sowLTfCVK2skJwaymkB-UgtPy1AYSKK8QuKjOhrXiA=CFZw@mail.gmail.com>
References: <CAC+sowLTfCVK2skJwaymkB-UgtPy1AYSKK8QuKjOhrXiA=CFZw@mail.gmail.com>
Message-ID: <CADTmJ6HN88LnRP85Tn_SfjL8knkR2DSvUO==qOPg6TkFX1s2SA@mail.gmail.com>

On Thu, Jul 26, 2012 at 2:12 PM, bf azi <bfazi90 at gmail.com> wrote:
> In my system london interaction played important role and I perform
> suggestion of Emine Kucukbenli (for input_dft="vdW-DF2" use a
> revised-PW86), next question is:

> Is necessary for london=.True.?

no. not at all. london=.true. uses DFT-D
which is an empirical correction to "regular"
functionals like BLYP and PBE and alike.
this is different from what emine was
talking about.

please have a good look at the related publications
that are mentioned in the input documentation.

axel.

>
> and in ATOMIC_SPECIES , Which kind of pseudopotential better for revised-PW86?
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



-- 
Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

From lmartinsamos at gmail.com  Thu Jul 26 16:55:26 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Thu, 26 Jul 2012 16:55:26 +0200
Subject: [Pw_forum] release espresso 5.0.1
Message-ID: <CAGCSmJQFKD42XyDJJ10e12mYzAiS4+V-XqPc5Sgi7W5dVkHmzA@mail.gmail.com>

Dear all, Quantum ESPRESSO release 5.0.1 is now available at
http://qe-forge.org/frs/?group_id=10. The webpage documentation has been
updated accordingly.

best regards

Paolo and Layla
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From giannozz at democritos.it  Thu Jul 26 17:48:32 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 26 Jul 2012 17:48:32 +0200
Subject: [Pw_forum] read out settings for ld1.x run from UPF-file
In-Reply-To: <50112EFE.3070202@theochem.tu-muenchen.de>
References: <50112EFE.3070202@theochem.tu-muenchen.de>
Message-ID: <894B8672-0E4C-4566-B133-DAD3E6C58DF8@democritos.it>


On Jul 26, 2012, at 13:50 , Cheng-chau Chiu wrote:

> is there a possibility to read from as .UPF- file what the input
> was for the pseudopotnetial generation using ld1.x?

since v.5.0.1 ld1.x saves the input data into the UPF file.
Unfortunately this works only for newly-generated pseudopotentials

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Thu Jul 26 17:52:20 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 26 Jul 2012 17:52:20 +0200
Subject: [Pw_forum] vc-md_NOT-STOP
In-Reply-To: <CAL9r4=K=iLWRZ6VfFL8ozN=di4KXffex05Nj7UiOWJGWKsfApw@mail.gmail.com>
References: <CAL9r4=K=iLWRZ6VfFL8ozN=di4KXffex05Nj7UiOWJGWKsfApw@mail.gmail.com>
Message-ID: <EE7B776C-6FF2-48B5-88D8-844077C8823F@democritos.it>


On Jul 26, 2012, at 9:39 , Ranber Thakur wrote:

> VC-md calculations does not stop after nstep. It keep running
> forever. What does this mean? Is there some strange bug?

sort of. More exactly: nobody has ever cared about this.
It will likely be fixed whenever a long-overdue cleanup of
the molecular dynamics code will be done

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From ranber14 at gmail.com  Thu Jul 26 20:07:42 2012
From: ranber14 at gmail.com (Ranber Thakur)
Date: Thu, 26 Jul 2012 23:37:42 +0530
Subject: [Pw_forum] vc-md_NOT-STOP
In-Reply-To: <EE7B776C-6FF2-48B5-88D8-844077C8823F@democritos.it>
References: <CAL9r4=K=iLWRZ6VfFL8ozN=di4KXffex05Nj7UiOWJGWKsfApw@mail.gmail.com>
	<EE7B776C-6FF2-48B5-88D8-844077C8823F@democritos.it>
Message-ID: <CAL9r4=LgzNGacE7sjowRzMt=qjGzj8HWKR3G5dMiYZLcmSp1Hg@mail.gmail.com>

It was, in fact, very simple. I have fixed it. I add few more options in
vcsmd.f90.
It is now ok.


On Thu, Jul 26, 2012 at 9:22 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Jul 26, 2012, at 9:39 , Ranber Thakur wrote:
>
> > VC-md calculations does not stop after nstep. It keep running
> > forever. What does this mean? Is there some strange bug?
>
> sort of. More exactly: nobody has ever cared about this.
> It will likely be fixed whenever a long-overdue cleanup of
> the molecular dynamics code will be done
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From tkaloni at gmail.com  Thu Jul 26 20:20:37 2012
From: tkaloni at gmail.com (Thaneshwor Kaloni)
Date: Thu, 26 Jul 2012 21:20:37 +0300
Subject: [Pw_forum] k points weights
Message-ID: <CABvS7QJ42OYsNgGSgXsbnMXfvrn025rM2M-iEhHzoRZiXTozQg@mail.gmail.com>

Message: 1
Date: Thu, 26 Jul 2012 19:10:07 +0800 (SGT)
From: Sohail Ahmad <sohailphysics at yahoo.co.in>
Subject: [Pw_forum] k points weights
To: Plane Wave <pw_forum at pwscf.org>
Message-ID:
        <1343301007.14468.YahooMailClassic at web190902.mail.sg3.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Pw users

In example 01 of version QE-4.2.3
In band.in file k points are given as
?K_POINTS
?28
?? 0.0 0.0 0.0 1.0
?? 0.0 0.0 0.1 1.0
?? 0.0 0.0 0.2 1.0

while
 in lab exercise2
 day1 (given by Prof Shobhana Narasimhan on july 20, 2009) tutorial held
 in Santa Barbara
http://media.quantum-espresso.org/santa_barbara_2009_07/
36
?? 0.5 0.5 0.5? 1
?? 0.4 0.4 0.4? 2
?? 0.3 0.3 0.3? 3
?? 0.2 0.2 0.2? 4
?? 0.1 0.1 0.1? 5

Now my question is whether i should write weights or the simply serial no.
in band.in file
i believe it should be its weitghs then the question is how to claculate

Sohail Ahmad
King Khalid University
Saudi Arbia
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>the question is how to claculate

use kpoints.x command.

Kaloni
http://cpms.kaust.edu.sa/Pages/People.aspx
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From masoudnahali at gmail.com  Fri Jul 27 02:31:26 2012
From: masoudnahali at gmail.com (m)
Date: Fri, 27 Jul 2012 02:31:26 +0200
Subject: [Pw_forum] plotrho and atom core !
Message-ID: <CAM-1hSui1f1W-342m7D9bmkN6+h6UtbATiFsrJxTDaUoucAZNw@mail.gmail.com>

Hi

As it seems the atom cores (black circles) that are sketched by plotrho
code have identical sizes for different atoms. So it can make some plots
that have less taste for a chemist.
For example in my system I have C-C and C-H bonds with 1.4 and 1.1 angstrom
lengths respectively; I can see the density of electrons between the two
carbon atoms clearly however for
the C-H the two atom cores are tangent to each other and one cannot see the
density of electrons between the two atoms as clear as the former case. I
'd better mention that I can understand that there is a chemical bond with
the lines (contours) that come from the side of the circles but it would be
nicer if they had different sizes. Does it seem sensible to make a bit
change in the code ? or any comment to make the plot nicer ? Many thanks,
Sincerely Yours.


Ciao, m





----------------------------------------
Masoud Nahali
International School for Advanced Studies (SISSA)
masoud.nahali at gmail.com
alum.sharif.edu/~m_nahali
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From aakimov at z.rochester.edu  Fri Jul 27 04:21:35 2012
From: aakimov at z.rochester.edu (Alexey Akimov)
Date: Thu, 26 Jul 2012 22:21:35 -0400 (EDT)
Subject: [Pw_forum] convergence problem for charged simulation cell
In-Reply-To: <493056282.84267.1343355678118.JavaMail.root@asems02.its.rochester.edu>
Message-ID: <1412189396.84274.1343355695489.JavaMail.root@asems02.its.rochester.edu>

Dear all,

I'm trying to calculate md of a system with the positive charge (+1) of the simulation cell. However it seems like a hard task,
because even the first step is not converging (electronic iteration). I used setup to allow up to 100 electronic iterations, but
this is not enough to achieve the convergence. I also tried to decrease the mixing parameter to 0.4, as was suggested in some of the
previous posts. I tried to increase charge density cutoff to 10*ecutwfc.

Also the program warns me that:
     (first iteration)
     WARNING: integrated charge=  2046.60000000, expected=  2047.00000000

     (10-th iteration)
     WARNING: integrated charge=  2046.01617514, expected=  2047.00000000

I do not know why program expects the charge corresponding to neutral system, while i ask for the positively charged one (tot_charge = 1.0)
I'm using version PWSCF v.4.3.2  with 4 processors. By the way, for neutral system the convergence does not give any problem.

Is there any ideas how to achieve the convergence for the charged simulation cell? Also i'm curious about those warning messages - can they be disregarded or it is me, who is missing something? May it be some bug of PWScf?

Thank you,
Alexey

-- 
Dr. Alexey V. Akimov

Postdoctoral Research Associate
Department of Chemistry
University of Rochester

aakimov at z.rochester.edu 

From d.tiana at bath.ac.uk  Fri Jul 27 10:39:54 2012
From: d.tiana at bath.ac.uk (Davide Tiana)
Date: Fri, 27 Jul 2012 09:39:54 +0100
Subject: [Pw_forum] k points weights
In-Reply-To: <mailman.1.1343376233.12689.pw_forum@pwscf.org>
References: <mailman.1.1343376233.12689.pw_forum@pwscf.org>
Message-ID: <20120727093954.Horde.mRhpZs1vlIJQElPap7kyGQA@webmail.bath.ac.uk>

As remembered in many QE tutorials, weights are meaningless in NSCF  
calculations such as band ones.

by the way when required (for instance during optimisation) weights  
are simply related to the multiplicity of the points and can be  
obtained looking International Cryst tables or Bilbao Cryst server.

Regards
Davide

>
> Message: 1
> Date: Thu, 26 Jul 2012 19:10:07 +0800 (SGT)
> From: Sohail Ahmad <sohailphysics at yahoo.co.in>
> Subject: [Pw_forum] k points weights
> To: Plane Wave <pw_forum at pwscf.org>
> Message-ID:
>         <1343301007.14468.YahooMailClassic at web190902.mail.sg3.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Pw users
>
> In example 01 of version QE-4.2.3
> In band.in file k points are given as
> ?K_POINTS
> ?28
> ?? 0.0 0.0 0.0 1.0
> ?? 0.0 0.0 0.1 1.0
> ?? 0.0 0.0 0.2 1.0
>
> while
>  in lab exercise2
>  day1 (given by Prof Shobhana Narasimhan on july 20, 2009) tutorial held
>  in Santa Barbara
> http://media.quantum-espresso.org/santa_barbara_2009_07/
> 36
> ?? 0.5 0.5 0.5? 1
> ?? 0.4 0.4 0.4? 2
> ?? 0.3 0.3 0.3? 3
> ?? 0.2 0.2 0.2? 4
> ?? 0.1 0.1 0.1? 5
>
> Now my question is whether i should write weights or the simply serial no.
> in band.in file
> i believe it should be its weitghs then the question is how to claculate
>
> Sohail Ahmad
> King Khalid University
> Saudi Arbia



From zhanhit at hotmail.com  Fri Jul 27 11:48:03 2012
From: zhanhit at hotmail.com (Franklin Zhan)
Date: Fri, 27 Jul 2012 09:48:03 +0000
Subject: [Pw_forum] k points weights
In-Reply-To: <20120727093954.Horde.mRhpZs1vlIJQElPap7kyGQA@webmail.bath.ac.uk>
References: <mailman.1.1343376233.12689.pw_forum@pwscf.org>,
	<20120727093954.Horde.mRhpZs1vlIJQElPap7kyGQA@webmail.bath.ac.uk>
Message-ID: <BAY151-W3715DBFA8C2F7D9CC7C65BA7C10@phx.gbl>


I think k point weight affects the DOS result.
regards,

franklin




> Date: Fri, 27 Jul 2012 09:39:54 +0100
> From: d.tiana at bath.ac.uk
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] k points weights
> 
> As remembered in many QE tutorials, weights are meaningless in NSCF  
> calculations such as band ones.
> 
> by the way when required (for instance during optimisation) weights  
> are simply related to the multiplicity of the points and can be  
> obtained looking International Cryst tables or Bilbao Cryst server.
> 
> Regards
> Davide
> 
> >
> > Message: 1
> > Date: Thu, 26 Jul 2012 19:10:07 +0800 (SGT)
> > From: Sohail Ahmad <sohailphysics at yahoo.co.in>
> > Subject: [Pw_forum] k points weights
> > To: Plane Wave <pw_forum at pwscf.org>
> > Message-ID:
> >         <1343301007.14468.YahooMailClassic at web190902.mail.sg3.yahoo.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Dear Pw users
> >
> > In example 01 of version QE-4.2.3
> > In band.in file k points are given as
> > ?K_POINTS
> > ?28
> > ?? 0.0 0.0 0.0 1.0
> > ?? 0.0 0.0 0.1 1.0
> > ?? 0.0 0.0 0.2 1.0
> >
> > while
> >  in lab exercise2
> >  day1 (given by Prof Shobhana Narasimhan on july 20, 2009) tutorial held
> >  in Santa Barbara
> > http://media.quantum-espresso.org/santa_barbara_2009_07/
> > 36
> > ?? 0.5 0.5 0.5? 1
> > ?? 0.4 0.4 0.4? 2
> > ?? 0.3 0.3 0.3? 3
> > ?? 0.2 0.2 0.2? 4
> > ?? 0.1 0.1 0.1? 5
> >
> > Now my question is whether i should write weights or the simply serial no.
> > in band.in file
> > i believe it should be its weitghs then the question is how to claculate
> >
> > Sohail Ahmad
> > King Khalid University
> > Saudi Arbia
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
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From pchen at ion.chem.utk.edu  Fri Jul 27 19:41:00 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Fri, 27 Jul 2012 13:41:00 -0400
Subject: [Pw_forum] U calculation error
Message-ID: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>

Dear All,

There are some errors when I run r.x to calculate the U. I used
Espresso-5.0 and follow the steps in LSDA+U example. I am not sure what
could be wrong. And if you need other input/output, please let me know.

Image              PC        Routine            Line        Source
r.x                0822DACC  Unknown               Unknown  Unknown
r.x                0822C265  Unknown               Unknown  Unknown
r.x                082071FA  Unknown               Unknown  Unknown
r.x                081DDFDA  Unknown               Unknown  Unknown
r.x                081FA33B  Unknown               Unknown  Unknown
r.x                081F9C5C  Unknown               Unknown  Unknown
r.x                0804E38F  Unknown               Unknown  Unknown
r.x                0804824A  Unknown               Unknown  Unknown
r.x                0823805D  Unknown               Unknown  Unknown
r.x                08048131  Unknown               Unknown  Unknown
forrtl: severe (8): internal consistency check failure, file
./src/libfor/for_wseq_lis.c, line 635
Image              PC        Routine            Line        Source
r.x                0822DACC  Unknown               Unknown  Unknown
r.x                0822C265  Unknown               Unknown  Unknown
r.x                082071FA  Unknown               Unknown  Unknown
r.x                081DD664  Unknown               Unknown  Unknown
r.x                081F9AF7  Unknown               Unknown  Unknown
r.x                0804E38F  Unknown               Unknown  Unknown
r.x                0804824A  Unknown               Unknown  Unknown
r.x                0823805D  Unknown               Unknown  Unknown
r.x                08048131  Unknown               Unknown  Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC        Routine            Line        Source
r.x                0804DAED  Unknown               Unknown  Unknown
r.x                0804824A  Unknown               Unknown  Unknown
r.x                0823805D  Unknown               Unknown  Unknown
r.x                08048131  Unknown               Unknown  Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC        Routine            Line        Source
r.x                08253657  Unknown               Unknown  Unknown
r.x                081F4087  Unknown               Unknown  Unknown
r.x                081DCDB7  Unknown               Unknown  Unknown
r.x                081DF354  Unknown               Unknown  Unknown
r.x                081DD672  Unknown               Unknown  Unknown
r.x                081DF5E8  Unknown               Unknown  Unknown
Unknown            FFFFE600  Unknown               Unknown  Unknown
r.x                0804824A  Unknown               Unknown  Unknown
r.x                0823805D  Unknown               Unknown  Unknown
r.x                08048131  Unknown               Unknown  Unknown


-- 
  Best Regards.
        Peng
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From iurii.timrov at polytechnique.edu  Fri Jul 27 19:35:12 2012
From: iurii.timrov at polytechnique.edu (Iurii TIMROV)
Date: Fri, 27 Jul 2012 19:35:12 +0200
Subject: [Pw_forum] Bug in PW/pw_readfile
Message-ID: <445e5712c6b055cf1e2cefcb3c893f0a.squirrel@theory.polytechnique.fr>

Dear QE developers,

It seems there is a bug in the subroutine PW/pw_readfile. It shows up when
a phonon calculation is restarted. I checked QE v.5.0.1, the bug hasn't
been fixed. It is related to the unit "iunout". In the beginning of the 
pw_readfile, there is a look for an empty unit:

CALL iotk_free_unit( iunout, ierr )

Afterwards, in the subroutine "read_band_structure" the unit "iunout" is
used. But the problem is that in "read_band_structure" the unit "iunout"
is declared second time:

INTEGER :: iunout

Thus, "iunout" is a random number, which sometimes may be negative, and
therefore the data file cannot be read. Due to this, the code escapes from
this routine (return), the data file is not read, and the code crashes
somewhere else. It is strange to me, why the code escapes (return
statement) instead of giving an error message (it takes time to find such
bugs due to this).

The solution of the problem is simple: just to remove "INTEGER :: iunout".

If this is not a bug, please explain me why. But in my case the code
doesn't work with this.

Best,
Iurii


Iurii TIMROV
Doctorant (PhD student)
Laboratoire des Solides Irradies
Ecole Polytechnique
F-91128 Palaiseau
+33 1 69 33 45 08


From stewart at cnf.cornell.edu  Fri Jul 27 20:07:26 2012
From: stewart at cnf.cornell.edu (Derek Stewart)
Date: Fri, 27 Jul 2012 14:07:26 -0400
Subject: [Pw_forum] Question on Fractional occupation used to generate
	Mg.pw91-np-van.UPF
Message-ID: <5012D8DE.5000705@cnf.cornell.edu>

Hi everyone,

I would like to use the PW91 Mg pseudopotential for some calculations, 
but I noticed something odd in the occupation listed at the beginning of 
the pseudopotential.

nl pn  l   occ               Rcut            Rcut US             E pseu
2P  2  1  6.00     10.00000000000      2.00000000000     -3.69842610300
3S  3  0  1.00     10.00000000000      2.30000000000     -0.51455069900
3P  3  1  0.75     10.00000000000      2.00000000000     -0.23733335900
3D  3  2  0.00     10.00000000000      2.00000000000     -0.02607571400

The ground state configuration of Mg is 1s2 2p6 3s2 , however this 
pseudopotential uses 1s2 2p6 3s1 3p0.75 with 0.25 electrons missing.

Later on in the file, it does specify the total valence as 8 electrons.

Does someone know why this approach was taken in generating the 
pseudopotential?  Is this done to provide a better pseudopotential for 
ionic materials where Mg will have a positive charge?

Thanks,

Derek


-- 
################################
Derek Stewart, Ph. D.
Senior Research Associate
http://sites.google.com/site/dft4nano/
250 Duffield Hall
Cornell Nanoscale Facility (CNF)
Ithaca, NY 14853
stewart (at) cnf.cornell.edu
(607) 255-2856




From bfazi90 at gmail.com  Fri Jul 27 20:25:58 2012
From: bfazi90 at gmail.com (bf azi)
Date: Fri, 27 Jul 2012 22:55:58 +0430
Subject: [Pw_forum] two conflicting
Message-ID: <CAC+sowLcN8kTuLN2er6zoHAEjP3uzGcFw+BmLLsziWhDSZ4s2A@mail.gmail.com>

Dear all

when I set vdw2 for input_dft, and run scf, running is stoped and show
this error:
     from set_dft_value : error #         1
     two conflicting matching values

why?

Thanks a lot

Bani Adam
Faculty of Science
Egypt

From matteo at umn.edu  Fri Jul 27 21:02:16 2012
From: matteo at umn.edu (Matteo Cococcioni)
Date: Fri, 27 Jul 2012 14:02:16 -0500
Subject: [Pw_forum] U calculation error
In-Reply-To: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>
References: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>
Message-ID: <CAMZASgH3ZxSwGtXARSqN+khMe4CSttRRgTb81F3LX7GfKFtp6w@mail.gmail.com>

Dear Peng,

can you provide info about your system? maybe it is larger than the
maximum size allowed by r.x?

Matteo

On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
> Dear All,
>
> There are some errors when I run r.x to calculate the U. I used Espresso-5.0
> and follow the steps in LSDA+U example. I am not sure what could be wrong.
> And if you need other input/output, please let me know.
>
> Image              PC        Routine            Line        Source
> r.x                0822DACC  Unknown               Unknown  Unknown
> r.x                0822C265  Unknown               Unknown  Unknown
> r.x                082071FA  Unknown               Unknown  Unknown
> r.x                081DDFDA  Unknown               Unknown  Unknown
> r.x                081FA33B  Unknown               Unknown  Unknown
> r.x                081F9C5C  Unknown               Unknown  Unknown
> r.x                0804E38F  Unknown               Unknown  Unknown
> r.x                0804824A  Unknown               Unknown  Unknown
> r.x                0823805D  Unknown               Unknown  Unknown
> r.x                08048131  Unknown               Unknown  Unknown
> forrtl: severe (8): internal consistency check failure, file
> ./src/libfor/for_wseq_lis.c, line 635
> Image              PC        Routine            Line        Source
> r.x                0822DACC  Unknown               Unknown  Unknown
> r.x                0822C265  Unknown               Unknown  Unknown
> r.x                082071FA  Unknown               Unknown  Unknown
> r.x                081DD664  Unknown               Unknown  Unknown
> r.x                081F9AF7  Unknown               Unknown  Unknown
> r.x                0804E38F  Unknown               Unknown  Unknown
> r.x                0804824A  Unknown               Unknown  Unknown
> r.x                0823805D  Unknown               Unknown  Unknown
> r.x                08048131  Unknown               Unknown  Unknown
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image              PC        Routine            Line        Source
> r.x                0804DAED  Unknown               Unknown  Unknown
> r.x                0804824A  Unknown               Unknown  Unknown
> r.x                0823805D  Unknown               Unknown  Unknown
> r.x                08048131  Unknown               Unknown  Unknown
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image              PC        Routine            Line        Source
> r.x                08253657  Unknown               Unknown  Unknown
> r.x                081F4087  Unknown               Unknown  Unknown
> r.x                081DCDB7  Unknown               Unknown  Unknown
> r.x                081DF354  Unknown               Unknown  Unknown
> r.x                081DD672  Unknown               Unknown  Unknown
> r.x                081DF5E8  Unknown               Unknown  Unknown
> Unknown            FFFFE600  Unknown               Unknown  Unknown
> r.x                0804824A  Unknown               Unknown  Unknown
> r.x                0823805D  Unknown               Unknown  Unknown
> r.x                08048131  Unknown               Unknown  Unknown
>
>
> --
>   Best Regards.
>         Peng
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056    Fax +1 612 626 7246

From lorenzo.paulatto at impmc.upmc.fr  Sat Jul 28 00:52:54 2012
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Sat, 28 Jul 2012 00:52:54 +0200
Subject: [Pw_forum] Question on Fractional occupation used to generate
	Mg.pw91-np-van.UPF
In-Reply-To: <5012D8DE.5000705@cnf.cornell.edu>
References: <5012D8DE.5000705@cnf.cornell.edu>
Message-ID: <CAG+GtJfPTDrtLjDvjRtwSvkk_LzpxVkMS6VrvovscAZKx6k3Pg@mail.gmail.com>

On 27 July 2012 20:07, Derek Stewart <stewart at cnf.cornell.edu> wrote:

> I would like to use the PW91 Mg pseudopotential for some calculations,
> but I noticed something odd in the occupation listed at the beginning of
> the pseudopotential.
>
> Dear Derek,
a good quality pseudopotential works in a vast range of conditions, not
only in the generation occupations. I.e. if the pseudo is well tested, no
need to worry: the pw.x code will still use the "right" number of
electrons, your cell won't be charged.

-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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From pchen at ion.chem.utk.edu  Sat Jul 28 06:46:38 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Sat, 28 Jul 2012 00:46:38 -0400
Subject: [Pw_forum] U calculation error
In-Reply-To: <CAMZASgH3ZxSwGtXARSqN+khMe4CSttRRgTb81F3LX7GfKFtp6w@mail.gmail.com>
References: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>
	<CAMZASgH3ZxSwGtXARSqN+khMe4CSttRRgTb81F3LX7GfKFtp6w@mail.gmail.com>
Message-ID: <CAP_5U0fA-N8DhL1DYcbpLZ=hiG8T4EfmJXPqwuJXFvcG89gP-Q@mail.gmail.com>

Dear Dr. Matteo,

The primitive cell has 26 atoms with 3 different types. The pos and
resp_mat.in files are shown below:

5.6087 10.79 0.0
5.6087 -10.79 0.0
0.0 0.0   15.570873
0       0       0       1
0.5     0.5     0.5     -1
0.12286329      0.378190177     0.749934361     1
0.87713671      0.621809823     0.250065639     1
0.377137388     0.121809201     0.249932658     -1
0.622862612     0.878190799     0.750067342     -1
0.373618754     0.623612138     0.11586798      0
0.126381501     0.876388862     0.615868582     0
0.626381246     0.376387862     0.88413202      0
0.873618499     0.123611138     0.384131418     0
0.241839036     0.756304999     0.223613779     0
0.258160617     0.74369391      0.723611944     0
0.758160964     0.243695001     0.776386221     0
0.741839383     0.25630609      0.276388056     0
-0.000998332    1.000227439     0.243205274     0
0.500997862     0.499772508     0.743208489     0
1.000998332     -0.000227439    0.756794726     0
0.499002138     0.500227492     0.256791511     0
0.381099639     0.150692971     0.006796703     0
0.118898786     0.349304325     0.506798051     0
0.149581603     0.378555571     0.991989919     0
0.350419534     0.121445697     0.491991443     0
0.618900361     0.849307029     0.993205297     0
0.881101214     0.650695675     0.493203949     0
0.850418397     0.621444429     0.008012081     0
0.649580466     0.878554303     0.508010557     0

resp_mat.in :
 &input_mat
   ntyp = 3
   na(1) = 6
   na(2) = 4
   na(3) = 16
   nalfa = 5
   magn=.true.
   filepos = 'pos'
   back = 'no'
   filednda = 'file_afm'
   n1 = 2
   n2 = 2
   n3 = 2
 &end



On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni <matteo at umn.edu> wrote:

> Dear Peng,
>
> can you provide info about your system? maybe it is larger than the
> maximum size allowed by r.x?
>
> Matteo
>
> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen <pchen at ion.chem.utk.edu>
> wrote:
> > Dear All,
> >
> > There are some errors when I run r.x to calculate the U. I used
> Espresso-5.0
> > and follow the steps in LSDA+U example. I am not sure what could be
> wrong.
> > And if you need other input/output, please let me know.
> >
> > Image              PC        Routine            Line        Source
> > r.x                0822DACC  Unknown               Unknown  Unknown
> > r.x                0822C265  Unknown               Unknown  Unknown
> > r.x                082071FA  Unknown               Unknown  Unknown
> > r.x                081DDFDA  Unknown               Unknown  Unknown
> > r.x                081FA33B  Unknown               Unknown  Unknown
> > r.x                081F9C5C  Unknown               Unknown  Unknown
> > r.x                0804E38F  Unknown               Unknown  Unknown
> > r.x                0804824A  Unknown               Unknown  Unknown
> > r.x                0823805D  Unknown               Unknown  Unknown
> > r.x                08048131  Unknown               Unknown  Unknown
> > forrtl: severe (8): internal consistency check failure, file
> > ./src/libfor/for_wseq_lis.c, line 635
> > Image              PC        Routine            Line        Source
> > r.x                0822DACC  Unknown               Unknown  Unknown
> > r.x                0822C265  Unknown               Unknown  Unknown
> > r.x                082071FA  Unknown               Unknown  Unknown
> > r.x                081DD664  Unknown               Unknown  Unknown
> > r.x                081F9AF7  Unknown               Unknown  Unknown
> > r.x                0804E38F  Unknown               Unknown  Unknown
> > r.x                0804824A  Unknown               Unknown  Unknown
> > r.x                0823805D  Unknown               Unknown  Unknown
> > r.x                08048131  Unknown               Unknown  Unknown
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > Image              PC        Routine            Line        Source
> > r.x                0804DAED  Unknown               Unknown  Unknown
> > r.x                0804824A  Unknown               Unknown  Unknown
> > r.x                0823805D  Unknown               Unknown  Unknown
> > r.x                08048131  Unknown               Unknown  Unknown
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > Image              PC        Routine            Line        Source
> > r.x                08253657  Unknown               Unknown  Unknown
> > r.x                081F4087  Unknown               Unknown  Unknown
> > r.x                081DCDB7  Unknown               Unknown  Unknown
> > r.x                081DF354  Unknown               Unknown  Unknown
> > r.x                081DD672  Unknown               Unknown  Unknown
> > r.x                081DF5E8  Unknown               Unknown  Unknown
> > Unknown            FFFFE600  Unknown               Unknown  Unknown
> > r.x                0804824A  Unknown               Unknown  Unknown
> > r.x                0823805D  Unknown               Unknown  Unknown
> > r.x                08048131  Unknown               Unknown  Unknown
> >
> >
> > --
> >   Best Regards.
> >         Peng
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Matteo Cococcioni
> Department of Chemical Engineering and Materials Science,
> University of Minnesota
> 421 Washington Av. SE
> Minneapolis, MN 55455
> Tel. +1 612 624 9056    Fax +1 612 626 7246
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
  Best Regards.
        Peng
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From sohailphysics at yahoo.co.in  Sat Jul 28 11:13:00 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Sat, 28 Jul 2012 17:13:00 +0800 (SGT)
Subject: [Pw_forum] pw91 pseudopotential for Se
Message-ID: <1343466780.11334.YahooMailClassic@web190903.mail.sg3.yahoo.com>

Dear PW users

I am looking for GGA pseudo potential (pw91 type) for Se and Te
i checked on QE website and many other website, unfortunately its not available

Can any one provide me ???

Thanks in advance

Sohail Ahmad
KIng Khalid University
Saudi Arabia

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From pandey.bramha at gmail.com  Sat Jul 28 11:40:16 2012
From: pandey.bramha at gmail.com (bramha pandey)
Date: Sat, 28 Jul 2012 15:10:16 +0530
Subject: [Pw_forum] pw91 pseudopotential for Se
In-Reply-To: <1343466780.11334.YahooMailClassic@web190903.mail.sg3.yahoo.com>
References: <1343466780.11334.YahooMailClassic@web190903.mail.sg3.yahoo.com>
Message-ID: <CAC2dNGHWkOoG_=NR+vwBOngKiv=DnofC2Bip=0LrjFSjYn7EYA@mail.gmail.com>

you have to search in pslibray definetly you will find it for both.

On Sat, Jul 28, 2012 at 2:43 PM, Sohail Ahmad <sohailphysics at yahoo.co.in>wrote:

> Dear PW users
>
> I am looking for GGA pseudo potential (pw91 type) for Se and Te
> i checked on QE website and many other website, unfortunately its not
> available
>
> Can any one provide me ???
>
> Thanks in advance
>
> Sohail Ahmad
> KIng Khalid University
> Saudi Arabia
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Thanks and Regards
Bramha Prasad Pandey
Ph.D Student Indian School of Mines(ISM)
Dhanbad, INDIA.
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From zafartariq2003 at yahoo.com  Sat Jul 28 15:09:42 2012
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Sat, 28 Jul 2012 06:09:42 -0700 (PDT)
Subject: [Pw_forum] Error while compiling  Quantum Espresso
Message-ID: <1343480982.93555.YahooMailClassic@web121405.mail.ne1.yahoo.com>

Dear all
we are trying to install Quantum Espresoo-4.1.3 on Solaris 10 (Sun sparc). But it gives follwing error during when we try to configure it..

"Configure : error linking to fortran libraries from c fails."
and stops.
will any body help to configure it.

Muhammad Zafar

PhD Scholar

Department of Physics

The Islamia University of Bahawalpur,Pakistan
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From binukhn at gmail.com  Sat Jul 28 16:00:43 2012
From: binukhn at gmail.com (Amin Amin)
Date: Sat, 28 Jul 2012 17:00:43 +0300
Subject: [Pw_forum] Request
Message-ID: <CAOBLcoyW0hCH3YNwBSZonjZTUsHanaxxJYcYVBjQGtPwo09H6w@mail.gmail.com>

Dear PWSCF users,

I would like to perform a electronic structure of the CrO2 with
inclusion of SOC.
I could not find full relativistic pseudopotential for Cr.  Now the
point is: can I use the SOC
included  pseudopotential  from VASP for my calculations?

Best, Amin
King Abdullah University of Science and Technology, KSA

From degironc at sissa.it  Sat Jul 28 16:27:17 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sat, 28 Jul 2012 16:27:17 +0200
Subject: [Pw_forum] Request
In-Reply-To: <CAOBLcoyW0hCH3YNwBSZonjZTUsHanaxxJYcYVBjQGtPwo09H6w@mail.gmail.com>
References: <CAOBLcoyW0hCH3YNwBSZonjZTUsHanaxxJYcYVBjQGtPwo09H6w@mail.gmail.com>
Message-ID: <5013F6C5.7000302@sissa.it>

Dear Amin,

    since the Vasp people refused to provide information about their 
pseudopotental format and to distribute publicly their preudopotential 
files, it is not possible and, i guess, legally forbidden to use their 
pseudo in other codes.
    In case you wish to use their pseudo with QE you should first of all 
submit a request for authorization to the Vasp people and ask 
information on how to create a converter to the UPF format.
    best regards,
stefano

PS: have you checked in the ps_library distribution for a Cr pseudo with 
SOC ?



On 07/28/2012 04:00 PM, Amin Amin wrote:
> Dear PWSCF users,
>
> I would like to perform a electronic structure of the CrO2 with
> inclusion of SOC.
> I could not find full relativistic pseudopotential for Cr.  Now the
> point is: can I use the SOC
> included  pseudopotential  from VASP for my calculations?
>
> Best, Amin
> King Abdullah University of Science and Technology, KSA
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From matteo at umn.edu  Sat Jul 28 16:38:40 2012
From: matteo at umn.edu (Matteo Cococcioni)
Date: Sat, 28 Jul 2012 09:38:40 -0500
Subject: [Pw_forum] U calculation error
In-Reply-To: <CAP_5U0fA-N8DhL1DYcbpLZ=hiG8T4EfmJXPqwuJXFvcG89gP-Q@mail.gmail.com>
References: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>
	<CAMZASgH3ZxSwGtXARSqN+khMe4CSttRRgTb81F3LX7GfKFtp6w@mail.gmail.com>
	<CAP_5U0fA-N8DhL1DYcbpLZ=hiG8T4EfmJXPqwuJXFvcG89gP-Q@mail.gmail.com>
Message-ID: <CAMZASgFWbtt6oCCoUp5g=ah3ODVOrNth9dwmmf2p+0XauMKhrw@mail.gmail.com>

Dear Peng,

nothing looks wrong in your input. have you tried with n1, n2, n3 all
equal to 1? are you sure you compiled correctly?

Matteo



On Fri, Jul 27, 2012 at 11:46 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
> Dear Dr. Matteo,
>
> The primitive cell has 26 atoms with 3 different types. The pos and
> resp_mat.in files are shown below:
>
> 5.6087 10.79 0.0
> 5.6087 -10.79 0.0
> 0.0 0.0   15.570873
> 0       0       0       1
> 0.5     0.5     0.5     -1
> 0.12286329      0.378190177     0.749934361     1
> 0.87713671      0.621809823     0.250065639     1
> 0.377137388     0.121809201     0.249932658     -1
> 0.622862612     0.878190799     0.750067342     -1
> 0.373618754     0.623612138     0.11586798      0
> 0.126381501     0.876388862     0.615868582     0
> 0.626381246     0.376387862     0.88413202      0
> 0.873618499     0.123611138     0.384131418     0
> 0.241839036     0.756304999     0.223613779     0
> 0.258160617     0.74369391      0.723611944     0
> 0.758160964     0.243695001     0.776386221     0
> 0.741839383     0.25630609      0.276388056     0
> -0.000998332    1.000227439     0.243205274     0
> 0.500997862     0.499772508     0.743208489     0
> 1.000998332     -0.000227439    0.756794726     0
> 0.499002138     0.500227492     0.256791511     0
> 0.381099639     0.150692971     0.006796703     0
> 0.118898786     0.349304325     0.506798051     0
> 0.149581603     0.378555571     0.991989919     0
> 0.350419534     0.121445697     0.491991443     0
> 0.618900361     0.849307029     0.993205297     0
> 0.881101214     0.650695675     0.493203949     0
> 0.850418397     0.621444429     0.008012081     0
> 0.649580466     0.878554303     0.508010557     0
>
> resp_mat.in :
>  &input_mat
>    ntyp = 3
>    na(1) = 6
>    na(2) = 4
>    na(3) = 16
>    nalfa = 5
>    magn=.true.
>    filepos = 'pos'
>    back = 'no'
>    filednda = 'file_afm'
>    n1 = 2
>    n2 = 2
>    n3 = 2
>  &end
>
>
>
> On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni <matteo at umn.edu> wrote:
>>
>> Dear Peng,
>>
>> can you provide info about your system? maybe it is larger than the
>> maximum size allowed by r.x?
>>
>> Matteo
>>
>> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen <pchen at ion.chem.utk.edu>
>> wrote:
>> > Dear All,
>> >
>> > There are some errors when I run r.x to calculate the U. I used
>> > Espresso-5.0
>> > and follow the steps in LSDA+U example. I am not sure what could be
>> > wrong.
>> > And if you need other input/output, please let me know.
>> >
>> > Image              PC        Routine            Line        Source
>> > r.x                0822DACC  Unknown               Unknown  Unknown
>> > r.x                0822C265  Unknown               Unknown  Unknown
>> > r.x                082071FA  Unknown               Unknown  Unknown
>> > r.x                081DDFDA  Unknown               Unknown  Unknown
>> > r.x                081FA33B  Unknown               Unknown  Unknown
>> > r.x                081F9C5C  Unknown               Unknown  Unknown
>> > r.x                0804E38F  Unknown               Unknown  Unknown
>> > r.x                0804824A  Unknown               Unknown  Unknown
>> > r.x                0823805D  Unknown               Unknown  Unknown
>> > r.x                08048131  Unknown               Unknown  Unknown
>> > forrtl: severe (8): internal consistency check failure, file
>> > ./src/libfor/for_wseq_lis.c, line 635
>> > Image              PC        Routine            Line        Source
>> > r.x                0822DACC  Unknown               Unknown  Unknown
>> > r.x                0822C265  Unknown               Unknown  Unknown
>> > r.x                082071FA  Unknown               Unknown  Unknown
>> > r.x                081DD664  Unknown               Unknown  Unknown
>> > r.x                081F9AF7  Unknown               Unknown  Unknown
>> > r.x                0804E38F  Unknown               Unknown  Unknown
>> > r.x                0804824A  Unknown               Unknown  Unknown
>> > r.x                0823805D  Unknown               Unknown  Unknown
>> > r.x                08048131  Unknown               Unknown  Unknown
>> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> > Image              PC        Routine            Line        Source
>> > r.x                0804DAED  Unknown               Unknown  Unknown
>> > r.x                0804824A  Unknown               Unknown  Unknown
>> > r.x                0823805D  Unknown               Unknown  Unknown
>> > r.x                08048131  Unknown               Unknown  Unknown
>> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> > Image              PC        Routine            Line        Source
>> > r.x                08253657  Unknown               Unknown  Unknown
>> > r.x                081F4087  Unknown               Unknown  Unknown
>> > r.x                081DCDB7  Unknown               Unknown  Unknown
>> > r.x                081DF354  Unknown               Unknown  Unknown
>> > r.x                081DD672  Unknown               Unknown  Unknown
>> > r.x                081DF5E8  Unknown               Unknown  Unknown
>> > Unknown            FFFFE600  Unknown               Unknown  Unknown
>> > r.x                0804824A  Unknown               Unknown  Unknown
>> > r.x                0823805D  Unknown               Unknown  Unknown
>> > r.x                08048131  Unknown               Unknown  Unknown
>> >
>> >
>> > --
>> >   Best Regards.
>> >         Peng
>> >
>> > _______________________________________________
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>>
>>
>>
>> --
>> Matteo Cococcioni
>> Department of Chemical Engineering and Materials Science,
>> University of Minnesota
>> 421 Washington Av. SE
>> Minneapolis, MN 55455
>> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
>   Best Regards.
>         Peng
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056    Fax +1 612 626 7246

From lorenzo.paulatto at impmc.upmc.fr  Sat Jul 28 17:01:56 2012
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Sat, 28 Jul 2012 17:01:56 +0200
Subject: [Pw_forum] Error while compiling Quantum Espresso
In-Reply-To: <1343480982.93555.YahooMailClassic@web121405.mail.ne1.yahoo.com>
References: <1343480982.93555.YahooMailClassic@web121405.mail.ne1.yahoo.com>
Message-ID: <CAG+GtJfd0Pe5LFdLmj8P18FJqY32Waca4FuzzyWfemCRr-SPdQ@mail.gmail.com>

On 28 July 2012 15:09, zafar rasheed <zafartariq2003 at yahoo.com> wrote:

> Dear all
> we are trying to install Quantum Espresoo-4.1.3 on Solaris 10 (Sun sparc).
> But it gives follwing error during when we try to configure it..
>
> "Configure : error linking to fortran libraries from c fails."
> and stops.
> will any body help to configure it.
>
>
Dear Zafar,
this is a probaby a problem with Solaris, more than QE, but someone may
still be able to help if you provide at the very list a copy of your
make.sys file (please zip it, dear mail admins blocks .sys files...).
Anyway, why are you using such an old version of QE? Version 5.0.1 is out
by now, and can be downloaded for free, as always.
-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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From pchen at ion.chem.utk.edu  Sun Jul 29 04:10:37 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Sat, 28 Jul 2012 22:10:37 -0400
Subject: [Pw_forum] U calculation error
In-Reply-To: <CAMZASgFWbtt6oCCoUp5g=ah3ODVOrNth9dwmmf2p+0XauMKhrw@mail.gmail.com>
References: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>
	<CAMZASgH3ZxSwGtXARSqN+khMe4CSttRRgTb81F3LX7GfKFtp6w@mail.gmail.com>
	<CAP_5U0fA-N8DhL1DYcbpLZ=hiG8T4EfmJXPqwuJXFvcG89gP-Q@mail.gmail.com>
	<CAMZASgFWbtt6oCCoUp5g=ah3ODVOrNth9dwmmf2p+0XauMKhrw@mail.gmail.com>
Message-ID: <CAP_5U0cU4t-AYM7rhOwo8MhMEuwjKEq5NzMoteDsaCO6wPugsw@mail.gmail.com>

Dear Dr. Matteo,

I used command listed below to compile resp_mat.f90. No error in compiling.
 I am not sure if I did right in choosing the libs.
ifort  -o r.x resp_mat.f90 -L"/data/apps/intel/11.1.072/mkl/lib/em64t"
 -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_mc3  -lmkl_sequential -lmkl_core

The libs in mkl are shown below:
libmkl_avx.so                   libmkl_intel_sp2dp.so
libmkl_blacs_ilp64.a            libmkl_intel_thread.a
libmkl_blacs_intelmpi_ilp64.a   libmkl_intel_thread.so
libmkl_blacs_intelmpi_ilp64.so  libmkl_lapack95_ilp64.a
libmkl_blacs_intelmpi_lp64.a    libmkl_lapack95_lp64.a
libmkl_blacs_intelmpi_lp64.so   libmkl_lapack.so
libmkl_blacs_lp64.a             libmkl_mc3.so
libmkl_blacs_openmpi_ilp64.a    libmkl_mc.so
libmkl_blacs_openmpi_lp64.a     libmkl_p4n.so
libmkl_blacs_sgimpt_ilp64.a     libmkl_pgi_thread.a
libmkl_blacs_sgimpt_lp64.a      libmkl_pgi_thread.so
libmkl_blas95_ilp64.a           libmkl_scalapack_ilp64.a
libmkl_blas95_lp64.a            libmkl_scalapack_ilp64.so
libmkl_cdft_core.a              libmkl_scalapack_lp64.a
libmkl_core.a                   libmkl_scalapack_lp64.so
libmkl_core.so                  libmkl_sequential.a
libmkl_def.so                   libmkl_sequential.so
libmkl_gf_ilp64.a               libmkl_solver_ilp64.a
libmkl_gf_ilp64.so              libmkl_solver_ilp64_sequential.a
libmkl_gf_lp64.a                libmkl_solver_lp64.a
libmkl_gf_lp64.so               libmkl_solver_lp64_sequential.a
libmkl_gnu_thread.a             libmkl_vml_avx.so
libmkl_gnu_thread.so            libmkl_vml_def.so
libmkl_intel_ilp64.a            libmkl_vml_mc2.so
libmkl_intel_ilp64.so           libmkl_vml_mc3.so
libmkl_intel_lp64.a             libmkl_vml_mc.so
libmkl_intel_lp64.so            libmkl_vml_p4n.so
libmkl_intel_sp2dp.a            locale


Some errors in output:
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
r.x                0000000000445659  Unknown               Unknown  Unknown
r.x                000000000040A363  Unknown               Unknown  Unknown
r.x                000000000040338C  Unknown               Unknown  Unknown
libc.so.6          00002B85B9495994  Unknown               Unknown  Unknown
r.x                0000000000403289  Unknown               Unknown  Unknown


On Sat, Jul 28, 2012 at 10:38 AM, Matteo Cococcioni <matteo at umn.edu> wrote:

> Dear Peng,
>
> nothing looks wrong in your input. have you tried with n1, n2, n3 all
> equal to 1? are you sure you compiled correctly?
>
> Matteo
>
>
>
> On Fri, Jul 27, 2012 at 11:46 PM, Peng Chen <pchen at ion.chem.utk.edu>
> wrote:
> > Dear Dr. Matteo,
> >
> > The primitive cell has 26 atoms with 3 different types. The pos and
> > resp_mat.in files are shown below:
> >
> > 5.6087 10.79 0.0
> > 5.6087 -10.79 0.0
> > 0.0 0.0   15.570873
> > 0       0       0       1
> > 0.5     0.5     0.5     -1
> > 0.12286329      0.378190177     0.749934361     1
> > 0.87713671      0.621809823     0.250065639     1
> > 0.377137388     0.121809201     0.249932658     -1
> > 0.622862612     0.878190799     0.750067342     -1
> > 0.373618754     0.623612138     0.11586798      0
> > 0.126381501     0.876388862     0.615868582     0
> > 0.626381246     0.376387862     0.88413202      0
> > 0.873618499     0.123611138     0.384131418     0
> > 0.241839036     0.756304999     0.223613779     0
> > 0.258160617     0.74369391      0.723611944     0
> > 0.758160964     0.243695001     0.776386221     0
> > 0.741839383     0.25630609      0.276388056     0
> > -0.000998332    1.000227439     0.243205274     0
> > 0.500997862     0.499772508     0.743208489     0
> > 1.000998332     -0.000227439    0.756794726     0
> > 0.499002138     0.500227492     0.256791511     0
> > 0.381099639     0.150692971     0.006796703     0
> > 0.118898786     0.349304325     0.506798051     0
> > 0.149581603     0.378555571     0.991989919     0
> > 0.350419534     0.121445697     0.491991443     0
> > 0.618900361     0.849307029     0.993205297     0
> > 0.881101214     0.650695675     0.493203949     0
> > 0.850418397     0.621444429     0.008012081     0
> > 0.649580466     0.878554303     0.508010557     0
> >
> > resp_mat.in :
> >  &input_mat
> >    ntyp = 3
> >    na(1) = 6
> >    na(2) = 4
> >    na(3) = 16
> >    nalfa = 5
> >    magn=.true.
> >    filepos = 'pos'
> >    back = 'no'
> >    filednda = 'file_afm'
> >    n1 = 2
> >    n2 = 2
> >    n3 = 2
> >  &end
> >
> >
> >
> > On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni <matteo at umn.edu>
> wrote:
> >>
> >> Dear Peng,
> >>
> >> can you provide info about your system? maybe it is larger than the
> >> maximum size allowed by r.x?
> >>
> >> Matteo
> >>
> >> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen <pchen at ion.chem.utk.edu>
> >> wrote:
> >> > Dear All,
> >> >
> >> > There are some errors when I run r.x to calculate the U. I used
> >> > Espresso-5.0
> >> > and follow the steps in LSDA+U example. I am not sure what could be
> >> > wrong.
> >> > And if you need other input/output, please let me know.
> >> >
> >> > Image              PC        Routine            Line        Source
> >> > r.x                0822DACC  Unknown               Unknown  Unknown
> >> > r.x                0822C265  Unknown               Unknown  Unknown
> >> > r.x                082071FA  Unknown               Unknown  Unknown
> >> > r.x                081DDFDA  Unknown               Unknown  Unknown
> >> > r.x                081FA33B  Unknown               Unknown  Unknown
> >> > r.x                081F9C5C  Unknown               Unknown  Unknown
> >> > r.x                0804E38F  Unknown               Unknown  Unknown
> >> > r.x                0804824A  Unknown               Unknown  Unknown
> >> > r.x                0823805D  Unknown               Unknown  Unknown
> >> > r.x                08048131  Unknown               Unknown  Unknown
> >> > forrtl: severe (8): internal consistency check failure, file
> >> > ./src/libfor/for_wseq_lis.c, line 635
> >> > Image              PC        Routine            Line        Source
> >> > r.x                0822DACC  Unknown               Unknown  Unknown
> >> > r.x                0822C265  Unknown               Unknown  Unknown
> >> > r.x                082071FA  Unknown               Unknown  Unknown
> >> > r.x                081DD664  Unknown               Unknown  Unknown
> >> > r.x                081F9AF7  Unknown               Unknown  Unknown
> >> > r.x                0804E38F  Unknown               Unknown  Unknown
> >> > r.x                0804824A  Unknown               Unknown  Unknown
> >> > r.x                0823805D  Unknown               Unknown  Unknown
> >> > r.x                08048131  Unknown               Unknown  Unknown
> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> > Image              PC        Routine            Line        Source
> >> > r.x                0804DAED  Unknown               Unknown  Unknown
> >> > r.x                0804824A  Unknown               Unknown  Unknown
> >> > r.x                0823805D  Unknown               Unknown  Unknown
> >> > r.x                08048131  Unknown               Unknown  Unknown
> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> > Image              PC        Routine            Line        Source
> >> > r.x                08253657  Unknown               Unknown  Unknown
> >> > r.x                081F4087  Unknown               Unknown  Unknown
> >> > r.x                081DCDB7  Unknown               Unknown  Unknown
> >> > r.x                081DF354  Unknown               Unknown  Unknown
> >> > r.x                081DD672  Unknown               Unknown  Unknown
> >> > r.x                081DF5E8  Unknown               Unknown  Unknown
> >> > Unknown            FFFFE600  Unknown               Unknown  Unknown
> >> > r.x                0804824A  Unknown               Unknown  Unknown
> >> > r.x                0823805D  Unknown               Unknown  Unknown
> >> > r.x                08048131  Unknown               Unknown  Unknown
> >> >
> >> >
> >> > --
> >> >   Best Regards.
> >> >         Peng
> >> >
> >> > _______________________________________________
> >> > Pw_forum mailing list
> >> > Pw_forum at pwscf.org
> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >
> >>
> >>
> >>
> >> --
> >> Matteo Cococcioni
> >> Department of Chemical Engineering and Materials Science,
> >> University of Minnesota
> >> 421 Washington Av. SE
> >> Minneapolis, MN 55455
> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> >   Best Regards.
> >         Peng
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Matteo Cococcioni
> Department of Chemical Engineering and Materials Science,
> University of Minnesota
> 421 Washington Av. SE
> Minneapolis, MN 55455
> Tel. +1 612 624 9056    Fax +1 612 626 7246
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
  Best Regards.
        Peng
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From dalcorso at sissa.it  Sun Jul 29 08:51:25 2012
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Sun, 29 Jul 2012 08:51:25 +0200
Subject: [Pw_forum] Bug in PW/pw_readfile
In-Reply-To: <445e5712c6b055cf1e2cefcb3c893f0a.squirrel@theory.polytechnique.fr>
References: <445e5712c6b055cf1e2cefcb3c893f0a.squirrel@theory.polytechnique.fr>
Message-ID: <1343544685.2115.1.camel@localhost.localdomain>

Thank you for reporting this. You are right it is a bug that might
appear when lkpoint_dir=.false..

I have corrected the svn version.

Andrea


On Fri, 2012-07-27 at 19:35 +0200, Iurii TIMROV wrote:
> Dear QE developers,
> 
> It seems there is a bug in the subroutine PW/pw_readfile. It shows up when
> a phonon calculation is restarted. I checked QE v.5.0.1, the bug hasn't
> been fixed. It is related to the unit "iunout". In the beginning of the 
> pw_readfile, there is a look for an empty unit:
> 
> CALL iotk_free_unit( iunout, ierr )
> 
> Afterwards, in the subroutine "read_band_structure" the unit "iunout" is
> used. But the problem is that in "read_band_structure" the unit "iunout"
> is declared second time:
> 
> INTEGER :: iunout
> 
> Thus, "iunout" is a random number, which sometimes may be negative, and
> therefore the data file cannot be read. Due to this, the code escapes from
> this routine (return), the data file is not read, and the code crashes
> somewhere else. It is strange to me, why the code escapes (return
> statement) instead of giving an error message (it takes time to find such
> bugs due to this).
> 
> The solution of the problem is simple: just to remove "INTEGER :: iunout".
> 
> If this is not a bug, please explain me why. But in my case the code
> doesn't work with this.
> 
> Best,
> Iurii
> 
> 
> Iurii TIMROV
> Doctorant (PhD student)
> Laboratoire des Solides Irradies
> Ecole Polytechnique
> F-91128 Palaiseau
> +33 1 69 33 45 08
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



From sohailphysics at yahoo.co.in  Sun Jul 29 09:33:07 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Sun, 29 Jul 2012 15:33:07 +0800 (SGT)
Subject: [Pw_forum] MoS2 -monolayer input -
Message-ID: <1343547187.91481.YahooMailClassic@web190905.mail.sg3.yahoo.com>

Dear QE users

I am working on MoS2 which is hexagonal layered structure having 2 Mo and 4 S atoms
i wish to study now only a single layer (one Mo and two S). 
The only thing i understand that i 
will have to increase c axis to prevent interaction 
between the layers.
But when i do so i
 realise that all bond length got stretched.

both
 the two input file (bulk and monolayers are attached) 
pls compare the two inputs,
?i got the results for bulk perfectly comparable to the experiment when i run for mono sometimes it doesnot and sometimes it gives unwanted 20-30 GB files

I dont know where is the mistake

Thanks in Advance for any help

Sohail
 Ahmad
King Khalid University
Saudi Arabia

-----
Monolayer input

&control
? calculation = 'scf',
? restart_mode = 'from_scratch',
? prefix = 'MoS1l',
? pseudo_dir = '/home/sandeep/espresso-4.2.1/pseudo',
? outdir = './OUT',
?/
?&system
??? ibrav = 0, a= 3.16,c= 6.15,
??? cosac= 0.0, cosbc= 0.0, cosab= -0.5,
? nat = 3,
? ntyp = 2,
? ecutwfc = 70,
? ecutrho = 300,
? nbnd = 20,
? occupations = 'smearing', smearing = 'gaussian', degauss = 0.001,
? nspin = 2,
? starting_magnetization(1) = 0.5d0,
?/
? &electrons
? mixing_beta = 0.3,
? conv_thr = 1.0d-9,
?/
ATOMIC_SPECIES
Mo? 95.96? Mo.pw91-n-van.UPF
S?? 32.06? S.pw91-van_ak.UPF
CELL_PARAMETERS
 {hexagonal}
?1.00000000?????????? 0.00000000????????? 0.00000000
-0.50000000?????????? 0.86602540????????? 0.00000000
?0.00000000?????????? 0.00000000????????? 7.78000000 
ATOMIC_POSITIONS {Angstrom}
Mo? 1.58000000? 0.91221343? 3.07250000
S?? 1.58000000 -0.91221343? 1.47480000
S?? 1.58000000 -0.91221343? 4.67260000
K_POINTS AUTOMATIC
4 4 4 1 1 1 
--------
bulk input
&control
? calculation = 'scf',
? restart_mode = 'from_scratch',
? prefix = 'MoSb8',
? pseudo_dir = '/home/sandeep/espresso-4.2.1/pseudo',
? outdir =
 './OUT',
?/
?&system
? ibrav = 4, celldm(1) = 6.0281946, celldm(3) = 3.89, nat = 6, ntyp = 2,
? ecutwfc = 70,
? ecutrho = 300,
? nbnd = 30,
? occupations = 'smearing', smearing = 'gaussian', degauss = 0.001,
? nspin = 2,
? starting_magnetization(1) = 0.1d0,
?/
?&electrons
? mixing_beta = 0.3,
? conv_thr = 1.0d-9,
?/
ATOMIC_SPECIES
Mo? 95.96? Mo.pw91-n-van.UPF
S?? 32.06? S.pw91-van_ak.UPF
ATOMIC_POSITIONS {crystal}
Mo? 0.33333333? 0.66666667? 0.25000000
Mo? 0.66666667? 0.33333333? 0.75000000
S?? 0.33333333? 0.66666667? 0.62000000
S?? 0.66666667? 0.33333333? 0.12000000
S?? 0.66666667? 0.33333333 -0.62000000
S?? 0.33333333? 0.66666667 -0.12000000
K_POINTS AUTOMATIC
8 8 8 1 1
 1
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From csatya11 at gmail.com  Sun Jul 29 13:05:22 2012
From: csatya11 at gmail.com (csatya11 at gmail.com)
Date: Sun, 29 Jul 2012 06:05:22 -0500
Subject: [Pw_forum] Reminder: csatya11@gmail.com wants to follow you
Message-ID: <0.0.42.D0A.1CD6D7A0C268186.16FF@mail7.infoaxe.net>

Hi,

Satyananda Chab wants to follow you.

****** Is Satyananda Chab you friend? ******
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From konda.physics at gmail.com  Sun Jul 29 13:32:47 2012
From: konda.physics at gmail.com (Kondaiah Samudrala)
Date: Sun, 29 Jul 2012 17:02:47 +0530
Subject: [Pw_forum] Running QHA calculations for orthorhombic structure
Message-ID: <CAKjMXpZczycidY=TwyLZ9LK5xpz2jG4D5-+dx2ygdm9o68VS0Q@mail.gmail.com>

Dear all,

I am working on base centered orthorhombic structure with space group 64. I
run complete phonon dispersion for this compound, but i want to calculate
thermodynamic quantities such as specific heat, thermal expansion for this
compound. Whether it is possible to calculate these things using QHA for
base centered orthorhombic structure in pwscf???


with regards
S.Appalakondaiah
Research scholar
HCU
Hyd-500046
India
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From zafartariq2003 at yahoo.com  Sun Jul 29 14:47:25 2012
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Sun, 29 Jul 2012 05:47:25 -0700 (PDT)
Subject: [Pw_forum] Types of pseudopotentials
Message-ID: <1343566045.32045.YahooMailClassic@web121405.mail.ne1.yahoo.com>

Dear All 

I am a bit confused about the type of pseudopotentials. 

PW91 ===> LDA or GGA?

PZ====> LDA? ----is it right.

PBE ======> GGA?

BLYP======> GGA?

Muhammad Zafar

PhD Scholar

Department of Physics

The Islamia University of Bahawalpur,Pakistan
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From pandey.bramha at gmail.com  Sun Jul 29 15:21:18 2012
From: pandey.bramha at gmail.com (bramha pandey)
Date: Sun, 29 Jul 2012 18:51:18 +0530
Subject: [Pw_forum] Types of pseudopotentials
In-Reply-To: <1343566045.32045.YahooMailClassic@web121405.mail.ne1.yahoo.com>
References: <1343566045.32045.YahooMailClassic@web121405.mail.ne1.yahoo.com>
Message-ID: <CAC2dNGEBJ=xYcsjA=v25kzChs9Nc1Q+yE3u7xQiM6Tun=gS6gw@mail.gmail.com>

On Sun, Jul 29, 2012 at 6:17 PM, zafar rasheed <zafartariq2003 at yahoo.com>wrote:

> Dear All
> I am a bit confused about the type of pseudopotentials.
>


> PW91 ===> LDA or GGA? >>>>>  it is GGA..
>


> PZ====> LDA  ----is it right.....yes.
>


> PBE ======> GGA?...yes
>


> BLYP======> GGA? this is the another type of pseudopotentail whose
> property is similar to GGA means PBE.
>
> Better search at pw forum, you will find losts of info regarding this.

Muhammad Zafar
> PhD Scholar
> Department of Physics
> The Islamia University of Bahawalpur,Pakistan
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Thanks and Regards
Bramha Prasad Pandey
Ph.D Student Indian School of Mines(ISM)
Dhanbad, INDIA.
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From zafartariq2003 at yahoo.com  Sun Jul 29 15:33:15 2012
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Sun, 29 Jul 2012 06:33:15 -0700 (PDT)
Subject: [Pw_forum] Error while compiling Quantum Espresso
Message-ID: <1343568795.22962.YahooMailClassic@web121402.mail.ne1.yahoo.com>


Dear Lorenzo Paulatto
Thanks for your kind reply. Unfortunately make.system file not created...........
but information appear at screen during comilation , configure.log and make.sys.in file are attached here.

best regards
Muhammad Zafar

PhD Scholar

Department of Physics

The Islamia University of Bahawalpur,Pakistan
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From matteo at umn.edu  Sun Jul 29 17:27:16 2012
From: matteo at umn.edu (Matteo Cococcioni)
Date: Sun, 29 Jul 2012 10:27:16 -0500
Subject: [Pw_forum] U calculation error
In-Reply-To: <CAP_5U0cU4t-AYM7rhOwo8MhMEuwjKEq5NzMoteDsaCO6wPugsw@mail.gmail.com>
References: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>
	<CAMZASgH3ZxSwGtXARSqN+khMe4CSttRRgTb81F3LX7GfKFtp6w@mail.gmail.com>
	<CAP_5U0fA-N8DhL1DYcbpLZ=hiG8T4EfmJXPqwuJXFvcG89gP-Q@mail.gmail.com>
	<CAMZASgFWbtt6oCCoUp5g=ah3ODVOrNth9dwmmf2p+0XauMKhrw@mail.gmail.com>
	<CAP_5U0cU4t-AYM7rhOwo8MhMEuwjKEq5NzMoteDsaCO6wPugsw@mail.gmail.com>
Message-ID: <CAMZASgGFhiF15BgCwkWgE5ZQj9tMRYFopAsQOKX8pte6Vw-DEg@mail.gmail.com>

Dear Peng,

I'm not very expert of compiling codes. You have to make sure that all
the libraries are linked correctly for the code to work. I assume you
have QE installed on the same computer. You could give a look in the
make.sys to check what is the correct way to link them. If everything
is consistent, then you have to find out where the code is failing.
have you tried to run with n1 = n2 = n3 = 1? what did you get?

Matteo



On Sat, Jul 28, 2012 at 9:10 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
> Dear Dr. Matteo,
>
> I used command listed below to compile resp_mat.f90. No error in compiling.
> I am not sure if I did right in choosing the libs.
> ifort  -o r.x resp_mat.f90 -L"/data/apps/intel/11.1.072/mkl/lib/em64t"
> -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_mc3  -lmkl_sequential -lmkl_core
>
> The libs in mkl are shown below:
> libmkl_avx.so                   libmkl_intel_sp2dp.so
> libmkl_blacs_ilp64.a            libmkl_intel_thread.a
> libmkl_blacs_intelmpi_ilp64.a   libmkl_intel_thread.so
> libmkl_blacs_intelmpi_ilp64.so  libmkl_lapack95_ilp64.a
> libmkl_blacs_intelmpi_lp64.a    libmkl_lapack95_lp64.a
> libmkl_blacs_intelmpi_lp64.so   libmkl_lapack.so
> libmkl_blacs_lp64.a             libmkl_mc3.so
> libmkl_blacs_openmpi_ilp64.a    libmkl_mc.so
> libmkl_blacs_openmpi_lp64.a     libmkl_p4n.so
> libmkl_blacs_sgimpt_ilp64.a     libmkl_pgi_thread.a
> libmkl_blacs_sgimpt_lp64.a      libmkl_pgi_thread.so
> libmkl_blas95_ilp64.a           libmkl_scalapack_ilp64.a
> libmkl_blas95_lp64.a            libmkl_scalapack_ilp64.so
> libmkl_cdft_core.a              libmkl_scalapack_lp64.a
> libmkl_core.a                   libmkl_scalapack_lp64.so
> libmkl_core.so                  libmkl_sequential.a
> libmkl_def.so                   libmkl_sequential.so
> libmkl_gf_ilp64.a               libmkl_solver_ilp64.a
> libmkl_gf_ilp64.so              libmkl_solver_ilp64_sequential.a
> libmkl_gf_lp64.a                libmkl_solver_lp64.a
> libmkl_gf_lp64.so               libmkl_solver_lp64_sequential.a
> libmkl_gnu_thread.a             libmkl_vml_avx.so
> libmkl_gnu_thread.so            libmkl_vml_def.so
> libmkl_intel_ilp64.a            libmkl_vml_mc2.so
> libmkl_intel_ilp64.so           libmkl_vml_mc3.so
> libmkl_intel_lp64.a             libmkl_vml_mc.so
> libmkl_intel_lp64.so            libmkl_vml_p4n.so
> libmkl_intel_sp2dp.a            locale
>
>
> Some errors in output:
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image              PC                Routine            Line        Source
> r.x                0000000000445659  Unknown               Unknown  Unknown
> r.x                000000000040A363  Unknown               Unknown  Unknown
> r.x                000000000040338C  Unknown               Unknown  Unknown
> libc.so.6          00002B85B9495994  Unknown               Unknown  Unknown
> r.x                0000000000403289  Unknown               Unknown  Unknown
>
>
> On Sat, Jul 28, 2012 at 10:38 AM, Matteo Cococcioni <matteo at umn.edu> wrote:
>>
>> Dear Peng,
>>
>> nothing looks wrong in your input. have you tried with n1, n2, n3 all
>> equal to 1? are you sure you compiled correctly?
>>
>> Matteo
>>
>>
>>
>> On Fri, Jul 27, 2012 at 11:46 PM, Peng Chen <pchen at ion.chem.utk.edu>
>> wrote:
>> > Dear Dr. Matteo,
>> >
>> > The primitive cell has 26 atoms with 3 different types. The pos and
>> > resp_mat.in files are shown below:
>> >
>> > 5.6087 10.79 0.0
>> > 5.6087 -10.79 0.0
>> > 0.0 0.0   15.570873
>> > 0       0       0       1
>> > 0.5     0.5     0.5     -1
>> > 0.12286329      0.378190177     0.749934361     1
>> > 0.87713671      0.621809823     0.250065639     1
>> > 0.377137388     0.121809201     0.249932658     -1
>> > 0.622862612     0.878190799     0.750067342     -1
>> > 0.373618754     0.623612138     0.11586798      0
>> > 0.126381501     0.876388862     0.615868582     0
>> > 0.626381246     0.376387862     0.88413202      0
>> > 0.873618499     0.123611138     0.384131418     0
>> > 0.241839036     0.756304999     0.223613779     0
>> > 0.258160617     0.74369391      0.723611944     0
>> > 0.758160964     0.243695001     0.776386221     0
>> > 0.741839383     0.25630609      0.276388056     0
>> > -0.000998332    1.000227439     0.243205274     0
>> > 0.500997862     0.499772508     0.743208489     0
>> > 1.000998332     -0.000227439    0.756794726     0
>> > 0.499002138     0.500227492     0.256791511     0
>> > 0.381099639     0.150692971     0.006796703     0
>> > 0.118898786     0.349304325     0.506798051     0
>> > 0.149581603     0.378555571     0.991989919     0
>> > 0.350419534     0.121445697     0.491991443     0
>> > 0.618900361     0.849307029     0.993205297     0
>> > 0.881101214     0.650695675     0.493203949     0
>> > 0.850418397     0.621444429     0.008012081     0
>> > 0.649580466     0.878554303     0.508010557     0
>> >
>> > resp_mat.in :
>> >  &input_mat
>> >    ntyp = 3
>> >    na(1) = 6
>> >    na(2) = 4
>> >    na(3) = 16
>> >    nalfa = 5
>> >    magn=.true.
>> >    filepos = 'pos'
>> >    back = 'no'
>> >    filednda = 'file_afm'
>> >    n1 = 2
>> >    n2 = 2
>> >    n3 = 2
>> >  &end
>> >
>> >
>> >
>> > On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni <matteo at umn.edu>
>> > wrote:
>> >>
>> >> Dear Peng,
>> >>
>> >> can you provide info about your system? maybe it is larger than the
>> >> maximum size allowed by r.x?
>> >>
>> >> Matteo
>> >>
>> >> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen <pchen at ion.chem.utk.edu>
>> >> wrote:
>> >> > Dear All,
>> >> >
>> >> > There are some errors when I run r.x to calculate the U. I used
>> >> > Espresso-5.0
>> >> > and follow the steps in LSDA+U example. I am not sure what could be
>> >> > wrong.
>> >> > And if you need other input/output, please let me know.
>> >> >
>> >> > Image              PC        Routine            Line        Source
>> >> > r.x                0822DACC  Unknown               Unknown  Unknown
>> >> > r.x                0822C265  Unknown               Unknown  Unknown
>> >> > r.x                082071FA  Unknown               Unknown  Unknown
>> >> > r.x                081DDFDA  Unknown               Unknown  Unknown
>> >> > r.x                081FA33B  Unknown               Unknown  Unknown
>> >> > r.x                081F9C5C  Unknown               Unknown  Unknown
>> >> > r.x                0804E38F  Unknown               Unknown  Unknown
>> >> > r.x                0804824A  Unknown               Unknown  Unknown
>> >> > r.x                0823805D  Unknown               Unknown  Unknown
>> >> > r.x                08048131  Unknown               Unknown  Unknown
>> >> > forrtl: severe (8): internal consistency check failure, file
>> >> > ./src/libfor/for_wseq_lis.c, line 635
>> >> > Image              PC        Routine            Line        Source
>> >> > r.x                0822DACC  Unknown               Unknown  Unknown
>> >> > r.x                0822C265  Unknown               Unknown  Unknown
>> >> > r.x                082071FA  Unknown               Unknown  Unknown
>> >> > r.x                081DD664  Unknown               Unknown  Unknown
>> >> > r.x                081F9AF7  Unknown               Unknown  Unknown
>> >> > r.x                0804E38F  Unknown               Unknown  Unknown
>> >> > r.x                0804824A  Unknown               Unknown  Unknown
>> >> > r.x                0823805D  Unknown               Unknown  Unknown
>> >> > r.x                08048131  Unknown               Unknown  Unknown
>> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> >> > Image              PC        Routine            Line        Source
>> >> > r.x                0804DAED  Unknown               Unknown  Unknown
>> >> > r.x                0804824A  Unknown               Unknown  Unknown
>> >> > r.x                0823805D  Unknown               Unknown  Unknown
>> >> > r.x                08048131  Unknown               Unknown  Unknown
>> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> >> > Image              PC        Routine            Line        Source
>> >> > r.x                08253657  Unknown               Unknown  Unknown
>> >> > r.x                081F4087  Unknown               Unknown  Unknown
>> >> > r.x                081DCDB7  Unknown               Unknown  Unknown
>> >> > r.x                081DF354  Unknown               Unknown  Unknown
>> >> > r.x                081DD672  Unknown               Unknown  Unknown
>> >> > r.x                081DF5E8  Unknown               Unknown  Unknown
>> >> > Unknown            FFFFE600  Unknown               Unknown  Unknown
>> >> > r.x                0804824A  Unknown               Unknown  Unknown
>> >> > r.x                0823805D  Unknown               Unknown  Unknown
>> >> > r.x                08048131  Unknown               Unknown  Unknown
>> >> >
>> >> >
>> >> > --
>> >> >   Best Regards.
>> >> >         Peng
>> >> >
>> >> > _______________________________________________
>> >> > Pw_forum mailing list
>> >> > Pw_forum at pwscf.org
>> >> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Matteo Cococcioni
>> >> Department of Chemical Engineering and Materials Science,
>> >> University of Minnesota
>> >> 421 Washington Av. SE
>> >> Minneapolis, MN 55455
>> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> >> _______________________________________________
>> >> Pw_forum mailing list
>> >> Pw_forum at pwscf.org
>> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>> >
>> >
>> >
>> > --
>> >   Best Regards.
>> >         Peng
>> >
>> > _______________________________________________
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>>
>>
>>
>> --
>> Matteo Cococcioni
>> Department of Chemical Engineering and Materials Science,
>> University of Minnesota
>> 421 Washington Av. SE
>> Minneapolis, MN 55455
>> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
>   Best Regards.
>         Peng
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056    Fax +1 612 626 7246

From pchen at ion.chem.utk.edu  Sun Jul 29 19:00:44 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Sun, 29 Jul 2012 13:00:44 -0400
Subject: [Pw_forum] U calculation error
In-Reply-To: <CAMZASgGFhiF15BgCwkWgE5ZQj9tMRYFopAsQOKX8pte6Vw-DEg@mail.gmail.com>
References: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>
	<CAMZASgH3ZxSwGtXARSqN+khMe4CSttRRgTb81F3LX7GfKFtp6w@mail.gmail.com>
	<CAP_5U0fA-N8DhL1DYcbpLZ=hiG8T4EfmJXPqwuJXFvcG89gP-Q@mail.gmail.com>
	<CAMZASgFWbtt6oCCoUp5g=ah3ODVOrNth9dwmmf2p+0XauMKhrw@mail.gmail.com>
	<CAP_5U0cU4t-AYM7rhOwo8MhMEuwjKEq5NzMoteDsaCO6wPugsw@mail.gmail.com>
	<CAMZASgGFhiF15BgCwkWgE5ZQj9tMRYFopAsQOKX8pte6Vw-DEg@mail.gmail.com>
Message-ID: <CAP_5U0fYafiTLd+sNKK1HE2TefOn8ZVZ9+urU6VcTTw2yQxmqQ@mail.gmail.com>

Dear Dr. Matteo,

I compiled the code with the parameters in make.sys. The n1=n2=n3=1 case is
done without error, but the results for Ni and O are negative which should
not be correct.
26 -14.8678837915617 7.56505581785392 -0.681000339374195
I plot dn.1.da.1.dat and dn0.1.da.1.dat, the data in dn0.1.da.1.dat are not
linear. The scf calculation is converged to 0.001 Ry. So I am not sure what
can cause the problem.

I've attached the Umat_afm.1.out which may contain some useful information
for you. I also put below the input for scf and perturbation on Ni
(alpha=-0.15,-0.07,0.0,0.07,0.15). Same calculations are done for V and O
as well with perturbed V or O atom translated to the origin of the unit
cell.


scf calculation input:

&control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='nvoprim.afm.ucalc.Ni',
    pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
    outdir='/data/pchen/qe/'
    wf_collect=.TRUE.
 /
 &system
    ibrav=0, celldm(1)=11.19096,
     nat=26, ntyp=6,
  nspin = 2,  starting_magnetization(1)=0.6,
    starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
 starting_magnetization(4)=-0.5,
 ecutwfc = 100, ecutrho = 800,
 occupations ='smearing',
    smearing ='mv',
    degauss = 0.005,nbnd=135
  lda_plus_u = .true.
    Hubbard_U(1)= 1.d-20
    Hubbard_U(2)= 1.d-20
 Hubbard_U(3)= 1.d-20
 Hubbard_U(4)= 1.d-20
 Hubbard_U(5)= 1.d-20
 Hubbard_U(6)= 1.d-20
 /
 &electrons
    conv_thr = 1.0e-7
    mixing_beta = 0.3
 /
CELL_PARAMETERS
0.5 0.96015 0
0.5 -0.96015 0
0 0   1.38889
ATOMIC_SPECIES
 Ni1 58.6934 Ni.pz-n-rrkjus.UPF
 Ni2 58.6934 Ni.pz-n-rrkjus.UPF
 Ni3 58.6934 Ni.pz-n-rrkjus.UPF
 Ni4 58.6934 Ni.pz-n-rrkjus.UPF
 V 50.9415 V.pz-spn-rrkjus.UPF
 O  15.9994  O.pz-n-rrkjus.UPF
ATOMIC_POSITIONS crystal
Ni1      0.000000000   0.000000000   0.000000000
Ni2      0.500000000   0.500000000   0.500000000
Ni3      0.122863290   0.378190177   0.749934361
Ni3      0.877136710   0.621809823   0.250065639
Ni4      0.377137388   0.121809201   0.249932658
Ni4      0.622862612   0.878190799   0.750067342
V        0.373618754   0.623612138   0.115867980
V        0.126381501   0.876388862   0.615868582
V        0.626381246   0.376387862   0.884132020
V        0.873618499   0.123611138   0.384131418
O        0.241839036   0.756304999   0.223613779
O        0.258160617   0.743693910   0.723611944
O        0.758160964   0.243695001   0.776386221
O        0.741839383   0.256306090   0.276388056
O       -0.000998332   1.000227439   0.243205274
O        0.500997862   0.499772508   0.743208489
O        1.000998332  -0.000227439   0.756794726
O        0.499002138   0.500227492   0.256791511
O        0.381099639   0.150692971   0.006796703
O        0.118898786   0.349304325   0.506798051
O        0.149581603   0.378555571   0.991989919
O        0.350419534   0.121445697   0.491991443
O        0.618900361   0.849307029   0.993205297
O        0.881101214   0.650695675   0.493203949
O        0.850418397   0.621444429   0.008012081
O        0.649580466   0.878554303   0.508010557

K_POINTS (automatic)
 5 5 5 1 1 1

Perturbation on Ni with alpha=0.15 input:

&control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='nvoprim.afm.ucalc.Ni',
    pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
    outdir='/data/pchen/qe/'
   wf_collect=.TRUE.
 /
 &system
    ibrav=0, celldm(1)=11.19096,
     nat=26, ntyp=6,
  nspin = 2,  starting_magnetization(1)=0.6,
    starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
 starting_magnetization(4)=-0.5,
 ecutwfc = 100, ecutrho = 800,
 occupations ='smearing',
    smearing ='mv',
    degauss = 0.005,nbnd=135
  lda_plus_u = .true.
    Hubbard_U(1)= 1.d-20
    Hubbard_U(2)= 1.d-20
    Hubbard_U(3)= 1.d-20
Hubbard_U(4)= 1.d-20
Hubbard_U(5)= 1.d-20
Hubbard_U(6)= 1.d-20

    Hubbard_alpha(1)= 0.15
 /
 &electrons
    conv_thr = 1.0e-7
    mixing_beta = 0.3
  startingpot='file'
 startingwfc='file'
 diago_thr_init=5.09E-11,
 /
CELL_PARAMETERS
0.5 0.96015 0
0.5 -0.96015 0
0 0   1.38889
ATOMIC_SPECIES
 Ni1 58.6934 Ni.pz-n-rrkjus.UPF
 Ni2 58.6934 Ni.pz-n-rrkjus.UPF
 Ni3 58.6934 Ni.pz-n-rrkjus.UPF
 Ni4 58.6934 Ni.pz-n-rrkjus.UPF
 V 50.9415 V.pz-spn-rrkjus.UPF
 O  15.9994  O.pz-n-rrkjus.UPF
ATOMIC_POSITIONS crystal
Ni1      0.000000000   0.000000000   0.000000000
Ni2      0.500000000   0.500000000   0.500000000
Ni3      0.122863290   0.378190177   0.749934361
Ni3      0.877136710   0.621809823   0.250065639
Ni4      0.377137388   0.121809201   0.249932658
Ni4      0.622862612   0.878190799   0.750067342
V        0.373618754   0.623612138   0.115867980
V        0.126381501   0.876388862   0.615868582
V        0.626381246   0.376387862   0.884132020
V        0.873618499   0.123611138   0.384131418
O        0.241839036   0.756304999   0.223613779
O        0.258160617   0.743693910   0.723611944
O        0.758160964   0.243695001   0.776386221
O        0.741839383   0.256306090   0.276388056
O       -0.000998332   1.000227439   0.243205274
O        0.500997862   0.499772508   0.743208489
O        1.000998332  -0.000227439   0.756794726
O        0.499002138   0.500227492   0.256791511
O        0.381099639   0.150692971   0.006796703
O        0.118898786   0.349304325   0.506798051
O        0.149581603   0.378555571   0.991989919
O        0.350419534   0.121445697   0.491991443
O        0.618900361   0.849307029   0.993205297
O        0.881101214   0.650695675   0.493203949
O        0.850418397   0.621444429   0.008012081
O        0.649580466   0.878554303   0.508010557

K_POINTS (automatic)
 5 5 5 1 1 1



On Sun, Jul 29, 2012 at 11:27 AM, Matteo Cococcioni <matteo at umn.edu> wrote:

> Dear Peng,
>
> I'm not very expert of compiling codes. You have to make sure that all
> the libraries are linked correctly for the code to work. I assume you
> have QE installed on the same computer. You could give a look in the
> make.sys to check what is the correct way to link them. If everything
> is consistent, then you have to find out where the code is failing.
> have you tried to run with n1 = n2 = n3 = 1? what did you get?
>
> Matteo
>
>
>
> On Sat, Jul 28, 2012 at 9:10 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
> > Dear Dr. Matteo,
> >
> > I used command listed below to compile resp_mat.f90. No error in
> compiling.
> > I am not sure if I did right in choosing the libs.
> > ifort  -o r.x resp_mat.f90 -L"/data/apps/intel/11.1.072/mkl/lib/em64t"
> > -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_mc3  -lmkl_sequential
> -lmkl_core
> >
> > The libs in mkl are shown below:
> > libmkl_avx.so                   libmkl_intel_sp2dp.so
> > libmkl_blacs_ilp64.a            libmkl_intel_thread.a
> > libmkl_blacs_intelmpi_ilp64.a   libmkl_intel_thread.so
> > libmkl_blacs_intelmpi_ilp64.so  libmkl_lapack95_ilp64.a
> > libmkl_blacs_intelmpi_lp64.a    libmkl_lapack95_lp64.a
> > libmkl_blacs_intelmpi_lp64.so   libmkl_lapack.so
> > libmkl_blacs_lp64.a             libmkl_mc3.so
> > libmkl_blacs_openmpi_ilp64.a    libmkl_mc.so
> > libmkl_blacs_openmpi_lp64.a     libmkl_p4n.so
> > libmkl_blacs_sgimpt_ilp64.a     libmkl_pgi_thread.a
> > libmkl_blacs_sgimpt_lp64.a      libmkl_pgi_thread.so
> > libmkl_blas95_ilp64.a           libmkl_scalapack_ilp64.a
> > libmkl_blas95_lp64.a            libmkl_scalapack_ilp64.so
> > libmkl_cdft_core.a              libmkl_scalapack_lp64.a
> > libmkl_core.a                   libmkl_scalapack_lp64.so
> > libmkl_core.so                  libmkl_sequential.a
> > libmkl_def.so                   libmkl_sequential.so
> > libmkl_gf_ilp64.a               libmkl_solver_ilp64.a
> > libmkl_gf_ilp64.so              libmkl_solver_ilp64_sequential.a
> > libmkl_gf_lp64.a                libmkl_solver_lp64.a
> > libmkl_gf_lp64.so               libmkl_solver_lp64_sequential.a
> > libmkl_gnu_thread.a             libmkl_vml_avx.so
> > libmkl_gnu_thread.so            libmkl_vml_def.so
> > libmkl_intel_ilp64.a            libmkl_vml_mc2.so
> > libmkl_intel_ilp64.so           libmkl_vml_mc3.so
> > libmkl_intel_lp64.a             libmkl_vml_mc.so
> > libmkl_intel_lp64.so            libmkl_vml_p4n.so
> > libmkl_intel_sp2dp.a            locale
> >
> >
> > Some errors in output:
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > Image              PC                Routine            Line
>  Source
> > r.x                0000000000445659  Unknown               Unknown
>  Unknown
> > r.x                000000000040A363  Unknown               Unknown
>  Unknown
> > r.x                000000000040338C  Unknown               Unknown
>  Unknown
> > libc.so.6          00002B85B9495994  Unknown               Unknown
>  Unknown
> > r.x                0000000000403289  Unknown               Unknown
>  Unknown
> >
> >
> > On Sat, Jul 28, 2012 at 10:38 AM, Matteo Cococcioni <matteo at umn.edu>
> wrote:
> >>
> >> Dear Peng,
> >>
> >> nothing looks wrong in your input. have you tried with n1, n2, n3 all
> >> equal to 1? are you sure you compiled correctly?
> >>
> >> Matteo
> >>
> >>
> >>
> >> On Fri, Jul 27, 2012 at 11:46 PM, Peng Chen <pchen at ion.chem.utk.edu>
> >> wrote:
> >> > Dear Dr. Matteo,
> >> >
> >> > The primitive cell has 26 atoms with 3 different types. The pos and
> >> > resp_mat.in files are shown below:
> >> >
> >> > 5.6087 10.79 0.0
> >> > 5.6087 -10.79 0.0
> >> > 0.0 0.0   15.570873
> >> > 0       0       0       1
> >> > 0.5     0.5     0.5     -1
> >> > 0.12286329      0.378190177     0.749934361     1
> >> > 0.87713671      0.621809823     0.250065639     1
> >> > 0.377137388     0.121809201     0.249932658     -1
> >> > 0.622862612     0.878190799     0.750067342     -1
> >> > 0.373618754     0.623612138     0.11586798      0
> >> > 0.126381501     0.876388862     0.615868582     0
> >> > 0.626381246     0.376387862     0.88413202      0
> >> > 0.873618499     0.123611138     0.384131418     0
> >> > 0.241839036     0.756304999     0.223613779     0
> >> > 0.258160617     0.74369391      0.723611944     0
> >> > 0.758160964     0.243695001     0.776386221     0
> >> > 0.741839383     0.25630609      0.276388056     0
> >> > -0.000998332    1.000227439     0.243205274     0
> >> > 0.500997862     0.499772508     0.743208489     0
> >> > 1.000998332     -0.000227439    0.756794726     0
> >> > 0.499002138     0.500227492     0.256791511     0
> >> > 0.381099639     0.150692971     0.006796703     0
> >> > 0.118898786     0.349304325     0.506798051     0
> >> > 0.149581603     0.378555571     0.991989919     0
> >> > 0.350419534     0.121445697     0.491991443     0
> >> > 0.618900361     0.849307029     0.993205297     0
> >> > 0.881101214     0.650695675     0.493203949     0
> >> > 0.850418397     0.621444429     0.008012081     0
> >> > 0.649580466     0.878554303     0.508010557     0
> >> >
> >> > resp_mat.in :
> >> >  &input_mat
> >> >    ntyp = 3
> >> >    na(1) = 6
> >> >    na(2) = 4
> >> >    na(3) = 16
> >> >    nalfa = 5
> >> >    magn=.true.
> >> >    filepos = 'pos'
> >> >    back = 'no'
> >> >    filednda = 'file_afm'
> >> >    n1 = 2
> >> >    n2 = 2
> >> >    n3 = 2
> >> >  &end
> >> >
> >> >
> >> >
> >> > On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni <matteo at umn.edu>
> >> > wrote:
> >> >>
> >> >> Dear Peng,
> >> >>
> >> >> can you provide info about your system? maybe it is larger than the
> >> >> maximum size allowed by r.x?
> >> >>
> >> >> Matteo
> >> >>
> >> >> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen <pchen at ion.chem.utk.edu>
> >> >> wrote:
> >> >> > Dear All,
> >> >> >
> >> >> > There are some errors when I run r.x to calculate the U. I used
> >> >> > Espresso-5.0
> >> >> > and follow the steps in LSDA+U example. I am not sure what could be
> >> >> > wrong.
> >> >> > And if you need other input/output, please let me know.
> >> >> >
> >> >> > Image              PC        Routine            Line        Source
> >> >> > r.x                0822DACC  Unknown               Unknown  Unknown
> >> >> > r.x                0822C265  Unknown               Unknown  Unknown
> >> >> > r.x                082071FA  Unknown               Unknown  Unknown
> >> >> > r.x                081DDFDA  Unknown               Unknown  Unknown
> >> >> > r.x                081FA33B  Unknown               Unknown  Unknown
> >> >> > r.x                081F9C5C  Unknown               Unknown  Unknown
> >> >> > r.x                0804E38F  Unknown               Unknown  Unknown
> >> >> > r.x                0804824A  Unknown               Unknown  Unknown
> >> >> > r.x                0823805D  Unknown               Unknown  Unknown
> >> >> > r.x                08048131  Unknown               Unknown  Unknown
> >> >> > forrtl: severe (8): internal consistency check failure, file
> >> >> > ./src/libfor/for_wseq_lis.c, line 635
> >> >> > Image              PC        Routine            Line        Source
> >> >> > r.x                0822DACC  Unknown               Unknown  Unknown
> >> >> > r.x                0822C265  Unknown               Unknown  Unknown
> >> >> > r.x                082071FA  Unknown               Unknown  Unknown
> >> >> > r.x                081DD664  Unknown               Unknown  Unknown
> >> >> > r.x                081F9AF7  Unknown               Unknown  Unknown
> >> >> > r.x                0804E38F  Unknown               Unknown  Unknown
> >> >> > r.x                0804824A  Unknown               Unknown  Unknown
> >> >> > r.x                0823805D  Unknown               Unknown  Unknown
> >> >> > r.x                08048131  Unknown               Unknown  Unknown
> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> >> > Image              PC        Routine            Line        Source
> >> >> > r.x                0804DAED  Unknown               Unknown  Unknown
> >> >> > r.x                0804824A  Unknown               Unknown  Unknown
> >> >> > r.x                0823805D  Unknown               Unknown  Unknown
> >> >> > r.x                08048131  Unknown               Unknown  Unknown
> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> >> > Image              PC        Routine            Line        Source
> >> >> > r.x                08253657  Unknown               Unknown  Unknown
> >> >> > r.x                081F4087  Unknown               Unknown  Unknown
> >> >> > r.x                081DCDB7  Unknown               Unknown  Unknown
> >> >> > r.x                081DF354  Unknown               Unknown  Unknown
> >> >> > r.x                081DD672  Unknown               Unknown  Unknown
> >> >> > r.x                081DF5E8  Unknown               Unknown  Unknown
> >> >> > Unknown            FFFFE600  Unknown               Unknown  Unknown
> >> >> > r.x                0804824A  Unknown               Unknown  Unknown
> >> >> > r.x                0823805D  Unknown               Unknown  Unknown
> >> >> > r.x                08048131  Unknown               Unknown  Unknown
> >> >> >
> >> >> >
> >> >> > --
> >> >> >   Best Regards.
> >> >> >         Peng
> >> >> >
> >> >> > _______________________________________________
> >> >> > Pw_forum mailing list
> >> >> > Pw_forum at pwscf.org
> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Matteo Cococcioni
> >> >> Department of Chemical Engineering and Materials Science,
> >> >> University of Minnesota
> >> >> 421 Washington Av. SE
> >> >> Minneapolis, MN 55455
> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> >> _______________________________________________
> >> >> Pw_forum mailing list
> >> >> Pw_forum at pwscf.org
> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> >   Best Regards.
> >> >         Peng
> >> >
> >> > _______________________________________________
> >> > Pw_forum mailing list
> >> > Pw_forum at pwscf.org
> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >
> >>
> >>
> >>
> >> --
> >> Matteo Cococcioni
> >> Department of Chemical Engineering and Materials Science,
> >> University of Minnesota
> >> 421 Washington Av. SE
> >> Minneapolis, MN 55455
> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> >   Best Regards.
> >         Peng
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Matteo Cococcioni
> Department of Chemical Engineering and Materials Science,
> University of Minnesota
> 421 Washington Av. SE
> Minneapolis, MN 55455
> Tel. +1 612 624 9056    Fax +1 612 626 7246
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
  Best Regards.
        Peng
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From matteo at umn.edu  Sun Jul 29 19:17:59 2012
From: matteo at umn.edu (Matteo Cococcioni)
Date: Sun, 29 Jul 2012 12:17:59 -0500
Subject: [Pw_forum] U calculation error
In-Reply-To: <CAP_5U0fYafiTLd+sNKK1HE2TefOn8ZVZ9+urU6VcTTw2yQxmqQ@mail.gmail.com>
References: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>
	<CAMZASgH3ZxSwGtXARSqN+khMe4CSttRRgTb81F3LX7GfKFtp6w@mail.gmail.com>
	<CAP_5U0fA-N8DhL1DYcbpLZ=hiG8T4EfmJXPqwuJXFvcG89gP-Q@mail.gmail.com>
	<CAMZASgFWbtt6oCCoUp5g=ah3ODVOrNth9dwmmf2p+0XauMKhrw@mail.gmail.com>
	<CAP_5U0cU4t-AYM7rhOwo8MhMEuwjKEq5NzMoteDsaCO6wPugsw@mail.gmail.com>
	<CAMZASgGFhiF15BgCwkWgE5ZQj9tMRYFopAsQOKX8pte6Vw-DEg@mail.gmail.com>
	<CAP_5U0fYafiTLd+sNKK1HE2TefOn8ZVZ9+urU6VcTTw2yQxmqQ@mail.gmail.com>
Message-ID: <CAMZASgEoRBJRL1wSaWxAxAHOKvUw5Xci=3K4nVjP-YbyoEvuxQ@mail.gmail.com>

Dear Peng,

I advise you to run the example available from the QE webpage and try
to reproduce the same results.

On Sun, Jul 29, 2012 at 12:00 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
> Dear Dr. Matteo,
>
> I compiled the code with the parameters in make.sys. The n1=n2=n3=1 case is
> done without error, but the results for Ni and O are negative which should
> not be correct.


ok then maybe you can try to increase them one per time and see at
what level the code stops with error?


> 26 -14.8678837915617 7.56505581785392 -0.681000339374195
> I plot dn.1.da.1.dat and dn0.1.da.1.dat, the data in dn0.1.da.1.dat are not
> linear.


this is not related to the error message of r.x but is not right. if
you want reliable results you have to get these plots linear.



The scf calculation is converged to 0.001 Ry. So I am not sure what
> can cause the problem.


yes probably this is not enough. the inputs look fine (I haven't
looked inside the response matrix) but you have to make sure the scf
potential and wfc are saved after the unperturbed scf run and every
perturbed calculation starts from them.
do you really need 100 Ry cut off with US PP?

Matteo


>
> I've attached the Umat_afm.1.out which may contain some useful information
> for you. I also put below the input for scf and perturbation on Ni
> (alpha=-0.15,-0.07,0.0,0.07,0.15). Same calculations are done for V and O as
> well with perturbed V or O atom translated to the origin of the unit cell.
>
>
> scf calculation input:
>
> &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     prefix='nvoprim.afm.ucalc.Ni',
>     pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
>     outdir='/data/pchen/qe/'
>     wf_collect=.TRUE.
>  /
>  &system
>     ibrav=0, celldm(1)=11.19096,
>      nat=26, ntyp=6,
>   nspin = 2,  starting_magnetization(1)=0.6,
>     starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
>  starting_magnetization(4)=-0.5,
>  ecutwfc = 100, ecutrho = 800,
>  occupations ='smearing',
>     smearing ='mv',
>     degauss = 0.005,nbnd=135
>   lda_plus_u = .true.
>     Hubbard_U(1)= 1.d-20
>     Hubbard_U(2)= 1.d-20
>  Hubbard_U(3)= 1.d-20
>  Hubbard_U(4)= 1.d-20
>  Hubbard_U(5)= 1.d-20
>  Hubbard_U(6)= 1.d-20
>  /
>  &electrons
>     conv_thr = 1.0e-7
>     mixing_beta = 0.3
>  /
> CELL_PARAMETERS
> 0.5 0.96015 0
> 0.5 -0.96015 0
> 0 0   1.38889
> ATOMIC_SPECIES
>  Ni1 58.6934 Ni.pz-n-rrkjus.UPF
>  Ni2 58.6934 Ni.pz-n-rrkjus.UPF
>  Ni3 58.6934 Ni.pz-n-rrkjus.UPF
>  Ni4 58.6934 Ni.pz-n-rrkjus.UPF
>  V 50.9415 V.pz-spn-rrkjus.UPF
>  O  15.9994  O.pz-n-rrkjus.UPF
> ATOMIC_POSITIONS crystal
> Ni1      0.000000000   0.000000000   0.000000000
> Ni2      0.500000000   0.500000000   0.500000000
> Ni3      0.122863290   0.378190177   0.749934361
> Ni3      0.877136710   0.621809823   0.250065639
> Ni4      0.377137388   0.121809201   0.249932658
> Ni4      0.622862612   0.878190799   0.750067342
> V        0.373618754   0.623612138   0.115867980
> V        0.126381501   0.876388862   0.615868582
> V        0.626381246   0.376387862   0.884132020
> V        0.873618499   0.123611138   0.384131418
> O        0.241839036   0.756304999   0.223613779
> O        0.258160617   0.743693910   0.723611944
> O        0.758160964   0.243695001   0.776386221
> O        0.741839383   0.256306090   0.276388056
> O       -0.000998332   1.000227439   0.243205274
> O        0.500997862   0.499772508   0.743208489
> O        1.000998332  -0.000227439   0.756794726
> O        0.499002138   0.500227492   0.256791511
> O        0.381099639   0.150692971   0.006796703
> O        0.118898786   0.349304325   0.506798051
> O        0.149581603   0.378555571   0.991989919
> O        0.350419534   0.121445697   0.491991443
> O        0.618900361   0.849307029   0.993205297
> O        0.881101214   0.650695675   0.493203949
> O        0.850418397   0.621444429   0.008012081
> O        0.649580466   0.878554303   0.508010557
>
> K_POINTS (automatic)
>  5 5 5 1 1 1
>
> Perturbation on Ni with alpha=0.15 input:
>
> &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     prefix='nvoprim.afm.ucalc.Ni',
>     pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
>     outdir='/data/pchen/qe/'
>    wf_collect=.TRUE.
>  /
>  &system
>     ibrav=0, celldm(1)=11.19096,
>      nat=26, ntyp=6,
>   nspin = 2,  starting_magnetization(1)=0.6,
>     starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
>  starting_magnetization(4)=-0.5,
>  ecutwfc = 100, ecutrho = 800,
>  occupations ='smearing',
>     smearing ='mv',
>     degauss = 0.005,nbnd=135
>   lda_plus_u = .true.
>     Hubbard_U(1)= 1.d-20
>     Hubbard_U(2)= 1.d-20
>     Hubbard_U(3)= 1.d-20
> Hubbard_U(4)= 1.d-20
> Hubbard_U(5)= 1.d-20
> Hubbard_U(6)= 1.d-20
>
>     Hubbard_alpha(1)= 0.15
>  /
>  &electrons
>     conv_thr = 1.0e-7
>     mixing_beta = 0.3
>   startingpot='file'
>  startingwfc='file'
>  diago_thr_init=5.09E-11,
>  /
> CELL_PARAMETERS
> 0.5 0.96015 0
> 0.5 -0.96015 0
> 0 0   1.38889
> ATOMIC_SPECIES
>  Ni1 58.6934 Ni.pz-n-rrkjus.UPF
>  Ni2 58.6934 Ni.pz-n-rrkjus.UPF
>  Ni3 58.6934 Ni.pz-n-rrkjus.UPF
>  Ni4 58.6934 Ni.pz-n-rrkjus.UPF
>  V 50.9415 V.pz-spn-rrkjus.UPF
>  O  15.9994  O.pz-n-rrkjus.UPF
> ATOMIC_POSITIONS crystal
> Ni1      0.000000000   0.000000000   0.000000000
> Ni2      0.500000000   0.500000000   0.500000000
> Ni3      0.122863290   0.378190177   0.749934361
> Ni3      0.877136710   0.621809823   0.250065639
> Ni4      0.377137388   0.121809201   0.249932658
> Ni4      0.622862612   0.878190799   0.750067342
> V        0.373618754   0.623612138   0.115867980
> V        0.126381501   0.876388862   0.615868582
> V        0.626381246   0.376387862   0.884132020
> V        0.873618499   0.123611138   0.384131418
> O        0.241839036   0.756304999   0.223613779
> O        0.258160617   0.743693910   0.723611944
> O        0.758160964   0.243695001   0.776386221
> O        0.741839383   0.256306090   0.276388056
> O       -0.000998332   1.000227439   0.243205274
> O        0.500997862   0.499772508   0.743208489
> O        1.000998332  -0.000227439   0.756794726
> O        0.499002138   0.500227492   0.256791511
> O        0.381099639   0.150692971   0.006796703
> O        0.118898786   0.349304325   0.506798051
> O        0.149581603   0.378555571   0.991989919
> O        0.350419534   0.121445697   0.491991443
> O        0.618900361   0.849307029   0.993205297
> O        0.881101214   0.650695675   0.493203949
> O        0.850418397   0.621444429   0.008012081
> O        0.649580466   0.878554303   0.508010557
>
> K_POINTS (automatic)
>  5 5 5 1 1 1
>
>
>
> On Sun, Jul 29, 2012 at 11:27 AM, Matteo Cococcioni <matteo at umn.edu> wrote:
>>
>> Dear Peng,
>>
>> I'm not very expert of compiling codes. You have to make sure that all
>> the libraries are linked correctly for the code to work. I assume you
>> have QE installed on the same computer. You could give a look in the
>> make.sys to check what is the correct way to link them. If everything
>> is consistent, then you have to find out where the code is failing.
>> have you tried to run with n1 = n2 = n3 = 1? what did you get?
>>
>> Matteo
>>
>>
>>
>> On Sat, Jul 28, 2012 at 9:10 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
>> > Dear Dr. Matteo,
>> >
>> > I used command listed below to compile resp_mat.f90. No error in
>> > compiling.
>> > I am not sure if I did right in choosing the libs.
>> > ifort  -o r.x resp_mat.f90 -L"/data/apps/intel/11.1.072/mkl/lib/em64t"
>> > -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_mc3  -lmkl_sequential
>> > -lmkl_core
>> >
>> > The libs in mkl are shown below:
>> > libmkl_avx.so                   libmkl_intel_sp2dp.so
>> > libmkl_blacs_ilp64.a            libmkl_intel_thread.a
>> > libmkl_blacs_intelmpi_ilp64.a   libmkl_intel_thread.so
>> > libmkl_blacs_intelmpi_ilp64.so  libmkl_lapack95_ilp64.a
>> > libmkl_blacs_intelmpi_lp64.a    libmkl_lapack95_lp64.a
>> > libmkl_blacs_intelmpi_lp64.so   libmkl_lapack.so
>> > libmkl_blacs_lp64.a             libmkl_mc3.so
>> > libmkl_blacs_openmpi_ilp64.a    libmkl_mc.so
>> > libmkl_blacs_openmpi_lp64.a     libmkl_p4n.so
>> > libmkl_blacs_sgimpt_ilp64.a     libmkl_pgi_thread.a
>> > libmkl_blacs_sgimpt_lp64.a      libmkl_pgi_thread.so
>> > libmkl_blas95_ilp64.a           libmkl_scalapack_ilp64.a
>> > libmkl_blas95_lp64.a            libmkl_scalapack_ilp64.so
>> > libmkl_cdft_core.a              libmkl_scalapack_lp64.a
>> > libmkl_core.a                   libmkl_scalapack_lp64.so
>> > libmkl_core.so                  libmkl_sequential.a
>> > libmkl_def.so                   libmkl_sequential.so
>> > libmkl_gf_ilp64.a               libmkl_solver_ilp64.a
>> > libmkl_gf_ilp64.so              libmkl_solver_ilp64_sequential.a
>> > libmkl_gf_lp64.a                libmkl_solver_lp64.a
>> > libmkl_gf_lp64.so               libmkl_solver_lp64_sequential.a
>> > libmkl_gnu_thread.a             libmkl_vml_avx.so
>> > libmkl_gnu_thread.so            libmkl_vml_def.so
>> > libmkl_intel_ilp64.a            libmkl_vml_mc2.so
>> > libmkl_intel_ilp64.so           libmkl_vml_mc3.so
>> > libmkl_intel_lp64.a             libmkl_vml_mc.so
>> > libmkl_intel_lp64.so            libmkl_vml_p4n.so
>> > libmkl_intel_sp2dp.a            locale
>> >
>> >
>> > Some errors in output:
>> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> > Image              PC                Routine            Line
>> > Source
>> > r.x                0000000000445659  Unknown               Unknown
>> > Unknown
>> > r.x                000000000040A363  Unknown               Unknown
>> > Unknown
>> > r.x                000000000040338C  Unknown               Unknown
>> > Unknown
>> > libc.so.6          00002B85B9495994  Unknown               Unknown
>> > Unknown
>> > r.x                0000000000403289  Unknown               Unknown
>> > Unknown
>> >
>> >
>> > On Sat, Jul 28, 2012 at 10:38 AM, Matteo Cococcioni <matteo at umn.edu>
>> > wrote:
>> >>
>> >> Dear Peng,
>> >>
>> >> nothing looks wrong in your input. have you tried with n1, n2, n3 all
>> >> equal to 1? are you sure you compiled correctly?
>> >>
>> >> Matteo
>> >>
>> >>
>> >>
>> >> On Fri, Jul 27, 2012 at 11:46 PM, Peng Chen <pchen at ion.chem.utk.edu>
>> >> wrote:
>> >> > Dear Dr. Matteo,
>> >> >
>> >> > The primitive cell has 26 atoms with 3 different types. The pos and
>> >> > resp_mat.in files are shown below:
>> >> >
>> >> > 5.6087 10.79 0.0
>> >> > 5.6087 -10.79 0.0
>> >> > 0.0 0.0   15.570873
>> >> > 0       0       0       1
>> >> > 0.5     0.5     0.5     -1
>> >> > 0.12286329      0.378190177     0.749934361     1
>> >> > 0.87713671      0.621809823     0.250065639     1
>> >> > 0.377137388     0.121809201     0.249932658     -1
>> >> > 0.622862612     0.878190799     0.750067342     -1
>> >> > 0.373618754     0.623612138     0.11586798      0
>> >> > 0.126381501     0.876388862     0.615868582     0
>> >> > 0.626381246     0.376387862     0.88413202      0
>> >> > 0.873618499     0.123611138     0.384131418     0
>> >> > 0.241839036     0.756304999     0.223613779     0
>> >> > 0.258160617     0.74369391      0.723611944     0
>> >> > 0.758160964     0.243695001     0.776386221     0
>> >> > 0.741839383     0.25630609      0.276388056     0
>> >> > -0.000998332    1.000227439     0.243205274     0
>> >> > 0.500997862     0.499772508     0.743208489     0
>> >> > 1.000998332     -0.000227439    0.756794726     0
>> >> > 0.499002138     0.500227492     0.256791511     0
>> >> > 0.381099639     0.150692971     0.006796703     0
>> >> > 0.118898786     0.349304325     0.506798051     0
>> >> > 0.149581603     0.378555571     0.991989919     0
>> >> > 0.350419534     0.121445697     0.491991443     0
>> >> > 0.618900361     0.849307029     0.993205297     0
>> >> > 0.881101214     0.650695675     0.493203949     0
>> >> > 0.850418397     0.621444429     0.008012081     0
>> >> > 0.649580466     0.878554303     0.508010557     0
>> >> >
>> >> > resp_mat.in :
>> >> >  &input_mat
>> >> >    ntyp = 3
>> >> >    na(1) = 6
>> >> >    na(2) = 4
>> >> >    na(3) = 16
>> >> >    nalfa = 5
>> >> >    magn=.true.
>> >> >    filepos = 'pos'
>> >> >    back = 'no'
>> >> >    filednda = 'file_afm'
>> >> >    n1 = 2
>> >> >    n2 = 2
>> >> >    n3 = 2
>> >> >  &end
>> >> >
>> >> >
>> >> >
>> >> > On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni <matteo at umn.edu>
>> >> > wrote:
>> >> >>
>> >> >> Dear Peng,
>> >> >>
>> >> >> can you provide info about your system? maybe it is larger than the
>> >> >> maximum size allowed by r.x?
>> >> >>
>> >> >> Matteo
>> >> >>
>> >> >> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen <pchen at ion.chem.utk.edu>
>> >> >> wrote:
>> >> >> > Dear All,
>> >> >> >
>> >> >> > There are some errors when I run r.x to calculate the U. I used
>> >> >> > Espresso-5.0
>> >> >> > and follow the steps in LSDA+U example. I am not sure what could
>> >> >> > be
>> >> >> > wrong.
>> >> >> > And if you need other input/output, please let me know.
>> >> >> >
>> >> >> > Image              PC        Routine            Line        Source
>> >> >> > r.x                0822DACC  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0822C265  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                082071FA  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                081DDFDA  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                081FA33B  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                081F9C5C  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0804E38F  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0804824A  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0823805D  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                08048131  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > forrtl: severe (8): internal consistency check failure, file
>> >> >> > ./src/libfor/for_wseq_lis.c, line 635
>> >> >> > Image              PC        Routine            Line        Source
>> >> >> > r.x                0822DACC  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0822C265  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                082071FA  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                081DD664  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                081F9AF7  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0804E38F  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0804824A  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0823805D  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                08048131  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> >> >> > Image              PC        Routine            Line        Source
>> >> >> > r.x                0804DAED  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0804824A  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0823805D  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                08048131  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> >> >> > Image              PC        Routine            Line        Source
>> >> >> > r.x                08253657  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                081F4087  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                081DCDB7  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                081DF354  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                081DD672  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                081DF5E8  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > Unknown            FFFFE600  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0804824A  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0823805D  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                08048131  Unknown               Unknown
>> >> >> > Unknown
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> >   Best Regards.
>> >> >> >         Peng
>> >> >> >
>> >> >> > _______________________________________________
>> >> >> > Pw_forum mailing list
>> >> >> > Pw_forum at pwscf.org
>> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Matteo Cococcioni
>> >> >> Department of Chemical Engineering and Materials Science,
>> >> >> University of Minnesota
>> >> >> 421 Washington Av. SE
>> >> >> Minneapolis, MN 55455
>> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> >> >> _______________________________________________
>> >> >> Pw_forum mailing list
>> >> >> Pw_forum at pwscf.org
>> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >   Best Regards.
>> >> >         Peng
>> >> >
>> >> > _______________________________________________
>> >> > Pw_forum mailing list
>> >> > Pw_forum at pwscf.org
>> >> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Matteo Cococcioni
>> >> Department of Chemical Engineering and Materials Science,
>> >> University of Minnesota
>> >> 421 Washington Av. SE
>> >> Minneapolis, MN 55455
>> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> >> _______________________________________________
>> >> Pw_forum mailing list
>> >> Pw_forum at pwscf.org
>> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>> >
>> >
>> >
>> > --
>> >   Best Regards.
>> >         Peng
>> >
>> > _______________________________________________
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>>
>>
>>
>> --
>> Matteo Cococcioni
>> Department of Chemical Engineering and Materials Science,
>> University of Minnesota
>> 421 Washington Av. SE
>> Minneapolis, MN 55455
>> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
>   Best Regards.
>         Peng
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056    Fax +1 612 626 7246

From pchen at ion.chem.utk.edu  Sun Jul 29 22:01:08 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Sun, 29 Jul 2012 16:01:08 -0400
Subject: [Pw_forum] U calculation error
In-Reply-To: <CAMZASgEoRBJRL1wSaWxAxAHOKvUw5Xci=3K4nVjP-YbyoEvuxQ@mail.gmail.com>
References: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>
	<CAMZASgH3ZxSwGtXARSqN+khMe4CSttRRgTb81F3LX7GfKFtp6w@mail.gmail.com>
	<CAP_5U0fA-N8DhL1DYcbpLZ=hiG8T4EfmJXPqwuJXFvcG89gP-Q@mail.gmail.com>
	<CAMZASgFWbtt6oCCoUp5g=ah3ODVOrNth9dwmmf2p+0XauMKhrw@mail.gmail.com>
	<CAP_5U0cU4t-AYM7rhOwo8MhMEuwjKEq5NzMoteDsaCO6wPugsw@mail.gmail.com>
	<CAMZASgGFhiF15BgCwkWgE5ZQj9tMRYFopAsQOKX8pte6Vw-DEg@mail.gmail.com>
	<CAP_5U0fYafiTLd+sNKK1HE2TefOn8ZVZ9+urU6VcTTw2yQxmqQ@mail.gmail.com>
	<CAMZASgEoRBJRL1wSaWxAxAHOKvUw5Xci=3K4nVjP-YbyoEvuxQ@mail.gmail.com>
Message-ID: <CAP_5U0faBHn-_7JhoSWhbsD0U-FePKd1mxXaFo9wTU11sgqD6A@mail.gmail.com>

Dear Dr. Matteo,

Yes,  I ran the LSDA+U example successfully, the only difference is that
the U of Ni converged to 6.0 not 5.0.

For my calculation, if I use n1=n2=n3=2, the result is
208 NaN 6.899999999999315E-003 2.066666666665403E-003.
If n1=n2=n3=3, the size of Umat.out will continue to increase > 2G. And I
have to stop it before the space is used up.

The  potential and wfcs are saved and I used ecutwfc=100 to make the scf
energy converged to 0.001Ry. I can decrease it if that will help to get
correct U.

On Sun, Jul 29, 2012 at 1:17 PM, Matteo Cococcioni <matteo at umn.edu> wrote:

> Dear Peng,
>
> I advise you to run the example available from the QE webpage and try
> to reproduce the same results.
>
> On Sun, Jul 29, 2012 at 12:00 PM, Peng Chen <pchen at ion.chem.utk.edu>
> wrote:
> > Dear Dr. Matteo,
> >
> > I compiled the code with the parameters in make.sys. The n1=n2=n3=1 case
> is
> > done without error, but the results for Ni and O are negative which
> should
> > not be correct.
>
>
> ok then maybe you can try to increase them one per time and see at
> what level the code stops with error?
>
>
> > 26 -14.8678837915617 7.56505581785392 -0.681000339374195
> > I plot dn.1.da.1.dat and dn0.1.da.1.dat, the data in dn0.1.da.1.dat are
> not
> > linear.
>
>
> this is not related to the error message of r.x but is not right. if
> you want reliable results you have to get these plots linear.
>
>
>
> The scf calculation is converged to 0.001 Ry. So I am not sure what
> > can cause the problem.
>
>
> yes probably this is not enough. the inputs look fine (I haven't
> looked inside the response matrix) but you have to make sure the scf
> potential and wfc are saved after the unperturbed scf run and every
> perturbed calculation starts from them.
> do you really need 100 Ry cut off with US PP?
>
> Matteo
>
>
> >
> > I've attached the Umat_afm.1.out which may contain some useful
> information
> > for you. I also put below the input for scf and perturbation on Ni
> > (alpha=-0.15,-0.07,0.0,0.07,0.15). Same calculations are done for V and
> O as
> > well with perturbed V or O atom translated to the origin of the unit
> cell.
> >
> >
> > scf calculation input:
> >
> > &control
> >     calculation='scf'
> >     restart_mode='from_scratch',
> >     prefix='nvoprim.afm.ucalc.Ni',
> >     pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
> >     outdir='/data/pchen/qe/'
> >     wf_collect=.TRUE.
> >  /
> >  &system
> >     ibrav=0, celldm(1)=11.19096,
> >      nat=26, ntyp=6,
> >   nspin = 2,  starting_magnetization(1)=0.6,
> >     starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
> >  starting_magnetization(4)=-0.5,
> >  ecutwfc = 100, ecutrho = 800,
> >  occupations ='smearing',
> >     smearing ='mv',
> >     degauss = 0.005,nbnd=135
> >   lda_plus_u = .true.
> >     Hubbard_U(1)= 1.d-20
> >     Hubbard_U(2)= 1.d-20
> >  Hubbard_U(3)= 1.d-20
> >  Hubbard_U(4)= 1.d-20
> >  Hubbard_U(5)= 1.d-20
> >  Hubbard_U(6)= 1.d-20
> >  /
> >  &electrons
> >     conv_thr = 1.0e-7
> >     mixing_beta = 0.3
> >  /
> > CELL_PARAMETERS
> > 0.5 0.96015 0
> > 0.5 -0.96015 0
> > 0 0   1.38889
> > ATOMIC_SPECIES
> >  Ni1 58.6934 Ni.pz-n-rrkjus.UPF
> >  Ni2 58.6934 Ni.pz-n-rrkjus.UPF
> >  Ni3 58.6934 Ni.pz-n-rrkjus.UPF
> >  Ni4 58.6934 Ni.pz-n-rrkjus.UPF
> >  V 50.9415 V.pz-spn-rrkjus.UPF
> >  O  15.9994  O.pz-n-rrkjus.UPF
> > ATOMIC_POSITIONS crystal
> > Ni1      0.000000000   0.000000000   0.000000000
> > Ni2      0.500000000   0.500000000   0.500000000
> > Ni3      0.122863290   0.378190177   0.749934361
> > Ni3      0.877136710   0.621809823   0.250065639
> > Ni4      0.377137388   0.121809201   0.249932658
> > Ni4      0.622862612   0.878190799   0.750067342
> > V        0.373618754   0.623612138   0.115867980
> > V        0.126381501   0.876388862   0.615868582
> > V        0.626381246   0.376387862   0.884132020
> > V        0.873618499   0.123611138   0.384131418
> > O        0.241839036   0.756304999   0.223613779
> > O        0.258160617   0.743693910   0.723611944
> > O        0.758160964   0.243695001   0.776386221
> > O        0.741839383   0.256306090   0.276388056
> > O       -0.000998332   1.000227439   0.243205274
> > O        0.500997862   0.499772508   0.743208489
> > O        1.000998332  -0.000227439   0.756794726
> > O        0.499002138   0.500227492   0.256791511
> > O        0.381099639   0.150692971   0.006796703
> > O        0.118898786   0.349304325   0.506798051
> > O        0.149581603   0.378555571   0.991989919
> > O        0.350419534   0.121445697   0.491991443
> > O        0.618900361   0.849307029   0.993205297
> > O        0.881101214   0.650695675   0.493203949
> > O        0.850418397   0.621444429   0.008012081
> > O        0.649580466   0.878554303   0.508010557
> >
> > K_POINTS (automatic)
> >  5 5 5 1 1 1
> >
> > Perturbation on Ni with alpha=0.15 input:
> >
> > &control
> >     calculation='scf'
> >     restart_mode='from_scratch',
> >     prefix='nvoprim.afm.ucalc.Ni',
> >     pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
> >     outdir='/data/pchen/qe/'
> >    wf_collect=.TRUE.
> >  /
> >  &system
> >     ibrav=0, celldm(1)=11.19096,
> >      nat=26, ntyp=6,
> >   nspin = 2,  starting_magnetization(1)=0.6,
> >     starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
> >  starting_magnetization(4)=-0.5,
> >  ecutwfc = 100, ecutrho = 800,
> >  occupations ='smearing',
> >     smearing ='mv',
> >     degauss = 0.005,nbnd=135
> >   lda_plus_u = .true.
> >     Hubbard_U(1)= 1.d-20
> >     Hubbard_U(2)= 1.d-20
> >     Hubbard_U(3)= 1.d-20
> > Hubbard_U(4)= 1.d-20
> > Hubbard_U(5)= 1.d-20
> > Hubbard_U(6)= 1.d-20
> >
> >     Hubbard_alpha(1)= 0.15
> >  /
> >  &electrons
> >     conv_thr = 1.0e-7
> >     mixing_beta = 0.3
> >   startingpot='file'
> >  startingwfc='file'
> >  diago_thr_init=5.09E-11,
> >  /
> > CELL_PARAMETERS
> > 0.5 0.96015 0
> > 0.5 -0.96015 0
> > 0 0   1.38889
> > ATOMIC_SPECIES
> >  Ni1 58.6934 Ni.pz-n-rrkjus.UPF
> >  Ni2 58.6934 Ni.pz-n-rrkjus.UPF
> >  Ni3 58.6934 Ni.pz-n-rrkjus.UPF
> >  Ni4 58.6934 Ni.pz-n-rrkjus.UPF
> >  V 50.9415 V.pz-spn-rrkjus.UPF
> >  O  15.9994  O.pz-n-rrkjus.UPF
> > ATOMIC_POSITIONS crystal
> > Ni1      0.000000000   0.000000000   0.000000000
> > Ni2      0.500000000   0.500000000   0.500000000
> > Ni3      0.122863290   0.378190177   0.749934361
> > Ni3      0.877136710   0.621809823   0.250065639
> > Ni4      0.377137388   0.121809201   0.249932658
> > Ni4      0.622862612   0.878190799   0.750067342
> > V        0.373618754   0.623612138   0.115867980
> > V        0.126381501   0.876388862   0.615868582
> > V        0.626381246   0.376387862   0.884132020
> > V        0.873618499   0.123611138   0.384131418
> > O        0.241839036   0.756304999   0.223613779
> > O        0.258160617   0.743693910   0.723611944
> > O        0.758160964   0.243695001   0.776386221
> > O        0.741839383   0.256306090   0.276388056
> > O       -0.000998332   1.000227439   0.243205274
> > O        0.500997862   0.499772508   0.743208489
> > O        1.000998332  -0.000227439   0.756794726
> > O        0.499002138   0.500227492   0.256791511
> > O        0.381099639   0.150692971   0.006796703
> > O        0.118898786   0.349304325   0.506798051
> > O        0.149581603   0.378555571   0.991989919
> > O        0.350419534   0.121445697   0.491991443
> > O        0.618900361   0.849307029   0.993205297
> > O        0.881101214   0.650695675   0.493203949
> > O        0.850418397   0.621444429   0.008012081
> > O        0.649580466   0.878554303   0.508010557
> >
> > K_POINTS (automatic)
> >  5 5 5 1 1 1
> >
> >
> >
> > On Sun, Jul 29, 2012 at 11:27 AM, Matteo Cococcioni <matteo at umn.edu>
> wrote:
> >>
> >> Dear Peng,
> >>
> >> I'm not very expert of compiling codes. You have to make sure that all
> >> the libraries are linked correctly for the code to work. I assume you
> >> have QE installed on the same computer. You could give a look in the
> >> make.sys to check what is the correct way to link them. If everything
> >> is consistent, then you have to find out where the code is failing.
> >> have you tried to run with n1 = n2 = n3 = 1? what did you get?
> >>
> >> Matteo
> >>
> >>
> >>
> >> On Sat, Jul 28, 2012 at 9:10 PM, Peng Chen <pchen at ion.chem.utk.edu>
> wrote:
> >> > Dear Dr. Matteo,
> >> >
> >> > I used command listed below to compile resp_mat.f90. No error in
> >> > compiling.
> >> > I am not sure if I did right in choosing the libs.
> >> > ifort  -o r.x resp_mat.f90 -L"/data/apps/intel/11.1.072/mkl/lib/em64t"
> >> > -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_mc3  -lmkl_sequential
> >> > -lmkl_core
> >> >
> >> > The libs in mkl are shown below:
> >> > libmkl_avx.so                   libmkl_intel_sp2dp.so
> >> > libmkl_blacs_ilp64.a            libmkl_intel_thread.a
> >> > libmkl_blacs_intelmpi_ilp64.a   libmkl_intel_thread.so
> >> > libmkl_blacs_intelmpi_ilp64.so  libmkl_lapack95_ilp64.a
> >> > libmkl_blacs_intelmpi_lp64.a    libmkl_lapack95_lp64.a
> >> > libmkl_blacs_intelmpi_lp64.so   libmkl_lapack.so
> >> > libmkl_blacs_lp64.a             libmkl_mc3.so
> >> > libmkl_blacs_openmpi_ilp64.a    libmkl_mc.so
> >> > libmkl_blacs_openmpi_lp64.a     libmkl_p4n.so
> >> > libmkl_blacs_sgimpt_ilp64.a     libmkl_pgi_thread.a
> >> > libmkl_blacs_sgimpt_lp64.a      libmkl_pgi_thread.so
> >> > libmkl_blas95_ilp64.a           libmkl_scalapack_ilp64.a
> >> > libmkl_blas95_lp64.a            libmkl_scalapack_ilp64.so
> >> > libmkl_cdft_core.a              libmkl_scalapack_lp64.a
> >> > libmkl_core.a                   libmkl_scalapack_lp64.so
> >> > libmkl_core.so                  libmkl_sequential.a
> >> > libmkl_def.so                   libmkl_sequential.so
> >> > libmkl_gf_ilp64.a               libmkl_solver_ilp64.a
> >> > libmkl_gf_ilp64.so              libmkl_solver_ilp64_sequential.a
> >> > libmkl_gf_lp64.a                libmkl_solver_lp64.a
> >> > libmkl_gf_lp64.so               libmkl_solver_lp64_sequential.a
> >> > libmkl_gnu_thread.a             libmkl_vml_avx.so
> >> > libmkl_gnu_thread.so            libmkl_vml_def.so
> >> > libmkl_intel_ilp64.a            libmkl_vml_mc2.so
> >> > libmkl_intel_ilp64.so           libmkl_vml_mc3.so
> >> > libmkl_intel_lp64.a             libmkl_vml_mc.so
> >> > libmkl_intel_lp64.so            libmkl_vml_p4n.so
> >> > libmkl_intel_sp2dp.a            locale
> >> >
> >> >
> >> > Some errors in output:
> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> > Image              PC                Routine            Line
> >> > Source
> >> > r.x                0000000000445659  Unknown               Unknown
> >> > Unknown
> >> > r.x                000000000040A363  Unknown               Unknown
> >> > Unknown
> >> > r.x                000000000040338C  Unknown               Unknown
> >> > Unknown
> >> > libc.so.6          00002B85B9495994  Unknown               Unknown
> >> > Unknown
> >> > r.x                0000000000403289  Unknown               Unknown
> >> > Unknown
> >> >
> >> >
> >> > On Sat, Jul 28, 2012 at 10:38 AM, Matteo Cococcioni <matteo at umn.edu>
> >> > wrote:
> >> >>
> >> >> Dear Peng,
> >> >>
> >> >> nothing looks wrong in your input. have you tried with n1, n2, n3 all
> >> >> equal to 1? are you sure you compiled correctly?
> >> >>
> >> >> Matteo
> >> >>
> >> >>
> >> >>
> >> >> On Fri, Jul 27, 2012 at 11:46 PM, Peng Chen <pchen at ion.chem.utk.edu>
> >> >> wrote:
> >> >> > Dear Dr. Matteo,
> >> >> >
> >> >> > The primitive cell has 26 atoms with 3 different types. The pos and
> >> >> > resp_mat.in files are shown below:
> >> >> >
> >> >> > 5.6087 10.79 0.0
> >> >> > 5.6087 -10.79 0.0
> >> >> > 0.0 0.0   15.570873
> >> >> > 0       0       0       1
> >> >> > 0.5     0.5     0.5     -1
> >> >> > 0.12286329      0.378190177     0.749934361     1
> >> >> > 0.87713671      0.621809823     0.250065639     1
> >> >> > 0.377137388     0.121809201     0.249932658     -1
> >> >> > 0.622862612     0.878190799     0.750067342     -1
> >> >> > 0.373618754     0.623612138     0.11586798      0
> >> >> > 0.126381501     0.876388862     0.615868582     0
> >> >> > 0.626381246     0.376387862     0.88413202      0
> >> >> > 0.873618499     0.123611138     0.384131418     0
> >> >> > 0.241839036     0.756304999     0.223613779     0
> >> >> > 0.258160617     0.74369391      0.723611944     0
> >> >> > 0.758160964     0.243695001     0.776386221     0
> >> >> > 0.741839383     0.25630609      0.276388056     0
> >> >> > -0.000998332    1.000227439     0.243205274     0
> >> >> > 0.500997862     0.499772508     0.743208489     0
> >> >> > 1.000998332     -0.000227439    0.756794726     0
> >> >> > 0.499002138     0.500227492     0.256791511     0
> >> >> > 0.381099639     0.150692971     0.006796703     0
> >> >> > 0.118898786     0.349304325     0.506798051     0
> >> >> > 0.149581603     0.378555571     0.991989919     0
> >> >> > 0.350419534     0.121445697     0.491991443     0
> >> >> > 0.618900361     0.849307029     0.993205297     0
> >> >> > 0.881101214     0.650695675     0.493203949     0
> >> >> > 0.850418397     0.621444429     0.008012081     0
> >> >> > 0.649580466     0.878554303     0.508010557     0
> >> >> >
> >> >> > resp_mat.in :
> >> >> >  &input_mat
> >> >> >    ntyp = 3
> >> >> >    na(1) = 6
> >> >> >    na(2) = 4
> >> >> >    na(3) = 16
> >> >> >    nalfa = 5
> >> >> >    magn=.true.
> >> >> >    filepos = 'pos'
> >> >> >    back = 'no'
> >> >> >    filednda = 'file_afm'
> >> >> >    n1 = 2
> >> >> >    n2 = 2
> >> >> >    n3 = 2
> >> >> >  &end
> >> >> >
> >> >> >
> >> >> >
> >> >> > On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni <matteo at umn.edu
> >
> >> >> > wrote:
> >> >> >>
> >> >> >> Dear Peng,
> >> >> >>
> >> >> >> can you provide info about your system? maybe it is larger than
> the
> >> >> >> maximum size allowed by r.x?
> >> >> >>
> >> >> >> Matteo
> >> >> >>
> >> >> >> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen <
> pchen at ion.chem.utk.edu>
> >> >> >> wrote:
> >> >> >> > Dear All,
> >> >> >> >
> >> >> >> > There are some errors when I run r.x to calculate the U. I used
> >> >> >> > Espresso-5.0
> >> >> >> > and follow the steps in LSDA+U example. I am not sure what could
> >> >> >> > be
> >> >> >> > wrong.
> >> >> >> > And if you need other input/output, please let me know.
> >> >> >> >
> >> >> >> > Image              PC        Routine            Line
>  Source
> >> >> >> > r.x                0822DACC  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0822C265  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                082071FA  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                081DDFDA  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                081FA33B  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                081F9C5C  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0804E38F  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0804824A  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0823805D  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                08048131  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > forrtl: severe (8): internal consistency check failure, file
> >> >> >> > ./src/libfor/for_wseq_lis.c, line 635
> >> >> >> > Image              PC        Routine            Line
>  Source
> >> >> >> > r.x                0822DACC  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0822C265  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                082071FA  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                081DD664  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                081F9AF7  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0804E38F  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0804824A  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0823805D  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                08048131  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> >> >> > Image              PC        Routine            Line
>  Source
> >> >> >> > r.x                0804DAED  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0804824A  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0823805D  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                08048131  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> >> >> > Image              PC        Routine            Line
>  Source
> >> >> >> > r.x                08253657  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                081F4087  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                081DCDB7  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                081DF354  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                081DD672  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                081DF5E8  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > Unknown            FFFFE600  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0804824A  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0823805D  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                08048131  Unknown               Unknown
> >> >> >> > Unknown
> >> >> >> >
> >> >> >> >
> >> >> >> > --
> >> >> >> >   Best Regards.
> >> >> >> >         Peng
> >> >> >> >
> >> >> >> > _______________________________________________
> >> >> >> > Pw_forum mailing list
> >> >> >> > Pw_forum at pwscf.org
> >> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Matteo Cococcioni
> >> >> >> Department of Chemical Engineering and Materials Science,
> >> >> >> University of Minnesota
> >> >> >> 421 Washington Av. SE
> >> >> >> Minneapolis, MN 55455
> >> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> >> >> _______________________________________________
> >> >> >> Pw_forum mailing list
> >> >> >> Pw_forum at pwscf.org
> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> >   Best Regards.
> >> >> >         Peng
> >> >> >
> >> >> > _______________________________________________
> >> >> > Pw_forum mailing list
> >> >> > Pw_forum at pwscf.org
> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Matteo Cococcioni
> >> >> Department of Chemical Engineering and Materials Science,
> >> >> University of Minnesota
> >> >> 421 Washington Av. SE
> >> >> Minneapolis, MN 55455
> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> >> _______________________________________________
> >> >> Pw_forum mailing list
> >> >> Pw_forum at pwscf.org
> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> >   Best Regards.
> >> >         Peng
> >> >
> >> > _______________________________________________
> >> > Pw_forum mailing list
> >> > Pw_forum at pwscf.org
> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >
> >>
> >>
> >>
> >> --
> >> Matteo Cococcioni
> >> Department of Chemical Engineering and Materials Science,
> >> University of Minnesota
> >> 421 Washington Av. SE
> >> Minneapolis, MN 55455
> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> >   Best Regards.
> >         Peng
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Matteo Cococcioni
> Department of Chemical Engineering and Materials Science,
> University of Minnesota
> 421 Washington Av. SE
> Minneapolis, MN 55455
> Tel. +1 612 624 9056    Fax +1 612 626 7246
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
  Best Regards.
        Peng
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From matteo at umn.edu  Mon Jul 30 03:11:33 2012
From: matteo at umn.edu (Matteo Cococcioni)
Date: Sun, 29 Jul 2012 20:11:33 -0500
Subject: [Pw_forum] U calculation error
In-Reply-To: <CAP_5U0faBHn-_7JhoSWhbsD0U-FePKd1mxXaFo9wTU11sgqD6A@mail.gmail.com>
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Message-ID: <CAMZASgGaDy+cT=RYaxykMhv4foQhZNQ-wGMoZEXE74-iFgXviw@mail.gmail.com>

Dear Peng,

I'm not sure what the problem could be. sounds like a problem with the
memory of your computer.
I don't know what the line you report below is supposed to mean. NaN
usually comes out when the code tries to divide something by 0, or
things like that. try to track it in the source of the code and make
it print the quantities it uses to compute that output entry.
Have you tried to increase the max size of the matrices, or to
increase the threshold values within which the code assumes two
distances to be the same?

Matteo



On Sun, Jul 29, 2012 at 3:01 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
> Dear Dr. Matteo,
>
> Yes,  I ran the LSDA+U example successfully, the only difference is that the
> U of Ni converged to 6.0 not 5.0.
>
> For my calculation, if I use n1=n2=n3=2, the result is
> 208 NaN 6.899999999999315E-003 2.066666666665403E-003.
> If n1=n2=n3=3, the size of Umat.out will continue to increase > 2G. And I
> have to stop it before the space is used up.
>
> The  potential and wfcs are saved and I used ecutwfc=100 to make the scf
> energy converged to 0.001Ry. I can decrease it if that will help to get
> correct U.
>
> On Sun, Jul 29, 2012 at 1:17 PM, Matteo Cococcioni <matteo at umn.edu> wrote:
>>
>> Dear Peng,
>>
>> I advise you to run the example available from the QE webpage and try
>> to reproduce the same results.
>>
>> On Sun, Jul 29, 2012 at 12:00 PM, Peng Chen <pchen at ion.chem.utk.edu>
>> wrote:
>> > Dear Dr. Matteo,
>> >
>> > I compiled the code with the parameters in make.sys. The n1=n2=n3=1 case
>> > is
>> > done without error, but the results for Ni and O are negative which
>> > should
>> > not be correct.
>>
>>
>> ok then maybe you can try to increase them one per time and see at
>> what level the code stops with error?
>>
>>
>> > 26 -14.8678837915617 7.56505581785392 -0.681000339374195
>> > I plot dn.1.da.1.dat and dn0.1.da.1.dat, the data in dn0.1.da.1.dat are
>> > not
>> > linear.
>>
>>
>> this is not related to the error message of r.x but is not right. if
>> you want reliable results you have to get these plots linear.
>>
>>
>>
>> The scf calculation is converged to 0.001 Ry. So I am not sure what
>> > can cause the problem.
>>
>>
>> yes probably this is not enough. the inputs look fine (I haven't
>> looked inside the response matrix) but you have to make sure the scf
>> potential and wfc are saved after the unperturbed scf run and every
>> perturbed calculation starts from them.
>> do you really need 100 Ry cut off with US PP?
>>
>> Matteo
>>
>>
>> >
>> > I've attached the Umat_afm.1.out which may contain some useful
>> > information
>> > for you. I also put below the input for scf and perturbation on Ni
>> > (alpha=-0.15,-0.07,0.0,0.07,0.15). Same calculations are done for V and
>> > O as
>> > well with perturbed V or O atom translated to the origin of the unit
>> > cell.
>> >
>> >
>> > scf calculation input:
>> >
>> > &control
>> >     calculation='scf'
>> >     restart_mode='from_scratch',
>> >     prefix='nvoprim.afm.ucalc.Ni',
>> >     pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
>> >     outdir='/data/pchen/qe/'
>> >     wf_collect=.TRUE.
>> >  /
>> >  &system
>> >     ibrav=0, celldm(1)=11.19096,
>> >      nat=26, ntyp=6,
>> >   nspin = 2,  starting_magnetization(1)=0.6,
>> >     starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
>> >  starting_magnetization(4)=-0.5,
>> >  ecutwfc = 100, ecutrho = 800,
>> >  occupations ='smearing',
>> >     smearing ='mv',
>> >     degauss = 0.005,nbnd=135
>> >   lda_plus_u = .true.
>> >     Hubbard_U(1)= 1.d-20
>> >     Hubbard_U(2)= 1.d-20
>> >  Hubbard_U(3)= 1.d-20
>> >  Hubbard_U(4)= 1.d-20
>> >  Hubbard_U(5)= 1.d-20
>> >  Hubbard_U(6)= 1.d-20
>> >  /
>> >  &electrons
>> >     conv_thr = 1.0e-7
>> >     mixing_beta = 0.3
>> >  /
>> > CELL_PARAMETERS
>> > 0.5 0.96015 0
>> > 0.5 -0.96015 0
>> > 0 0   1.38889
>> > ATOMIC_SPECIES
>> >  Ni1 58.6934 Ni.pz-n-rrkjus.UPF
>> >  Ni2 58.6934 Ni.pz-n-rrkjus.UPF
>> >  Ni3 58.6934 Ni.pz-n-rrkjus.UPF
>> >  Ni4 58.6934 Ni.pz-n-rrkjus.UPF
>> >  V 50.9415 V.pz-spn-rrkjus.UPF
>> >  O  15.9994  O.pz-n-rrkjus.UPF
>> > ATOMIC_POSITIONS crystal
>> > Ni1      0.000000000   0.000000000   0.000000000
>> > Ni2      0.500000000   0.500000000   0.500000000
>> > Ni3      0.122863290   0.378190177   0.749934361
>> > Ni3      0.877136710   0.621809823   0.250065639
>> > Ni4      0.377137388   0.121809201   0.249932658
>> > Ni4      0.622862612   0.878190799   0.750067342
>> > V        0.373618754   0.623612138   0.115867980
>> > V        0.126381501   0.876388862   0.615868582
>> > V        0.626381246   0.376387862   0.884132020
>> > V        0.873618499   0.123611138   0.384131418
>> > O        0.241839036   0.756304999   0.223613779
>> > O        0.258160617   0.743693910   0.723611944
>> > O        0.758160964   0.243695001   0.776386221
>> > O        0.741839383   0.256306090   0.276388056
>> > O       -0.000998332   1.000227439   0.243205274
>> > O        0.500997862   0.499772508   0.743208489
>> > O        1.000998332  -0.000227439   0.756794726
>> > O        0.499002138   0.500227492   0.256791511
>> > O        0.381099639   0.150692971   0.006796703
>> > O        0.118898786   0.349304325   0.506798051
>> > O        0.149581603   0.378555571   0.991989919
>> > O        0.350419534   0.121445697   0.491991443
>> > O        0.618900361   0.849307029   0.993205297
>> > O        0.881101214   0.650695675   0.493203949
>> > O        0.850418397   0.621444429   0.008012081
>> > O        0.649580466   0.878554303   0.508010557
>> >
>> > K_POINTS (automatic)
>> >  5 5 5 1 1 1
>> >
>> > Perturbation on Ni with alpha=0.15 input:
>> >
>> > &control
>> >     calculation='scf'
>> >     restart_mode='from_scratch',
>> >     prefix='nvoprim.afm.ucalc.Ni',
>> >     pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
>> >     outdir='/data/pchen/qe/'
>> >    wf_collect=.TRUE.
>> >  /
>> >  &system
>> >     ibrav=0, celldm(1)=11.19096,
>> >      nat=26, ntyp=6,
>> >   nspin = 2,  starting_magnetization(1)=0.6,
>> >     starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
>> >  starting_magnetization(4)=-0.5,
>> >  ecutwfc = 100, ecutrho = 800,
>> >  occupations ='smearing',
>> >     smearing ='mv',
>> >     degauss = 0.005,nbnd=135
>> >   lda_plus_u = .true.
>> >     Hubbard_U(1)= 1.d-20
>> >     Hubbard_U(2)= 1.d-20
>> >     Hubbard_U(3)= 1.d-20
>> > Hubbard_U(4)= 1.d-20
>> > Hubbard_U(5)= 1.d-20
>> > Hubbard_U(6)= 1.d-20
>> >
>> >     Hubbard_alpha(1)= 0.15
>> >  /
>> >  &electrons
>> >     conv_thr = 1.0e-7
>> >     mixing_beta = 0.3
>> >   startingpot='file'
>> >  startingwfc='file'
>> >  diago_thr_init=5.09E-11,
>> >  /
>> > CELL_PARAMETERS
>> > 0.5 0.96015 0
>> > 0.5 -0.96015 0
>> > 0 0   1.38889
>> > ATOMIC_SPECIES
>> >  Ni1 58.6934 Ni.pz-n-rrkjus.UPF
>> >  Ni2 58.6934 Ni.pz-n-rrkjus.UPF
>> >  Ni3 58.6934 Ni.pz-n-rrkjus.UPF
>> >  Ni4 58.6934 Ni.pz-n-rrkjus.UPF
>> >  V 50.9415 V.pz-spn-rrkjus.UPF
>> >  O  15.9994  O.pz-n-rrkjus.UPF
>> > ATOMIC_POSITIONS crystal
>> > Ni1      0.000000000   0.000000000   0.000000000
>> > Ni2      0.500000000   0.500000000   0.500000000
>> > Ni3      0.122863290   0.378190177   0.749934361
>> > Ni3      0.877136710   0.621809823   0.250065639
>> > Ni4      0.377137388   0.121809201   0.249932658
>> > Ni4      0.622862612   0.878190799   0.750067342
>> > V        0.373618754   0.623612138   0.115867980
>> > V        0.126381501   0.876388862   0.615868582
>> > V        0.626381246   0.376387862   0.884132020
>> > V        0.873618499   0.123611138   0.384131418
>> > O        0.241839036   0.756304999   0.223613779
>> > O        0.258160617   0.743693910   0.723611944
>> > O        0.758160964   0.243695001   0.776386221
>> > O        0.741839383   0.256306090   0.276388056
>> > O       -0.000998332   1.000227439   0.243205274
>> > O        0.500997862   0.499772508   0.743208489
>> > O        1.000998332  -0.000227439   0.756794726
>> > O        0.499002138   0.500227492   0.256791511
>> > O        0.381099639   0.150692971   0.006796703
>> > O        0.118898786   0.349304325   0.506798051
>> > O        0.149581603   0.378555571   0.991989919
>> > O        0.350419534   0.121445697   0.491991443
>> > O        0.618900361   0.849307029   0.993205297
>> > O        0.881101214   0.650695675   0.493203949
>> > O        0.850418397   0.621444429   0.008012081
>> > O        0.649580466   0.878554303   0.508010557
>> >
>> > K_POINTS (automatic)
>> >  5 5 5 1 1 1
>> >
>> >
>> >
>> > On Sun, Jul 29, 2012 at 11:27 AM, Matteo Cococcioni <matteo at umn.edu>
>> > wrote:
>> >>
>> >> Dear Peng,
>> >>
>> >> I'm not very expert of compiling codes. You have to make sure that all
>> >> the libraries are linked correctly for the code to work. I assume you
>> >> have QE installed on the same computer. You could give a look in the
>> >> make.sys to check what is the correct way to link them. If everything
>> >> is consistent, then you have to find out where the code is failing.
>> >> have you tried to run with n1 = n2 = n3 = 1? what did you get?
>> >>
>> >> Matteo
>> >>
>> >>
>> >>
>> >> On Sat, Jul 28, 2012 at 9:10 PM, Peng Chen <pchen at ion.chem.utk.edu>
>> >> wrote:
>> >> > Dear Dr. Matteo,
>> >> >
>> >> > I used command listed below to compile resp_mat.f90. No error in
>> >> > compiling.
>> >> > I am not sure if I did right in choosing the libs.
>> >> > ifort  -o r.x resp_mat.f90
>> >> > -L"/data/apps/intel/11.1.072/mkl/lib/em64t"
>> >> > -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_mc3  -lmkl_sequential
>> >> > -lmkl_core
>> >> >
>> >> > The libs in mkl are shown below:
>> >> > libmkl_avx.so                   libmkl_intel_sp2dp.so
>> >> > libmkl_blacs_ilp64.a            libmkl_intel_thread.a
>> >> > libmkl_blacs_intelmpi_ilp64.a   libmkl_intel_thread.so
>> >> > libmkl_blacs_intelmpi_ilp64.so  libmkl_lapack95_ilp64.a
>> >> > libmkl_blacs_intelmpi_lp64.a    libmkl_lapack95_lp64.a
>> >> > libmkl_blacs_intelmpi_lp64.so   libmkl_lapack.so
>> >> > libmkl_blacs_lp64.a             libmkl_mc3.so
>> >> > libmkl_blacs_openmpi_ilp64.a    libmkl_mc.so
>> >> > libmkl_blacs_openmpi_lp64.a     libmkl_p4n.so
>> >> > libmkl_blacs_sgimpt_ilp64.a     libmkl_pgi_thread.a
>> >> > libmkl_blacs_sgimpt_lp64.a      libmkl_pgi_thread.so
>> >> > libmkl_blas95_ilp64.a           libmkl_scalapack_ilp64.a
>> >> > libmkl_blas95_lp64.a            libmkl_scalapack_ilp64.so
>> >> > libmkl_cdft_core.a              libmkl_scalapack_lp64.a
>> >> > libmkl_core.a                   libmkl_scalapack_lp64.so
>> >> > libmkl_core.so                  libmkl_sequential.a
>> >> > libmkl_def.so                   libmkl_sequential.so
>> >> > libmkl_gf_ilp64.a               libmkl_solver_ilp64.a
>> >> > libmkl_gf_ilp64.so              libmkl_solver_ilp64_sequential.a
>> >> > libmkl_gf_lp64.a                libmkl_solver_lp64.a
>> >> > libmkl_gf_lp64.so               libmkl_solver_lp64_sequential.a
>> >> > libmkl_gnu_thread.a             libmkl_vml_avx.so
>> >> > libmkl_gnu_thread.so            libmkl_vml_def.so
>> >> > libmkl_intel_ilp64.a            libmkl_vml_mc2.so
>> >> > libmkl_intel_ilp64.so           libmkl_vml_mc3.so
>> >> > libmkl_intel_lp64.a             libmkl_vml_mc.so
>> >> > libmkl_intel_lp64.so            libmkl_vml_p4n.so
>> >> > libmkl_intel_sp2dp.a            locale
>> >> >
>> >> >
>> >> > Some errors in output:
>> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> >> > Image              PC                Routine            Line
>> >> > Source
>> >> > r.x                0000000000445659  Unknown               Unknown
>> >> > Unknown
>> >> > r.x                000000000040A363  Unknown               Unknown
>> >> > Unknown
>> >> > r.x                000000000040338C  Unknown               Unknown
>> >> > Unknown
>> >> > libc.so.6          00002B85B9495994  Unknown               Unknown
>> >> > Unknown
>> >> > r.x                0000000000403289  Unknown               Unknown
>> >> > Unknown
>> >> >
>> >> >
>> >> > On Sat, Jul 28, 2012 at 10:38 AM, Matteo Cococcioni <matteo at umn.edu>
>> >> > wrote:
>> >> >>
>> >> >> Dear Peng,
>> >> >>
>> >> >> nothing looks wrong in your input. have you tried with n1, n2, n3
>> >> >> all
>> >> >> equal to 1? are you sure you compiled correctly?
>> >> >>
>> >> >> Matteo
>> >> >>
>> >> >>
>> >> >>
>> >> >> On Fri, Jul 27, 2012 at 11:46 PM, Peng Chen <pchen at ion.chem.utk.edu>
>> >> >> wrote:
>> >> >> > Dear Dr. Matteo,
>> >> >> >
>> >> >> > The primitive cell has 26 atoms with 3 different types. The pos
>> >> >> > and
>> >> >> > resp_mat.in files are shown below:
>> >> >> >
>> >> >> > 5.6087 10.79 0.0
>> >> >> > 5.6087 -10.79 0.0
>> >> >> > 0.0 0.0   15.570873
>> >> >> > 0       0       0       1
>> >> >> > 0.5     0.5     0.5     -1
>> >> >> > 0.12286329      0.378190177     0.749934361     1
>> >> >> > 0.87713671      0.621809823     0.250065639     1
>> >> >> > 0.377137388     0.121809201     0.249932658     -1
>> >> >> > 0.622862612     0.878190799     0.750067342     -1
>> >> >> > 0.373618754     0.623612138     0.11586798      0
>> >> >> > 0.126381501     0.876388862     0.615868582     0
>> >> >> > 0.626381246     0.376387862     0.88413202      0
>> >> >> > 0.873618499     0.123611138     0.384131418     0
>> >> >> > 0.241839036     0.756304999     0.223613779     0
>> >> >> > 0.258160617     0.74369391      0.723611944     0
>> >> >> > 0.758160964     0.243695001     0.776386221     0
>> >> >> > 0.741839383     0.25630609      0.276388056     0
>> >> >> > -0.000998332    1.000227439     0.243205274     0
>> >> >> > 0.500997862     0.499772508     0.743208489     0
>> >> >> > 1.000998332     -0.000227439    0.756794726     0
>> >> >> > 0.499002138     0.500227492     0.256791511     0
>> >> >> > 0.381099639     0.150692971     0.006796703     0
>> >> >> > 0.118898786     0.349304325     0.506798051     0
>> >> >> > 0.149581603     0.378555571     0.991989919     0
>> >> >> > 0.350419534     0.121445697     0.491991443     0
>> >> >> > 0.618900361     0.849307029     0.993205297     0
>> >> >> > 0.881101214     0.650695675     0.493203949     0
>> >> >> > 0.850418397     0.621444429     0.008012081     0
>> >> >> > 0.649580466     0.878554303     0.508010557     0
>> >> >> >
>> >> >> > resp_mat.in :
>> >> >> >  &input_mat
>> >> >> >    ntyp = 3
>> >> >> >    na(1) = 6
>> >> >> >    na(2) = 4
>> >> >> >    na(3) = 16
>> >> >> >    nalfa = 5
>> >> >> >    magn=.true.
>> >> >> >    filepos = 'pos'
>> >> >> >    back = 'no'
>> >> >> >    filednda = 'file_afm'
>> >> >> >    n1 = 2
>> >> >> >    n2 = 2
>> >> >> >    n3 = 2
>> >> >> >  &end
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni
>> >> >> > <matteo at umn.edu>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> Dear Peng,
>> >> >> >>
>> >> >> >> can you provide info about your system? maybe it is larger than
>> >> >> >> the
>> >> >> >> maximum size allowed by r.x?
>> >> >> >>
>> >> >> >> Matteo
>> >> >> >>
>> >> >> >> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen
>> >> >> >> <pchen at ion.chem.utk.edu>
>> >> >> >> wrote:
>> >> >> >> > Dear All,
>> >> >> >> >
>> >> >> >> > There are some errors when I run r.x to calculate the U. I used
>> >> >> >> > Espresso-5.0
>> >> >> >> > and follow the steps in LSDA+U example. I am not sure what
>> >> >> >> > could
>> >> >> >> > be
>> >> >> >> > wrong.
>> >> >> >> > And if you need other input/output, please let me know.
>> >> >> >> >
>> >> >> >> > Image              PC        Routine            Line
>> >> >> >> > Source
>> >> >> >> > r.x                0822DACC  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                0822C265  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                082071FA  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                081DDFDA  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                081FA33B  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                081F9C5C  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                0804E38F  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                0804824A  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                0823805D  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                08048131  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > forrtl: severe (8): internal consistency check failure, file
>> >> >> >> > ./src/libfor/for_wseq_lis.c, line 635
>> >> >> >> > Image              PC        Routine            Line
>> >> >> >> > Source
>> >> >> >> > r.x                0822DACC  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                0822C265  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                082071FA  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                081DD664  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                081F9AF7  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                0804E38F  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                0804824A  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                0823805D  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                08048131  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> >> >> >> > Image              PC        Routine            Line
>> >> >> >> > Source
>> >> >> >> > r.x                0804DAED  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                0804824A  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                0823805D  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                08048131  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> >> >> >> > Image              PC        Routine            Line
>> >> >> >> > Source
>> >> >> >> > r.x                08253657  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                081F4087  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                081DCDB7  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                081DF354  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                081DD672  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                081DF5E8  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > Unknown            FFFFE600  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                0804824A  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                0823805D  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> > r.x                08048131  Unknown               Unknown
>> >> >> >> > Unknown
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> >   Best Regards.
>> >> >> >> >         Peng
>> >> >> >> >
>> >> >> >> > _______________________________________________
>> >> >> >> > Pw_forum mailing list
>> >> >> >> > Pw_forum at pwscf.org
>> >> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >> >> >
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >> Matteo Cococcioni
>> >> >> >> Department of Chemical Engineering and Materials Science,
>> >> >> >> University of Minnesota
>> >> >> >> 421 Washington Av. SE
>> >> >> >> Minneapolis, MN 55455
>> >> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> >> >> >> _______________________________________________
>> >> >> >> Pw_forum mailing list
>> >> >> >> Pw_forum at pwscf.org
>> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> >   Best Regards.
>> >> >> >         Peng
>> >> >> >
>> >> >> > _______________________________________________
>> >> >> > Pw_forum mailing list
>> >> >> > Pw_forum at pwscf.org
>> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Matteo Cococcioni
>> >> >> Department of Chemical Engineering and Materials Science,
>> >> >> University of Minnesota
>> >> >> 421 Washington Av. SE
>> >> >> Minneapolis, MN 55455
>> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> >> >> _______________________________________________
>> >> >> Pw_forum mailing list
>> >> >> Pw_forum at pwscf.org
>> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >   Best Regards.
>> >> >         Peng
>> >> >
>> >> > _______________________________________________
>> >> > Pw_forum mailing list
>> >> > Pw_forum at pwscf.org
>> >> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Matteo Cococcioni
>> >> Department of Chemical Engineering and Materials Science,
>> >> University of Minnesota
>> >> 421 Washington Av. SE
>> >> Minneapolis, MN 55455
>> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> >> _______________________________________________
>> >> Pw_forum mailing list
>> >> Pw_forum at pwscf.org
>> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>> >
>> >
>> >
>> > --
>> >   Best Regards.
>> >         Peng
>> >
>> > _______________________________________________
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>>
>>
>>
>> --
>> Matteo Cococcioni
>> Department of Chemical Engineering and Materials Science,
>> University of Minnesota
>> 421 Washington Av. SE
>> Minneapolis, MN 55455
>> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
>   Best Regards.
>         Peng
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056    Fax +1 612 626 7246

From pchen at ion.chem.utk.edu  Mon Jul 30 03:52:01 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Sun, 29 Jul 2012 21:52:01 -0400
Subject: [Pw_forum] U calculation error
In-Reply-To: <CAMZASgGaDy+cT=RYaxykMhv4foQhZNQ-wGMoZEXE74-iFgXviw@mail.gmail.com>
References: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>
	<CAMZASgH3ZxSwGtXARSqN+khMe4CSttRRgTb81F3LX7GfKFtp6w@mail.gmail.com>
	<CAP_5U0fA-N8DhL1DYcbpLZ=hiG8T4EfmJXPqwuJXFvcG89gP-Q@mail.gmail.com>
	<CAMZASgFWbtt6oCCoUp5g=ah3ODVOrNth9dwmmf2p+0XauMKhrw@mail.gmail.com>
	<CAP_5U0cU4t-AYM7rhOwo8MhMEuwjKEq5NzMoteDsaCO6wPugsw@mail.gmail.com>
	<CAMZASgGFhiF15BgCwkWgE5ZQj9tMRYFopAsQOKX8pte6Vw-DEg@mail.gmail.com>
	<CAP_5U0fYafiTLd+sNKK1HE2TefOn8ZVZ9+urU6VcTTw2yQxmqQ@mail.gmail.com>
	<CAMZASgEoRBJRL1wSaWxAxAHOKvUw5Xci=3K4nVjP-YbyoEvuxQ@mail.gmail.com>
	<CAP_5U0faBHn-_7JhoSWhbsD0U-FePKd1mxXaFo9wTU11sgqD6A@mail.gmail.com>
	<CAMZASgGaDy+cT=RYaxykMhv4foQhZNQ-wGMoZEXE74-iFgXviw@mail.gmail.com>
Message-ID: <CAP_5U0dSxeb8HK-HZ9D7As4zVGaD4Ac_N_4JN_7+DSKVKcst9A@mail.gmail.com>

Dear Dr. Matteo,

 Do you mean to increase the size of vectors in the pos file?
5.6087 10.79 0.0
5.6087 -10.79 0.0
0.0 0.0   15.570873

I still can not obtain linear behavior of dn0.1.da.1.dat which should
related with scf and perturbation calculations. What's your suggestions on
this part?

File dn0.1.da.1.dat:

 -0.15   8.63607
  -0.07   8.59247
  0.0   8.56719
  0.07   8.52053
  0.15   8.46247



On Sun, Jul 29, 2012 at 9:11 PM, Matteo Cococcioni <matteo at umn.edu> wrote:

> Dear Peng,
>
> I'm not sure what the problem could be. sounds like a problem with the
> memory of your computer.
> I don't know what the line you report below is supposed to mean. NaN
> usually comes out when the code tries to divide something by 0, or
> things like that. try to track it in the source of the code and make
> it print the quantities it uses to compute that output entry.
> Have you tried to increase the max size of the matrices, or to
> increase the threshold values within which the code assumes two
> distances to be the same?
>
> Matteo
>
>
>
> On Sun, Jul 29, 2012 at 3:01 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
> > Dear Dr. Matteo,
> >
> > Yes,  I ran the LSDA+U example successfully, the only difference is that
> the
> > U of Ni converged to 6.0 not 5.0.
> >
> > For my calculation, if I use n1=n2=n3=2, the result is
> > 208 NaN 6.899999999999315E-003 2.066666666665403E-003.
> > If n1=n2=n3=3, the size of Umat.out will continue to increase > 2G. And I
> > have to stop it before the space is used up.
> >
> > The  potential and wfcs are saved and I used ecutwfc=100 to make the scf
> > energy converged to 0.001Ry. I can decrease it if that will help to get
> > correct U.
> >
> > On Sun, Jul 29, 2012 at 1:17 PM, Matteo Cococcioni <matteo at umn.edu>
> wrote:
> >>
> >> Dear Peng,
> >>
> >> I advise you to run the example available from the QE webpage and try
> >> to reproduce the same results.
> >>
> >> On Sun, Jul 29, 2012 at 12:00 PM, Peng Chen <pchen at ion.chem.utk.edu>
> >> wrote:
> >> > Dear Dr. Matteo,
> >> >
> >> > I compiled the code with the parameters in make.sys. The n1=n2=n3=1
> case
> >> > is
> >> > done without error, but the results for Ni and O are negative which
> >> > should
> >> > not be correct.
> >>
> >>
> >> ok then maybe you can try to increase them one per time and see at
> >> what level the code stops with error?
> >>
> >>
> >> > 26 -14.8678837915617 7.56505581785392 -0.681000339374195
> >> > I plot dn.1.da.1.dat and dn0.1.da.1.dat, the data in dn0.1.da.1.dat
> are
> >> > not
> >> > linear.
> >>
> >>
> >> this is not related to the error message of r.x but is not right. if
> >> you want reliable results you have to get these plots linear.
> >>
> >>
> >>
> >> The scf calculation is converged to 0.001 Ry. So I am not sure what
> >> > can cause the problem.
> >>
> >>
> >> yes probably this is not enough. the inputs look fine (I haven't
> >> looked inside the response matrix) but you have to make sure the scf
> >> potential and wfc are saved after the unperturbed scf run and every
> >> perturbed calculation starts from them.
> >> do you really need 100 Ry cut off with US PP?
> >>
> >> Matteo
> >>
> >>
> >> >
> >> > I've attached the Umat_afm.1.out which may contain some useful
> >> > information
> >> > for you. I also put below the input for scf and perturbation on Ni
> >> > (alpha=-0.15,-0.07,0.0,0.07,0.15). Same calculations are done for V
> and
> >> > O as
> >> > well with perturbed V or O atom translated to the origin of the unit
> >> > cell.
> >> >
> >> >
> >> > scf calculation input:
> >> >
> >> > &control
> >> >     calculation='scf'
> >> >     restart_mode='from_scratch',
> >> >     prefix='nvoprim.afm.ucalc.Ni',
> >> >     pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
> >> >     outdir='/data/pchen/qe/'
> >> >     wf_collect=.TRUE.
> >> >  /
> >> >  &system
> >> >     ibrav=0, celldm(1)=11.19096,
> >> >      nat=26, ntyp=6,
> >> >   nspin = 2,  starting_magnetization(1)=0.6,
> >> >     starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
> >> >  starting_magnetization(4)=-0.5,
> >> >  ecutwfc = 100, ecutrho = 800,
> >> >  occupations ='smearing',
> >> >     smearing ='mv',
> >> >     degauss = 0.005,nbnd=135
> >> >   lda_plus_u = .true.
> >> >     Hubbard_U(1)= 1.d-20
> >> >     Hubbard_U(2)= 1.d-20
> >> >  Hubbard_U(3)= 1.d-20
> >> >  Hubbard_U(4)= 1.d-20
> >> >  Hubbard_U(5)= 1.d-20
> >> >  Hubbard_U(6)= 1.d-20
> >> >  /
> >> >  &electrons
> >> >     conv_thr = 1.0e-7
> >> >     mixing_beta = 0.3
> >> >  /
> >> > CELL_PARAMETERS
> >> > 0.5 0.96015 0
> >> > 0.5 -0.96015 0
> >> > 0 0   1.38889
> >> > ATOMIC_SPECIES
> >> >  Ni1 58.6934 Ni.pz-n-rrkjus.UPF
> >> >  Ni2 58.6934 Ni.pz-n-rrkjus.UPF
> >> >  Ni3 58.6934 Ni.pz-n-rrkjus.UPF
> >> >  Ni4 58.6934 Ni.pz-n-rrkjus.UPF
> >> >  V 50.9415 V.pz-spn-rrkjus.UPF
> >> >  O  15.9994  O.pz-n-rrkjus.UPF
> >> > ATOMIC_POSITIONS crystal
> >> > Ni1      0.000000000   0.000000000   0.000000000
> >> > Ni2      0.500000000   0.500000000   0.500000000
> >> > Ni3      0.122863290   0.378190177   0.749934361
> >> > Ni3      0.877136710   0.621809823   0.250065639
> >> > Ni4      0.377137388   0.121809201   0.249932658
> >> > Ni4      0.622862612   0.878190799   0.750067342
> >> > V        0.373618754   0.623612138   0.115867980
> >> > V        0.126381501   0.876388862   0.615868582
> >> > V        0.626381246   0.376387862   0.884132020
> >> > V        0.873618499   0.123611138   0.384131418
> >> > O        0.241839036   0.756304999   0.223613779
> >> > O        0.258160617   0.743693910   0.723611944
> >> > O        0.758160964   0.243695001   0.776386221
> >> > O        0.741839383   0.256306090   0.276388056
> >> > O       -0.000998332   1.000227439   0.243205274
> >> > O        0.500997862   0.499772508   0.743208489
> >> > O        1.000998332  -0.000227439   0.756794726
> >> > O        0.499002138   0.500227492   0.256791511
> >> > O        0.381099639   0.150692971   0.006796703
> >> > O        0.118898786   0.349304325   0.506798051
> >> > O        0.149581603   0.378555571   0.991989919
> >> > O        0.350419534   0.121445697   0.491991443
> >> > O        0.618900361   0.849307029   0.993205297
> >> > O        0.881101214   0.650695675   0.493203949
> >> > O        0.850418397   0.621444429   0.008012081
> >> > O        0.649580466   0.878554303   0.508010557
> >> >
> >> > K_POINTS (automatic)
> >> >  5 5 5 1 1 1
> >> >
> >> > Perturbation on Ni with alpha=0.15 input:
> >> >
> >> > &control
> >> >     calculation='scf'
> >> >     restart_mode='from_scratch',
> >> >     prefix='nvoprim.afm.ucalc.Ni',
> >> >     pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
> >> >     outdir='/data/pchen/qe/'
> >> >    wf_collect=.TRUE.
> >> >  /
> >> >  &system
> >> >     ibrav=0, celldm(1)=11.19096,
> >> >      nat=26, ntyp=6,
> >> >   nspin = 2,  starting_magnetization(1)=0.6,
> >> >     starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
> >> >  starting_magnetization(4)=-0.5,
> >> >  ecutwfc = 100, ecutrho = 800,
> >> >  occupations ='smearing',
> >> >     smearing ='mv',
> >> >     degauss = 0.005,nbnd=135
> >> >   lda_plus_u = .true.
> >> >     Hubbard_U(1)= 1.d-20
> >> >     Hubbard_U(2)= 1.d-20
> >> >     Hubbard_U(3)= 1.d-20
> >> > Hubbard_U(4)= 1.d-20
> >> > Hubbard_U(5)= 1.d-20
> >> > Hubbard_U(6)= 1.d-20
> >> >
> >> >     Hubbard_alpha(1)= 0.15
> >> >  /
> >> >  &electrons
> >> >     conv_thr = 1.0e-7
> >> >     mixing_beta = 0.3
> >> >   startingpot='file'
> >> >  startingwfc='file'
> >> >  diago_thr_init=5.09E-11,
> >> >  /
> >> > CELL_PARAMETERS
> >> > 0.5 0.96015 0
> >> > 0.5 -0.96015 0
> >> > 0 0   1.38889
> >> > ATOMIC_SPECIES
> >> >  Ni1 58.6934 Ni.pz-n-rrkjus.UPF
> >> >  Ni2 58.6934 Ni.pz-n-rrkjus.UPF
> >> >  Ni3 58.6934 Ni.pz-n-rrkjus.UPF
> >> >  Ni4 58.6934 Ni.pz-n-rrkjus.UPF
> >> >  V 50.9415 V.pz-spn-rrkjus.UPF
> >> >  O  15.9994  O.pz-n-rrkjus.UPF
> >> > ATOMIC_POSITIONS crystal
> >> > Ni1      0.000000000   0.000000000   0.000000000
> >> > Ni2      0.500000000   0.500000000   0.500000000
> >> > Ni3      0.122863290   0.378190177   0.749934361
> >> > Ni3      0.877136710   0.621809823   0.250065639
> >> > Ni4      0.377137388   0.121809201   0.249932658
> >> > Ni4      0.622862612   0.878190799   0.750067342
> >> > V        0.373618754   0.623612138   0.115867980
> >> > V        0.126381501   0.876388862   0.615868582
> >> > V        0.626381246   0.376387862   0.884132020
> >> > V        0.873618499   0.123611138   0.384131418
> >> > O        0.241839036   0.756304999   0.223613779
> >> > O        0.258160617   0.743693910   0.723611944
> >> > O        0.758160964   0.243695001   0.776386221
> >> > O        0.741839383   0.256306090   0.276388056
> >> > O       -0.000998332   1.000227439   0.243205274
> >> > O        0.500997862   0.499772508   0.743208489
> >> > O        1.000998332  -0.000227439   0.756794726
> >> > O        0.499002138   0.500227492   0.256791511
> >> > O        0.381099639   0.150692971   0.006796703
> >> > O        0.118898786   0.349304325   0.506798051
> >> > O        0.149581603   0.378555571   0.991989919
> >> > O        0.350419534   0.121445697   0.491991443
> >> > O        0.618900361   0.849307029   0.993205297
> >> > O        0.881101214   0.650695675   0.493203949
> >> > O        0.850418397   0.621444429   0.008012081
> >> > O        0.649580466   0.878554303   0.508010557
> >> >
> >> > K_POINTS (automatic)
> >> >  5 5 5 1 1 1
> >> >
> >> >
> >> >
> >> > On Sun, Jul 29, 2012 at 11:27 AM, Matteo Cococcioni <matteo at umn.edu>
> >> > wrote:
> >> >>
> >> >> Dear Peng,
> >> >>
> >> >> I'm not very expert of compiling codes. You have to make sure that
> all
> >> >> the libraries are linked correctly for the code to work. I assume you
> >> >> have QE installed on the same computer. You could give a look in the
> >> >> make.sys to check what is the correct way to link them. If everything
> >> >> is consistent, then you have to find out where the code is failing.
> >> >> have you tried to run with n1 = n2 = n3 = 1? what did you get?
> >> >>
> >> >> Matteo
> >> >>
> >> >>
> >> >>
> >> >> On Sat, Jul 28, 2012 at 9:10 PM, Peng Chen <pchen at ion.chem.utk.edu>
> >> >> wrote:
> >> >> > Dear Dr. Matteo,
> >> >> >
> >> >> > I used command listed below to compile resp_mat.f90. No error in
> >> >> > compiling.
> >> >> > I am not sure if I did right in choosing the libs.
> >> >> > ifort  -o r.x resp_mat.f90
> >> >> > -L"/data/apps/intel/11.1.072/mkl/lib/em64t"
> >> >> > -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_mc3  -lmkl_sequential
> >> >> > -lmkl_core
> >> >> >
> >> >> > The libs in mkl are shown below:
> >> >> > libmkl_avx.so                   libmkl_intel_sp2dp.so
> >> >> > libmkl_blacs_ilp64.a            libmkl_intel_thread.a
> >> >> > libmkl_blacs_intelmpi_ilp64.a   libmkl_intel_thread.so
> >> >> > libmkl_blacs_intelmpi_ilp64.so  libmkl_lapack95_ilp64.a
> >> >> > libmkl_blacs_intelmpi_lp64.a    libmkl_lapack95_lp64.a
> >> >> > libmkl_blacs_intelmpi_lp64.so   libmkl_lapack.so
> >> >> > libmkl_blacs_lp64.a             libmkl_mc3.so
> >> >> > libmkl_blacs_openmpi_ilp64.a    libmkl_mc.so
> >> >> > libmkl_blacs_openmpi_lp64.a     libmkl_p4n.so
> >> >> > libmkl_blacs_sgimpt_ilp64.a     libmkl_pgi_thread.a
> >> >> > libmkl_blacs_sgimpt_lp64.a      libmkl_pgi_thread.so
> >> >> > libmkl_blas95_ilp64.a           libmkl_scalapack_ilp64.a
> >> >> > libmkl_blas95_lp64.a            libmkl_scalapack_ilp64.so
> >> >> > libmkl_cdft_core.a              libmkl_scalapack_lp64.a
> >> >> > libmkl_core.a                   libmkl_scalapack_lp64.so
> >> >> > libmkl_core.so                  libmkl_sequential.a
> >> >> > libmkl_def.so                   libmkl_sequential.so
> >> >> > libmkl_gf_ilp64.a               libmkl_solver_ilp64.a
> >> >> > libmkl_gf_ilp64.so              libmkl_solver_ilp64_sequential.a
> >> >> > libmkl_gf_lp64.a                libmkl_solver_lp64.a
> >> >> > libmkl_gf_lp64.so               libmkl_solver_lp64_sequential.a
> >> >> > libmkl_gnu_thread.a             libmkl_vml_avx.so
> >> >> > libmkl_gnu_thread.so            libmkl_vml_def.so
> >> >> > libmkl_intel_ilp64.a            libmkl_vml_mc2.so
> >> >> > libmkl_intel_ilp64.so           libmkl_vml_mc3.so
> >> >> > libmkl_intel_lp64.a             libmkl_vml_mc.so
> >> >> > libmkl_intel_lp64.so            libmkl_vml_p4n.so
> >> >> > libmkl_intel_sp2dp.a            locale
> >> >> >
> >> >> >
> >> >> > Some errors in output:
> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> >> > Image              PC                Routine            Line
> >> >> > Source
> >> >> > r.x                0000000000445659  Unknown               Unknown
> >> >> > Unknown
> >> >> > r.x                000000000040A363  Unknown               Unknown
> >> >> > Unknown
> >> >> > r.x                000000000040338C  Unknown               Unknown
> >> >> > Unknown
> >> >> > libc.so.6          00002B85B9495994  Unknown               Unknown
> >> >> > Unknown
> >> >> > r.x                0000000000403289  Unknown               Unknown
> >> >> > Unknown
> >> >> >
> >> >> >
> >> >> > On Sat, Jul 28, 2012 at 10:38 AM, Matteo Cococcioni <
> matteo at umn.edu>
> >> >> > wrote:
> >> >> >>
> >> >> >> Dear Peng,
> >> >> >>
> >> >> >> nothing looks wrong in your input. have you tried with n1, n2, n3
> >> >> >> all
> >> >> >> equal to 1? are you sure you compiled correctly?
> >> >> >>
> >> >> >> Matteo
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> On Fri, Jul 27, 2012 at 11:46 PM, Peng Chen <
> pchen at ion.chem.utk.edu>
> >> >> >> wrote:
> >> >> >> > Dear Dr. Matteo,
> >> >> >> >
> >> >> >> > The primitive cell has 26 atoms with 3 different types. The pos
> >> >> >> > and
> >> >> >> > resp_mat.in files are shown below:
> >> >> >> >
> >> >> >> > 5.6087 10.79 0.0
> >> >> >> > 5.6087 -10.79 0.0
> >> >> >> > 0.0 0.0   15.570873
> >> >> >> > 0       0       0       1
> >> >> >> > 0.5     0.5     0.5     -1
> >> >> >> > 0.12286329      0.378190177     0.749934361     1
> >> >> >> > 0.87713671      0.621809823     0.250065639     1
> >> >> >> > 0.377137388     0.121809201     0.249932658     -1
> >> >> >> > 0.622862612     0.878190799     0.750067342     -1
> >> >> >> > 0.373618754     0.623612138     0.11586798      0
> >> >> >> > 0.126381501     0.876388862     0.615868582     0
> >> >> >> > 0.626381246     0.376387862     0.88413202      0
> >> >> >> > 0.873618499     0.123611138     0.384131418     0
> >> >> >> > 0.241839036     0.756304999     0.223613779     0
> >> >> >> > 0.258160617     0.74369391      0.723611944     0
> >> >> >> > 0.758160964     0.243695001     0.776386221     0
> >> >> >> > 0.741839383     0.25630609      0.276388056     0
> >> >> >> > -0.000998332    1.000227439     0.243205274     0
> >> >> >> > 0.500997862     0.499772508     0.743208489     0
> >> >> >> > 1.000998332     -0.000227439    0.756794726     0
> >> >> >> > 0.499002138     0.500227492     0.256791511     0
> >> >> >> > 0.381099639     0.150692971     0.006796703     0
> >> >> >> > 0.118898786     0.349304325     0.506798051     0
> >> >> >> > 0.149581603     0.378555571     0.991989919     0
> >> >> >> > 0.350419534     0.121445697     0.491991443     0
> >> >> >> > 0.618900361     0.849307029     0.993205297     0
> >> >> >> > 0.881101214     0.650695675     0.493203949     0
> >> >> >> > 0.850418397     0.621444429     0.008012081     0
> >> >> >> > 0.649580466     0.878554303     0.508010557     0
> >> >> >> >
> >> >> >> > resp_mat.in :
> >> >> >> >  &input_mat
> >> >> >> >    ntyp = 3
> >> >> >> >    na(1) = 6
> >> >> >> >    na(2) = 4
> >> >> >> >    na(3) = 16
> >> >> >> >    nalfa = 5
> >> >> >> >    magn=.true.
> >> >> >> >    filepos = 'pos'
> >> >> >> >    back = 'no'
> >> >> >> >    filednda = 'file_afm'
> >> >> >> >    n1 = 2
> >> >> >> >    n2 = 2
> >> >> >> >    n3 = 2
> >> >> >> >  &end
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni
> >> >> >> > <matteo at umn.edu>
> >> >> >> > wrote:
> >> >> >> >>
> >> >> >> >> Dear Peng,
> >> >> >> >>
> >> >> >> >> can you provide info about your system? maybe it is larger than
> >> >> >> >> the
> >> >> >> >> maximum size allowed by r.x?
> >> >> >> >>
> >> >> >> >> Matteo
> >> >> >> >>
> >> >> >> >> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen
> >> >> >> >> <pchen at ion.chem.utk.edu>
> >> >> >> >> wrote:
> >> >> >> >> > Dear All,
> >> >> >> >> >
> >> >> >> >> > There are some errors when I run r.x to calculate the U. I
> used
> >> >> >> >> > Espresso-5.0
> >> >> >> >> > and follow the steps in LSDA+U example. I am not sure what
> >> >> >> >> > could
> >> >> >> >> > be
> >> >> >> >> > wrong.
> >> >> >> >> > And if you need other input/output, please let me know.
> >> >> >> >> >
> >> >> >> >> > Image              PC        Routine            Line
> >> >> >> >> > Source
> >> >> >> >> > r.x                0822DACC  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                0822C265  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                082071FA  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                081DDFDA  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                081FA33B  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                081F9C5C  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                0804E38F  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                0804824A  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                0823805D  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                08048131  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > forrtl: severe (8): internal consistency check failure, file
> >> >> >> >> > ./src/libfor/for_wseq_lis.c, line 635
> >> >> >> >> > Image              PC        Routine            Line
> >> >> >> >> > Source
> >> >> >> >> > r.x                0822DACC  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                0822C265  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                082071FA  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                081DD664  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                081F9AF7  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                0804E38F  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                0804824A  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                0823805D  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                08048131  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> >> >> >> > Image              PC        Routine            Line
> >> >> >> >> > Source
> >> >> >> >> > r.x                0804DAED  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                0804824A  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                0823805D  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                08048131  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> >> >> >> > Image              PC        Routine            Line
> >> >> >> >> > Source
> >> >> >> >> > r.x                08253657  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                081F4087  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                081DCDB7  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                081DF354  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                081DD672  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                081DF5E8  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > Unknown            FFFFE600  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                0804824A  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                0823805D  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> > r.x                08048131  Unknown               Unknown
> >> >> >> >> > Unknown
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> > --
> >> >> >> >> >   Best Regards.
> >> >> >> >> >         Peng
> >> >> >> >> >
> >> >> >> >> > _______________________________________________
> >> >> >> >> > Pw_forum mailing list
> >> >> >> >> > Pw_forum at pwscf.org
> >> >> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >> >> >
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> Matteo Cococcioni
> >> >> >> >> Department of Chemical Engineering and Materials Science,
> >> >> >> >> University of Minnesota
> >> >> >> >> 421 Washington Av. SE
> >> >> >> >> Minneapolis, MN 55455
> >> >> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> >> >> >> _______________________________________________
> >> >> >> >> Pw_forum mailing list
> >> >> >> >> Pw_forum at pwscf.org
> >> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > --
> >> >> >> >   Best Regards.
> >> >> >> >         Peng
> >> >> >> >
> >> >> >> > _______________________________________________
> >> >> >> > Pw_forum mailing list
> >> >> >> > Pw_forum at pwscf.org
> >> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Matteo Cococcioni
> >> >> >> Department of Chemical Engineering and Materials Science,
> >> >> >> University of Minnesota
> >> >> >> 421 Washington Av. SE
> >> >> >> Minneapolis, MN 55455
> >> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> >> >> _______________________________________________
> >> >> >> Pw_forum mailing list
> >> >> >> Pw_forum at pwscf.org
> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> >   Best Regards.
> >> >> >         Peng
> >> >> >
> >> >> > _______________________________________________
> >> >> > Pw_forum mailing list
> >> >> > Pw_forum at pwscf.org
> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Matteo Cococcioni
> >> >> Department of Chemical Engineering and Materials Science,
> >> >> University of Minnesota
> >> >> 421 Washington Av. SE
> >> >> Minneapolis, MN 55455
> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> >> _______________________________________________
> >> >> Pw_forum mailing list
> >> >> Pw_forum at pwscf.org
> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> >   Best Regards.
> >> >         Peng
> >> >
> >> > _______________________________________________
> >> > Pw_forum mailing list
> >> > Pw_forum at pwscf.org
> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >
> >>
> >>
> >>
> >> --
> >> Matteo Cococcioni
> >> Department of Chemical Engineering and Materials Science,
> >> University of Minnesota
> >> 421 Washington Av. SE
> >> Minneapolis, MN 55455
> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> >   Best Regards.
> >         Peng
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Matteo Cococcioni
> Department of Chemical Engineering and Materials Science,
> University of Minnesota
> 421 Washington Av. SE
> Minneapolis, MN 55455
> Tel. +1 612 624 9056    Fax +1 612 626 7246
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
  Best Regards.
        Peng
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From magerode at gmail.com  Mon Jul 30 11:27:17 2012
From: magerode at gmail.com (DENIS MAGERO)
Date: Mon, 30 Jul 2012 12:27:17 +0300
Subject: [Pw_forum] Error in QHA calculations
Message-ID: <CAEmqt8XQoToDYKGiQYSovhZDsc=yzGjkLRysd4OONfX_Zo9s7w@mail.gmail.com>

Dear all,
I,m calculating thermodynamic properties using QHA for magnesium hydride.
There is however a value of NaN for values of entropy and F_vibration.
Could someone please help.

Attached is the file.

# Zero vibration energy:      0.0053709107  (Ry/cell)
# Phonon DOS norm      :      1.998766      ! 3N for check purpose, N
number of atoms in the unit cell
# T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N
modes), S in k_B
#
#   T         E_internal        F_vibration          Specific heat
(C_v)       Entropy
############################################################################################################
    5.00      0.0053761511               NaN
0.0024038079                   NaN
   10.00      0.0053762656               NaN
0.0048307667                   NaN
   15.00      0.0053764576               NaN
0.0073049072                   NaN
   20.00      0.0053767292               NaN
0.0098829693                   NaN
   25.00      0.0053770872               NaN
0.0128304742                   NaN
   30.00      0.0053775527               NaN
0.0168191020                   NaN
   35.00      0.0053781734               NaN
0.0227957550                   NaN
   40.00      0.0053790267               NaN
0.0316241179                   NaN
   45.00      0.0053802120               NaN
0.0438189128                   NaN
   50.00      0.0053818386               NaN
0.0594854231                   NaN
   55.00      0.0053840137               NaN
0.0783989719                   NaN
   60.00      0.0053868337               NaN
0.1001298120                   NaN
   65.00      0.0053903795               NaN
0.1241557017                   NaN
   70.00      0.0053947154               NaN
0.1499421117                   NaN
   75.00      0.0053998891               NaN
0.1769907068                   NaN
   80.00      0.0054059335               NaN
0.2048639362                   NaN
   85.00      0.0054128686               NaN
0.2331939897                   NaN
   90.00      0.0054207041               NaN
0.2616824973                   NaN
   95.00      0.0054294410               NaN
0.2900952630                   NaN
  100.00      0.0054390741               NaN
0.3182546901                   NaN


-- 
Dennis Magero,
M.Sc Student,
Computational group,
Chepkoilel University College, ELDORET
KENYA.
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From lorenzo.paulatto at impmc.upmc.fr  Mon Jul 30 11:39:34 2012
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Mon, 30 Jul 2012 11:39:34 +0200
Subject: [Pw_forum] Error while compiling Quantum Espresso
In-Reply-To: <1343568795.22962.YahooMailClassic@web121402.mail.ne1.yahoo.com>
References: <1343568795.22962.YahooMailClassic@web121402.mail.ne1.yahoo.com>
Message-ID: <CAG+GtJeCA3VJF+6=w=+1Ghj_uKt0Boiyyqm+ohMi26k5oZcD_A@mail.gmail.com>

On 29 July 2012 15:33, zafar rasheed <zafartariq2003 at yahoo.com> wrote:

>
> Dear Lorenzo Paulatto
> Thanks for your kind reply. Unfortunately make.system file not
> created...........
> but information appear at screen during comilation , configure.log and
> make.sys.in file are attached here.
>
> best regards
>
>
No file attached here..
btw, make.sys.in  is the same for everyone, so no need to attach it.

-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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From bfazi90 at gmail.com  Mon Jul 30 14:02:01 2012
From: bfazi90 at gmail.com (bf azi)
Date: Mon, 30 Jul 2012 16:32:01 +0430
Subject: [Pw_forum] LDA contribution
Message-ID: <CAC+sowKr9=GdKTLgiQYcxmN_3M+5nXHNYKkJ4vEyp0BaRLXzzw@mail.gmail.com>

Dear all

when I set "sla+pw+rw86" for input_dft,(input_dft="sla+pw+rw86") ,
this error appeared:

from set_dft_from_name : error
revPW86 already contains LDA contribution

What am I doing?

Thanks a lot

Bani Adam
Faculty of Science
Egypt

From akohlmey at gmail.com  Mon Jul 30 14:07:33 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Mon, 30 Jul 2012 14:07:33 +0200
Subject: [Pw_forum] LDA contribution
In-Reply-To: <CAC+sowKr9=GdKTLgiQYcxmN_3M+5nXHNYKkJ4vEyp0BaRLXzzw@mail.gmail.com>
References: <CAC+sowKr9=GdKTLgiQYcxmN_3M+5nXHNYKkJ4vEyp0BaRLXzzw@mail.gmail.com>
Message-ID: <CADTmJ6E9ZiHPZ5BNTXf+Uhx_Xgd4x--qvouPBWzm+eLhXu4m+A@mail.gmail.com>

On Mon, Jul 30, 2012 at 2:02 PM, bf azi <bfazi90 at gmail.com> wrote:
> Dear all
>
> when I set "sla+pw+rw86" for input_dft,(input_dft="sla+pw+rw86") ,
> this error appeared:
>
> from set_dft_from_name : error
> revPW86 already contains LDA contribution
>
> What am I doing?

too much?  ;)

axel.

>
> Thanks a lot
>
> Bani Adam
> Faculty of Science
> Egypt
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



-- 
Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

From pandey.bramha at gmail.com  Mon Jul 30 15:04:46 2012
From: pandey.bramha at gmail.com (bramha pandey)
Date: Mon, 30 Jul 2012 18:34:46 +0530
Subject: [Pw_forum] Error in QHA calculations
In-Reply-To: <CAEmqt8XQoToDYKGiQYSovhZDsc=yzGjkLRysd4OONfX_Zo9s7w@mail.gmail.com>
References: <CAEmqt8XQoToDYKGiQYSovhZDsc=yzGjkLRysd4OONfX_Zo9s7w@mail.gmail.com>
Message-ID: <CAC2dNGE_9vfdBEZ0XyAS=Bj0GA+gyK-XbqTujXimNU5RO+2E3Q@mail.gmail.com>

Dear Denis,
Firstly you have to check your Phonon dos norm is coming correct or not???
I think there is a problem calculating with phonon frequency(Omega).
Here i am giving you a reference from where you can get the important clue.

""""First-principles calculations of phonon and thermodynamic properties
of AlRE (RE= Y, Gd, Pr, Yb) intermetallic compounds ?
Rui Wang? Shaofeng Wang, and Xiaozhi Wu""""""
,



Department of Physics and Institute for Structure and Function, Chongqing
University,
Chongqing 400044, P. R. China.


On Mon, Jul 30, 2012 at 2:57 PM, DENIS MAGERO <magerode at gmail.com> wrote:

> Dear all,
> I,m calculating thermodynamic properties using QHA for magnesium hydride.
> There is however a value of NaN for values of entropy and F_vibration.
> Could someone please help.
>
> Attached is the file.
>
> # Zero vibration energy:      0.0053709107  (Ry/cell)
> # Phonon DOS norm      :      1.998766      ! 3N for check purpose, N
> number of atoms in the unit cell
> # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N
> modes), S in k_B
> #
> #   T         E_internal        F_vibration          Specific heat
> (C_v)       Entropy
>
> ############################################################################################################
>     5.00      0.0053761511               NaN
> 0.0024038079                   NaN
>    10.00      0.0053762656               NaN
> 0.0048307667                   NaN
>    15.00      0.0053764576               NaN
> 0.0073049072                   NaN
>    20.00      0.0053767292               NaN
> 0.0098829693                   NaN
>    25.00      0.0053770872               NaN
> 0.0128304742                   NaN
>    30.00      0.0053775527               NaN
> 0.0168191020                   NaN
>    35.00      0.0053781734               NaN
> 0.0227957550                   NaN
>    40.00      0.0053790267               NaN
> 0.0316241179                   NaN
>    45.00      0.0053802120               NaN
> 0.0438189128                   NaN
>    50.00      0.0053818386               NaN
> 0.0594854231                   NaN
>    55.00      0.0053840137               NaN
> 0.0783989719                   NaN
>    60.00      0.0053868337               NaN
> 0.1001298120                   NaN
>    65.00      0.0053903795               NaN
> 0.1241557017                   NaN
>    70.00      0.0053947154               NaN
> 0.1499421117                   NaN
>    75.00      0.0053998891               NaN
> 0.1769907068                   NaN
>    80.00      0.0054059335               NaN
> 0.2048639362                   NaN
>    85.00      0.0054128686               NaN
> 0.2331939897                   NaN
>    90.00      0.0054207041               NaN
> 0.2616824973                   NaN
>    95.00      0.0054294410               NaN
> 0.2900952630                   NaN
>   100.00      0.0054390741               NaN
> 0.3182546901                   NaN
>
>
> --
> Dennis Magero,
> M.Sc Student,
> Computational group,
> Chepkoilel University College, ELDORET
> KENYA.
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Thanks and Regards
Bramha Prasad Pandey
Ph.D Student Indian School of Mines(ISM)
Dhanbad, INDIA.
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From amirhosseinba67 at gmail.com  Mon Jul 30 15:10:07 2012
From: amirhosseinba67 at gmail.com (Amir hosseini)
Date: Mon, 30 Jul 2012 17:40:07 +0430
Subject: [Pw_forum] BAD TERMINATION
Message-ID: <CABGPTx0zSC5ZMxqe-5QaZ6PvFTfpsgP_+f5gVMhe1n1Ujj8RsQ@mail.gmail.com>

Dear all

When I performe "pwcond.x" run is stopped and this error appear in cond.out

=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 9
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=====================================================================================
APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)

Help me please
Thanks

From pandey.bramha at gmail.com  Mon Jul 30 15:12:22 2012
From: pandey.bramha at gmail.com (bramha pandey)
Date: Mon, 30 Jul 2012 18:42:22 +0530
Subject: [Pw_forum] Running QHA calculations for orthorhombic structure
In-Reply-To: <CAKjMXpZczycidY=TwyLZ9LK5xpz2jG4D5-+dx2ygdm9o68VS0Q@mail.gmail.com>
References: <CAKjMXpZczycidY=TwyLZ9LK5xpz2jG4D5-+dx2ygdm9o68VS0Q@mail.gmail.com>
Message-ID: <CAC2dNGEtf_nJrD5nFbSsop00XHqaqqsJ1MVBbD0QM3MSyuCzPg@mail.gmail.com>

On Sun, Jul 29, 2012 at 5:02 PM, Kondaiah Samudrala <konda.physics at gmail.com
> wrote:

> Dear all,
>
> I am working on base centered orthorhombic structure with space group 64.
> I run complete phonon dispersion for this compound, but i want to calculate
> thermodynamic quantities such as specific heat, thermal expansion for this
> compound. Whether it is possible to calculate these things using QHA for
> base centered orthorhombic structure in pwscf???
>
Dear Samudrala,
if you are able to calculate the PHDOS for this structure, then in QHA
approximation you can easily able to calculate all the thermodynamical
properties.


>
>
> with regards
> S.Appalakondaiah
> Research scholar
> HCU
> Hyd-500046
> India
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Thanks and Regards
Bramha Prasad Pandey
Ph.D Student Indian School of Mines(ISM)
Dhanbad, INDIA.
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From ttduyle at gmail.com  Mon Jul 30 15:28:52 2012
From: ttduyle at gmail.com (Duy Le)
Date: Mon, 30 Jul 2012 09:28:52 -0400
Subject: [Pw_forum] BAD TERMINATION
In-Reply-To: <CABGPTx0zSC5ZMxqe-5QaZ6PvFTfpsgP_+f5gVMhe1n1Ujj8RsQ@mail.gmail.com>
References: <CABGPTx0zSC5ZMxqe-5QaZ6PvFTfpsgP_+f5gVMhe1n1Ujj8RsQ@mail.gmail.com>
Message-ID: <CAF-j6z8MSVqCwFczcr4TeBBPkuzPzKB8Xx_dYc-ZCFacAL9Kmg@mail.gmail.com>

This should not be pwscf-related. It is from your mpi application.
----------------------------------------------------
Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Mon, Jul 30, 2012 at 9:10 AM, Amir hosseini
<amirhosseinba67 at gmail.com> wrote:
> BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

From matteo at umn.edu  Mon Jul 30 16:20:28 2012
From: matteo at umn.edu (Matteo Cococcioni)
Date: Mon, 30 Jul 2012 09:20:28 -0500
Subject: [Pw_forum] U calculation error
In-Reply-To: <CAP_5U0dSxeb8HK-HZ9D7As4zVGaD4Ac_N_4JN_7+DSKVKcst9A@mail.gmail.com>
References: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>
	<CAMZASgH3ZxSwGtXARSqN+khMe4CSttRRgTb81F3LX7GfKFtp6w@mail.gmail.com>
	<CAP_5U0fA-N8DhL1DYcbpLZ=hiG8T4EfmJXPqwuJXFvcG89gP-Q@mail.gmail.com>
	<CAMZASgFWbtt6oCCoUp5g=ah3ODVOrNth9dwmmf2p+0XauMKhrw@mail.gmail.com>
	<CAP_5U0cU4t-AYM7rhOwo8MhMEuwjKEq5NzMoteDsaCO6wPugsw@mail.gmail.com>
	<CAMZASgGFhiF15BgCwkWgE5ZQj9tMRYFopAsQOKX8pte6Vw-DEg@mail.gmail.com>
	<CAP_5U0fYafiTLd+sNKK1HE2TefOn8ZVZ9+urU6VcTTw2yQxmqQ@mail.gmail.com>
	<CAMZASgEoRBJRL1wSaWxAxAHOKvUw5Xci=3K4nVjP-YbyoEvuxQ@mail.gmail.com>
	<CAP_5U0faBHn-_7JhoSWhbsD0U-FePKd1mxXaFo9wTU11sgqD6A@mail.gmail.com>
	<CAMZASgGaDy+cT=RYaxykMhv4foQhZNQ-wGMoZEXE74-iFgXviw@mail.gmail.com>
	<CAP_5U0dSxeb8HK-HZ9D7As4zVGaD4Ac_N_4JN_7+DSKVKcst9A@mail.gmail.com>
Message-ID: <CAMZASgFB81Jv+Si9zh4th1fr7DcpkvktD=1vD=tdN2x0EmtoEg@mail.gmail.com>

Dear Peng,

On Sun, Jul 29, 2012 at 8:52 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
> Dear Dr. Matteo,
>
>  Do you mean to increase the size of vectors in the pos file?
> 5.6087 10.79 0.0
> 5.6087 -10.79 0.0
> 0.0 0.0   15.570873
>


no, I meant to increase the dimension of the matrices in the code r.x.


> I still can not obtain linear behavior of dn0.1.da.1.dat which should
> related with scf and perturbation calculations. What's your suggestions on
> this part?
>
> File dn0.1.da.1.dat:
>
>  -0.15   8.63607
>   -0.07   8.59247
>   0.0   8.56719
>   0.07   8.52053
>   0.15   8.46247
>


I'm not sure what to suggest. are you sure the first iteration was
sufficiently converged? is your system a metal to start with?

Matteo



>
>
> On Sun, Jul 29, 2012 at 9:11 PM, Matteo Cococcioni <matteo at umn.edu> wrote:
>>
>> Dear Peng,
>>
>> I'm not sure what the problem could be. sounds like a problem with the
>> memory of your computer.
>> I don't know what the line you report below is supposed to mean. NaN
>> usually comes out when the code tries to divide something by 0, or
>> things like that. try to track it in the source of the code and make
>> it print the quantities it uses to compute that output entry.
>> Have you tried to increase the max size of the matrices, or to
>> increase the threshold values within which the code assumes two
>> distances to be the same?
>>
>> Matteo
>>
>>
>>
>> On Sun, Jul 29, 2012 at 3:01 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
>> > Dear Dr. Matteo,
>> >
>> > Yes,  I ran the LSDA+U example successfully, the only difference is that
>> > the
>> > U of Ni converged to 6.0 not 5.0.
>> >
>> > For my calculation, if I use n1=n2=n3=2, the result is
>> > 208 NaN 6.899999999999315E-003 2.066666666665403E-003.
>> > If n1=n2=n3=3, the size of Umat.out will continue to increase > 2G. And
>> > I
>> > have to stop it before the space is used up.
>> >
>> > The  potential and wfcs are saved and I used ecutwfc=100 to make the scf
>> > energy converged to 0.001Ry. I can decrease it if that will help to get
>> > correct U.
>> >
>> > On Sun, Jul 29, 2012 at 1:17 PM, Matteo Cococcioni <matteo at umn.edu>
>> > wrote:
>> >>
>> >> Dear Peng,
>> >>
>> >> I advise you to run the example available from the QE webpage and try
>> >> to reproduce the same results.
>> >>
>> >> On Sun, Jul 29, 2012 at 12:00 PM, Peng Chen <pchen at ion.chem.utk.edu>
>> >> wrote:
>> >> > Dear Dr. Matteo,
>> >> >
>> >> > I compiled the code with the parameters in make.sys. The n1=n2=n3=1
>> >> > case
>> >> > is
>> >> > done without error, but the results for Ni and O are negative which
>> >> > should
>> >> > not be correct.
>> >>
>> >>
>> >> ok then maybe you can try to increase them one per time and see at
>> >> what level the code stops with error?
>> >>
>> >>
>> >> > 26 -14.8678837915617 7.56505581785392 -0.681000339374195
>> >> > I plot dn.1.da.1.dat and dn0.1.da.1.dat, the data in dn0.1.da.1.dat
>> >> > are
>> >> > not
>> >> > linear.
>> >>
>> >>
>> >> this is not related to the error message of r.x but is not right. if
>> >> you want reliable results you have to get these plots linear.
>> >>
>> >>
>> >>
>> >> The scf calculation is converged to 0.001 Ry. So I am not sure what
>> >> > can cause the problem.
>> >>
>> >>
>> >> yes probably this is not enough. the inputs look fine (I haven't
>> >> looked inside the response matrix) but you have to make sure the scf
>> >> potential and wfc are saved after the unperturbed scf run and every
>> >> perturbed calculation starts from them.
>> >> do you really need 100 Ry cut off with US PP?
>> >>
>> >> Matteo
>> >>
>> >>
>> >> >
>> >> > I've attached the Umat_afm.1.out which may contain some useful
>> >> > information
>> >> > for you. I also put below the input for scf and perturbation on Ni
>> >> > (alpha=-0.15,-0.07,0.0,0.07,0.15). Same calculations are done for V
>> >> > and
>> >> > O as
>> >> > well with perturbed V or O atom translated to the origin of the unit
>> >> > cell.
>> >> >
>> >> >
>> >> > scf calculation input:
>> >> >
>> >> > &control
>> >> >     calculation='scf'
>> >> >     restart_mode='from_scratch',
>> >> >     prefix='nvoprim.afm.ucalc.Ni',
>> >> >     pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
>> >> >     outdir='/data/pchen/qe/'
>> >> >     wf_collect=.TRUE.
>> >> >  /
>> >> >  &system
>> >> >     ibrav=0, celldm(1)=11.19096,
>> >> >      nat=26, ntyp=6,
>> >> >   nspin = 2,  starting_magnetization(1)=0.6,
>> >> >     starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
>> >> >  starting_magnetization(4)=-0.5,
>> >> >  ecutwfc = 100, ecutrho = 800,
>> >> >  occupations ='smearing',
>> >> >     smearing ='mv',
>> >> >     degauss = 0.005,nbnd=135
>> >> >   lda_plus_u = .true.
>> >> >     Hubbard_U(1)= 1.d-20
>> >> >     Hubbard_U(2)= 1.d-20
>> >> >  Hubbard_U(3)= 1.d-20
>> >> >  Hubbard_U(4)= 1.d-20
>> >> >  Hubbard_U(5)= 1.d-20
>> >> >  Hubbard_U(6)= 1.d-20
>> >> >  /
>> >> >  &electrons
>> >> >     conv_thr = 1.0e-7
>> >> >     mixing_beta = 0.3
>> >> >  /
>> >> > CELL_PARAMETERS
>> >> > 0.5 0.96015 0
>> >> > 0.5 -0.96015 0
>> >> > 0 0   1.38889
>> >> > ATOMIC_SPECIES
>> >> >  Ni1 58.6934 Ni.pz-n-rrkjus.UPF
>> >> >  Ni2 58.6934 Ni.pz-n-rrkjus.UPF
>> >> >  Ni3 58.6934 Ni.pz-n-rrkjus.UPF
>> >> >  Ni4 58.6934 Ni.pz-n-rrkjus.UPF
>> >> >  V 50.9415 V.pz-spn-rrkjus.UPF
>> >> >  O  15.9994  O.pz-n-rrkjus.UPF
>> >> > ATOMIC_POSITIONS crystal
>> >> > Ni1      0.000000000   0.000000000   0.000000000
>> >> > Ni2      0.500000000   0.500000000   0.500000000
>> >> > Ni3      0.122863290   0.378190177   0.749934361
>> >> > Ni3      0.877136710   0.621809823   0.250065639
>> >> > Ni4      0.377137388   0.121809201   0.249932658
>> >> > Ni4      0.622862612   0.878190799   0.750067342
>> >> > V        0.373618754   0.623612138   0.115867980
>> >> > V        0.126381501   0.876388862   0.615868582
>> >> > V        0.626381246   0.376387862   0.884132020
>> >> > V        0.873618499   0.123611138   0.384131418
>> >> > O        0.241839036   0.756304999   0.223613779
>> >> > O        0.258160617   0.743693910   0.723611944
>> >> > O        0.758160964   0.243695001   0.776386221
>> >> > O        0.741839383   0.256306090   0.276388056
>> >> > O       -0.000998332   1.000227439   0.243205274
>> >> > O        0.500997862   0.499772508   0.743208489
>> >> > O        1.000998332  -0.000227439   0.756794726
>> >> > O        0.499002138   0.500227492   0.256791511
>> >> > O        0.381099639   0.150692971   0.006796703
>> >> > O        0.118898786   0.349304325   0.506798051
>> >> > O        0.149581603   0.378555571   0.991989919
>> >> > O        0.350419534   0.121445697   0.491991443
>> >> > O        0.618900361   0.849307029   0.993205297
>> >> > O        0.881101214   0.650695675   0.493203949
>> >> > O        0.850418397   0.621444429   0.008012081
>> >> > O        0.649580466   0.878554303   0.508010557
>> >> >
>> >> > K_POINTS (automatic)
>> >> >  5 5 5 1 1 1
>> >> >
>> >> > Perturbation on Ni with alpha=0.15 input:
>> >> >
>> >> > &control
>> >> >     calculation='scf'
>> >> >     restart_mode='from_scratch',
>> >> >     prefix='nvoprim.afm.ucalc.Ni',
>> >> >     pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
>> >> >     outdir='/data/pchen/qe/'
>> >> >    wf_collect=.TRUE.
>> >> >  /
>> >> >  &system
>> >> >     ibrav=0, celldm(1)=11.19096,
>> >> >      nat=26, ntyp=6,
>> >> >   nspin = 2,  starting_magnetization(1)=0.6,
>> >> >     starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
>> >> >  starting_magnetization(4)=-0.5,
>> >> >  ecutwfc = 100, ecutrho = 800,
>> >> >  occupations ='smearing',
>> >> >     smearing ='mv',
>> >> >     degauss = 0.005,nbnd=135
>> >> >   lda_plus_u = .true.
>> >> >     Hubbard_U(1)= 1.d-20
>> >> >     Hubbard_U(2)= 1.d-20
>> >> >     Hubbard_U(3)= 1.d-20
>> >> > Hubbard_U(4)= 1.d-20
>> >> > Hubbard_U(5)= 1.d-20
>> >> > Hubbard_U(6)= 1.d-20
>> >> >
>> >> >     Hubbard_alpha(1)= 0.15
>> >> >  /
>> >> >  &electrons
>> >> >     conv_thr = 1.0e-7
>> >> >     mixing_beta = 0.3
>> >> >   startingpot='file'
>> >> >  startingwfc='file'
>> >> >  diago_thr_init=5.09E-11,
>> >> >  /
>> >> > CELL_PARAMETERS
>> >> > 0.5 0.96015 0
>> >> > 0.5 -0.96015 0
>> >> > 0 0   1.38889
>> >> > ATOMIC_SPECIES
>> >> >  Ni1 58.6934 Ni.pz-n-rrkjus.UPF
>> >> >  Ni2 58.6934 Ni.pz-n-rrkjus.UPF
>> >> >  Ni3 58.6934 Ni.pz-n-rrkjus.UPF
>> >> >  Ni4 58.6934 Ni.pz-n-rrkjus.UPF
>> >> >  V 50.9415 V.pz-spn-rrkjus.UPF
>> >> >  O  15.9994  O.pz-n-rrkjus.UPF
>> >> > ATOMIC_POSITIONS crystal
>> >> > Ni1      0.000000000   0.000000000   0.000000000
>> >> > Ni2      0.500000000   0.500000000   0.500000000
>> >> > Ni3      0.122863290   0.378190177   0.749934361
>> >> > Ni3      0.877136710   0.621809823   0.250065639
>> >> > Ni4      0.377137388   0.121809201   0.249932658
>> >> > Ni4      0.622862612   0.878190799   0.750067342
>> >> > V        0.373618754   0.623612138   0.115867980
>> >> > V        0.126381501   0.876388862   0.615868582
>> >> > V        0.626381246   0.376387862   0.884132020
>> >> > V        0.873618499   0.123611138   0.384131418
>> >> > O        0.241839036   0.756304999   0.223613779
>> >> > O        0.258160617   0.743693910   0.723611944
>> >> > O        0.758160964   0.243695001   0.776386221
>> >> > O        0.741839383   0.256306090   0.276388056
>> >> > O       -0.000998332   1.000227439   0.243205274
>> >> > O        0.500997862   0.499772508   0.743208489
>> >> > O        1.000998332  -0.000227439   0.756794726
>> >> > O        0.499002138   0.500227492   0.256791511
>> >> > O        0.381099639   0.150692971   0.006796703
>> >> > O        0.118898786   0.349304325   0.506798051
>> >> > O        0.149581603   0.378555571   0.991989919
>> >> > O        0.350419534   0.121445697   0.491991443
>> >> > O        0.618900361   0.849307029   0.993205297
>> >> > O        0.881101214   0.650695675   0.493203949
>> >> > O        0.850418397   0.621444429   0.008012081
>> >> > O        0.649580466   0.878554303   0.508010557
>> >> >
>> >> > K_POINTS (automatic)
>> >> >  5 5 5 1 1 1
>> >> >
>> >> >
>> >> >
>> >> > On Sun, Jul 29, 2012 at 11:27 AM, Matteo Cococcioni <matteo at umn.edu>
>> >> > wrote:
>> >> >>
>> >> >> Dear Peng,
>> >> >>
>> >> >> I'm not very expert of compiling codes. You have to make sure that
>> >> >> all
>> >> >> the libraries are linked correctly for the code to work. I assume
>> >> >> you
>> >> >> have QE installed on the same computer. You could give a look in the
>> >> >> make.sys to check what is the correct way to link them. If
>> >> >> everything
>> >> >> is consistent, then you have to find out where the code is failing.
>> >> >> have you tried to run with n1 = n2 = n3 = 1? what did you get?
>> >> >>
>> >> >> Matteo
>> >> >>
>> >> >>
>> >> >>
>> >> >> On Sat, Jul 28, 2012 at 9:10 PM, Peng Chen <pchen at ion.chem.utk.edu>
>> >> >> wrote:
>> >> >> > Dear Dr. Matteo,
>> >> >> >
>> >> >> > I used command listed below to compile resp_mat.f90. No error in
>> >> >> > compiling.
>> >> >> > I am not sure if I did right in choosing the libs.
>> >> >> > ifort  -o r.x resp_mat.f90
>> >> >> > -L"/data/apps/intel/11.1.072/mkl/lib/em64t"
>> >> >> > -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_mc3  -lmkl_sequential
>> >> >> > -lmkl_core
>> >> >> >
>> >> >> > The libs in mkl are shown below:
>> >> >> > libmkl_avx.so                   libmkl_intel_sp2dp.so
>> >> >> > libmkl_blacs_ilp64.a            libmkl_intel_thread.a
>> >> >> > libmkl_blacs_intelmpi_ilp64.a   libmkl_intel_thread.so
>> >> >> > libmkl_blacs_intelmpi_ilp64.so  libmkl_lapack95_ilp64.a
>> >> >> > libmkl_blacs_intelmpi_lp64.a    libmkl_lapack95_lp64.a
>> >> >> > libmkl_blacs_intelmpi_lp64.so   libmkl_lapack.so
>> >> >> > libmkl_blacs_lp64.a             libmkl_mc3.so
>> >> >> > libmkl_blacs_openmpi_ilp64.a    libmkl_mc.so
>> >> >> > libmkl_blacs_openmpi_lp64.a     libmkl_p4n.so
>> >> >> > libmkl_blacs_sgimpt_ilp64.a     libmkl_pgi_thread.a
>> >> >> > libmkl_blacs_sgimpt_lp64.a      libmkl_pgi_thread.so
>> >> >> > libmkl_blas95_ilp64.a           libmkl_scalapack_ilp64.a
>> >> >> > libmkl_blas95_lp64.a            libmkl_scalapack_ilp64.so
>> >> >> > libmkl_cdft_core.a              libmkl_scalapack_lp64.a
>> >> >> > libmkl_core.a                   libmkl_scalapack_lp64.so
>> >> >> > libmkl_core.so                  libmkl_sequential.a
>> >> >> > libmkl_def.so                   libmkl_sequential.so
>> >> >> > libmkl_gf_ilp64.a               libmkl_solver_ilp64.a
>> >> >> > libmkl_gf_ilp64.so              libmkl_solver_ilp64_sequential.a
>> >> >> > libmkl_gf_lp64.a                libmkl_solver_lp64.a
>> >> >> > libmkl_gf_lp64.so               libmkl_solver_lp64_sequential.a
>> >> >> > libmkl_gnu_thread.a             libmkl_vml_avx.so
>> >> >> > libmkl_gnu_thread.so            libmkl_vml_def.so
>> >> >> > libmkl_intel_ilp64.a            libmkl_vml_mc2.so
>> >> >> > libmkl_intel_ilp64.so           libmkl_vml_mc3.so
>> >> >> > libmkl_intel_lp64.a             libmkl_vml_mc.so
>> >> >> > libmkl_intel_lp64.so            libmkl_vml_p4n.so
>> >> >> > libmkl_intel_sp2dp.a            locale
>> >> >> >
>> >> >> >
>> >> >> > Some errors in output:
>> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> >> >> > Image              PC                Routine            Line
>> >> >> > Source
>> >> >> > r.x                0000000000445659  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                000000000040A363  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                000000000040338C  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > libc.so.6          00002B85B9495994  Unknown               Unknown
>> >> >> > Unknown
>> >> >> > r.x                0000000000403289  Unknown               Unknown
>> >> >> > Unknown
>> >> >> >
>> >> >> >
>> >> >> > On Sat, Jul 28, 2012 at 10:38 AM, Matteo Cococcioni
>> >> >> > <matteo at umn.edu>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> Dear Peng,
>> >> >> >>
>> >> >> >> nothing looks wrong in your input. have you tried with n1, n2, n3
>> >> >> >> all
>> >> >> >> equal to 1? are you sure you compiled correctly?
>> >> >> >>
>> >> >> >> Matteo
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> On Fri, Jul 27, 2012 at 11:46 PM, Peng Chen
>> >> >> >> <pchen at ion.chem.utk.edu>
>> >> >> >> wrote:
>> >> >> >> > Dear Dr. Matteo,
>> >> >> >> >
>> >> >> >> > The primitive cell has 26 atoms with 3 different types. The pos
>> >> >> >> > and
>> >> >> >> > resp_mat.in files are shown below:
>> >> >> >> >
>> >> >> >> > 5.6087 10.79 0.0
>> >> >> >> > 5.6087 -10.79 0.0
>> >> >> >> > 0.0 0.0   15.570873
>> >> >> >> > 0       0       0       1
>> >> >> >> > 0.5     0.5     0.5     -1
>> >> >> >> > 0.12286329      0.378190177     0.749934361     1
>> >> >> >> > 0.87713671      0.621809823     0.250065639     1
>> >> >> >> > 0.377137388     0.121809201     0.249932658     -1
>> >> >> >> > 0.622862612     0.878190799     0.750067342     -1
>> >> >> >> > 0.373618754     0.623612138     0.11586798      0
>> >> >> >> > 0.126381501     0.876388862     0.615868582     0
>> >> >> >> > 0.626381246     0.376387862     0.88413202      0
>> >> >> >> > 0.873618499     0.123611138     0.384131418     0
>> >> >> >> > 0.241839036     0.756304999     0.223613779     0
>> >> >> >> > 0.258160617     0.74369391      0.723611944     0
>> >> >> >> > 0.758160964     0.243695001     0.776386221     0
>> >> >> >> > 0.741839383     0.25630609      0.276388056     0
>> >> >> >> > -0.000998332    1.000227439     0.243205274     0
>> >> >> >> > 0.500997862     0.499772508     0.743208489     0
>> >> >> >> > 1.000998332     -0.000227439    0.756794726     0
>> >> >> >> > 0.499002138     0.500227492     0.256791511     0
>> >> >> >> > 0.381099639     0.150692971     0.006796703     0
>> >> >> >> > 0.118898786     0.349304325     0.506798051     0
>> >> >> >> > 0.149581603     0.378555571     0.991989919     0
>> >> >> >> > 0.350419534     0.121445697     0.491991443     0
>> >> >> >> > 0.618900361     0.849307029     0.993205297     0
>> >> >> >> > 0.881101214     0.650695675     0.493203949     0
>> >> >> >> > 0.850418397     0.621444429     0.008012081     0
>> >> >> >> > 0.649580466     0.878554303     0.508010557     0
>> >> >> >> >
>> >> >> >> > resp_mat.in :
>> >> >> >> >  &input_mat
>> >> >> >> >    ntyp = 3
>> >> >> >> >    na(1) = 6
>> >> >> >> >    na(2) = 4
>> >> >> >> >    na(3) = 16
>> >> >> >> >    nalfa = 5
>> >> >> >> >    magn=.true.
>> >> >> >> >    filepos = 'pos'
>> >> >> >> >    back = 'no'
>> >> >> >> >    filednda = 'file_afm'
>> >> >> >> >    n1 = 2
>> >> >> >> >    n2 = 2
>> >> >> >> >    n3 = 2
>> >> >> >> >  &end
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni
>> >> >> >> > <matteo at umn.edu>
>> >> >> >> > wrote:
>> >> >> >> >>
>> >> >> >> >> Dear Peng,
>> >> >> >> >>
>> >> >> >> >> can you provide info about your system? maybe it is larger
>> >> >> >> >> than
>> >> >> >> >> the
>> >> >> >> >> maximum size allowed by r.x?
>> >> >> >> >>
>> >> >> >> >> Matteo
>> >> >> >> >>
>> >> >> >> >> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen
>> >> >> >> >> <pchen at ion.chem.utk.edu>
>> >> >> >> >> wrote:
>> >> >> >> >> > Dear All,
>> >> >> >> >> >
>> >> >> >> >> > There are some errors when I run r.x to calculate the U. I
>> >> >> >> >> > used
>> >> >> >> >> > Espresso-5.0
>> >> >> >> >> > and follow the steps in LSDA+U example. I am not sure what
>> >> >> >> >> > could
>> >> >> >> >> > be
>> >> >> >> >> > wrong.
>> >> >> >> >> > And if you need other input/output, please let me know.
>> >> >> >> >> >
>> >> >> >> >> > Image              PC        Routine            Line
>> >> >> >> >> > Source
>> >> >> >> >> > r.x                0822DACC  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                0822C265  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                082071FA  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                081DDFDA  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                081FA33B  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                081F9C5C  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                0804E38F  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                0804824A  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                0823805D  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                08048131  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > forrtl: severe (8): internal consistency check failure, file
>> >> >> >> >> > ./src/libfor/for_wseq_lis.c, line 635
>> >> >> >> >> > Image              PC        Routine            Line
>> >> >> >> >> > Source
>> >> >> >> >> > r.x                0822DACC  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                0822C265  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                082071FA  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                081DD664  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                081F9AF7  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                0804E38F  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                0804824A  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                0823805D  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                08048131  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> >> >> >> >> > Image              PC        Routine            Line
>> >> >> >> >> > Source
>> >> >> >> >> > r.x                0804DAED  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                0804824A  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                0823805D  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                08048131  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> >> >> >> >> > Image              PC        Routine            Line
>> >> >> >> >> > Source
>> >> >> >> >> > r.x                08253657  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                081F4087  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                081DCDB7  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                081DF354  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                081DD672  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                081DF5E8  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > Unknown            FFFFE600  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                0804824A  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                0823805D  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> > r.x                08048131  Unknown               Unknown
>> >> >> >> >> > Unknown
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > --
>> >> >> >> >> >   Best Regards.
>> >> >> >> >> >         Peng
>> >> >> >> >> >
>> >> >> >> >> > _______________________________________________
>> >> >> >> >> > Pw_forum mailing list
>> >> >> >> >> > Pw_forum at pwscf.org
>> >> >> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >> >> >> >
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> --
>> >> >> >> >> Matteo Cococcioni
>> >> >> >> >> Department of Chemical Engineering and Materials Science,
>> >> >> >> >> University of Minnesota
>> >> >> >> >> 421 Washington Av. SE
>> >> >> >> >> Minneapolis, MN 55455
>> >> >> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> >> >> >> >> _______________________________________________
>> >> >> >> >> Pw_forum mailing list
>> >> >> >> >> Pw_forum at pwscf.org
>> >> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> >   Best Regards.
>> >> >> >> >         Peng
>> >> >> >> >
>> >> >> >> > _______________________________________________
>> >> >> >> > Pw_forum mailing list
>> >> >> >> > Pw_forum at pwscf.org
>> >> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >> >> >
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >> Matteo Cococcioni
>> >> >> >> Department of Chemical Engineering and Materials Science,
>> >> >> >> University of Minnesota
>> >> >> >> 421 Washington Av. SE
>> >> >> >> Minneapolis, MN 55455
>> >> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> >> >> >> _______________________________________________
>> >> >> >> Pw_forum mailing list
>> >> >> >> Pw_forum at pwscf.org
>> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> >   Best Regards.
>> >> >> >         Peng
>> >> >> >
>> >> >> > _______________________________________________
>> >> >> > Pw_forum mailing list
>> >> >> > Pw_forum at pwscf.org
>> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Matteo Cococcioni
>> >> >> Department of Chemical Engineering and Materials Science,
>> >> >> University of Minnesota
>> >> >> 421 Washington Av. SE
>> >> >> Minneapolis, MN 55455
>> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> >> >> _______________________________________________
>> >> >> Pw_forum mailing list
>> >> >> Pw_forum at pwscf.org
>> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >   Best Regards.
>> >> >         Peng
>> >> >
>> >> > _______________________________________________
>> >> > Pw_forum mailing list
>> >> > Pw_forum at pwscf.org
>> >> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Matteo Cococcioni
>> >> Department of Chemical Engineering and Materials Science,
>> >> University of Minnesota
>> >> 421 Washington Av. SE
>> >> Minneapolis, MN 55455
>> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> >> _______________________________________________
>> >> Pw_forum mailing list
>> >> Pw_forum at pwscf.org
>> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>> >
>> >
>> >
>> > --
>> >   Best Regards.
>> >         Peng
>> >
>> > _______________________________________________
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>>
>>
>>
>> --
>> Matteo Cococcioni
>> Department of Chemical Engineering and Materials Science,
>> University of Minnesota
>> 421 Washington Av. SE
>> Minneapolis, MN 55455
>> Tel. +1 612 624 9056    Fax +1 612 626 7246
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
>   Best Regards.
>         Peng
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056    Fax +1 612 626 7246

From mayankaditya at gmail.com  Mon Jul 30 16:32:54 2012
From: mayankaditya at gmail.com (mayank gupta)
Date: Mon, 30 Jul 2012 20:02:54 +0530
Subject: [Pw_forum] Force constant from short range and long range
	interaction
Message-ID: <CAHNEyD8v-=YQd31FVJTJoZwW87PHGbPFJcDbPRm6r6j8QFYk1A@mail.gmail.com>

Dear Users and experts


Is it possible to calculate the force constant matrix  from long range and
short range interaction separately.

Thanks
-- 
--
Mayank

 BARC
MUMBAI, INDIA
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From d.tiana at bath.ac.uk  Mon Jul 30 18:52:21 2012
From: d.tiana at bath.ac.uk (Davide Tiana)
Date: Mon, 30 Jul 2012 17:52:21 +0100
Subject: [Pw_forum] band vs plotband output.
Message-ID: <20120730175221.Horde.eyc0V0KGDPZQFrvFzzoFXFA@webmail.bath.ac.uk>


Dear all,
I found some cases where after reorganise the bands output with plot  
bands, the homo - lumo are swapped. Why does his happen? More  
important to calculate the Band Gap what values should I used?

here an example: electron = 94, homo band numb 47.
band.out
           k = 0.0000 0.0000 0.0000     band energies (ev):

    -55.9850 -55.9850 -27.9953 -27.9953 -27.9793 -27.9793 -27.9357 -27.9357
    -20.6223 -20.5647 -19.6426 -17.8930 -17.1262 -15.8489 -15.6076 -14.4238
    -13.4669 -12.7303 -11.1590 -10.9066 -10.8380 -10.8160 -10.7731  -9.7812
     -9.6601  -8.6932  -7.8692  -7.7732  -7.7280  -7.1303  -6.6701  -6.6130
     -6.1019  -6.0213  -5.5373  -5.2958  -5.0030  -4.4158  -4.2662  -4.0390
     -3.8182  -3.7469  -3.6889  -3.6568  -2.7622  -2.1193  -1.5121  -1.4329
     -1.0247  -0.6744   0.1096   0.2954   0.4064   0.7536   0.8100   1.0277
...
           k = 0.0000 0.0000 0.8327     band energies (ev):

    -55.9850 -55.9850 -27.9953 -27.9953 -27.9793 -27.9793 -27.9357 -27.9357
    -20.6203 -20.5647 -19.6429 -17.9201 -17.1113 -15.9214 -15.4652 -14.2886
    -13.7199 -12.6999 -11.5050 -10.9082 -10.8380 -10.8359 -10.6059  -9.7363
     -9.1694  -8.6237  -8.2259  -7.6547  -7.4356  -7.3467  -6.8330  -6.5799
     -6.3278  -5.8338  -5.4976  -5.2352  -4.9676  -4.7183  -4.5833  -4.1295
     -4.0561  -3.6146  -3.2923  -2.9937  -2.9251  -2.6585  -1.5326  -1.4329
     -0.9754  -0.6156   0.3641   0.4861   0.5199   0.5499   0.5910   1.0285

bands.dat
0.000000  0.000000  0.000000
  -55.985 -55.985 -27.995 -27.995 -27.979 -27.979 -27.936 -27.936  
-20.622 -20.565
  -19.643 -17.893 -17.126 -15.849 -15.608 -14.424 -13.467 -12.730  
-11.159 -10.907
  -10.838 -10.816 -10.773  -9.781  -9.660  -8.693  -7.869  -7.773   
-7.728  -7.130
   -6.670  -6.613  -6.102  -6.021  -5.537  -5.296  -5.003  -4.416   
-4.266  -4.039
   -3.818  -3.747  -3.689  -3.657  -2.762  -2.119  -1.512  -1.433   
-1.025  -0.674
    0.110   0.295   0.406   0.754   0.810   1.028
..            0.000000  0.000000  0.832734
  -55.985 -55.985 -27.995 -27.995 -27.979 -27.979 -27.936 -27.936  
-20.620 -20.565
  -19.643 -17.920 -17.111 -15.921 -15.465 -14.289 -13.720 -12.700  
-11.505 -10.908
  -10.838 -10.836 -10.606  -9.736  -9.169  -8.624  -7.436  -8.226   
-7.655  -7.347
   -6.328  -6.833  -6.580  -5.834  -5.498  -5.235  -4.968  -4.718   
-4.583  -4.056
   -3.292  -4.129  -2.925  -3.615  -2.994  -2.658  -1.433  -1.533   
-0.975  -0.616
    0.550   0.364   0.520   0.486   0.591   1.028

band.out
HOMO -1.5121  LUMO -1.4329
HOMO -1.5326  LUMO -1.4329

bands.dat
HOMO -1.512  LUMO -1.433
HOMO -1.433  LUMO -1.533

Thank you for helping me



From pchen at ion.chem.utk.edu  Mon Jul 30 22:11:17 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Mon, 30 Jul 2012 16:11:17 -0400
Subject: [Pw_forum] U calculation error
In-Reply-To: <CAMZASgFB81Jv+Si9zh4th1fr7DcpkvktD=1vD=tdN2x0EmtoEg@mail.gmail.com>
References: <CAP_5U0d=B=ELuAfhFGu-SRT7C+dgb7cPuVtpk7yUz0A2BkBnuQ@mail.gmail.com>
	<CAMZASgH3ZxSwGtXARSqN+khMe4CSttRRgTb81F3LX7GfKFtp6w@mail.gmail.com>
	<CAP_5U0fA-N8DhL1DYcbpLZ=hiG8T4EfmJXPqwuJXFvcG89gP-Q@mail.gmail.com>
	<CAMZASgFWbtt6oCCoUp5g=ah3ODVOrNth9dwmmf2p+0XauMKhrw@mail.gmail.com>
	<CAP_5U0cU4t-AYM7rhOwo8MhMEuwjKEq5NzMoteDsaCO6wPugsw@mail.gmail.com>
	<CAMZASgGFhiF15BgCwkWgE5ZQj9tMRYFopAsQOKX8pte6Vw-DEg@mail.gmail.com>
	<CAP_5U0fYafiTLd+sNKK1HE2TefOn8ZVZ9+urU6VcTTw2yQxmqQ@mail.gmail.com>
	<CAMZASgEoRBJRL1wSaWxAxAHOKvUw5Xci=3K4nVjP-YbyoEvuxQ@mail.gmail.com>
	<CAP_5U0faBHn-_7JhoSWhbsD0U-FePKd1mxXaFo9wTU11sgqD6A@mail.gmail.com>
	<CAMZASgGaDy+cT=RYaxykMhv4foQhZNQ-wGMoZEXE74-iFgXviw@mail.gmail.com>
	<CAP_5U0dSxeb8HK-HZ9D7As4zVGaD4Ac_N_4JN_7+DSKVKcst9A@mail.gmail.com>
	<CAMZASgFB81Jv+Si9zh4th1fr7DcpkvktD=1vD=tdN2x0EmtoEg@mail.gmail.com>
Message-ID: <CAP_5U0dnYNd2t30UkpaROxd3OvE2G0kDGPohh=szPv1i11ONmA@mail.gmail.com>

Dear Dr. Matteo,

I did scf convergence test with ecutwfc, ecutrho, degauss, and kpoints. The
energy is converged. The system is supposed to be an insulator. LSDA
calculation gave a result very close to the metal which is the reason I
need LSDA+U. And it looks more difficult to obtain U than I thought.

On Mon, Jul 30, 2012 at 10:20 AM, Matteo Cococcioni <matteo at umn.edu> wrote:

> Dear Peng,
>
> On Sun, Jul 29, 2012 at 8:52 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
> > Dear Dr. Matteo,
> >
> >  Do you mean to increase the size of vectors in the pos file?
> > 5.6087 10.79 0.0
> > 5.6087 -10.79 0.0
> > 0.0 0.0   15.570873
> >
>
>
> no, I meant to increase the dimension of the matrices in the code r.x.
>
>
> > I still can not obtain linear behavior of dn0.1.da.1.dat which should
> > related with scf and perturbation calculations. What's your suggestions
> on
> > this part?
> >
> > File dn0.1.da.1.dat:
> >
> >  -0.15   8.63607
> >   -0.07   8.59247
> >   0.0   8.56719
> >   0.07   8.52053
> >   0.15   8.46247
> >
>
>
> I'm not sure what to suggest. are you sure the first iteration was
> sufficiently converged? is your system a metal to start with?
>
> Matteo
>
>
>
> >
> >
> > On Sun, Jul 29, 2012 at 9:11 PM, Matteo Cococcioni <matteo at umn.edu>
> wrote:
> >>
> >> Dear Peng,
> >>
> >> I'm not sure what the problem could be. sounds like a problem with the
> >> memory of your computer.
> >> I don't know what the line you report below is supposed to mean. NaN
> >> usually comes out when the code tries to divide something by 0, or
> >> things like that. try to track it in the source of the code and make
> >> it print the quantities it uses to compute that output entry.
> >> Have you tried to increase the max size of the matrices, or to
> >> increase the threshold values within which the code assumes two
> >> distances to be the same?
> >>
> >> Matteo
> >>
> >>
> >>
> >> On Sun, Jul 29, 2012 at 3:01 PM, Peng Chen <pchen at ion.chem.utk.edu>
> wrote:
> >> > Dear Dr. Matteo,
> >> >
> >> > Yes,  I ran the LSDA+U example successfully, the only difference is
> that
> >> > the
> >> > U of Ni converged to 6.0 not 5.0.
> >> >
> >> > For my calculation, if I use n1=n2=n3=2, the result is
> >> > 208 NaN 6.899999999999315E-003 2.066666666665403E-003.
> >> > If n1=n2=n3=3, the size of Umat.out will continue to increase > 2G.
> And
> >> > I
> >> > have to stop it before the space is used up.
> >> >
> >> > The  potential and wfcs are saved and I used ecutwfc=100 to make the
> scf
> >> > energy converged to 0.001Ry. I can decrease it if that will help to
> get
> >> > correct U.
> >> >
> >> > On Sun, Jul 29, 2012 at 1:17 PM, Matteo Cococcioni <matteo at umn.edu>
> >> > wrote:
> >> >>
> >> >> Dear Peng,
> >> >>
> >> >> I advise you to run the example available from the QE webpage and try
> >> >> to reproduce the same results.
> >> >>
> >> >> On Sun, Jul 29, 2012 at 12:00 PM, Peng Chen <pchen at ion.chem.utk.edu>
> >> >> wrote:
> >> >> > Dear Dr. Matteo,
> >> >> >
> >> >> > I compiled the code with the parameters in make.sys. The n1=n2=n3=1
> >> >> > case
> >> >> > is
> >> >> > done without error, but the results for Ni and O are negative which
> >> >> > should
> >> >> > not be correct.
> >> >>
> >> >>
> >> >> ok then maybe you can try to increase them one per time and see at
> >> >> what level the code stops with error?
> >> >>
> >> >>
> >> >> > 26 -14.8678837915617 7.56505581785392 -0.681000339374195
> >> >> > I plot dn.1.da.1.dat and dn0.1.da.1.dat, the data in dn0.1.da.1.dat
> >> >> > are
> >> >> > not
> >> >> > linear.
> >> >>
> >> >>
> >> >> this is not related to the error message of r.x but is not right. if
> >> >> you want reliable results you have to get these plots linear.
> >> >>
> >> >>
> >> >>
> >> >> The scf calculation is converged to 0.001 Ry. So I am not sure what
> >> >> > can cause the problem.
> >> >>
> >> >>
> >> >> yes probably this is not enough. the inputs look fine (I haven't
> >> >> looked inside the response matrix) but you have to make sure the scf
> >> >> potential and wfc are saved after the unperturbed scf run and every
> >> >> perturbed calculation starts from them.
> >> >> do you really need 100 Ry cut off with US PP?
> >> >>
> >> >> Matteo
> >> >>
> >> >>
> >> >> >
> >> >> > I've attached the Umat_afm.1.out which may contain some useful
> >> >> > information
> >> >> > for you. I also put below the input for scf and perturbation on Ni
> >> >> > (alpha=-0.15,-0.07,0.0,0.07,0.15). Same calculations are done for V
> >> >> > and
> >> >> > O as
> >> >> > well with perturbed V or O atom translated to the origin of the
> unit
> >> >> > cell.
> >> >> >
> >> >> >
> >> >> > scf calculation input:
> >> >> >
> >> >> > &control
> >> >> >     calculation='scf'
> >> >> >     restart_mode='from_scratch',
> >> >> >     prefix='nvoprim.afm.ucalc.Ni',
> >> >> >     pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
> >> >> >     outdir='/data/pchen/qe/'
> >> >> >     wf_collect=.TRUE.
> >> >> >  /
> >> >> >  &system
> >> >> >     ibrav=0, celldm(1)=11.19096,
> >> >> >      nat=26, ntyp=6,
> >> >> >   nspin = 2,  starting_magnetization(1)=0.6,
> >> >> >     starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
> >> >> >  starting_magnetization(4)=-0.5,
> >> >> >  ecutwfc = 100, ecutrho = 800,
> >> >> >  occupations ='smearing',
> >> >> >     smearing ='mv',
> >> >> >     degauss = 0.005,nbnd=135
> >> >> >   lda_plus_u = .true.
> >> >> >     Hubbard_U(1)= 1.d-20
> >> >> >     Hubbard_U(2)= 1.d-20
> >> >> >  Hubbard_U(3)= 1.d-20
> >> >> >  Hubbard_U(4)= 1.d-20
> >> >> >  Hubbard_U(5)= 1.d-20
> >> >> >  Hubbard_U(6)= 1.d-20
> >> >> >  /
> >> >> >  &electrons
> >> >> >     conv_thr = 1.0e-7
> >> >> >     mixing_beta = 0.3
> >> >> >  /
> >> >> > CELL_PARAMETERS
> >> >> > 0.5 0.96015 0
> >> >> > 0.5 -0.96015 0
> >> >> > 0 0   1.38889
> >> >> > ATOMIC_SPECIES
> >> >> >  Ni1 58.6934 Ni.pz-n-rrkjus.UPF
> >> >> >  Ni2 58.6934 Ni.pz-n-rrkjus.UPF
> >> >> >  Ni3 58.6934 Ni.pz-n-rrkjus.UPF
> >> >> >  Ni4 58.6934 Ni.pz-n-rrkjus.UPF
> >> >> >  V 50.9415 V.pz-spn-rrkjus.UPF
> >> >> >  O  15.9994  O.pz-n-rrkjus.UPF
> >> >> > ATOMIC_POSITIONS crystal
> >> >> > Ni1      0.000000000   0.000000000   0.000000000
> >> >> > Ni2      0.500000000   0.500000000   0.500000000
> >> >> > Ni3      0.122863290   0.378190177   0.749934361
> >> >> > Ni3      0.877136710   0.621809823   0.250065639
> >> >> > Ni4      0.377137388   0.121809201   0.249932658
> >> >> > Ni4      0.622862612   0.878190799   0.750067342
> >> >> > V        0.373618754   0.623612138   0.115867980
> >> >> > V        0.126381501   0.876388862   0.615868582
> >> >> > V        0.626381246   0.376387862   0.884132020
> >> >> > V        0.873618499   0.123611138   0.384131418
> >> >> > O        0.241839036   0.756304999   0.223613779
> >> >> > O        0.258160617   0.743693910   0.723611944
> >> >> > O        0.758160964   0.243695001   0.776386221
> >> >> > O        0.741839383   0.256306090   0.276388056
> >> >> > O       -0.000998332   1.000227439   0.243205274
> >> >> > O        0.500997862   0.499772508   0.743208489
> >> >> > O        1.000998332  -0.000227439   0.756794726
> >> >> > O        0.499002138   0.500227492   0.256791511
> >> >> > O        0.381099639   0.150692971   0.006796703
> >> >> > O        0.118898786   0.349304325   0.506798051
> >> >> > O        0.149581603   0.378555571   0.991989919
> >> >> > O        0.350419534   0.121445697   0.491991443
> >> >> > O        0.618900361   0.849307029   0.993205297
> >> >> > O        0.881101214   0.650695675   0.493203949
> >> >> > O        0.850418397   0.621444429   0.008012081
> >> >> > O        0.649580466   0.878554303   0.508010557
> >> >> >
> >> >> > K_POINTS (automatic)
> >> >> >  5 5 5 1 1 1
> >> >> >
> >> >> > Perturbation on Ni with alpha=0.15 input:
> >> >> >
> >> >> > &control
> >> >> >     calculation='scf'
> >> >> >     restart_mode='from_scratch',
> >> >> >     prefix='nvoprim.afm.ucalc.Ni',
> >> >> >     pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
> >> >> >     outdir='/data/pchen/qe/'
> >> >> >    wf_collect=.TRUE.
> >> >> >  /
> >> >> >  &system
> >> >> >     ibrav=0, celldm(1)=11.19096,
> >> >> >      nat=26, ntyp=6,
> >> >> >   nspin = 2,  starting_magnetization(1)=0.6,
> >> >> >     starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
> >> >> >  starting_magnetization(4)=-0.5,
> >> >> >  ecutwfc = 100, ecutrho = 800,
> >> >> >  occupations ='smearing',
> >> >> >     smearing ='mv',
> >> >> >     degauss = 0.005,nbnd=135
> >> >> >   lda_plus_u = .true.
> >> >> >     Hubbard_U(1)= 1.d-20
> >> >> >     Hubbard_U(2)= 1.d-20
> >> >> >     Hubbard_U(3)= 1.d-20
> >> >> > Hubbard_U(4)= 1.d-20
> >> >> > Hubbard_U(5)= 1.d-20
> >> >> > Hubbard_U(6)= 1.d-20
> >> >> >
> >> >> >     Hubbard_alpha(1)= 0.15
> >> >> >  /
> >> >> >  &electrons
> >> >> >     conv_thr = 1.0e-7
> >> >> >     mixing_beta = 0.3
> >> >> >   startingpot='file'
> >> >> >  startingwfc='file'
> >> >> >  diago_thr_init=5.09E-11,
> >> >> >  /
> >> >> > CELL_PARAMETERS
> >> >> > 0.5 0.96015 0
> >> >> > 0.5 -0.96015 0
> >> >> > 0 0   1.38889
> >> >> > ATOMIC_SPECIES
> >> >> >  Ni1 58.6934 Ni.pz-n-rrkjus.UPF
> >> >> >  Ni2 58.6934 Ni.pz-n-rrkjus.UPF
> >> >> >  Ni3 58.6934 Ni.pz-n-rrkjus.UPF
> >> >> >  Ni4 58.6934 Ni.pz-n-rrkjus.UPF
> >> >> >  V 50.9415 V.pz-spn-rrkjus.UPF
> >> >> >  O  15.9994  O.pz-n-rrkjus.UPF
> >> >> > ATOMIC_POSITIONS crystal
> >> >> > Ni1      0.000000000   0.000000000   0.000000000
> >> >> > Ni2      0.500000000   0.500000000   0.500000000
> >> >> > Ni3      0.122863290   0.378190177   0.749934361
> >> >> > Ni3      0.877136710   0.621809823   0.250065639
> >> >> > Ni4      0.377137388   0.121809201   0.249932658
> >> >> > Ni4      0.622862612   0.878190799   0.750067342
> >> >> > V        0.373618754   0.623612138   0.115867980
> >> >> > V        0.126381501   0.876388862   0.615868582
> >> >> > V        0.626381246   0.376387862   0.884132020
> >> >> > V        0.873618499   0.123611138   0.384131418
> >> >> > O        0.241839036   0.756304999   0.223613779
> >> >> > O        0.258160617   0.743693910   0.723611944
> >> >> > O        0.758160964   0.243695001   0.776386221
> >> >> > O        0.741839383   0.256306090   0.276388056
> >> >> > O       -0.000998332   1.000227439   0.243205274
> >> >> > O        0.500997862   0.499772508   0.743208489
> >> >> > O        1.000998332  -0.000227439   0.756794726
> >> >> > O        0.499002138   0.500227492   0.256791511
> >> >> > O        0.381099639   0.150692971   0.006796703
> >> >> > O        0.118898786   0.349304325   0.506798051
> >> >> > O        0.149581603   0.378555571   0.991989919
> >> >> > O        0.350419534   0.121445697   0.491991443
> >> >> > O        0.618900361   0.849307029   0.993205297
> >> >> > O        0.881101214   0.650695675   0.493203949
> >> >> > O        0.850418397   0.621444429   0.008012081
> >> >> > O        0.649580466   0.878554303   0.508010557
> >> >> >
> >> >> > K_POINTS (automatic)
> >> >> >  5 5 5 1 1 1
> >> >> >
> >> >> >
> >> >> >
> >> >> > On Sun, Jul 29, 2012 at 11:27 AM, Matteo Cococcioni <
> matteo at umn.edu>
> >> >> > wrote:
> >> >> >>
> >> >> >> Dear Peng,
> >> >> >>
> >> >> >> I'm not very expert of compiling codes. You have to make sure that
> >> >> >> all
> >> >> >> the libraries are linked correctly for the code to work. I assume
> >> >> >> you
> >> >> >> have QE installed on the same computer. You could give a look in
> the
> >> >> >> make.sys to check what is the correct way to link them. If
> >> >> >> everything
> >> >> >> is consistent, then you have to find out where the code is
> failing.
> >> >> >> have you tried to run with n1 = n2 = n3 = 1? what did you get?
> >> >> >>
> >> >> >> Matteo
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> On Sat, Jul 28, 2012 at 9:10 PM, Peng Chen <
> pchen at ion.chem.utk.edu>
> >> >> >> wrote:
> >> >> >> > Dear Dr. Matteo,
> >> >> >> >
> >> >> >> > I used command listed below to compile resp_mat.f90. No error in
> >> >> >> > compiling.
> >> >> >> > I am not sure if I did right in choosing the libs.
> >> >> >> > ifort  -o r.x resp_mat.f90
> >> >> >> > -L"/data/apps/intel/11.1.072/mkl/lib/em64t"
> >> >> >> > -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_mc3  -lmkl_sequential
> >> >> >> > -lmkl_core
> >> >> >> >
> >> >> >> > The libs in mkl are shown below:
> >> >> >> > libmkl_avx.so                   libmkl_intel_sp2dp.so
> >> >> >> > libmkl_blacs_ilp64.a            libmkl_intel_thread.a
> >> >> >> > libmkl_blacs_intelmpi_ilp64.a   libmkl_intel_thread.so
> >> >> >> > libmkl_blacs_intelmpi_ilp64.so  libmkl_lapack95_ilp64.a
> >> >> >> > libmkl_blacs_intelmpi_lp64.a    libmkl_lapack95_lp64.a
> >> >> >> > libmkl_blacs_intelmpi_lp64.so   libmkl_lapack.so
> >> >> >> > libmkl_blacs_lp64.a             libmkl_mc3.so
> >> >> >> > libmkl_blacs_openmpi_ilp64.a    libmkl_mc.so
> >> >> >> > libmkl_blacs_openmpi_lp64.a     libmkl_p4n.so
> >> >> >> > libmkl_blacs_sgimpt_ilp64.a     libmkl_pgi_thread.a
> >> >> >> > libmkl_blacs_sgimpt_lp64.a      libmkl_pgi_thread.so
> >> >> >> > libmkl_blas95_ilp64.a           libmkl_scalapack_ilp64.a
> >> >> >> > libmkl_blas95_lp64.a            libmkl_scalapack_ilp64.so
> >> >> >> > libmkl_cdft_core.a              libmkl_scalapack_lp64.a
> >> >> >> > libmkl_core.a                   libmkl_scalapack_lp64.so
> >> >> >> > libmkl_core.so                  libmkl_sequential.a
> >> >> >> > libmkl_def.so                   libmkl_sequential.so
> >> >> >> > libmkl_gf_ilp64.a               libmkl_solver_ilp64.a
> >> >> >> > libmkl_gf_ilp64.so              libmkl_solver_ilp64_sequential.a
> >> >> >> > libmkl_gf_lp64.a                libmkl_solver_lp64.a
> >> >> >> > libmkl_gf_lp64.so               libmkl_solver_lp64_sequential.a
> >> >> >> > libmkl_gnu_thread.a             libmkl_vml_avx.so
> >> >> >> > libmkl_gnu_thread.so            libmkl_vml_def.so
> >> >> >> > libmkl_intel_ilp64.a            libmkl_vml_mc2.so
> >> >> >> > libmkl_intel_ilp64.so           libmkl_vml_mc3.so
> >> >> >> > libmkl_intel_lp64.a             libmkl_vml_mc.so
> >> >> >> > libmkl_intel_lp64.so            libmkl_vml_p4n.so
> >> >> >> > libmkl_intel_sp2dp.a            locale
> >> >> >> >
> >> >> >> >
> >> >> >> > Some errors in output:
> >> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> >> >> > Image              PC                Routine            Line
> >> >> >> > Source
> >> >> >> > r.x                0000000000445659  Unknown
> Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                000000000040A363  Unknown
> Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                000000000040338C  Unknown
> Unknown
> >> >> >> > Unknown
> >> >> >> > libc.so.6          00002B85B9495994  Unknown
> Unknown
> >> >> >> > Unknown
> >> >> >> > r.x                0000000000403289  Unknown
> Unknown
> >> >> >> > Unknown
> >> >> >> >
> >> >> >> >
> >> >> >> > On Sat, Jul 28, 2012 at 10:38 AM, Matteo Cococcioni
> >> >> >> > <matteo at umn.edu>
> >> >> >> > wrote:
> >> >> >> >>
> >> >> >> >> Dear Peng,
> >> >> >> >>
> >> >> >> >> nothing looks wrong in your input. have you tried with n1, n2,
> n3
> >> >> >> >> all
> >> >> >> >> equal to 1? are you sure you compiled correctly?
> >> >> >> >>
> >> >> >> >> Matteo
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> On Fri, Jul 27, 2012 at 11:46 PM, Peng Chen
> >> >> >> >> <pchen at ion.chem.utk.edu>
> >> >> >> >> wrote:
> >> >> >> >> > Dear Dr. Matteo,
> >> >> >> >> >
> >> >> >> >> > The primitive cell has 26 atoms with 3 different types. The
> pos
> >> >> >> >> > and
> >> >> >> >> > resp_mat.in files are shown below:
> >> >> >> >> >
> >> >> >> >> > 5.6087 10.79 0.0
> >> >> >> >> > 5.6087 -10.79 0.0
> >> >> >> >> > 0.0 0.0   15.570873
> >> >> >> >> > 0       0       0       1
> >> >> >> >> > 0.5     0.5     0.5     -1
> >> >> >> >> > 0.12286329      0.378190177     0.749934361     1
> >> >> >> >> > 0.87713671      0.621809823     0.250065639     1
> >> >> >> >> > 0.377137388     0.121809201     0.249932658     -1
> >> >> >> >> > 0.622862612     0.878190799     0.750067342     -1
> >> >> >> >> > 0.373618754     0.623612138     0.11586798      0
> >> >> >> >> > 0.126381501     0.876388862     0.615868582     0
> >> >> >> >> > 0.626381246     0.376387862     0.88413202      0
> >> >> >> >> > 0.873618499     0.123611138     0.384131418     0
> >> >> >> >> > 0.241839036     0.756304999     0.223613779     0
> >> >> >> >> > 0.258160617     0.74369391      0.723611944     0
> >> >> >> >> > 0.758160964     0.243695001     0.776386221     0
> >> >> >> >> > 0.741839383     0.25630609      0.276388056     0
> >> >> >> >> > -0.000998332    1.000227439     0.243205274     0
> >> >> >> >> > 0.500997862     0.499772508     0.743208489     0
> >> >> >> >> > 1.000998332     -0.000227439    0.756794726     0
> >> >> >> >> > 0.499002138     0.500227492     0.256791511     0
> >> >> >> >> > 0.381099639     0.150692971     0.006796703     0
> >> >> >> >> > 0.118898786     0.349304325     0.506798051     0
> >> >> >> >> > 0.149581603     0.378555571     0.991989919     0
> >> >> >> >> > 0.350419534     0.121445697     0.491991443     0
> >> >> >> >> > 0.618900361     0.849307029     0.993205297     0
> >> >> >> >> > 0.881101214     0.650695675     0.493203949     0
> >> >> >> >> > 0.850418397     0.621444429     0.008012081     0
> >> >> >> >> > 0.649580466     0.878554303     0.508010557     0
> >> >> >> >> >
> >> >> >> >> > resp_mat.in :
> >> >> >> >> >  &input_mat
> >> >> >> >> >    ntyp = 3
> >> >> >> >> >    na(1) = 6
> >> >> >> >> >    na(2) = 4
> >> >> >> >> >    na(3) = 16
> >> >> >> >> >    nalfa = 5
> >> >> >> >> >    magn=.true.
> >> >> >> >> >    filepos = 'pos'
> >> >> >> >> >    back = 'no'
> >> >> >> >> >    filednda = 'file_afm'
> >> >> >> >> >    n1 = 2
> >> >> >> >> >    n2 = 2
> >> >> >> >> >    n3 = 2
> >> >> >> >> >  &end
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> > On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni
> >> >> >> >> > <matteo at umn.edu>
> >> >> >> >> > wrote:
> >> >> >> >> >>
> >> >> >> >> >> Dear Peng,
> >> >> >> >> >>
> >> >> >> >> >> can you provide info about your system? maybe it is larger
> >> >> >> >> >> than
> >> >> >> >> >> the
> >> >> >> >> >> maximum size allowed by r.x?
> >> >> >> >> >>
> >> >> >> >> >> Matteo
> >> >> >> >> >>
> >> >> >> >> >> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen
> >> >> >> >> >> <pchen at ion.chem.utk.edu>
> >> >> >> >> >> wrote:
> >> >> >> >> >> > Dear All,
> >> >> >> >> >> >
> >> >> >> >> >> > There are some errors when I run r.x to calculate the U. I
> >> >> >> >> >> > used
> >> >> >> >> >> > Espresso-5.0
> >> >> >> >> >> > and follow the steps in LSDA+U example. I am not sure what
> >> >> >> >> >> > could
> >> >> >> >> >> > be
> >> >> >> >> >> > wrong.
> >> >> >> >> >> > And if you need other input/output, please let me know.
> >> >> >> >> >> >
> >> >> >> >> >> > Image              PC        Routine            Line
> >> >> >> >> >> > Source
> >> >> >> >> >> > r.x                0822DACC  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                0822C265  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                082071FA  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                081DDFDA  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                081FA33B  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                081F9C5C  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                0804E38F  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                0804824A  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                0823805D  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                08048131  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > forrtl: severe (8): internal consistency check failure,
> file
> >> >> >> >> >> > ./src/libfor/for_wseq_lis.c, line 635
> >> >> >> >> >> > Image              PC        Routine            Line
> >> >> >> >> >> > Source
> >> >> >> >> >> > r.x                0822DACC  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                0822C265  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                082071FA  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                081DD664  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                081F9AF7  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                0804E38F  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                0804824A  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                0823805D  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                08048131  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> >> >> >> >> > Image              PC        Routine            Line
> >> >> >> >> >> > Source
> >> >> >> >> >> > r.x                0804DAED  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                0804824A  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                0823805D  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                08048131  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> >> >> >> >> > Image              PC        Routine            Line
> >> >> >> >> >> > Source
> >> >> >> >> >> > r.x                08253657  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                081F4087  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                081DCDB7  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                081DF354  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                081DD672  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                081DF5E8  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > Unknown            FFFFE600  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                0804824A  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                0823805D  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> > r.x                08048131  Unknown               Unknown
> >> >> >> >> >> > Unknown
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> > --
> >> >> >> >> >> >   Best Regards.
> >> >> >> >> >> >         Peng
> >> >> >> >> >> >
> >> >> >> >> >> > _______________________________________________
> >> >> >> >> >> > Pw_forum mailing list
> >> >> >> >> >> > Pw_forum at pwscf.org
> >> >> >> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >> >> >> >
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> --
> >> >> >> >> >> Matteo Cococcioni
> >> >> >> >> >> Department of Chemical Engineering and Materials Science,
> >> >> >> >> >> University of Minnesota
> >> >> >> >> >> 421 Washington Av. SE
> >> >> >> >> >> Minneapolis, MN 55455
> >> >> >> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> >> >> >> >> _______________________________________________
> >> >> >> >> >> Pw_forum mailing list
> >> >> >> >> >> Pw_forum at pwscf.org
> >> >> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> > --
> >> >> >> >> >   Best Regards.
> >> >> >> >> >         Peng
> >> >> >> >> >
> >> >> >> >> > _______________________________________________
> >> >> >> >> > Pw_forum mailing list
> >> >> >> >> > Pw_forum at pwscf.org
> >> >> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >> >> >
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> Matteo Cococcioni
> >> >> >> >> Department of Chemical Engineering and Materials Science,
> >> >> >> >> University of Minnesota
> >> >> >> >> 421 Washington Av. SE
> >> >> >> >> Minneapolis, MN 55455
> >> >> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> >> >> >> _______________________________________________
> >> >> >> >> Pw_forum mailing list
> >> >> >> >> Pw_forum at pwscf.org
> >> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > --
> >> >> >> >   Best Regards.
> >> >> >> >         Peng
> >> >> >> >
> >> >> >> > _______________________________________________
> >> >> >> > Pw_forum mailing list
> >> >> >> > Pw_forum at pwscf.org
> >> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Matteo Cococcioni
> >> >> >> Department of Chemical Engineering and Materials Science,
> >> >> >> University of Minnesota
> >> >> >> 421 Washington Av. SE
> >> >> >> Minneapolis, MN 55455
> >> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> >> >> _______________________________________________
> >> >> >> Pw_forum mailing list
> >> >> >> Pw_forum at pwscf.org
> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> >   Best Regards.
> >> >> >         Peng
> >> >> >
> >> >> > _______________________________________________
> >> >> > Pw_forum mailing list
> >> >> > Pw_forum at pwscf.org
> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Matteo Cococcioni
> >> >> Department of Chemical Engineering and Materials Science,
> >> >> University of Minnesota
> >> >> 421 Washington Av. SE
> >> >> Minneapolis, MN 55455
> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> >> _______________________________________________
> >> >> Pw_forum mailing list
> >> >> Pw_forum at pwscf.org
> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> >   Best Regards.
> >> >         Peng
> >> >
> >> > _______________________________________________
> >> > Pw_forum mailing list
> >> > Pw_forum at pwscf.org
> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >
> >>
> >>
> >>
> >> --
> >> Matteo Cococcioni
> >> Department of Chemical Engineering and Materials Science,
> >> University of Minnesota
> >> 421 Washington Av. SE
> >> Minneapolis, MN 55455
> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> >   Best Regards.
> >         Peng
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Matteo Cococcioni
> Department of Chemical Engineering and Materials Science,
> University of Minnesota
> 421 Washington Av. SE
> Minneapolis, MN 55455
> Tel. +1 612 624 9056    Fax +1 612 626 7246
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
  Best Regards.
        Peng
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From mojdeh.akhavan at gmail.com  Tue Jul 31 10:18:15 2012
From: mojdeh.akhavan at gmail.com (mojdeh akhavan)
Date: Tue, 31 Jul 2012 12:48:15 +0430
Subject: [Pw_forum] strange DOS for an antiferromagnetic system
Message-ID: <CAKUnNLc1ifKXQWQFxPtwrG4ftgDvKb=UVnj55-sfMgwSGT8nvg@mail.gmail.com>

Dear users
Hi

I have studied a nanotube with an adsorbed metal atom. After scf
calculation, the total and absolute magnetic moments are 0.00 and 1.86. I
concluded that my system has antiferromagnetic spin ordering. I have read
in literature that in such cases the difference in up/down DOS is only
possible for subsets of atoms. However, when I calculate TDOS for the whole
system, the spin-up and spin-down curves are completely different!!! What's
wrong about this?

Thank you very much in advance

M. Akhavan, Ph.D.
Post-Doctoral Research Fellow
School of Nano-Science
Institute for Research in Fundamental Sciences (IPM)
P.O. Box 19395-5531 Tehran, Iran
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From zafartariq2003 at yahoo.com  Tue Jul 31 12:28:29 2012
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Tue, 31 Jul 2012 03:28:29 -0700 (PDT)
Subject: [Pw_forum] Error while compiling Quantum Espresso
In-Reply-To: <mailman.207.1343653809.1439.pw_forum@pwscf.org>
Message-ID: <1343730509.395.YahooMailClassic@web121403.mail.ne1.yahoo.com>

Dear Lorenzo Paulatto
Check the ziped file. A copy of output will be there. We are trying to cover up the problem. I told you last time that make.sys file is not created.

Best regards

Muhammad Zafar

PhD Scholar

Department of Physics

The Islamia University of Bahawalpur,Pakistan

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From zafartariq2003 at yahoo.com  Tue Jul 31 12:32:45 2012
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Tue, 31 Jul 2012 03:32:45 -0700 (PDT)
Subject: [Pw_forum] Error in QHA calculations
In-Reply-To: <mailman.207.1343653809.1439.pw_forum@pwscf.org>
Message-ID: <1343730765.85440.YahooMailClassic@web121405.mail.ne1.yahoo.com>


?Dear DENIS MAGERO

This problem is discussed in group so many time. Just increase [tr2_ph = below default value mean default value is { 1.0d-10 to 1.0d-18 any value ] and then try. This error is due to some negative frequency. Hope this will help you.

Muhammad Zafar

PhD Scholar

Department of Physics

The Islamia University of Bahawalpur,Pakistan

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From gkucukdalyan at gmail.com  Tue Jul 31 21:37:19 2012
From: gkucukdalyan at gmail.com (Gulcin Kucukdalyan)
Date: Tue, 31 Jul 2012 15:37:19 -0400
Subject: [Pw_forum] Hirshfeld Charges
Message-ID: <CAOwUK0CiKBTPgcrn1E=A1qFKwg67YFxNANWhODRE75MSbRnBug@mail.gmail.com>

Hi All,

I want to calculate Hirshfeld on each carbon and lithium for
graphene-lithium system to be able to analyze the charge transfer from
lithium to graphene.

Can someone please explain to me how can i do it by using quantum-espresso?

Thanks,

Gulcin
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From bogus@does.not.exist.com  Sat Jul 21 16:05:02 2012
From: bogus@does.not.exist.com ()
Date: Sat, 21 Jul 2012 14:05:02 -0000
Subject: No subject
Message-ID: <mailman.0.1348848214.1433.pw_forum@pwscf.org>

Is it possible to save the ionic POSITION and VELOCITY at every MD step
in a separate file in pw.x  (I know its possible for CP.x)?
what keyword I have to use?
can anyone explain, what is printed in  pwscf.md, pwscf.mix1

Here is my input
 &CONTROL
  nstep        = 50,
  dt           = 10.D0,
  calculation  = "md",
  outdir       = "./",
  pseudo_dir      = "./",
  restart_mode = "restart",
  disk_io="high"
  verbosity="high"
/
&SYSTEM
  nosym       = .TRUE.,
  ibrav       = 1,
  celldm(1)   = 10.D0,
  nat         = 4,
  ntyp        = 2,
  ecutwfc     = 24.0D0,
  ecutrho     = 144.0D0,
  occupations = "smearing",
  degauss     = 0.01D0,
  smearing    = "gauss",
/
&ELECTRONS
  diagonalization='cg'
  conv_thr    = 1.D-7,
  mixing_beta = 0.5D0,
/
&IONS
  tempw             = 500.D0,
  ion_temperature   = "rescaling",
  nraise            = 1,
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/
ATOMIC_SPECIES
H   1.0  H.US_PBE.RRKJ3.UPF
C  12.0  C.US_PBE.RRKJ3.UPF
ATOMIC_POSITIONS { bohr }
C        0.000000000   0.000000000   0.000000000  0 0 0
C        2.100000000   0.000000000   0.000000000
H       -1.600000000   0.400000000   0.000000000
H        3.600000000  -0.400000000   0.000000000
K_POINTS { gamma }

Thanking You
A