From masoudnahali at gmail.com  Fri Jul  1 00:38:24 2011
From: masoudnahali at gmail.com (Masoud Nahali)
Date: Fri, 1 Jul 2011 03:08:24 +0430
Subject: [Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
Message-ID: <BANLkTiks_MJUG7AAT4HtydftzNXgj4-XZg@mail.gmail.com>

Dear Quantum Espresso Users

In QE (version 4.2) the code read and open shared objects without any error
but in QE (version 4.3 and 4.3.1) the code cannot open libmkl_intel_lp64.so
file and so I cannot run the examples of QE successfully.
The MKL libraries path was exactly included in the .bashrc file,  mpif90
works well, and all versions were compiled without any error. The versions
were configured by "./configure MPIF90=mpif90 F77=gfortran" and then made.
But, only I can run all examples of QE (version 4.2) successfully and for
the 4.3 and 4.3.1 ones I get the error while loading shared libraries:
libmkl_intel_lp64.so: cannot open shared object file: No such file or
directory. It is strange for me what makes such difference.
Thank you for your help in advance. I appreciate the answers.


Best Wishes

 Masoud



--------------
Masoud Nahali, Sharif University of Technology
masoud.nahali at gmail.com;
alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali>

P Please don't print this e-mail unless you really need to.
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From zhaohscas at yahoo.com.cn  Fri Jul  1 02:11:47 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Fri, 01 Jul 2011 08:11:47 +0800
Subject: [Pw_forum] error in vc-md at 700K, 72GPa calculations
In-Reply-To: <BANLkTinmzTBQfNfrEHWbufBsH6uFceWfPA@mail.gmail.com>
References: <BANLkTin=JKJf4chMsiwfX-cnHg0JgBbt9A@mail.gmail.com>	<3C92746F-ECA9-4B52-B357-D7A8CC747A80@democritos.it>
	<BANLkTinmzTBQfNfrEHWbufBsH6uFceWfPA@mail.gmail.com>
Message-ID: <4E0D10C3.3080504@yahoo.com.cn>

On 06/30/2011 10:42 PM, WANG Wei wrote:
> Prof. Giannozzi,
> It should be press=720     ! 72GPa.
> By the way, what are the values of ave,  avec,  e,  eal,   p,   tv files
> in the vc-md calculations.

 From where you know  the unit for press should be Gpa in default?  I 
think for the other things you mentioned above, perhaps you can find 
hints from the same place.

Regards.
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From mayankaditya at gmail.com  Fri Jul  1 06:17:43 2011
From: mayankaditya at gmail.com (mayank gupta)
Date: Fri, 1 Jul 2011 09:47:43 +0530
Subject: [Pw_forum] phonon at q=0
Message-ID: <BANLkTimUgVaXt_gokrWn=NVU2qwVqkRtrA@mail.gmail.com>

Dear All
I have a query ragrdin phonon calculations at q=0. When I performed
the phonon caclualtion at q=0, we didn't get zero enrgy for acoustic
branches, however they can be set to zero by using acoustic/ crystal
sum rules. My question is if the zone center acoustic braches values
are too large (4 THz) even we have implemented very high convergence,
it is ok to apply ASR.

Thanks

-- 
Mayank

BHABHA ATOMIC RESEARCH CENTER
MUMBAI, INDIA
Office: ?022-25595606
Home: 9920397437 / 9869834437

From baroni at sissa.it  Fri Jul  1 07:25:24 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 1 Jul 2011 07:25:24 +0200
Subject: [Pw_forum] Query regarding real space interatomic force constant
In-Reply-To: <11E9D1A89846924196F177C70CCBDACB159A7C03DF@EXPO17.exchange.mit.edu>
References: <11E9D1A89846924196F177C70CCBDACB159A7C03DF@EXPO17.exchange.mit.edu>
Message-ID: <88EE9D44-783B-4119-9C7E-ACF7A17EE11B@sissa.it>

Dear Sandeep,

sure it can, if you take all the periodic replica of any atom into account (as one should).

SB

On Jun 30, 2011, at 7:28 PM, Sandeep Kumar wrote:

> Dear PWSCF users,
> I have carried out linear response phonon calculations for Al over a 4 * 4 * 4 grid of q-points. This corresponds to a calculation in a supercell comprised of 4 * 4* 4 unit cells (primitive).
> We recall that the lattice vectors in fractional coordinate system of a fcc primitive cell are-
> a=(0.5, 0.5, 0.0)
> b=(0.0, 0.5, 0.5)
> c=(0.5, 0.0, 0.5)
> 
>> From the force-constant file (Al44.fc)  I obtained the force constant matrix Phi(i1,i2, na, nb) for pairs of atoms in the super-cell with the relative positions given  by
> R = (i-1)*a + (j-1)*b +(k-1)*c
> where i j and k are read from Al444.fc file.
> However, such a supercell does not include the pair of atoms located along the cube axis direction i.e R = (a,0,0) or (0,a,0) or (0,0,a), and hence the calculation CAN NOT give us the force-constant matrices along those pair of atoms.
> How do we obtain the force-constant matrices for pair of atoms located along the cube axes direction.
> I will be VERY VERY GRATEFUL to any help in this regard.
> 
> Sandeep K. Lahiri
> Department of Mechanical Engineering
> Massachusetts Institute of Technology
> Cambridge, MA
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
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

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From baroni at sissa.it  Fri Jul  1 07:29:16 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 1 Jul 2011 07:29:16 +0200
Subject: [Pw_forum] phonon at q=0
In-Reply-To: <BANLkTimUgVaXt_gokrWn=NVU2qwVqkRtrA@mail.gmail.com>
References: <BANLkTimUgVaXt_gokrWn=NVU2qwVqkRtrA@mail.gmail.com>
Message-ID: <E2932345-C772-4814-959E-33FB60981DBC@sissa.it>

Dear Mayanka,

is this a polar material? If so, the violation of the ASR may be justified by the use of too coarse a k-point mesh. Please, provide more details on the system and the calculations you are doing. 

SB

On Jul 1, 2011, at 6:17 AM, mayank gupta wrote:

> Dear All
> I have a query ragrdin phonon calculations at q=0. When I performed
> the phonon caclualtion at q=0, we didn't get zero enrgy for acoustic
> branches, however they can be set to zero by using acoustic/ crystal
> sum rules. My question is if the zone center acoustic braches values
> are too large (4 THz) even we have implemented very high convergence,
> it is ok to apply ASR.
> 
> Thanks
> 
> -- 
> Mayank
> 
> BHABHA ATOMIC RESEARCH CENTER
> MUMBAI, INDIA
> Office:  022-25595606
> Home: 9920397437 / 9869834437
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
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

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From giannozz at democritos.it  Fri Jul  1 08:58:58 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 01 Jul 2011 08:58:58 +0200
Subject: [Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
In-Reply-To: <BANLkTiks_MJUG7AAT4HtydftzNXgj4-XZg@mail.gmail.com>
References: <BANLkTiks_MJUG7AAT4HtydftzNXgj4-XZg@mail.gmail.com>
Message-ID: <1309503538.27434.5.camel@fe12lx.fisica.uniud.it>

On Fri, 2011-07-01 at 03:08 +0430, Masoud Nahali wrote:

> The MKL libraries path was exactly included in the .bashrc file,
>   ...] I can run all examples of QE (version 4.2) successfully and for
> the 4.3 and 4.3.1 ones I get the error while loading shared libraries:
> libmkl_intel_lp64.so: cannot open shared object file: No such file or
> directory. It is strange for me what makes such difference. 

if I remember correctly, v.4.2 was linking *.a (static) mkl libraries,
while v 4.3 links *.so (shared) libraries, by default. You can verify
this using "ldd executable-file-name". If a compiled code doesn't
find shared libraries, there is something incorrect in your init files.

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From degironc at sissa.it  Fri Jul  1 09:18:07 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 01 Jul 2011 09:18:07 +0200
Subject: [Pw_forum] error in vc-md at 700K, 72GPa calculations
In-Reply-To: <4E0D10C3.3080504@yahoo.com.cn>
References: <BANLkTin=JKJf4chMsiwfX-cnHg0JgBbt9A@mail.gmail.com>	<3C92746F-ECA9-4B52-B357-D7A8CC747A80@democritos.it>	<BANLkTinmzTBQfNfrEHWbufBsH6uFceWfPA@mail.gmail.com>
	<4E0D10C3.3080504@yahoo.com.cn>
Message-ID: <4E0D74AF.9010804@sissa.it>

the unit of pressure is KBar.. you can know it from the documentation, 
for instance INPUT_PW.html

sometime it's useful.
stefano

On 07/01/2011 02:11 AM, Hongsheng Zhao wrote:
> On 06/30/2011 10:42 PM, WANG Wei wrote:
>> Prof. Giannozzi,
>> It should be press=720     ! 72GPa.
>> By the way, what are the values of ave,  avec,  e,  eal,   p,   tv files
>> in the vc-md calculations.
>    From where you know  the unit for press should be Gpa in default?  I
> think for the other things you mentioned above, perhaps you can find
> hints from the same place.
>
> Regards.


From giannozz at democritos.it  Fri Jul  1 09:45:34 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 01 Jul 2011 09:45:34 +0200
Subject: [Pw_forum] init_london Error
In-Reply-To: <BANLkTin+VVugkjJLH8RVGE16GvTvfy+z3Q@mail.gmail.com>
References: <BANLkTi=Mv+k3E4gdy0cte-=QH_AokHUoQg@mail.gmail.com>
	<201106231152.33600.giuseppe.mattioli@mlib.ism.cnr.it>
	<BANLkTimh1nVwwzbMfoKe3JpwXcNiHzicHw@mail.gmail.com>
	<201106301112.40013.giuseppe.mattioli@mlib.ism.cnr.it>
	<BANLkTin+VVugkjJLH8RVGE16GvTvfy+z3Q@mail.gmail.com>
Message-ID: <1309506334.27434.14.camel@fe12lx.fisica.uniud.it>

On Thu, 2011-06-30 at 12:36 -0400, Vikas Varshney wrote:

> Lets say for my system of interest, I want to use LDA functionals with
> vdw-DF setting (which will modify the wavefunctions) and run an SCF
> calculation on a previously relaxed geometry. Then, I do the phonon
> dispersion calculation (...). In that case, will the calculated 
> dynamical matrix include the interactions from vdw forces as well?

only in part, because you will start from vdw-aware wavefunctions,
but you will miss the vdw term in the second derivative of the
exchange-correlation functional. I just heard rumors that this
will be soon implemented, though

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From degironc at sissa.it  Fri Jul  1 09:49:54 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 01 Jul 2011 09:49:54 +0200
Subject: [Pw_forum] init_london Error
In-Reply-To: <1309506334.27434.14.camel@fe12lx.fisica.uniud.it>
References: <BANLkTi=Mv+k3E4gdy0cte-=QH_AokHUoQg@mail.gmail.com>	<201106231152.33600.giuseppe.mattioli@mlib.ism.cnr.it>	<BANLkTimh1nVwwzbMfoKe3JpwXcNiHzicHw@mail.gmail.com>	<201106301112.40013.giuseppe.mattioli@mlib.ism.cnr.it>	<BANLkTin+VVugkjJLH8RVGE16GvTvfy+z3Q@mail.gmail.com>
	<1309506334.27434.14.camel@fe12lx.fisica.uniud.it>
Message-ID: <4E0D7C22.9040803@sissa.it>

vdW-DF is not yet implemented in the DFPT part.
we are working on that,
stefano
-
Stefano de Gironcoli - SISSA and DEMOCRITOS

On 07/01/2011 09:45 AM, Paolo Giannozzi wrote:
> On Thu, 2011-06-30 at 12:36 -0400, Vikas Varshney wrote:
>
>> Lets say for my system of interest, I want to use LDA functionals with
>> vdw-DF setting (which will modify the wavefunctions) and run an SCF
>> calculation on a previously relaxed geometry. Then, I do the phonon
>> dispersion calculation (...). In that case, will the calculated
>> dynamical matrix include the interactions from vdw forces as well?
> only in part, because you will start from vdw-aware wavefunctions,
> but you will miss the vdw term in the second derivative of the
> exchange-correlation functional. I just heard rumors that this
> will be soon implemented, though
>
> P.


From dalcorso at sissa.it  Fri Jul  1 10:01:48 2011
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Fri, 01 Jul 2011 10:01:48 +0200
Subject: [Pw_forum] Problem with high accuracy and parallel ph.x
In-Reply-To: <BANLkTikjpAMV4t4eyN80dCn4+uNjznF63Q@mail.gmail.com>
References: <BANLkTikjpAMV4t4eyN80dCn4+uNjznF63Q@mail.gmail.com>
Message-ID: <1309507308.2219.17.camel@localhost.localdomain>

Please note that the maximum number of k points is still a parameter in
QE (presently set to 40000), so to make phonon calculations with a very
large mesh of k points you have to increase the value of npk in
Modules/parameters.f90. 


HTH,

Andrea


On Thu, 2011-06-30 at 11:58 +0330, Mohammad Saghayezhian wrote:
> Dear All,
> 
> When I perform the scf calculation with high kp (45 45 45) and cut-off
> (42 Ry), the parallel execution ph.x fails and stops (q-points in
> ph.in: 4 4 3). but lowering the kp (15 15 15) and cut-off (22 Ry)
> solves the problem and the parallel ph.x goes on without any problem.
> Does this mean that I can not calculate phonon spectra with this
> accuracy?
> Also, the calculations are for metals.
> 
> 
> > Dear PWscf users,
> >
> > I have encountered a problem during parallel execution of ph,x
> >
> > Actually the parallel pw,x performs good and without any error, but
> ph.x does not work,
> > I lowered the kpoints and kinetic-energy cut-off and the problem
> solved and ph.x works properly.
> > I need high accuracy in my calculation, so I cannot lower the
> kpoints and cut-off.
> > How can I perform parallel ph.x without lowering the computational
> parameters?
> >
> > Any help would be appreciated.
> > Thanks.
> >
> > ------------------------------
> -------------------------------------
> > Mohammad Saghayezhian
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> 
> ---
> 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
> 
> Please, if possible, don't  send me MS Word or PowerPoint attachments
> Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html
> 
> 
> 
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> 
> -- 
> -------------------------------------------------------------------
> Mohammad Saghayezhian
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



From giuseppe.mattioli at mlib.ism.cnr.it  Fri Jul  1 11:19:17 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Fri, 1 Jul 2011 11:19:17 +0200
Subject: [Pw_forum] charged defect in a unit cell
In-Reply-To: <BANLkTinEB68iOy57qLX8SVyEe29E1n4W=Q@mail.gmail.com>
References: <BANLkTinEB68iOy57qLX8SVyEe29E1n4W=Q@mail.gmail.com>
Message-ID: <201107011119.17132.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Tram Bui
First, you may want to carefully read the following paper:

Van de Walle, C. G.; Neugebauer, J. J. Appl. Phys. 95, 3851 (2004)

HTH
Giuseppe

On Thursday 30 June 2011 23:33:21 Tram Bui wrote:
> Hi Everyone,
>      I'm working with the beta- SiC, zinc-blend structure, and I have come
> across some paper talking about the energy formation of a charged defect,
> e.g. carbon vacancy with positive charge 1, or positive charge 2, or
> silicon vacancy with positive charge 1 or negative charge 1.  For example,
> if I'd like to calculate the energy for carbon vacancy with positive charge
> 2, how would I do that? So would anyone please give me some information on
> how to make the cell charged in quantum espresso?
>
> Regards,
>
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu



-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
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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.
********************************************************

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? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? 
? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ?
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? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From masoudnahali at gmail.com  Fri Jul  1 11:26:12 2011
From: masoudnahali at gmail.com (Masoud Nahali)
Date: Fri, 1 Jul 2011 13:56:12 +0430
Subject: [Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
Message-ID: <BANLkTimUG86OxxotwU3RMdfUmkwxks0E+Q@mail.gmail.com>

Dear Paolo

Thanks for your reply; it is the results of list dynamic dependencies
command for pw.x binary of QE (4.2) and QE (4.3.1) :

*looki at looki:~$ ldd /home/looki/QE4.3.1/QE/bin/pw.x*

    linux-vdso.so.1 =>  (0x00007fff489e2000)
    libfftw3.so.3 => /usr/lib/libfftw3.so.3 (0x00007fe662b13000)
    libmkl_intel_lp64.so => not found
    libmkl_sequential.so => not found
    libmkl_core.so => not found
    libmpi_f90.so.0 => /usr/lib/libmpi_f90.so.0 (0x00007fe66290e000)
    libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x00007fe6626d5000)
    libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007fe662425000)
    libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007fe6621d9000)
    libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007fe661f64000)
    libdl.so.2 => /lib/libdl.so.2 (0x00007fe661d60000)
    libnsl.so.1 => /lib/libnsl.so.1 (0x00007fe661b46000)
    libutil.so.1 => /lib/libutil.so.1 (0x00007fe661942000)
    libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007fe661655000)
    libm.so.6 => /lib/libm.so.6 (0x00007fe6613d2000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fe6611ba000)
    libpthread.so.0 => /lib/libpthread.so.0 (0x00007fe660f9d000)
    libc.so.6 => /lib/libc.so.6 (0x00007fe660c1a000)
    /lib64/ld-linux-x86-64.so.2 (0x00007fe662e30000)

*looki at looki:~$ ldd /home/looki/QE4.2/QE/bin/pw.x *

    linux-vdso.so.1 =>  (0x00007fff61dff000)
    libfftw3.so.3 => /usr/lib/libfftw3.so.3 (0x00007f4ae2c3f000)
    libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x00007f4ae22a4000)
    libmpi_f90.so.0 => /usr/lib/libmpi_f90.so.0 (0x00007f4ae209f000)
    libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x00007f4ae1e67000)
    libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007f4ae1bb7000)
    libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007f4ae196a000)
    libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007f4ae16f6000)
    libdl.so.2 => /lib/libdl.so.2 (0x00007f4ae14f2000)
    libnsl.so.1 => /lib/libnsl.so.1 (0x00007f4ae12d7000)
    libutil.so.1 => /lib/libutil.so.1 (0x00007f4ae10d4000)
    libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f4ae0de7000)
    libm.so.6 => /lib/libm.so.6 (0x00007f4ae0b63000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f4ae094c000)
    libpthread.so.0 => /lib/libpthread.so.0 (0x00007f4ae072f000)
    libc.so.6 => /lib/libc.so.6 (0x00007f4ae03ab000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f4ae2f5c000)


   Although the exact path of MKL libraries was included in .bashrc file, as
it is shown "libmkl_intel_lp64.so" and some other *.so files were not found
by QE (4.3.1).  In addition, I have copied the library files to /usr/lib and
for a test the code was configured with including the path of library
directory by LIBDIR. In all tries both QE (4.2) and QE(4.3.1) compiles well
but QE (4.3.1) could not find shared libraries such as libmkl_intel_lp64.so
and stopped. I appreciate your help in advance.


Best Wishes

 Masoud



--------------
Masoud Nahali, Sharif University of Technology
masoud.nahali at gmail.com;
alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali>

P Please don't print this e-mail unless you really need to.


> On Fri, 2011-07-01 at 03:08 +0430, Masoud Nahali wrote:
>
> > The MKL libraries path was exactly included in the .bashrc file,
> >   ...] I can run all examples of QE (version 4.2) successfully and for
> > the 4.3 and 4.3.1 ones I get the error while loading shared libraries:
> > libmkl_intel_lp64.so: cannot open shared object file: No such file or
> > directory. It is strange for me what makes such difference.
>


    On Fri, Jul 1, 2011 at 11:48 AM, Paolo Giannozzi wrote:

 if I remember correctly, v.4.2 was linking *.a (static) mkl libraries,
> while v 4.3 links *.so (shared) libraries, by default. You can verify
> this using "ldd executable-file-name". If a compiled code doesn't
> find shared libraries, there is something incorrect in your init files.
>
> P.
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
>
>
>
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From m.saghayezhian at gmail.com  Fri Jul  1 12:17:01 2011
From: m.saghayezhian at gmail.com (Mohammad Saghayezhian)
Date: Fri, 1 Jul 2011 06:17:01 -0400
Subject: [Pw_forum] Problem with high accuracy and parallel ph.x
	(Mohammad Saghayezhian)
Message-ID: <BANLkTimjt6JEgMYNPjm0oHNkNQ5KP8mj=w@mail.gmail.com>

Dear Andrea,

Thanks for reply.

The nkp in my calculation is far less than 40000. As I know, the symmetry
reduces nkp,
therefore for a mesh of 30*30*28 the max nkp is 25200, So if the problem
rooted in max nkp parameter,
above mesh should not make any problem, there are some
tests that I did for checking the valid nkp and cut-off energy:
Cut-off(Ry) , Kpoints: 33, 22*22*18 (OK)
                                35, 25*25*22 (OK)
                                35, 30*30*26 ()
                                38, 22*22*18 (OK)
                                38, 30*30*26 (Failed)
                                40, 30*30*26 (Failed)
All of above number kpoints are lower that nkp max (40000). I also run the
calculation
without npool option to provide higher memory for large cut-off. but still I
wonder why
the last two calculation did not worked!

Could it be due to optimization deficiency in compilation of ph.x files?
Please take a look at this links:
http://www.democritos.it/pipermail/pw_forum/2005-February/002070.html
 http://www.democritos.it/pipermail/pw_forum/2005-February/002074.html
Thanks a lot



On Thu, Fri, 01 Jul 2011 10:01:48 +0200,  Andrea Dal Corso wrote:
>Please note that the maximum number of k points is still a parameter in
>QE (presently set to 40000), so to make phonon calculations with a very
>large mesh of k points you have to increase the value of npk in
>Modules/parameters.f90.


>HTH,

>Andrea



On Thu, 2011-06-30 at 11:58 +0330, Mohammad Saghayezhian wrote:
> Dear All,
>
> When I perform the scf calculation with high kp (45 45 45) and cut-off
> (42 Ry), the parallel execution ph.x fails and stops (q-points in
> ph.in: 4 4 3). but lowering the kp (15 15 15) and cut-off (22 Ry)
> solves the problem and the parallel ph.x goes on without any problem.
> Does this mean that I can not calculate phonon spectra with this
> accuracy?
> Also, the calculations are for metals.
-- 
-------------------------------------------------------------------
Mohammad Saghayezhian
Computational Condensed Matter Research Lab
Physics Department, Isfahan University of Technology, Isfahan, Iran

Tel lab: +98 311 391 3731     Fax Office: +98311 391 3746
-------------------------------------------------------------------
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From giannozz at democritos.it  Fri Jul  1 12:28:56 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 01 Jul 2011 12:28:56 +0200
Subject: [Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
In-Reply-To: <BANLkTimUG86OxxotwU3RMdfUmkwxks0E+Q@mail.gmail.com>
References: <BANLkTimUG86OxxotwU3RMdfUmkwxks0E+Q@mail.gmail.com>
Message-ID: <1309516136.27434.38.camel@fe12lx.fisica.uniud.it>

On Fri, 2011-07-01 at 13:56 +0430, Masoud Nahali wrote:


>  In all tries both QE (4.2) and QE(4.3.1) compiles well but QE (4.3.1)
> could not find shared libraries such as libmkl_intel_lp64.so and stopped

once again: it is a problem of your software setup, not of QE.
You should put in your .basrch, .profile, .cshrc, .whatever,
the correct initialization for MKL libraries. What you have
is either not correct or not executed when it is needed. 

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From dalcorso at sissa.it  Fri Jul  1 13:03:34 2011
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Fri, 01 Jul 2011 13:03:34 +0200
Subject: [Pw_forum] Problem with high accuracy and parallel
	ph.x	(Mohammad Saghayezhian)
In-Reply-To: <BANLkTimjt6JEgMYNPjm0oHNkNQ5KP8mj=w@mail.gmail.com>
References: <BANLkTimjt6JEgMYNPjm0oHNkNQ5KP8mj=w@mail.gmail.com>
Message-ID: <20110701130334.xho2bjdn6s8g8k8c@webmail.sissa.it>

Which is the error message, if there is one. Note that the phonon code
at a low symmetry q point requires much more k points than the pw.x code.

Andrea


Quoting Mohammad Saghayezhian <m.saghayezhian at gmail.com>:

> Dear Andrea,
>
> Thanks for reply.
>
> The nkp in my calculation is far less than 40000. As I know, the symmetry
> reduces nkp,
> therefore for a mesh of 30*30*28 the max nkp is 25200, So if the problem
> rooted in max nkp parameter,
> above mesh should not make any problem, there are some
> tests that I did for checking the valid nkp and cut-off energy:
> Cut-off(Ry) , Kpoints: 33, 22*22*18 (OK)
>                                 35, 25*25*22 (OK)
>                                 35, 30*30*26 ()
>                                 38, 22*22*18 (OK)
>                                 38, 30*30*26 (Failed)
>                                 40, 30*30*26 (Failed)
> All of above number kpoints are lower that nkp max (40000). I also run the
> calculation
> without npool option to provide higher memory for large cut-off. but still I
> wonder why
> the last two calculation did not worked!
>
> Could it be due to optimization deficiency in compilation of ph.x files?
> Please take a look at this links:
> http://www.democritos.it/pipermail/pw_forum/2005-February/002070.html
>  http://www.democritos.it/pipermail/pw_forum/2005-February/002074.html
> Thanks a lot
>
>
>
> On Thu, Fri, 01 Jul 2011 10:01:48 +0200,  Andrea Dal Corso wrote:
>> Please note that the maximum number of k points is still a parameter in
>> QE (presently set to 40000), so to make phonon calculations with a very
>> large mesh of k points you have to increase the value of npk in
>> Modules/parameters.f90.
>
>
>> HTH,
>
>> Andrea
>
>
>
> On Thu, 2011-06-30 at 11:58 +0330, Mohammad Saghayezhian wrote:
>> Dear All,
>>
>> When I perform the scf calculation with high kp (45 45 45) and cut-off
>> (42 Ry), the parallel execution ph.x fails and stops (q-points in
>> ph.in: 4 4 3). but lowering the kp (15 15 15) and cut-off (22 Ry)
>> solves the problem and the parallel ph.x goes on without any problem.
>> Does this mean that I can not calculate phonon spectra with this
>> accuracy?
>> Also, the calculations are for metals.
> --
> -------------------------------------------------------------------
> Mohammad Saghayezhian
> Computational Condensed Matter Research Lab
> Physics Department, Isfahan University of Technology, Isfahan, Iran
>
> Tel lab: +98 311 391 3731     Fax Office: +98311 391 3746
> -------------------------------------------------------------------
>



----------------------------------------------------------------
   SISSA Webmail https://webmail.sissa.it/
   Powered by Horde http://www.horde.org/



From zhaohscas at yahoo.com.cn  Fri Jul  1 13:05:54 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Fri, 01 Jul 2011 19:05:54 +0800
Subject: [Pw_forum] error in vc-md at 700K, 72GPa calculations
In-Reply-To: <4E0D74AF.9010804@sissa.it>
References: <BANLkTin=JKJf4chMsiwfX-cnHg0JgBbt9A@mail.gmail.com>	<3C92746F-ECA9-4B52-B357-D7A8CC747A80@democritos.it>	<BANLkTinmzTBQfNfrEHWbufBsH6uFceWfPA@mail.gmail.com>	<4E0D10C3.3080504@yahoo.com.cn>
	<4E0D74AF.9010804@sissa.it>
Message-ID: <4E0DAA12.7000905@yahoo.com.cn>

On 07/01/2011 03:18 PM, Stefano de Gironcoli wrote:
> the unit of pressure is KBar.. you can know it from the documentation,
> for instance INPUT_PW.html

Thanks a lot for your hints.

Best.
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From zhaohscas at yahoo.com.cn  Fri Jul  1 13:14:28 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Fri, 01 Jul 2011 19:14:28 +0800
Subject: [Pw_forum] About the md in pwscf.
Message-ID: <4E0DAC14.5040504@yahoo.com.cn>

Hi all,

I've some puzzles on the md method fulfilled in pwscf.

I know should be cp-based md within the pwscf.  The issue of mine is: 
for which properties/systems should I consider to do a md relative 
calations using pwscf (md, vc-md)?  Thank your for any  hints.

Best
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From baroni at sissa.it  Fri Jul  1 14:11:49 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 1 Jul 2011 14:11:49 +0200
Subject: [Pw_forum] About the md in pwscf.
In-Reply-To: <4E0DAC14.5040504@yahoo.com.cn>
References: <4E0DAC14.5040504@yahoo.com.cn>
Message-ID: <BDE47E10-15D5-4281-92B0-16A86BC6A424@sissa.it>


On Jul 1, 2011, at 1:14 PM, Hongsheng Zhao wrote:

> Hi all,
> 
> I've some puzzles on the md method fulfilled in pwscf.
> 
> I know should be cp-based md within the pwscf.  

NO pw.x performs Born-Oppenheimer MD. CP MD is performed by cp.x

> The issue of mine is: 
> for which properties/systems should I consider to do a md relative 
> calations using pwscf (md, vc-md)?  Thank your for any  hints.

Not sure I understand the question.

SB

> Best
> -- 
> Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
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

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From giuseppe.mattioli at mlib.ism.cnr.it  Fri Jul  1 14:30:28 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Fri, 1 Jul 2011 14:30:28 +0200
Subject: [Pw_forum] init_london Error
In-Reply-To: <4E0D7C22.9040803@sissa.it>
References: <BANLkTi=Mv+k3E4gdy0cte-=QH_AokHUoQg@mail.gmail.com>
	<1309506334.27434.14.camel@fe12lx.fisica.uniud.it>
	<4E0D7C22.9040803@sissa.it>
Message-ID: <201107011430.28909.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Vikas
A final remark: 

> I am using GGA functionals
> for my relaxation. So, as you mentioned vdw-DF is improved for LDA
> type of functionals, I will stick with the london option.

The vdW-DF functional is not a simple LDA xc functional. It contains a 
long-range LDA correlation contribution. Some lines extracted from the 
Modules/funct.f90 file may help to explain:

  !              "pz"    = "sla+pz"            = Perdew-Zunger LDA
  !              "pbe"   = "sla+pw+pbx+pbc"    = PBE
  !              "revpbe"= "sla+pw+rpb+pbc"    = revPBE (Zhang-Yang)
  !              "vdw-df"= "sla+pw+rpb+vdw"    = vdW-DF
  !
  ! Exchange: 
  !              "sla"    Slater (alpha=2/3)             
  !
  ! Correlation: "noc"    none                           
  !              "pz"     Perdew-Zunger                  
  !              "pw"     Perdew-Wang                    
  !
  ! Gradient Correction on Exchange:
  !              "pbx"    Perdew-Burke-Ernzenhof exch   
  !              "rpb"    revised PBE by Zhang-Yang      
  !
  ! Gradient Correction on Correlation:
  !
  !              "pbc"    Perdew-Burke-Ernzenhof corr    
  !
  ! Van der Waals functionals
  !              "nonlc"   none                           
  !              "vdw1"    vdW-DF1                       
  !              "vdw2"    vdW-DF2                       
  !
  ! References:
  !              pz      J.P.Perdew and A.Zunger, PRB 23, 5048 (1981) 
  !              pbe     J.P.Perdew, K.Burke, M.Ernzerhof, PRL 77, 3865 (1996)
  !              pw91    J.P.Perdew and Y. Wang, PRB 46, 6671 (1992)
  !              revPBE  Zhang and Yang, PRL 80, 890 (1998)
  !              vdW-DF  M. Dion et al., PRL 92, 246401 (2004)
  !                      T. Thonhauser et al., PRB 76, 125112 (2007)

Yours
Giuseppe

On Friday 01 July 2011 09:49:54 Stefano de Gironcoli wrote:
> vdW-DF is not yet implemented in the DFPT part.
> we are working on that,
> stefano
> -
> Stefano de Gironcoli - SISSA and DEMOCRITOS
>
> On 07/01/2011 09:45 AM, Paolo Giannozzi wrote:
> > On Thu, 2011-06-30 at 12:36 -0400, Vikas Varshney wrote:
> >> Lets say for my system of interest, I want to use LDA functionals with
> >> vdw-DF setting (which will modify the wavefunctions) and run an SCF
> >> calculation on a previously relaxed geometry. Then, I do the phonon
> >> dispersion calculation (...). In that case, will the calculated
> >> dynamical matrix include the interactions from vdw forces as well?
> >
> > only in part, because you will start from vdw-aware wavefunctions,
> > but you will miss the vdw term in the second derivative of the
> > exchange-correlation functional. I just heard rumors that this
> > will be soon implemented, though
> >
> > P.
>
> _______________________________________________
> 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 zhaohscas at yahoo.com.cn  Fri Jul  1 14:42:07 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Fri, 01 Jul 2011 20:42:07 +0800
Subject: [Pw_forum] About the md in pwscf.
In-Reply-To: <BDE47E10-15D5-4281-92B0-16A86BC6A424@sissa.it>
References: <4E0DAC14.5040504@yahoo.com.cn>
	<BDE47E10-15D5-4281-92B0-16A86BC6A424@sissa.it>
Message-ID: <4E0DC09F.7000501@yahoo.com.cn>

On 07/01/2011 08:11 PM, Stefano Baroni wrote:
>
> On Jul 1, 2011, at 1:14 PM, Hongsheng Zhao wrote:
>
>> Hi all,
>>
>> I've some puzzles on the md method fulfilled in pwscf.
>>
>> I know should be cp-based md within the pwscf.
>
> NO pw.x performs Born-Oppenheimer MD. CP MD is performed by cp.x

Thanks for this explanation.

>
>> The issue of mine is:
>> for which properties/systems should I consider to do a md relative
>> calations using pwscf (md, vc-md)? Thank your for any hints.
>
> Not sure I understand the question.

It's me that should give more detailed/specific descriptions on my issue.

By saying Born-Oppenheimer MD, I think it has the same meaning of "First 
principle molecular dynamics", am I right?

Furthermore, I've learned that the "Full-potential linear Muffin Tin 
orbital combination method" is also an implementation of "First 
principle molecular dynamics".  It's well knows that the FP-LMTO is 
among the most accurate DFT calculations.
So, for a specific calculation, say, bandstructure, should I select MD 
or common DFT within   Quantum Espresso?

Regards.
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From vv0210 at gmail.com  Fri Jul  1 15:40:38 2011
From: vv0210 at gmail.com (Vikas Varshney)
Date: Fri, 1 Jul 2011 09:40:38 -0400
Subject: [Pw_forum] init_london Error
In-Reply-To: <201107011430.28909.giuseppe.mattioli@mlib.ism.cnr.it>
References: <BANLkTi=Mv+k3E4gdy0cte-=QH_AokHUoQg@mail.gmail.com>
	<1309506334.27434.14.camel@fe12lx.fisica.uniud.it>
	<4E0D7C22.9040803@sissa.it>
	<201107011430.28909.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <BANLkTim44u3sszZXBEL16Vijr43p78BFWA@mail.gmail.com>

Thank you all of you (Pablo, Stefano and Giuseppe)
It did clarify many of my confusions.

Best Wishes,
Vikas

On Fri, Jul 1, 2011 at 8:30 AM, Giuseppe Mattioli
<giuseppe.mattioli at mlib.ism.cnr.it> wrote:
>
> Dear Vikas
> A final remark:
>
>> I am using GGA functionals
>> for my relaxation. So, as you mentioned vdw-DF is improved for LDA
>> type of functionals, I will stick with the london option.
>
> The vdW-DF functional is not a simple LDA xc functional. It contains a
> long-range LDA correlation contribution. Some lines extracted from the
> Modules/funct.f90 file may help to explain:
>
> ?! ? ? ? ? ? ? ?"pz" ? ?= "sla+pz" ? ? ? ? ? ?= Perdew-Zunger LDA
> ?! ? ? ? ? ? ? ?"pbe" ? = "sla+pw+pbx+pbc" ? ?= PBE
> ?! ? ? ? ? ? ? ?"revpbe"= "sla+pw+rpb+pbc" ? ?= revPBE (Zhang-Yang)
> ?! ? ? ? ? ? ? ?"vdw-df"= "sla+pw+rpb+vdw" ? ?= vdW-DF
> ?!
> ?! Exchange:
> ?! ? ? ? ? ? ? ?"sla" ? ?Slater (alpha=2/3)
> ?!
> ?! Correlation: "noc" ? ?none
> ?! ? ? ? ? ? ? ?"pz" ? ? Perdew-Zunger
> ?! ? ? ? ? ? ? ?"pw" ? ? Perdew-Wang
> ?!
> ?! Gradient Correction on Exchange:
> ?! ? ? ? ? ? ? ?"pbx" ? ?Perdew-Burke-Ernzenhof exch
> ?! ? ? ? ? ? ? ?"rpb" ? ?revised PBE by Zhang-Yang
> ?!
> ?! Gradient Correction on Correlation:
> ?!
> ?! ? ? ? ? ? ? ?"pbc" ? ?Perdew-Burke-Ernzenhof corr
> ?!
> ?! Van der Waals functionals
> ?! ? ? ? ? ? ? ?"nonlc" ? none
> ?! ? ? ? ? ? ? ?"vdw1" ? ?vdW-DF1
> ?! ? ? ? ? ? ? ?"vdw2" ? ?vdW-DF2
> ?!
> ?! References:
> ?! ? ? ? ? ? ? ?pz ? ? ?J.P.Perdew and A.Zunger, PRB 23, 5048 (1981)
> ?! ? ? ? ? ? ? ?pbe ? ? J.P.Perdew, K.Burke, M.Ernzerhof, PRL 77, 3865 (1996)
> ?! ? ? ? ? ? ? ?pw91 ? ?J.P.Perdew and Y. Wang, PRB 46, 6671 (1992)
> ?! ? ? ? ? ? ? ?revPBE ?Zhang and Yang, PRL 80, 890 (1998)
> ?! ? ? ? ? ? ? ?vdW-DF ?M. Dion et al., PRL 92, 246401 (2004)
> ?! ? ? ? ? ? ? ? ? ? ? ?T. Thonhauser et al., PRB 76, 125112 (2007)
>
> Yours
> Giuseppe
>
> On Friday 01 July 2011 09:49:54 Stefano de Gironcoli wrote:
>> vdW-DF is not yet implemented in the DFPT part.
>> we are working on that,
>> stefano
>> -
>> Stefano de Gironcoli - SISSA and DEMOCRITOS
>>
>> On 07/01/2011 09:45 AM, Paolo Giannozzi wrote:
>> > On Thu, 2011-06-30 at 12:36 -0400, Vikas Varshney wrote:
>> >> Lets say for my system of interest, I want to use LDA functionals with
>> >> vdw-DF setting (which will modify the wavefunctions) and run an SCF
>> >> calculation on a previously relaxed geometry. Then, I do the phonon
>> >> dispersion calculation (...). In that case, will the calculated
>> >> dynamical matrix include the interactions from vdw forces as well?
>> >
>> > only in part, because you will start from vdw-aware wavefunctions,
>> > but you will miss the vdw term in the second derivative of the
>> > exchange-correlation functional. I just heard rumors that this
>> > will be soon implemented, though
>> >
>> > P.
>>
>> _______________________________________________
>> 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
>

From baroni at sissa.it  Fri Jul  1 16:13:04 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 1 Jul 2011 16:13:04 +0200
Subject: [Pw_forum] About the md in pwscf.
In-Reply-To: <4E0DC09F.7000501@yahoo.com.cn>
References: <4E0DAC14.5040504@yahoo.com.cn>
	<BDE47E10-15D5-4281-92B0-16A86BC6A424@sissa.it>
	<4E0DC09F.7000501@yahoo.com.cn>
Message-ID: <871EFA29-5351-4586-AC16-66C6F25778AC@sissa.it>


On Jul 1, 2011, at 2:42 PM, Hongsheng Zhao wrote:

> It's me that should give more detailed/specific descriptions on my issue.
> 
> By saying Born-Oppenheimer MD, I think it has the same meaning of "First 
> principle molecular dynamics", am I right?

NO - both the Car-Parrinello and Born-Oppenheimer flavors of MD are respectable "first-principles molecular dynamics"

> Furthermore, I've learned that the "Full-potential linear Muffin Tin 
> orbital combination method" is also an implementation of "First 
> principle molecular dynamics".

I am afraid there is a whole lot of confusion, here. "Full-potential etc." is a technique to perform electronic-structure calculations. Whether or not FPLMTO implementations of AIMD exist, I do not know. QE is entireley based on pseudopotentials.

>  It's well knows that the FP-LMTO is 
> among the most accurate DFT calculations.
> So, for a specific calculation, say, bandstructure, should I select MD 
> or common DFT within   Quantum Espresso?

I wonder how you could calculate a band structure via molecular dynamics (ab initio or other)

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

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From wonvein at gmail.com  Fri Jul  1 18:37:01 2011
From: wonvein at gmail.com (WANG Wei)
Date: Sat, 2 Jul 2011 01:37:01 +0900
Subject: [Pw_forum] Problems with vc-relaxed calculation
Message-ID: <BANLkTi=XWx35VwU0foPF90yRGH9s4m2z8A@mail.gmail.com>

Dear QE users,

Why are the total energy and press of the final step of vc-relax
calculation different from those of the scf calculation using the same
structure?  Especially for the values of press, what makes this great
difference between the final step of vc-relax calculation and the final scf
calculation (after the vc-relax calculation)?

(1) For the final step of vc-relax calculation, the press and total energy
are:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
!    total energy              =     -73.74310183 Ry

          total   stress  (Ry/bohr**3)                   (kbar)     P=
-0.03
  -0.00000009   0.00000001   0.00000000         -0.01      0.00      0.00
   0.00000001  -0.00000008   0.00000000          0.00     -0.01      0.00
   0.00000000   0.00000000  -0.00000048          0.00      0.00     -0.07
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

(2) For the final scf calculations, the press and total energy are:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
!    total energy              =     -74.60031750 Ry

          total   stress  (Ry/bohr**3)                   (kbar)     P=
638.94
   0.00760001  -0.00000151   0.00000000       1118.00     -0.22      0.00
  -0.00000151   0.00759826   0.00000000         -0.22   1117.74      0.00
   0.00000000   0.00000000  -0.00216804          0.00      0.00   -318.93
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Regards,
WANG
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From wonvein at gmail.com  Fri Jul  1 18:37:46 2011
From: wonvein at gmail.com (WANG Wei)
Date: Sat, 2 Jul 2011 01:37:46 +0900
Subject: [Pw_forum] MD+vdW-DF is not implemented?
In-Reply-To: <4197EB00-27D9-4078-9E42-885CF40E77EC@democritos.it>
References: <BANLkTinXUZ1kf8hcZefyBE6ymYNPx3XGkQ@mail.gmail.com>
	<4197EB00-27D9-4078-9E42-885CF40E77EC@democritos.it>
Message-ID: <BANLkTiny_R2-Dara+1B_FJjdm9KKf8rvsw@mail.gmail.com>

Dear Prof. Giannozzi,

Thank you for your reply. That's a good news for me! I am performing some
BOMD tests with vdW-DF.

Sincererly yours?
WANG

On 30 June 2011 22:45, Paolo Giannozzi <giannozz at democritos.it> wrote:

>
> On Jun 30, 2011, at 8:01 , WANG Wei wrote:
>
> > I note that the vdW-DF is not implemented in MD calculations
> > (md, vc-md, and cp)?
>
> is this a question or a statement? in any case: vW-dDF is not
> implemented for Car-Parrinello dynamics (code CP) and in
> linear-response (phonon) calculations
>
> 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 vv0210 at gmail.com  Fri Jul  1 18:43:10 2011
From: vv0210 at gmail.com (Vikas Varshney)
Date: Fri, 1 Jul 2011 12:43:10 -0400
Subject: [Pw_forum] Problems with vc-relaxed calculation
In-Reply-To: <BANLkTi=XWx35VwU0foPF90yRGH9s4m2z8A@mail.gmail.com>
References: <BANLkTi=XWx35VwU0foPF90yRGH9s4m2z8A@mail.gmail.com>
Message-ID: <BANLkTim2ir2F-H8xCHYzvOfbVeaozXwsSQ@mail.gmail.com>

Did you update the cell dimensions correctly? For example, if your
celldm(1) and celldm(3) before relax are a and c. Lets say after
relax, they become 1.1a and 1.2c. In the final scf calculation, new a
should be 1.1a and and new c shsould be (1.2/1.1)*c.

I dont know if this is the case but just wanted to tell that. Not much
help can be done until more input is provided.

Hope this helps
Vikas


On Fri, Jul 1, 2011 at 12:37 PM, WANG Wei <wonvein at gmail.com> wrote:
> Dear QE users,
>
> Why?are?the total energy and press?of the final step of vc-relax
> calculation?different from those of?the scf?calculation?using the same
> structure?? Especially for the?values of press, what makes this great
> difference between the final step of vc-relax calculation and the final scf
> calculation (after the vc-relax calculation)?
>
> (1) For the final step of vc-relax calculation, the press and total energy
> are:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> !??? total energy????????????? =???? -73.74310183 Ry
>
> ????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=
> -0.03
> ? -0.00000009?? 0.00000001?? 0.00000000???????? -0.01????? 0.00????? 0.00
> ?? 0.00000001? -0.00000008?? 0.00000000????????? 0.00???? -0.01????? 0.00
> ?? 0.00000000?? 0.00000000? -0.00000048????????? 0.00????? 0.00???? -0.07
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> (2) For the final scf calculations, the press and total energy are:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> !??? total energy????????????? =???? -74.60031750 Ry
>
> ????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=
> 638.94
> ?? 0.00760001? -0.00000151?? 0.00000000?????? 1118.00???? -0.22????? 0.00
> ? -0.00000151?? 0.00759826?? 0.00000000???????? -0.22?? 1117.74????? 0.00
> ?? 0.00000000?? 0.00000000? -0.00216804????????? 0.00????? 0.00?? -318.93
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> Regards,
> WANG
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From wonvein at gmail.com  Fri Jul  1 18:45:58 2011
From: wonvein at gmail.com (WANG Wei)
Date: Sat, 2 Jul 2011 01:45:58 +0900
Subject: [Pw_forum] error in vc-md at 700K, 72GPa calculations
In-Reply-To: <4E0D74AF.9010804@sissa.it>
References: <BANLkTin=JKJf4chMsiwfX-cnHg0JgBbt9A@mail.gmail.com>
	<3C92746F-ECA9-4B52-B357-D7A8CC747A80@democritos.it>
	<BANLkTinmzTBQfNfrEHWbufBsH6uFceWfPA@mail.gmail.com>
	<4E0D10C3.3080504@yahoo.com.cn> <4E0D74AF.9010804@sissa.it>
Message-ID: <BANLkTimOy7fobRpqF3tQxC3TLDj0Y8Q4GQ@mail.gmail.com>

Thank you, Stefano de Gironcoli. But I could not find the meanings of
valules in the ave,  avec,  e,  eal,   p,   tv files.
I note that the these values are defined in vcsmd.f90. However, I could not
understand of some variables. Where can I find the declarations of these
variables?

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     WRITE( iun_e,   101 ) ut, ekint, edyn, pv, nst
     WRITE( iun_eal, 103 ) uta, eka, eta, utl, ekla, etl, nst
     WRITE( iun_ave, 104 ) avu, avk, nst
     WRITE( iun_p,   105 ) press, p, avp, nst

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

On 1 July 2011 16:18, Stefano de Gironcoli <degironc at sissa.it> wrote:

> the unit of pressure is KBar.. you can know it from the documentation,
> for instance INPUT_PW.html
>
> sometime it's useful.
> stefano
>
> On 07/01/2011 02:11 AM, Hongsheng Zhao wrote:
> > On 06/30/2011 10:42 PM, WANG Wei wrote:
> >> Prof. Giannozzi,
> >> It should be press=720     ! 72GPa.
> >> By the way, what are the values of ave,  avec,  e,  eal,   p,   tv files
> >> in the vc-md calculations.
> >    From where you know  the unit for press should be Gpa in default?  I
> > think for the other things you mentioned above, perhaps you can find
> > hints from the same place.
> >
> > Regards.
>
>  _______________________________________________
> 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  Fri Jul  1 18:51:39 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 1 Jul 2011 18:51:39 +0200
Subject: [Pw_forum] error in vc-md at 700K, 72GPa calculations
In-Reply-To: <BANLkTimOy7fobRpqF3tQxC3TLDj0Y8Q4GQ@mail.gmail.com>
References: <BANLkTin=JKJf4chMsiwfX-cnHg0JgBbt9A@mail.gmail.com>
	<3C92746F-ECA9-4B52-B357-D7A8CC747A80@democritos.it>
	<BANLkTinmzTBQfNfrEHWbufBsH6uFceWfPA@mail.gmail.com>
	<4E0D10C3.3080504@yahoo.com.cn> <4E0D74AF.9010804@sissa.it>
	<BANLkTimOy7fobRpqF3tQxC3TLDj0Y8Q4GQ@mail.gmail.com>
Message-ID: <DB7FF000-1ECF-46A5-8D51-7B53C8F952E2@democritos.it>


On Jul 1, 2011, at 18:45 , WANG Wei wrote:

> But I could not find the meanings of values in the ave,  avec,  e,   
> eal,
> p,   tv files. [...]. Where can I find the declarations of these  
> variables?

  these variables are undocumented

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 wonvein at gmail.com  Fri Jul  1 18:55:09 2011
From: wonvein at gmail.com (WANG Wei)
Date: Sat, 2 Jul 2011 01:55:09 +0900
Subject: [Pw_forum] Problems with vc-relaxed calculation
In-Reply-To: <BANLkTim2ir2F-H8xCHYzvOfbVeaozXwsSQ@mail.gmail.com>
References: <BANLkTi=XWx35VwU0foPF90yRGH9s4m2z8A@mail.gmail.com>
	<BANLkTim2ir2F-H8xCHYzvOfbVeaozXwsSQ@mail.gmail.com>
Message-ID: <BANLkTim5qf+GDaACvAX3ZzfFAX2g8k3R7A@mail.gmail.com>

Vikas, I mean that the values of the the last-step (scf) calculation  are
significantly different from those of second-step calculation (vc-relax)
from bottom.  Thank you!


&control
   calculation = 'vc-relax'
!   restart_mode='from_scratch',
   prefix='graphite',
   tstress = .true.
   tprnfor = .true.
    pseudo_dir   = "/home/wangvei/works/quantum-espresso/pseudo",
    outdir       = "./",
    disk_io  = 'none'
    forc_conv_thr = 1.0e-3
/
&system
    ibrav           = 4
    celldm(1)       = 4.68
    celldm(3)       = 2.70
    nat             = 4
    ntyp            = 1
    occupations = "smearing",
    smearing    = "gaussian",
    degauss     = 0.002D0,
    ecutwfc         = 40.0
    ecutrho         = 200
!    input_dft       = 'vdw1'
/
&electrons
    conv_thr        = 1.0d-8
/
&ions
/
&cell
    press_conv_thr  = 0.5D0
    press           = 0.D0
    cell_dynamics   = 'bfgs'
/
ATOMIC_SPECIES
C   12.00   C.pbe-paw_kj.UPF
ATOMIC_POSITIONS {crystal}
 C     0.00000   0.00000   0.25000
 C     0.00000   0.00000   0.75000
 C     0.33333   0.66667   0.25000
 C     0.66667   0.33333   0.75000
K_POINTS automatic
9 9 4 0 0 0




On 2 July 2011 01:43, Vikas Varshney <vv0210 at gmail.com> wrote:

> Did you update the cell dimensions correctly? For example, if your
> celldm(1) and celldm(3) before relax are a and c. Lets say after
> relax, they become 1.1a and 1.2c. In the final scf calculation, new a
> should be 1.1a and and new c shsould be (1.2/1.1)*c.
>
> I dont know if this is the case but just wanted to tell that. Not much
> help can be done until more input is provided.
>
> Hope this helps
> Vikas
>
>
> On Fri, Jul 1, 2011 at 12:37 PM, WANG Wei <wonvein at gmail.com> wrote:
> > Dear QE users,
> >
> > Why are the total energy and press of the final step of vc-relax
> > calculation different from those of the scf calculation using the same
> > structure?  Especially for the values of press, what makes this great
> > difference between the final step of vc-relax calculation and the final
> scf
> > calculation (after the vc-relax calculation)?
> >
> > (1) For the final step of vc-relax calculation, the press and total
> energy
> > are:
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > !    total energy              =     -73.74310183 Ry
> >
> >           total   stress  (Ry/bohr**3)                   (kbar)     P=
> > -0.03
> >   -0.00000009   0.00000001   0.00000000         -0.01      0.00      0.00
> >    0.00000001  -0.00000008   0.00000000          0.00     -0.01      0.00
> >    0.00000000   0.00000000  -0.00000048          0.00      0.00     -0.07
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> > (2) For the final scf calculations, the press and total energy are:
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > !    total energy              =     -74.60031750 Ry
> >
> >           total   stress  (Ry/bohr**3)                   (kbar)     P=
> > 638.94
> >    0.00760001  -0.00000151   0.00000000       1118.00     -0.22      0.00
> >   -0.00000151   0.00759826   0.00000000         -0.22   1117.74      0.00
> >    0.00000000   0.00000000  -0.00216804          0.00      0.00   -318.93
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> > Regards,
> > WANG
> >
> > _______________________________________________
> > 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 giannozz at democritos.it  Fri Jul  1 18:58:20 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 1 Jul 2011 18:58:20 +0200
Subject: [Pw_forum] Problems with vc-relaxed calculation
In-Reply-To: <BANLkTi=XWx35VwU0foPF90yRGH9s4m2z8A@mail.gmail.com>
References: <BANLkTi=XWx35VwU0foPF90yRGH9s4m2z8A@mail.gmail.com>
Message-ID: <2AE6BE32-0645-4723-9C9D-43DEA18DDE5A@democritos.it>


On Jul 1, 2011, at 18:37 , WANG Wei wrote:

>  Why are the total energy and press of the final step of vc-relax
> calculation different from those of the scf calculation using the  
> same structure?

this question has been asked 10^8 times. Either it is not the same  
structrure,
or if it is the same, the plane wave basis set is not the same, for  
reasons that
have been explained 10^8 times

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 wonvein at gmail.com  Fri Jul  1 19:01:58 2011
From: wonvein at gmail.com (WANG Wei)
Date: Sat, 2 Jul 2011 02:01:58 +0900
Subject: [Pw_forum] Problems with vc-relaxed calculation
In-Reply-To: <2AE6BE32-0645-4723-9C9D-43DEA18DDE5A@democritos.it>
References: <BANLkTi=XWx35VwU0foPF90yRGH9s4m2z8A@mail.gmail.com>
	<2AE6BE32-0645-4723-9C9D-43DEA18DDE5A@democritos.it>
Message-ID: <BANLkTineD0_B=f6eCNxYD1EahDnVpNAGww@mail.gmail.com>

Thank you, Prof. Giannozzi.  :)

On 2 July 2011 01:58, Paolo Giannozzi <giannozz at democritos.it> wrote:

>
> On Jul 1, 2011, at 18:37 , WANG Wei wrote:
>
> >  Why are the total energy and press of the final step of vc-relax
> > calculation different from those of the scf calculation using the
> > same structure?
>
> this question has been asked 10^8 times. Either it is not the same
> structrure,
> or if it is the same, the plane wave basis set is not the same, for
> reasons that
> have been explained 10^8 times
>
> 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 wonvein at gmail.com  Fri Jul  1 19:10:17 2011
From: wonvein at gmail.com (WANG Wei)
Date: Sat, 2 Jul 2011 02:10:17 +0900
Subject: [Pw_forum] The overestimation of graphite lattice using
	vc-relax+vdW-DF
Message-ID: <BANLkTimUn_zgPQpZnfOqs=pFMDDeMHcBSg@mail.gmail.com>

Hello, everyone. As a benchmark test, I performed the vc-relax+vdW-DF
calculations for graphite. The opitimized lattice constants seem to be
unreasonable using vc-relax+vdW-DF. It is overestimated about about 29% for
a. I don't know what the problem is.

#############################################################################################
          total   stress  (Ry/bohr**3)                   (kbar)     P=
-0.01
  -0.00000002   0.00000000   0.00000000          0.00      0.00      0.00
   0.00000000  -0.00000002   0.00000000          0.00      0.00      0.00
   0.00000000   0.00000000  -0.00000007          0.00      0.00     -0.01

     The maximum number of steps has been reached.
     End of BFGS Geometry Optimization
Begin final coordinates
     new unit-cell volume =    450.28054 a.u.^3 (    66.72469 Ang^3 )
CELL_PARAMETERS (alat=  4.68000000)
   1.292794235  -0.000000090   0.000000000
  -0.646397196   1.119592604   0.000000000
   0.000000000   0.000000000   3.034982637
ATOMIC_POSITIONS (crystal)
C       -0.000001693   0.000001693   0.250000000
C        0.000001693  -0.000001693   0.750000000
C        0.333331648   0.666668352   0.250000000
C        0.666668352   0.333331648   0.750000000
End final coordinates
######################################################################################



&control
   calculation = 'vc-relax'
!   restart_mode='from_scratch',
   prefix='graphite',
   tstress = .true.
   tprnfor = .true.
    pseudo_dir   = "/home/wangvei/works/quantum-espresso/pseudo",
    outdir       = "./",
    disk_io  = 'none'
    forc_conv_thr = 1.0e-3
   nstep =  45  ,
               etot_conv_thr = 1.0E-4 ,
               forc_conv_thr = 1.0D-3 ,
                      iprint = 1 ,
                 max_seconds = 36000 ,
                          dt = 100 ,
/
&system
    ibrav           = 4
    celldm(1)       = 4.68
    celldm(3)       = 2.70
    nat             = 4
    ntyp            = 1
    occupations = "smearing",
    smearing    = "gaussian",
    degauss     = 0.002D0,
    ecutwfc         = 40.0
    ecutrho         = 200
    input_dft       = 'vdw1'
/
&electrons
    conv_thr        = 1.0d-8
/
&ions
/
&cell
    press_conv_thr  = 0.0D0
    press           = 0.D0
    cell_dynamics   = 'bfgs'
!    cell_dofree     = 'z'
/
ATOMIC_SPECIES
C   12.00   C.pbe-paw_kj.UPF
ATOMIC_POSITIONS {crystal}
 C     0.00000   0.00000   0.25000
 C     0.00000   0.00000   0.75000
 C     0.33333   0.66667   0.25000
 C     0.66667   0.33333   0.75000
K_POINTS automatic
9 9 4 0 0 0
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From wonvein at gmail.com  Sat Jul  2 03:10:10 2011
From: wonvein at gmail.com (WANG Wei)
Date: Sat, 2 Jul 2011 10:10:10 +0900
Subject: [Pw_forum] The overestimation of graphite lattice using
	vc-relax+vdW-DF
In-Reply-To: <BANLkTimUn_zgPQpZnfOqs=pFMDDeMHcBSg@mail.gmail.com>
References: <BANLkTimUn_zgPQpZnfOqs=pFMDDeMHcBSg@mail.gmail.com>
Message-ID: <BANLkTinWqbvSdec_GOgYkPEMvEsg8p7A8A@mail.gmail.com>

Is it a bug? The optimized lattice constants of vdW-DF is so different from
those of vdw1, namely,

When I set input_dft       = 'vdw-DF', I got the


          total   stress  (Ry/bohr**3)                   (kbar)     P=
0.03
   0.00000033   0.00000000   0.00000000          0.05      0.00      0.00
   0.00000000   0.00000033   0.00000000          0.00      0.05      0.00
   0.00000000   0.00000000  -0.00000003          0.00      0.00      0.00

 CELL_PARAMETERS (alat=  4.68000000)
   1.000251032   0.000000003   0.000000000
  -0.500125514   0.866242806   0.000000000
   0.000000000   0.000000000   2.845991200


However,  I set input_dft       = 'vdw1', I got the

          total   stress  (Ry/bohr**3)                   (kbar)     P=
-0.01
  -0.00000002   0.00000000   0.00000000          0.00      0.00      0.00
   0.00000000  -0.00000002   0.00000000          0.00      0.00      0.00
   0.00000000   0.00000000  -0.00000007          0.00      0.00     -0.01

CELL_PARAMETERS (alat=  4.68000000)
   1.292794235  -0.000000090   0.000000000
  -0.646397196   1.119592604   0.000000000
   0.000000000   0.000000000   3.034982637
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From giannozz at democritos.it  Sat Jul  2 10:07:49 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 2 Jul 2011 10:07:49 +0200
Subject: [Pw_forum] The overestimation of graphite lattice using
	vc-relax+vdW-DF
In-Reply-To: <BANLkTinWqbvSdec_GOgYkPEMvEsg8p7A8A@mail.gmail.com>
References: <BANLkTimUn_zgPQpZnfOqs=pFMDDeMHcBSg@mail.gmail.com>
	<BANLkTinWqbvSdec_GOgYkPEMvEsg8p7A8A@mail.gmail.com>
Message-ID: <CF42636C-778E-464E-B9C1-F6F8CDC5AF75@democritos.it>


On Jul 2, 2011, at 3:10 , WANG Wei wrote:

> However,  I set input_dft       = 'vdw1', I got the

'vdw1' /= 'vdw-DF', as explained in the documentation
and reprinted in the output. The correct name is 'vdw-DF'.

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 mayankaditya at gmail.com  Sat Jul  2 12:02:50 2011
From: mayankaditya at gmail.com (mayank gupta)
Date: Sat, 2 Jul 2011 15:32:50 +0530
Subject: [Pw_forum] Phonon at q=0
Message-ID: <CAHNEyD9gFQiyRKoX7cZ-QOyZQAE5DEyDV1Te9-sKCQAV=CXO_Q@mail.gmail.com>

Thanks Sir for your response.

I am doing all these calculations for oxides. for example I have done
the phonon calculations for Cu2O and Ag2O system the details are as
follow

Ag2O ecutwfc 70 Ry.  Mesh  (8x8x8)        zone ceneter acoustic
mode=1.6 THz (with PBE)
Cu2O ecutwfc  95 Ry. Mesh  (8x8x8)        zone centre acoustic mode =
1.33 THz (PW)

I have performed above calculation using tr2_ph=1.0e-14, but the
values are almost same. the ecutrho=20times of ecutwfc.


Mayank


> Dear Mayanka,
>
> is this a polar material? If so, the violation of the ASR may be justified
> by the use of too coarse a k-point mesh. Please, provide more details on the
> system and the calculations you are doing.
>
> SB
>
> On Jul 1, 2011, at 6:17 AM, mayank gupta wrote:
>
>> Dear All
>> I have a query ragrdin phonon calculations at q=0. When I performed
>> the phonon caclualtion at q=0, we didn't get zero enrgy for acoustic
>> branches, however they can be set to zero by using acoustic/ crystal
>> sum rules. My question is if the zone center acoustic braches values
>> are too large (4 THz) even we have implemented very high convergence,
>> it is ok to apply ASR.
>>
>> Thanks
>>
>> --
>> Mayank


BHABHA ATOMIC RESEARCH CENTER
MUMBAI, INDIA
Office:  022-25595606
Home: 9920397437 / 9869834437

From baroni at sissa.it  Sat Jul  2 16:17:33 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Sat, 2 Jul 2011 16:17:33 +0200
Subject: [Pw_forum] Phonon at q=0
In-Reply-To: <CAHNEyD9gFQiyRKoX7cZ-QOyZQAE5DEyDV1Te9-sKCQAV=CXO_Q@mail.gmail.com>
References: <CAHNEyD9gFQiyRKoX7cZ-QOyZQAE5DEyDV1Te9-sKCQAV=CXO_Q@mail.gmail.com>
Message-ID: <80AC6D24-FCEC-4D84-A441-36C53155534F@sissa.it>

Try to increase the number of k points and let us know what happens. If, as I guess, the zone-center acoustic modes soften, try to understand why, starting from the early literature on DFPT. A good starting point could be e.g., http://link.aps.org/doi/10.1103/PhysRevB.33.7017 and http://link.aps.org/doi/10.1103/PhysRevLett.62.2853 .
Hope this helps
Stefano Baroni

On Jul 2, 2011, at 12:02 PM, mayank gupta wrote:

> Thanks Sir for your response.
> 
> I am doing all these calculations for oxides. for example I have done
> the phonon calculations for Cu2O and Ag2O system the details are as
> follow
> 
> Ag2O ecutwfc 70 Ry.  Mesh  (8x8x8)        zone ceneter acoustic
> mode=1.6 THz (with PBE)
> Cu2O ecutwfc  95 Ry. Mesh  (8x8x8)        zone centre acoustic mode =
> 1.33 THz (PW)
> 
> I have performed above calculation using tr2_ph=1.0e-14, but the
> values are almost same. the ecutrho=20times of ecutwfc.
> 
> 
> Mayank
> 
> 
>> Dear Mayanka,
>> 
>> is this a polar material? If so, the violation of the ASR may be justified
>> by the use of too coarse a k-point mesh. Please, provide more details on the
>> system and the calculations you are doing.
>> 
>> SB
>> 
>> On Jul 1, 2011, at 6:17 AM, mayank gupta wrote:
>> 
>>> Dear All
>>> I have a query ragrdin phonon calculations at q=0. When I performed
>>> the phonon caclualtion at q=0, we didn't get zero enrgy for acoustic
>>> branches, however they can be set to zero by using acoustic/ crystal
>>> sum rules. My question is if the zone center acoustic braches values
>>> are too large (4 THz) even we have implemented very high convergence,
>>> it is ok to apply ASR.
>>> 
>>> Thanks
>>> 
>>> --
>>> Mayank
> 
> 
> BHABHA ATOMIC RESEARCH CENTER
> MUMBAI, INDIA
> Office:  022-25595606
> Home: 9920397437 / 9869834437
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
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

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From masoudnahali at gmail.com  Sat Jul  2 16:43:08 2011
From: masoudnahali at gmail.com (Masoud Nahali)
Date: Sat, 2 Jul 2011 19:13:08 +0430
Subject: [Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
Message-ID: <CAM-1hSvznhamShy+_HqsgcUXvUN_RBf5nprxzYrV9-SH0-pW+g@mail.gmail.com>

Dear Paolo and QE Users

I am writing since maybe it is useful for others; I replaced the MKL
(10.2.3.029) by MKL (10.3.4.191, version of 2011.4.19) and got rid of the
error. Now, all examples run well.


Best Wishes

 Masoud



--------------
Masoud Nahali, Sharif University of Technology
masoud.nahali at gmail.com;
alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali>

P Please don't print this e-mail unless you really need to.




> On Fri, 2011-07-01 at 13:56 +0430, Masoud Nahali wrote:
>
>
> >  In all tries both QE (4.2) and QE(4.3.1) compiles well but QE (4.3.1)
> > could not find shared libraries such as libmkl_intel_lp64.so and stopped
>
> once again: it is a problem of your software setup, not of QE.
> You should put in your .basrch, .profile, .cshrc, .whatever,
> the correct initialization for MKL libraries. What you have
> is either not correct or not executed when it is needed.
>
> P.
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
>
>
>
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From baroni at sissa.it  Sat Jul  2 18:00:27 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Sat, 2 Jul 2011 18:00:27 +0200
Subject: [Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
In-Reply-To: <CAM-1hSvznhamShy+_HqsgcUXvUN_RBf5nprxzYrV9-SH0-pW+g@mail.gmail.com>
References: <CAM-1hSvznhamShy+_HqsgcUXvUN_RBf5nprxzYrV9-SH0-pW+g@mail.gmail.com>
Message-ID: <94706FFC-D2EC-4EFE-9024-E87DC166B977@sissa.it>

Masoud: we do appreciate your sharing the info. Thanks. Best regards - SB

On Jul 2, 2011, at 4:43 PM, Masoud Nahali wrote:

> 
> 
> Dear Paolo and QE Users
> 
> I am writing since maybe it is useful for others; I replaced the MKL (10.2.3.029) by MKL (10.3.4.191, version of 2011.4.19) and got rid of the error. Now, all examples run well. 
> 
> 
> Best Wishes
> 
>  Masoud
> 
> 
> 
> --------------
> Masoud Nahali, Sharif University of Technology
> masoud.nahali at gmail.com; alum.sharif.edu/~m_nahali
> P Please don't print this e-mail unless you really need to.
> 
> 
> 
> 
> 
> On Fri, 2011-07-01 at 13:56 +0430, Masoud Nahali wrote:
> 
> 
> >  In all tries both QE (4.2) and QE(4.3.1) compiles well but QE (4.3.1)
> > could not find shared libraries such as libmkl_intel_lp64.so and stopped
> 
> once again: it is a problem of your software setup, not of QE.
> You should put in your .basrch, .profile, .cshrc, .whatever,
> the correct initialization for MKL libraries. What you have
> is either not correct or not executed when it is needed.
> 
> 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

---
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

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From wangqj1 at 126.com  Sun Jul  3 05:20:11 2011
From: wangqj1 at 126.com (Q.J.Wang)
Date: Sun, 3 Jul 2011 11:20:11 +0800 (CST)
Subject: [Pw_forum] switch the direction of electric field
Message-ID: <27d00310.175.130ee02b0a4.Coremail.wangqj1@126.com>

Dear all
I want to add a sawlike potential on the slab, however, I don't know how to add a inverse sawlike potential. Does it set the parameter 'eamp' negative or exchange the value of 'emaxpos' and 'eopreg'?
Thank you in advance for your suggestions and help on this problem.

--

Best regards
 
Q.J.Wang
 
XiangTan University
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From zhaohscas at yahoo.com.cn  Sun Jul  3 09:43:29 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Sun, 03 Jul 2011 15:43:29 +0800
Subject: [Pw_forum] charged defect in a unit cell
In-Reply-To: <201107011119.17132.giuseppe.mattioli@mlib.ism.cnr.it>
References: <BANLkTinEB68iOy57qLX8SVyEe29E1n4W=Q@mail.gmail.com>
	<201107011119.17132.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <4E101DA1.7040407@yahoo.com.cn>

On 07/01/2011 05:19 PM, Giuseppe Mattioli wrote:
> Dear Tram Bui
> First, you may want to carefully read the following paper:
>
> Van de Walle, C. G.; Neugebauer, J. J. Appl. Phys. 95, 3851 (2004)

Should be J. Appl. Phys. 95, 3851 (2004).

Best
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From hqzhou at nju.edu.cn  Sun Jul  3 09:53:49 2011
From: hqzhou at nju.edu.cn (=?gbk?B?aHF6aG91IA==?=)
Date: Sun, 3 Jul 2011 15:53:49 +0800 (CST)
Subject: [Pw_forum] =?gbk?b?u9i4tKO6IFJlOiAgbGlibWtsX2ludGVsX2xwNjQgKFFF?=
 =?gbk?b?IDQuMiB2cyA0LjMp?=
In-Reply-To: <BANLkTimUG86OxxotwU3RMdfUmkwxks0E+Q@mail.gmail.com>
Message-ID: <73093103.232579.1309679629364.JavaMail.root@mailtmp.tmailer.org>

Masoud,

While you used generic BLAS/LAPACK libraries when you compiled your
qe 4.2, you were using MKL in compiling qe 4.3.1. But the compiler
never found where the MKL libraries are. How did you set the environment
for MKL? You should "source" the mklvarsem64t.sh in .bashrc or 
.bash_profile as below:

source /your ROOT of MKL installation/tools/environment/mklvarsem64t.sh

If your version of MKL is 11.1-073 and was installed in default directory, 
the sentence above should be:

source /opt/intel/Compiler/11.1/073/mkl/tools/environment/mklvarsem64t.sh 

Hope this help you.

zhou huiqun
@earth sciences, nanjing university, china


----- ???? -----
???: Masoud Nahali <masoudnahali at gmail.com>
???: pw forum <pw_forum at pwscf.org>
?????: Fri, 01 Jul 2011 17:26:12 +0800 (CST)
??: Re: [Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)

Dear Paolo

Thanks for your reply; it is the results of list dynamic dependencies
command for pw.x binary of QE (4.2) and QE (4.3.1) :

*looki at looki:~$ ldd /home/looki/QE4.3.1/QE/bin/pw.x*

    linux-vdso.so.1 =>  (0x00007fff489e2000)
    libfftw3.so.3 => /usr/lib/libfftw3.so.3 (0x00007fe662b13000)
    libmkl_intel_lp64.so => not found
    libmkl_sequential.so => not found
    libmkl_core.so => not found
    libmpi_f90.so.0 => /usr/lib/libmpi_f90.so.0 (0x00007fe66290e000)
    libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x00007fe6626d5000)
    libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007fe662425000)
    libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007fe6621d9000)
    libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007fe661f64000)
    libdl.so.2 => /lib/libdl.so.2 (0x00007fe661d60000)
    libnsl.so.1 => /lib/libnsl.so.1 (0x00007fe661b46000)
    libutil.so.1 => /lib/libutil.so.1 (0x00007fe661942000)
    libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007fe661655000)
    libm.so.6 => /lib/libm.so.6 (0x00007fe6613d2000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fe6611ba000)
    libpthread.so.0 => /lib/libpthread.so.0 (0x00007fe660f9d000)
    libc.so.6 => /lib/libc.so.6 (0x00007fe660c1a000)
    /lib64/ld-linux-x86-64.so.2 (0x00007fe662e30000)

*looki at looki:~$ ldd /home/looki/QE4.2/QE/bin/pw.x *

    linux-vdso.so.1 =>  (0x00007fff61dff000)
    libfftw3.so.3 => /usr/lib/libfftw3.so.3 (0x00007f4ae2c3f000)
    libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x00007f4ae22a4000)
    libmpi_f90.so.0 => /usr/lib/libmpi_f90.so.0 (0x00007f4ae209f000)
    libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x00007f4ae1e67000)
    libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007f4ae1bb7000)
    libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007f4ae196a000)
    libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007f4ae16f6000)
    libdl.so.2 => /lib/libdl.so.2 (0x00007f4ae14f2000)
    libnsl.so.1 => /lib/libnsl.so.1 (0x00007f4ae12d7000)
    libutil.so.1 => /lib/libutil.so.1 (0x00007f4ae10d4000)
    libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f4ae0de7000)
    libm.so.6 => /lib/libm.so.6 (0x00007f4ae0b63000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f4ae094c000)
    libpthread.so.0 => /lib/libpthread.so.0 (0x00007f4ae072f000)
    libc.so.6 => /lib/libc.so.6 (0x00007f4ae03ab000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f4ae2f5c000)


   Although the exact path of MKL libraries was included in .bashrc file, as
it is shown "libmkl_intel_lp64.so" and some other *.so files were not found
by QE (4.3.1).  In addition, I have copied the library files to /usr/lib and
for a test the code was configured with including the path of library
directory by LIBDIR. In all tries both QE (4.2) and QE(4.3.1) compiles well
but QE (4.3.1) could not find shared libraries such as libmkl_intel_lp64.so
and stopped. I appreciate your help in advance.


Best Wishes

 Masoud



--------------
Masoud Nahali, Sharif University of Technology
masoud.nahali at gmail.com;
alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali>

P Please don't print this e-mail unless you really need to.


> On Fri, 2011-07-01 at 03:08 +0430, Masoud Nahali wrote:
>
> > The MKL libraries path was exactly included in the .bashrc file,
> >   ...] I can run all examples of QE (version 4.2) successfully and for
> > the 4.3 and 4.3.1 ones I get the error while loading shared libraries:
> > libmkl_intel_lp64.so: cannot open shared object file: No such file or
> > directory. It is strange for me what makes such difference.
>


    On Fri, Jul 1, 2011 at 11:48 AM, Paolo Giannozzi wrote:

 if I remember correctly, v.4.2 was linking *.a (static) mkl libraries,
> while v 4.3 links *.so (shared) libraries, by default. You can verify
> this using "ldd executable-file-name". If a compiled code doesn't
> find shared libraries, there is something incorrect in your init files.
>
> P.
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
>
>
>


From yhho at pub.iams.sinica.edu.tw  Sun Jul  3 10:03:37 2011
From: yhho at pub.iams.sinica.edu.tw (yhho)
Date: Sun, 3 Jul 2011 16:03:37 +0800
Subject: [Pw_forum] About q2r.x problem
Message-ID: <002a01cc3957$b664d060$61706d8c@mychatd6d7d1f2>

Dear all
I am doing the phonon calculation now.
There's a waring message in output file when I was runing the q2r.x.

      fft-check warning: sum of imaginary terms = .1207107E-07

And when I ran matdyn.x, the other error appeared:

     Message from routine matdyn:
     Z* not found in file AuC444.fc, TO-LO splitting at q=0 will be absent!
     A direction for q was not specified:TO-LO splitting will be absent
     Message from routine matdyn:
     Z* not found in file AuC444.fc, TO-LO splitting at q=0 will be absent!
     A direction for q was not specified:TO-LO splitting will be absent

Although I still can get the xxx.freq to plot phonon dispersion, but the result was not great. 
I would like to ask that wether those warning and error are important or not?
How could I improve that?

 (scf.in)
 &control
    calculation ='scf'
    restart_mode ='from_scratch'
    pseudo_dir ='/lustre/lwork/dyyang/bin/espresso-4.0.3/pseudo/'
    outdir ='./'
    prefix ='AuC'
 /
 &system
    ibrav =4
    celldm(1)=  4.65217057370607
    celldm(3)=  6.0000
    nat =  4 ,
    ntyp =  1 ,
    ecutwfc = 60.0,
    ecutrho =  600.0,
    nosym=.FALSE.
    occupations ='smearing',
    smearing = "fd"
    degauss= 0.01
 /
 &electrons
    conv_thr =   1.0d-12
    electron_maxstep = 100
 /
&IONS
    ion_dynamics = 'bfgs',
/
 &CELL
     cell_dynamics='bfgs',
/
ATOMIC_SPECIES
  C 12.0107 C.pbe-rrkjus.UPF
ATOMIC_POSITIONS {crystal}
C        0.000000000   1.000000000  -0.109494500
C        0.333333333   0.666666667  -0.109385116
C        0.666666667  -0.666666667   0.468858184
C        0.333333333   0.666666667   0.468747968

K_POINTS automatic
6 6 4 0 0 0


 (ph.in)
phonons of AuC
 &inputph
  tr2_ph=1.0d-15,
  ldisp=.true.,
  nq1=8, nq2=8, nq3=1
  amass(1)= 12.0107
  prefix='AuC',
  outdir='./'
  fildyn='AuC.dyn',
  fildrho='disp.drho'
 /


thanks a lot

Best regards,

--
Yu-Han Ho
Research Assistant
Institute of Atomic and Molecular Sciences(IAMS), lab503
No. 1, Roosevelt Rd., Sec. 4, Taipei, 10617, Taiwan
Tel: 886-2-2362-0212

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From syuva2987 at gmail.com  Sun Jul  3 15:25:00 2011
From: syuva2987 at gmail.com (yuva rani)
Date: Sun, 3 Jul 2011 18:55:00 +0530
Subject: [Pw_forum] (no subject)
In-Reply-To: <BANLkTinPVv1gF4UbgteO3gRsiGn6e4sr3A@mail.gmail.com>
References: <BANLkTinPVv1gF4UbgteO3gRsiGn6e4sr3A@mail.gmail.com>
Message-ID: <CAM6Xv8mhp_JrK=MRo+x3UK6Gh+RfxAoJsccUjD3ZUs7syJf1Jg@mail.gmail.com>

On 6/27/11, yuva rani <syuva2987 at gmail.com> wrote:
> Sir I have just started working with quantum espresso. I am
> constructing a aluminium layer with 112 atom - 2 layers. I relaxed the
> structure obtaininga negative energy. But for the same parameters the
> SCF calculation has energy in terms of positive values. Whether it is
> correct or wrong, and here in the total energy sum the ewald
> contribution is more. How should I decrease this ewald contributiion
> and what parameter should be adjusted in the input.
> Here I have attached the input and output file for the aluminium
> pentacene stacking in which pentacene is at a distance of 3.5
> angstrom. Here the total system is not relaxed and only the SCF
> calculations are perfomed.
> Please any one suggest idea on this results and also give me the
> detailed usage of constraints and how to apply constraints in this
> problem during relaxation.
> Thanks in advance.
>

From mayankaditya at gmail.com  Mon Jul  4 08:07:23 2011
From: mayankaditya at gmail.com (mayank gupta)
Date: Mon, 4 Jul 2011 11:37:23 +0530
Subject: [Pw_forum] ACOUSTIC SUM RULES
Message-ID: <CAHNEyD-ZYi-GxvU2a+b70DRxbJtwyJ1GqdxepqDHt7NtyP999Q@mail.gmail.com>

Dear Users

Real space force constant calculations (q2r.x) and calculation of
phonon frequencies  (matdyn.x), we have to select acoustic sum rule
(ASR).  there are various type of sum rule,which sum rule should be
use (ACOUSTIC/CRYSTAL)  and in q2r.x and matdyn.x calculations the ASR
should be same or they can be different.

-- 
Mayank

BHABHA ATOMIC RESEARCH CENTER
MUMBAI, INDIA
Office: ?022-25595606
Home: 9920397437 / 9869834437

From trambui at u.boisestate.edu  Mon Jul  4 08:16:30 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Mon, 4 Jul 2011 00:16:30 -0600
Subject: [Pw_forum] charged defect in a unit cell
In-Reply-To: <4E101DA1.7040407@yahoo.com.cn>
References: <BANLkTinEB68iOy57qLX8SVyEe29E1n4W=Q@mail.gmail.com>
	<201107011119.17132.giuseppe.mattioli@mlib.ism.cnr.it>
	<4E101DA1.7040407@yahoo.com.cn>
Message-ID: <CANzxBn8e53M-nVMKKf0V3QxgVMY=KvSNQkueunF_D-tds1=+iA@mail.gmail.com>

Dear Giuseppe and Hongsheng,
 Thank you very much for your information. The paper was a great source. I
have read the paper couple times and also google here and there but there is
something I don't quite understand is the shallow acceptor. I take the
courage to ask you a little further into the paper. The authors mentioned of
the case where they took Mg acceptor in GaN, and the term Ecorr was used
 (eq. 3) in the shallow centers. Can some one help me to understand what a
shallow acceptor means? my guess was it is the energy level of the acceptor
(Mg in GaN) if lower than the thermal energy-->shallow, if higher--->deep.
Is that correct? I really appreciate your help.

Great Respect,
Tram

On Sun, Jul 3, 2011 at 1:43 AM, Hongsheng Zhao <zhaohscas at yahoo.com.cn>wrote:

> On 07/01/2011 05:19 PM, Giuseppe Mattioli wrote:
> > Dear Tram Bui
> > First, you may want to carefully read the following paper:
> >
> > Van de Walle, C. G.; Neugebauer, J. J. Appl. Phys. 95, 3851 (2004)
>
> Should be J. Appl. Phys. 95, 3851 (2004).
>
> Best
> --
> Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From Lorenzo.Paulatto at impmc.upmc.fr  Mon Jul  4 10:19:19 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Mon, 04 Jul 2011 10:19:19 +0200
Subject: [Pw_forum] About q2r.x problem
In-Reply-To: <002a01cc3957$b664d060$61706d8c@mychatd6d7d1f2>
References: <002a01cc3957$b664d060$61706d8c@mychatd6d7d1f2>
Message-ID: <op.vx25ehvwxuur8c@vanoxite.impmc.jussieu.fr>

On Sun, 03 Jul 2011 10:03:37 +0200, yhho <yhho at pub.iams.sinica.edu.tw>  
wrote:
> There's a waring message in output file when I was runing the q2r.x.
>
>       fft-check warning: sum of imaginary terms = .1207107E-07

Such a small amount of imaginary components in the dynamical matrices  
should pose no problem.

>      Message from routine matdyn:
>      Z* not found in file AuC444.fc, TO-LO splitting at q=0 will be  
> absent!
>      A direction for q was not specified:TO-LO splitting will be absent
>      Message from routine matdyn:
>      Z* not found in file AuC444.fc, TO-LO splitting at q=0 will be  
> absent!
>      A direction for q was not specified:TO-LO splitting will be absent
>
> Although I still can get the xxx.freq to plot phonon dispersion, but the  
> result was not great.

If your are NOT studying a polar material, there is no need for the  
effective charge (Z*) long range LO-TO splitting: you can safely ignore  
this warning.

> I would like to ask that wether those warning and error are important or  
> not?

I think they are not.

> How could I improve that?

If I understand your input correctly you are studying 2 very distant  
planes of graphene (why 2 of them??); converging graphene's phonons can be  
tricky especially w.r.t. the k-points. I think you may try to reduce the  
smearing and/or use a more efficient smearing scheme, while increasing the  
k-point sampling along x and y. You can also probably reduce the number of  
k-points along the z direction from 4 to 1; I doubt there is any  
significant interaction between planes that are more then 10 bohr apart!


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

From kangbugy at lycos.co.kr  Mon Jul  4 10:26:00 2011
From: kangbugy at lycos.co.kr (=?UTF-8?B?a2FuZ2J1Z3lAbHljb3MuY28ua3I=?=)
Date: Mon, 04 Jul 2011 17:26:00 +0900
Subject: [Pw_forum] =?utf-8?q?phonon_calculation_error?=
Message-ID: <52f988944f377e823c57f3b03efe7c9f$5c6718fe@pcmail3.nate.com>

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From mehrnooshhazrati at gmail.com  Mon Jul  4 12:47:51 2011
From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati)
Date: Mon, 4 Jul 2011 15:17:51 +0430
Subject: [Pw_forum] Charge Density
Message-ID: <CAHbvuiQ-qiCrMVsbz4kdiNeUxUBi=8y1PZv9AN3udk3P_+jp5w@mail.gmail.com>

Hi everyone,

I need to calculate the charge density of a graphene sheet, but i don't know
how can i choose e1, e2 and x0 for my system.

Thank you in advance
-- 
*

*
*
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
**** Mehrnoosh Kh. Hazrati ****
**** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
 *** Phone : +989123436300 ***
*** Mail : mehrnooshhazrati at gmail.com ***
*
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
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From songsong19840614 at gmail.com  Tue Jul  5 04:12:37 2011
From: songsong19840614 at gmail.com (lucking-pine)
Date: Tue, 5 Jul 2011 10:12:37 +0800
Subject: [Pw_forum] phonon partial density
Message-ID: <CAEBBOkLRsg3bHY_4XXnRgds0F6HDiMdv4WwBn56TSuzOrSJwLQ@mail.gmail.com>

I want to calculate the phonon partial density.But the example of pwscf have
not it.And I also find the method after searching Pw_forum mailist from
google.
I know the phonon dos is matdyn.x:
&input
asr='simple', amass(1)=65.003, amass(3)=16.000 flfrc='ZnO.fc',
flfrq='ZnO,freq', dos=.true.
fldos='ZnOphonon.dos', nk1=6, nk2=6, nk3=6, ndos=50

So how could I calculate the pdos,using projwfc.x or matdyn.x?
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From physics.skgupta at gmail.com  Tue Jul  5 05:04:10 2011
From: physics.skgupta at gmail.com (Sanjeev Gupta)
Date: Tue, 5 Jul 2011 08:34:10 +0530
Subject: [Pw_forum] phonon partial density
In-Reply-To: <CAEBBOkLRsg3bHY_4XXnRgds0F6HDiMdv4WwBn56TSuzOrSJwLQ@mail.gmail.com>
References: <CAEBBOkLRsg3bHY_4XXnRgds0F6HDiMdv4WwBn56TSuzOrSJwLQ@mail.gmail.com>
Message-ID: <CAB4TLPKzpuMUPzf-B9QWfA4pgYhjjqJdL4NRTTq8MDBUXsfi7g@mail.gmail.com>

Please first provide your affiliation.
The answer for your question is QHA, which is implemented in espresso.
Read the manual, and see old post, which is very useful.

Regrads
Sanjeev

On Tue, Jul 5, 2011 at 7:42 AM, lucking-pine <songsong19840614 at gmail.com>wrote:

> I want to calculate the phonon partial density.But the example of pwscf
> have not it.And I also find the method after searching Pw_forum mailist from
> google.
> I know the phonon dos is matdyn.x:
> &input
> asr='simple', amass(1)=65.003, amass(3)=16.000 flfrc='ZnO.fc',
> flfrq='ZnO,freq', dos=.true.
> fldos='ZnOphonon.dos', nk1=6, nk2=6, nk3=6, ndos=50
>
> So how could I calculate the pdos,using projwfc.x or matdyn.x?
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
*Dr. Sanjeev Kumar Gupta*
*Post Doctoral Fellow,

Department of Physics,
Bhavnagar University, Bhavnagar-364 022
Gujarat, India*
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From songsong19840614 at gmail.com  Tue Jul  5 05:54:40 2011
From: songsong19840614 at gmail.com (lucking-pine)
Date: Tue, 5 Jul 2011 11:54:40 +0800
Subject: [Pw_forum] phonon partial density
In-Reply-To: <CAB4TLPKzpuMUPzf-B9QWfA4pgYhjjqJdL4NRTTq8MDBUXsfi7g@mail.gmail.com>
References: <CAEBBOkLRsg3bHY_4XXnRgds0F6HDiMdv4WwBn56TSuzOrSJwLQ@mail.gmail.com>
	<CAB4TLPKzpuMUPzf-B9QWfA4pgYhjjqJdL4NRTTq8MDBUXsfi7g@mail.gmail.com>
Message-ID: <CAEBBOkJho-PrqcT5FsJ+35-_1UG=WbmEoYoVWGMiU++Ya4vK2Q@mail.gmail.com>

Thanks for your help.I will search it.
Best Regards
Pine.

2011/7/5 Sanjeev Gupta <physics.skgupta at gmail.com>

> Please first provide your affiliation.
> The answer for your question is QHA, which is implemented in espresso.
> Read the manual, and see old post, which is very useful.
>
> Regrads
> Sanjeev
>
>   On Tue, Jul 5, 2011 at 7:42 AM, lucking-pine <songsong19840614 at gmail.com
> > wrote:
>
>>   I want to calculate the phonon partial density.But the example of pwscf
>> have not it.And I also find the method after searching Pw_forum mailist from
>> google.
>> I know the phonon dos is matdyn.x:
>> &input
>> asr='simple', amass(1)=65.003, amass(3)=16.000 flfrc='ZnO.fc',
>> flfrq='ZnO,freq', dos=.true.
>> fldos='ZnOphonon.dos', nk1=6, nk2=6, nk3=6, ndos=50
>>
>> So how could I calculate the pdos,using projwfc.x or matdyn.x?
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> *Dr. Sanjeev Kumar Gupta*
> *Post Doctoral Fellow,
>
> Department of Physics,
> Bhavnagar University, Bhavnagar-364 022
> Gujarat, India*
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From bamideleibrahim at yahoo.com  Tue Jul  5 07:47:53 2011
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Mon, 4 Jul 2011 22:47:53 -0700 (PDT)
Subject: [Pw_forum] can pwscf compute elastic constant?
Message-ID: <1309844873.43602.YahooMailClassic@web39412.mail.mud.yahoo.com>

Dear All,
? I want to know if the pwscf code can compute the elastic constant. If this is possible, can anybody with an idea give a description of how the input file for the calculation would look like. I will be delighted to read some lines from the forum.

Ciao 

Adetunji Bamidele Ibrahim

Department of physics,University of Agriculture,

Abeokuta, Ogun State,Nigeria.
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From physics.skgupta at gmail.com  Tue Jul  5 09:07:46 2011
From: physics.skgupta at gmail.com (Sanjeev Gupta)
Date: Tue, 5 Jul 2011 12:37:46 +0530
Subject: [Pw_forum] can pwscf compute elastic constant?
In-Reply-To: <1309844873.43602.YahooMailClassic@web39412.mail.mud.yahoo.com>
References: <1309844873.43602.YahooMailClassic@web39412.mail.mud.yahoo.com>
Message-ID: <CAB4TLPLPeCHX0V0k+OvJn6=4tTGJQmpYJkgDvX1m3VVpr58rKQ@mail.gmail.com>

i do not understand, why u asked same question, while your answer was given
in old post.
Please see and dont make separate.

Best
Sanjeev



On Tue, Jul 5, 2011 at 11:17 AM, bamidele ibrahim <bamideleibrahim at yahoo.com
> wrote:

> Dear All,
>   I want to know if the pwscf code can compute the elastic constant. If
> this is possible, can anybody with an idea give a description of how the
> input file for the calculation would look like. I will be delighted to read
> some lines from the forum.
>
> Ciao
>
> Adetunji Bamidele Ibrahim
> 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
>
>


-- 
*Dr. Sanjeev Kumar Gupta*
*Post Doctoral Fellow,
Department of Physics,
Bhavnagar University, Bhavnagar-364 022
Gujarat, India*
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From fratesi at mater.unimib.it  Tue Jul  5 16:02:16 2011
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Tue, 5 Jul 2011 16:02:16 +0200 (CEST)
Subject: [Pw_forum] Different adsorbate dipole moments from 4.3.1 and 4.0.1
Message-ID: <alpine.DEB.2.00.1107051559460.4793@localhost.localdomain,>

Dear all,

I'm experiencing some differences when computing dipole moments for
adsorbates on surfaces with pw.x from newer versions (>4.2) with
respect to previous calculations I did with QE-4.0.1. They amount to
few percent in the computed dipole in my cases. I expect they follow
the restructuring of the associated routines, PW/compute_dip.f90 and
PW/add_efield.f90, performed in 2009.

The systems are generally quite large (alkali adatoms on top of a
metal slab with about 80 atoms) so I extracted a smaller case which
already highlights some discrepancies: a neutral OH molecule in a cell
10x10x40au^3, which I submit here to your consideration if you are
interested and/or can give me some advice.

Let us focus on the dipole moment computed as a function of the
variables emaxpos/eopreg defining the saw-like potential. The cell is
very large along z (40au) so the position of emaxpos can be varied
considerably without affecting the results (the molecule is around the
origin). I now compare versions 4.0.1 and 4.3.1. They give the same
dipole moment P=0.6223au and energy Etot when emaxpos is far from the
atoms (distance d in the tables below). However, when emaxpos
approaches the atoms, the new version 4.3.1 deviates much more rapidly
from this value than the former 4.0.1 one.

Although the the percentual error in P is relatively small also for
QE-4.3.1, amounting to 1% only for d smaller than about 2.8au (quite
small indeed) the very different P-vs-d behavior deserves in my
opinion some attention, and it may have more dramatic effects in other
cases.

Thank you for your kind consideration,
Guido Fratesi

Tables and test-script follow. I will send you detailed input/output
files if you wish.

This with 4.0.1:
eopreg	emaxpos	d(au)	Etot(Ry)	P(au)	dE(meV)	dP(%)
0.05	0.475	18.10	-32.74822138	-0.6223	0.00	0.00
0.10	0.450	17.10	-32.74822138	-0.6223	0.00	0.00
0.15	0.425	16.10	-32.74822138	-0.6223	0.00	0.00
0.20	0.400	15.10	-32.74822138	-0.6223	0.00	0.00
0.25	0.375	14.10	-32.74822138	-0.6223	0.00	0.00
0.30	0.350	13.10	-32.74822138	-0.6223	0.00	0.00
0.35	0.325	12.10	-32.74822138	-0.6223	0.00	0.00
0.40	0.300	11.10	-32.74822138	-0.6223	0.00	0.00
0.45	0.275	10.10	-32.74822138	-0.6223	0.00	0.00
0.50	0.250	9.10	-32.74822138	-0.6223	0.00	0.00
0.55	0.225	8.10	-32.74822138	-0.6223	0.00	0.00
0.60	0.200	7.10	-32.74822138	-0.6223	0.00	0.00
0.65	0.175	6.10	-32.74822138	-0.6223	0.00	0.00
0.70	0.150	5.10	-32.74822137	-0.6223	0.00	0.00
0.75	0.125	4.10	-32.74822136	-0.6223	0.00	0.01
0.76	0.120	3.90	-32.74822136	-0.6223	0.00	0.01
0.77	0.115	3.70	-32.74822135	-0.6224	0.00	0.02
0.78	0.110	3.50	-32.74822134	-0.6224	0.00	0.02
0.79	0.105	3.30	-32.74822132	-0.6225	0.00	0.03
0.80	0.100	3.10	-32.74822130	-0.6225	0.00	0.03
0.81	0.095	2.90	-32.74822126	-0.6226	0.00	0.05
0.82	0.090	2.70	-32.74822121	-0.6227	0.00	0.07
0.83	0.085	2.50	-32.74822112	-0.6229	0.00	0.10
0.84	0.080	2.30	-32.74822100	-0.6231	0.01	0.12
0.85	0.075	2.10	-32.74822083	-0.6233	0.01	0.17
0.86	0.070	1.90	-32.74822057	-0.6237	0.01	0.22
0.87	0.065	1.70	-32.74822020	-0.6241	0.02	0.29
0.88	0.060	1.50	-32.74821975	-0.6246	0.02	0.36
0.89	0.055	1.30	-32.74821905	-0.6252	0.03	0.47
0.90	0.050	1.10	-32.74821809	-0.6260	0.04	0.60
0.91	0.045	0.90	-32.74821684	-0.6269	0.06	0.75
0.92	0.040	0.70	-32.74821523	-0.6281	0.08	0.93
0.93	0.035	0.50	-32.74821325	-0.6293	0.11	1.13
0.94	0.030	0.30	-32.74821090	-0.6307	0.14	1.35
0.95	0.025	0.10	-32.74820813	-0.6321	0.18	1.57

This with 4.3.1:
eopreg	emaxpos	d(au)	Etot(Ry)	P(au)	dE(meV)	dP(%)
0.05	0.475	18.10	-32.74822138	-0.6223	0.00	0.00
0.10	0.450	17.10	-32.74822138	-0.6223	0.00	0.00
0.15	0.425	16.10	-32.74822138	-0.6223	0.00	0.00
0.20	0.400	15.10	-32.74822138	-0.6223	0.00	0.00
0.25	0.375	14.10	-32.74822138	-0.6223	0.00	0.00
0.30	0.350	13.10	-32.74822138	-0.6223	0.00	0.00
0.35	0.325	12.10	-32.74822138	-0.6223	0.00	0.00
0.40	0.300	11.10	-32.74822139	-0.6223	0.00	0.00
0.45	0.275	10.10	-32.74822139	-0.6223	0.00	0.00
0.50	0.250	9.10	-32.74822139	-0.6223	0.00	0.00
0.55	0.225	8.10	-32.74822139	-0.6223	0.00	0.00
0.60	0.200	7.10	-32.74822140	-0.6223	0.00	0.00
0.65	0.175	6.10	-32.74822143	-0.6223	0.00	0.00
0.70	0.150	5.10	-32.74822163	-0.6222	0.00	-0.02
0.75	0.125	4.10	-32.74822308	-0.6219	-0.02	-0.06
0.76	0.120	3.90	-32.74822393	-0.6217	-0.03	-0.10
0.77	0.115	3.70	-32.74822521	-0.6214	-0.05	-0.14
0.78	0.110	3.50	-32.74822713	-0.6209	-0.08	-0.22
0.79	0.105	3.30	-32.74823004	-0.6203	-0.12	-0.32
0.80	0.100	3.10	-32.74823448	-0.6192	-0.18	-0.50
0.81	0.095	2.90	-32.74824122	-0.6176	-0.27	-0.76
0.82	0.090	2.70	-32.74825141	-0.6151	-0.41	-1.16
0.83	0.085	2.50	-32.74826676	-0.6114	-0.62	-1.75
0.84	0.080	2.30	-32.74828988	-0.6056	-0.93	-2.68
0.85	0.075	2.10	-32.74832476	-0.5968	-1.41	-4.10
0.86	0.070	1.90	-32.74837714	-0.5832	-2.12	-6.28
0.87	0.065	1.70	-32.74845479	-0.5624	-3.18	-9.63
0.88	0.060	1.50	-32.74856764	-0.5306	-4.71	-14.74
0.89	0.055	1.30	-32.74872674	-0.4820	-6.88	-22.55
0.90	0.050	1.10	-32.74893929	-0.4078	-9.77	-34.47
0.91	0.045	0.90	-32.74919357	-0.2949	-13.23	-52.61
0.92	0.040	0.70	-32.74942151	-0.1249	-16.33	-79.93
0.93	0.035	0.50	-32.74942170	0.1248	-16.33	-120.05
0.94	0.030	0.30	-32.74875527	0.4751	-7.26	-176.35
0.95	0.025	0.10	-32.74669998	0.9359	20.70	-250.39


################################################################################


#!/bin/bash

PSEUDO_DIR=../pseudo/
TMP_DIR=../tmp/

pw[0]=/opt/Q-E.d/espresso-4.0.1/bin/pw.x
pw[1]=/opt/Q-E.d/espresso-4.3.1/bin/pw.x
pp[0]=/opt/Q-E.d/espresso-4.0.1/bin/pp.x
pp[1]=/opt/Q-E.d/espresso-4.3.1/bin/pp.x

for code in 0 1 ; do

cat > oh.scf.$code.in << EOF
&CONTROL
   calculation   = 'scf'
   prefix        = 'OH$code'
   restart_mode  = 'from_scratch'
   outdir        = '$TMP_DIR'
   PSEUDO_DIR    = '$PSEUDO_DIR'
/
&SYSTEM
     ibrav     = 6
     celldm(1) = 10.d0
     celldm(3) = 4.d0
     nat       = 2
     ntyp      = 2
     ecutwfc   = 27.0d0
     ecutrho   = 216.0d0
     occupations = 'smearing'
     degauss     = 0.01D0
     smearing    = 'mp'
     nspin = 2
     starting_magnetization = 0.7
/
&ELECTRONS
     conv_thr    = 1.0d-9
     mixing_mode = 'plain'
     mixing_beta = 0.3d0
/
ATOMIC_SPECIES
H     1.00   H.vbc.UPF
O    16.00   O.pz-rrkjus.UPF
ATOMIC_POSITIONS (bohr)
H        0 0 -0.9
O        0 0  0.9
K_POINTS gamma
EOF

${pw[$code]} < oh.scf.$code.in > oh.scf.$code.out

#dummy is eopreg*100
for dummy in 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 ; do
eopreg=`echo $dummy  | awk '{printf "%4.2f",$1/100}'`
tst=${eopreg:2:2}
emaxpos=`dc -e "6k 1 $eopreg - 2/p"`

cat > oh.dip.scf.$code.$tst.in << EOF
&CONTROL
   calculation   = 'scf'
   prefix        = 'OH$code'
   restart_mode  = 'from_scratch'
   outdir        = '$TMP_DIR'
   PSEUDO_DIR    = '$PSEUDO_DIR'
   dipfield = .true. , tefield = .true.
/
&SYSTEM
     ibrav     = 6
     celldm(1) = 10.d0
     celldm(3) = 4.d0
     nat       = 2
     ntyp      = 2
     ecutwfc   = 27.0d0
     ecutrho   = 216.0d0
     occupations = 'smearing'
     degauss     = 0.01D0
     smearing    = 'mp'
     nspin = 2
     starting_magnetization = 0.7
     edir=3,    eamp=0,    emaxpos=$emaxpos,   eopreg=$eopreg
/
&ELECTRONS
     startingpot = 'file'
     startingwfc = 'file'
     conv_thr    = 1.0d-9
     mixing_mode = 'plain'
     mixing_beta = 0.3d0
/
ATOMIC_SPECIES
H     1.00   H.vbc.UPF
O    16.00   O.pz-rrkjus.UPF
ATOMIC_POSITIONS (bohr)
H        0 0 -0.9
O        0 0  0.9
K_POINTS gamma
EOF

${pw[$code]} < oh.dip.scf.$code.$tst.in > oh.dip.scf.$code.$tst.out

done
done

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
Milano, Italy

From flux_ray12 at 163.com  Tue Jul  5 15:53:41 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Tue, 5 Jul 2011 21:53:41 +0800 (CST)
Subject: [Pw_forum] Charge Density
In-Reply-To: <CAHbvuiQ-qiCrMVsbz4kdiNeUxUBi=8y1PZv9AN3udk3P_+jp5w@mail.gmail.com>
References: <CAHbvuiQ-qiCrMVsbz4kdiNeUxUBi=8y1PZv9AN3udk3P_+jp5w@mail.gmail.com>
Message-ID: <be6f4a9.d57e.130fa93655b.Coremail.flux_ray12@163.com>

As shown in /Doc/Input_PP.*, ei(j) is the vector (lattice line), and x0(j) the origin of line (intersection of two lattice line).

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-04 18:47:51?"Mehrnoosh Hazrati" <mehrnooshhazrati at gmail.com> wrote:


Hi everyone,
 
I need to calculate the charge density of a graphene sheet, but i don't know how can i choose e1, e2 and x0 for my system.
 
Thank you in advance
--

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
***Mehrnoosh Kh. Hazrati***
***Master Student of Computational Physical Chemistry,KNTU,Tehran***
 ***Phone : +989123436300***
***Mail :mehrnooshhazrati at gmail.com***
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 
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From giuseppe.mattioli at mlib.ism.cnr.it  Tue Jul  5 17:41:44 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Tue, 5 Jul 2011 17:41:44 +0200
Subject: [Pw_forum] charged defect in a unit cell
In-Reply-To: <CANzxBn8e53M-nVMKKf0V3QxgVMY=KvSNQkueunF_D-tds1=+iA@mail.gmail.com>
References: <BANLkTinEB68iOy57qLX8SVyEe29E1n4W=Q@mail.gmail.com>
	<4E101DA1.7040407@yahoo.com.cn>
	<CANzxBn8e53M-nVMKKf0V3QxgVMY=KvSNQkueunF_D-tds1=+iA@mail.gmail.com>
Message-ID: <201107051741.44457.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Tram
I am afraid that your question cannot be answered in a short e-mail... I can 
suggest you to read at least one among many semiconductor physics books.
a quite simple, application oriented one is 

B. G. Streetman
Solid State electronic devices
Prentice-Hall International editions

But you can surely find plenty of alternatives...
HTH

Giuseppe  

On Monday 04 July 2011 08:16:30 Tram Bui wrote:
> Dear Giuseppe and Hongsheng,
>  Thank you very much for your information. The paper was a great source. I
> have read the paper couple times and also google here and there but there
> is something I don't quite understand is the shallow acceptor. I take the
> courage to ask you a little further into the paper. The authors mentioned
> of the case where they took Mg acceptor in GaN, and the term Ecorr was used
> (eq. 3) in the shallow centers. Can some one help me to understand what a
> shallow acceptor means? my guess was it is the energy level of the acceptor
> (Mg in GaN) if lower than the thermal energy-->shallow, if higher--->deep.
> Is that correct? I really appreciate your help.
>
> Great Respect,
> Tram
>
> On Sun, Jul 3, 2011 at 1:43 AM, Hongsheng Zhao 
<zhaohscas at yahoo.com.cn>wrote:
> > On 07/01/2011 05:19 PM, Giuseppe Mattioli wrote:
> > > Dear Tram Bui
> > > First, you may want to carefully read the following paper:
> > >
> > > Van de Walle, C. G.; Neugebauer, J. J. Appl. Phys. 95, 3851 (2004)
> >
> > Should be J. Appl. Phys. 95, 3851 (2004).
> >
> > Best
> > --
> > Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> > School of Physics and Electrical Information Science,
> > Ningxia University, Yinchuan 750021, China
> > _______________________________________________
> > 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 wonvein at gmail.com  Wed Jul  6 06:56:43 2011
From: wonvein at gmail.com (WANG Wei)
Date: Wed, 6 Jul 2011 13:56:43 +0900
Subject: [Pw_forum] Problem with vdW-DF2
Message-ID: <CAOcD3SLRi__2NrwMifAufHeAEcZ_SrSs8uxABXJgHh3UWaPCmA@mail.gmail.com>

Dear QE developers,

I found that the vdW-DF2 is defined in funct.f90:

###############################################

  else if ('VDW-DF2' .EQ. TRIM(dftout) ) then
    ! Special case vdW-DF2
       call set_dft_value (iexch, 0)
       call set_dft_value (icorr, 4)
       call set_dft_value (igcx, 13)
       call set_dft_value (igcc, 0)
       call set_dft_value (inlc, 2)
       dft_defined = .true.

###############################################

However, when I performed calculations using vdW-DF2, I noted the the
informations of vdW-DF2 in log files (out file) is
Exchange-correlation      = VDW-DF2 ( 1 413 0 2).
Is the value of iexch in vdW-DF2 redefined? namely iexch=1?

Regards,
WANG
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From forsdan at gmail.com  Wed Jul  6 11:54:37 2011
From: forsdan at gmail.com (Dan Fors)
Date: Wed, 6 Jul 2011 11:54:37 +0200
Subject: [Pw_forum] negative dr2
Message-ID: <CAOpLxAGB6PhXJedPrh3MT3szbOhzf5LpT7iDMazQ=Y3+v5t-=w@mail.gmail.com>

Dear users,

I am running a simple 2-atomic non-magnetic (NM) bcc Cr system (see
below for the input file)  with v.4.2.1 and I keep getting an error
message regarding a negative dr2:

     from mix_rho : error #         1
     negative dr2

This error occurs for values close to as well as away from the
estimated equilibrium volume. What is the possible the origins of this
error and how may I eliminate it?

I have tried to change the mixing_beta in the range 0.1 to 0.8, as
well as changing the mixing mode to 'TF'. I have also tried to set
nspin = 2 with a zero start magnetisation since an anti-ferromagnetic
(AFM) start configuration does not give rise to the problem (but
yields the AFM solution instead of the NM one). However. this also
gives the error. Finally, I tested to use ibrav = 3 and with only one
atom in the cell, but I still get the above error.

What I have noticed is that in the AFM case I get a couple of very
flat bands in the bandstructure just above the Fermi level. If I
change to a USPP potential or an alternative PAW potential these bands
disappear, and the above error does not occur. Can the potential I use
in the present case be the source to the error, and if yes, what is
the reason behind it?

I would appreciate any help or suggestions.

Dan



%-------------------------------------

&CONTROL
	calculation = 'scf',
	restart_mode = 'from_scratch',
	prefix = 'Cr',
	tstress = .true.,
	tprnfor = .true.,
	pseudo_dir = '/home/forsdan/PROGRAMS/QUANTUM_ESPRESSO/espresso-4.2.1_intel/pseudo/',
	outdir = '/home/forsdan/FeCr_PROJECT/TEMP_PAW/'
/
&SYSTEM
	ibrav =  1, celldm(1) = 5.378798, nat =  2, ntyp = 1,
	ecutwfc = 40.0, ecutrho = 180.0, nbnd = 14
	occupations = 'smearing',
	smearing = 'mp', degauss = 0.022,
	nspin = 1,
/
&ELECTRONS
	electron_maxstep = 100,
	conv_thr =  1.0d-8,
	diagonalization = 'cg',
	mixing_mode = 'plain',
	mixing_beta = 0.3
/
ATOMIC_SPECIES
 Cr  51.996  Cr.pbe-paw_kj_6.UPF
ATOMIC_POSITIONS {crystal}
 Cr 0.00 0.00 0.00
 Cr 0.50 0.50 0.50
K_POINTS {automatic}
 12 12 12 0 0 0

%-------------------------------------

From natalie at wfu.edu  Wed Jul  6 14:58:56 2011
From: natalie at wfu.edu (Holzwarth, Natalie)
Date: Wed, 6 Jul 2011 08:58:56 -0400
Subject: [Pw_forum] negative dr2
In-Reply-To: <CAOpLxAGB6PhXJedPrh3MT3szbOhzf5LpT7iDMazQ=Y3+v5t-=w@mail.gmail.com>
References: <CAOpLxAGB6PhXJedPrh3MT3szbOhzf5LpT7iDMazQ=Y3+v5t-=w@mail.gmail.com>
Message-ID: <CAH3a32=yEipg4oH1iaVbVhKLSC=p9RgRSOPQcOiACcd3qdaKww@mail.gmail.com>

Dear Dan,

I have seen this error in several cases particularly for transition metals
and
for basis and projector functions generated by our atompaw program.  My
understanding
(based on a discussion with Stefano de Gironcoli) is that the program stops
when the
program detects a certain product of one-center terms to be negative.   In
my experience
these terms can be negative before convergence and I have commented out the
offending
line.   In my tests, this allows the program to converge consistently in the
tests I have done.
This is not necessarily safe or well-tested and I did promise to look into
it further.   In case
you would like to also try, the offending line in 4.2.1 is line 553 in
sct_mod.f90:

  IF (okpaw)         rho_ddot = rho_ddot + paw_ddot(rho1%bec, rho2%bec)

I repeat that commenting out this line may not be a good idea, but it has
worked for me in
limited tests.  (I still hope to do more tests.)


 Sincerely,

      Natalie Holzwarth

N. A. W. Holzwarth                                       email:
natalie at wfu.edu
Department of Physics                                 web:
http://www.wfu.edu/~natalie
Wake Forest University                                 phone:
1-336-758-5510
Winston-Salem, NC 27109 USA                     office: Rm. 300 Olin
Physical Lab

On Wed, Jul 6, 2011 at 5:54 AM, Dan Fors <forsdan at gmail.com> wrote:

> Dear users,
>
> I am running a simple 2-atomic non-magnetic (NM) bcc Cr system (see
> below for the input file)  with v.4.2.1 and I keep getting an error
> message regarding a negative dr2:
>
>     from mix_rho : error #         1
>     negative dr2
>
> This error occurs for values close to as well as away from the
> estimated equilibrium volume. What is the possible the origins of this
> error and how may I eliminate it?
>
> I have tried to change the mixing_beta in the range 0.1 to 0.8, as
> well as changing the mixing mode to 'TF'. I have also tried to set
> nspin = 2 with a zero start magnetisation since an anti-ferromagnetic
> (AFM) start configuration does not give rise to the problem (but
> yields the AFM solution instead of the NM one). However. this also
> gives the error. Finally, I tested to use ibrav = 3 and with only one
> atom in the cell, but I still get the above error.
>
> What I have noticed is that in the AFM case I get a couple of very
> flat bands in the bandstructure just above the Fermi level. If I
> change to a USPP potential or an alternative PAW potential these bands
> disappear, and the above error does not occur. Can the potential I use
> in the present case be the source to the error, and if yes, what is
> the reason behind it?
>
> I would appreciate any help or suggestions.
>
> Dan
>
>
>
> %-------------------------------------
>
> &CONTROL
>        calculation = 'scf',
>        restart_mode = 'from_scratch',
>        prefix = 'Cr',
>        tstress = .true.,
>        tprnfor = .true.,
>        pseudo_dir =
> '/home/forsdan/PROGRAMS/QUANTUM_ESPRESSO/espresso-4.2.1_intel/pseudo/',
>        outdir = '/home/forsdan/FeCr_PROJECT/TEMP_PAW/'
> /
> &SYSTEM
>        ibrav =  1, celldm(1) = 5.378798, nat =  2, ntyp = 1,
>        ecutwfc = 40.0, ecutrho = 180.0, nbnd = 14
>        occupations = 'smearing',
>        smearing = 'mp', degauss = 0.022,
>        nspin = 1,
> /
> &ELECTRONS
>        electron_maxstep = 100,
>        conv_thr =  1.0d-8,
>        diagonalization = 'cg',
>        mixing_mode = 'plain',
>        mixing_beta = 0.3
> /
> ATOMIC_SPECIES
>  Cr  51.996  Cr.pbe-paw_kj_6.UPF
> ATOMIC_POSITIONS {crystal}
>  Cr 0.00 0.00 0.00
>  Cr 0.50 0.50 0.50
> K_POINTS {automatic}
>  12 12 12 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 mehrnooshhazrati at gmail.com  Wed Jul  6 15:10:24 2011
From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati)
Date: Wed, 6 Jul 2011 17:40:24 +0430
Subject: [Pw_forum] OCCUPATION , example 11
Message-ID: <CAHbvuiSRB23_mH41HgGhKJN8e6j7V1T1T1db9QzypPFjUj7Wig@mail.gmail.com>

Dear QE users,
I want to calculate the formation energy of my system and need the chemical
potential of Nitrogen. I used Example 11, but i don't know how to choose
OCCUPATIONS.
any suggest will be appreciated.
My INPUT :
 &control
calculation='scf',
pseudo_dir = './',
outdir='./',
prefix='n',
/
&system
ibrav =1,
celldm(1) =20.0,
nat =1,
ntyp =1,
nbnd =5,
nosym=.true.,
ecutwfc=15.0,
occupations='./',
/
&electrons
conv_thr=1.0d-7
mixing_beta = 0.5,
/
ATOMIC_SPECIES
N 14.006 N.pw91-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
N 0.00 0.00 0.00
K_POINTS AUTOMATIC
1 1 1 0 0 0
OCCUPATIONS
????

-- 
*

*
*
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
**** Mehrnoosh Kh. Hazrati ****
**** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
*** Phone : +989123436300 ***
*** Mail : mehrnooshhazrati at gmail.com ***
*
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*


-- 
*

*
*
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
**** Mehrnoosh Kh. Hazrati ****
**** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
 *** Phone : +989123436300 ***
*** Mail : mehrnooshhazrati at gmail.com ***
*
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
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From guntram.schmidt at chemie.uni-halle.de  Wed Jul  6 17:10:04 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Wed, 06 Jul 2011 17:10:04 +0200
Subject: [Pw_forum] Fwd: pp convergence once more
Message-ID: <4E147ACC.7000407@chemie.uni-halle.de>

Hello together!

I started using QE to calculate some total energies of molecular
crystals. It was said, that using rpb-pseudopotentials together with
input_dft = 'vdW-DF'
should lead to good results.
So I created the potentials using the PSlibrary-code. Some elements
didn't converge, but the ones, which generated a UPF-file should be fine
- aren't they?

To find the ECUTWFC it was said to be sufficient, to just calculate one
atom of the type you are interested in, so I took the following input:

&control
    calculation = 'scf'
    restart_mode='from_scratch',
    prefix='',
    tstress = .false.
    tprnfor = .false.
    pseudo_dir = '/gpfs/home/aasfu/espresso-4.3.1/pseudo/',
    outdir='/gpfs/home/aasfu/tmp/'
    verbosity = 'high'
/
&system
  ibrav=0,
  celldm(1)=2,
  nat = 1,
  ntyp = 1,
  ecutwfc = 30,
  ecutrho = 120,
  input_dft = 'vdW-DF',
  occupations='smearing',
  smearing='gaussian',
  degauss=0.01,
  force_pairing = .true.

/
&electrons
     conv_thr        = 1.0d-8
     electron_maxstep= 1000
/

CELL_PARAMETERS cubic
10.0 	0.0 	0.0
0		10.0	0
0.0	 	0.0		10.0

ATOMIC_SPECIES
  O 1.0 O.rpb-rrkjus.UPF

ATOMIC_POSITIONS angstrom
  O      0 0 0

K_POINTS automatic
1 1 1 0 0 0



for the elements of interest (H, C, N, O, P, Sn) with increasing
cutoff-value and different multiplicators to get ecutrho (4 times
ecutwfc and 10 times ecutwfc (ultrasoft?) ).

Some of them converge (e.g, C at 36 / 140 and 37 / 370 for rpb-rrkjus),
but others do oscillate quite large (O, Sn).

What is a good convergence criterium?
I found numbers like 1mRy but also 5mRy per atom
(http://users.aims.ac.za/~daniel/hands_on/Brandon_workshop_handout.pdf)!
Does this mean, the more atoms I have in my structure (will be ~200),
the bigger the allowed deviation (1Ry in my case)?
I always took the difference between n Ry and n+1 Ry in ecutwfc as a
criteria - is this right?

Or is it better to test convergence with small molecules, which contain
the atoms in the configuration of my molecule (sp2-carbons, carboxylate
functions etc.)?

Thanks a lot for clearification,
Guntram

From syuva2987 at gmail.com  Wed Jul  6 18:40:48 2011
From: syuva2987 at gmail.com (yuva rani)
Date: Wed, 6 Jul 2011 22:10:48 +0530
Subject: [Pw_forum] constraint
Message-ID: <CAM6Xv8kkEuiRNt+UDXsVZ4gduXLZg_qTbLr=vfoGivWEJyrOpQ@mail.gmail.com>

Dear QE users,
 I am constructing a metal-organic interface.I built an layered
structure using matreial studio and the cartesian coordinates are
taken using chemcraft. Here I have to relax the stacked structure
using constraints. But I did not know much about the usage of
constraints. so please anyone help me with the input example involving
constraints.

Thanks in advance.

From bamideleibrahim at yahoo.com  Wed Jul  6 20:17:35 2011
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Wed, 6 Jul 2011 11:17:35 -0700 (PDT)
Subject: [Pw_forum] can pwscf compute elastic constant?
In-Reply-To: <CAB4TLPLPeCHX0V0k+OvJn6=4tTGJQmpYJkgDvX1m3VVpr58rKQ@mail.gmail.com>
Message-ID: <1309976255.98526.YahooMailClassic@web39402.mail.mud.yahoo.com>

Dear Sanjeev,
? I understand the theoretical aspect of this concept, but i don't know how to do the calculation with pwscf. This is the reason why i repeated the question on the forum if anybody can give me the description of how the input file will look like. And if you cab help with the description, i will appreciate it.

Thanks,
Ibrahim

Adetunji Bamidele Ibrahim

Department of physics,University of Agriculture,

Abeokuta, Ogun State,Nigeria.

--- On Tue, 7/5/11, Sanjeev Gupta <physics.skgupta at gmail.com> wrote:

From: Sanjeev Gupta <physics.skgupta at gmail.com>
Subject: Re: [Pw_forum] can pwscf compute elastic constant?
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Tuesday, July 5, 2011, 12:07 AM

i do not understand, why u asked same question, while your answer was given in old post.Please see and dont make?separate.
Best?Sanjeev



On Tue, Jul 5, 2011 at 11:17 AM, bamidele ibrahim <bamideleibrahim at yahoo.com> wrote:

Dear All,
? I want to know if the pwscf code can compute the elastic constant. If this is possible, can anybody with an idea give a description of how the input file for the calculation would look like. I will be delighted to read some lines from the forum.


Ciao 

Adetunji Bamidele Ibrahim

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





-- 
Dr. Sanjeev Kumar Gupta
Post Doctoral Fellow,
Department of Physics,

Bhavnagar University, Bhavnagar-364 022
Gujarat, India




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From mirnezhad.mm at gmail.com  Wed Jul  6 23:39:08 2011
From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad)
Date: Wed, 6 Jul 2011 14:39:08 -0700
Subject: [Pw_forum] hysteresis Loop
Message-ID: <CAOMa7Cx12Vvvw38-j-nQ5ZN3VDCQ5Dn5_Jkj-e1Oh8Cng6_KMA@mail.gmail.com>

Dear Developers,
I want to study the hysteresis loop by using the DFT calculation. DFT
simply calculates the Ground State of the physical system, it is not
involve the memory of system. Could any body introduce me a DFT or
"DFT like" method for this kind of calculations?
Thanks in advance

----------------------------------------------------------------------------
Mahdi Mirnezhad
MSc student of Mechanical engineering,
Guilan University.

From maxradin at umich.edu  Thu Jul  7 00:27:57 2011
From: maxradin at umich.edu (maxradin at umich.edu)
Date: Wed, 06 Jul 2011 18:27:57 -0400
Subject: [Pw_forum] SiO2 xanes calculation
Message-ID: <d5360c67d8b89e63994a959436f4846e@umich.edu>

Hi,

I'm trying to repeat the ultrasoft core-hole calculation of the Si K-edge
in Matteo's paper:

"First-principles calculations of x-ray absorption in a scheme 
based on ultrasoft pseudopotentials: From alpha-quartz to 
high-Tc  compounds"

I haved used the same parameters given in that article (cell size, cutoff
energies, kpoints) but the spectrum that I get does not at all look right.
Is it possible that this discrepancy is due to the choice of
pseudopotentials? For the absorbing atom I am using 

http://www.quantum-espresso.org/pseudo/1.3/UPF/Si.star1s-pbe-van_gipaw.UPF

which I think is the same one used in the paper. For the other atoms I am
using the ultrasoft pseudopotentials included with the xspectra SiO2
example (Si_PBE_USPP.UPF and O_PBE_USPP.UPF).

Also, I obtained the fermi level from the output of the scf calculation
(converted from eV to Ry). Is this the correct way to choose the ef_r
parameter? My input files are attached.

Regards,

Max 
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From trambui at u.boisestate.edu  Thu Jul  7 06:47:35 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Wed, 6 Jul 2011 22:47:35 -0600
Subject: [Pw_forum] "relax" vs. "vc-relax" calculation
Message-ID: <CANzxBn8y8C0et3tKoEoLaZ0LgRDe_YWofcR8nwuEPPzkUQocow@mail.gmail.com>

Dear Everyone,
     I have a quick question regarding the "relax" vs. "vc-relax"
calculation for my SiC structure. As I run the " scf" calculation with a
single defect, e.g. interstitial or sustitutional, the lattice parameter of
the unit cell is expected to be stretched. And as I checked, the lattice
constant got larger when introduced defect. Now, I'm just wondering between
the "relax" calculation (which will only relax the atomic position ) and the
"vc-relax" one (which will relax both atomic position and the lattice of the
unit cell), which one would you recommend to use?

Thank you very much,

Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From baroni at sissa.it  Thu Jul  7 07:11:13 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 7 Jul 2011 07:11:13 +0200
Subject: [Pw_forum] can pwscf compute elastic constant?
In-Reply-To: <1309976255.98526.YahooMailClassic@web39402.mail.mud.yahoo.com>
References: <1309976255.98526.YahooMailClassic@web39402.mail.mud.yahoo.com>
Message-ID: <0722C87B-2922-4A51-BEFB-805B838C5704@sissa.it>

calculate the stress corresponding to different strain states and interpolate in-between. beware that, if you have internal degrees of freedom (which is usally the case) you have to minimize the energy with respect to internal coordinates, corresponding to each strain state. SB


On Jul 6, 2011, at 8:17 PM, bamidele ibrahim wrote:

> Dear Sanjeev,
>   I understand the theoretical aspect of this concept, but i don't know how to do the calculation with pwscf. This is the reason why i repeated the question on the forum if anybody can give me the description of how the input file will look like. And if you cab help with the description, i will appreciate it.
> 
> Thanks,
> Ibrahim
> 
> Adetunji Bamidele Ibrahim
> Department of physics,University of Agriculture,
> Abeokuta, Ogun State,Nigeria.
> 
> --- On Tue, 7/5/11, Sanjeev Gupta <physics.skgupta at gmail.com> wrote:
> 
> From: Sanjeev Gupta <physics.skgupta at gmail.com>
> Subject: Re: [Pw_forum] can pwscf compute elastic constant?
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Tuesday, July 5, 2011, 12:07 AM
> 
> i do not understand, why u asked same question, while your answer was given in old post.
> Please see and dont make separate.
> 
> Best 
> Sanjeev
> 
> 
> 
> On Tue, Jul 5, 2011 at 11:17 AM, bamidele ibrahim <bamideleibrahim at yahoo.com> wrote:
> Dear All,
>   I want to know if the pwscf code can compute the elastic constant. If this is possible, can anybody with an idea give a description of how the input file for the calculation would look like. I will be delighted to read some lines from the forum.
> 
> Ciao 
> 
> Adetunji Bamidele Ibrahim
> 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
> 
> 
> 
> 
> -- 
> Dr. Sanjeev Kumar Gupta
> Post Doctoral Fellow,
> Department of Physics,
> Bhavnagar University, Bhavnagar-364 022
> Gujarat, India
> 
> 
> -----Inline Attachment Follows-----
> 
> _______________________________________________
> 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

---
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

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From matteo.calandra at impmc.jussieu.fr  Thu Jul  7 09:25:54 2011
From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra)
Date: Thu, 07 Jul 2011 09:25:54 +0200
Subject: [Pw_forum] SiO2 xanes calculation
In-Reply-To: <mailman.13752.1310015476.1814.pw_forum@pwscf.org>
References: <mailman.13752.1310015476.1814.pw_forum@pwscf.org>
Message-ID: <4E155F82.7050500@impmc.jussieu.fr>

 >Message: 3
 >Date: Wed, 06 Jul 2011 18:27:57 -0400
 >From: <maxradin at umich.edu>
 >Subject: [Pw_forum] SiO2 xanes calculation
 >To: pw_forum at pwscf.org
 >Message-ID: <d5360c67d8b89e63994a959436f4846e at umich.edu>
 >Content-Type: text/plain; charset="utf-8"
 >
 >Hi,
 >
 >I'm trying to repeat the ultrasoft core-hole calculation of the Si >K-edge
 >in Matteo's paper:
 >
 >"First-principles calculations of x-ray absorption in a scheme
 >based on ultrasoft pseudopotentials: From alpha-quartz to
 >high-Tc  compounds"

 >I haved used the same parameters given in that article (cell size, >cutoff
 >energies, kpoints) but the spectrum that I get does not at all look 
 >right.
 >Is it possible that this discrepancy is due to the choice of
 >pseudopotentials? For the absorbing atom I am using

Dear Max,

   the pseudo you use are correct, however this is not the case for
the k-points in your Xanes calculation. In the paper it is stated
that you need "the Lanczos method was performed
using a centered 3x3x3 k-points grid of the 72
atoms supercell." (see just below Eq. 27).

The second thing is that in an insulator, there is no Fermi level.
Are you sure you're cutting eliminated the occupied states at the right 
energy position ?

Can you try yo see if you reproduce the results of the QE XSpectra 
example directory ?

all the best,

Matteo

-- 
* * * *
Matteo Calandra, Directeur de Recherche (DR2)
Institut de Mineralogie et de Physique des Milieux Condenses de Paris
Universite Pierre et Marie Curie, tour 23, 3eme etage, case 115
4 Place Jussieu, 75252 Paris Cedex 05 France
Tel: +33-1-44 27 52 16       Fax: +33-1-44 27 37 85
http://www.impmc.jussieu.fr/~calandra

From masoudnahali at gmail.com  Thu Jul  7 10:32:43 2011
From: masoudnahali at gmail.com (Masoud Nahali)
Date: Thu, 7 Jul 2011 01:32:43 -0700
Subject: [Pw_forum] "relax" vs. "vc-relax" calculation
Message-ID: <CAM-1hSs5XPP92HyoH_9TArTtTk-V1-QqZ+mta71Q-Ew+kMzcug@mail.gmail.com>

     Dear Tram

         I think that vc-relax calculation is more convenient for your case;
in addition you should glance over the below tutorial about defects :

http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_defects.pdf

         I hope it is useful.


Best Wishes

 Masoud



--------------
Masoud Nahali, Sharif University of Technology
masoud.nahali at gmail.com;
alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali>

P Please don't print this e-mail unless you really need to.


*Tram wrote on Thu Jul 7 06:47:35 CEST 2011*
>
Dear Everyone,
     I have a quick question regarding the "relax" vs. "vc-relax"
calculation for my SiC structure. As I run the " scf" calculation with a
single defect, e.g. interstitial or sustitutional, the lattice parameter of
the unit cell is expected to be stretched. And as I checked, the lattice
constant got larger when introduced defect. Now, I'm just wondering between
the "relax" calculation (which will only relax the atomic position ) and the
"vc-relax" one (which will relax both atomic position and the lattice of the
unit cell), which one would you recommend to use?

Thank you very much,

Tram Bui

M.S. Materials Science & Engineeringtrambui at u.boisestate.edu
<http://www.democritos.it/mailman/listinfo/pw_forum>
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From goodluck_1982 at 163.com  Thu Jul  7 11:39:58 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Thu, 07 Jul 2011 17:39:58 +0800
Subject: [Pw_forum] What's wrong in my calculation of epsilon of fcc Au?
In-Reply-To: <d5360c67d8b89e63994a959436f4846e@umich.edu>
References: <d5360c67d8b89e63994a959436f4846e@umich.edu>
Message-ID: <4E157EEE.4050309@163.com>

Dear all,

       I want to calculate dielectric function of carbon nanotube, but I 
have no experiences of calculating dielectric function before. Hence, I 
decide to start with a simple case of fcc gold, because there are 
referable results from wien2k (wien2k is capable of simple case such as 
fcc Au, but too resource consumptive to deal with large cells such as CNT).
       Because epsilon.x doesn't support USPP, the UPF file of Au is got 
by converting fhi file from abinit using fhi2upf.x. I calculate fcc Au 
with a=7.71bohr and 15x15x15 k-mesh using both pwscf(v4.3) and wien2k. 
First I check the band structures and find that the results from both 
softwares agree well (see attachments). But the results of epsilon from 
pwscf is not satisfactory as the results from wien2k:

       (1) Figures imag_eps and real_eps are the compares with only 
interband contribution. (note that for pwscf, I subtract the intraband 
contribution [-omega_p^2/omega^2] to get only interband contribution for 
compares). We can see the differences are notable. What's the reason? 
BTW, I use a homogeneous k-mesh also 15x15x15 generated by myself for 
epsilon calculation (see input file fccAu.nscf4eps.in).
------input for epsilon.x--------
&inputpp
      outdir='./work'
      prefix='fccAu'
      calculation='eps'
/
&energy_grid
      smeartype='gauss'
      intersmear=0.1d0
      intrasmear=0d0
      wmax=20d0
      wmin=0d0
      nw=600
      shift=0d0
/
--------------------------------

      (2) As for the intraband contribution, wien2k gives the plasma 
frequency 9.0075eV which agrees well with experimental value (ref: 
http://wave-scattering.com/drudefit.html), but the result from epsilon.x 
is puzzling.
Specifically, plasma frequency given in the output of epsilon.x is 
dependent on the input parameters:
<1>. intrasmear=0,   wmax=20d0  -->   The bulk xx plasmon frequency [eV] 
is:    14.877926200
<2>. intrasmear=0,   wmax=10d0  -->   The bulk xx plasmon frequency [eV] 
is:    7.625822195
<3>. intrasmear=0,   wmax=6d0   -->   The bulk xx plasmon frequency [eV] 
is:    3.156554381
<4>. intrasmear=0.1, wmax=20d0  -->   The bulk xx plasmon frequency [eV] 
is:    15.766403193
<5>. intrasmear=0.1, wmax=10d0  -->   The bulk xx plasmon frequency [eV] 
is:    9.322251787
<6>. intrasmear=0.1, wmax=20d0  -->   The bulk xx plasmon frequency [eV] 
is:    6.263713572
However, none of these values is the one got by fitting the results 
using Drude model [ 1 - omega_p^2/(omega^2+i*omega*gamma), gamma is the 
intrasmear here ]. By fitting the results using Drude model, I get 
omega_p=5.528769eV, for all the cases above (<1>~<6>). But this omega_p 
is far from the experimental value (~9 eV)! What's wrong? And what are 
the meanings of the values given in <1>~<6> ?

       How can I get more accurate results like the ones from wien2k?
       Please help me if you know something about this, thanks in advance!

Best regards!

                    Liu Guibin
                Postdoctoral Fellow,
                Department of Physics,
                The University of Hong Kong
                gbliu at hku.hk





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From e110658 at metu.edu.tr  Thu Jul  7 12:05:26 2011
From: e110658 at metu.edu.tr (?nkaya Ugur Yigit)
Date: Thu, 07 Jul 2011 13:05:26 +0300
Subject: [Pw_forum] Inability of PWgui version 4.3 to open an example input
	file
Message-ID: <20110707130526.62925jieo7gk6ew6@horde.metu.edu.tr>

Dear users,

Although PWgui version 4.3, which I have installed in my Ubuntu 11.04  
machine, could browse the example input file al.band.cg.in contained  
in ../espresso-4.3.1/examples/example01/results, it was not able to  
open the file. The paths for QE version 4.3.1 and pwgui executable is  
the following, where inkaya is both the root name and my user name:

/home/inkaya/espresso-4.3.1

/home/inkaya/espresso-4.3.1/PWgui-4.3/pwgui

Also a log file for the error has been attached. The problem might be  
elementary but I am not an experienced Ubuntu user, so any answer  
could be important for me to save time. Thanks in advance.

Ugur Yigit Inkaya
PhD student
Middle East Technical University





----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

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From Lorenzo.Paulatto at impmc.upmc.fr  Thu Jul  7 12:08:55 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 07 Jul 2011 12:08:55 +0200
Subject: [Pw_forum] Inability of PWgui version 4.3 to open an example
 input file
In-Reply-To: <20110707130526.62925jieo7gk6ew6@horde.metu.edu.tr>
References: <20110707130526.62925jieo7gk6ew6@horde.metu.edu.tr>
Message-ID: <op.vx8ug5qaxuur8c@vanoxite.impmc.jussieu.fr>

On Thu, 07 Jul 2011 12:05:26 +0200, ?nkaya Ugur Yigit  
<e110658 at metu.edu.tr> wrote:
> /home/inkaya/espresso-4.3.1
>
> /home/inkaya/espresso-4.3.1/PWgui-4.3/pwgui
>

As long as the directory actually exists (note that examples have to be  
donwloaded separately in 4.3.1) this is absolutely NOT a Quantum-ESPRESSO.  
You should refer to the Ubuntu communit support instead:  
http://www.ubuntu.com/support


-- 
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

From m.abbasnejad at gmail.com  Thu Jul  7 13:01:57 2011
From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad)
Date: Thu, 7 Jul 2011 15:31:57 +0430
Subject: [Pw_forum] oxygen pseudopotential in tio2
In-Reply-To: <1309224464.1474.YahooMailClassic@web125505.mail.ne1.yahoo.com>
References: <1309224464.1474.YahooMailClassic@web125505.mail.ne1.yahoo.com>
Message-ID: <CAF3mdWNcyJnYhudZ9JL+p0dTtAHuA8LUiFKpT7a+ZbAuCVAAbQ@mail.gmail.com>

Dear Dr. Deyu Lu

I am looking for a Ti norm-conserving PSP.
I was wondering if I could have the generated Ti-PSP by you.

Best Regards,
Mohaddeseh
---------------------------------------------------------
Mohaddeseh Abbasnejad,
Room No. 323, Department of Physics,
University of Tehran, North Karegar Ave.,
Tehran, P.O. Box: 14395-547- IRAN
Tel. No.: +98 21 6111 8634  & Fax No.: +98 21 8800 4781
Cellphone: +98 917 731 7514
E-Mail:     m.abbasnejad at gmail.com
Website:  http://physics.ut.ac.ir
---------------------------------------------------------


On Tue, Jun 28, 2011 at 5:57 AM, Deyu Lu <deyulu at yahoo.com> wrote:

> Dear PW developers and users:
>     I have been doing norm-conserving PSP (PBE) calculations to
> study the structure of rutile tio2. During my study, I found the
> resulting lattice constant is sensitive to some fine details of
> the PSPs I used. Such effect is kind of counter-intuitive. Perhaps
> someone with a better understanding can clarify it for me. The story is a
> bit long, which I summarize below. Input files and some PSPs are attached.
>
> All the calculations are carried out on a Linux cluster with QE 4.2.1.
> The code is compiled with Intel compiler (ifort) and mvapich2-1.2,
> and is linked to the mkl library accompanied with the code. Main
> results are verified on a Cray XE6 machine (hopper at NERSC) with the same
> version of QE.
>
> The Ti PBE PSP was generated from an ionic configuration
> 3s2 3p6 3d0 4s0, with semi-core included explicitly. A small rcut
> (0.9 0.9 1.0 for 3s 3p 3d) was used to ensure a good transferability.
> The psp was generated from opium, and the convergence can be
> reached at ecutwfn=160 Ry.
>
> The structure of Rutile TiO2 was calculated using this Ti PSP
> and O.pbe-mt.UPF from QE library. The lattice constant 4.587 angstrom
> is in excellent agreement with experiment (4.587 and 4.582 angstrom)
> but at odds with all the known theoretical results (ultrasoft and paw)  in
> the literature (4.63 - 4.65). The error is about 1.1%. So our good agreement
> seems to be accidental. In order to obtain a better understanding, I
> performed the calculations using paw (vasp) and norm-conserving PSP with HGH
> (abinit library Theor. Chem. Acc. 114, 145 (2005)) which is known to be very
> accurate. Indeed, the results are consistent with literature.
>
> The 1% difference was later found to be related to the Oxygen PSP.
> Different Oxygen PSPs are used in the following tests.
>
> 1.d: 08-O.PBE.fhi.UPF (abinit PSP library, converted to UPF, lmax=3,
> local=2)
>     a=4.633 angstrom
>
> 2.d: O.pbe-mt.UPF (QE PSP library, lmax=2, local=2)
>     a=4.587 angstrom
>
> In order to see if the f channel can cause any difference, 08-O.PBE.fhi.UPF
> is modified (08-O.PBE.fake.UPF) by removing f channel and making
> corresponding changes in DIJ.
> No difference is found as compared to 1.d.
>
> 6.d: 08-O.PBE.fake.UPF (modified version, lmax=2, local=2)
>     a=4.633 angstrom
>
> There seems to be a bug in the <PP_HEADER> section of O.pbe-mt.UPF, where
> Max angular momentum component is set to 1 instead of 2. I manually changed
> it to 2 (O.pbe-mt.9.UPF), and no difference found in output as compared to
> 2.d. So this field is not sensitive in the calculation.
>
> 9.d: O.pbe-mt.9.UPF (minor modification of O.pbe-mt.UPF)
>     a=4.587 angstrom
>
> In the rest of tests, the "Max angular momentum component" is left
> unchanged.
>
> To find out the difference between 08-O.PBE.fake.UPF and O.pbe-mt.UPF, I
> plot term by term for two PSPs, and the results are shown in the xmgrace
> plots for mesh, local, and nonlocal parts of the PSP. The two meshes have
> the same size, with a max difference within 5d-3 a.u (mesh.agr). There is no
> difference found in local and non-local components of the PSP (local.agr and
> nonlocal.agr). In the inset of local.agr, we see that even the small wiggle
> at the origin is id
> entical. My conclusion is that the two PSPs are literally the same.
>
> Further tests were done by replace local PP and Beta sections in
> O.pbe-mt.UPF one by one by the corresponding section from 08-O.PBE.fake.UPF,
> and the difference is negligible as compared to 2.d.
>
> In the end, I replaced </PP_MESH> section in O.pbe-mt.UPF with that from
> 08-O.PBE.fake.UPF, and kept everything else unchanged, the lattice constant
> increased from 4.587 to 4.633.
>
> 8.d: O.pbe-mt.8.UPF ( </PP_MESH> section modified)
>     a=4.633
>
> In the end, I was quite confused about the fact that a very small change in
> the mesh (<5d-3 max at 80 a.u.) can cause a difference in the lattice
> constant by 1%.
>
> Best
> Deyu Lu
>
> ************************************************
> Deyu Lu
> Assistant Physicist, Theory & Computation Group
> the Center for Functional Nanomaterials
> Building 735, Brookhaven National Lab
> Upton, NY, 11973
> ************************************************
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From zhaohscas at yahoo.com.cn  Thu Jul  7 13:40:45 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Thu, 07 Jul 2011 19:40:45 +0800
Subject: [Pw_forum] can pwscf compute elastic constant?
In-Reply-To: <0722C87B-2922-4A51-BEFB-805B838C5704@sissa.it>
References: <1309976255.98526.YahooMailClassic@web39402.mail.mud.yahoo.com>
	<0722C87B-2922-4A51-BEFB-805B838C5704@sissa.it>
Message-ID: <4E159B3D.8080107@yahoo.com.cn>

On 07/07/2011 01:11 PM, Stefano Baroni wrote:
> calculate the stress corresponding to different strain states and
> interpolate in-between. beware that, if you have internal degrees of
> freedom (which is usally the case) you have to minimize the energy with
> respect to internal coordinates, corresponding to each strain state. SB

I.e., in general case, you should do "calculation = relax " for each 
strain when minimizing the energy.

Regards.
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From sclauzer at sissa.it  Thu Jul  7 14:57:25 2011
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Thu, 7 Jul 2011 14:57:25 +0200
Subject: [Pw_forum] hysteresis Loop
In-Reply-To: <CAOMa7Cx12Vvvw38-j-nQ5ZN3VDCQ5Dn5_Jkj-e1Oh8Cng6_KMA@mail.gmail.com>
References: <CAOMa7Cx12Vvvw38-j-nQ5ZN3VDCQ5Dn5_Jkj-e1Oh8Cng6_KMA@mail.gmail.com>
Message-ID: <08D158F2-5FF1-4225-AD1B-C88581AB9734@sissa.it>

Il giorno 06/lug/2011, alle ore 23.39, Mahdi Mirnezhad ha scritto:

> Dear Developers,
> I want to study the hysteresis loop by using the DFT calculation.

Hysteresis loops can arise in several physics phenomena and in different situations, so it is not clear to me what you are referring to.
Please make your question more specific, for instance by pointing to some work in the scientific literature! Are you speaking about dynamics, magnetism, other...?


GS

> DFT
> simply calculates the Ground State of the physical system, it is not
> involve the memory of system. Could any body introduce me a DFT or
> "DFT like" method for this kind of calculations?
> Thanks in advance
> 
> ----------------------------------------------------------------------------
> Mahdi Mirnezhad
> MSc student of Mechanical engineering,
> Guilan University.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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

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From sclauzer at sissa.it  Thu Jul  7 15:02:59 2011
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Thu, 7 Jul 2011 15:02:59 +0200
Subject: [Pw_forum] OCCUPATION , example 11
In-Reply-To: <CAHbvuiSRB23_mH41HgGhKJN8e6j7V1T1T1db9QzypPFjUj7Wig@mail.gmail.com>
References: <CAHbvuiSRB23_mH41HgGhKJN8e6j7V1T1T1db9QzypPFjUj7Wig@mail.gmail.com>
Message-ID: <8BDDE5BC-9B15-414F-855A-5B80D821DABA@sissa.it>

Have you looked into the documentation?

See, e.g.

http://www.quantum-espresso.org/input-syntax/INPUT_PW.html#id2469938


HTH

GS

Il giorno 06/lug/2011, alle ore 15.10, Mehrnoosh Hazrati ha scritto:

> Dear QE users,
> I want to calculate the formation energy of my system and need the chemical potential of Nitrogen. I used Example 11, but i don't know how to choose OCCUPATIONS.
> any suggest will be appreciated.
> My INPUT :
> &control
> calculation='scf',
> pseudo_dir = './',
> outdir='./',
> prefix='n',
> /
> &system
> ibrav =1,
> celldm(1) =20.0,
> nat =1,
> ntyp =1,
> nbnd =5,
> nosym=.true.,
> ecutwfc=15.0,
> occupations='./',
> /
> &electrons
> conv_thr=1.0d-7
> mixing_beta = 0.5,
> /
> ATOMIC_SPECIES
> N 14.006 N.pw91-van_ak.UPF
> ATOMIC_POSITIONS {angstrom}
> N 0.00 0.00 0.00
> K_POINTS AUTOMATIC
> 1 1 1 0 0 0
> OCCUPATIONS
> ????
> 
> -- 
> """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> *** Mehrnoosh Kh. Hazrati ***
> *** Master Student of Computational Physical Chemistry,KNTU,Tehran ***
> *** Phone : +989123436300 ***
> *** Mail : mehrnooshhazrati at gmail.com ***
> """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> 
> 
> -- 
> """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> *** Mehrnoosh Kh. Hazrati ***
> *** Master Student of Computational Physical Chemistry,KNTU,Tehran ***
>  *** Phone : +989123436300 ***
> *** Mail : mehrnooshhazrati at gmail.com ***
> """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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

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From fratesi at mater.unimib.it  Thu Jul  7 16:30:59 2011
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Thu, 7 Jul 2011 16:30:59 +0200 (CEST)
Subject: [Pw_forum] Different adsorbate dipole moments from 4.3.1 and
	4.0.1
In-Reply-To: <alpine.DEB.2.00.1107051559460.4793@localhost.localdomain,>
References: <alpine.DEB.2.00.1107051559460.4793@localhost.localdomain,>
Message-ID: <alpine.DEB.2.00.1107071611580.7496@localhost.localdomain,>

Replying myself to my own message...

The differences between the old and new PW/compute_dip.f90 (see function 
saw()) actually explain my apparently weird results for 4.3.1, which occur 
when there is electron charge in the region where the electric field is 
reverted.

  In the previous version 4.0.1 this was not a problem for the calculation 
of the dipole itself, but the application of such an electric field is 
probably incorrect in most cases of physical interests.

  The two lead to the same result for a well-constructed cell setup.

Guido Fratesi

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
Milano, Italy

From Lorenzo.Paulatto at impmc.upmc.fr  Thu Jul  7 17:23:25 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 07 Jul 2011 17:23:25 +0200
Subject: [Pw_forum] Inability of PWgui version 4.3 to open an example
 input file
In-Reply-To: <op.vx8ug5qaxuur8c@vanoxite.impmc.jussieu.fr>
References: <20110707130526.62925jieo7gk6ew6@horde.metu.edu.tr>
	<op.vx8ug5qaxuur8c@vanoxite.impmc.jussieu.fr>
Message-ID: <op.vx881bioxuur8c@vanoxite.impmc.jussieu.fr>

On Thu, 07 Jul 2011 12:08:55 +0200, Lorenzo Paulatto  
<Lorenzo.Paulatto at impmc.upmc.fr> wrote:
> As long as the directory actually exists (note that examples have to be
> donwloaded separately in 4.3.1) this is absolutely NOT a  
> Quantum-ESPRESSO.

Actually I misread your message... it appears to actually BE a problem of  
pwgui... however I have no idea how to fix it.

Let's wait to see if the author of the program (Tone Kokalj) has the time  
to check 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

From mehrnooshhazrati at gmail.com  Thu Jul  7 17:25:34 2011
From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati)
Date: Thu, 7 Jul 2011 19:55:34 +0430
Subject: [Pw_forum] OCCUPATION , example 11
In-Reply-To: <8BDDE5BC-9B15-414F-855A-5B80D821DABA@sissa.it>
References: <CAHbvuiSRB23_mH41HgGhKJN8e6j7V1T1T1db9QzypPFjUj7Wig@mail.gmail.com>
	<8BDDE5BC-9B15-414F-855A-5B80D821DABA@sissa.it>
Message-ID: <CAHbvuiSXh=iDpfDoSzjV9tBcsqQwJkNKUj9QU2r5YUus0T1CPw@mail.gmail.com>

Thank you dear Gabriele :)

On Thu, Jul 7, 2011 at 5:32 PM, Gabriele Sclauzero <sclauzer at sissa.it>wrote:

> Have you looked into the documentation?
>
> See, e.g.
>
> http://www.quantum-espresso.org/input-syntax/INPUT_PW.html#id2469938
>
>
> HTH
>
> GS
>
> Il giorno 06/lug/2011, alle ore 15.10, Mehrnoosh Hazrati ha scritto:
>
> Dear QE users,
> I want to calculate the formation energy of my system and need the chemical
> potential of Nitrogen. I used Example 11, but i don't know how to choose
> OCCUPATIONS.
>  any suggest will be appreciated.
> My INPUT :
>  &control
> calculation='scf',
> pseudo_dir = './',
> outdir='./',
> prefix='n',
> /
> &system
> ibrav =1,
> celldm(1) =20.0,
> nat =1,
> ntyp =1,
> nbnd =5,
> nosym=.true.,
> ecutwfc=15.0,
> occupations='./',
> /
> &electrons
> conv_thr=1.0d-7
> mixing_beta = 0.5,
> /
> ATOMIC_SPECIES
> N 14.006 N.pw91-van_ak.UPF
> ATOMIC_POSITIONS {angstrom}
> N 0.00 0.00 0.00
> K_POINTS AUTOMATIC
> 1 1 1 0 0 0
> OCCUPATIONS
> ????
>
> --
> *
>
> *
> *
> """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> *
> **** Mehrnoosh Kh. Hazrati ****
> **** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
>  *** Phone : +989123436300 ***
> *** Mail : mehrnooshhazrati at gmail.com ***
> *
> """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> *
>
>
> --
> *
>
> *
> *
> """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> *
> **** Mehrnoosh Kh. Hazrati ****
> **** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
>  *** Phone : +989123436300 ***
> *** Mail : mehrnooshhazrati at gmail.com ***
> *
> """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> *
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *   PH H2 462, Station 3, CH-1015 Lausanne*
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
*

*
*
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
**** Mehrnoosh Kh. Hazrati ****
**** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
 *** Phone : +989123436300 ***
*** Mail : mehrnooshhazrati at gmail.com ***
*
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
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From mirnezhad.mm at gmail.com  Thu Jul  7 18:17:09 2011
From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad)
Date: Thu, 7 Jul 2011 09:17:09 -0700
Subject: [Pw_forum] hysteresis Loop
In-Reply-To: <08D158F2-5FF1-4225-AD1B-C88581AB9734@sissa.it>
References: <CAOMa7Cx12Vvvw38-j-nQ5ZN3VDCQ5Dn5_Jkj-e1Oh8Cng6_KMA@mail.gmail.com>
	<08D158F2-5FF1-4225-AD1B-C88581AB9734@sissa.it>
Message-ID: <CAOMa7CzJcxarQ_=usReDF51pdtvRR6_04AnfmxXmw-a=roEL8g@mail.gmail.com>

Dear Developers,
I want to study the hysteresis loop by using the DFT calculation.

We want to draw a graph of residual stress (strain).

DFT
simply calculates the Ground State of the physical system, it is not
involve the memory of system. Could any body introduce me a DFT or
"DFT like" method for this kind of calculations?
Thanks in advance


Mahdi Mirnezhad
MSc student of Mechanical engineering,
Guilan University.


On 7/7/11, Gabriele Sclauzero <sclauzer at sissa.it> wrote:
> Il giorno 06/lug/2011, alle ore 23.39, Mahdi Mirnezhad ha scritto:
>
>> Dear Developers,
>> I want to study the hysteresis loop by using the DFT calculation.
>
> Hysteresis loops can arise in several physics phenomena and in different
> situations, so it is not clear to me what you are referring to.
> Please make your question more specific, for instance by pointing to some
> work in the scientific literature! Are you speaking about dynamics,
> magnetism, other...?
>
>
> GS
>
>> DFT
>> simply calculates the Ground State of the physical system, it is not
>> involve the memory of system. Could any body introduce me a DFT or
>> "DFT like" method for this kind of calculations?
>> Thanks in advance
>>
>> ----------------------------------------------------------------------------
>> Mahdi Mirnezhad
>> MSc student of Mechanical engineering,
>> Guilan University.
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>    PH H2 462, Station 3, CH-1015 Lausanne
>
>

From hashemifar at cc.iut.ac.ir  Thu Jul  7 19:13:08 2011
From: hashemifar at cc.iut.ac.ir (Seyed Javad Hashemifar)
Date: Thu, 7 Jul 2011 19:13:08 +0200
Subject: [Pw_forum] hysteresis Loop
In-Reply-To: <CAOMa7CzJcxarQ_=usReDF51pdtvRR6_04AnfmxXmw-a=roEL8g@mail.gmail.com>
References: <CAOMa7Cx12Vvvw38-j-nQ5ZN3VDCQ5Dn5_Jkj-e1Oh8Cng6_KMA@mail.gmail.com>
	<08D158F2-5FF1-4225-AD1B-C88581AB9734@sissa.it>
	<CAOMa7CzJcxarQ_=usReDF51pdtvRR6_04AnfmxXmw-a=roEL8g@mail.gmail.com>
Message-ID: <CAKScr_r8aPz6dDomknEJJJhhsiF8TsQfEgYDBUxfB-CY=kvCzA@mail.gmail.com>

I am not sure but my understanding is that studying hysteresis phenomena
needs to phenomenological models and I doubt if it is possible to study
directly this macroscopic phenomena by first principles calculations without
any phenomenology. As far as I know husteresis is s macroscopic phenomena
wich originates from domain structure of the system. For example in the case
of ferromagnetic hysteresis, the magnetic domain structure of the system
give rises to hysteresis effect. Hence I guess you have to develop or find a
phenomenological model based on some physical parameters such as domain wall
energy to be able to draw hysteresis loop. The physical parameters of
phenomenological models could be calculated by direct first principles
computations.

SJ Hashemifar

======================================
Seyed Javad  Hashemifar
Physics Department, Isfahan University of Technology
84156-83111 Isfahan, Iran
Tel: +98 311 391 2375     Fax:+98 311 3912376
Email:  hashemifar at cc.iut.ac.ir
Homepage:  http://hashemifar.iut.ac.ir
---------------------------------------------------------------------------


On Thu, Jul 7, 2011 at 6:17 PM, Mahdi Mirnezhad <mirnezhad.mm at gmail.com>wrote:

> Dear Developers,
> I want to study the hysteresis loop by using the DFT calculation.
>
> We want to draw a graph of residual stress (strain).
>
> DFT
> simply calculates the Ground State of the physical system, it is not
> involve the memory of system. Could any body introduce me a DFT or
> "DFT like" method for this kind of calculations?
> Thanks in advance
>
>
> Mahdi Mirnezhad
> MSc student of Mechanical engineering,
> Guilan University.
>
>
> On 7/7/11, Gabriele Sclauzero <sclauzer at sissa.it> wrote:
> > Il giorno 06/lug/2011, alle ore 23.39, Mahdi Mirnezhad ha scritto:
> >
> >> Dear Developers,
> >> I want to study the hysteresis loop by using the DFT calculation.
> >
> > Hysteresis loops can arise in several physics phenomena and in different
> > situations, so it is not clear to me what you are referring to.
> > Please make your question more specific, for instance by pointing to some
> > work in the scientific literature! Are you speaking about dynamics,
> > magnetism, other...?
> >
> >
> > GS
> >
> >> DFT
> >> simply calculates the Ground State of the physical system, it is not
> >> involve the memory of system. Could any body introduce me a DFT or
> >> "DFT like" method for this kind of calculations?
> >> Thanks in advance
> >>
> >>
> ----------------------------------------------------------------------------
> >> Mahdi Mirnezhad
> >> MSc student of Mechanical engineering,
> >> Guilan University.
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> > ? Gabriele Sclauzero, EPFL SB ITP CSEA
> >    PH H2 462, Station 3, CH-1015 Lausanne
> >
> >
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From maxradin at umich.edu  Thu Jul  7 20:18:28 2011
From: maxradin at umich.edu (maxradin at umich.edu)
Date: Thu, 07 Jul 2011 14:18:28 -0400
Subject: [Pw_forum] SiO2 xanes calculation
In-Reply-To: <mailman.1.1310025042.7590.pw_forum@pwscf.org>
References: <mailman.1.1310025042.7590.pw_forum@pwscf.org>
Message-ID: <49b7663c124a7dce522b7706e3a38eca@umich.edu>


>  >Hi,
>  >
>  >I'm trying to repeat the ultrasoft core-hole calculation of the Si
>  >>K-edge
>  >in Matteo's paper:
>  >
>  >"First-principles calculations of x-ray absorption in a scheme
>  >based on ultrasoft pseudopotentials: From alpha-quartz to
>  >high-Tc  compounds"
> 
>  >I haved used the same parameters given in that article (cell size,
>  >>cutoff
>  >energies, kpoints) but the spectrum that I get does not at all look 
>  >right.
>  >Is it possible that this discrepancy is due to the choice of
>  >pseudopotentials? For the absorbing atom I am using
> 
> Dear Max,
> 
>    the pseudo you use are correct, however this is not the case for
> the k-points in your Xanes calculation. In the paper it is stated
> that you need "the Lanczos method was performed
> using a centered 3x3x3 k-points grid of the 72
> atoms supercell." (see just below Eq. 27).
> 
> The second thing is that in an insulator, there is no Fermi level.
> Are you sure you're cutting eliminated the occupied states at the right 
> energy position ?
> 
> Can you try yo see if you reproduce the results of the QE XSpectra 
> example directory ?
> 
> all the best,
> 
> Matteo

After closer inspection, the major problem was due to unit conversion
(lattice constants were in Angstroms instead of Bohr). But regarding the
occupied states: as I understand it, for insulators, one should do an scf
calculation (without smearing) followed by an xspectra fermi level
calculation to find the energy to cut the occupied states. In the case of a
gamma only
kpoint grid, could one simply use the energy of the highest occupied band 
instead of doing the fermi level calculation? 

Thanks,

Max

From guntram.schmidt at chemie.uni-halle.de  Fri Jul  8 00:38:20 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Fri, 08 Jul 2011 00:38:20 +0200
Subject: [Pw_forum] dE0s is positive which should never happen
Message-ID: <4E16355C.4050708@chemie.uni-halle.de>

Dear All,

I tried to optimize a crystal structure of a molecular compound and get 
this strange error. Is there something I've forgotten in the input file?
I've chosen a small ecutwfc to make some "preoptimization" - is it okay 
to do so (I'm still not able to converge the cutoffs - see my other post)?

&control
    calculation = 'relax'
    restart_mode='from_scratch',
    prefix='i2t0480',
    tstress = .true.
    tprnfor = .true.
    pseudo_dir = '/gpfs/home/aasfu/espresso-4.3.1/pseudo/',
    outdir='/gpfs/home/aasfu/tmp/'
    verbosity = 'high'
/
&system
  ibrav = 14,
  A = 8.2555,
  B = 17.0986,
  C = 16.3082,
  cosAB = 0,
  cosAC = -.4968073528,
  cosBC = 0,
  nat = 196,
  ntyp = 5,
  occupations = 'fixed',
  ecutwfc = 20,
  ecutrho = 80,
  input_dft = 'vdW-DF'
/
&electrons
     conv_thr        = 1.0d-5
     electron_maxstep= 1000
/
&ions
/

ATOMIC_SPECIES
  P 39.974 P.rpb-nc.UPF
  O 15.999 O.rpb-nc.UPF
  N 14.007 N.rpb-nc.UPF
  C 12.011 C.rpb-nc.UPF
  H 1.0079 H.rpb-nc.UPF


ATOMIC_POSITIONS angstrom
  H      -4.163902    3.036540    7.286078 1 1 1
  C      -3.730208    5.027159    7.959787 1 1 1
  H      -2.669409    4.951703    7.725352 1 1 1
  C      -4.231111    6.183196    8.511764 1 1 1
  H      -3.568842    7.024960    8.708593 1 1 1
and 210 more atoms...



The output says after 41 cycles of geometry optimizations in the 
subroutine stress:



    0:     number of scf cycles    =  30
    0:     number of bfgs steps    =  28
    0:
    0:     energy   old            =   -1592.2501932245 Ry
    0:     energy   new            =   -1547.5620256423 Ry
    0:
    0:     CASE: energy  _new > energy  _old
    0:
    0:
    0: 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    0:     from bfgs : error #         1
    0:     dE0s is positive which should never happen
    0: 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    0:
    0:     stopping ...

The strange thing is, that the energy was not -1592... before at all:
grep '!' i2t0480.xyz.relax.20.rpb-nc.UPF.out
    0:!    total energy              =   -1542.41391161 Ry
    0:!    total energy              =   -1544.87249615 Ry
    0:!    total energy              =   -1546.30689086 Ry
    0:!    total energy              =   -1546.89859418 Ry
    0:!    total energy              =   -1547.07908001 Ry
    0:!    total energy              =   -1547.12438175 Ry
    0:!    total energy              =   -1547.16304879 Ry
    0:!    total energy              =   -1547.21850898 Ry
    0:!    total energy              =   -1547.26799568 Ry
    0:!    total energy              =   -1547.31147437 Ry
    0:!    total energy              =   -1547.33202922 Ry
    0:!    total energy              =   -1547.35963149 Ry
    0:!    total energy              =   -1547.36650754 Ry
    0:!    total energy              =   -1547.38045447 Ry
    0:!    total energy              =   -1547.38597654 Ry
    0:!    total energy              =   -1547.39351928 Ry
    0:!    total energy              =   -1547.40184806 Ry
    0:!    total energy              =   -1547.41383843 Ry
    0:!    total energy              =   -1547.43030750 Ry
    0:!    total energy              =   -1547.45110560 Ry
    0:!    total energy              =   -1547.47294386 Ry
    0:!    total energy              =   -1547.48424959 Ry
    0:!    total energy              =   -1547.48774725 Ry
    0:!    total energy              =   -1547.49458349 Ry
    0:!    total energy              =   -1547.50098365 Ry
    0:!    total energy              =   -1547.50487139 Ry
    0:!    total energy              =   -1547.50802242 Ry
    0:!    total energy              =   -1547.51133404 Ry
    0:!    total energy              =   -1547.51564694 Ry
    0:!    total energy              =   -1547.52054790 Ry
    0:!    total energy              =   -1547.52614229 Ry
    0:!    total energy              =   -1547.53597920 Ry
    0:!    total energy              =   -1547.54614655 Ry
    0:!    total energy              =   -1547.55021920 Ry
    0:!    total energy              =   -1547.55191818 Ry
    0:!    total energy              =   -1547.55360256 Ry
    0:!    total energy              =   -1547.55527582 Ry
    0:!    total energy              =   -1547.55697509 Ry
    0:!    total energy              =   -1547.55871207 Ry
    0:!    total energy              =   -1547.56042619 Ry
    0:!    total energy              =   -1547.56202564 Ry


Thanks a lot for help,
Guntram

From goodluck_1982 at 163.com  Fri Jul  8 05:28:26 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Fri, 08 Jul 2011 11:28:26 +0800
Subject: [Pw_forum] What's wrong in my calculation of epsilon of fcc Au?
In-Reply-To: <CAEQ9wfAAJhdXbPTiLXWowbRioQ_N=Ssi6BVyOwiE73Unv8oLAA@mail.gmail.com>
References: <d5360c67d8b89e63994a959436f4846e@umich.edu>	<4E157EEE.4050309@163.com>
	<CAEQ9wfAAJhdXbPTiLXWowbRioQ_N=Ssi6BVyOwiE73Unv8oLAA@mail.gmail.com>
Message-ID: <4E16795A.9060409@163.com>

Dear Sun,

    Thanks for your reply.  I know this. Automatic k-mesh is only used 
in the scf run. In the following *nscf *run I used a self defined 
k-mesh,  which can be seen in the attached file fccAu.nscf4eps.in of the 
original mail.

Best regards,
Liu Gui-Bin

? 2011/7/7 23:53, Tao Sun ??:
> Hi.
>
> I have never done dielectric function calculations.  But the kmesh you
> are using "15 15 15 1 1 1" automatic seems to be inconsistent with
> this manual.  https://ir.library.dc-uoit.ca/bitstream/10155/159/3/McNelles_Phillip_appendixA.pdf.
>    Maybe this is worth checking, i.e. set the full kmesh by hand,
> without symmetry.
>
> Best
>
> Tao
>
> On Thu, Jul 7, 2011 at 4:39 AM, gbliu<goodluck_1982 at 163.com>  wrote:
>> Dear all,
>>
>>       I want to calculate dielectric function of carbon nanotube, but I have
>> no experiences of calculating dielectric function before. Hence, I decide to
>> start with a simple case of fcc gold, because there are referable results
>> from wien2k (wien2k is capable of simple case such as fcc Au, but too
>> resource consumptive to deal with large cells such as CNT).
>>       Because epsilon.x doesn't support USPP, the UPF file of Au is got by
>> converting fhi file from abinit using fhi2upf.x. I calculate fcc Au with
>> a=7.71bohr and 15x15x15 k-mesh using both pwscf(v4.3) and wien2k. First I
>> check the band structures and find that the results from both softwares
>> agree well (see attachments). But the results of epsilon from pwscf is not
>> satisfactory as the results from wien2k:
>>
>>       (1) Figures imag_eps and real_eps are the compares with only interband
>> contribution. (note that for pwscf, I subtract the intraband contribution
>> [-omega_p^2/omega^2] to get only interband contribution for compares). We
>> can see the differences are notable. What's the reason?/*  */_*BTW, I use a
>> homogeneous k-mesh also 15x15x15 generated by myself for epsilon calculation
>> (see input file fccAu.nscf4eps.in).*_
>> ------input for epsilon.x--------
>> &inputpp
>>      outdir='./work'
>>      prefix='fccAu'
>>      calculation='eps'
>> /
>> &energy_grid
>>      smeartype='gauss'
>>      intersmear=0.1d0
>>      intrasmear=0d0
>>      wmax=20d0
>>      wmin=0d0
>>      nw=600
>>      shift=0d0
>> /
>> --------------------------------
>>
>>      (2) As for the intraband contribution, wien2k gives the plasma frequency
>> 9.0075eV which agrees well with experimental value (ref:
>> http://wave-scattering.com/drudefit.html), but the result from epsilon.x is
>> puzzling.
>> Specifically, plasma frequency given in the output of epsilon.x is dependent
>> on the input parameters:
>> <1>. intrasmear=0,   wmax=20d0  -->     The bulk xx plasmon frequency [eV] is:
>>     14.877926200
>> <2>. intrasmear=0,   wmax=10d0  -->     The bulk xx plasmon frequency [eV] is:
>>     7.625822195
>> <3>. intrasmear=0,   wmax=6d0   -->     The bulk xx plasmon frequency [eV] is:
>>     3.156554381
>> <4>. intrasmear=0.1, wmax=20d0  -->     The bulk xx plasmon frequency [eV] is:
>>     15.766403193
>> <5>. intrasmear=0.1, wmax=10d0  -->     The bulk xx plasmon frequency [eV] is:
>>     9.322251787
>> <6>. intrasmear=0.1, wmax=20d0  -->     The bulk xx plasmon frequency [eV] is:
>>     6.263713572
>> However, none of these values is the one got by fitting the results using
>> Drude model [ 1 - omega_p^2/(omega^2+i*omega*gamma), gamma is the intrasmear
>> here ]. By fitting the results using Drude model, I get omega_p=5.528769eV,
>> for all the cases above (<1>~<6>). But this omega_p is far from the
>> experimental value (~9 eV)! What's wrong? And what are the meanings of the
>> values given in<1>~<6>  ?
>>
>>       How can I get more accurate results like the ones from wien2k?
>>       Please help me if you know something about this, thanks in advance!
>>
>> Best regards!
>>
>>                    Liu Guibin
>>                Postdoctoral Fellow,
>>                Department of Physics,
>>                The University of Hong Kong
>>                gbliu at hku.hk
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>

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From nedward at MIT.EDU  Fri Jul  8 09:20:37 2011
From: nedward at MIT.EDU (Nicholas Edward Miller)
Date: Fri, 08 Jul 2011 03:20:37 -0400
Subject: [Pw_forum] dE0s is positive which should never happen
In-Reply-To: <4E16355C.4050708@chemie.uni-halle.de>
References: <4E16355C.4050708@chemie.uni-halle.de>
Message-ID: <20110708032037.epfglzgs00okk04c@webmail.mit.edu>

Hi Guntram,

Without really looking at the rest of the setup, I noticed you specify
'nat=196', but actually claim to have 215 atoms in the system.

-Nick

Quoting Guntram Schmidt <guntram.schmidt at chemie.uni-halle.de>:

> Dear All,
>
> I tried to optimize a crystal structure of a molecular compound and get
> this strange error. Is there something I've forgotten in the input file?
> I've chosen a small ecutwfc to make some "preoptimization" - is it okay
> to do so (I'm still not able to converge the cutoffs - see my other post)?
>
> &control
>    calculation = 'relax'
>    restart_mode='from_scratch',
>    prefix='i2t0480',
>    tstress = .true.
>    tprnfor = .true.
>    pseudo_dir = '/gpfs/home/aasfu/espresso-4.3.1/pseudo/',
>    outdir='/gpfs/home/aasfu/tmp/'
>    verbosity = 'high'
> /
> &system
>  ibrav = 14,
>  A = 8.2555,
>  B = 17.0986,
>  C = 16.3082,
>  cosAB = 0,
>  cosAC = -.4968073528,
>  cosBC = 0,
>  nat = 196,
>  ntyp = 5,
>  occupations = 'fixed',
>  ecutwfc = 20,
>  ecutrho = 80,
>  input_dft = 'vdW-DF'
> /
> &electrons
>     conv_thr        = 1.0d-5
>     electron_maxstep= 1000
> /
> &ions
> /
>
> ATOMIC_SPECIES
>  P 39.974 P.rpb-nc.UPF
>  O 15.999 O.rpb-nc.UPF
>  N 14.007 N.rpb-nc.UPF
>  C 12.011 C.rpb-nc.UPF
>  H 1.0079 H.rpb-nc.UPF
>
>
> ATOMIC_POSITIONS angstrom
>  H      -4.163902    3.036540    7.286078 1 1 1
>  C      -3.730208    5.027159    7.959787 1 1 1
>  H      -2.669409    4.951703    7.725352 1 1 1
>  C      -4.231111    6.183196    8.511764 1 1 1
>  H      -3.568842    7.024960    8.708593 1 1 1
> and 210 more atoms...
>
>
>
> The output says after 41 cycles of geometry optimizations in the
> subroutine stress:
>
>
>
>    0:     number of scf cycles    =  30
>    0:     number of bfgs steps    =  28
>    0:
>    0:     energy   old            =   -1592.2501932245 Ry
>    0:     energy   new            =   -1547.5620256423 Ry
>    0:
>    0:     CASE: energy  _new > energy  _old
>    0:
>    0:
>    0:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>    0:     from bfgs : error #         1
>    0:     dE0s is positive which should never happen
>    0:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>    0:
>    0:     stopping ...
>
> The strange thing is, that the energy was not -1592... before at all:
> grep '!' i2t0480.xyz.relax.20.rpb-nc.UPF.out
>    0:!    total energy              =   -1542.41391161 Ry
>    0:!    total energy              =   -1544.87249615 Ry
>    0:!    total energy              =   -1546.30689086 Ry
>    0:!    total energy              =   -1546.89859418 Ry
>    0:!    total energy              =   -1547.07908001 Ry
>    0:!    total energy              =   -1547.12438175 Ry
>    0:!    total energy              =   -1547.16304879 Ry
>    0:!    total energy              =   -1547.21850898 Ry
>    0:!    total energy              =   -1547.26799568 Ry
>    0:!    total energy              =   -1547.31147437 Ry
>    0:!    total energy              =   -1547.33202922 Ry
>    0:!    total energy              =   -1547.35963149 Ry
>    0:!    total energy              =   -1547.36650754 Ry
>    0:!    total energy              =   -1547.38045447 Ry
>    0:!    total energy              =   -1547.38597654 Ry
>    0:!    total energy              =   -1547.39351928 Ry
>    0:!    total energy              =   -1547.40184806 Ry
>    0:!    total energy              =   -1547.41383843 Ry
>    0:!    total energy              =   -1547.43030750 Ry
>    0:!    total energy              =   -1547.45110560 Ry
>    0:!    total energy              =   -1547.47294386 Ry
>    0:!    total energy              =   -1547.48424959 Ry
>    0:!    total energy              =   -1547.48774725 Ry
>    0:!    total energy              =   -1547.49458349 Ry
>    0:!    total energy              =   -1547.50098365 Ry
>    0:!    total energy              =   -1547.50487139 Ry
>    0:!    total energy              =   -1547.50802242 Ry
>    0:!    total energy              =   -1547.51133404 Ry
>    0:!    total energy              =   -1547.51564694 Ry
>    0:!    total energy              =   -1547.52054790 Ry
>    0:!    total energy              =   -1547.52614229 Ry
>    0:!    total energy              =   -1547.53597920 Ry
>    0:!    total energy              =   -1547.54614655 Ry
>    0:!    total energy              =   -1547.55021920 Ry
>    0:!    total energy              =   -1547.55191818 Ry
>    0:!    total energy              =   -1547.55360256 Ry
>    0:!    total energy              =   -1547.55527582 Ry
>    0:!    total energy              =   -1547.55697509 Ry
>    0:!    total energy              =   -1547.55871207 Ry
>    0:!    total energy              =   -1547.56042619 Ry
>    0:!    total energy              =   -1547.56202564 Ry
>
>
> Thanks a lot for help,
> Guntram
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



From matteo.calandra at impmc.jussieu.fr  Fri Jul  8 09:47:01 2011
From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra)
Date: Fri, 08 Jul 2011 09:47:01 +0200
Subject: [Pw_forum] XANES SiO2
In-Reply-To: <mailman.13789.1310095763.1814.pw_forum@pwscf.org>
References: <mailman.13789.1310095763.1814.pw_forum@pwscf.org>
Message-ID: <4E16B5F5.3040503@impmc.jussieu.fr>


>
> After closer inspection, the major problem was due to unit conversion
> (lattice constants were in Angstroms instead of Bohr). But regarding the
> occupied states: as I understand it, for insulators, one should do an scf
> calculation (without smearing) followed by an xspectra fermi level
> calculation to find the energy to cut the occupied states. In the case of a
> gamma only
> kpoint grid, could one simply use the energy of the highest occupied band
> instead of doing the fermi level calculation?
>
> Thanks,
>
> Max
>


Dear Max,

    it is in general a good idea to print out forces/stress, if you had
Angstrom instead of Bohr you probably would have totally absurd values 
for Forces and Stress.

Regarding the question about Fermi level in insulators. In general you 
can choose your Fermi level as you prefer inside the gap of the system 
WITH a core-hole.

All the best, M.

>
> ------------------------------
>
> Message: 4
> Date: Fri, 08 Jul 2011 00:38:20 +0200
> From: Guntram Schmidt<guntram.schmidt at chemie.uni-halle.de>
> Subject: [Pw_forum] dE0s is positive which should never happen
> To: pw_forum at pwscf.org
> Message-ID:<4E16355C.4050708 at chemie.uni-halle.de>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
> Dear All,
>
> I tried to optimize a crystal structure of a molecular compound and get
> this strange error. Is there something I've forgotten in the input file?
> I've chosen a small ecutwfc to make some "preoptimization" - is it okay
> to do so (I'm still not able to converge the cutoffs - see my other post)?
>
> &control
>      calculation = 'relax'
>      restart_mode='from_scratch',
>      prefix='i2t0480',
>      tstress = .true.
>      tprnfor = .true.
>      pseudo_dir = '/gpfs/home/aasfu/espresso-4.3.1/pseudo/',
>      outdir='/gpfs/home/aasfu/tmp/'
>      verbosity = 'high'
> /
> &system
>    ibrav = 14,
>    A = 8.2555,
>    B = 17.0986,
>    C = 16.3082,
>    cosAB = 0,
>    cosAC = -.4968073528,
>    cosBC = 0,
>    nat = 196,
>    ntyp = 5,
>    occupations = 'fixed',
>    ecutwfc = 20,
>    ecutrho = 80,
>    input_dft = 'vdW-DF'
> /
> &electrons
>       conv_thr        = 1.0d-5
>       electron_maxstep= 1000
> /
> &ions
> /
>
> ATOMIC_SPECIES
>    P 39.974 P.rpb-nc.UPF
>    O 15.999 O.rpb-nc.UPF
>    N 14.007 N.rpb-nc.UPF
>    C 12.011 C.rpb-nc.UPF
>    H 1.0079 H.rpb-nc.UPF
>
>
> ATOMIC_POSITIONS angstrom
>    H      -4.163902    3.036540    7.286078 1 1 1
>    C      -3.730208    5.027159    7.959787 1 1 1
>    H      -2.669409    4.951703    7.725352 1 1 1
>    C      -4.231111    6.183196    8.511764 1 1 1
>    H      -3.568842    7.024960    8.708593 1 1 1
> and 210 more atoms...
>
>
>
> The output says after 41 cycles of geometry optimizations in the
> subroutine stress:
>
>
>
>      0:     number of scf cycles    =  30
>      0:     number of bfgs steps    =  28
>      0:
>      0:     energy   old            =   -1592.2501932245 Ry
>      0:     energy   new            =   -1547.5620256423 Ry
>      0:
>      0:     CASE: energy  _new>  energy  _old
>      0:
>      0:
>      0:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      0:     from bfgs : error #         1
>      0:     dE0s is positive which should never happen
>      0:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      0:
>      0:     stopping ...
>
> The strange thing is, that the energy was not -1592... before at all:
> grep '!' i2t0480.xyz.relax.20.rpb-nc.UPF.out
>      0:!    total energy              =   -1542.41391161 Ry
>      0:!    total energy              =   -1544.87249615 Ry
>      0:!    total energy              =   -1546.30689086 Ry
>      0:!    total energy              =   -1546.89859418 Ry
>      0:!    total energy              =   -1547.07908001 Ry
>      0:!    total energy              =   -1547.12438175 Ry
>      0:!    total energy              =   -1547.16304879 Ry
>      0:!    total energy              =   -1547.21850898 Ry
>      0:!    total energy              =   -1547.26799568 Ry
>      0:!    total energy              =   -1547.31147437 Ry
>      0:!    total energy              =   -1547.33202922 Ry
>      0:!    total energy              =   -1547.35963149 Ry
>      0:!    total energy              =   -1547.36650754 Ry
>      0:!    total energy              =   -1547.38045447 Ry
>      0:!    total energy              =   -1547.38597654 Ry
>      0:!    total energy              =   -1547.39351928 Ry
>      0:!    total energy              =   -1547.40184806 Ry
>      0:!    total energy              =   -1547.41383843 Ry
>      0:!    total energy              =   -1547.43030750 Ry
>      0:!    total energy              =   -1547.45110560 Ry
>      0:!    total energy              =   -1547.47294386 Ry
>      0:!    total energy              =   -1547.48424959 Ry
>      0:!    total energy              =   -1547.48774725 Ry
>      0:!    total energy              =   -1547.49458349 Ry
>      0:!    total energy              =   -1547.50098365 Ry
>      0:!    total energy              =   -1547.50487139 Ry
>      0:!    total energy              =   -1547.50802242 Ry
>      0:!    total energy              =   -1547.51133404 Ry
>      0:!    total energy              =   -1547.51564694 Ry
>      0:!    total energy              =   -1547.52054790 Ry
>      0:!    total energy              =   -1547.52614229 Ry
>      0:!    total energy              =   -1547.53597920 Ry
>      0:!    total energy              =   -1547.54614655 Ry
>      0:!    total energy              =   -1547.55021920 Ry
>      0:!    total energy              =   -1547.55191818 Ry
>      0:!    total energy              =   -1547.55360256 Ry
>      0:!    total energy              =   -1547.55527582 Ry
>      0:!    total energy              =   -1547.55697509 Ry
>      0:!    total energy              =   -1547.55871207 Ry
>      0:!    total energy              =   -1547.56042619 Ry
>      0:!    total energy              =   -1547.56202564 Ry
>
>
> Thanks a lot for help,
> Guntram
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 08 Jul 2011 11:28:26 +0800
> From: gbliu<goodluck_1982 at 163.com>
> Subject: Re: [Pw_forum] What's wrong in my calculation of epsilon of
> 	fcc Au?
> To: PWSCF Forum<pw_forum at pwscf.org>, Tao Sun<taotao.sun at gmail.com>
> Message-ID:<4E16795A.9060409 at 163.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Sun,
>
>      Thanks for your reply.  I know this. Automatic k-mesh is only used
> in the scf run. In the following *nscf *run I used a self defined
> k-mesh,  which can be seen in the attached file fccAu.nscf4eps.in of the
> original mail.
>
> Best regards,
> Liu Gui-Bin
>
> ? 2011/7/7 23:53, Tao Sun ??:
>> Hi.
>>
>> I have never done dielectric function calculations.  But the kmesh you
>> are using "15 15 15 1 1 1" automatic seems to be inconsistent with
>> this manual.  https://ir.library.dc-uoit.ca/bitstream/10155/159/3/McNelles_Phillip_appendixA.pdf.
>>     Maybe this is worth checking, i.e. set the full kmesh by hand,
>> without symmetry.
>>
>> Best
>>
>> Tao
>>
>> On Thu, Jul 7, 2011 at 4:39 AM, gbliu<goodluck_1982 at 163.com>   wrote:
>>> Dear all,
>>>
>>>        I want to calculate dielectric function of carbon nanotube, but I have
>>> no experiences of calculating dielectric function before. Hence, I decide to
>>> start with a simple case of fcc gold, because there are referable results
>>> from wien2k (wien2k is capable of simple case such as fcc Au, but too
>>> resource consumptive to deal with large cells such as CNT).
>>>        Because epsilon.x doesn't support USPP, the UPF file of Au is got by
>>> converting fhi file from abinit using fhi2upf.x. I calculate fcc Au with
>>> a=7.71bohr and 15x15x15 k-mesh using both pwscf(v4.3) and wien2k. First I
>>> check the band structures and find that the results from both softwares
>>> agree well (see attachments). But the results of epsilon from pwscf is not
>>> satisfactory as the results from wien2k:
>>>
>>>        (1) Figures imag_eps and real_eps are the compares with only interband
>>> contribution. (note that for pwscf, I subtract the intraband contribution
>>> [-omega_p^2/omega^2] to get only interband contribution for compares). We
>>> can see the differences are notable. What's the reason?/*  */_*BTW, I use a
>>> homogeneous k-mesh also 15x15x15 generated by myself for epsilon calculation
>>> (see input file fccAu.nscf4eps.in).*_
>>> ------input for epsilon.x--------
>>> &inputpp
>>>       outdir='./work'
>>>       prefix='fccAu'
>>>       calculation='eps'
>>> /
>>> &energy_grid
>>>       smeartype='gauss'
>>>       intersmear=0.1d0
>>>       intrasmear=0d0
>>>       wmax=20d0
>>>       wmin=0d0
>>>       nw=600
>>>       shift=0d0
>>> /
>>> --------------------------------
>>>
>>>       (2) As for the intraband contribution, wien2k gives the plasma frequency
>>> 9.0075eV which agrees well with experimental value (ref:
>>> http://wave-scattering.com/drudefit.html), but the result from epsilon.x is
>>> puzzling.
>>> Specifically, plasma frequency given in the output of epsilon.x is dependent
>>> on the input parameters:
>>> <1>. intrasmear=0,   wmax=20d0  -->      The bulk xx plasmon frequency [eV] is:
>>>      14.877926200
>>> <2>. intrasmear=0,   wmax=10d0  -->      The bulk xx plasmon frequency [eV] is:
>>>      7.625822195
>>> <3>. intrasmear=0,   wmax=6d0   -->      The bulk xx plasmon frequency [eV] is:
>>>      3.156554381
>>> <4>. intrasmear=0.1, wmax=20d0  -->      The bulk xx plasmon frequency [eV] is:
>>>      15.766403193
>>> <5>. intrasmear=0.1, wmax=10d0  -->      The bulk xx plasmon frequency [eV] is:
>>>      9.322251787
>>> <6>. intrasmear=0.1, wmax=20d0  -->      The bulk xx plasmon frequency [eV] is:
>>>      6.263713572
>>> However, none of these values is the one got by fitting the results using
>>> Drude model [ 1 - omega_p^2/(omega^2+i*omega*gamma), gamma is the intrasmear
>>> here ]. By fitting the results using Drude model, I get omega_p=5.528769eV,
>>> for all the cases above (<1>~<6>). But this omega_p is far from the
>>> experimental value (~9 eV)! What's wrong? And what are the meanings of the
>>> values given in<1>~<6>   ?
>>>
>>>        How can I get more accurate results like the ones from wien2k?
>>>        Please help me if you know something about this, thanks in advance!
>>>
>>> Best regards!
>>>
>>>                     Liu Guibin
>>>                 Postdoctoral Fellow,
>>>                 Department of Physics,
>>>                 The University of Hong Kong
>>>                 gbliu at hku.hk
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
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> ****************************************


-- 
* * * *
Matteo Calandra, Directeur de Recherche (DR2)
Institut de Mineralogie et de Physique des Milieux Condenses de Paris
Universite Pierre et Marie Curie, tour 23, 3eme etage, case 115
4 Place Jussieu, 75252 Paris Cedex 05 France
Tel: +33-1-44 27 52 16       Fax: +33-1-44 27 37 85
http://www.impmc.jussieu.fr/~calandra

From Lorenzo.Paulatto at impmc.upmc.fr  Fri Jul  8 09:55:46 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Fri, 08 Jul 2011 09:55:46 +0200
Subject: [Pw_forum] dE0s is positive which should never happen
In-Reply-To: <4E16355C.4050708@chemie.uni-halle.de>
References: <4E16355C.4050708@chemie.uni-halle.de>
Message-ID: <op.vyaiy8xsxuur8c@vanoxite.impmc.jussieu.fr>

On Fri, 08 Jul 2011 00:38:20 +0200, Guntram Schmidt  
<guntram.schmidt at chemie.uni-halle.de> wrote:
> I tried to optimize a crystal structure of a molecular compound and get
> this strange error.

dear Guntran,

It could be a small bug in the BFGS algorithm, or a compiler error or a  
bug in some algebra library... it's very difficult to tell and probably  
almost impossible to reproduce. I would just take the last optimized  
coordinates and bfgs thrust radius and continue (i.e. restart by hand)  
 from there.

If it happens again and/or regularly please report so we have a look at it.

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

From giannozz at democritos.it  Fri Jul  8 10:08:53 2011
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Fri, 08 Jul 2011 10:08:53 +0200
Subject: [Pw_forum] dE0s is positive which should never happen
In-Reply-To: <op.vyaiy8xsxuur8c@vanoxite.impmc.jussieu.fr>
References: <4E16355C.4050708@chemie.uni-halle.de>
	<op.vyaiy8xsxuur8c@vanoxite.impmc.jussieu.fr>
Message-ID: <20110708100853.42jczkowg84sw00s@mail.democritos.it>

Quoting Lorenzo Paulatto <Lorenzo.Paulatto at impmc.upmc.fr>:

> It could be a small bug in the BFGS algorithm, or a compiler error or a
> bug in some algebra library...

or another job running in the same directory

P.

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From xjin.xmu at gmail.com  Fri Jul  8 11:18:07 2011
From: xjin.xmu at gmail.com (jinxi)
Date: Fri, 08 Jul 2011 17:18:07 +0800
Subject: [Pw_forum] Raman cross section for metals
Message-ID: <4E16CB4F.6070706@gmail.com>

Dear all:

Why DFPT methods can't calculate Raman cross section for metals?
What method should I employ for calculating the coefficients for metals?

Many Thanks.

Xi Jin

From e110658 at metu.edu.tr  Fri Jul  8 16:03:04 2011
From: e110658 at metu.edu.tr (?nkaya Ugur Yigit)
Date: Fri, 08 Jul 2011 17:03:04 +0300
Subject: [Pw_forum] Inability of PWgui version 4.3 to open an example input
	file
Message-ID: <20110708170304.21357n8gyymwdn2w@horde.metu.edu.tr>

Dear users,

Although PWgui version 4.3, which I have installed in my Ubuntu 11.04  
machine, could browse the example input file al.band.cg.in contained  
in ../espresso-4.3.1/examples/example01/results, it was not able to  
open the file. The paths for QE version 4.3.1 and pwgui executable is  
the following, where inkaya is both the root name and my user name:

/home/inkaya/espresso-4.3.1

/home/inkaya/espresso-4.3.1/PWgui-4.3/pwgui

Also a log file for the error has been attached. The problem might be  
elementary but I am not an experienced Ubuntu user, so any answer  
could be important for me to save time. In addition to this problem,  
README of PWgui-4.3 does not contain sufficient information to operate  
QE via PWgui. Thanks in advance.

Regards,

Ugur Yigit Inkaya
PhD student
Middle East Technical University


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From guntram.schmidt at chemie.uni-halle.de  Fri Jul  8 16:33:14 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Fri, 08 Jul 2011 16:33:14 +0200
Subject: [Pw_forum] dE0s is positive which should never happen
In-Reply-To: <20110708100853.42jczkowg84sw00s@mail.democritos.it>
References: <4E16355C.4050708@chemie.uni-halle.de>
	<op.vyaiy8xsxuur8c@vanoxite.impmc.jussieu.fr>
	<20110708100853.42jczkowg84sw00s@mail.democritos.it>
Message-ID: <4E17152A.8000205@chemie.uni-halle.de>

Hello!

What is the "running" directory? The place where I started the mpiexec 
from, the tmp-directory?
Does 'prefix' not prevent such problems?

In fact, I have now a lot of jobs, just crashing without some things like:


    3:"xc_vdW_DF.f90", line 1746: 1525-108 Error encountered while 
attempting to allocate a data object.  The program will stop.
    6:"xc_vdW_DF.f90", line 1746: 1525-108 Error encountered while 
attempting to allocate a data object.  The program will stop.
    2:"xc_vdW_DF.f90", line 1746: 1525-108 Error encountered while 
attempting to allocate a data object.  The program will stop.


in the standard output.

Any ideas?

Thanks,
Guntram


Am 08.07.2011 10:08, schrieb giannozz at democritos.it:
> Quoting Lorenzo Paulatto<Lorenzo.Paulatto at impmc.upmc.fr>:
>
>> It could be a small bug in the BFGS algorithm, or a compiler error or a
>> bug in some algebra library...
>
> or another job running in the same directory
>
> P.
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

From goodluck_1982 at 163.com  Fri Jul  8 18:14:41 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Sat, 09 Jul 2011 00:14:41 +0800
Subject: [Pw_forum] What's wrong in my calculation of epsilon of fcc Au?
In-Reply-To: <CAEQ9wfCjE+gwoH8egEkrtMvOW4yY1sDy6qMUuVVMqQVBGBMT2g@mail.gmail.com>
References: <d5360c67d8b89e63994a959436f4846e@umich.edu>	<4E157EEE.4050309@163.com>	<CAEQ9wfAAJhdXbPTiLXWowbRioQ_N=Ssi6BVyOwiE73Unv8oLAA@mail.gmail.com>	<4E16795A.9060409@163.com>
	<CAEQ9wfCjE+gwoH8egEkrtMvOW4yY1sDy6qMUuVVMqQVBGBMT2g@mail.gmail.com>
Message-ID: <4E172CF1.4010103@163.com>

Hi Tao,

In my scf run with shifted kmesh, it also gives out P=-1708.63 kbar, 
Etot=-65.80769644 Ry.
As for the stress (or pressure), I'm not clear whether this value is too 
large. In my opinion, the stress comes from that I just use the 
experimental lattice constant a=4.08Angstrom=7.71bohr and no volume 
optimization is done.

Because the band structure is as good as the result from wien2k, I think 
the pseudopotential file is just ok and the energy cutoff 25Ry also 
should be ok.

About the k-mesh, I just calculated shifted 15x15x15 and shifted 
30x30x30 (total 27000 kpoints should be enough, I think). But the 
results are similar, hence not good either. I don't know why.

BTW: Mailing to the adress pw_forum at pwscf.org is just ok. Then the mail 
will appear in the mailing list.

Best,

Gui-Bin

? 2011/7/8 14:40, Tao Sun ??:
> Hi Gui-Bin,
>
> Sorry about that...
>
> I just used your nscf file as an input to do a scf calculation.  I got
> a total energy of -65.80738250 Ry.  The pressure I got is more than
> -170 GPa, which is not right. Did you get the same value in your
> shifted mesh scf?  I hope it is not because I am running from a mac...
> If the pressure is wrong, then maybe 25 Ry is a bit small for a
> norm-conserved pseudopotential, or the unshift 15x15x15 mesh is not
> dense enough.  This is just my guess. It would be a bit surprising to
> me if the problem is due to pseudo versus lapw, or there is a bug in
> epsilon.x.
>
> Best
>
> Tao




From victor.bermudez at nrl.navy.mil  Fri Jul  8 19:15:40 2011
From: victor.bermudez at nrl.navy.mil (Vic Bermudez)
Date: Fri, 8 Jul 2011 13:15:40 -0400
Subject: [Pw_forum] Problem with NEB Images (vers. 4.3.1)
Message-ID: <LEEKKBMDPAJFIINCBCGIOEMKDNAA.victor.bermudez@nrl.navy.mil>

Hello,

	I'm attempting, for the first time, to do a NEB calculation (using QE 4.3.1). The
attached is simply a test run for an HF molecule reacting with an SiOH group on a
SiC(0001) surface. The NEB job submission script (attached) correctly copies the first
image to the .in file (see attached). However, what gets passed to pw_x is a modified
structure where some of the surface atoms have been switched around. As can be seen in the
PW.out file, the F atom has changed places with an H that was in an SiOH group, and the O
atom in an SiOH has changed places with the H in the HF molecule. Naturally, the
calculation doesn't work very well with this modified starting structure. The rest of the
structure seems to be OK, i.e., nothing has changed between the .in file and the starting
structure in the .out file. Nothing like this happens when doing an ordinary pw-x 'relax'
or 'scf' calculation.
	Has anyone seen this sort of behavior before ?  I've looked for, and not found, anything
relevant in previous postings.

	Thanks,
	Vic Bermudez

************
Victor M. Bermudez
Code 6876
U.S. Naval Research Laboratory
4555 Overlook Ave., S.W.
Washington, DC 20375-5347

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From guntram.schmidt at chemie.uni-halle.de  Fri Jul  8 19:40:41 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Fri, 08 Jul 2011 19:40:41 +0200
Subject: [Pw_forum] dE0s is positive which should never happen
In-Reply-To: <20110708100853.42jczkowg84sw00s@mail.democritos.it>
References: <4E16355C.4050708@chemie.uni-halle.de>
	<op.vyaiy8xsxuur8c@vanoxite.impmc.jussieu.fr>
	<20110708100853.42jczkowg84sw00s@mail.democritos.it>
Message-ID: <4E174119.9060204@chemie.uni-halle.de>

I now ran the jobs from different directories and with different 
tmp-files, but I get the same error again and again (but some jobs seem 
to run fine).
Here is a sample input file:

&control
    calculation = 'scf',
    restart_mode='from_scratch',
    prefix='i2t0480n.xyz.201.804',
    tstress = .true.,
    tprnfor = .true.,
    pseudo_dir = '/gpfs/home/aasfu/espresso-4.3.1/pseudo/',
    outdir='/gpfs/home/aasfu/tmp/i2t0480n.xyz.201.804/',
    verbosity = 'high',
/
&system
  ibrav = 1,
  A = 20.0,
  B = 20.0,
  C = 20.0,
  cosAB = 0,
  cosAC = 0,
  cosBC = 0,
  nat = 49,
  ntyp = 5,
  occupations = 'fixed',
  ecutwfc = 201,
  ecutrho = 804,
  input_dft = 'vdW-DF',
/
&electrons
     conv_thr        = 1.0d-8,
     electron_maxstep= 1000,
/


ATOMIC_SPECIES
  O 1.0 O.rpb-nc.UPF
  P 1.0 P.rpb-nc.UPF
  H 1.0 H.rpb-nc.UPF
  N 1.0 N.rpb-nc.UPF
  C 1.0 C.rpb-nc.UPF


ATOMIC_POSITIONS angstrom
  C    2.53409    1.15758    5.90615
  C    3.15019   -0.07455    5.54807
  C    2.44131    2.12177    4.88712
  N    2.08837    1.31488    7.20825
  H    3.31810   -0.82944    6.31480
  C    3.53738   -0.33017    4.25447
  C    2.81937    1.85588    3.58926
  H    2.05732    3.11106    5.13159
  P    1.27411    2.59232    7.67785
  H    3.99492   -1.28895    4.01502
  C    3.35466    0.61367    3.23968
  H    2.70012    2.62397    2.82653
  C    2.32361    4.03989    7.96545
  C   -0.07967    3.08476    6.58551
  C    0.49920    2.23274    9.26472
  C    3.67968    0.32829    1.84558
  C    3.68044    3.95508    7.70220
  C    1.82454    5.21456    8.53441
  C   -0.99973    2.10073    6.24441
  C   -0.20939    4.36596    6.04202
  C    1.10848    1.38858   10.18043
  C   -0.66577    2.90557    9.63412
  O    3.33385    1.17929    0.95421
  O    4.28137   -0.76191    1.55162
  H    4.09160    3.03654    7.28608
  C    4.52529    5.02716    7.95979
  C    2.67299    6.27587    8.81889
  H    0.76162    5.29841    8.75594
  H   -0.88822    1.09226    6.63997
  C   -2.05731    2.39962    5.40230
  C   -1.25305    4.65424    5.19000
  H    0.51734    5.13775    6.29126
  H    2.01595    0.85160    9.90827
  C    0.56079    1.22802   11.44290
  C   -1.21257    2.72996   10.90225
  H   -1.15056    3.57429    8.92439
  H    3.53933    0.98640    0.00205
  H    5.58609    4.95170    7.72535
  C    4.02439    6.18320    8.51176
  H    2.27935    7.17994    9.28108
  H   -2.78394    1.63041    5.14492
  C   -2.19087    3.68406    4.88570
  H   -1.34098    5.64888    4.75538
  H    1.04561    0.56629   12.15913
  C   -0.59516    1.89743   11.80664
  H   -2.12784    3.25179   11.17774
  H    4.68666    7.02496    8.70859
  H   -3.03465    3.92651    4.24136
  H   -1.01367    1.76534   12.80330

K_POINTS automatic
1 1 1 0 0 0


and the errormessage in the loadleveler-logfile:

ATTENTION: 0031-408  4 tasks allocated by LoadLeveler, continuing...
ATTENTION: 0031-606 Unrecognized environment variable, MP_STACK_OVERFLOW.
    0:"recvec.f90", line 106: 1525-108 Error encountered while 
attempting to allocate a data object.  The program will stop.
    1:"recvec.f90", line 106: 1525-108 Error encountered while 
attempting to allocate a data object.  The program will stop.
    2:"recvec.f90", line 106: 1525-108 Error encountered while 
attempting to allocate a data object.  The program will stop.
    3:"recvec.f90", line 108: 1525-108 Error encountered while 
attempting to allocate a data object.  The program will stop.
ERROR: 0031-300  Forcing all remote tasks to exit due to exit code 1 in 
task 2


Any ideas?
Thank you,
Guntram


PS: last post was badly written - i didn't mean "without some things" 
but "with some things"


Am 08.07.2011 10:08, schrieb giannozz at democritos.it:
> Quoting Lorenzo Paulatto<Lorenzo.Paulatto at impmc.upmc.fr>:
>
>> It could be a small bug in the BFGS algorithm, or a compiler error or a
>> bug in some algebra library...
>
> or another job running in the same directory
>
> P.
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

From giannozz at democritos.it  Fri Jul  8 21:50:34 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 8 Jul 2011 21:50:34 +0200
Subject: [Pw_forum] Problem with NEB Images (vers. 4.3.1)
In-Reply-To: <LEEKKBMDPAJFIINCBCGIOEMKDNAA.victor.bermudez@nrl.navy.mil>
References: <LEEKKBMDPAJFIINCBCGIOEMKDNAA.victor.bermudez@nrl.navy.mil>
Message-ID: <4E5D30EE-D7C9-40AC-AF2F-82A61266A95E@democritos.it>


On Jul 8, 2011, at 19:15 , Vic Bermudez wrote:

> what gets passed to pw_x is a modified structure where some of the
> surface atoms have been switched around.

I guess that the ordering of atoms must be the same in all images.
In your input, the F atom is #1 in the first image, #7 in the last  
image.

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 degironc at sissa.it  Fri Jul  8 21:53:52 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 08 Jul 2011 21:53:52 +0200
Subject: [Pw_forum] Raman cross section for metals
In-Reply-To: <4E16CB4F.6070706@gmail.com>
References: <4E16CB4F.6070706@gmail.com>
Message-ID: <4E176050.1050107@sissa.it>

non resonant raman cross-section is defined in terms of the derivative 
of the static dielectric constant wrt phonon displacement...
in metals epsilon is infty and the derivative is not well defined... or 
at least no one has worked out a well defined  espression

stefano

On 07/08/2011 11:18 AM, jinxi wrote:
> Dear all:
>
> Why DFPT methods can't calculate Raman cross section for metals?
> What method should I employ for calculating the coefficients for metals?
>
> Many Thanks.
>
> Xi Jin
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From giannozz at democritos.it  Fri Jul  8 21:53:46 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 8 Jul 2011 21:53:46 +0200
Subject: [Pw_forum] dE0s is positive which should never happen
In-Reply-To: <4E174119.9060204@chemie.uni-halle.de>
References: <4E16355C.4050708@chemie.uni-halle.de>
	<op.vyaiy8xsxuur8c@vanoxite.impmc.jussieu.fr>
	<20110708100853.42jczkowg84sw00s@mail.democritos.it>
	<4E174119.9060204@chemie.uni-halle.de>
Message-ID: <83A6D420-FB26-420B-87AD-33AF41619802@democritos.it>


On Jul 8, 2011, at 19:40 , Guntram Schmidt wrote:

>   ecutwfc = 201,

that's a lot: are you really interested in such a high accuracy?

> K_POINTS automatic
> 1 1 1 0 0 0

for simple scf or optimization calculations, it is convenient to use
K_POINTS Gamma

>     0:"recvec.f90", line 106: 1525-108 Error encountered while
> attempting to allocate a data object.  The program will stop.

not enough memory

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  Fri Jul  8 21:54:36 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 8 Jul 2011 21:54:36 +0200
Subject: [Pw_forum] dE0s is positive which should never happen
In-Reply-To: <4E17152A.8000205@chemie.uni-halle.de>
References: <4E16355C.4050708@chemie.uni-halle.de>
	<op.vyaiy8xsxuur8c@vanoxite.impmc.jussieu.fr>
	<20110708100853.42jczkowg84sw00s@mail.democritos.it>
	<4E17152A.8000205@chemie.uni-halle.de>
Message-ID: <0E42BB43-9B00-4C6F-A9C1-E16A0B400492@democritos.it>


On Jul 8, 2011, at 16:33 , Guntram Schmidt wrote:

> What is the "running" directory? The place where I started the mpiexec
> from, the tmp-directory?

no, $outdir/$prefix

> Does 'prefix' not prevent such problems?

it should, if properly 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 bamideleibrahim at yahoo.com  Sat Jul  9 00:08:18 2011
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Fri, 8 Jul 2011 15:08:18 -0700 (PDT)
Subject: [Pw_forum] I need norm conserving pseudopotetial for Zinc that can
	work with pwscf
Message-ID: <1310162898.81940.YahooMailClassic@web39413.mail.mud.yahoo.com>


Dear all,
? I needed to run epsilo.x to get optical properties, but the pseudopotentials available on the QE page for Zinc has no norm conserving pseudopotential. So, i will appreciate it if an assistance can come from anybody from the forum. Also, if there is a way to make epsilo.x recognised the USPP. Kindly put me through.

Thanks
?
Adetunji Bamidele Ibrahim

Department of physics,University of Agriculture,

Abeokuta, Ogun State,Nigeria.
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From vovi47 at yahoo.com  Sat Jul  9 01:25:08 2011
From: vovi47 at yahoo.com (Vi Vo)
Date: Fri, 8 Jul 2011 16:25:08 -0700 (PDT)
Subject: [Pw_forum] reading atomic position in *.save
Message-ID: <1310167508.72605.YahooMailRC@web114504.mail.gq1.yahoo.com>

Dear All,

I apprciate if any of you could you show me which subroutine that allow for  
reading the atomic positions in the file "data-file.xml" in *.save  directory.  


Thank you very much,

Vi

Chemical Engineering,
University of Houston  
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From ma at nano.ku.dk  Sat Jul  9 09:12:49 2011
From: ma at nano.ku.dk (Martin Andersson)
Date: Sat, 09 Jul 2011 09:12:49 +0200
Subject: [Pw_forum] I need norm conserving pseudopotetial for Zinc that
 can work with pwscf
In-Reply-To: <1310162898.81940.YahooMailClassic@web39413.mail.mud.yahoo.com>
References: <1310162898.81940.YahooMailClassic@web39413.mail.mud.yahoo.com>
Message-ID: <4E17FF71.7020604@nano.ku.dk>

Hi,

You can download either LDA or PBE pseudopotentials for Zn from:

http://fpmd.ucdavis.edu/potentials/index.htm

and convert them to QE using the conversion tool qso2upf downloaded from:

http://eslab.ucdavis.edu/software/index.htm


Or you can convert pseudopotentials from www.abinit.org with converters 
in the QE distribution. Or you can generate your own...

Good luck,
Martin Andersson,
University of Copenhagen



On 7/9/2011 12:08 AM, bamidele ibrahim wrote:
>
> Dear all,
>   I needed to run epsilo.x to get optical properties, but the 
> pseudopotentials available on the QE page for Zinc has no norm 
> conserving pseudopotential. So, i will appreciate it if an assistance 
> can come from anybody from the forum. Also, if there is a way to make 
> epsilo.x recognised the USPP. Kindly put me through.
>
> Thanks
>
> Adetunji Bamidele Ibrahim
> 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 giannozz at democritos.it  Sat Jul  9 09:50:48 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 9 Jul 2011 09:50:48 +0200
Subject: [Pw_forum] reading atomic position in *.save
In-Reply-To: <1310167508.72605.YahooMailRC@web114504.mail.gq1.yahoo.com>
References: <1310167508.72605.YahooMailRC@web114504.mail.gq1.yahoo.com>
Message-ID: <A39904E9-E429-4385-9EDB-8529BBFD62E8@democritos.it>


On Jul 9, 2011, at 1:25 , Vi Vo wrote:

> I apprciate if any of you could you show me which subroutine that  
> allow
> for reading the atomic positions in the file "data-file.xml" in  
> *.save directory.

read_ions in PW/pw_restart.f90 . See also PP/qexml.f90

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 guntram.schmidt at chemie.uni-halle.de  Sat Jul  9 10:50:11 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Sat, 09 Jul 2011 10:50:11 +0200
Subject: [Pw_forum] dE0s is positive which should never happen
In-Reply-To: <83A6D420-FB26-420B-87AD-33AF41619802@democritos.it>
References: <4E16355C.4050708@chemie.uni-halle.de>
	<op.vyaiy8xsxuur8c@vanoxite.impmc.jussieu.fr>
	<20110708100853.42jczkowg84sw00s@mail.democritos.it>
	<4E174119.9060204@chemie.uni-halle.de>
	<83A6D420-FB26-420B-87AD-33AF41619802@democritos.it>
Message-ID: <4E181643.9040305@chemie.uni-halle.de>

Thanks for the reply!


2011/7/8 Paolo Giannozzi <giannozz at democritos.it>:
 > >
 > > On Jul 8, 2011, at 19:40 , Guntram Schmidt wrote:
 > >
 >> >>   ecutwfc = 201,
 > >
 > > that's a lot: are you really interested in such a high accuracy?


I lateron want to compare the total energy of two polymorphs - energy 
didn't converge until 200! I take 1 mRy energy difference per Ry cutoff
difference as criterium - is this too accurate?


 >> >> K_POINTS automatic
 >> >> 1 1 1 0 0 0
 > >
 > > for simple scf or optimization calculations, it is convenient to use
 > > K_POINTS Gamma
 > >
 >> >>     0:"recvec.f90", line 106: 1525-108 Error encountered while
 >> >> attempting to allocate a data object.  The program will stop.
 > >
 > > not enough memory


Is there a way to preestimate the needed memory per job? I couldn't
find any hint on this.
If it would be just this simple memory problem, I would be happy!



 > >
 > > 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 guntram.schmidt at chemie.uni-halle.de  Sat Jul  9 12:38:48 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Sat, 09 Jul 2011 12:38:48 +0200
Subject: [Pw_forum] dE0s is positive which should never happen
In-Reply-To: <83A6D420-FB26-420B-87AD-33AF41619802@democritos.it>
References: <4E16355C.4050708@chemie.uni-halle.de>
	<op.vyaiy8xsxuur8c@vanoxite.impmc.jussieu.fr>
	<20110708100853.42jczkowg84sw00s@mail.democritos.it>
	<4E174119.9060204@chemie.uni-halle.de>
	<83A6D420-FB26-420B-87AD-33AF41619802@democritos.it>
Message-ID: <4E182FB8.7030900@chemie.uni-halle.de>

>>      0:"recvec.f90", line 106: 1525-108 Error encountered while
>> attempting to allocate a data object.  The program will stop.
>
> not enough memory


There seems to be more than this.
When I start the same job (different prefix and outdir) on the same 
machine (without any other jobs running), but two times using half the 
processors, one of the latter jobs crashes and the other survives.

E.g.:
One job, consuming 7.000MB with 8 processors (56.000MB in total - the 
amount of the machine, where it is running) --> runs fine

Two jobs, consuming 7.000MB with 4 processors, each (= 56.000 in total, 
too) --> one job "survives", the other crashes:

   0:"xc_vdW_DF.f90", line 348: 1525-108 Error encountered while 
attempting to allocate a data object.  The program will stop.
    1:"xc_vdW_DF.f90", line 348: 1525-108 Error encountered while 
attempting to allocate a data object.  The program will stop.

Any idea?

The machine is a IBM 575 
(http://www-01.ibm.com/common/ssi/cgi-bin/ssialias?infotype=AN&subtype=CA&htmlfid=897/ENUS107-675&appname=USN) 
running Powerlinux/SLES 11 with loadleveler-job-balancing.

Thanks,
Guntram

From goodluck_1982 at 163.com  Sat Jul  9 15:32:44 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Sat, 09 Jul 2011 21:32:44 +0800
Subject: [Pw_forum] I need norm conserving pseudopotetial for Zinc that
 can	work with pwscf
In-Reply-To: <1310162898.81940.YahooMailClassic@web39413.mail.mud.yahoo.com>
References: <1310162898.81940.YahooMailClassic@web39413.mail.mud.yahoo.com>
Message-ID: <4E18587C.7070504@163.com>


You can use pp file of ABINIT, then use upftools/fhi2upf.x to covert the 
.fhi file to .upf file.

Best wishes,
Liu Gui-Bin
Dept. Physics, HKU

? 2011/7/9 6:08, bamidele ibrahim ??:
>
> Dear all,
>   I needed to run epsilo.x to get optical properties, but the 
> pseudopotentials available on the QE page for Zinc has no norm 
> conserving pseudopotential. So, i will appreciate it if an assistance 
> can come from anybody from the forum. Also, if there is a way to make 
> epsilo.x recognised the USPP. Kindly put me through.
>
> Thanks
>
> Adetunji Bamidele Ibrahim
> 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 pascal.boulet at univ-provence.fr  Sat Jul  9 18:13:35 2011
From: pascal.boulet at univ-provence.fr (pascal boulet)
Date: Sat, 09 Jul 2011 18:13:35 +0200
Subject: [Pw_forum] problem with symmetry recognition
Message-ID: <4E187E2F.6020402@univ-provence.fr>

Dear all,

I am struggling to make QE recognize the symmetry of a solid compound.
The group number is 116, it is a tetragonal primitive structure with 9
atoms in the primitive unit cell.
 

In the input file I give the reduced coordinates I obtained from the
Pearson database. I tried the following structure descriptions:

alat  = 1.,  ibrav = 0
CELL_PARAMETERS cubic
10.461 0. 0.
0. 10.461 0.
0. 0. 33.172

then:
celldm(1)=10.461, celldm(3)=3.171, ibrav=6

No way!

The idea is to optimize the cell parameters, so I would like QE to
retain the crystal symmetry.

Does anybody have an idea what could be wrong?

Thank you
Pascal


    * Anglais - d?tect?
    * Anglais
    * Fran?ais

    * Anglais
    * Fran?ais

<javascript:void(0);>

From victor.bermudez at nrl.navy.mil  Sat Jul  9 19:58:06 2011
From: victor.bermudez at nrl.navy.mil (Vic Bermudez)
Date: Sat, 9 Jul 2011 13:58:06 -0400
Subject: [Pw_forum] problem with symmetry recognition
In-Reply-To: <4E187E2F.6020402@univ-provence.fr>
Message-ID: <AKEFIBNCPJEJJMHNOPHICEGICHAA.victor.bermudez@nrl.navy.mil>

Hi Pascal,

	If I understand correctly, you're trying to optimize the unit cell while
constraining 2 of the lattice constants to remain equal, as required by
symmetry. I don't think that QE allows this. If you do a "vc-relax", what
seems to happen is that symmetry is ignored, and all lattice constants are
varied independently. I've attached a script written by a colleague that
does repeated single-point runs for a range of lattice constants. You can
then fit points near the total-energy minimum to find the exact minimum. Of
course, this has to be done iteratively if more than one lattice constant is
being optimized.
	Hope this helps.

	Best Wishes,
	Vic Bermudez

Victor M. Bermudez
Code 6876
U.S. Naval Research Laboratory
4555 Overlook Ave., S.W.
Washington, DC 20375-5347

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From degironc at sissa.it  Sat Jul  9 21:28:14 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sat, 09 Jul 2011 21:28:14 +0200
Subject: [Pw_forum] problem with symmetry recognition
In-Reply-To: <AKEFIBNCPJEJJMHNOPHICEGICHAA.victor.bermudez@nrl.navy.mil>
References: <AKEFIBNCPJEJJMHNOPHICEGICHAA.victor.bermudez@nrl.navy.mil>
Message-ID: <4E18ABCE.3020501@sissa.it>

this is not correct.
if the code finds some symmetry, forces and stress components will be 
symmetrized accordingly  and vc-relax will keep it.

There may be two reasons why the code does not find a symmetry:

- the symmetry is not there... check your coordinates. Beware that you 
need to specify ALL the atomic positions of a given structure not just 
the inequivalent ones, hoping the code to fill the others.

- the symmetry is there but involves a fractionary translations that 
cannot be written as a multiple of the FFT grid spacing.  the code 
writes a message saying that the symmetry is discarded due to a problem 
with fractionary translation and says what the translation would be in 
crystal coordinates. one can manually set the FFT dimensions (nr1,nr2, 
and/or nr3) so that the translation is in register with the FFT grid and 
the code can accept it

HTH

stefano
-
Stefano de Gironcoli - SISSA and DEMOCRITOS



On 07/09/2011 07:58 PM, Vic Bermudez wrote:
> Hi Pascal,
>
> 	If I understand correctly, you're trying to optimize the unit cell while
> constraining 2 of the lattice constants to remain equal, as required by
> symmetry. I don't think that QE allows this. If you do a "vc-relax", what
> seems to happen is that symmetry is ignored, and all lattice constants are
> varied independently. I've attached a script written by a colleague that
> does repeated single-point runs for a range of lattice constants. You can
> then fit points near the total-energy minimum to find the exact minimum. Of
> course, this has to be done iteratively if more than one lattice constant is
> being optimized.
> 	Hope this helps.
>
> 	Best Wishes,
> 	Vic Bermudez
>
> Victor M. Bermudez
> Code 6876
> U.S. Naval Research Laboratory
> 4555 Overlook Ave., S.W.
> Washington, DC 20375-5347
>
>
>
> _______________________________________________
> 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 mlib.ism.cnr.it  Sat Jul  9 22:46:33 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it)
Date: Sat,  9 Jul 2011 22:46:33 +0200
Subject: [Pw_forum] problem with symmetry recognition
In-Reply-To: <4E18ABCE.3020501@sissa.it>
References: <AKEFIBNCPJEJJMHNOPHICEGICHAA.victor.bermudez@nrl.navy.mil>
	<4E18ABCE.3020501@sissa.it>
Message-ID: <20110709224633.7bgqpfpbcwokccw0@webmail.sic.rm.cnr.it>


Dear Stefano, dear all.
Ok, but suppose that I would like to put a (quite useful) constraint  
like: "I say that the lattice is cubic because I know that it MUST be  
cubic (or tetragonal or monoclinic or so...), than KEEP IT CUBIC while  
performing a vc-relax, irrespective of the stress tensor! Change the  
volume, change the a/c ratio (if the lattice is, e.g., tetragonal) but  
retain the space group. I often have to perform a (boring) multi  
dimensional fit by changing the lattice parameters by hand on a grid  
near to the "expected" minimum...
I do not know exactly if Pascal's question was similar to mine;  
nevertheless I hope this can help...

Yours

Giuseppe


Quoting Stefano de Gironcoli <degironc at sissa.it>:

> this is not correct.
> if the code finds some symmetry, forces and stress components will be
> symmetrized accordingly  and vc-relax will keep it.
>
> There may be two reasons why the code does not find a symmetry:
>
> - the symmetry is not there... check your coordinates. Beware that you
> need to specify ALL the atomic positions of a given structure not just
> the inequivalent ones, hoping the code to fill the others.
>
> - the symmetry is there but involves a fractionary translations that
> cannot be written as a multiple of the FFT grid spacing.  the code
> writes a message saying that the symmetry is discarded due to a problem
> with fractionary translation and says what the translation would be in
> crystal coordinates. one can manually set the FFT dimensions (nr1,nr2,
> and/or nr3) so that the translation is in register with the FFT grid
> and the code can accept it
>
> HTH
>
> stefano
> -
> Stefano de Gironcoli - SISSA and DEMOCRITOS
>
>
>
> On 07/09/2011 07:58 PM, Vic Bermudez wrote:
>> Hi Pascal,
>>
>> 	If I understand correctly, you're trying to optimize the unit cell while
>> constraining 2 of the lattice constants to remain equal, as required by
>> symmetry. I don't think that QE allows this. If you do a "vc-relax", what
>> seems to happen is that symmetry is ignored, and all lattice constants are
>> varied independently. I've attached a script written by a colleague that
>> does repeated single-point runs for a range of lattice constants. You can
>> then fit points near the total-energy minimum to find the exact minimum. Of
>> course, this has to be done iteratively if more than one lattice constant is
>> being optimized.
>> 	Hope this helps.
>>
>> 	Best Wishes,
>> 	Vic Bermudez
>>
>> Victor M. Bermudez
>> Code 6876
>> U.S. Naval Research Laboratory
>> 4555 Overlook Ave., S.W.
>> Washington, DC 20375-5347
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum





From zhaohscas at yahoo.com.cn  Sun Jul 10 06:33:17 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Sun, 10 Jul 2011 12:33:17 +0800
Subject: [Pw_forum] On the doping modeling: how to determine all of the
 non-equivalent doping configurations?
Message-ID: <4E192B8D.2000701@yahoo.com.cn>

Dear All,

I use the 2*2*2 supercell of Wurtzite ZnO to construct the doping model. 
   In my case,   two Zn atoms will be substituted by Al in this 
supercell.  I want to calculate all of the non-equivalent doping 
configurations by geometry optimization and then find the  structure 
with lowest total energy.

The issue is the how to determine these non-equivalent doping 
configurations and then construct the correspond input file for each.

Any hints will be highly appreciated.

Best regards.
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China


From vovi47 at yahoo.com  Sun Jul 10 06:33:23 2011
From: vovi47 at yahoo.com (Vi Vo)
Date: Sat, 9 Jul 2011 21:33:23 -0700 (PDT)
Subject: [Pw_forum] reading atomic position in *.save
In-Reply-To: <A39904E9-E429-4385-9EDB-8529BBFD62E8@democritos.it>
References: <1310167508.72605.YahooMailRC@web114504.mail.gq1.yahoo.com>
	<A39904E9-E429-4385-9EDB-8529BBFD62E8@democritos.it>
Message-ID: <1310272403.16976.YahooMailRC@web114507.mail.gq1.yahoo.com>

Dear Paolo,

Thank you very much.

Vi





________________________________
From: Paolo Giannozzi <giannozz at democritos.it>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Sat, July 9, 2011 12:50:48 AM
Subject: Re: [Pw_forum] reading atomic position in *.save


On Jul 9, 2011, at 1:25 , Vi Vo wrote:

> I apprciate if any of you could you show me which subroutine that  
> allow
> for reading the atomic positions in the file "data-file.xml" in  
> *.save directory.

read_ions in PW/pw_restart.f90 . See also PP/qexml.f90

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  Sun Jul 10 09:15:04 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 10 Jul 2011 09:15:04 +0200
Subject: [Pw_forum] dE0s is positive which should never happen
In-Reply-To: <4E181643.9040305@chemie.uni-halle.de>
References: <4E16355C.4050708@chemie.uni-halle.de>
	<op.vyaiy8xsxuur8c@vanoxite.impmc.jussieu.fr>
	<20110708100853.42jczkowg84sw00s@mail.democritos.it>
	<4E174119.9060204@chemie.uni-halle.de>
	<83A6D420-FB26-420B-87AD-33AF41619802@democritos.it>
	<4E181643.9040305@chemie.uni-halle.de>
Message-ID: <BB4F6AA3-DDF9-4AAD-869C-F1CBAD427A54@democritos.it>


On Jul 9, 2011, at 10:50 , Guntram Schmidt wrote:

> I lateron want to compare the total energy of two polymorphs - energy
> didn't converge until 200!

energy differences between different structures converge much more
quickly than absolute energies

> Is there a way to preestimate the needed memory per job?
> I couldn't find any hint on this.

run a few smaller job and extrapolate. See also:
http://www.quantum-espresso.org/user_guide/node47.html
http://www.quantum-espresso.org/user_guide/node48.html

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 pascal.boulet at univ-provence.fr  Sun Jul 10 12:10:22 2011
From: pascal.boulet at univ-provence.fr (pascal boulet)
Date: Sun, 10 Jul 2011 12:10:22 +0200
Subject: [Pw_forum]  problem with symmetry recognition
Message-ID: <4E197A8E.5060306@univ-provence.fr>


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Hash: SHA1


Dear Vic, Stefano and Giuseppe,



Thank you for your help and sorry for this lengthy post.



Following Stefano's comment I need to provide ALL the atomic positions,
which I did not do! I gave only the positions in the primitive unit cell
(UC).

But then, if I provide all the positions (I guess in the full UC) why
should QE fill the others?

In addition, I did some calculations on Mg2Si (FCC, 12 atoms in the full
UC) by providing only the 3 atoms of the primitive UC. QE found 48
symmetry elements, which is correct, and the optimized cell parameters
seemed OK. So, still, is it wrong?

I have just tried Mn4Si7 with the full UC (44 atoms) and QE found 8
symmetry operations which is correct.

I also checked with the Bilbao Jmol applet that my structure is correct.


BTW, I also noticed something that looks strange to me. The coordinates
reported by QE in the output are not those I give in the input: X and Y
are the same but not Z which is scaled by c/a. So, for me, the distance
between the atoms is changed in the Z direction(?). That could explain
why the SCF converge is so difficult...(?) See the second set of
coordinates I copied from QE output, below.


For those who are interested, I provide here all the positions (cell
parameters: celldm(1)=10.46100d0,celldm(3)=3.17100d0, ibrav=6). The atom
positions with more digits are those of the atoms in the reduced UC (I
generated all the positions with the Bilbao website).



Input file:
ATOMIC_POSITIONS crystal
Si 0.16270000 0.67910000 0.18150000
Si 0.837300 0.320900 0.181500
Si 0.679100 0.837300 0.818500
Si 0.320900 0.162700 0.818500
Si 0.162700 0.320900 0.681500
Si 0.837300 0.679100 0.681500
Si 0.679100 0.162700 0.318500
Si 0.320900 0.837300 0.318500
Si 0.19330000 0.15070000 0.11290000
Si 0.806700 0.849300 0.112900
Si 0.150700 0.806700 0.887100
Si 0.849300 0.193300 0.887100
Si 0.193300 0.849300 0.612900
Si 0.806700 0.150700 0.612900
Si 0.150700 0.193300 0.387100
Si 0.849300 0.806700 0.387100
Si 0.34360000 0.22790000 0.54090000
Si 0.656400 0.772100 0.540900
Si 0.227900 0.656400 0.459100
Si 0.772100 0.343600 0.459100
Si 0.343600 0.772100 0.040900
Si 0.656400 0.227900 0.040900
Si 0.227900 0.343600 0.959100
Si 0.772100 0.656400 0.959100
Si 0.333333333333333 0.333333333333333 0.25000000
Si 0.666666666666667 0.666666666666667 0.2500
Si 0.333333333333333 0.666666666666667 0.7500
Si 0.666666666666667 0.333333333333333 0.7500
Mn 0.00000000 0.50000000 0.06250000
Mn 0.500000 0.000000 0.937500
Mn 0.000000 0.500000 0.562500
Mn 0.500000 0.000000 0.437500
Mn 0.00000000 0.50000000 0.31250000
Mn 0.500000 0.000000 0.687500
Mn 0.000000 0.500000 0.812500
Mn 0.500000 0.000000 0.187500
Mn 0.50000000 0.50000000 0.12500000
Mn 0.500000 0.500000 0.875000
Mn 0.500000 0.500000 0.625000
Mn 0.500000 0.500000 0.375000
Mn 0.00000000 0.00000000 0.00000000
Mn 0.000000 0.000000 0.500000
Mn 0.00000000 0.00000000 0.25000000
Mn 0.000000 0.000000 0.750000

- From output file:
[...]

      8 Sym.Ops. (no inversion)


   Cartesian axes

     site n.     atom                  positions (alat units)
         1           Si  tau(  1) = (   0.1627000   0.6791000   0.5755365  )
         2           Si  tau(  2) = (   0.8373000   0.3209000   0.5755365  )
         3           Si  tau(  3) = (   0.6791000   0.8373000   2.5954635  )
         4           Si  tau(  4) = (   0.3209000   0.1627000   2.5954635  )
         5           Si  tau(  5) = (   0.1627000   0.3209000   2.1610365  )
         6           Si  tau(  6) = (   0.8373000   0.6791000   2.1610365  )
         7           Si  tau(  7) = (   0.6791000   0.1627000   1.0099635  )
         8           Si  tau(  8) = (   0.3209000   0.8373000   1.0099635  )
         9           Si  tau(  9) = (   0.1933000   0.1507000   0.3580059  )
        10           Si  tau( 10) = (   0.8067000   0.8493000   0.3580059  )
        11           Si  tau( 11) = (   0.1507000   0.8067000   2.8129941  )
        12           Si  tau( 12) = (   0.8493000   0.1933000   2.8129941  )
        13           Si  tau( 13) = (   0.1933000   0.8493000   1.9435059  )
        14           Si  tau( 14) = (   0.8067000   0.1507000   1.9435059  )
        15           Si  tau( 15) = (   0.1507000   0.1933000   1.2274941  )
        16           Si  tau( 16) = (   0.8493000   0.8067000   1.2274941  )
        17           Si  tau( 17) = (   0.3436000   0.2279000   1.7151939  )
        18           Si  tau( 18) = (   0.6564000   0.7721000   1.7151939  )
        19           Si  tau( 19) = (   0.2279000   0.6564000   1.4558061  )
        20           Si  tau( 20) = (   0.7721000   0.3436000   1.4558061  )
        21           Si  tau( 21) = (   0.3436000   0.7721000   0.1296939  )
        22           Si  tau( 22) = (   0.6564000   0.2279000   0.1296939  )
        23           Si  tau( 23) = (   0.2279000   0.3436000   3.0413061  )
        24           Si  tau( 24) = (   0.7721000   0.6564000   3.0413061  )
        25           Si  tau( 25) = (   0.3333333   0.3333333   0.7927500  )
        26           Si  tau( 26) = (   0.6666667   0.6666667   0.7927500  )
        27           Si  tau( 27) = (   0.3333333   0.6666667   2.3782500  )
        28           Si  tau( 28) = (   0.6666667   0.3333333   2.3782500  )
        29           Mn  tau( 29) = (   0.0000000   0.5000000   0.1981875  )
        30           Mn  tau( 30) = (   0.5000000   0.0000000   2.9728125  )
        31           Mn  tau( 31) = (   0.0000000   0.5000000   1.7836875  )
        32           Mn  tau( 32) = (   0.5000000   0.0000000   1.3873125  )
        33           Mn  tau( 33) = (   0.0000000   0.5000000   0.9909375  )
        34           Mn  tau( 34) = (   0.5000000   0.0000000   2.1800625  )
        35           Mn  tau( 35) = (   0.0000000   0.5000000   2.5764375  )
        36           Mn  tau( 36) = (   0.5000000   0.0000000   0.5945625  )
        37           Mn  tau( 37) = (   0.5000000   0.5000000   0.3963750  )
        38           Mn  tau( 38) = (   0.5000000   0.5000000   2.7746250  )
        39           Mn  tau( 39) = (   0.5000000   0.5000000   1.9818750  )
        40           Mn  tau( 40) = (   0.5000000   0.5000000   1.1891250  )
        41           Mn  tau( 41) = (   0.0000000   0.0000000   0.0000000  )
        42           Mn  tau( 42) = (   0.0000000   0.0000000   1.5855000  )
        43           Mn  tau( 43) = (   0.0000000   0.0000000   0.7927500  )
        44           Mn  tau( 44) = (   0.0000000   0.0000000   2.3782500  )


Yours

Pascal
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From giannozz at democritos.it  Sun Jul 10 14:08:40 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 10 Jul 2011 14:08:40 +0200
Subject: [Pw_forum] problem with symmetry recognition
In-Reply-To: <4E197A8E.5060306@univ-provence.fr>
References: <4E197A8E.5060306@univ-provence.fr>
Message-ID: <2AF3362B-C94B-434A-9997-8BD7D6113EAC@democritos.it>


On Jul 10, 2011, at 12:10 , pascal boulet wrote:

> Following Stefano's comment I need to provide ALL the atomic  
> positions,
> which I did not do! I gave only the positions in the primitive unit  
> cell (UC).

what you call "primitive", I would call "irreducible" (like the  
irreducible
segment of the Brillouin Zone)

> But then, if I provide all the positions (I guess in the full UC)

what you call "full", I would call "primitive"

> why should QE fill the others?

which others?

> In addition, I did some calculations on Mg2Si (FCC, 12 atoms in the  
> full UC)

antifluorite structure? what you call "full" here, I would call  
"conventional"

> by providing only the 3 atoms of the primitive UC. QE found 48  
> symmetry
> elements, which is correct, and the optimized cell parameters  
> seemed OK.
> So, still, is it wrong?

no, because you provided all the needed atoms (3 in the unit cell of the
FCC lattice in the [anti]fluorite structure)

> BTW, I also noticed something that looks strange to me. The  
> coordinates
> reported by QE in the output are not those I give in the input: X  
> and Y
> are the same but not Z which is scaled by c/a.

nothing strange: atomic positions in input are in crystal coodinates:

> ATOMIC_POSITIONS crystal

atomic positions in output are in xyz coordinates, divided by a:

>    Cartesian axes
>
>      site n.     atom                  positions (alat units)

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 bamideleibrahim at yahoo.com  Sun Jul 10 16:08:32 2011
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Sun, 10 Jul 2011 07:08:32 -0700 (PDT)
Subject: [Pw_forum] I need norm conserving pseudopotetial for Zinc that
	can work with pwscf
In-Reply-To: <4E18587C.7070504@163.com>
Message-ID: <1310306912.94059.YahooMailClassic@web39413.mail.mud.yahoo.com>

Dear Liu,
? I have downloaded the .fhi file from abinit pseudopotential site, and i used the command given by you as follows;

?? ./fhi2upf.x /home/adetunji/Desktop/30-Zn.LDA.fhi 

after the command, here is the result of the process.
read_fhi: assuming abinit format
Pseudopotential without NLCC successfully read
Wavefunction # 1: label, occupancy > 

please, what is the next step.


Adetunji Bamidele Ibrahim

Department of physics,University of Agriculture,

Abeokuta, Ogun State,Nigeria.

--- On Sat, 7/9/11, gbliu <goodluck_1982 at 163.com> wrote:

From: gbliu <goodluck_1982 at 163.com>
Subject: Re: [Pw_forum] I need norm conserving pseudopotetial for Zinc that can work with pwscf
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Saturday, July 9, 2011, 6:32 AM



  

    
  

    You can use pp file of ABINIT, then use upftools/fhi2upf.x to covert
    the .fhi file to .upf file.

    

    Best wishes,

    Liu Gui-Bin

    Dept. Physics, HKU

    

    ? 2011/7/9 6:08, bamidele ibrahim ??:
    
      
        
          
            

              Dear all,

              ? I needed to run epsilo.x to get optical properties, but
              the pseudopotentials available on the QE page for Zinc has
              no norm conserving pseudopotential. So, i will appreciate
              it if an assistance can come from anybody from the forum.
              Also, if there is a way to make epsilo.x recognised the
              USPP. Kindly put me through.

              

              Thanks

              ?

              Adetunji Bamidele Ibrahim

              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 goodluck_1982 at 163.com  Sun Jul 10 16:51:28 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Sun, 10 Jul 2011 22:51:28 +0800
Subject: [Pw_forum] What's wrong in my calculation of epsilon of fcc Au?
In-Reply-To: <4E157EEE.4050309@163.com>
References: <d5360c67d8b89e63994a959436f4846e@umich.edu>
	<4E157EEE.4050309@163.com>
Message-ID: <4E19BC70.1060908@163.com>

Dear all,

   Now, I know that the bad results of dielectric function relate the 
pseudopotential(PP)!
   The PP I used is from abinit by fhi2upf.
   After that, I tested another qso PP, which is from 
http://fpmd.ucdavis.edu/potentials/index.htm and
http://eslab.ucdavis.edu/software/index.htm . Using this PP, the profile 
of the dielectric function curve is similar with the result from wien2k. 
But, this PP gives out somewhat bad band structures!

   So, it confuses me that a PP which can give good band structure 
results in bad dielectric function, while a PP which gives somewhat bad 
band structure results in a dielectric function comparable with wien2k. 
Can anyone give some explanations? (see attachments)

   Another question aslo confuses me as mentioned in the original email: 
what's the meaning of the "plasmon frequency" given by epsilon.x? And 
why it depends on the input parameter intrasmear and even wmax?

Best regards!

                    Liu Guibin
                Postdoctoral Fellow,
                Department of Physics,
                The University of Hong Kong
                gbliu at hku.hk


? 2011/7/7 17:39, gbliu ??:
> Dear all,
>
>       I want to calculate dielectric function of carbon nanotube, but 
> I have no experiences of calculating dielectric function before. 
> Hence, I decide to start with a simple case of fcc gold, because there 
> are referable results from wien2k (wien2k is capable of simple case 
> such as fcc Au, but too resource consumptive to deal with large cells 
> such as CNT).
>       Because epsilon.x doesn't support USPP, the UPF file of Au is 
> got by converting fhi file from abinit using fhi2upf.x. I calculate 
> fcc Au with a=7.71bohr and 15x15x15 k-mesh using both pwscf(v4.3) and 
> wien2k. First I check the band structures and find that the results 
> from both softwares agree well (see attachments). But the results of 
> epsilon from pwscf is not satisfactory as the results from wien2k:
>
>       (1) Figures imag_eps and real_eps are the compares with only 
> interband contribution. (note that for pwscf, I subtract the intraband 
> contribution [-omega_p^2/omega^2] to get only interband contribution 
> for compares). We can see the differences are notable. What's the 
> reason? BTW, I use a homogeneous k-mesh also 15x15x15 generated by 
> myself for epsilon calculation (see input file fccAu.nscf4eps.in).
> ------input for epsilon.x--------
> &inputpp
>      outdir='./work'
>      prefix='fccAu'
>      calculation='eps'
> /
> &energy_grid
>      smeartype='gauss'
>      intersmear=0.1d0
>      intrasmear=0d0
>      wmax=20d0
>      wmin=0d0
>      nw=600
>      shift=0d0
> /
> --------------------------------
>
>      (2) As for the intraband contribution, wien2k gives the plasma 
> frequency 9.0075eV which agrees well with experimental value (ref: 
> http://wave-scattering.com/drudefit.html), but the result from 
> epsilon.x is puzzling.
> Specifically, plasma frequency given in the output of epsilon.x is 
> dependent on the input parameters:
> <1>. intrasmear=0,   wmax=20d0  -->   The bulk xx plasmon frequency 
> [eV] is:    14.877926200
> <2>. intrasmear=0,   wmax=10d0  -->   The bulk xx plasmon frequency 
> [eV] is:    7.625822195
> <3>. intrasmear=0,   wmax=6d0   -->   The bulk xx plasmon frequency 
> [eV] is:    3.156554381
> <4>. intrasmear=0.1, wmax=20d0  -->   The bulk xx plasmon frequency 
> [eV] is:    15.766403193
> <5>. intrasmear=0.1, wmax=10d0  -->   The bulk xx plasmon frequency 
> [eV] is:    9.322251787
> <6>. intrasmear=0.1, wmax=20d0  -->   The bulk xx plasmon frequency 
> [eV] is:    6.263713572
> However, none of these values is the one got by fitting the results 
> using Drude model [ 1 - omega_p^2/(omega^2+i*omega*gamma), gamma is 
> the intrasmear here ]. By fitting the results using Drude model, I get 
> omega_p=5.528769eV, for all the cases above (<1>~<6>). But this 
> omega_p is far from the experimental value (~9 eV)! What's wrong? And 
> what are the meanings of the values given in <1>~<6> ?
>
>       How can I get more accurate results like the ones from wien2k?
>       Please help me if you know something about this, thanks in advance!
>
> Best regards!
>
>                    Liu Guibin
>                Postdoctoral Fellow,
>                Department of Physics,
>                The University of Hong Kong
>                gbliu at hku.hk
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From goodluck_1982 at 163.com  Sun Jul 10 17:05:02 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Sun, 10 Jul 2011 23:05:02 +0800
Subject: [Pw_forum] I need norm conserving pseudopotetial for Zinc that
 can work with pwscf
In-Reply-To: <1310306912.94059.YahooMailClassic@web39413.mail.mud.yahoo.com>
References: <1310306912.94059.YahooMailClassic@web39413.mail.mud.yahoo.com>
Message-ID: <4E19BF9E.6040201@163.com>

Hi Adetunji,

     I'm so sorry that I'm not good at generating pesudopotential file.
     I only used fhi2upf once and casually guess some values for 
"Wavefunction # ...:"

good luck.

Liu

? 2011/7/10 22:08, bamidele ibrahim ??:
> Dear Liu,
>   I have downloaded the .fhi file from abinit pseudopotential site, 
> and i used the command given by you as follows;
>
>    ./fhi2upf.x /home/adetunji/Desktop/30-Zn.LDA.fhi
>
> after the command, here is the result of the process.
> read_fhi: assuming abinit format
> Pseudopotential without NLCC successfully read
> Wavefunction # 1: label, occupancy >
>
> please, what is the next step.
>
>
> Adetunji Bamidele Ibrahim
> Department of physics,University of Agriculture,
> Abeokuta, Ogun State,Nigeria.
>
> --- On *Sat, 7/9/11, gbliu /<goodluck_1982 at 163.com>/* wrote:
>
>
>     From: gbliu <goodluck_1982 at 163.com>
>     Subject: Re: [Pw_forum] I need norm conserving pseudopotetial for
>     Zinc that can work with pwscf
>     To: "PWSCF Forum" <pw_forum at pwscf.org>
>     Date: Saturday, July 9, 2011, 6:32 AM
>
>
>     You can use pp file of ABINIT, then use upftools/fhi2upf.x to
>     covert the .fhi file to .upf file.
>
>     Best wishes,
>     Liu Gui-Bin
>     Dept. Physics, HKU
>
>     ? 2011/7/9 6:08, bamidele ibrahim ??:
>>
>>     Dear all,
>>       I needed to run epsilo.x to get optical properties, but the
>>     pseudopotentials available on the QE page for Zinc has no norm
>>     conserving pseudopotential. So, i will appreciate it if an
>>     assistance can come from anybody from the forum. Also, if there
>>     is a way to make epsilo.x recognised the USPP. Kindly put me through.
>>
>>     Thanks
>>
>>     Adetunji Bamidele Ibrahim
>>     Department of physics,University of Agriculture,
>>     Abeokuta, Ogun State,Nigeria.
>>
>>
>>     _______________________________________________
>>     Pw_forum mailing list
>>     Pw_forum at pwscf.org  </mc/compose?to=Pw_forum at pwscf.org>
>>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>     -----Inline Attachment Follows-----
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org </mc/compose?to=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 mayankaditya at gmail.com  Sun Jul 10 17:20:48 2011
From: mayankaditya at gmail.com (mayank gupta)
Date: Sun, 10 Jul 2011 20:50:48 +0530
Subject: [Pw_forum] XX and YY component in stress matrix are not same for
 body centred tetragonal structure
Message-ID: <CAHNEyD-CZ6CKZ-Pfg4T3pqGJ55VA+VLiJM9d8aWDwBksOyUWyQ@mail.gmail.com>

Dear All


I am doing total energy calculation of body centered tetragonal
structure. but I am not getting the same stress along a and b
direction ( XX and YY component in stress matrix). I have given the
atomic position in angstrom. relaxed the structure but still i didn't
get the symmetry in stress.
Thanks in advance
-- 
Mayank

BHABHA ATOMIC RESEARCH CENTER
MUMBAI, INDIA
Office:  022-25595606
Home: 9920397437 / 9869834437

From tsun at grad.physics.sunysb.edu  Sun Jul 10 18:36:38 2011
From: tsun at grad.physics.sunysb.edu (Tao Sun)
Date: Sun, 10 Jul 2011 11:36:38 -0500
Subject: [Pw_forum] What's wrong in my calculation of epsilon of fcc Au?
In-Reply-To: <4E19BC70.1060908@163.com>
References: <d5360c67d8b89e63994a959436f4846e@umich.edu>
	<4E157EEE.4050309@163.com> <4E19BC70.1060908@163.com>
Message-ID: <CAEQ9wfCKhB6ene3xZUkZRSjf-HCOeDYyuugT7C==grGDg+TuKA@mail.gmail.com>

Hi Guibin,

As far as I understand, the imaginary part of epsilon is closely
related to the joint density of the states of the valence and
conduction band electrons.  If LAPW and pseudo really give the same
band structure, they should give the same jdos, even the actual wave
functions are different.

It is a bit unthinkable to me that the previous pseudopotential can
give the correct band structure, while its jdos is so off the mark.
Something must be wrong.  Have you compared the DOS calculated  by
LAPW and pseudo, or a dispersion along a less symmetric direction?
Are they really the same?

These questions may not really help you much... I am just curious.

Best wishes.

Tao

From goodluck_1982 at 163.com  Sun Jul 10 20:16:19 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Mon, 11 Jul 2011 02:16:19 +0800
Subject: [Pw_forum] What's wrong in my calculation of epsilon of fcc Au?
In-Reply-To: <CAEQ9wfCKhB6ene3xZUkZRSjf-HCOeDYyuugT7C==grGDg+TuKA@mail.gmail.com>
References: <d5360c67d8b89e63994a959436f4846e@umich.edu>	<4E157EEE.4050309@163.com>
	<4E19BC70.1060908@163.com>
	<CAEQ9wfCKhB6ene3xZUkZRSjf-HCOeDYyuugT7C==grGDg+TuKA@mail.gmail.com>
Message-ID: <4E19EC73.9050204@163.com>

Hi Tao,

I'm clear now that the "plasmon frequency" given by eplilon.x is just 
caculated from the sum rule
int_0^inf w*Im[epsilon(w)] dw = pi/2 * omeag_p^2

I calculated and compared the DOS, they should be good. See attachments.
Now that the band structure is ok, the DOS should be ok, I think.

Best regards.

Liu Gui-Bin

? 2011/7/11 0:36, Tao Sun ??:
> Hi Guibin,
>
> As far as I understand, the imaginary part of epsilon is closely
> related to the joint density of the states of the valence and
> conduction band electrons.  If LAPW and pseudo really give the same
> band structure, they should give the same jdos, even the actual wave
> functions are different.
>
> It is a bit unthinkable to me that the previous pseudopotential can
> give the correct band structure, while its jdos is so off the mark.
> Something must be wrong.  Have you compared the DOS calculated  by
> LAPW and pseudo, or a dispersion along a less symmetric direction?
> Are they really the same?
>
> These questions may not really help you much... I am just curious.
>
> Best wishes.
>
> Tao
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From tsun at grad.physics.sunysb.edu  Sun Jul 10 21:02:50 2011
From: tsun at grad.physics.sunysb.edu (Tao Sun)
Date: Sun, 10 Jul 2011 14:02:50 -0500
Subject: [Pw_forum] What's wrong in my calculation of epsilon of fcc Au?
In-Reply-To: <4E19EC73.9050204@163.com>
References: <d5360c67d8b89e63994a959436f4846e@umich.edu>
	<4E157EEE.4050309@163.com> <4E19BC70.1060908@163.com>
	<CAEQ9wfCKhB6ene3xZUkZRSjf-HCOeDYyuugT7C==grGDg+TuKA@mail.gmail.com>
	<4E19EC73.9050204@163.com>
Message-ID: <CAEQ9wfAJJbLpnwxE+vtRZUn8EzuyypMuEQn3umrFj6zscWp=hg@mail.gmail.com>

Hi Gui-Bin,

Thanks!

I am puzzled.  Have you calculated the joint DOS of the three?  If
they are as similar as their DOS, then the only thing left is the wave
functions...  From the imaginary part of the epsilon, I had thought
that the pbe-fhi must have a very different joint DOS comparing to the
other two.

Best wishes.

Tao


On Sun, Jul 10, 2011 at 1:16 PM, gbliu <goodluck_1982 at 163.com> wrote:
> Hi Tao,
>
> I'm clear now that the "plasmon frequency" given by eplilon.x is just
> caculated from the sum rule
> int_0^inf w*Im[epsilon(w)] dw = pi/2 * omeag_p^2
>
> I calculated and compared the DOS, they should be good. See attachments.
> Now that the band structure is ok, the DOS should be ok, I think.
>
> Best regards.
>
> Liu Gui-Bin
>

From giuseppe.mattioli at mlib.ism.cnr.it  Sun Jul 10 21:09:05 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it)
Date: Sun, 10 Jul 2011 21:09:05 +0200
Subject: [Pw_forum] problem with symmetry recognition
Message-ID: <20110710210905.ipfpuwzro0cc0gsg@webmail.sic.rm.cnr.it>


Dear all
I was thinking again about keeping the space group symmetry fixed  
along a vc-relax calculation. Actually, I did not directly ask my main  
question...:-) Is there a way to put the above constraint which I am  
not aware of?
Yours

Giuseppe

ISM-CNR
Italy

Quoting Paolo Giannozzi <giannozz at democritos.it>:

>
> On Jul 10, 2011, at 12:10 , pascal boulet wrote:
>
>> Following Stefano's comment I need to provide ALL the atomic
>> positions,
>> which I did not do! I gave only the positions in the primitive unit
>> cell (UC).
>
> what you call "primitive", I would call "irreducible" (like the
> irreducible
> segment of the Brillouin Zone)
>
>> But then, if I provide all the positions (I guess in the full UC)
>
> what you call "full", I would call "primitive"
>
>> why should QE fill the others?
>
> which others?
>
>> In addition, I did some calculations on Mg2Si (FCC, 12 atoms in the
>> full UC)
>
> antifluorite structure? what you call "full" here, I would call
> "conventional"
>
>> by providing only the 3 atoms of the primitive UC. QE found 48
>> symmetry
>> elements, which is correct, and the optimized cell parameters
>> seemed OK.
>> So, still, is it wrong?
>
> no, because you provided all the needed atoms (3 in the unit cell of the
> FCC lattice in the [anti]fluorite structure)
>
>> BTW, I also noticed something that looks strange to me. The
>> coordinates
>> reported by QE in the output are not those I give in the input: X
>> and Y
>> are the same but not Z which is scaled by c/a.
>
> nothing strange: atomic positions in input are in crystal coodinates:
>
>> ATOMIC_POSITIONS crystal
>
> atomic positions in output are in xyz coordinates, divided by a:
>
>>    Cartesian axes
>>
>>      site n.     atom                  positions (alat units)
>
> 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 degironc at sissa.it  Sun Jul 10 21:24:51 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sun, 10 Jul 2011 21:24:51 +0200
Subject: [Pw_forum] problem with symmetry recognition
In-Reply-To: <20110709224633.7bgqpfpbcwokccw0@webmail.sic.rm.cnr.it>
References: <AKEFIBNCPJEJJMHNOPHICEGICHAA.victor.bermudez@nrl.navy.mil>	<4E18ABCE.3020501@sissa.it>
	<20110709224633.7bgqpfpbcwokccw0@webmail.sic.rm.cnr.it>
Message-ID: <4E19FC83.6090202@sissa.it>

cell_dofree ?
i never used it but it may do something similar to what you look for.
stefano


On 07/09/2011 10:46 PM, giuseppe.mattioli at mlib.ism.cnr.it wrote:
> Dear Stefano, dear all.
> Ok, but suppose that I would like to put a (quite useful) constraint
> like: "I say that the lattice is cubic because I know that it MUST be
> cubic (or tetragonal or monoclinic or so...), than KEEP IT CUBIC while
> performing a vc-relax, irrespective of the stress tensor! Change the
> volume, change the a/c ratio (if the lattice is, e.g., tetragonal) but
> retain the space group. I often have to perform a (boring) multi
> dimensional fit by changing the lattice parameters by hand on a grid
> near to the "expected" minimum...
> I do not know exactly if Pascal's question was similar to mine;
> nevertheless I hope this can help...
>
> Yours
>
> Giuseppe
>
>
> Quoting Stefano de Gironcoli<degironc at sissa.it>:
>
>> this is not correct.
>> if the code finds some symmetry, forces and stress components will be
>> symmetrized accordingly  and vc-relax will keep it.
>>
>> There may be two reasons why the code does not find a symmetry:
>>
>> - the symmetry is not there... check your coordinates. Beware that you
>> need to specify ALL the atomic positions of a given structure not just
>> the inequivalent ones, hoping the code to fill the others.
>>
>> - the symmetry is there but involves a fractionary translations that
>> cannot be written as a multiple of the FFT grid spacing.  the code
>> writes a message saying that the symmetry is discarded due to a problem
>> with fractionary translation and says what the translation would be in
>> crystal coordinates. one can manually set the FFT dimensions (nr1,nr2,
>> and/or nr3) so that the translation is in register with the FFT grid
>> and the code can accept it
>>
>> HTH
>>
>> stefano
>> -
>> Stefano de Gironcoli - SISSA and DEMOCRITOS
>>
>>
>>
>> On 07/09/2011 07:58 PM, Vic Bermudez wrote:
>>> Hi Pascal,
>>>
>>> 	If I understand correctly, you're trying to optimize the unit cell while
>>> constraining 2 of the lattice constants to remain equal, as required by
>>> symmetry. I don't think that QE allows this. If you do a "vc-relax", what
>>> seems to happen is that symmetry is ignored, and all lattice constants are
>>> varied independently. I've attached a script written by a colleague that
>>> does repeated single-point runs for a range of lattice constants. You can
>>> then fit points near the total-energy minimum to find the exact minimum. Of
>>> course, this has to be done iteratively if more than one lattice constant is
>>> being optimized.
>>> 	Hope this helps.
>>>
>>> 	Best Wishes,
>>> 	Vic Bermudez
>>>
>>> Victor M. Bermudez
>>> Code 6876
>>> U.S. Naval Research Laboratory
>>> 4555 Overlook Ave., S.W.
>>> Washington, DC 20375-5347
>>>
>>>
>>>
>>> _______________________________________________
>>> 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


From degironc at sissa.it  Sun Jul 10 23:20:08 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sun, 10 Jul 2011 23:20:08 +0200
Subject: [Pw_forum] problem with symmetry recognition
In-Reply-To: <20110710210905.ipfpuwzro0cc0gsg@webmail.sic.rm.cnr.it>
References: <20110710210905.ipfpuwzro0cc0gsg@webmail.sic.rm.cnr.it>
Message-ID: <4E1A1788.3050302@sissa.it>

If the symmetry is recognized vc-relax should keep it
if it is not there vc-relax cannot produce it unless the minimum the 
system converges to has that symmetry.
there  are codes (I recently discovered GULP) that can accept input 
structure defined by the positions of the irreducible atoms + space 
group definition...
pw.x does not have this capabiloity but if you generate the full list of 
coordinates with one of such codes then pw.x should be able to recognize 
the symmetry and keep it during relaxation.

stefano
-
Stefano de Gironcoli - SISSA and DEMOCRITOS





On 07/10/2011 09:09 PM, giuseppe.mattioli at mlib.ism.cnr.it wrote:
> Dear all
> I was thinking again about keeping the space group symmetry fixed
> along a vc-relax calculation. Actually, I did not directly ask my main
> question...:-) Is there a way to put the above constraint which I am
> not aware of?
> Yours
>
> Giuseppe
>
> ISM-CNR
> Italy
>


From trambui at u.boisestate.edu  Mon Jul 11 01:25:15 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Sun, 10 Jul 2011 17:25:15 -0600
Subject: [Pw_forum] "relax" vs. "vc-relax" calculation
In-Reply-To: <CAM-1hSs5XPP92HyoH_9TArTtTk-V1-QqZ+mta71Q-Ew+kMzcug@mail.gmail.com>
References: <CAM-1hSs5XPP92HyoH_9TArTtTk-V1-QqZ+mta71Q-Ew+kMzcug@mail.gmail.com>
Message-ID: <CANzxBn-YWR_uiVw0G5zPL8W6+FmjU3jdG_q2=fU0UME8szZCPQ@mail.gmail.com>

Dear Masoud,

 Thank you for your information. The tutorial is also very helpful. I have
some small questions related to the tutorial, I hope you don't mind. on the
slide # 11, the author has used the "?" sign, and what does it represent?.
also on the slide # 32, there is a warning sign saying "the total number of
electron is odd", so the degauss value was marked very low, as 0.0037. So
does it mean that the degauss should be low for odd number of electron and
higher for even cases?

I really appreciate your helps!
Tram


On Thu, Jul 7, 2011 at 2:32 AM, Masoud Nahali <masoudnahali at gmail.com>wrote:

>
>      Dear Tram
>
>          I think that vc-relax calculation is more convenient for your
> case; in addition you should glance over the below tutorial about defects :
>
> http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_defects.pdf
>
>          I hope it is useful.
>
>
> Best Wishes
>
>  Masoud
>
>
>
> --------------
> Masoud Nahali, Sharif University of Technology
> masoud.nahali at gmail.com; alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali>
>
> P Please don't print this e-mail unless you really need to.
>
>
> *Tram wrote on Thu Jul 7 06:47:35 CEST 2011*
>>
> Dear Everyone,
>      I have a quick question regarding the "relax" vs. "vc-relax"
> calculation for my SiC structure. As I run the " scf" calculation with a
> single defect, e.g. interstitial or sustitutional, the lattice parameter of
> the unit cell is expected to be stretched. And as I checked, the lattice
> constant got larger when introduced defect. Now, I'm just wondering between
> the "relax" calculation (which will only relax the atomic position ) and the
> "vc-relax" one (which will relax both atomic position and the lattice of the
> unit cell), which one would you recommend to use?
>
> Thank you very much,
>
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu <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
>
>


-- 
Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From mahdi_fn109 at yahoo.com  Mon Jul 11 03:27:51 2011
From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri)
Date: Sun, 10 Jul 2011 18:27:51 -0700 (PDT)
Subject: [Pw_forum] draw a ELF diagram using XCrysDen
Message-ID: <1310347671.78483.YahooMailNeo@web43141.mail.sp1.yahoo.com>

Dear all,

I want to draw a
ELF diagram using XCrysDen, but i don't find any good example for this purpose

. Anyonecanguidemeinthis matter?   


Mahdi Faghih nasiri
MSC,
Guilan University,
Rasht, Iran.
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From psavita at crlindia.com  Mon Jul 11 06:53:09 2011
From: psavita at crlindia.com (psavita at crlindia.com)
Date: Mon, 11 Jul 2011 10:23:09 +0530
Subject: [Pw_forum] draw a ELF diagram using XCrysDen (Mahdi Faqieh
	nasiri)
In-Reply-To: <mailman.13907.1310347674.1814.pw_forum@pwscf.org>
References: <mailman.13907.1310347674.1814.pw_forum@pwscf.org>
Message-ID: <OFE75AC3C8.C1BB0885-ON652578CA.001AD6BE-652578CA.001AD6CB@crlindia.com>

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From masoudnahali at gmail.com  Mon Jul 11 08:47:52 2011
From: masoudnahali at gmail.com (Masoud Nahali)
Date: Mon, 11 Jul 2011 11:17:52 +0430
Subject: [Pw_forum] "relax" vs. "vc-relax" calculation
Message-ID: <CAM-1hSsVgU+FXfTMn_=GyB7JY-5pNd6s28j0q3BTDpa_x0RE8A@mail.gmail.com>

Dear Tram

To specify how metallicity is treated you should use "smearing" and have to
determine degauss value (smearing width). These options not only use for
metallic systems but also for spin-polarized systems. If the mean of
Alessandra is performing a spin polarized calculation he should set nspin=2
and set a starting_magnetization otherwise his case is a metallic one !! . I
think you should plot E VS. degauss to find the convergence value of
degauss. About "Omega" (slide 11) I don't exactly know his mean. I hope it
is helpful.

Best Wishes

 Masoud



--------------
Masoud Nahali, Sharif University of Technology
masoud.nahali at gmail.com;
alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali>

P Save a Tree . . . Please don't print this e-mail unless you really need
to.

On Mon, Jul 11, 2011 at 5:57 AM, Tram wrote:

>
>
>  Dear Masoud,
>
>  Thank you for your information. The tutorial is also very helpful. I have
> some small questions related to the tutorial, I hope you don't mind. on the
> slide # 11, the author has used the "?" sign, and what does it represent?.
> also on the slide # 32, there is a warning sign saying "the total number of
> electron is odd", so the degauss value was marked very low, as 0.0037. So
> does it mean that the degauss should be low for odd number of electron and
> higher for even cases?
>
> I really appreciate your helps!
> Tram
>
>
> On Thu, Jul 7, 2011 at 2:32 AM, Masoud Nahali <masoudnahali at gmail.com
> >wrote:
>
> >
> >      Dear Tram
> >
> >          I think that vc-relax calculation is more convenient for your
> > case; in addition you should glance over the below tutorial about defects
> :
> >
> > http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_defects.pdf
> >
> >          I hope it is useful.
> >
> >
> > Best Wishes
> >
> >  Masoud
> >
> >
> >
> > --------------
> > Masoud Nahali, Sharif University of Technology
> > masoud.nahali at gmail.com; alum.sharif.edu/~m_nahali<
> http://alum.sharif.edu/%7Em_nahali>
> >
> > P Please don't print this e-mail unless you really need to.
> >
> >
> > *Tram wrote on Thu Jul 7 06:47:35 CEST 2011*
> >>
> > Dear Everyone,
> >      I have a quick question regarding the "relax" vs. "vc-relax"
> > calculation for my SiC structure. As I run the " scf" calculation with a
> > single defect, e.g. interstitial or sustitutional, the lattice parameter
> of
> > the unit cell is expected to be stretched. And as I checked, the lattice
> > constant got larger when introduced defect. Now, I'm just wondering
> between
> > the "relax" calculation (which will only relax the atomic position ) and
> the
> > "vc-relax" one (which will relax both atomic position and the lattice of
> the
> > unit cell), which one would you recommend to use?
> >
> > Thank you very much,
> >
> > Tram Bui
> >
> > M.S. Materials Science & Engineering
> > trambui at u.boisestate.edu <
> http://www.democritos.it/mailman/listinfo/pw_forum>
> >
>
>
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From mayankaditya at gmail.com  Mon Jul 11 10:11:34 2011
From: mayankaditya at gmail.com (mayank gupta)
Date: Mon, 11 Jul 2011 13:41:34 +0530
Subject: [Pw_forum] Vc-relax error with option cell_dofree
Message-ID: <CAHNEyD_sJafwnaVQFa1i1041-FfWUEqJBXdQf+tqZA756UWQnA@mail.gmail.com>

Dear all


I have relaxed body centered tetragonal system using ?vc-relax? method
with option cell_dofree='xz' as well as 'xyz', but i got error message
"check all symmetry error? after calculating the forces and position
in first cycle.
-- 
Mayank

BHABHA ATOMIC RESEARCH CENTER
MUMBAI, INDIA
Office: ?022-25595606
Home: 9920397437 / 9869834437

From giuseppe.mattioli at mlib.ism.cnr.it  Mon Jul 11 11:06:06 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Mon, 11 Jul 2011 11:06:06 +0200
Subject: [Pw_forum] problem with symmetry recognition
In-Reply-To: <4E1A1788.3050302@sissa.it>
References: <20110710210905.ipfpuwzro0cc0gsg@webmail.sic.rm.cnr.it>
	<4E1A1788.3050302@sissa.it>
Message-ID: <201107111106.06667.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Stefano, dear all.
cell_dofree is useful when, for instance, you want to keep at least 
orthorombic a starting cubic cell, because you can force alpha, beta and 
gamma to be pi/2 (cell_dofree='xyz'). But there is no way (at least, no way 
that I'm aware of) to change all a, b and c and, at the same time, keep 
a=b=c. Suppose that you want to optimise a CoO rocksalt antiferromagnetic 
supercell: you need to differentiate the starting spin up and spin down Co 
atoms (Co1 and Co2). This lowers the symmetry, and the supercell becomes 
tetragonal along the simulation. I could provide further examples, and I 
think that a cell_dofree flag which allows one to retain the initial ibrav 
would be quite useful. I do not like to ask for things that I cannot 
implement by myself, but I may suggest that it could be a useful 
improvement...

Yours

Giuseppe

On Sunday 10 July 2011 23:20:08 Stefano de Gironcoli wrote:
> If the symmetry is recognized vc-relax should keep it
> if it is not there vc-relax cannot produce it unless the minimum the
> system converges to has that symmetry.
> there  are codes (I recently discovered GULP) that can accept input
> structure defined by the positions of the irreducible atoms + space
> group definition...
> pw.x does not have this capabiloity but if you generate the full list of
> coordinates with one of such codes then pw.x should be able to recognize
> the symmetry and keep it during relaxation.
>
> stefano
> -
> Stefano de Gironcoli - SISSA and DEMOCRITOS
>
> On 07/10/2011 09:09 PM, giuseppe.mattioli at mlib.ism.cnr.it wrote:
> > Dear all
> > I was thinking again about keeping the space group symmetry fixed
> > along a vc-relax calculation. Actually, I did not directly ask my main
> > question...:-) Is there a way to put the above constraint which I am
> > not aware of?
> > Yours
> >
> > Giuseppe
> >
> > ISM-CNR
> > Italy
>
> _______________________________________________
> 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 goodluck_1982 at 163.com  Mon Jul 11 11:36:50 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Mon, 11 Jul 2011 17:36:50 +0800
Subject: [Pw_forum] What's wrong in my calculation of epsilon of fcc Au?
In-Reply-To: <CAEQ9wfAJJbLpnwxE+vtRZUn8EzuyypMuEQn3umrFj6zscWp=hg@mail.gmail.com>
References: <d5360c67d8b89e63994a959436f4846e@umich.edu>	<4E157EEE.4050309@163.com>
	<4E19BC70.1060908@163.com>	<CAEQ9wfCKhB6ene3xZUkZRSjf-HCOeDYyuugT7C==grGDg+TuKA@mail.gmail.com>	<4E19EC73.9050204@163.com>
	<CAEQ9wfAJJbLpnwxE+vtRZUn8EzuyypMuEQn3umrFj6zscWp=hg@mail.gmail.com>
Message-ID: <4E1AC432.70305@163.com>

Hi Tao,

Attachments are the jdos for the three cases.
But I'm not aware of how to analyze them.
And it's strange that the two cases of pwscf are similar, but differ in 
magnitude far from the wien2k result. However, their shape are similar.
What information can you get from the jdos's?

Best regards,
Liu Gui-Bin


? 2011/7/11 3:02, Tao Sun ??:
> Hi Gui-Bin,
>
> Thanks!
>
> I am puzzled.  Have you calculated the joint DOS of the three?  If
> they are as similar as their DOS, then the only thing left is the wave
> functions...  From the imaginary part of the epsilon, I had thought
> that the pbe-fhi must have a very different joint DOS comparing to the
> other two.
>
> Best wishes.
>
> Tao
>
>
> On Sun, Jul 10, 2011 at 1:16 PM, gbliu<goodluck_1982 at 163.com>  wrote:
>> Hi Tao,
>>
>> I'm clear now that the "plasmon frequency" given by eplilon.x is just
>> caculated from the sum rule
>> int_0^inf w*Im[epsilon(w)] dw = pi/2 * omeag_p^2
>>
>> I calculated and compared the DOS, they should be good. See attachments.
>> Now that the band structure is ok, the DOS should be ok, I think.
>>
>> Best regards.
>>
>> Liu Gui-Bin
>>
> _______________________________________________
> 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  Mon Jul 11 12:25:57 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 11 Jul 2011 12:25:57 +0200
Subject: [Pw_forum] problem with symmetry recognition
In-Reply-To: <201107111106.06667.giuseppe.mattioli@mlib.ism.cnr.it>
References: <20110710210905.ipfpuwzro0cc0gsg@webmail.sic.rm.cnr.it>
	<4E1A1788.3050302@sissa.it>
	<201107111106.06667.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <F086C168-28ED-4B17-9221-7A69EF6DA759@democritos.it>


On Jul 11, 2011, at 11:06 , Giuseppe Mattioli wrote:

> I think that a cell_dofree flag which allows one to retain the initial
> ibrav would be quite useful

retaining the starting lattice should be straightforward, because all
the symmetries of the starting bravais lattice are calculated and
available. Retaining a higher symmetry is more involved.

> I do not like to ask for things that I cannot implement by myself

...are you sure you cannot?

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  Mon Jul 11 15:40:53 2011
From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri)
Date: Mon, 11 Jul 2011 06:40:53 -0700 (PDT)
Subject: [Pw_forum] draw a ELF diagram using XCrysDen
Message-ID: <1310391653.96606.YahooMailNeo@web43144.mail.sp1.yahoo.com>

Dear?Savita Pundlik,
thanks your attention
i use this input file for ELF ?calculation in pp.x
but, output files not suitable for Xcrysden.?
xrysden dosen't able to open output files.
it just open files with *.xsf format.
Xcrysden 'Tools - Data grid'? option is?inactive.

?&INPUTPP
?? ?outdir = '/home/mahdi../../..1'
?? ?filplot = 'ELF'
?? ?plot_num= 8
?/
?&PLOT
?? ?nfile = 1
?? ?filepp(1) = 'ELF'
?? ?weight(1) = 1.0
?? ?iflag = 2?
?? ?output_format = 3
?? ?fileout = 'ELF.dat'
?? ?e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0,
?? ?e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
?? ?x0(1) =0.0, x0(2)=0.0, x0(0)=0.0?
?? ?nx=56, ny=40 ?
?/

?
Mahdi Faghih nasiri
MSC,
Guilan University,
Rasht, Iran.
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From mehrnooshhazrati at gmail.com  Mon Jul 11 16:15:40 2011
From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati)
Date: Mon, 11 Jul 2011 18:45:40 +0430
Subject: [Pw_forum] Charge Density
In-Reply-To: <be6f4a9.d57e.130fa93655b.Coremail.flux_ray12@163.com>
References: <CAHbvuiQ-qiCrMVsbz4kdiNeUxUBi=8y1PZv9AN3udk3P_+jp5w@mail.gmail.com>
	<be6f4a9.d57e.130fa93655b.Coremail.flux_ray12@163.com>
Message-ID: <CAHbvuiR09O+hzZYc4XyTOYd2a=nCOB3+Zi4GRo-=iSj83O28Pw@mail.gmail.com>

thank you :)

2011/7/5 GAO Zhe <flux_ray12 at 163.com>

> As shown in /Doc/Input_PP.*, ei(j) is the vector (lattice line), and x0(j)
> the origin of line (intersection of two lattice line).
> --
> GAO Zhe
> CMC Lab, MSE, SNU, Seoul, S.Korea
>
> At 2011-07-04 18:47:51?"Mehrnoosh Hazrati" <mehrnooshhazrati at gmail.com>
> wrote:
>
>
> Hi everyone,
>
> I need to calculate the charge density of a graphene sheet, but i don't
> know how can i choose e1, e2 and x0 for my system.
>
> Thank you in advance
> --
> *
>
> *
> *
> """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> *
> **** Mehrnoosh Kh. Hazrati ****
> **** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
>  *** Phone : +989123436300 ***
> *** Mail : mehrnooshhazrati at gmail.com ***
> *
> """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> *
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
*

*
*
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
**** Mehrnoosh Kh. Hazrati ****
**** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
 *** Phone : +989123436300 ***
*** Mail : mehrnooshhazrati at gmail.com ***
*
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
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From tsun at grad.physics.sunysb.edu  Mon Jul 11 16:54:43 2011
From: tsun at grad.physics.sunysb.edu (Tao Sun)
Date: Mon, 11 Jul 2011 09:54:43 -0500
Subject: [Pw_forum] What's wrong in my calculation of epsilon of fcc Au?
In-Reply-To: <4E1AC432.70305@163.com>
References: <d5360c67d8b89e63994a959436f4846e@umich.edu>
	<4E157EEE.4050309@163.com> <4E19BC70.1060908@163.com>
	<CAEQ9wfCKhB6ene3xZUkZRSjf-HCOeDYyuugT7C==grGDg+TuKA@mail.gmail.com>
	<4E19EC73.9050204@163.com>
	<CAEQ9wfAJJbLpnwxE+vtRZUn8EzuyypMuEQn3umrFj6zscWp=hg@mail.gmail.com>
	<4E1AC432.70305@163.com>
Message-ID: <CAEQ9wfDkhK7sg9n0nbUrv-MMugrPg7jXechLFu6anv35qch8-g@mail.gmail.com>

Hi Gui-Bin,

Here is reference calculation of the dielectric functions of Au
online, http://www.mri.psu.edu/conferences/WIEN/ProgramFiles/2009-06-WIEN2k-Optics-Sofo.pdf.

The reported jdos differ completely from all of your jdos, while the
final dielectric functions seem to be similar to yours. Maybe it is
due to a different definition?

Best wishes.

Tao

Postdoc,  CEMS. UMN.

On Mon, Jul 11, 2011 at 4:36 AM, gbliu <goodluck_1982 at 163.com> wrote:
> Hi Tao,
>
> Attachments are the jdos for the three cases.
> But I'm not aware of how to analyze them.
> And it's strange that the two cases of pwscf are similar, but differ in
> magnitude far from the wien2k result. However, their shape are similar.
> What information can you get from the jdos's?
>
> Best regards,
> Liu Gui-Bin
>

From tsun at grad.physics.sunysb.edu  Mon Jul 11 17:28:21 2011
From: tsun at grad.physics.sunysb.edu (Tao Sun)
Date: Mon, 11 Jul 2011 10:28:21 -0500
Subject: [Pw_forum] What's wrong in my calculation of epsilon of fcc Au?
In-Reply-To: <CAEQ9wfDkhK7sg9n0nbUrv-MMugrPg7jXechLFu6anv35qch8-g@mail.gmail.com>
References: <d5360c67d8b89e63994a959436f4846e@umich.edu>
	<4E157EEE.4050309@163.com> <4E19BC70.1060908@163.com>
	<CAEQ9wfCKhB6ene3xZUkZRSjf-HCOeDYyuugT7C==grGDg+TuKA@mail.gmail.com>
	<4E19EC73.9050204@163.com>
	<CAEQ9wfAJJbLpnwxE+vtRZUn8EzuyypMuEQn3umrFj6zscWp=hg@mail.gmail.com>
	<4E1AC432.70305@163.com>
	<CAEQ9wfDkhK7sg9n0nbUrv-MMugrPg7jXechLFu6anv35qch8-g@mail.gmail.com>
Message-ID: <CAEQ9wfCanhpz_hvLhBt_NVvzeL5n0AsaSq3kBfz4rnYYOT3wGA@mail.gmail.com>

Hi Gui-Bin,

Sorry...

The reported graph is

JDOS(w)/w^2

which, when the matrix element is a constant, is proportional to Im(\epsilon).

Best wishes.

Tao

From scandolo at ictp.it  Mon Jul 11 17:40:13 2011
From: scandolo at ictp.it (Sandro Scandolo)
Date: Mon, 11 Jul 2011 17:40:13 +0200
Subject: [Pw_forum] =?windows-1252?q?S=E3o_Paulo_ICTP/TWAS_Advanced_School?=
 =?windows-1252?q?_on_Computational_Materials_Science?=
Message-ID: <4E1B195D.9060603@ictp.it>

DEADLINE APPROACHING (15 JULY)!!


S?o Paulo ICTP/TWAS Advanced School on Computational Materials Science
for Energy and Environmental Applications

5 ? 16 September 2011
(Santo Andre' - Brazil)

The Abdus Salam International Centre for Theoretical Physics is
organizing in collaboration with the  Funda??o de Amparo ? Pesquisa do
Estado de S?o Paulo, Brazil (FAPESP), the Universidade Federal do ABC
(UFABC), the CNR-IOM Democritos Simulation Center, Trieste, and the
Academy of Sciences for the Developing World (TWAS) an Advanced School
on Computational Materials Science for Energy and Environmental
Applications to be held in Santo Andr?, Brazil from 5 to 16 September
2011.

The necessity to satisfy environmentally friendly the demand of energy
in the World has lead to increasing interest in the use of renewable
and clean sources of energy. At the same time, new sources and
methodologies are needed to efficiently explore alternative fossil
fuels and biofuels. These energy and environmental issues are
particularly important for Latin America and Africa continents due to
the technological gap, specially the use of hydrogen and solar energy.
In addition, advanced technologies are needed to better explore oil
and biofuel resources, in which Latin America and Africa, are large
producers, in particular Brazil. The School will provide an overview
on the advanced computational methods to address the problem of
materials for energy and environmental applications. Topics will
include: Functionals development and modeling dispersion forces,
Electrical and thermal transport, Large scale DFT and TDDFT,
Interatomic potentials development, Integrated and Multi-scale
modeling, Theoretical spectroscopy, Ab-initio thermodynamics,
Catalysis and Materials for energy and environmental applications.

The School will include a series of advanced talks covering the latest
developments as well as a series of hands-on tutorials based on public
license computer codes, high-performance computing and classical
molecular dynamics and Monte Carlo codes.

Applicants from all countries that are members of the United Nations,
UNESCO or IAEA may attend. As the Workshop will be conducted in
English, participants should have an adequate working knowledge of
this language. Limited funds are available for participants who are
not more than 45 years old. Such support is available only to those
attending the entire activity. There is no registration fee.

HOW TO APPLY FOR PARTICIPATION
The Online Application can be accessed at the activity website:
http://agenda.ictp.it/smr.php?2277.
Comprehensive instructions will guide you step-by-step on how to fill
out and submit the application form. Kindly send all file attachments
in Word or Acrobat format.

Secretariat: Ms. Rosa del Rio (smr 2277)
the Abdus Salam International Centre for Theoretical Physics
Strada Costiera 11 - 34151 Trieste, Italy
Telephone: +39-040-2240396 - Telefax: +39-040-22407396
E-mail:smr2277 at ictp.it
http://agenda.ictp.it/smr.php?2277

Application DEADLINES:
19 June 2011 (if requiring Visa)
or 15 July 2011 (if not requiring Visa)

Directors
Edison Zacarias da Silva
Layla Martin-Samos
Caetano Rodriques Miranda
Sandro Scandolo

Lecturers include
Alex Antonelli (Unicamp - Brazil)
Francesca Baletto(Kings College - UK)
?ngela Burlamaqui Klautau (UFPA - Brazil)
Giovani Bussi(SISSA - Italy)
Marilia Caldas (USP ? Brazil)
Rodrigo Capaz (UFRJ - Brazil)
Klaus Capelle (UFABC - Brazil)
Roberto Car (Princeton -USA
Juarez L. F. da Silva (USP-SC - Brazil)
Maurice de Koning (Unicamp - Brazil
Stefano de Gironcoli (Democritos - Italy)
Rex W. Godby (York ? UK)
Stefano Fabris (Democritos - Italy)
Adalberto Fazzio (USP - Brazil)
Ralph Gebauer (ICTP - Italy)
Alexandre Leit?o (UFJF - Brazil)
Andrea Marini (Roma ?Tor Vergata" - Italy)
Layla Martin Samos (Democritos - Italy)
Nicola Marzari (Oxford - UK)
Caetano R. Miranda(UFABC - Brazil)
Pablo Ordejon (CSIC-ICN-Spain)
Helena Petrilli (USP ? Brazil)
Alexandre Reyle (UFABC - Brazil)
Matthias Scheffler (FHI - Germany
Dami?n Scherlis Perel (UBA - Argentina)
Paolo Umari(Democritos - Italy)
Pedro Venezuela(UFF-Brazil)
Renata Wentzcovitch (Minnesota) - USA



-- 
Sandro Scandolo -- http:/www.ictp.it/~scandolo


From goodluck_1982 at 163.com  Mon Jul 11 17:43:41 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Mon, 11 Jul 2011 23:43:41 +0800
Subject: [Pw_forum] What's wrong in my calculation of epsilon of fcc Au?
In-Reply-To: <CAEQ9wfDkhK7sg9n0nbUrv-MMugrPg7jXechLFu6anv35qch8-g@mail.gmail.com>
References: <d5360c67d8b89e63994a959436f4846e@umich.edu>	<4E157EEE.4050309@163.com>
	<4E19BC70.1060908@163.com>	<CAEQ9wfCKhB6ene3xZUkZRSjf-HCOeDYyuugT7C==grGDg+TuKA@mail.gmail.com>	<4E19EC73.9050204@163.com>	<CAEQ9wfAJJbLpnwxE+vtRZUn8EzuyypMuEQn3umrFj6zscWp=hg@mail.gmail.com>	<4E1AC432.70305@163.com>
	<CAEQ9wfDkhK7sg9n0nbUrv-MMugrPg7jXechLFu6anv35qch8-g@mail.gmail.com>
Message-ID: <4E1B1A2D.3090101@163.com>

Hi Tao,

I've been read this slide. The jdos data give by wien2k have 3 columns: 
the first is energy, the second is labelled as "JDOS", and the third is 
labelled as "JDOS/E^2".
What I plot is the second column, and the figure in the slide uses the 
third column. There are consistent.

Best wishes

Liu Gui-Bin

? 2011/7/11 22:54, Tao Sun ??:
> Hi Gui-Bin,
>
> Here is reference calculation of the dielectric functions of Au
> online, http://www.mri.psu.edu/conferences/WIEN/ProgramFiles/2009-06-WIEN2k-Optics-Sofo.pdf.
>
> The reported jdos differ completely from all of your jdos, while the
> final dielectric functions seem to be similar to yours. Maybe it is
> due to a different definition?
>
> Best wishes.
>
> Tao
>
> Postdoc,  CEMS. UMN.
>
> On Mon, Jul 11, 2011 at 4:36 AM, gbliu<goodluck_1982 at 163.com>  wrote:
>> Hi Tao,
>>
>> Attachments are the jdos for the three cases.
>> But I'm not aware of how to analyze them.
>> And it's strange that the two cases of pwscf are similar, but differ in
>> magnitude far from the wien2k result. However, their shape are similar.
>> What information can you get from the jdos's?
>>
>> Best regards,
>> Liu Gui-Bin
>>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum




From goodluck_1982 at 163.com  Tue Jul 12 04:52:57 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Tue, 12 Jul 2011 10:52:57 +0800
Subject: [Pw_forum] What's wrong in my calculation of epsilon of fcc Au?
In-Reply-To: <CAEQ9wfANhbd59z=YqAriK4e9WqX7gUjLtY3zzZmyLCR_X1zMWw@mail.gmail.com>
References: <d5360c67d8b89e63994a959436f4846e@umich.edu>	<4E157EEE.4050309@163.com>	<4E19BC70.1060908@163.com>	<CAEQ9wfCKhB6ene3xZUkZRSjf-HCOeDYyuugT7C==grGDg+TuKA@mail.gmail.com>	<4E19EC73.9050204@163.com>	<CAEQ9wfAJJbLpnwxE+vtRZUn8EzuyypMuEQn3umrFj6zscWp=hg@mail.gmail.com>	<4E1AC432.70305@163.com>	<CAEQ9wfDkhK7sg9n0nbUrv-MMugrPg7jXechLFu6anv35qch8-g@mail.gmail.com>	<4E1B1A2D.3090101@163.com>
	<CAEQ9wfANhbd59z=YqAriK4e9WqX7gUjLtY3zzZmyLCR_X1zMWw@mail.gmail.com>
Message-ID: <4E1BB709.5090305@163.com>


OK. However, no progress now.

Best
Liu

? 2011/7/12 1:02, Tao Sun ??:
> Thank you for the clarification Gui-Bin.
>
> Have you made any new progress on understanding the puzzle?  Correct
> band structure, completely wrong wave functions?  Hard to believe...
> If you understand more why this happens, please let me know.
>
> Best wishes.
>
> Tao
>
> On Mon, Jul 11, 2011 at 10:43 AM, gbliu<goodluck_1982 at 163.com>  wrote:
>> Hi Tao,
>>
>> I've been read this slide. The jdos data give by wien2k have 3 columns:
>> the first is energy, the second is labelled as "JDOS", and the third is
>> labelled as "JDOS/E^2".
>> What I plot is the second column, and the figure in the slide uses the
>> third column. There are consistent.
>>
>> Best wishes
>>
>> Liu Gui-Bin




From psavita at crlindia.com  Tue Jul 12 08:24:36 2011
From: psavita at crlindia.com (psavita at crlindia.com)
Date: Tue, 12 Jul 2011 11:54:36 +0530
Subject: [Pw_forum] draw a ELF diagram using XCrysDen (Mahdi Faqieh
	nasiri)
In-Reply-To: <mailman.13935.1310398818.1814.pw_forum@pwscf.org>
References: <mailman.13935.1310398818.1814.pw_forum@pwscf.org>
Message-ID: <OFF5CFA2C3.2DC4595E-ON652578CB.0023364D-652578CB.0023365B@crlindia.com>

An HTML attachment was scrubbed...
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From baroni at sissa.it  Tue Jul 12 08:42:54 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Tue, 12 Jul 2011 08:42:54 +0200
Subject: [Pw_forum] draw a ELF diagram using XCrysDen (Mahdi Faqieh
	nasiri)
In-Reply-To: <OFF5CFA2C3.2DC4595E-ON652578CB.0023364D-652578CB.0023365B@crlindia.com>
References: <mailman.13935.1310398818.1814.pw_forum@pwscf.org>
	<OFF5CFA2C3.2DC4595E-ON652578CB.0023364D-652578CB.0023365B@crlindia.com>
Message-ID: <B8F8A2F9-6D3B-47CF-B7C8-C9A7FA82A2FF@sissa.it>

If anything else fails, you may want to refer to the xcrysden mailing list. SB

On Jul 12, 2011, at 8:24 AM, psavita at crlindia.com wrote:

> Hello Mahdi,
> 
> I think your input file for pp is fine, only you need to specify fileout='...,xsf' or copy this file to one with .xsf.
> To run Xcrysden you might as well use a command 'xcrysden --xsf .....xsf'. Once you get the structure,
> click the 'Tools' option on screen and then select 'Data Grid'. On success, you will get a menu to select
> isosurface/plane parameters.
> 
> Hope things work now for you.
> 
> Good luck and regards,
>  
> Savita Pundlik
> Computational Materials Applied Research Group
> Computational Research Laboratories Ltd.,
> Taco House, Damle Path, Off Law College Road
> Pune - 411004, India.
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
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

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From goodluck_1982 at 163.com  Tue Jul 12 19:04:28 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Wed, 13 Jul 2011 01:04:28 +0800
Subject: [Pw_forum] Why dielectric function of only interband contribution
 has the features of intraband?
In-Reply-To: <B8F8A2F9-6D3B-47CF-B7C8-C9A7FA82A2FF@sissa.it>
References: <mailman.13935.1310398818.1814.pw_forum@pwscf.org>	<OFF5CFA2C3.2DC4595E-ON652578CB.0023364D-652578CB.0023365B@crlindia.com>
	<B8F8A2F9-6D3B-47CF-B7C8-C9A7FA82A2FF@sissa.it>
Message-ID: <4E1C7E9C.5000402@163.com>

Dear PW users,

     I calculated the dielectric function of (3,3) Carbon nanotube 
(CNT). However, the results for only interband contribution has the 
features of intraband contribution! Attached figures show the results of 
parallel polarization compared with wien2k (a FP-LAPW software). Using 
"intrasmear = 0", the direct result of epsi.dat should gives out only 
interband contributions, while epsr.dat is added by  "omega_p^2/omega^2" 
to get the interband contributions only.  And omega_p is obtained as 
*3.5679eV* by fitting the difference of data with intrasmear=0 and 
intrasmear=0.1 using Drude model  "\epsilon_{intra}=1- 
omega_p^2/(omega^2+i*omega*intrasmear)". How to understand this?

     Another problem is, fitted omega_p = 3.5679eV. This is far from the 
result given by wien2k, 24.5eV!  Which one is more reasonable? And why?

    Can anyone help me?  Thanks in advance!

Best wishes,

Liu Gui-Bin
Dept. of Physics, The University of Hong Kong

---------------input file for epsilon.x----------
&inputpp
    outdir='./work'
    prefix='cnt33'
    calculation='eps'
/
&energy_grid
    smeartype='gauss'
    intersmear=0.1d0
    intrasmear=0d0
    wmax=30d0
    wmin=0d0
    nw=2000
    shift=0d0
/
----------------------------------------------------------
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From izaakw89 at yahoo.com  Tue Jul 12 20:01:01 2011
From: izaakw89 at yahoo.com (Izaak Williamson)
Date: Tue, 12 Jul 2011 11:01:01 -0700 (PDT)
Subject: [Pw_forum] Opening .xml files on linux
In-Reply-To: <CANxi7+O8VJ6He1JsH0jV06tWaLEangyW2g4g8JXzTk2JRWXg0g@mail.gmail.com>
References: <CANxi7+O8VJ6He1JsH0jV06tWaLEangyW2g4g8JXzTk2JRWXg0g@mail.gmail.com>
Message-ID: <1310493661.76035.YahooMailNeo@web43412.mail.sp1.yahoo.com>

Hello everyone,


I noticed the new version of QUANTUM ESPRESSO (4.3.1) has changed all of its documentation files to .xml (instead of the former .txt). The problem is, when I try to open these files through firefox, none of the formatting is kept. Everything is written as one continuous paragraph making it very difficult to read. How are these files meant to be opened? Is there an add-on or program that I will need to download?

Thanks in advance.

-- 
Izaak Williamson
Research Assistant
Physics Department
Boise State University
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From guntram.schmidt at chemie.uni-halle.de  Tue Jul 12 20:20:00 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Tue, 12 Jul 2011 20:20:00 +0200
Subject: [Pw_forum] assistance with QHA
Message-ID: <4E1C9050.7060705@chemie.uni-halle.de>

Dear All,

i've two questions concerning the qha-code.
I'd like to calculate and compare the Free Energy (= Gibbs Energy, the 
G=H-TS thing ;-) ) of two polymorphs of one molecule at room temperature.
QHA should do this, but I didn't find a documentation, how to use it. 
The examples provided are not easy to follow, as I have very little 
materials background.

Is there anybody who could provide me a short step-by-step-guide on how 
to do it? Looking through the examples is seems to be problematic to 
have monoclinic or orthorhombic phases?

Thanks!



Second question is, how to compile this part of QE without having ifort?
I tried to symlink ifort to our mpifort - without success.
After the first compilations, I get

"
The NOSTRICT option (default at OPT(3)) has the potential to alter the 
semantics of a program.  Please refer to documentation on the 
STRICT/NOSTRICT option for more information.
"

warnings and then

"
"Debye.f90", line 18.0: 1515-005 (S) Continuation line is not permitted 
at beginning of program or after INCLUDE, EJECT, @PROCESS statements or 
comment directive.  Line is ignored.
"
and so on...

Any ideas?

Thanks a lot,
Guntram

From modaresi.mohsen at gmail.com  Tue Jul 12 21:16:05 2011
From: modaresi.mohsen at gmail.com (mohsen modaresi)
Date: Tue, 12 Jul 2011 12:16:05 -0700
Subject: [Pw_forum] assistance with QHA
In-Reply-To: <4E1C9050.7060705@chemie.uni-halle.de>
References: <4E1C9050.7060705@chemie.uni-halle.de>
Message-ID: <CAM2BXVDesvNF06W3GaJPgmkNPayqXJBwx6xx+406ASobyi05Hw@mail.gmail.com>

Dear Guntram,
about your second question, we install QHA by using gfortran in a parallel
machine. You should simply change "ifort" to "gfortran" in the makefile in
different folders of QHA and then compile it.
I hope it helps.

On Tue, Jul 12, 2011 at 11:20 AM, Guntram Schmidt <
guntram.schmidt at chemie.uni-halle.de> wrote:

> Dear All,
>
> i've two questions concerning the qha-code.
> I'd like to calculate and compare the Free Energy (= Gibbs Energy, the
> G=H-TS thing ;-) ) of two polymorphs of one molecule at room temperature.
> QHA should do this, but I didn't find a documentation, how to use it.
> The examples provided are not easy to follow, as I have very little
> materials background.
>
> Is there anybody who could provide me a short step-by-step-guide on how
> to do it? Looking through the examples is seems to be problematic to
> have monoclinic or orthorhombic phases?
>
> Thanks!
>
>
>
> Second question is, how to compile this part of QE without having ifort?
> I tried to symlink ifort to our mpifort - without success.
> After the first compilations, I get
>
> "
> The NOSTRICT option (default at OPT(3)) has the potential to alter the
> semantics of a program.  Please refer to documentation on the
> STRICT/NOSTRICT option for more information.
> "
>
> warnings and then
>
> "
> "Debye.f90", line 18.0: 1515-005 (S) Continuation line is not permitted
> at beginning of program or after INCLUDE, EJECT, @PROCESS statements or
> comment directive.  Line is ignored.
> "
> and so on...
>
> Any ideas?
>
> Thanks a lot,
> Guntram
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Mohsen Modarresi,
PhD student of Solid State Physics, Ferdowsi University of Mashhad, Iran.
Phone +98-9133452131
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From izaakw89 at yahoo.com  Tue Jul 12 22:12:40 2011
From: izaakw89 at yahoo.com (Izaak Williamson)
Date: Tue, 12 Jul 2011 13:12:40 -0700 (PDT)
Subject: [Pw_forum] What occupation should be used
In-Reply-To: <CANxi7+PyCZGCzUhU_HMLmU8ZnBkjnPxjhMWoZ8VCKTe=+cD0Vw@mail.gmail.com>
References: <CANxi7+PyCZGCzUhU_HMLmU8ZnBkjnPxjhMWoZ8VCKTe=+cD0Vw@mail.gmail.com>
Message-ID: <1310501560.64667.YahooMailNeo@web43402.mail.sp1.yahoo.com>

Hello everyone,


I am doing calculations on Cu3N which is found theoretically to have a band gap around 0.3eV whereas experiments give a value around 1eV. My question is, should I use smearing for this system?

Thanks

-- 
Izaak Williamson
Research Assistant
Physics Department
Boise State University
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From izaakw89 at yahoo.com  Tue Jul 12 22:41:40 2011
From: izaakw89 at yahoo.com (Izaak Williamson)
Date: Tue, 12 Jul 2011 13:41:40 -0700 (PDT)
Subject: [Pw_forum] Using the outdir from vc-relax
In-Reply-To: <CANxi7+NOJv6tVENDphaqB_pB3Uu3Y2k6LLV6W6PY4t1KW-SYYg@mail.gmail.com>
References: <CANxi7+NOJv6tVENDphaqB_pB3Uu3Y2k6LLV6W6PY4t1KW-SYYg@mail.gmail.com>
Message-ID: <1310503300.7780.YahooMailNeo@web43403.mail.sp1.yahoo.com>

Hello everyone,


When I run a vc-relax calculations and attempt running projwfc, it does not give me the correct charge on the atoms. When I run projwfc on relax calculations (for the same system), however, it works fine. Is there a problem with vc-relax that is not allowing projwfc to work with its outdir files properly? Do I need to run an scf calculation on the vc-relax output before running projwfc?

Thanks for any help.

-- 
Izaak Williamson
Research Assistant
Physics Department
Boise State University
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From kangbugy at lycos.co.kr  Wed Jul 13 06:28:40 2011
From: kangbugy at lycos.co.kr (=?UTF-8?B?a2FuZ2J1Z3lAbHljb3MuY28ua3I=?=)
Date: Wed, 13 Jul 2011 13:28:40 +0900
Subject: [Pw_forum] =?utf-8?q?bravais_lattice_of_Cmca?=
Message-ID: <a516df3bfe4a39f8323c44eb34676492$5c6718fe@pcmail3.nate.com>

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From karandeepster at gmail.com  Wed Jul 13 08:18:43 2011
From: karandeepster at gmail.com (karan deep)
Date: Wed, 13 Jul 2011 11:48:43 +0530
Subject: [Pw_forum] Confusion in choosing rlderiv
Message-ID: <CA+PV1XAi8WAWpCPpF8W33UtTS83ShW9W_24SErkT7RtrMyoCcA@mail.gmail.com>

In pseudo-gen.pdf in atomic_doc by Paolo Giannozzi it is written that

*rlderiv( rd) should be of the order of the ionic or covalent radius, and
larger than any of the rc ?s (cut of radius for each pseudo wave function)*
*
*
*But *in some of the examples given in same doc, the used value of rd's  are
smaller then that of rc's.

also according to  some posts here, the value of rd should be *in the order
of half a typical bond-bond *

*distance. i*s it mean that rc's should be less then this value ???


Thanks to all readers.


Karandeep
Research Scholar
Physics Department,
IIT,  Delhi
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From giuseppe.mattioli at mlib.ism.cnr.it  Wed Jul 13 10:01:06 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Wed, 13 Jul 2011 10:01:06 +0200
Subject: [Pw_forum] What occupation should be used
In-Reply-To: <1310501560.64667.YahooMailNeo@web43402.mail.sp1.yahoo.com>
References: <CANxi7+PyCZGCzUhU_HMLmU8ZnBkjnPxjhMWoZ8VCKTe=+cD0Vw@mail.gmail.com>
	<1310501560.64667.YahooMailNeo@web43402.mail.sp1.yahoo.com>
Message-ID: <201107131001.07045.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Izaak
What does pw.x say? does it explicitly requires smearing? Does the scf cycle 
converge without smearing? You may set a small degauss value (i.e. 0.01) and 
check if the -TS contribution in the pw.x output is reassuringly 
negligible...
HTH
Giuseppe

On Tuesday 12 July 2011 22:12:40 Izaak Williamson wrote:
> Hello everyone,
>
>
> I am doing calculations on Cu3N which is found theoretically to have a band
> gap around 0.3eV whereas experiments give a value around 1eV. My question
> is, should I use smearing for this system?
>
> Thanks



-- 
********************************************************
- 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 giuseppe.mattioli at mlib.ism.cnr.it  Wed Jul 13 10:04:17 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Wed, 13 Jul 2011 10:04:17 +0200
Subject: [Pw_forum] Using the outdir from vc-relax
In-Reply-To: <1310503300.7780.YahooMailNeo@web43403.mail.sp1.yahoo.com>
References: <CANxi7+NOJv6tVENDphaqB_pB3Uu3Y2k6LLV6W6PY4t1KW-SYYg@mail.gmail.com>
	<1310503300.7780.YahooMailNeo@web43403.mail.sp1.yahoo.com>
Message-ID: <201107131004.17668.giuseppe.mattioli@mlib.ism.cnr.it>


Which QE version are you using? The newest ones should perform an scf cycle at 
the end of a vc-relax calculation, which should allow one to obtain 
meaningful projwfc.x results.

On Tuesday 12 July 2011 22:41:40 Izaak Williamson wrote:
> Hello everyone,
>
>
> When I run a vc-relax calculations and attempt running projwfc, it does not
> give me the correct charge on the atoms. When I run projwfc on relax
> calculations (for the same system), however, it works fine. Is there a
> problem with vc-relax that is not allowing projwfc to work with its outdir
> files properly? Do I need to run an scf calculation on the vc-relax output
> before running projwfc?
>
> Thanks for any help.



-- 
********************************************************
- 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 zafartariq2003 at yahoo.com  Wed Jul 13 13:22:09 2011
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Wed, 13 Jul 2011 04:22:09 -0700 (PDT)
Subject: [Pw_forum] phonon_dos.x not created........
Message-ID: <1310556129.14735.YahooMailClassic@web65412.mail.ac4.yahoo.com>











Dear Users
I want to use QHA for thermodynamic properties. I change fortran compiler ifort to gfortran?(fedora core 7)in makefiles of Debay,Include,Phonon_Dos,SRC diretories . This change creates all *.x files except Phonon_dos.x .
The process after compilation is?as follows
?
[root at localhost QHA]# ./Compile 
gfortran -O3 -c tetra.f
gfortran -O3 -c k_brillouin.f
gfortran -O3 -c generate_tetra.f
In file generate_tetra.f:84
IF(S-.0001)3,3,1 
1
Warning: Obsolete: arithmetic IF statement at (1)
gfortran -O3 -c det3.f
gfortran -O3 -c det4.f
gfortran -static -o tetra.x tetra.o k_brillouin.o generate_tetra.o det3.o det4.o 
gfortran -O3 -c phonon_dos.f
In file phonon_dos.f:122
open(unit=8,file='PHDOS.out',access='sequential',form='formatted'
1
Error: Syntax error in OPEN statement at (1)
make: *** [phonon_dos.o] Error 1
gfortran -O3 -c Debye.f90
In file Debye.f90:144
do T = T_low_start, T_low, T_low_delta
1
Warning: Obsolete: REAL DO loop iterator at (1)
In file Debye.f90:177
do T = T_low+5, T_high, T_high_delta
1
Warning: Obsolete: REAL DO loop iterator at (1)
gfortran -O3 -c Debye_T.f
gfortran -O3 -c debye3.f
gfortran -O3 -c cheval.f
gfortran -O3 -c d1mach.f
gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o 
gfortran -FR -c Mean_square_displacement.f90
In file Mean_square_displacement.f90:162
do T=T_start,T_end,T_delta
1
Warning: Obsolete: REAL DO loop iterator at (1)
gfortran -static -o Mean_square_displacement.x Mean_square_displacement.o 
gfortran -FR -c Atom_projected_properties.f90
In file Atom_projected_properties.f90:180
do T=T_start, T_end, T_delta
1
Warning: Obsolete: REAL DO loop iterator at (1)
gfortran -static -o Atom_projected_properties.x Atom_projected_properties.o 
gfortran -FR -c F_QHA.f90
In file F_QHA.f90:134
do T=T_start,T_end,T_delta
1
Warning: Obsolete: REAL DO loop iterator at (1)
gfortran -static -o F_QHA.x F_QHA.o 
gfortran -FR -c Ghost_DOS.f90
gfortran -static -o Ghost_DOS.x Ghost_DOS.o 
gfortran -FR -c Partial_phonon_DOS.f90
gfortran -static -o Partial_phonon_DOS.x Partial_phonon_DOS.o 
gfortran -FR -c atom_info.f90
gfortran -static -o atom_info.x atom_info.o 
?
Muhammad Zafar
PhD Scholar
Department of Physics
The Islamia University of Bahawalpur,Pakistan
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From guntram.schmidt at chemie.uni-halle.de  Wed Jul 13 14:04:52 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Wed, 13 Jul 2011 14:04:52 +0200
Subject: [Pw_forum] phonon_dos.x not created........
In-Reply-To: <1310556129.14735.YahooMailClassic@web65412.mail.ac4.yahoo.com>
References: <1310556129.14735.YahooMailClassic@web65412.mail.ac4.yahoo.com>
Message-ID: <4E1D89E4.3070304@chemie.uni-halle.de>

Dear Muhammad Zafar,

have you removed the

FFLAGS = -O3

and used the linux-proposed:

FFLAGS = -O3 -ffast-math -fno-f2c

in each makefile?
In my case, this was important.

Good luck,
Guntram


Am 13.07.2011 13:22, schrieb zafar rasheed:
>
>
>
>     Dear Users
>     I want to use QHA for thermodynamic properties. I change fortran
>     compiler ifort to gfortran (fedora core 7)in makefiles of
>     Debay,Include,Phonon_Dos,SRC diretories . This change creates all
>     *.x files except Phonon_dos.x .
>     The process after compilation is as follows
>     ?
>     [root at localhost QHA]# ./Compile
>     gfortran -O3 -c tetra.f
>     gfortran -O3 -c k_brillouin.f
>     gfortran -O3 -c generate_tetra.f
>     In file generate_tetra.f:84
>     IF(S-.0001)3,3,1
>     1
>     Warning: Obsolete: arithmetic IF statement at (1)
>     gfortran -O3 -c det3.f
>     gfortran -O3 -c det4.f
>     gfortran -static -o tetra.x tetra.o k_brillouin.o generate_tetra.o
>     det3.o det4.o
>     gfortran -O3 -c phonon_dos.f
>     In file phonon_dos.f:122
>     open(unit=8,file='PHDOS.out',access='sequential',form='formatted'
>     1
>     Error: Syntax error in OPEN statement at (1)
>     make: *** [phonon_dos.o] Error 1
>     gfortran -O3 -c Debye.f90
>     In file Debye.f90:144
>     do T = T_low_start, T_low, T_low_delta
>     1
>     Warning: Obsolete: REAL DO loop iterator at (1)
>     In file Debye.f90:177
>     do T = T_low+5, T_high, T_high_delta
>     1
>     Warning: Obsolete: REAL DO loop iterator at (1)
>     gfortran -O3 -c Debye_T.f
>     gfortran -O3 -c debye3.f
>     gfortran -O3 -c cheval.f
>     gfortran -O3 -c d1mach.f
>     gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o
>     d1mach.o
>     gfortran -FR -c Mean_square_displacement.f90
>     In file Mean_square_displacement.f90:162
>     do T=T_start,T_end,T_delta
>     1
>     Warning: Obsolete: REAL DO loop iterator at (1)
>     gfortran -static -o Mean_square_displacement.x
>     Mean_square_displacement.o
>     gfortran -FR -c Atom_projected_properties.f90
>     In file Atom_projected_properties.f90:180
>     do T=T_start, T_end, T_delta
>     1
>     Warning: Obsolete: REAL DO loop iterator at (1)
>     gfortran -static -o Atom_projected_properties.x
>     Atom_projected_properties.o
>     gfortran -FR -c F_QHA.f90
>     In file F_QHA.f90:134
>     do T=T_start,T_end,T_delta
>     1
>     Warning: Obsolete: REAL DO loop iterator at (1)
>     gfortran -static -o F_QHA.x F_QHA.o
>     gfortran -FR -c Ghost_DOS.f90
>     gfortran -static -o Ghost_DOS.x Ghost_DOS.o
>     gfortran -FR -c Partial_phonon_DOS.f90
>     gfortran -static -o Partial_phonon_DOS.x Partial_phonon_DOS.o
>     gfortran -FR -c atom_info.f90
>     gfortran -static -o atom_info.x atom_info.o
>     ?
>
>     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

From guntram.schmidt at chemie.uni-halle.de  Wed Jul 13 14:52:57 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Wed, 13 Jul 2011 14:52:57 +0200
Subject: [Pw_forum] assistance with QHA
In-Reply-To: <CAM2BXVDesvNF06W3GaJPgmkNPayqXJBwx6xx+406ASobyi05Hw@mail.gmail.com>
References: <4E1C9050.7060705@chemie.uni-halle.de>
	<CAM2BXVDesvNF06W3GaJPgmkNPayqXJBwx6xx+406ASobyi05Hw@mail.gmail.com>
Message-ID: <4E1D9529.40302@chemie.uni-halle.de>

Dear Mohsen,

as already posted in another thread - the solution was to also put the
FFLAGS = -O3 -ffast-math -fno-f2c
into every make-file.

Using xlf it now finished compiling. I'll start the examples now - but 
the reference data is missing :-(. Where can I find it? Was it supplied 
with older versions of QE?

And can anybody please help me with "simply" calculating the 
gibbs-energy of my molecular crystals?


Thanks,
Guntram




Am 12.07.2011 21:16, schrieb mohsen modaresi:
> Dear Guntram,
> about your second question, we install QHA by using gfortran in a
> parallel machine. You should simply change "ifort" to "gfortran" in the
> makefile in different folders of QHA and then compile it.
> I hope it helps.
>
> On Tue, Jul 12, 2011 at 11:20 AM, Guntram Schmidt
> <guntram.schmidt at chemie.uni-halle.de
> <mailto:guntram.schmidt at chemie.uni-halle.de>> wrote:
>
>     Dear All,
>
>     i've two questions concerning the qha-code.
>     I'd like to calculate and compare the Free Energy (= Gibbs Energy, the
>     G=H-TS thing ;-) ) of two polymorphs of one molecule at room
>     temperature.
>     QHA should do this, but I didn't find a documentation, how to use it.
>     The examples provided are not easy to follow, as I have very little
>     materials background.
>
>     Is there anybody who could provide me a short step-by-step-guide on how
>     to do it? Looking through the examples is seems to be problematic to
>     have monoclinic or orthorhombic phases?
>
>     Thanks!
>
>
>
>     Second question is, how to compile this part of QE without having ifort?
>     I tried to symlink ifort to our mpifort - without success.
>     After the first compilations, I get
>
>     "
>     The NOSTRICT option (default at OPT(3)) has the potential to alter the
>     semantics of a program.  Please refer to documentation on the
>     STRICT/NOSTRICT option for more information.
>     "
>
>     warnings and then
>
>     "
>     "Debye.f90", line 18.0: 1515-005 (S) Continuation line is not permitted
>     at beginning of program or after INCLUDE, EJECT, @PROCESS statements or
>     comment directive.  Line is ignored.
>     "
>     and so on...
>
>     Any ideas?
>
>     Thanks a lot,
>     Guntram
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
> Mohsen Modarresi,
> PhD student of Solid State Physics, Ferdowsi University of Mashhad, Iran.
> Phone +98-9133452131
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

From guntram.schmidt at chemie.uni-halle.de  Wed Jul 13 16:47:39 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Wed, 13 Jul 2011 16:47:39 +0200
Subject: [Pw_forum] from matdyn : error #        49
In-Reply-To: <CAM2BXVDesvNF06W3GaJPgmkNPayqXJBwx6xx+406ASobyi05Hw@mail.gmail.com>
References: <4E1C9050.7060705@chemie.uni-halle.de>
	<CAM2BXVDesvNF06W3GaJPgmkNPayqXJBwx6xx+406ASobyi05Hw@mail.gmail.com>
Message-ID: <4E1DB00B.2000005@chemie.uni-halle.de>

Dear All,

I'm trying to get QHA working on our clusters.
When I try to run the first example (Al), I get the above error.
I don't know this matdyn - here is the corresponding input-file, created 
by Run_Me:


&input
     amass(1)=26.98,
     asr='crystal',
     flfrc=Al4.fc,
     flfrq='frequency'
&end
  455
        .50000    .50000    .00000   1.00000
...
...
...
        .50000    .04167    .04167   1.00000
        .50000    .00000    .00000   1.00000
EOF


The error message is:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    0:     from matdyn : error #        49
    0:     reading input namelist
    0: 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    0:
    0:     stopping ...


I had to start it via our mpi-loadleveler - which shouldn't affect this 
errors, imho.

Any ideas on this?
Thanks,
Guntram

From izaakw89 at yahoo.com  Wed Jul 13 19:21:52 2011
From: izaakw89 at yahoo.com (Izaak Williamson)
Date: Wed, 13 Jul 2011 10:21:52 -0700 (PDT)
Subject: [Pw_forum] Using the outdir from vc-relax
In-Reply-To: <201107131004.17668.giuseppe.mattioli@mlib.ism.cnr.it>
References: <CANxi7+NOJv6tVENDphaqB_pB3Uu3Y2k6LLV6W6PY4t1KW-SYYg@mail.gmail.com>
	<1310503300.7780.YahooMailNeo@web43403.mail.sp1.yahoo.com>
	<201107131004.17668.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <1310577712.60379.YahooMailNeo@web43415.mail.sp1.yahoo.com>

Thank you for your response.

The version I was using was espresso-4.1.3. On which version did they start running an scf at the end of a vc-relax calculation?



________________________________
From: Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Wednesday, July 13, 2011 1:04 AM
Subject: Re: [Pw_forum] Using the outdir from vc-relax


Which QE version are you using? The newest ones should perform an scf cycle at 
the end of a vc-relax calculation, which should allow one to obtain 
meaningful projwfc.x results.

On Tuesday 12 July 2011 22:41:40 Izaak Williamson wrote:
> Hello everyone,
>
>
> When I run a vc-relax calculations and attempt running projwfc, it does not
> give me the correct charge on the atoms. When I run projwfc on relax
> calculations (for the same system), however, it works fine. Is there a
> problem with vc-relax that is not allowing projwfc to work with its outdir
> files properly? Do I need to run an scf calculation on the vc-relax output
> before running projwfc?
>
> Thanks for any help.



-- 
********************************************************
- 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 trambui at u.boisestate.edu  Wed Jul 13 20:26:44 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Wed, 13 Jul 2011 12:26:44 -0600
Subject: [Pw_forum] charged defects
Message-ID: <CANzxBn_yseaZ+ir6DsFWB3oWV-XwPpbdfKcHQyEOPHxQp5iX-Q@mail.gmail.com>

Dear Everyone,
      would you give me some information on how one can determine the
possible charge states for a defect? e.g. Mg substitution Ga in GaN. or Ag
substitution Si in SiC.

Regards,

Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From degironc at sissa.it  Wed Jul 13 20:58:18 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 13 Jul 2011 20:58:18 +0200
Subject: [Pw_forum] charged defects
In-Reply-To: <CANzxBn_yseaZ+ir6DsFWB3oWV-XwPpbdfKcHQyEOPHxQp5iX-Q@mail.gmail.com>
References: <CANzxBn_yseaZ+ir6DsFWB3oWV-XwPpbdfKcHQyEOPHxQp5iX-Q@mail.gmail.com>
Message-ID: <20110713205818.28ukruvl8og484w4@webmail.sissa.it>

I would start with some reading...
there are a number of research papers and review papers, notably by  
Chris Van de Walle, on the subject
stefano
-
Stefano de Gironcoli - SISSA and DEMOCRITOS

Quoting Tram Bui <trambui at u.boisestate.edu>:

> Dear Everyone,
>       would you give me some information on how one can determine the
> possible charge states for a defect? e.g. Mg substitution Ga in GaN. or Ag
> substitution Si in SiC.
>
> Regards,
>
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>



----------------------------------------------------------------
   SISSA Webmail https://webmail.sissa.it/
   Powered by Horde http://www.horde.org/



From flux_ray12 at 163.com  Thu Jul 14 08:24:03 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 14 Jul 2011 14:24:03 +0800 (CST)
Subject: [Pw_forum] phonon_dos.x not created........
In-Reply-To: <1310556129.14735.YahooMailClassic@web65412.mail.ac4.yahoo.com>
References: <1310556129.14735.YahooMailClassic@web65412.mail.ac4.yahoo.com>
Message-ID: <47497475.15238.1312750f8a9.Coremail.flux_ray12@163.com>

I compiled QHA in this way and successed. This is the biggining of makefile in my Phonon_DOS folder:
.SUFFIXES: .f .o
FC = mpif90#ifort
LD = $(FC) #-static
DOS  = phonon_dos.x
TET  = tetra.x
#Linux
#FFLAGS = -O3 -ffast-math -fno-f2c
FFLAGS = -O3
OBJ1 =    phonon_dos.o k_brillouin.o generate_tetra.o  det3.o det4.o \
    Tetrahedra.o Integration.o
.......

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-13 19:22:09?"zafar rasheed" <zafartariq2003 at yahoo.com> wrote:






Dear Users
I want to use QHA for thermodynamic properties. I change fortran compiler ifort to gfortran (fedora core 7)in makefiles of Debay,Include,Phonon_Dos,SRC diretories . This change creates all *.x files except Phonon_dos.x .
The process after compilation is as follows
?
[root at localhost QHA]# ./Compile
gfortran -O3 -c tetra.f
gfortran -O3 -c k_brillouin.f
gfortran -O3 -c generate_tetra.f
In file generate_tetra.f:84
IF(S-.0001)3,3,1
1
Warning: Obsolete: arithmetic IF statement at (1)
gfortran -O3 -c det3.f
gfortran -O3 -c det4.f
gfortran -static -o tetra.x tetra.o k_brillouin.o generate_tetra.o det3.o det4.o
gfortran -O3 -c phonon_dos.f
In file phonon_dos.f:122
open(unit=8,file='PHDOS.out',access='sequential',form='formatted'
1
Error: Syntax error in OPEN statement at (1)
make: *** [phonon_dos.o] Error 1
gfortran -O3 -c Debye.f90
In file Debye.f90:144
do T = T_low_start, T_low, T_low_delta
1
Warning: Obsolete: REAL DO loop iterator at (1)
In file Debye.f90:177
do T = T_low+5, T_high, T_high_delta
1
Warning: Obsolete: REAL DO loop iterator at (1)
gfortran -O3 -c Debye_T.f
gfortran -O3 -c debye3.f
gfortran -O3 -c cheval.f
gfortran -O3 -c d1mach.f
gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o
gfortran -FR -c Mean_square_displacement.f90
In file Mean_square_displacement.f90:162
do T=T_start,T_end,T_delta
1
Warning: Obsolete: REAL DO loop iterator at (1)
gfortran -static -o Mean_square_displacement.x Mean_square_displacement.o
gfortran -FR -c Atom_projected_properties.f90
In file Atom_projected_properties.f90:180
do T=T_start, T_end, T_delta
1
Warning: Obsolete: REAL DO loop iterator at (1)
gfortran -static -o Atom_projected_properties.x Atom_projected_properties.o
gfortran -FR -c F_QHA.f90
In file F_QHA.f90:134
do T=T_start,T_end,T_delta
1
Warning: Obsolete: REAL DO loop iterator at (1)
gfortran -static -o F_QHA.x F_QHA.o
gfortran -FR -c Ghost_DOS.f90
gfortran -static -o Ghost_DOS.x Ghost_DOS.o
gfortran -FR -c Partial_phonon_DOS.f90
gfortran -static -o Partial_phonon_DOS.x Partial_phonon_DOS.o
gfortran -FR -c atom_info.f90
gfortran -static -o atom_info.x atom_info.o
?

Muhammad Zafar
PhD Scholar
Department of Physics
The Islamia University of Bahawalpur,Pakistan
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From flux_ray12 at 163.com  Thu Jul 14 08:14:03 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 14 Jul 2011 14:14:03 +0800 (CST)
Subject: [Pw_forum] from matdyn : error #        49
In-Reply-To: <4E1DB00B.2000005@chemie.uni-halle.de>
References: <4E1DB00B.2000005@chemie.uni-halle.de>
	<4E1C9050.7060705@chemie.uni-halle.de>
	<CAM2BXVDesvNF06W3GaJPgmkNPayqXJBwx6xx+406ASobyi05Hw@mail.gmail.com>
Message-ID: <1f882333.14f33.1312747d189.Coremail.flux_ray12@163.com>

Please modify flfrc line from flfrc = Al4.fc to flfrc = 'Al4.fc' ~~~~ It is a small careless mistake~

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea




At 2011-07-13 22:47:39?"Guntram Schmidt" <guntram.schmidt at chemie.uni-halle.de> wrote:

>Dear All,
>
>I'm trying to get QHA working on our clusters.
>When I try to run the first example (Al), I get the above error.
>I don't know this matdyn - here is the corresponding input-file, created 
>by Run_Me:
>
>
>&input
>     amass(1)=26.98,
>     asr='crystal',
>     flfrc=Al4.fc,
>     flfrq='frequency'
>&end
>  455
>        .50000    .50000    .00000   1.00000
>...
>...
>...
>        .50000    .04167    .04167   1.00000
>        .50000    .00000    .00000   1.00000
>EOF
>
>
>The error message is:
>
>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>    0:     from matdyn : error #        49
>    0:     reading input namelist
>    0: 
>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>    0:
>    0:     stopping ...
>
>
>I had to start it via our mpi-loadleveler - which shouldn't affect this 
>errors, imho.
>
>Any ideas on this?
>Thanks,
>Guntram
>_______________________________________________
>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  Thu Jul 14 08:15:58 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 14 Jul 2011 14:15:58 +0800 (CST)
Subject: [Pw_forum] assistance with QHA
In-Reply-To: <4E1C9050.7060705@chemie.uni-halle.de>
References: <4E1C9050.7060705@chemie.uni-halle.de>
Message-ID: <3ca32d3f.14fb3.131274992ad.Coremail.flux_ray12@163.com>

For the First question:
Please read the scripts in QHA/Examples carefully, or you can just modify the scripts for your model.

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea




At 2011-07-13 02:20:00?"Guntram Schmidt" <guntram.schmidt at chemie.uni-halle.de> wrote:

>Dear All,
>
>i've two questions concerning the qha-code.
>I'd like to calculate and compare the Free Energy (= Gibbs Energy, the 
>G=H-TS thing ;-) ) of two polymorphs of one molecule at room temperature.
>QHA should do this, but I didn't find a documentation, how to use it. 
>The examples provided are not easy to follow, as I have very little 
>materials background.
>
>Is there anybody who could provide me a short step-by-step-guide on how 
>to do it? Looking through the examples is seems to be problematic to 
>have monoclinic or orthorhombic phases?
>
>Thanks!
>
>
>
>Second question is, how to compile this part of QE without having ifort?
>I tried to symlink ifort to our mpifort - without success.
>After the first compilations, I get
>
>"
>The NOSTRICT option (default at OPT(3)) has the potential to alter the 
>semantics of a program.  Please refer to documentation on the 
>STRICT/NOSTRICT option for more information.
>"
>
>warnings and then
>
>"
>"Debye.f90", line 18.0: 1515-005 (S) Continuation line is not permitted 
>at beginning of program or after INCLUDE, EJECT, @PROCESS statements or 
>comment directive.  Line is ignored.
>"
>and so on...
>
>Any ideas?
>
>Thanks a lot,
>Guntram
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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From raji.phy at gmail.com  Thu Jul 14 12:38:19 2011
From: raji.phy at gmail.com (Raji)
Date: Thu, 14 Jul 2011 16:08:19 +0530
Subject: [Pw_forum] QE installation probelm in linux PC (Red hat EL)
Message-ID: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>

Dear all,

I am trying to install QE 4.3.1 in a ia32  PC - OS: RHEL.
I do have installed gfortran and C.

*QE Compilation seems to work *

[root at localhost espresso-4.3.1]# ./configure
..............
checking for Fortran 77 name-mangling scheme... lower case, underscore, no
extra underscore
checking for library containing dgemm... no
MKL not found
in /opt/intel/Compiler/*/*/mkl/lib/32: checking for library containing
dgemm... no
MKL not found
in /opt/intel/mkl/*/lib/32: checking for library containing dgemm... no
MKL not found
in /opt/intel/mkl*/lib/32: checking for library containing dgemm... no
MKL not found
checking for library containing dgemm... no
in /usr/local/lib: checking for library containing dgemm... no
checking for library containing dgemm... -lblas
checking for library containing dspev... -llapack
.........
The following libraries have been found
  BLAS_LIBS= -lblas
  LAPACK_LIBS= -llapack  -lblas
  FFT_LIBS= -lfftw3
Please check if this is what you expect.
Parallel environment not detected \(is this a parallel machine?\).\
Configured for compilation of serial executables.
...
configure: success
*
After i type make all, program exits with following message.
*
[root at localhost espresso-4.3.1]# make all
...............
make[2]: Entering directory `/root/QE/espresso-4.3.1/S3DE/iotk/src'
gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW3
-I../include  -c iotk_scan.f90
iotk_scan.spp: In function ?iotk_scan_tag_x?:
iotk_scan.spp:452: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://bugzilla.redhat.com/bugzilla> for instructions.
make[2]: *** [iotk_scan.o] Error 1
make[2]: Leaving directory `/root/QE/espresso-4.3.1/S3DE/iotk/src'
make[1]: *** [libiotk] Error 2
make[1]: Leaving directory `/root/QE/espresso-4.3.1/extlibs'
make: *** [libiotk] Error 2

I have googled the previous quires, but nothing seems to workout.
I would greatly appreaciate any help or suggestion to sort out this.

 Raji.
***************************************
M. Rajarajeswari
Research Scholar
Madurai Kamaraj University
Madurai - 625 021 Tamil Nadu
India.
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From flux_ray12 at 163.com  Thu Jul 14 14:27:30 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 14 Jul 2011 20:27:30 +0800 (CST)
Subject: [Pw_forum] QE installation probelm in linux PC (Red hat EL)
In-Reply-To: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
Message-ID: <7ac8cb29.1af22.131289dbaed.Coremail.flux_ray12@163.com>

Why not try:
/opt/intel/bin/compilervars.sh ia32
./configure FC=ifort
?
I saw you have installed intel fortran compiler.
Or, if you do not want to change from gfortran to ifort, you can also try the parameter:
./configure FFLAGS=-O0
Good Luck.

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-14 18:38:19?Raji <raji.phy at gmail.com> wrote:


Dear all,

I am trying to install QE 4.3.1 in a ia32  PC - OS: RHEL.
I do have installed gfortran and C.

QE Compilation seems to work 

[root at localhost espresso-4.3.1]# ./configure
..............
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking for library containing dgemm... no
MKL not found
in /opt/intel/Compiler/*/*/mkl/lib/32: checking for library containing dgemm... no
MKL not found
in /opt/intel/mkl/*/lib/32: checking for library containing dgemm... no
MKL not found
in /opt/intel/mkl*/lib/32: checking for library containing dgemm... no
MKL not found
checking for library containing dgemm... no
in /usr/local/lib: checking for library containing dgemm... no
checking for library containing dgemm... -lblas
checking for library containing dspev... -llapack
.........
The following libraries have been found
  BLAS_LIBS= -lblas
  LAPACK_LIBS= -llapack  -lblas
  FFT_LIBS= -lfftw3
Please check if this is what you expect.
Parallel environment not detected \(is this a parallel machine?\).\
Configured for compilation of serial executables.
...
configure: success

After i type make all, program exits with following message.

[root at localhost espresso-4.3.1]# make all
...............
make[2]: Entering directory `/root/QE/espresso-4.3.1/S3DE/iotk/src'
gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW3 -I../include  -c iotk_scan.f90
iotk_scan.spp: In function ?iotk_scan_tag_x?:
iotk_scan.spp:452: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://bugzilla.redhat.com/bugzilla> for instructions.
make[2]: *** [iotk_scan.o] Error 1
make[2]: Leaving directory `/root/QE/espresso-4.3.1/S3DE/iotk/src'
make[1]: *** [libiotk] Error 2
make[1]: Leaving directory `/root/QE/espresso-4.3.1/extlibs'
make: *** [libiotk] Error 2

I have googled the previous quires, but nothing seems to workout.
I would greatly appreaciate any help or suggestion to sort out this.



Raji.
***************************************
M. Rajarajeswari
Research Scholar
Madurai Kamaraj University
Madurai - 625 021 Tamil Nadu
India.
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From bamideleibrahim at yahoo.com  Thu Jul 14 15:44:58 2011
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Thu, 14 Jul 2011 06:44:58 -0700 (PDT)
Subject: [Pw_forum] how to extract data from phonon calculation to plot
	phonon frequency dispersion curve
Message-ID: <1310651098.17544.YahooMailClassic@web39408.mail.mud.yahoo.com>

Dear all,
?I want to plot phonon dispersion frequency curve. i perform scf and phonon calculation at gamma point(0,0,0), where i have an output file .dynG. Inside this file, there? are some data which i think is to be use to plot the phonon frequency dispersion curve. but to extract these data is a problem. Can anybody help me out? Your assistance will be appreciated.
thanks,
ibrahim 

Adetunji Bamidele Ibrahim

Department of physics,University of Agriculture,

Abeokuta, Ogun State,Nigeria.
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From eyvaz_isaev at yahoo.com  Thu Jul 14 16:02:55 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 14 Jul 2011 07:02:55 -0700 (PDT)
Subject: [Pw_forum] Back to the forum
Message-ID: <1310652175.24221.YahooMailNeo@web65709.mail.ac4.yahoo.com>

Dear all,

I would like to thank the forum members for some discussions of the QHA code and fixing the 

problems. Hopefully, I will be more active later.

Best regards,
Eyvaz.

?
-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
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From eyvaz_isaev at yahoo.com  Thu Jul 14 16:11:33 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 14 Jul 2011 07:11:33 -0700 (PDT)
Subject: [Pw_forum] how to extract data from phonon calculation to plot
	phonon frequency dispersion curve
In-Reply-To: <1310651098.17544.YahooMailClassic@web39408.mail.mud.yahoo.com>
References: <1310651098.17544.YahooMailClassic@web39408.mail.mud.yahoo.com>
Message-ID: <1310652693.5776.YahooMailNeo@web65711.mail.ac4.yahoo.com>

Hi,

In order to plot phonon dispersion relations you need interatomic force constants matrix, *.fc file. To get it you have to calculate dynamical matrices for a given number of q-points defined via (nq1 x nq2 x nq3) mesh, then perform FFT to get F(R) - the *.fc file (using q2r.x). Then you can use PlotPhon utility to plot phonon dispersion relations. 


Best regards,
Eyvaz.? 

?
-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


________________________________
From: bamidele ibrahim <bamideleibrahim at yahoo.com>
To: pw_forum at pwscf.org
Sent: Thursday, July 14, 2011 5:44 PM
Subject: [Pw_forum] how to extract data from phonon calculation to plot phonon frequency dispersion curve


Dear all,
?I want to plot phonon dispersion frequency curve. i perform scf and phonon calculation at gamma point(0,0,0), where i have an output file .dynG. Inside this file, there? are some data which i think is to be use to plot the phonon frequency dispersion curve. but to extract these data is a problem. Can anybody help me out? Your assistance will be appreciated.
thanks,
ibrahim 

Adetunji Bamidele Ibrahim
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 mashiatalaaii at gmail.com  Thu Jul 14 17:33:34 2011
From: mashiatalaaii at gmail.com (mashiat alaaii)
Date: Thu, 14 Jul 2011 11:33:34 -0400
Subject: [Pw_forum] projected wavefunction
Message-ID: <CAOdEC1kfShiEfGAY+CtV_pjb-AECiW6FkfP4AkE4yhWvAeBY4A@mail.gmail.com>

Dear All,
Hello.

   1. I would appreciate if anybody could refer me to an article or site
   which explains how to get the projected wavefunction on atoms OR
   equivalently describe the output of projwfc.x.
   2. I would be grateful if anybody refer me to an input file which shows
   how to move a couple of atoms in a big structure to find their final
   position.

I am really thankful of any kind of help and advice.
I look forward to hearing from you.
Yours
M Alaaii
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From giuseppe.mattioli at mlib.ism.cnr.it  Thu Jul 14 17:36:06 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Thu, 14 Jul 2011 17:36:06 +0200
Subject: [Pw_forum] Using the outdir from vc-relax
In-Reply-To: <1310577712.60379.YahooMailNeo@web43415.mail.sp1.yahoo.com>
References: <CANxi7+NOJv6tVENDphaqB_pB3Uu3Y2k6LLV6W6PY4t1KW-SYYg@mail.gmail.com>
	<201107131004.17668.giuseppe.mattioli@mlib.ism.cnr.it>
	<1310577712.60379.YahooMailNeo@web43415.mail.sp1.yahoo.com>
Message-ID: <201107141736.06611.giuseppe.mattioli@mlib.ism.cnr.it>


Not sure; it should be the 4.2 one, but I suppose that the best thing is to 
try with the most recent stable 4.3.1 version...
G.

On Wednesday 13 July 2011 19:21:52 Izaak Williamson wrote:
> Thank you for your response.
>
> The version I was using was espresso-4.1.3. On which version did they start
> running an scf at the end of a vc-relax calculation?
>
>
>
> ________________________________
> From: Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
> To: PWSCF Forum <pw_forum at pwscf.org>
> Sent: Wednesday, July 13, 2011 1:04 AM
> Subject: Re: [Pw_forum] Using the outdir from vc-relax
>
>
> Which QE version are you using? The newest ones should perform an scf cycle
> at the end of a vc-relax calculation, which should allow one to obtain
> meaningful projwfc.x results.
>
> On Tuesday 12 July 2011 22:41:40 Izaak Williamson wrote:
> > Hello everyone,
> >
> >
> > When I run a vc-relax calculations and attempt running projwfc, it does
> > not give me the correct charge on the atoms. When I run projwfc on relax
> > calculations (for the same system), however, it works fine. Is there a
> > problem with vc-relax that is not allowing projwfc to work with its
> > outdir files properly? Do I need to run an scf calculation on the
> > vc-relax output before running projwfc?
> >
> > Thanks for any help.



-- 
********************************************************
- 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 giannozz at democritos.it  Thu Jul 14 23:30:03 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 14 Jul 2011 23:30:03 +0200
Subject: [Pw_forum] Confusion in choosing rlderiv
In-Reply-To: <CA+PV1XAi8WAWpCPpF8W33UtTS83ShW9W_24SErkT7RtrMyoCcA@mail.gmail.com>
References: <CA+PV1XAi8WAWpCPpF8W33UtTS83ShW9W_24SErkT7RtrMyoCcA@mail.gmail.com>
Message-ID: <50704F14-8E02-4BB9-A37A-C23DE70026C4@democritos.it>


On Jul 13, 2011, at 8:18 , karan deep wrote:

> rlderiv( rd) should be of the order of the ionic or covalent radius,
> and larger than any of the rc ?s (cut of radius for each pseudo  
> wave function)

it is not a strict rule, as long as rd is not much smaller than rc
>
> also according to  some posts here, the value of rd should be in  
> the order of
> half a typical bond-bond distance. is it mean that rc's should be  
> less then this
> value ???

it is preferrable that the "core" regions (i.e. the region of space  
where the pseudo
and all-electron orbitals appreciably differ) do not overlap. Again,  
not a strict rule.

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 14 23:32:57 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 14 Jul 2011 23:32:57 +0200
Subject: [Pw_forum] QE installation probelm in linux PC (Red hat EL)
In-Reply-To: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
Message-ID: <35FCD62C-4AA5-4CA3-ADDC-41E33CED5569@democritos.it>


On Jul 14, 2011, at 12:38 , Raji wrote:
> iotk_scan.spp:452: internal compiler error
>
as explained in the user guide, this invariably means that the
compiler is buggy. If lowering the optimization level (-O0)
doesn't work, you need a different compiler

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 mtorabi at uwo.ca  Fri Jul 15 00:07:37 2011
From: mtorabi at uwo.ca (Amin Torabi)
Date: Thu, 14 Jul 2011 18:07:37 -0400
Subject: [Pw_forum] Pressure-induced phase transition
Message-ID: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>

Dear experts!

Forgive me for my naive question... but I am interested in pressure-induced
phase transitions of diborane. Could you please have a look at my input
file, attached to this message.

The following is what I think I should do: (correct me if I'm wrong!)

1. doing separate vc-relax calculation at each pressure
2. comparing the optimized cell_parameters at each pressure to see when the
structure changes

I am wondering how I can use the enthalpy or unit cell volume at each
pressure to make sure that a phase transition has occurred

Thanks in advance


-- 
Amin Torabi
Ph.D. Student
Chemistry Department
*The* University *of* Western Ontario
London, On Canada, N6A 5B7
Phone: 519-661-2111 Ext: 87871
****************************************
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From elie.moujaes at hotmail.co.uk  Fri Jul 15 03:00:23 2011
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Fri, 15 Jul 2011 02:00:23 +0100
Subject: [Pw_forum] simple question about plotband.x
Message-ID: <DUB110-W210F3DCD537449810ED909D3490@phx.gbl>


Dear all,
I am doing calculations on grain boundaries of graphene. When I use plotband.x  and restrict the limit of the energies between say -2.1 and 2.1 eV , The produced curve has limits between -2.7 and 1.8. Why is that the case? This is also affecting the graph in the sense that when I set the fermi energy as a reference , the dashed line at the zero is lower than the actual Fermi energy where bands intersect..See graph attached (in the graph the point 0.0 is lower than 0.3299 where the bands intersect). Howvere the general band structure is correct. How can I solve this problem

Thanks
Elias MoukaesUniversity of NottsUKNG7 2RD
 		 	   		  
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From germaneau at gucas.ac.cn  Fri Jul 15 15:16:27 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Fri, 15 Jul 2011 09:16:27 -0400
Subject: [Pw_forum] simple question about plotband.x
In-Reply-To: <510691538.30723@test1.gucas.ac.cn>
References: <510691538.30723@test1.gucas.ac.cn>
Message-ID: <4E203DAB.9060602@gucas.ac.cn>

Hey Elias,

You may not use enough points I think.
Try with more k-vectors to see.
Best,

        ?ric.

On 07/14/2011 09:00 PM, Elie Moujaes wrote:
> Dear all,
>
> I am doing calculations on grain boundaries of graphene. When I use 
> *plotband.x*  and restrict the limit of the energies between say -2.1 
> and 2.1 eV , The produced curve has limits between -2.7 and 1.8. Why 
> is that the case? This is also affecting the graph in the sense that 
> when I set the fermi energy as a reference , the dashed line at the 
> zero is lower than the actual Fermi energy where bands intersect..See 
> graph attached (in the graph the point 0.0 is lower than 0.3299 where 
> the bands intersect). Howvere the general band structure is correct. 
> How can I solve this problem
>
>
> Thanks
>
> Elias Moukaes
> University of Notts
> UK
> NG7 2RD
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html /

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From eariel99 at gmail.com  Fri Jul 15 08:10:04 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Fri, 15 Jul 2011 02:10:04 -0400
Subject: [Pw_forum] Pw_forum Digest, Vol 49, Issue 33
In-Reply-To: <mailman.13968.1310490301.1814.pw_forum@pwscf.org>
References: <mailman.13968.1310490301.1814.pw_forum@pwscf.org>
Message-ID: <CAM5Vcw-emcZrBH=eqidEaOjVmLqYEkW5V9SjYuwpphs_+20Uqg@mail.gmail.com>

Hi Gui-Bin

To avoid intraband contribution it is not enough to use intrasmear=0, you
also need to set occupations='fixed' in the PW calculations, at least for
the nscf one. The following reads in the manual of epsilon.

\emph{intrasmear} is the broadening parameter for the intraband, i.e. metal
Drude like term (again in eV),
the intraband contribution is calculated only if a Gaussian broadening or
tetrahedron method it's been
applied in PW calculations.


On the other hand, it seems from the epsi plot,  that the Wien calculation
considers automatically a larger number of bands. You must set manually the
parameter nbnd in the  nscf calculations, and increase it until the
dielectric function is converged. Check specially the convergence of epsr.
nbnd determine the number of transitions (the peaks) observed in epsri. High
energy transitions contribute in shifting the low energy values of epsr, as
you can see looking at the Kramers-Kronig relations.

Best wishes
Eduardo


"
>
> Today's Topics:
>
>   1. Why dielectric function of only interband contribution has
>      the features of intraband? (gbliu)
>
>
> ---------- Mensaje reenviado ----------
> From: gbliu <goodluck_1982 at 163.com>
> To: PWSCF Forum <pw_forum at pwscf.org>
> Date: Wed, 13 Jul 2011 01:04:28 +0800
> Subject: [Pw_forum] Why dielectric function of only interband contribution
> has the features of intraband?
> **
> Dear PW users,
>
>     I calculated the dielectric function of (3,3) Carbon nanotube (CNT).
> However, the results for only interband contribution has the features of
> intraband contribution! Attached figures show the results of parallel
> polarization compared with wien2k (a FP-LAPW software). Using "intrasmear =
> 0", the direct result of epsi.dat should gives out only interband
> contributions, while epsr.dat is added by  "omega_p^2/omega^2" to get the
> interband contributions only.  And omega_p is obtained as *3.5679eV* by
> fitting the difference of data with intrasmear=0 and intrasmear=0.1 using
> Drude model  "\epsilon_{intra}=1- omega_p^2/(omega^2+i*omega*intrasmear)".
> How to understand this?
>
>     Another problem is, fitted omega_p = 3.5679eV. This is far from the
> result given by wien2k, 24.5eV!  Which one is more reasonable? And why?
>
>    Can anyone help me?  Thanks in advance!
>
> Best wishes,
>
> Liu Gui-Bin
> Dept. of Physics, The University of Hong Kong
>
> ---------------input file for epsilon.x----------
>  &inputpp
>    outdir='./work'
>    prefix='cnt33'
>    calculation='eps'
> /
> &energy_grid
>    smeartype='gauss'
>    intersmear=0.1d0
>    intrasmear=0d0
>    wmax=30d0
>    wmin=0d0
>    nw=2000
>    shift=0d0
> /
> ----------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de
su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su
grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

Translate from spanish here
http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en
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From eariel99 at gmail.com  Fri Jul 15 08:11:42 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Fri, 15 Jul 2011 02:11:42 -0400
Subject: [Pw_forum] Why dielectric function of only interband
 contribution has the features of intraband?
Message-ID: <CAM5Vcw-_1fU1wmcAsWuj4jUbtqkk8Xa9SAoKoU3TrY7F3VhCbw@mail.gmail.com>

Hi Gui-Bin

To avoid intraband contribution it is not enough to use intrasmear=0, you
also need to set occupations='fixed' in the PW calculations, at least for
the nscf one. The following reads in the manual of epsilon.

\emph{intrasmear} is the broadening parameter for the intraband, i.e. metal
Drude like term (again in eV),
the intraband contribution is calculated only if a Gaussian broadening or
tetrahedron method it's been
applied in PW calculations.


On the other hand, it seems from the epsi plot,  that the Wien calculation
considers automatically a larger number of bands. You must set manually the
parameter nbnd in the  nscf calculations, and increase it until the
dielectric function is converged. Check specially the convergence of epsr.
nbnd determine the number of transitions (the peaks) observed in epsri. High
energy transitions contribute in shifting the low energy values of epsr, as
you can see looking at the Kramers-Kronig relations.

Best wishes
Eduardo



>
> "
>>
>> Today's Topics:
>>
>>   1. Why dielectric function of only interband contribution has
>>      the features of intraband? (gbliu)
>>
>>
>> ---------- Mensaje reenviado ----------
>> From: gbliu <goodluck_1982 at 163.com>
>> To: PWSCF Forum <pw_forum at pwscf.org>
>> Date: Wed, 13 Jul 2011 01:04:28 +0800
>> Subject: [Pw_forum] Why dielectric function of only interband contribution
>> has the features of intraband?
>> **
>> Dear PW users,
>>
>>     I calculated the dielectric function of (3,3) Carbon nanotube (CNT).
>> However, the results for only interband contribution has the features of
>> intraband contribution! Attached figures show the results of parallel
>> polarization compared with wien2k (a FP-LAPW software). Using "intrasmear =
>> 0", the direct result of epsi.dat should gives out only interband
>> contributions, while epsr.dat is added by  "omega_p^2/omega^2" to get the
>> interband contributions only.  And omega_p is obtained as *3.5679eV* by
>> fitting the difference of data with intrasmear=0 and intrasmear=0.1 using
>> Drude model  "\epsilon_{intra}=1- omega_p^2/(omega^2+i*omega*intrasmear)".
>> How to understand this?
>>
>>     Another problem is, fitted omega_p = 3.5679eV. This is far from the
>> result given by wien2k, 24.5eV!  Which one is more reasonable? And why?
>>
>>    Can anyone help me?  Thanks in advance!
>>
>> Best wishes,
>>
>> Liu Gui-Bin
>> Dept. of Physics, The University of Hong Kong
>>
>> ---------------input file for epsilon.x----------
>>  &inputpp
>>    outdir='./work'
>>    prefix='cnt33'
>>    calculation='eps'
>> /
>> &energy_grid
>>    smeartype='gauss'
>>    intersmear=0.1d0
>>    intrasmear=0d0
>>    wmax=30d0
>>    wmin=0d0
>>    nw=2000
>>    shift=0d0
>> /
>> ----------------------------------------------------------
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>>
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
>
>
> Eduardo Menendez Proupin
> Departamento de Qu?mica Fisica Aplicada
> Facultad de Ciencias
> Universidad Aut?noma de Madrid
> Phone: +34 91 497 6706
>
> On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
> Chile URL: http://fisica.ciencias.uchile.cl/~emenendez
>
> "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
> padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
> pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
> que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
> mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
> grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
> inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
> reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de
> su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su
> grandeza, su m?xima medida en el Reino de este Mundo*".
> Alejo Carpentier, El reino de este mundo, (1949).
>
> Translate from spanish here
> http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en
>
>


-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de
su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su
grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

Translate from spanish here
http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en
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From guntram.schmidt at chemie.uni-halle.de  Fri Jul 15 12:14:42 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Fri, 15 Jul 2011 12:14:42 +0200
Subject: [Pw_forum] phonon_dos.x not created........
In-Reply-To: <47497475.15238.1312750f8a9.Coremail.flux_ray12@163.com>
References: <1310556129.14735.YahooMailClassic@web65412.mail.ac4.yahoo.com>
	<47497475.15238.1312750f8a9.Coremail.flux_ray12@163.com>
Message-ID: <4E201312.2030809@chemie.uni-halle.de>

Thanks a lot - this works!

Phonon_DOS/makefile:
.SUFFIXES: .f .o
FC = /usr/bin/gfortran-4.3 #ifort
LD = $(FC) #-static
DOS  = phonon_dos.x
TET  = tetra.x

#Linux
# FFLAGS = -O3 -ffast-math -fno-f2c

FFLAGS = -O3
....

Debye/makefile
.SUFFIXES: .f90 .f .o
FC = /usr/bin/gfortran-4.3
LD = $(FC) #-static
Debye_x = Debye.x

FFLAGS = -O3
...

SRC/makefile
.SUFFIXES: .f90 .o
FC = /usr/bin/gfortran-4.3
LD = $(FC) #-static
...

The only errors I get when compiling are:
----------------------------------
Debye.f90:144.9:

      do T = T_low_start, T_low, T_low_delta
         1
Warning: Deleted feature: Loop variable at (1) must be integer
---------------------------------
at different positions in different files.
Seems to work, nevertheless - but as I don't have the results to compare 
the results.

For the examples, don't forget to edit "Edit_Me" in every folder and add 
the ' :

     flfrc='$FC_file',

Good luck!


Am 14.07.2011 08:24, schrieb GAO Zhe:
> I compiled QHA in this way and successed. This is the biggining of
> makefile in my Phonon_DOS folder:
> .SUFFIXES: .f .o
> FC = mpif90#ifort
> LD = $(FC)#-static
> DOS = phonon_dos.x
> TET = tetra.x
> #Linux
> #FFLAGS = -O3 -ffast-math -fno-f2c
> FFLAGS = -O3
> OBJ1 = phonon_dos.o k_brillouin.o generate_tetra.o det3.o det4.o \
> Tetrahedra.o Integration.o
> .......
> --
> GAO Zhe
> CMC Lab, MSE, SNU, Seoul, S.Korea
>
> At 2011-07-13 19:22:09??"zafar rasheed" <zafartariq2003 at yahoo.com> wrote:
>
>
>
>
>         Dear Users
>         I want to use QHA for thermodynamic properties. I change fortran
>         compiler ifort to gfortran (fedora core 7)in makefiles of
>         Debay,Include,Phonon_Dos,SRC diretories . This change creates
>         all *.x files except Phonon_dos.x .
>         The process after compilation is as follows
>         ??
>         [root at localhost QHA]# ./Compile
>         gfortran -O3 -c tetra.f
>         gfortran -O3 -c k_brillouin.f
>         gfortran -O3 -c generate_tetra.f
>         In file generate_tetra.f:84
>         IF(S-.0001)3,3,1
>         1
>         Warning: Obsolete: arithmetic IF statement at (1)
>         gfortran -O3 -c det3.f
>         gfortran -O3 -c det4.f
>         gfortran -static -o tetra.x tetra.o k_brillouin.o
>         generate_tetra.o det3.o det4.o
>         gfortran -O3 -c phonon_dos.f
>         In file phonon_dos.f:122
>         open(unit=8,file='PHDOS.out',access='sequential',form='formatted'
>         1
>         Error: Syntax error in OPEN statement at (1)
>         make: *** [phonon_dos.o] Error 1
>         gfortran -O3 -c Debye.f90
>         In file Debye.f90:144
>         do T = T_low_start, T_low, T_low_delta
>         1
>         Warning: Obsolete: REAL DO loop iterator at (1)
>         In file Debye.f90:177
>         do T = T_low+5, T_high, T_high_delta
>         1
>         Warning: Obsolete: REAL DO loop iterator at (1)
>         gfortran -O3 -c Debye_T.f
>         gfortran -O3 -c debye3.f
>         gfortran -O3 -c cheval.f
>         gfortran -O3 -c d1mach.f
>         gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o
>         d1mach.o
>         gfortran -FR -c Mean_square_displacement.f90
>         In file Mean_square_displacement.f90:162
>         do T=T_start,T_end,T_delta
>         1
>         Warning: Obsolete: REAL DO loop iterator at (1)
>         gfortran -static -o Mean_square_displacement.x
>         Mean_square_displacement.o
>         gfortran -FR -c Atom_projected_properties.f90
>         In file Atom_projected_properties.f90:180
>         do T=T_start, T_end, T_delta
>         1
>         Warning: Obsolete: REAL DO loop iterator at (1)
>         gfortran -static -o Atom_projected_properties.x
>         Atom_projected_properties.o
>         gfortran -FR -c F_QHA.f90
>         In file F_QHA.f90:134
>         do T=T_start,T_end,T_delta
>         1
>         Warning: Obsolete: REAL DO loop iterator at (1)
>         gfortran -static -o F_QHA.x F_QHA.o
>         gfortran -FR -c Ghost_DOS.f90
>         gfortran -static -o Ghost_DOS.x Ghost_DOS.o
>         gfortran -FR -c Partial_phonon_DOS.f90
>         gfortran -static -o Partial_phonon_DOS.x Partial_phonon_DOS.o
>         gfortran -FR -c atom_info.f90
>         gfortran -static -o atom_info.x atom_info.o
>         ??
>
>         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

From bamideleibrahim at yahoo.com  Fri Jul 15 23:28:52 2011
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Fri, 15 Jul 2011 14:28:52 -0700 (PDT)
Subject: [Pw_forum] how to extract data from phonon calculation to plot
	phonon frequency dispersion curve
In-Reply-To: <1310652693.5776.YahooMailNeo@web65711.mail.ac4.yahoo.com>
Message-ID: <1310765332.55884.YahooMailClassic@web39423.mail.mud.yahoo.com>

Dear Prof. Eyvaz,
? Thanks for that information. I have obtain the necessary files but i don't understand how to use the PlotPhon. The PlotPhon is not part of the executable in the /bin. I tried to used plotband.x but i was asked to input the value of Efermi, which i have not calculated in my calculation. I will be very happy if you can enlightened me more on this.

Thanks,
Ibrahim? ? 

Adetunji Bamidele Ibrahim

Department of physics,University of Agriculture,

Abeokuta, Ogun State,Nigeria.

--- On Thu, 7/14/11, Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:

From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
Subject: Re: [Pw_forum] how to extract data from phonon calculation to plot phonon frequency dispersion curve
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Thursday, July 14, 2011, 7:11 AM

Hi,
In order to plot phonon dispersion relations you need interatomic force constants matrix, *.fc file. To get it you have to calculate dynamical matrices for a given number of q-points defined via (nq1 x nq2 x nq3) mesh, then perform FFT to get F(R) - the *.fc file (using q2r.x). Then you can use PlotPhon utility to plot phonon dispersion relations. 

Best regards,Eyvaz.? 
?-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
From: bamidele ibrahim <bamideleibrahim at yahoo.com>
To: pw_forum at pwscf.org
Sent: Thursday, July 14, 2011 5:44 PM
Subject: [Pw_forum] how to extract data from phonon calculation to plot phonon frequency dispersion curve

Dear all,
?I want to plot phonon dispersion frequency curve. i perform scf and phonon calculation at gamma point(0,0,0), where i have an output
 file .dynG. Inside this file, there? are some data which i think is to be use to plot the phonon frequency dispersion curve. but to extract these data is a problem. Can anybody help me out? Your assistance will be appreciated.
thanks,
ibrahim 

Adetunji Bamidele Ibrahim

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 scandolo at ictp.it  Sat Jul 16 00:17:08 2011
From: scandolo at ictp.it (Sandro Scandolo)
Date: Sat, 16 Jul 2011 00:17:08 +0200
Subject: [Pw_forum] bravais lattice of Cmca
In-Reply-To: <a516df3bfe4a39f8323c44eb34676492$5c6718fe@pcmail3.nate.com>
References: <a516df3bfe4a39f8323c44eb34676492$5c6718fe@pcmail3.nate.com>
Message-ID: <4E20BC64.2020506@ictp.it>

Hi,

> I calculate the Cmca(#64) structure.
> But I wonder which ibrav number is.
> This structure is orthorhombic.

it's base-centered orthorhombic, ibrav=9.

> I could check the other program.
> It is C-center based orthorhombic.
> Also, I got the atomic position.
> But I didn't get a correct result.
>

Notice that QE assumes that the centering occurs on the ab basal plane. 
Moreover if using "crystal" for the atomic positions, QE assumes that 
positions are expressed in terms of the primitive cell, not in terms of 
the conventional (orthorhombic) cell.

Sandro


-- 
Sandro Scandolo -- http:/www.ictp.it/~scandolo


From flux_ray12 at 163.com  Sat Jul 16 05:40:36 2011
From: flux_ray12 at 163.com (=?UTF-8?Q?GAO=C2=A0Zhe?=)
Date: Sat, 16 Jul 2011 11:40:36 +0800 (CST)
Subject: [Pw_forum] ph.x cannot reach convergence within 100 steps
Message-ID: <4fe46835.f662.13131080d5a.Coremail.flux_ray12@163.com>

Dear QE developer and users:
Recently, I am trying to calculate phonon dispersion via ph.x. However, in some cases, ph.x cannot reach convergence within 100 steps and stop automaticly.
I have tested the convergent lattice parameter, cut-off energy and k-points (M-P grid), and the thresholds of force and stress were also very low. Even if I increase the tr2_ph from 1.0d-12 (default) to 1.0d-10, the |ddv_scf|^2  values was around 10^(-6) or 10^(-7) magnitude. The problem usually occurred at the second q-point, but sometimes, even if lucky enough, it would definitely occur at the third q-point (4 q-points in 3x3x3 case).
Are there any methods to solve this problem? Any suggestion will be welcome.
Calculations were used GGA-PBE USPP.
This is my input file:
cat >W25.relax.in <<EOF
&control
     calculation = 'vc-relax' ,
     disk_io = 'low' ,
     prefix = 'W' ,
     outdir = '$TempDIR/' ,
     pseudo_dir = '$PseudoDIR/' ,
     etot_conv_thr = 1.0d-12 ,
     forc_conv_thr = 1.0d-4 ,
/
&system
     ibrav = 1 ,
     celldm(1) = ******* ,
     nat = ** ,
     ntyp = 3 ,
     nbnd = 100 ,
     ecutwfc = 47.5 ,
     ecutrho = 450 ,
     occupations = 'smearing' ,
     smearing = 'mp' ,
     degauss = 0.003 ,
/
&electrons
     conv_thr = 1.0d-12 ,
     startingpot = 'atomic' ,
     startingwfc = 'atomic+random' ,
     diagonalization = 'cg' ,
     electron_maxstep = 150 ,
/
&ions
     ion_dynamics = 'bfgs' ,
/
&cell
     cell_dynamics = 'bfgs' ,
     press_conv_thr = 0.01 ,
/
ATOMIC_SPECIES
  V   50.9415   V.pbe-n-van.UPF
  W   183.800   W.pbe-nsp-van.UPF
  C   12.0110   C.pbe-van_ak.UPF
ATOMIC_POSITIONS crystal
  V   0.50  0.50  0.00
...........
  C   0.50  0.50  0.50
K_POINTS automatic
13  13  13   0  0  0
EOF
echo -e "  Relaxing Structure...\c"
$MPIBIN/mpirun -n 6 pw.x -npool 2 <W.relax.in >W.relax.out
echo -e " DONE"

cat >W.ph.in <<EOF
Phonon Calculation
&inputph
     outdir = '$TempDIR/' ,
     prefix = 'W' ,
     ldisp = .true. ,
     nq1 = 3 ,
     nq2 = 3 ,
     nq3 = 3 ,
     tr2_ph = 1.0d-10 ,
     fildyn = 'W.dyn' ,
/
EOF
echo -e "  Calculating Dynamic Matrix...\c"
$MPIBIN/mpirun -n 6 ph.x -npool 2 <W.ph.in >W.ph.out
echo -e " DONE"



--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea
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From mehrnooshhazrati at gmail.com  Sat Jul 16 08:20:43 2011
From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati)
Date: Sat, 16 Jul 2011 10:50:43 +0430
Subject: [Pw_forum] simple question about plotband.x
In-Reply-To: <DUB110-W210F3DCD537449810ED909D3490@phx.gbl>
References: <DUB110-W210F3DCD537449810ED909D3490@phx.gbl>
Message-ID: <CAHbvuiSc_5QLiBjWQcOzGrF0w1QKS+k2ZMrgSDrD2Ntr4BkYVw@mail.gmail.com>

Dear Elias,

about your first question, i should say that the fermi energy can move the
limit of the energies you choose, so if you want to restrict the limit
between -2.1 and 2.1, you should sum min and max energy that you choose with
fermi energy (approximately).

I hope that it helps !

Regards
Mehrnoosh
On Fri, Jul 15, 2011 at 5:30 AM, Elie Moujaes <elie.moujaes at hotmail.co.uk>wrote:

>  Dear all,
>
> I am doing calculations on grain boundaries of graphene. When I use *
> plotband.x*  and restrict the limit of the energies between say -2.1 and
> 2.1 eV , The produced curve has limits between -2.7 and 1.8. Why is that the
> case? This is also affecting the graph in the sense that when I set the
> fermi energy as a reference , the dashed line at the zero is lower than the
> actual Fermi energy where bands intersect..See graph attached (in the graph
> the point 0.0 is lower than 0.3299 where the bands intersect). Howvere the
> general band structure is correct. How can I solve this problem
>
>
> Thanks
>
> Elias Moukaes
> University of Notts
> UK
> NG7 2RD
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
*

*
*
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
**** Mehrnoosh Kh. Hazrati ****
**** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
 *** Phone : +989123436300 ***
*** Mail : mehrnooshhazrati at gmail.com ***
*
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
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From eyvaz_isaev at yahoo.com  Sat Jul 16 10:39:40 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 16 Jul 2011 01:39:40 -0700 (PDT)
Subject: [Pw_forum] ph.x cannot reach convergence within 100 steps
In-Reply-To: <4fe46835.f662.13131080d5a.Coremail.flux_ray12@163.com>
References: <4fe46835.f662.13131080d5a.Coremail.flux_ray12@163.com>
Message-ID: <1310805580.13329.YahooMailNeo@web65711.mail.ac4.yahoo.com>

Hi, 


>Recently, I am trying to calculate phonon dispersion via ph.x. However, 
in some cases, ph.x cannot reach convergence within 100 steps and stop 
>automaticly.
?
1. You should? perform 'scf', not 'vc-relax' before phonon calculations.
2. You have a rather large system (nbnd=100), but used alpha_mix(1) by default (0.7). Try it around 0.1.
3. Try changing nmix_ph (by default 4).
4. If this does not help change 'maxter=100' in phcom.f90 and recompile.

Bests,
Eyvaz.


-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


________________________________
From: GAO?Zhe <flux_ray12 at 163.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Saturday, July 16, 2011 7:40 AM
Subject: [Pw_forum] ph.x cannot reach convergence within 100 steps


Dear QE developer and users:
Recently, I am trying to calculate phonon dispersion via ph.x. However, in some cases, ph.x cannot reach convergence within 100 steps and stop automaticly.
I have tested the convergent lattice parameter, cut-off energy and k-points (M-P grid), and the thresholds of force and stress were also very low. Even if I increase the tr2_ph from 1.0d-12 (default) to 1.0d-10, the |ddv_scf|^2? values was around 10^(-6) or 10^(-7) magnitude. The problem usually occurred at the second q-point, but sometimes, even if lucky enough, it would definitely occur at the third q-point (4 q-points in 3x3x3 case).
Are there any methods to solve this problem? Any suggestion will be welcome.
Calculations were used GGA-PBE USPP.
This is my input file:
cat >W25.relax.in <<EOF
&control
???? calculation = 'vc-relax' ,
???? disk_io = 'low' ,
???? prefix = 'W' ,
???? outdir = '$TempDIR/' ,
???? pseudo_dir = '$PseudoDIR/' ,
???? etot_conv_thr = 1.0d-12 ,
???? forc_conv_thr = 1.0d-4 ,
/
&system
???? ibrav = 1 ,
???? celldm(1) = ******* ,
???? nat = ** ,
???? ntyp = 3 ,
???? nbnd = 100 ,
???? ecutwfc = 47.5 ,
???? ecutrho = 450 ,
???? occupations = 'smearing' ,
???? smearing = 'mp' ,
???? degauss = 0.003 ,
/
&electrons
???? conv_thr = 1.0d-12 ,
???? startingpot = 'atomic' ,
???? startingwfc = 'atomic+random' ,
???? diagonalization = 'cg' ,
???? electron_maxstep = 150 ,
/
&ions
???? ion_dynamics = 'bfgs' ,
/
&cell
???? cell_dynamics = 'bfgs' ,
???? press_conv_thr = 0.01 ,
/
ATOMIC_SPECIES
? V?? 50.9415?? V.pbe-n-van.UPF
? W?? 183.800?? W.pbe-nsp-van.UPF
? C?? 12.0110?? C.pbe-van_ak.UPF
ATOMIC_POSITIONS crystal
? V?? 0.50? 0.50? 0.00
...........
? C?? 0.50? 0.50? 0.50
K_POINTS automatic
13? 13? 13?? 0? 0? 0
EOF
echo -e "? Relaxing Structure...\c"
$MPIBIN/mpirun -n 6 pw.x -npool 2 <W.relax.in >W.relax.out
echo -e " DONE"

cat >W.ph.in <<EOF
Phonon Calculation
&inputph
???? outdir = '$TempDIR/' ,
???? prefix = 'W' ,
???? ldisp = .true. ,
???? nq1 = 3 ,
???? nq2 = 3 ,
???? nq3 = 3 ,
???? tr2_ph = 1.0d-10 ,
???? fildyn = 'W.dyn' ,
/
EOF
echo -e "? Calculating Dynamic Matrix...\c"
$MPIBIN/mpirun -n 6 ph.x -npool 2 <W.ph.in >W.ph.out
echo -e " DONE"



--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea



_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From bamideleibrahim at yahoo.com  Sat Jul 16 15:37:23 2011
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Sat, 16 Jul 2011 06:37:23 -0700 (PDT)
Subject: [Pw_forum] can pwscf calculate temperature dependence of the
	vibrational contribution to the free energy?
Message-ID: <1310823443.28311.YahooMailClassic@web39423.mail.mud.yahoo.com>


Dear all,

? I am interested in studying the effect of temperature on the vibrational contribution to the free energy, enthalpy, heat capacity. So, i don't know if the pwscf can do this. I will appreciate an idea on how to do this if it is possible to do it will pwscf.

Thanks,
Ibrahim

Adetunji Bamidele Ibrahim

Department of physics,University of Agriculture,

Abeokuta, Ogun State,Nigeria.
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From eyvaz_isaev at yahoo.com  Sat Jul 16 19:38:23 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 16 Jul 2011 10:38:23 -0700 (PDT)
Subject: [Pw_forum] can pwscf calculate temperature dependence of the
	vibrational contribution to the free energy?
In-Reply-To: <1310823443.28311.YahooMailClassic@web39423.mail.mud.yahoo.com>
References: <1310823443.28311.YahooMailClassic@web39423.mail.mud.yahoo.com>
Message-ID: <1310837903.32420.YahooMailNeo@web65701.mail.ac4.yahoo.com>

All you need (and more)? is implemented in the QHA? code, see your QE package. The only limitation is the number of lattices, but hopefully this will be eliminated soon.
I am working on this problem. 


But you can not calculate temperature dependence of phonon frequencies using DFPT. It is another story.

As concerns basics you can read any textbook (for example, M. Dove, Introduction to lattice dynamics,? or Structure and dynamics: an atomic view of materials) 
or our recent paper: Baroni S, Giannozzi P, Isaev E (2010) Density-functional perturbation theory for quasi-harmonic calculations.
Rev Mineral Geochem 71:39-57

Bests,
Eyvaz.


-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


________________________________
From: bamidele ibrahim <bamideleibrahim at yahoo.com>
To: pw_forum at pwscf.org
Sent: Saturday, July 16, 2011 5:37 PM
Subject: [Pw_forum] can pwscf calculate temperature dependence of the vibrational contribution to the free energy?



Dear all,

? I am interested in studying the effect of temperature on the vibrational contribution to the free energy, enthalpy, heat capacity. So, i don't know if the pwscf can do this. I will appreciate an idea on how to do this if it is possible to do it will pwscf.

Thanks,
Ibrahim

Adetunji Bamidele Ibrahim
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 zhaohscas at yahoo.com.cn  Sun Jul 17 05:24:22 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Sun, 17 Jul 2011 11:24:22 +0800
Subject: [Pw_forum] Input file for  MgB2C2.
Message-ID: <4E2255E6.90609@yahoo.com.cn>

Hi all,

I obtain the xyz format crystal structure information for MgB2C2 - with 
the spacegroup of Cmca (#64) - from the following webpage:

http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos

The contents of this file is as follows:

------------
    102
Mg B_2 C_2 & Cmca D_{2h}^{18} #64 & oC80 & Worle&Nesper, J. 
Alloy&Compounds 216
C      2.73050000     5.42020690     5.59425000
B      2.73050000     8.56598940     5.59425000
B      2.73050000     3.83548940     5.59425000
C      2.73050000     0.68970690     5.59425000
Mg     1.67576250     9.46100000     0.00000000
Mg     0.00000000     6.81371760     0.08428670
B      8.19150000     8.56598940     5.59425000
B      0.00000000     8.62275540     5.78818400
C      8.19150000     5.42020690     5.59425000
C      8.19150000     0.68970690     5.59425000
C      0.00000000     8.71168880     1.72601260
Mg     1.67576250     9.46100000     7.45900000
B      0.00000000     3.89225540     5.40031600
B      1.39583160     6.23006850     5.64049580
B      1.39583160     7.96143150     1.91099580
B      1.39583160     1.49956850     5.54800420
C      1.35978900     7.80532500     5.79489710
C      1.35978900     6.38617500     2.06539710
C      1.35978900     3.07482500     5.39360290
B      5.46100000     8.62275540     5.40031600
B      6.85683160     6.23006850     5.54800420
C      6.82078900     7.80532500     5.39360290
Mg     1.67576250     0.00000000     0.00000000
Mg     1.67576250     4.73050000     3.72950000
Mg     0.00000000     2.08321760     3.64521330
Mg     0.00000000     7.37778240     3.81378670
B      2.73050000     0.89501060     1.86475000
B      8.19150000     3.83548940     5.59425000
B      2.73050000     5.62551060     1.86475000
B      0.00000000     5.56874460     2.05868400
B      1.39583160     3.23093150     1.81850420
C      2.73050000     8.77129310     1.86475000
C      0.00000000     5.47981120     5.45551260
C      0.00000000     3.98118880     2.00348740
C      1.35978900     1.65567500     1.66410290
Mg     1.67576250     0.00000000     7.45900000
Mg     0.00000000     2.64728240     7.37471330
C      0.00000000     0.74931120     5.73298740
Mg     7.13676250     4.73050000     0.00000000
Mg     3.78523750     4.73050000     0.00000000
Mg     3.78523750     9.46100000     3.72950000
Mg     7.13676250     9.46100000     3.72950000
Mg     5.46100000     6.81371760     3.64521330
Mg     5.46100000     2.08321760     0.08428670
B      8.19150000     5.62551060     1.86475000
B      5.46100000     3.89225540     5.78818400
B      6.85683160     7.96143150     1.81850420
B      4.06516840     6.23006850     5.54800420
B      4.06516840     7.96143150     1.81850420
C      5.46100000     3.98118880     1.72601260
C      5.46100000     8.71168880     2.00348740
C      6.82078900     6.38617500     1.66410290
C      4.10121100     7.80532500     5.39360290
C      4.10121100     6.38617500     1.66410290
Mg     7.13676250     4.73050000     7.45900000
Mg     3.78523750     4.73050000     7.45900000
Mg     5.46100000     7.37778240     7.37471330
B      6.85683160     1.49956850     5.64049580
B      4.06516840     1.49956850     5.64049580
B      6.85683160     3.23093150     1.91099580
C      5.46100000     5.47981120     5.73298740
C      6.82078900     3.07482500     5.79489710
C      4.10121100     3.07482500     5.79489710
C      6.82078900     1.65567500     2.06539710
Mg     9.24623750     9.46100000     0.00000000
Mg    10.92200000     6.81371760     0.08428670
B     10.92200000     8.62275540     5.78818400
C     10.92200000     8.71168880     1.72601260
Mg     9.24623750     9.46100000     7.45900000
B     10.92200000     3.89225540     5.40031600
B      9.52616840     6.23006850     5.64049580
C      9.56221100     7.80532500     5.79489710
B      0.00000000     0.83824460     1.67081600
C      2.73050000     4.04079310     1.86475000
Mg     3.78523750     0.00000000     3.72950000
Mg     7.13676250     0.00000000     3.72950000
Mg     5.46100000     2.64728240     3.81378670
B      8.19150000     0.89501060     1.86475000
B      5.46100000     0.83824460     2.05868400
B      5.46100000     5.56874460     1.67081600
B      4.06516840     3.23093150     1.91099580
C      8.19150000     4.04079310     1.86475000
C      8.19150000     8.77129310     1.86475000
C      5.46100000     0.74931120     5.45551260
C      4.10121100     1.65567500     2.06539710
Mg     9.24623750     0.00000000     0.00000000
Mg     9.24623750     4.73050000     3.72950000
Mg    10.92200000     2.08321760     3.64521330
Mg    10.92200000     7.37778240     3.81378670
B     10.92200000     5.56874460     2.05868400
B      9.52616840     1.49956850     5.54800420
B      9.52616840     7.96143150     1.91099580
B      9.52616840     3.23093150     1.81850420
C     10.92200000     5.47981120     5.45551260
C     10.92200000     3.98118880     2.00348740
C      9.56221100     3.07482500     5.39360290
C      9.56221100     6.38617500     2.06539710
C      9.56221100     1.65567500     1.66410290
Mg     9.24623750     0.00000000     7.45900000
Mg    10.92200000     2.64728240     7.37471330
C     10.92200000     0.74931120     5.73298740
B     10.92200000     0.83824460     1.67081600


****************************************


Primitive vectors
a(1) =   5.46100000 -4.73050000  0.00000000
a(2) =   5.46100000  4.73050000  0.00000000
a(3) =   0.00000000  0.00000000  7.45900000


Volume = 385.38058014


Reciprocal vectors
b(1) =   0.09155832 -0.10569707  0.00000000
b(2) =   0.09155832  0.10569707  0.00000000
b(3) =   0.00000000  0.00000000  0.13406623


Basis Vectors:
Atom    Lattice Coordinates                Cartesian Coordinates

Mg  0.15343000  0.15343000  0.00000000     1.67576250  0.00000000 0.00000000
Mg -0.15343000 -0.15343000  0.00000000    -1.67576250  0.00000000 0.00000000
Mg -0.65343000  0.34657000  0.50000000    -1.67576250  4.73050000 3.72950000
Mg -0.34657000  0.65343000  0.50000000     1.67576250  4.73050000 3.72950000
Mg -0.27981000  0.27981000 -0.01130000     0.00000000  2.64728240 
-0.08428670
Mg -0.22019000  0.22019000  0.48870000     0.00000000  2.08321760 3.64521330
Mg -0.77981000  0.77981000  0.51130000     0.00000000  7.37778240 3.81378670
Mg  0.27981000 -0.27981000  0.01130000     0.00000000 -2.64728240 0.08428670
B   0.15540000  0.34460000  0.25000000     2.73050000  0.89501060 1.86475000
B   0.34460000  1.15540000  0.75000000     8.19150000  3.83548940 5.59425000
B   0.84460000  0.65540000  0.75000000     8.19150000 -0.89501060 5.59425000
B  -0.34460000  0.84460000  0.25000000     2.73050000  5.62551060 1.86475000
B  -0.58860000  0.58860000  0.27600000     0.00000000  5.56874460 2.05868400
B   0.08860000 -0.08860000  0.77600000     0.00000000 -0.83824460 5.78818400
B  -1.08860000  1.08860000  0.22400000     0.00000000 10.29924460 1.67081600
B   0.58860000 -0.58860000 -0.27600000     0.00000000 -5.56874460 
-2.05868400
B  -0.21370000  0.46930000  0.24380000     1.39583160  3.23093150 1.81850420
B  -0.28630000  0.03070000  0.74380000    -1.39583160  1.49956850 5.54800420
B  -0.96930000  0.71370000  0.25620000    -1.39583160  7.96143150 1.91099580
B   0.46930000 -0.21370000 -0.24380000     1.39583160 -3.23093150 
-1.81850420
B   0.21370000 -0.46930000 -0.24380000    -1.39583160 -3.23093150 
-1.81850420
B   0.28630000 -0.03070000 -0.74380000     1.39583160 -1.49956850 
-5.54800420
B   0.96930000 -0.71370000 -0.25620000     1.39583160 -7.96143150 
-1.91099580
B  -0.46930000  0.21370000  0.24380000    -1.39583160  3.23093150 1.81850420
C  -0.67710000  1.17710000  0.25000000     2.73050000  8.77129310 1.86475000
C   1.17710000  0.32290000  0.75000000     8.19150000 -4.04079310 5.59425000
C   1.67710000 -0.17710000  0.75000000     8.19150000 -8.77129310 5.59425000
C  -1.17710000  1.67710000  0.25000000     2.73050000 13.50179310 1.86475000
C   0.07920000 -0.07920000  0.23140000     0.00000000 -0.74931120 1.72601260
C  -0.57920000  0.57920000  0.73140000     0.00000000  5.47981120 5.45551260
C  -0.42080000  0.42080000  0.26860000     0.00000000  3.98118880 2.00348740
C  -0.07920000  0.07920000 -0.23140000     0.00000000  0.74931120 
-1.72601260
C  -0.05050000  0.29950000  0.22310000     1.35978900  1.65567500 1.66410290
C  -0.44950000  0.20050000  0.72310000    -1.35978900  3.07482500 5.39360290
C  -0.79950000  0.55050000  0.27690000    -1.35978900  6.38617500 2.06539710
C   0.29950000 -0.05050000 -0.22310000     1.35978900 -1.65567500 
-1.66410290
C   0.05050000 -0.29950000 -0.22310000    -1.35978900 -1.65567500 
-1.66410290
C   0.44950000 -0.20050000 -0.72310000     1.35978900 -3.07482500 
-5.39360290
C   0.79950000 -0.55050000 -0.27690000     1.35978900 -6.38617500 
-2.06539710
C  -0.29950000  0.05050000  0.22310000    -1.35978900  1.65567500 1.66410290
------------

I want to construct the corresponding crystal structure information for 
pwscf based on the above content.  Any hints?

Regards
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China


From eyvaz_isaev at yahoo.com  Sun Jul 17 08:38:07 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 16 Jul 2011 23:38:07 -0700 (PDT)
Subject: [Pw_forum] Input file for  MgB2C2.
In-Reply-To: <4E2255E6.90609@yahoo.com.cn>
References: <4E2255E6.90609@yahoo.com.cn>
Message-ID: <1310884687.65570.YahooMailNeo@web65705.mail.ac4.yahoo.com>


> I want to construct the corresponding crystal structure information for 
> pwscf based on the above content.? Any hints?

You have all the information to build the crystal structure. Please read carefully the page info. 


Bests,
Eyvaz.

?
-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


________________________________
From: Hongsheng Zhao <zhaohscas at yahoo.com.cn>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Sunday, July 17, 2011 7:24 AM
Subject: [Pw_forum] Input file for  MgB2C2.

Hi all,

I obtain the xyz format crystal structure information for MgB2C2 - with 
the spacegroup of Cmca (#64) - from the following webpage:

http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos

?

I want to construct the corresponding crystal structure information for 
pwscf based on the above content.? Any hints?

Regards
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

_______________________________________________
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 17 08:48:25 2011
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Sat, 16 Jul 2011 23:48:25 -0700 (PDT)
Subject: [Pw_forum] Request for gfortran4.3
Message-ID: <1310885305.12868.YahooMailClassic@web65408.mail.ac4.yahoo.com>


?
Dear All
I need gfortran 4.3 compiler. I try it from gnu site but due to server problem at my end I cannot download it. ?Will any body send it to me? I am using fedora core 07 (Fedora core 7 uses gfortran-4.1).
Best regards

?

Muhammad Zafar
PhD Scholar
Department of Physics
The Islamia University of Bahawalpur,Pakistan
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From flux_ray12 at 163.com  Sun Jul 17 09:27:24 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Sun, 17 Jul 2011 15:27:24 +0800 (CST)
Subject: [Pw_forum] Request for gfortran4.3
In-Reply-To: <1310885305.12868.YahooMailClassic@web65408.mail.ac4.yahoo.com>
References: <1310885305.12868.YahooMailClassic@web65408.mail.ac4.yahoo.com>
Message-ID: <79bab2b8.2b94.13136fe0ef9.Coremail.flux_ray12@163.com>

You can try RPM package, too, since you are using Red Hat based Linux. However, I am not sure whether you can use a higher version of gcc because of your old OS version.
You may try to download RPMs here: http://rpmfind.net/linux/rpm2html/search.php?query=gcc-gfortran, or google it for a better speed of downloading

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-17 14:48:25?"zafar rasheed" <zafartariq2003 at yahoo.com> wrote:


 

Dear All

I need gfortran 4.3 compiler. I try it from gnu site but due to server problem at my end I cannot download it. Will any body send it to me? I am using fedora core 07 (Fedora core 7 uses gfortran-4.1).

Best regards

 

Muhammad Zafar
PhD Scholar
Department of Physics
The Islamia University of Bahawalpur,Pakistan
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From flux_ray12 at 163.com  Sun Jul 17 09:33:56 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Sun, 17 Jul 2011 15:33:56 +0800 (CST)
Subject: [Pw_forum] ph.x cannot reach convergence within 100 steps
In-Reply-To: <1310805580.13329.YahooMailNeo@web65711.mail.ac4.yahoo.com>
References: <1310805580.13329.YahooMailNeo@web65711.mail.ac4.yahoo.com>
	<4fe46835.f662.13131080d5a.Coremail.flux_ray12@163.com>
Message-ID: <7c36558a.2c24.13137040a7b.Coremail.flux_ray12@163.com>

Thank you very much, Prof. Isaev.
I tried all of 'scf', 'relax' and 'vc-relax' before ph.x, but got the same problem in each case~
I was not sure whether this problem caused by empty-band number, so I increase nbnd. It may too large for my model~ Now, I am trying to change the values of alpha_mix(1) and nmix_ph for a better convergent.
Thank you, again ^_^

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-16 16:39:40?"Eyvaz Isaev" <eyvaz_isaev at yahoo.com> wrote:

Hi,



>Recently, I am trying to calculate phonon dispersion via ph.x. However, in some cases, ph.x cannot reach convergence within 100 steps and stop >automaticly.
 
1. You should  perform 'scf', not 'vc-relax' before phonon calculations.
2. You have a rather large system (nbnd=100), but used alpha_mix(1) by default (0.7). Try it around 0.1.
3. Try changing nmix_ph (by default 4).
4. If this does not help change 'maxter=100' in phcom.f90 and recompile.

Bests,
Eyvaz.


-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
isaev at ifm.liu.se,eyvaz_isaev at yahoo.com

From: GAO Zhe <flux_ray12 at 163.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Saturday, July 16, 2011 7:40 AM
Subject: [Pw_forum] ph.x cannot reach convergence within 100 steps


Dear QE developer and users:
Recently, I am trying to calculate phonon dispersion via ph.x. However, in some cases, ph.x cannot reach convergence within 100 steps and stop automaticly.
I have tested the convergent lattice parameter, cut-off energy and k-points (M-P grid), and the thresholds of force and stress were also very low. Even if I increase the tr2_ph from 1.0d-12 (default) to 1.0d-10, the |ddv_scf|^2  values was around 10^(-6) or 10^(-7) magnitude. The problem usually occurred at the second q-point, but sometimes, even if lucky enough, it would definitely occur at the third q-point (4 q-points in 3x3x3 case).
Are there any methods to solve this problem? Any suggestion will be welcome.
Calculations were used GGA-PBE USPP.
This is my input file:
cat >W25.relax.in <<EOF
&control
     calculation = 'vc-relax' ,
     disk_io = 'low' ,
     prefix = 'W' ,
     outdir = '$TempDIR/' ,
     pseudo_dir = '$PseudoDIR/' ,
     etot_conv_thr = 1.0d-12 ,
     forc_conv_thr = 1.0d-4 ,
/
&system
     ibrav = 1 ,
     celldm(1) = ******* ,
     nat = ** ,
     ntyp = 3 ,
     nbnd = 100 ,
     ecutwfc = 47.5 ,
     ecutrho = 450 ,
     occupations = 'smearing' ,
     smearing = 'mp' ,
     degauss = 0.003 ,
/
&electrons
     conv_thr = 1.0d-12 ,
     startingpot = 'atomic' ,
     startingwfc = 'atomic+random' ,
     diagonalization = 'cg' ,
     electron_maxstep = 150 ,
/
&ions
     ion_dynamics = 'bfgs' ,
/
&cell
     cell_dynamics = 'bfgs' ,
     press_conv_thr = 0.01 ,
/
ATOMIC_SPECIES
  V   50.9415   V.pbe-n-van.UPF
  W   183.800   W.pbe-nsp-van.UPF
  C   12.0110   C.pbe-van_ak.UPF
ATOMIC_POSITIONS crystal
  V   0.50  0.50  0.00
...........
  C   0.50  0.50  0.50
K_POINTS automatic
13  13  13   0  0  0
EOF
echo -e "  Relaxing Structure...\c"
$MPIBIN/mpirun -n 6 pw.x -npool 2 <W.relax.in >W.relax.out
echo -e " DONE"

cat >W.ph.in <<EOF
Phonon Calculation
&inputph
     outdir = '$TempDIR/' ,
     prefix = 'W' ,
     ldisp = .true. ,
     nq1 = 3 ,
     nq2 = 3 ,
     nq3 = 3 ,
     tr2_ph = 1.0d-10 ,
     fildyn = 'W.dyn' ,
/
EOF
echo -e "  Calculating Dynamic Matrix...\c"
$MPIBIN/mpirun -n 6 ph.x -npool 2 <W.ph.in >W.ph.out
echo -e " DONE"



--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea





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

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From flux_ray12 at 163.com  Sun Jul 17 09:36:11 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Sun, 17 Jul 2011 15:36:11 +0800 (CST)
Subject: [Pw_forum] can pwscf calculate temperature dependence of the
 vibrational contribution to the free energy?
In-Reply-To: <1310823443.28311.YahooMailClassic@web39423.mail.mud.yahoo.com>
References: <1310823443.28311.YahooMailClassic@web39423.mail.mud.yahoo.com>
Message-ID: <1002c8d1.2c6c.13137061621.Coremail.flux_ray12@163.com>

Phonon calculation (ph.x, q2r.x, matdyn.x in PH folder) + QHA method~

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-16 21:37:23?"bamidele ibrahim" <bamideleibrahim at yahoo.com> wrote:


Dear all,

  I am interested in studying the effect of temperature on the vibrational contribution to the free energy, enthalpy, heat capacity. So, i don't know if the pwscf can do this. I will appreciate an idea on how to do this if it is possible to do it will pwscf.

Thanks,
Ibrahim

Adetunji Bamidele Ibrahim
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.
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From eyvaz_isaev at yahoo.com  Sun Jul 17 09:39:13 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sun, 17 Jul 2011 00:39:13 -0700 (PDT)
Subject: [Pw_forum] ph.x cannot reach convergence within 100 steps
In-Reply-To: <7c36558a.2c24.13137040a7b.Coremail.flux_ray12@163.com>
References: <1310805580.13329.YahooMailNeo@web65711.mail.ac4.yahoo.com>
	<4fe46835.f662.13131080d5a.Coremail.flux_ray12@163.com>
	<7c36558a.2c24.13137040a7b.Coremail.flux_ray12@163.com>
Message-ID: <1310888353.20005.YahooMailNeo@web65703.mail.ac4.yahoo.com>

> I was not sure whether this problem caused by empty-band number, so I increase nbnd.
?
You should increase nbnd if you see "too few bands" message? in *.ph.out file. 

Bests,
Eyvaz. 
?

?


________________________________
From: GAO Zhe <flux_ray12 at 163.com>
To: Eyvaz Isaev <eyvaz_isaev at yahoo.com>; PWSCF Forum <pw_forum at pwscf.org>
Sent: Sunday, July 17, 2011 11:33 AM
Subject: Re: [Pw_forum] ph.x cannot reach convergence within 100 steps


Thank you very much, Prof. Isaev.
I tried all of 'scf', 'relax' and 'vc-relax' before ph.x, but got the same problem in each case~
I was not sure whether this problem caused by empty-band number, so I increase nbnd. It may too large for my model~ Now, I am trying to change the values of alpha_mix(1) and nmix_ph for a better convergent.
Thank you, again ^_^

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea

At 2011-07-16 16:39:40?"Eyvaz?Isaev"?<eyvaz_isaev at yahoo.com> wrote:

Hi, 
>
>
>
>>Recently, I am trying to calculate phonon dispersion via ph.x. However, 
in some cases, ph.x cannot reach convergence within 100 steps and stop 
>automaticly.
>?
>1. You should? perform 'scf', not 'vc-relax' before phonon calculations.
>2. You have a rather large system (nbnd=100), but used alpha_mix(1) by default (0.7). Try it around 0.1.
>3. Try changing nmix_ph (by default 4).
>4. If this does not help change 'maxter=100' in phcom.f90 and recompile.
>
>Bests,
>Eyvaz.
>
>
>-------------------------------------------------------------------
>Prof. Eyvaz Isaev, 
>Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
>Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
>isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
>________________________________
>From: GAO?Zhe <flux_ray12 at 163.com>
>To: PWSCF Forum <pw_forum at pwscf.org>
>Sent: Saturday, July 16, 2011 7:40 AM
>Subject: [Pw_forum] ph.x cannot reach convergence within 100 steps
>
>
>Dear QE developer and users:
>Recently, I am trying to calculate phonon dispersion via ph.x. However, in some cases, ph.x cannot reach convergence within 100 steps and stop automaticly.
>I have tested the convergent lattice parameter, cut-off energy and k-points (M-P grid), and the thresholds of force and stress were also very low. Even if I increase the tr2_ph from 1.0d-12 (default) to 1.0d-10, the |ddv_scf|^2? values was around 10^(-6) or 10^(-7) magnitude. The problem usually occurred at the second q-point, but sometimes, even if lucky enough, it would definitely occur at
 the third q-point (4 q-points in 3x3x3 case).
>Are there any methods to solve this problem? Any suggestion will be welcome.
>Calculations were used GGA-PBE USPP.
>This is my input file:
>cat >W25.relax.in <<EOF
>&control
>???? calculation = 'vc-relax' ,
>???? disk_io = 'low' ,
>???? prefix = 'W' ,
>???? outdir = '$TempDIR/' ,
>???? pseudo_dir = '$PseudoDIR/' ,
>???? etot_conv_thr = 1.0d-12 ,
>???? forc_conv_thr = 1.0d-4 ,
>/
>&system
>???? ibrav = 1 ,
>???? celldm(1) = ******* ,
>???? nat = ** ,
>???? ntyp = 3 ,
>???? nbnd = 100 ,
>???? ecutwfc = 47.5 ,
>???? ecutrho = 450 ,
>???? occupations =
 'smearing' ,
>???? smearing = 'mp' ,
>???? degauss = 0.003 ,
>/
>&electrons
>???? conv_thr = 1.0d-12 ,
>???? startingpot = 'atomic' ,
>???? startingwfc = 'atomic+random' ,
>???? diagonalization = 'cg' ,
>???? electron_maxstep = 150 ,
>/
>&ions
>???? ion_dynamics = 'bfgs' ,
>/
>&cell
>???? cell_dynamics = 'bfgs' ,
>???? press_conv_thr = 0.01 ,
>/
>ATOMIC_SPECIES
>? V?? 50.9415?? V.pbe-n-van.UPF
>? W?? 183.800?? W.pbe-nsp-van.UPF
>? C?? 12.0110?? C.pbe-van_ak.UPF
>ATOMIC_POSITIONS crystal
>? V?? 0.50? 0.50? 0.00
>...........
>? C?? 0.50? 0.50? 0.50
>K_POINTS
 automatic
>13? 13? 13?? 0? 0? 0
>EOF
>echo -e "? Relaxing Structure...\c"
>$MPIBIN/mpirun -n 6 pw.x -npool 2 <W.relax.in >W.relax.out
>echo -e " DONE"
>
>cat >W.ph.in <<EOF
>Phonon Calculation
>&inputph
>???? outdir = '$TempDIR/' ,
>???? prefix = 'W' ,
>???? ldisp = .true. ,
>???? nq1 = 3 ,
>???? nq2 = 3 ,
>???? nq3 = 3 ,
>???? tr2_ph = 1.0d-10 ,
>???? fildyn = 'W.dyn' ,
>/
>EOF
>echo -e "? Calculating Dynamic Matrix...\c"
>$MPIBIN/mpirun -n 6 ph.x -npool 2 <W.ph.in >W.ph.out
>echo -e " DONE"
>
>
>
>--
>GAO Zhe
>CMC Lab, MSE, SNU, Seoul, S.Korea
>
>
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>


_______________________________________________
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From zhaohscas at yahoo.com.cn  Sun Jul 17 09:54:23 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Sun, 17 Jul 2011 15:54:23 +0800
Subject: [Pw_forum] Input file for  MgB2C2.
In-Reply-To: <1310884687.65570.YahooMailNeo@web65705.mail.ac4.yahoo.com>
References: <4E2255E6.90609@yahoo.com.cn>
	<1310884687.65570.YahooMailNeo@web65705.mail.ac4.yahoo.com>
Message-ID: <4E22952F.6000207@yahoo.com.cn>

On 07/17/2011 02:38 PM, Eyvaz Isaev wrote:
>
>  > I want to construct the corresponding crystal structure information for
>  > pwscf based on the above content. Any hints?
>
> You have all the information to build the crystal structure. Please read
> carefully the page info.

I've some puzzles on which are the lattice vectors should be used for 
this case.  In detail, you can find the following information from the 
webpage: http://cst-www.nrl.navy.mil/lattice/struk/mgb2c2.html

-----------------
   Primitive Vectors:
A1 	 =  	? a X - ? b Y
A2 	 =  	? a X + ? b Y
A3 	 =  	c Z
---------------------

On the other hand, you can find the following information from within 
the mgb2c2.pos file downloaded from here: 
http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos:

--------------
Primitive vectors
a(1) =   5.46100000 -4.73050000  0.00000000
a(2) =   5.46100000  4.73050000  0.00000000
a(3) =   0.00000000  0.00000000  7.45900000
--------------

So in this case, what's the lattice vectors should I used to construct 
the unit cell, i.e., the [a(1),a(2), a(3)] or the [a,b,c] should be used?

Furthermore, you can find fourty basis vectors listed for MgB2C2 on the 
webpage: http://cst-www.nrl.navy.mil/lattice/struk/mgb2c2.html.  What's 
the usage of these basis vectors?

Regards
>
> Bests,
> Eyvaz.
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping
> University, Sweden
> Theoretical Physics Department, Moscow State Institute of Steel &
> Alloys, Russia,
> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
> ------------------------------------------------------------------------
> *From:* Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> *To:* PWSCF Forum <pw_forum at pwscf.org>
> *Sent:* Sunday, July 17, 2011 7:24 AM
> *Subject:* [Pw_forum] Input file for MgB2C2.
>
> Hi all,
>
> I obtain the xyz format crystal structure information for MgB2C2 - with
> the spacegroup of Cmca (#64) - from the following webpage:
>
> http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos
>
>
>
> I want to construct the corresponding crystal structure information for
> pwscf based on the above content. Any hints?
>
> Regards
> --
> Hongsheng Zhao <zhaohscas at yahoo.com.cn <mailto:zhaohscas at yahoo.com.cn>>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
>
> _______________________________________________
> 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


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From eyvaz_isaev at yahoo.com  Sun Jul 17 10:19:00 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sun, 17 Jul 2011 01:19:00 -0700 (PDT)
Subject: [Pw_forum] Input file for  MgB2C2.
In-Reply-To: <4E22952F.6000207@yahoo.com.cn>
References: <4E2255E6.90609@yahoo.com.cn>
	<1310884687.65570.YahooMailNeo@web65705.mail.ac4.yahoo.com>
	<4E22952F.6000207@yahoo.com.cn>
Message-ID: <1310890740.25256.YahooMailNeo@web65712.mail.ac4.yahoo.com>

You have all the info. Please take your decision for which nobody should be responsible.
Analyze the data you have, it is a very good way to learn the code and basics. Read INPUT_PW.txt,? it is very useful. 


Bests,
Eyvaz. 

?

________________________________
From: Hongsheng Zhao <zhaohscas at yahoo.com.cn>
To: pw_forum at pwscf.org
Sent: Sunday, July 17, 2011 11:54 AM
Subject: Re: [Pw_forum] Input file for  MgB2C2.

On 07/17/2011 02:38 PM, Eyvaz Isaev wrote:
>
>? > I want to construct the corresponding crystal structure information for
>? > pwscf based on the above content. Any hints?
>
> You have all the information to build the crystal structure. Please read
> carefully the page info.

I've some puzzles on which are the lattice vectors should be used for 
this case.? In detail, you can find the following information from the 
webpage: http://cst-www.nrl.navy.mil/lattice/struk/mgb2c2.html

-----------------
?  Primitive Vectors:
A1 ???  =? ??? ? a X - ? b Y
A2 ???  =? ??? ? a X + ? b Y
A3 ???  =? ??? c Z
---------------------

On the other hand, you can find the following information from within 
the mgb2c2.pos file downloaded from here: 
http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos:

--------------
Primitive vectors
a(1) =?  5.46100000 -4.73050000? 0.00000000
a(2) =?  5.46100000? 4.73050000? 0.00000000
a(3) =?  0.00000000? 0.00000000? 7.45900000
--------------

So in this case, what's the lattice vectors should I used to construct 
the unit cell, i.e., the [a(1),a(2), a(3)] or the [a,b,c] should be used?

Furthermore, you can find fourty basis vectors listed for MgB2C2 on the 
webpage: http://cst-www.nrl.navy.mil/lattice/struk/mgb2c2.html.? What's 
the usage of these basis vectors?

Regards
>
> Bests,
> Eyvaz.
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping
> University, Sweden
> Theoretical Physics Department, Moscow State Institute of Steel &
> Alloys, Russia,
> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
> ------------------------------------------------------------------------
> *From:* Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> *To:* PWSCF Forum <pw_forum at pwscf.org>
> *Sent:* Sunday, July 17, 2011 7:24 AM
> *Subject:* [Pw_forum] Input file for MgB2C2.
>
> Hi all,
>
> I obtain the xyz format crystal structure information for MgB2C2 - with
> the spacegroup of Cmca (#64) - from the following webpage:
>
> http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos
>
>
>
> I want to construct the corresponding crystal structure information for
> pwscf based on the above content. Any hints?
>
> Regards
> --
> Hongsheng Zhao <zhaohscas at yahoo.com.cn <mailto:zhaohscas at yahoo.com.cn>>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
>
> _______________________________________________
> 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


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China
_______________________________________________
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  Sun Jul 17 10:30:11 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Sun, 17 Jul 2011 16:30:11 +0800 (CST)
Subject: [Pw_forum] Input file for  MgB2C2.
In-Reply-To: <4E22952F.6000207@yahoo.com.cn>
References: <4E22952F.6000207@yahoo.com.cn> <4E2255E6.90609@yahoo.com.cn>
	<1310884687.65570.YahooMailNeo@web65705.mail.ac4.yahoo.com>
Message-ID: <a71c5fc.31f8.1313737865f.Coremail.flux_ray12@163.com>

Or, you can use the structrue information like below, after all, it may be easier for you when you do not have or do not want to have crystallography knowledge:
Coll Code   79587
Rec  Date   1996/10/14
Chem Name   Magnesium Boride Carbide (1/2/2)
Structured  Mg B2 C2
Sum         C2 B2 Mg1
Title       Mg B2 C2, a new graphite-related refractory compound
Author(s)   Woerle, M.;Nesper, R.
Reference   Journal of Alloys Compd.
            (1994), 216, 75-83
Unit Cell   10.922(2) 9.461(2) 7.459(1) 90. 90. 90.
Vol         770.76
Z           16
Space Group C m c a
SG Number   64
Cryst Sys   orthorhombic
Atom  #   OX   SITE      x           y           z           SOF      H
 Mg   1  +0    8 d   0.15343(6)  0           0              1.         0   
 Mg   2  +0    8 f   0           0.27981(6)  -.0113(1)      1.         0   
 B    1  +0    8 e   0.25        0.0946(2)   0.25           1.         0   
 B    2  +0    8 f   0           0.5886(2)   0.2760(3)      1.         0   
 B    3  +0    16 g  0.1278(2)   0.3415(1)   0.2438(2)      1.         0   
 C    1  +0    8 e   0.25        0.9271(2)   0.25           1.         0   
 C    2  +0    8 f   0           -.0792(2)   0.2314(2)      1.         0   
 C    3  +0    16 g  0.1245(2)   0.1750(1)   0.2231(1)      1.         0   

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea




At 2011-07-17 15:54:23?"Hongsheng Zhao" <zhaohscas at yahoo.com.cn> wrote:

>On 07/17/2011 02:38 PM, Eyvaz Isaev wrote:
>>
>>  > I want to construct the corresponding crystal structure information for
>>  > pwscf based on the above content. Any hints?
>>
>> You have all the information to build the crystal structure. Please read
>> carefully the page info.
>
>I've some puzzles on which are the lattice vectors should be used for 
>this case.  In detail, you can find the following information from the 
>webpage: http://cst-www.nrl.navy.mil/lattice/struk/mgb2c2.html
>
>-----------------
>   Primitive Vectors:
>A1 	 =  	? a X - ? b Y
>A2 	 =  	? a X + ? b Y
>A3 	 =  	c Z
>---------------------
>
>On the other hand, you can find the following information from within 
>the mgb2c2.pos file downloaded from here: 
>http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos:
>
>--------------
>Primitive vectors
>a(1) =   5.46100000 -4.73050000  0.00000000
>a(2) =   5.46100000  4.73050000  0.00000000
>a(3) =   0.00000000  0.00000000  7.45900000
>--------------
>
>So in this case, what's the lattice vectors should I used to construct 
>the unit cell, i.e., the [a(1),a(2), a(3)] or the [a,b,c] should be used?
>
>Furthermore, you can find fourty basis vectors listed for MgB2C2 on the 
>webpage: http://cst-www.nrl.navy.mil/lattice/struk/mgb2c2.html.  What's 
>the usage of these basis vectors?
>
>Regards
>>
>> Bests,
>> Eyvaz.
>> -------------------------------------------------------------------
>> Prof. Eyvaz Isaev,
>> Department of Physics, Chemistry, and Biology (IFM), Linkoping
>> University, Sweden
>> Theoretical Physics Department, Moscow State Institute of Steel &
>> Alloys, Russia,
>> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>> ------------------------------------------------------------------------
>> *From:* Hongsheng Zhao <zhaohscas at yahoo.com.cn>
>> *To:* PWSCF Forum <pw_forum at pwscf.org>
>> *Sent:* Sunday, July 17, 2011 7:24 AM
>> *Subject:* [Pw_forum] Input file for MgB2C2.
>>
>> Hi all,
>>
>> I obtain the xyz format crystal structure information for MgB2C2 - with
>> the spacegroup of Cmca (#64) - from the following webpage:
>>
>> http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos
>>
>>
>>
>> I want to construct the corresponding crystal structure information for
>> pwscf based on the above content. Any hints?
>>
>> Regards
>> --
>> Hongsheng Zhao <zhaohscas at yahoo.com.cn <mailto:zhaohscas at yahoo.com.cn>>
>> School of Physics and Electrical Information Science,
>> Ningxia University, Yinchuan 750021, China
>>
>> _______________________________________________
>> 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
>
>
>-- 
>Hongsheng Zhao <zhaohscas at yahoo.com.cn>
>School of Physics and Electrical Information Science,
>Ningxia University, Yinchuan 750021, China
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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From zhaohscas at yahoo.com.cn  Sun Jul 17 11:16:25 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Sun, 17 Jul 2011 17:16:25 +0800
Subject: [Pw_forum] Input file for  MgB2C2.
In-Reply-To: <a71c5fc.31f8.1313737865f.Coremail.flux_ray12@163.com>
References: <4E22952F.6000207@yahoo.com.cn>
	<4E2255E6.90609@yahoo.com.cn>	<1310884687.65570.YahooMailNeo@web65705.mail.ac4.yahoo.com>
	<a71c5fc.31f8.1313737865f.Coremail.flux_ray12@163.com>
Message-ID: <4E22A869.80301@yahoo.com.cn>

On 07/17/2011 04:30 PM, GAO Zhe wrote:
> Or, you can use the structrue information like below, after all, it may
> be easier for you when you do not have or do not want to have
> crystallography knowledge:
> /*Coll Code* 79587
> *Rec Date * 1996/10/14
> *Chem Name * Magnesium Boride Carbide (1/2/2)
> *Structured* Mg B2 C2
> *Sum* C2 B2 Mg1
> *Title* Mg B2 C2, a new graphite-related refractory compound
> *Author(s)* Woerle, M.;Nesper, R.
> *Reference * Journal of Alloys Compd.
> (1994), 216, 75-83
> *Unit Cell * 10.922(2) 9.461(2) 7.459(1) 90. 90. 90.
> *Vol* 770.76
> *Z* 16
> *Space Group* C m c a
> *SG Number* 64
> *Cryst Sys* orthorhombic
> *Atom # OX SITE x y z SOF H *
> Mg 1 +0 8 d 0.15343(6) 0 0 1. 0
> Mg 2 +0 8 f 0 0.27981(6) -.0113(1) 1. 0
> B 1 +0 8 e 0.25 0.0946(2) 0.25 1. 0
> B 2 +0 8 f 0 0.5886(2) 0.2760(3) 1. 0
> B 3 +0 16 g 0.1278(2) 0.3415(1) 0.2438(2) 1. 0
> C 1 +0 8 e 0.25 0.9271(2) 0.25 1. 0
> C 2 +0 8 f 0 -.0792(2) 0.2314(2) 1. 0
> C 3 +0 16 g 0.1245(2) 0.1750(1) 0.2231(1) 1. 0 /
> --
> GAO Zhe
> CMC Lab, MSE, SNU, Seoul, S.Korea

 From where do you obtain these informations?

Regards
>
>
> At  2011-07-17  15:54:23?"Hongsheng  Zhao"  <zhaohscas at yahoo.com.cn>  wrote:
>
>>On  07/17/2011  02:38  PM,  Eyvaz  Isaev  wrote:
>>>
>>>    >  I  want  to  construct  the  corresponding  crystal  structure  information  for
>>>    >  pwscf  based  on  the  above  content.  Any  hints?
>>>
>>>  You  have  all  the  information  to  build  the  crystal  structure.  Please  read
>>>  carefully  the  page  info.
>>
>>I've  some  puzzles  on  which  are  the  lattice  vectors  should  be  used  for
>>this  case.    In  detail,  you  can  find  the  following  information  from  the
>>webpage:  http://cst-www.nrl.navy.mil/lattice/struk/mgb2c2.html
>>
>>-----------------
>>      Primitive  Vectors:
>>A1  	  =    	?  a  X  -  ?  b  Y
>>A2  	  =    	?  a  X  +  ?  b  Y
>>A3  	  =    	c  Z
>>---------------------
>>
>>On  the  other  hand,  you  can  find  the  following  information  from  within
>>the  mgb2c2.pos  file  downloaded  from  here:
>>http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos:
>>
>>--------------
>>Primitive  vectors
>>a(1)  =      5.46100000  -4.73050000    0.00000000
>>a(2)  =      5.46100000    4.73050000    0.00000000
>>a(3)  =      0.00000000    0.00000000    7.45900000
>>--------------
>>
>>So  in  this  case,  what's  the  lattice  vectors  should  I  used  to  construct
>>the  unit  cell,  i.e.,  the  [a(1),a(2),  a(3)]  or  the  [a,b,c]  should  be  used?
>>
>>Furthermore,  you  can  find  fourty  basis  vectors  listed  for  MgB2C2  on  the
>>webpage:  http://cst-www.nrl.navy.mil/lattice/struk/mgb2c2.html.    What's
>>the  usage  of  these  basis  vectors?
>>
>>Regards
>>>
>>>  Bests,
>>>  Eyvaz.
>>>  -------------------------------------------------------------------
>>>  Prof.  Eyvaz  Isaev,
>>>  Department  of  Physics,  Chemistry,  and  Biology  (IFM),  Linkoping
>>>  University,  Sweden
>>>  Theoretical  Physics  Department,  Moscow  State  Institute  of  Steel  &
>>>  Alloys,  Russia,
>>>  isaev at ifm.liu.se,  eyvaz_isaev at yahoo.com
>>>  ------------------------------------------------------------------------
>>>  *From:*  Hongsheng  Zhao  <zhaohscas at yahoo.com.cn>
>>>  *To:*  PWSCF  Forum  <pw_forum at pwscf.org>
>>>  *Sent:*  Sunday,  July  17,  2011  7:24  AM
>>>  *Subject:*  [Pw_forum]  Input  file  for  MgB2C2.
>>>
>>>  Hi  all,
>>>
>>>  I  obtain  the  xyz  format  crystal  structure  information  for  MgB2C2  -  with
>>>  the  spacegroup  of  Cmca  (#64)  -  from  the  following  webpage:
>>>
>>>  http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos
>>>
>>>
>>>
>>>  I  want  to  construct  the  corresponding  crystal  structure  information  for
>>>  pwscf  based  on  the  above  content.  Any  hints?
>>>
>>>  Regards
>>>  --
>>>  Hongsheng  Zhao  <zhaohscas at yahoo.com.cn  <mailto:zhaohscas at yahoo.com.cn>>
>>>  School  of  Physics  and  Electrical  Information  Science,
>>>  Ningxia  University,  Yinchuan  750021,  China
>>>
>>>  _______________________________________________
>>>  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
>>
>>
>>--
>>Hongsheng  Zhao  <zhaohscas at yahoo.com.cn>
>>School  of  Physics  and  Electrical  Information  Science,
>>Ningxia  University,  Yinchuan  750021,  China
>>_______________________________________________
>>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


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From mtorabi at uwo.ca  Mon Jul 18 03:40:28 2011
From: mtorabi at uwo.ca (Amin Torabi)
Date: Sun, 17 Jul 2011 21:40:28 -0400
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>
Message-ID: <CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>

Dear experts!

Forgive me for my naive question... but I am interested in pressure-induced
phase transitions of diborane. Could you please have a look at my input
file, attached to this message.

The following is what I think I should do: (correct me if I'm wrong!)

1. doing separate vc-relax calculation at each pressure
2. comparing the optimized cell_parameters at each pressure to see when the
structure changes

I am wondering how I can use the enthalpy or unit cell volume at each
pressure to make sure that a phase transition has occurred

Thanks in advance


-- 
Amin Torabi
Ph.D. Student
Chemistry Department
*The* University *of* Western Ontario
London, On Canada, N6A 5B7
Phone: 519-661-2111 Ext: 87871
****************************************
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From wonvein at gmail.com  Mon Jul 18 04:10:02 2011
From: wonvein at gmail.com (WANG Wei)
Date: Mon, 18 Jul 2011 11:10:02 +0900
Subject: [Pw_forum] Problem with NEB.x in QE-4.3
Message-ID: <CAOcD3SLHbygsNq_iYTwTDMgHy6_s-oAyYdGPPTvDv4X1CA+TRQ@mail.gmail.com>

Dear QE users,

When I performed a NEB test (example17) by using the command "neb.x -inp
H2+H.in  > H2+H.out", an error occurs:

parsing_file_name: H2+H.in
PGFIO-F-209/OPEN/unit=99/'OLD' specified for file which does not exist.
 File name = H2+H.in
 In source file path_gen_inputs.F90, at line number 27

By the way, the example17 is always failed.  I have no idea about it because
I am a new learner.

#######################################################
BEGIN
BEGIN_PATH_INPUT
&PATH
  restart_mode      = 'from_scratch'
  string_method     = 'neb',
  nstep_path        = 20,
  ds                = 2.D0,
  opt_scheme        = "broyden",
  num_of_images     = 11,
  k_max             = 0.3D0,
  k_min             = 0.2D0,
  CI_scheme         = "auto",
  path_thr          = 0.1D0,
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
  prefix         = "H2+H"
  outdir         = "/home/wangvei/tmp",
  pseudo_dir     =
"/home/wangvei/works/quantum-espresso/espresso-4.3.1/pseudo",
/
&SYSTEM
  ibrav                  = 0,
  celldm(1)              = 1.D0,
  nat                    = 3,
  ntyp                   = 1,
  ecutwfc                = 20.0D0,
  ecutrho                = 100.0D0,
  nspin                  = 2,
  starting_magnetization = 0.5D0,
  occupations            = "smearing",
  degauss                = 0.03D0,
/
&ELECTRONS
  conv_thr    = 1.D-8,
  mixing_beta = 0.3D0,
/
&IONS
/
ATOMIC_SPECIES
H  1.00794  HUSPBE.RRKJ3
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS { bohr }
H   -4.56670009      0.00000000      0.00000000  1  0  0
H    0.00000000      0.00000000      0.00000000  0  0  0
H    1.55776676      0.00000000      0.00000000  1  0  0
LAST_IMAGE
ATOMIC_POSITIONS { bohr }
H   -1.55776676      0.00000000      0.00000000
H    0.00000000      0.00000000      0.00000000
H    4.56670009      0.00000000      0.00000000
END_POSITIONS
K_POINTS { gamma }
CELL_PARAMETERS { cubic }
  12.00000  0.00000  0.00000
   0.00000  5.00000  0.00000
   0.00000  0.00000  5.00000
END_ENGINE_INPUT
END
#######################################################

Best Regards,
WANG <http://dict.youdao.com/search?q=new&keyfrom=E2Ctranslation>
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From hqzhou at nju.edu.cn  Mon Jul 18 05:31:53 2011
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Mon, 18 Jul 2011 11:31:53 +0800
Subject: [Pw_forum] Input file for  MgB2C2.
References: <4E2255E6.90609@yahoo.com.cn><1310884687.65570.YahooMailNeo@web65705.mail.ac4.yahoo.com>
	<4E22952F.6000207@yahoo.com.cn>
Message-ID: <8CC7A1612C9746B8B070A84F73B1EA09@solarflare>

You should have already got the crystal structure from the information
you provided, haven't you?

1/2a = 5.461
1/2b = 4.7305
c = 7.459

And because your structure is base centered orthorhombic (bco),
so your ibrav = 9.

Hope this help you.

zhou huiqun
@earth sciences, nanjing university, china


----- Original Message ----- 
From: "Hongsheng Zhao" <zhaohscas at yahoo.com.cn>
To: <pw_forum at pwscf.org>
Sent: Sunday, July 17, 2011 3:54 PM
Subject: Re: [Pw_forum] Input file for MgB2C2.


On 07/17/2011 02:38 PM, Eyvaz Isaev wrote:
>
>  > I want to construct the corresponding crystal structure information for
>  > pwscf based on the above content. Any hints?
>
> You have all the information to build the crystal structure. Please read
> carefully the page info.

I've some puzzles on which are the lattice vectors should be used for
this case.  In detail, you can find the following information from the
webpage: http://cst-www.nrl.navy.mil/lattice/struk/mgb2c2.html

-----------------
   Primitive Vectors:
A1 =  ? a X - ? b Y
A2 =  ? a X + ? b Y
A3 =  c Z
---------------------

On the other hand, you can find the following information from within
the mgb2c2.pos file downloaded from here:
http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos:

--------------
Primitive vectors
a(1) =   5.46100000 -4.73050000  0.00000000
a(2) =   5.46100000  4.73050000  0.00000000
a(3) =   0.00000000  0.00000000  7.45900000
--------------

So in this case, what's the lattice vectors should I used to construct
the unit cell, i.e., the [a(1),a(2), a(3)] or the [a,b,c] should be used?

Furthermore, you can find fourty basis vectors listed for MgB2C2 on the
webpage: http://cst-www.nrl.navy.mil/lattice/struk/mgb2c2.html.  What's
the usage of these basis vectors?

Regards
>
> Bests,
> Eyvaz.
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping
> University, Sweden
> Theoretical Physics Department, Moscow State Institute of Steel &
> Alloys, Russia,
> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
> ------------------------------------------------------------------------
> *From:* Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> *To:* PWSCF Forum <pw_forum at pwscf.org>
> *Sent:* Sunday, July 17, 2011 7:24 AM
> *Subject:* [Pw_forum] Input file for MgB2C2.
>
> Hi all,
>
> I obtain the xyz format crystal structure information for MgB2C2 - with
> the spacegroup of Cmca (#64) - from the following webpage:
>
> http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos
>
>
>
> I want to construct the corresponding crystal structure information for
> pwscf based on the above content. Any hints?
>
> Regards
> --
> Hongsheng Zhao <zhaohscas at yahoo.com.cn <mailto:zhaohscas at yahoo.com.cn>>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
>
> _______________________________________________
> 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


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum



From lmartinsamos at gmail.com  Mon Jul 18 08:43:44 2011
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Mon, 18 Jul 2011 08:43:44 +0200
Subject: [Pw_forum] Problem with NEB.x in QE-4.3
In-Reply-To: <CAOcD3SLHbygsNq_iYTwTDMgHy6_s-oAyYdGPPTvDv4X1CA+TRQ@mail.gmail.com>
References: <CAOcD3SLHbygsNq_iYTwTDMgHy6_s-oAyYdGPPTvDv4X1CA+TRQ@mail.gmail.com>
Message-ID: <CAGCSmJTRVN5h1CUF3cGQBT1L30+vnc5jfGx_DNv6jx6WTrXDRw@mail.gmail.com>

Dear Wang, is a strange error message. Can you try with the svn espresso
version (some small bug have been fixed there for neb)? you can download it
at http://qe-forge.org/scm/?group_id=10

bests

Layla

2011/7/18 WANG Wei <wonvein at gmail.com>

> Dear QE users,
>
> When I performed a NEB test (example17) by using the command "neb.x -inp
> H2+H.in  > H2+H.out", an error occurs:
>
> parsing_file_name: H2+H.in
> PGFIO-F-209/OPEN/unit=99/'OLD' specified for file which does not exist.
>  File name = H2+H.in
>  In source file path_gen_inputs.F90, at line number 27
>
> By the way, the example17 is always failed.  I have no idea about it
> because I am a new learner.
>
> #######################################################
> BEGIN
> BEGIN_PATH_INPUT
> &PATH
>   restart_mode      = 'from_scratch'
>   string_method     = 'neb',
>   nstep_path        = 20,
>   ds                = 2.D0,
>   opt_scheme        = "broyden",
>   num_of_images     = 11,
>   k_max             = 0.3D0,
>   k_min             = 0.2D0,
>   CI_scheme         = "auto",
>   path_thr          = 0.1D0,
> /
> END_PATH_INPUT
> BEGIN_ENGINE_INPUT
> &CONTROL
>   prefix         = "H2+H"
>   outdir         = "/home/wangvei/tmp",
>   pseudo_dir     =
> "/home/wangvei/works/quantum-espresso/espresso-4.3.1/pseudo",
> /
> &SYSTEM
>   ibrav                  = 0,
>   celldm(1)              = 1.D0,
>   nat                    = 3,
>   ntyp                   = 1,
>   ecutwfc                = 20.0D0,
>   ecutrho                = 100.0D0,
>   nspin                  = 2,
>   starting_magnetization = 0.5D0,
>   occupations            = "smearing",
>   degauss                = 0.03D0,
> /
> &ELECTRONS
>   conv_thr    = 1.D-8,
>   mixing_beta = 0.3D0,
> /
> &IONS
> /
> ATOMIC_SPECIES
> H  1.00794  HUSPBE.RRKJ3
> BEGIN_POSITIONS
> FIRST_IMAGE
> ATOMIC_POSITIONS { bohr }
> H   -4.56670009      0.00000000      0.00000000  1  0  0
> H    0.00000000      0.00000000      0.00000000  0  0  0
> H    1.55776676      0.00000000      0.00000000  1  0  0
> LAST_IMAGE
> ATOMIC_POSITIONS { bohr }
> H   -1.55776676      0.00000000      0.00000000
> H    0.00000000      0.00000000      0.00000000
> H    4.56670009      0.00000000      0.00000000
> END_POSITIONS
> K_POINTS { gamma }
> CELL_PARAMETERS { cubic }
>   12.00000  0.00000  0.00000
>    0.00000  5.00000  0.00000
>    0.00000  0.00000  5.00000
> END_ENGINE_INPUT
> END
> #######################################################
>
> Best Regards,
> WANG <http://dict.youdao.com/search?q=new&keyfrom=E2Ctranslation>
> _______________________________________________
> 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  Mon Jul 18 08:58:20 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 18 Jul 2011 08:58:20 +0200
Subject: [Pw_forum] Problem with NEB.x in QE-4.3
In-Reply-To: <CAOcD3SLHbygsNq_iYTwTDMgHy6_s-oAyYdGPPTvDv4X1CA+TRQ@mail.gmail.com>
References: <CAOcD3SLHbygsNq_iYTwTDMgHy6_s-oAyYdGPPTvDv4X1CA+TRQ@mail.gmail.com>
Message-ID: <F3E9914B-A1E0-4CF6-AED8-A447B38AC4FE@democritos.it>


On Jul 18, 2011, at 4:10 , WANG Wei wrote:

> By the way, the example17 is always failed.  I have no idea about  
> it because I am a new learner.


if you do not try to figure out what does not work and why and how to  
fix it,
you will be forever a new learner

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 zhaohscas at yahoo.com.cn  Mon Jul 18 10:04:32 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Mon, 18 Jul 2011 16:04:32 +0800
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>
	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>
Message-ID: <4E23E910.1050004@yahoo.com.cn>

On 07/18/2011 09:40 AM, Amin Torabi wrote:
> Dear experts!
>
> Forgive me for my naive question... but I am interested in
> pressure-induced phase transitions of diborane. Could you please have a
> look at my input file, attached to this message.
>
> The following is what I think I should do: (correct me if I'm wrong!)
>
> 1. doing separate vc-relax calculation at each pressure

By using this method, there are some limitations.  You should have known 
in advance the different phases between them the phase transition maybe 
occur when we change the pressure.  Then you can use this method to 
determine the phase transition path.  But I'm not so sure this method 
can predict all of the possible phases for a system when we change the 
external pressure.  To do a more reasonable and complete phase 
transition prediction and even searching for unknown phases, you should 
use some third-party code like uspex for this type of job.

In addition, I think you should do relax, not vc-relax calculation at 
each pressure.  If you do vc-relax, then the pressure imposed to the 
system will be released.  So you won't get the *Pressure-induced* phase 
transition.

> 2. comparing the optimized cell_parameters at each pressure to see when
> the structure changes
>
> I am wondering how I can use the enthalpy or unit cell volume at each
> pressure to make sure that a phase transition has occurred

For the other questions, see this thread on this list:  About the method 
to obtain the common tangent for determing the phase transition 
pressure.  HTH.

Regards
>
> Thanks in advance
>
>
> --
> Amin Torabi
> Ph.D. Student
> Chemistry Department
> /The/ University /of/ Western Ontario
> London, On Canada, N6A 5B7
> Phone: 519-661-2111 Ext: 87871
> ****************************************
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From sclauzer at sissa.it  Mon Jul 18 10:59:20 2011
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 18 Jul 2011 10:59:20 +0200
Subject: [Pw_forum] Opening .xml files on linux
In-Reply-To: <1310493661.76035.YahooMailNeo@web43412.mail.sp1.yahoo.com>
References: <CANxi7+O8VJ6He1JsH0jV06tWaLEangyW2g4g8JXzTk2JRWXg0g@mail.gmail.com>
	<1310493661.76035.YahooMailNeo@web43412.mail.sp1.yahoo.com>
Message-ID: <4A6933F2-7335-42F5-83E4-6DDD81A9DE34@sissa.it>

Have you tried with
   make doc
after running configure? The .txt and .html files should appear in the Doc directory.

HTH

GS

Il giorno 12/lug/2011, alle ore 20.01, Izaak Williamson ha scritto:

> Hello everyone,
> 
> I noticed the new version of QUANTUM ESPRESSO (4.3.1) has changed all of its documentation files to .xml (instead of the former .txt). The problem is, when I try to open these files through firefox, none of the formatting is kept. Everything is written as one continuous paragraph making it very difficult to read. How are these files meant to be opened? Is there an add-on or program that I will need to download?
> 
> Thanks in advance.
> 
> -- 
> Izaak Williamson
> Research Assistant
> Physics Department
> Boise State University
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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

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From germaneau at gucas.ac.cn  Tue Jul 19 03:23:54 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Mon, 18 Jul 2011 21:23:54 -0400
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <510975832.04103@test1.gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>
	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>
	<510975832.04103@test1.gucas.ac.cn>
Message-ID: <4E24DCAA.7000709@gucas.ac.cn>

Hey Amin,

The approach you proposed is ok but you should relax the cell as well.
By keeping the cell fix the system does not feel the pressure you wish 
to apply.
You can also change the volume, relax the positions only and compute the 
pressure.
The best is to compute the free energy as function of pressure ans so 
the QHA method is the best way to go.
Note that at first you can ignore the thermal effect and compute the 
free energy from a regular phonon calculations.
I'm also very interested in such calculations but don't have experiences 
doing this by mean of first principal calculations.

I hope that helps,
Good luck,

                               ?ric.

On 07/18/2011 04:04 AM, Hongsheng Zhao wrote:
> On 07/18/2011 09:40 AM, Amin Torabi wrote:
>> Dear experts!
>>
>> Forgive me for my naive question... but I am interested in
>> pressure-induced phase transitions of diborane. Could you please have a
>> look at my input file, attached to this message.
>>
>> The following is what I think I should do: (correct me if I'm wrong!)
>>
>> 1. doing separate vc-relax calculation at each pressure
> By using this method, there are some limitations.  You should have known
> in advance the different phases between them the phase transition maybe
> occur when we change the pressure.  Then you can use this method to
> determine the phase transition path.  But I'm not so sure this method
> can predict all of the possible phases for a system when we change the
> external pressure.  To do a more reasonable and complete phase
> transition prediction and even searching for unknown phases, you should
> use some third-party code like uspex for this type of job.
>
> In addition, I think you should do relax, not vc-relax calculation at
> each pressure.  If you do vc-relax, then the pressure imposed to the
> system will be released.  So you won't get the *Pressure-induced* phase
> transition.
>
>> 2. comparing the optimized cell_parameters at each pressure to see when
>> the structure changes
>>
>> I am wondering how I can use the enthalpy or unit cell volume at each
>> pressure to make sure that a phase transition has occurred
> For the other questions, see this thread on this list:  About the method
> to obtain the common tangent for determing the phase transition
> pressure.  HTH.
>
> Regards
>> Thanks in advance
>>
>>
>> --
>> Amin Torabi
>> Ph.D. Student
>> Chemistry Department
>> /The/ University /of/ Western Ontario
>> London, On Canada, N6A 5B7
>> Phone: 519-661-2111 Ext: 87871
>> ****************************************
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html /

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From zhaohscas at yahoo.com.cn  Mon Jul 18 16:45:39 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Mon, 18 Jul 2011 22:45:39 +0800
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <4E24DCAA.7000709@gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<510975832.04103@test1.gucas.ac.cn>
	<4E24DCAA.7000709@gucas.ac.cn>
Message-ID: <4E244713.5060008@yahoo.com.cn>

On 07/19/2011 09:23 AM, Eric Germaneau wrote:
> Hey Amin,
>
> The approach you proposed is ok but you should relax the cell as well.
> By keeping the cell fix the system does not feel the pressure you wish
> to apply.

Not so clear about the meaning of this sentence, could you please give 
some more explanations? ;-(

> You can also change the volume, relax the positions only and compute the
> pressure.
> The best is to compute the free energy as function of pressure ans so
> the QHA method is the best way to go.

I think this method cann't do the job of structure-searching-and-finding 
for unknown phases when we changing the external pressure.

Regards

> Note that at first you can ignore the thermal effect and compute the
> free energy from a regular phonon calculations.
> I'm also very interested in such calculations but don't have experiences
> doing this by mean of first principal calculations.
>
> I hope that helps,
> Good luck,


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From mtorabi at uwo.ca  Mon Jul 18 18:45:12 2011
From: mtorabi at uwo.ca (Amin Torabi)
Date: Mon, 18 Jul 2011 12:45:12 -0400
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <4E23E910.1050004@yahoo.com.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>
	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>
	<4E23E910.1050004@yahoo.com.cn>
Message-ID: <CAEXRF5z8Qzw9cy1D7=Dt-bumGwvjyZ0bQ1yQ=Ja1Zn8j7pD0Ww@mail.gmail.com>

Dear Hongsheng,

I don't understand why I should use relax instead of vc-relax. As far as I
understand, when a system is under pressure, both the atomic positions
inside a unit cell, as well as the dimensions of the unit cell changes. So,
why should I keep the unit cell parameters fixed if I am interested in
finding phase transitions?

Thanks

On Mon, Jul 18, 2011 at 4:04 AM, Hongsheng Zhao <zhaohscas at yahoo.com.cn>wrote:

> On 07/18/2011 09:40 AM, Amin Torabi wrote:
> > Dear experts!
> >
> > Forgive me for my naive question... but I am interested in
> > pressure-induced phase transitions of diborane. Could you please have a
> > look at my input file, attached to this message.
> >
> > The following is what I think I should do: (correct me if I'm wrong!)
> >
> > 1. doing separate vc-relax calculation at each pressure
>
> By using this method, there are some limitations.  You should have known
> in advance the different phases between them the phase transition maybe
> occur when we change the pressure.  Then you can use this method to
> determine the phase transition path.  But I'm not so sure this method
> can predict all of the possible phases for a system when we change the
> external pressure.  To do a more reasonable and complete phase
> transition prediction and even searching for unknown phases, you should
> use some third-party code like uspex for this type of job.
>
> In addition, I think you should do relax, not vc-relax calculation at
> each pressure.  If you do vc-relax, then the pressure imposed to the
> system will be released.  So you won't get the *Pressure-induced* phase
> transition.
>
> > 2. comparing the optimized cell_parameters at each pressure to see when
> > the structure changes
> >
> > I am wondering how I can use the enthalpy or unit cell volume at each
> > pressure to make sure that a phase transition has occurred
>
> For the other questions, see this thread on this list:  About the method
> to obtain the common tangent for determing the phase transition
> pressure.  HTH.
>
> Regards
> >
> > Thanks in advance
> >
> >
> > --
> > Amin Torabi
> > Ph.D. Student
> > Chemistry Department
> > /The/ University /of/ Western Ontario
> > London, On Canada, N6A 5B7
> > Phone: 519-661-2111 Ext: 87871
> > ****************************************
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> --
> Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Amin Torabi
Ph.D. Student
Chemistry Department
*The* University *of* Western Ontario
London, On Canada, N6A 5B7
Phone: 519-661-2111 Ext: 87871
****************************************
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From izaakw89 at yahoo.com  Mon Jul 18 22:50:14 2011
From: izaakw89 at yahoo.com (Izaak Williamson)
Date: Mon, 18 Jul 2011 13:50:14 -0700 (PDT)
Subject: [Pw_forum] Opening .xml files on linux
In-Reply-To: <1311013149.22516.YahooMailNeo@web43407.mail.sp1.yahoo.com>
References: <CANxi7+O8VJ6He1JsH0jV06tWaLEangyW2g4g8JXzTk2JRWXg0g@mail.gmail.com>
	<1310493661.76035.YahooMailNeo@web43412.mail.sp1.yahoo.com>
	<4A6933F2-7335-42F5-83E4-6DDD81A9DE34@sissa.it>
	<1311013149.22516.YahooMailNeo@web43407.mail.sp1.yahoo.com>
Message-ID: <1311022214.3759.YahooMailNeo@web43408.mail.sp1.yahoo.com>

After running ./configure I used the command "make all" and usually, the Doc file is created with the necessary .txt and .html files. With the newest version (4.3.1) however, instead of having INPUT_PW.txt for example, it has INPUT_PW.xml. There are no .txt or .html files anymore. I do not mind that the .txt files are not there, I just want to be able to open the .xml files properly.


Thanks for the help.



________________________________
From: Gabriele Sclauzero <sclauzer at sissa.it>
To: Izaak Williamson <izaakw89 at yahoo.com>; PWSCF Forum <pw_forum at pwscf.org>
Sent: Monday, July 18, 2011 1:59 AM
Subject: Re: [Pw_forum] Opening .xml files on linux


Have you tried with
?? make doc
after running configure? The .txt and .html files should appear in the Doc directory.

HTH

GS


Il giorno 12/lug/2011, alle ore 20.01, Izaak Williamson ha scritto:

Hello everyone,
>
>
>I noticed the new version of QUANTUM ESPRESSO (4.3.1) has changed all of its documentation files to .xml (instead of the former .txt). The problem is, when I try to open these files through firefox, none of the formatting is kept. Everything is written as one continuous paragraph making it very difficult to read. How are these files meant to be opened? Is there an add-on or program that I will need to download?
>
>Thanks in advance.
>
>-- 
>Izaak Williamson
>Research Assistant
>Physics Department
>Boise State University
>
>
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>


? Gabriele Sclauzero,?EPFL SB ITP CSEA
?? PH H2 462, Station 3,?CH-1015 Lausanne 
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From germaneau at gucas.ac.cn  Tue Jul 19 12:49:17 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Tue, 19 Jul 2011 06:49:17 -0400
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <510999887.17934@test1.gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<510975832.04103@test1.gucas.ac.cn>
	<4E24DCAA.7000709@gucas.ac.cn> <510999887.17934@test1.gucas.ac.cn>
Message-ID: <4E25612D.4090704@gucas.ac.cn>



On 07/18/2011 10:45 AM, Hongsheng Zhao wrote:
> On 07/19/2011 09:23 AM, Eric Germaneau wrote:
>> Hey Amin,
>>
>> The approach you proposed is ok but you should relax the cell as well.
>> By keeping the cell fix the system does not feel the pressure you wish
>> to apply.
> Not so clear about the meaning of this sentence, could you please give
> some more explanations? ;-(
Under pressure keeping the unit cell fix is useless since the system 
won't feel it.
It just makes sense.
So, if you wish to see the effect of the pressure you have to perform 
vc-relax calculation.
Take it that way, in thermodynamic you have 2 important ensembles, 
isochoric and isobaric.
So either the volume is fix and you get out the corresponding pressure, 
or the pressure is fix and you get out the corresponding volume.
Note that the volume of gas for instance decreases inversely 
proportionally to pressure.
The pressure is the intensive variable related to the volume (extensive).
You simply can not have both of them constant at the same time.
Hope it helps.
>
>> You can also change the volume, relax the positions only and compute the
>> pressure.
>> The best is to compute the free energy as function of pressure ans so
>> the QHA method is the best way to go.
> I think this method cann't do the job of structure-searching-and-finding
> for unknown phases when we changing the external pressure.
Yes, it can but in the case of  structure-searching it's very expensive.
In that case you'd better generate random unit cell parameters, random 
positions and run vc-relax.
Even this can be expensive since you have to do it a lot of times ....
Just take a look to this papers, PRL 97 1 (2006) 
<http://link.aps.org/doi/10.1103/PhysRevLett.97.045504> and JPCM 23 
053201 (2011) 
<http://stacks.iop.org/0953-8984/23/i=5/a=053201?key=crossref.44087776832bc9a0edd0dc492a67d376>.
It is the main work of Professor Pickard 
<http://www.st-andrews.ac.uk/physics/condmat/pickard/Crystals%20ex%20nihilo.html>.
Best.

>
> Regards
>
>> Note that at first you can ignore the thermal effect and compute the
>> free energy from a regular phonon calculations.
>> I'm also very interested in such calculations but don't have experiences
>> doing this by mean of first principal calculations.
>>
>> I hope that helps,
>> Good luck,
>

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html /

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From zhaohscas at yahoo.com.cn  Tue Jul 19 02:15:07 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 19 Jul 2011 08:15:07 +0800
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <CAEXRF5z8Qzw9cy1D7=Dt-bumGwvjyZ0bQ1yQ=Ja1Zn8j7pD0Ww@mail.gmail.com>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<4E23E910.1050004@yahoo.com.cn>
	<CAEXRF5z8Qzw9cy1D7=Dt-bumGwvjyZ0bQ1yQ=Ja1Zn8j7pD0Ww@mail.gmail.com>
Message-ID: <4E24CC8B.4050407@yahoo.com.cn>

On 07/19/2011 12:45 AM, Amin Torabi wrote:
> Dear Hongsheng,
>
> I don't understand why I should use relax instead of vc-relax. As far as
> I understand, when a system is under pressure, both the atomic positions
> inside a unit cell, as well as the dimensions of the unit cell changes.
> So, why should I keep the unit cell parameters fixed if I am interested
> in finding phase transitions?

In fact, you can do relax or  vc-relax, it depend on the actual ways 
used by you to study the   Pressure-induced phase transition.  Let me 
give you a more detailed description as follows:

1-  If you only use one type of initial phase to do this type of study. 
  Then you should use the vc-relax when changing the external pressure. 
  And then see what's the ultimate unit cell looks like for each 
pressure step.  For convenience, you can also plot the 
binding-energy/formation-energy vs external-pressure to see whether 
there are some abrupt change points - of course, there are many other 
physical properties you can consider to assist you judging the first 
order phase transition, I just give you a example here - on the plot.

2-  If you have two or more  initial phases and want to find the phase 
transition pressure among them.  In this case, you can do the relax 
calculation for each phase  by impose external pressure in certain 
range.  And then you can plot the E-V or H-V plots for each phase in the 
same Cartesian system  to find the  phase transition point.

Basically, the first method (vc-relax) enable you to find or predict 
some possible phase you don't known in advance.  The second method 
(relax) enable you find the phase transition pressure for known phases.

But, even by using the vc-relax, I don't think it can be served as a 
perfect method for new-phase finding an searching technology.  This is 
because the vc-relax just changing the unit cells ( cell parameters and 
atoms positions ) in a series of localized positions.  So I don't think 
by using this method you can do the job like universal structure 
prediction just as the uspex or similar codes done for you.

Regards
>
> Thanks


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From zhaohscas at yahoo.com.cn  Tue Jul 19 02:23:55 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 19 Jul 2011 08:23:55 +0800
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <4E24CC8B.4050407@yahoo.com.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<4E23E910.1050004@yahoo.com.cn>
	<CAEXRF5z8Qzw9cy1D7=Dt-bumGwvjyZ0bQ1yQ=Ja1Zn8j7pD0Ww@mail.gmail.com>
	<4E24CC8B.4050407@yahoo.com.cn>
Message-ID: <4E24CE9B.50705@yahoo.com.cn>

On 07/19/2011 08:15 AM, Hongsheng Zhao wrote:
>
> 1-  If you only use one type of initial phase to do this type of study.
>   Then you should use the vc-relax when changing the external pressure.
>   And then see what's the ultimate unit cell looks like for each
> pressure step.  For convenience, you can also plot the
> binding-energy/formation-energy vs external-pressure to see whether
> there are some abrupt change points - of course, there are many other
> physical properties you can consider to assist you judging the first
> order phase transition, I just give you a example here - on the plot.

Even in this case, you can also do the relax calculation for each 
external pressure step.  Then you plot the 
binding-energy/formation-energy vs external-pressure and find the abrupt 
change point on the plot.   Subsequently, you do the  vc-relax 
calculation for you system by imposing the pressure neighboring to 
abrupt change point and see what's you system should looks like.  By 
this method, you can save some computation times.

Best
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From germaneau at gucas.ac.cn  Tue Jul 19 14:27:33 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Tue, 19 Jul 2011 08:27:33 -0400
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <511034047.29551@test1.gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<4E23E910.1050004@yahoo.com.cn>
	<CAEXRF5z8Qzw9cy1D7=Dt-bumGwvjyZ0bQ1yQ=Ja1Zn8j7pD0Ww@mail.gmail.com>
	<511034047.29551@test1.gucas.ac.cn>
Message-ID: <4E257835.70409@gucas.ac.cn>



On 07/18/2011 08:15 PM, Hongsheng Zhao wrote:
> On 07/19/2011 12:45 AM, Amin Torabi wrote:
>> Dear Hongsheng,
>>
>> I don't understand why I should use relax instead of vc-relax. As far as
>> I understand, when a system is under pressure, both the atomic positions
>> inside a unit cell, as well as the dimensions of the unit cell changes.
>> So, why should I keep the unit cell parameters fixed if I am interested
>> in finding phase transitions?
> In fact, you can do relax or  vc-relax, it depend on the actual ways
> used by you to study the   Pressure-induced phase transition.  Let me
> give you a more detailed description as follows:
>
> 1-  If you only use one type of initial phase to do this type of study.
>    Then you should use the vc-relax when changing the external pressure.
>    And then see what's the ultimate unit cell looks like for each
> pressure step.  For convenience, you can also plot the
> binding-energy/formation-energy vs external-pressure to see whether
> there are some abrupt change points - of course, there are many other
> physical properties you can consider to assist you judging the first
> order phase transition, I just give you a example here - on the plot.
>
> 2-  If you have two or more  initial phases and want to find the phase
> transition pressure among them.  In this case, you can do the relax
> calculation for each phase  by impose external pressure in certain
> range.  And then you can plot the E-V or H-V plots for each phase in the
> same Cartesian system  to find the  phase transition point.
>
> Basically, the first method (vc-relax) enable you to find or predict
> some possible phase you don't known in advance.  The second method
> (relax) enable you find the phase transition pressure for known phases.
>
> But, even by using the vc-relax, I don't think it can be served as a
> perfect method for new-phase finding an searching technology.  This is
> because the vc-relax just changing the unit cells ( cell parameters and
> atoms positions ) in a series of localized positions.  So I don't think
> by using this method you can do the job like universal structure
> prediction just as the uspex or similar codes done for you.
They use the free energy and so it's more accurate.
The cell relaxation procedure can give good results (See the work of 
Prof. Pickard).
Anyway, I don't want to debate who is right or wrong. I simply don't 
believe in that.
The guy wanted our opening, I got it.
Best,

            ?ric.
>
> Regards
>> Thanks
>

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html /

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From zhaohscas at yahoo.com.cn  Tue Jul 19 03:12:38 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 19 Jul 2011 09:12:38 +0800
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <4E24CC8B.4050407@yahoo.com.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<4E23E910.1050004@yahoo.com.cn>	<CAEXRF5z8Qzw9cy1D7=Dt-bumGwvjyZ0bQ1yQ=Ja1Zn8j7pD0Ww@mail.gmail.com>
	<4E24CC8B.4050407@yahoo.com.cn>
Message-ID: <4E24DA06.2040703@yahoo.com.cn>

On 07/19/2011 08:15 AM, Hongsheng Zhao wrote:
> 2-  If you have two or more  initial phases and want to find the phase
> transition pressure among them.  In this case, you can do the relax
> calculation for each phase  by impose external pressure in certain
> range.  And then you can plot the E-V or H-V plots for each phase in the
> same Cartesian system  to find the  phase transition point.

Sorry for my posts on this thread, I'm  confused by some other 
calculatoins with this, say, elastic constans.  Dear Amin, the things 
said by Eric is right.  in any case, for studying the  Pressure-induced 
phase transition, you do always do  vc-relax calculations.  Sorry for my 
misleading disscussions in this thread.

Regards
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From zhaohscas at yahoo.com.cn  Tue Jul 19 03:22:41 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 19 Jul 2011 09:22:41 +0800
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <4E24CC8B.4050407@yahoo.com.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<4E23E910.1050004@yahoo.com.cn>	<CAEXRF5z8Qzw9cy1D7=Dt-bumGwvjyZ0bQ1yQ=Ja1Zn8j7pD0Ww@mail.gmail.com>
	<4E24CC8B.4050407@yahoo.com.cn>
Message-ID: <4E24DC61.2090309@yahoo.com.cn>

On 07/19/2011 08:15 AM, Hongsheng Zhao wrote:
> 2-  If you have two or more  initial phases and want to find the phase
> transition pressure among them.  In this case, you can do the relax
> calculation for each phase  by impose external pressure in certain
> range.  And then you can plot the E-V or H-V plots for each phase in the
> same Cartesian system  to find the  phase transition point.

Sorry for my posts on this thread, I'm  confused by some other 
calculatoins with this, say, elastic constans.  Dear Amin, the things 
said by Eric is right.  in any case, for studying the  Pressure-induced 
phase transition, you do always do  vc-relax calculations.  Sorry for my 
misleading disscussions in this thread.

Regards
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From zhaohscas at yahoo.com.cn  Tue Jul 19 03:28:49 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 19 Jul 2011 09:28:49 +0800
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <4E25612D.4090704@gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<510975832.04103@test1.gucas.ac.cn>	<4E24DCAA.7000709@gucas.ac.cn>
	<510999887.17934@test1.gucas.ac.cn> <4E25612D.4090704@gucas.ac.cn>
Message-ID: <4E24DDD1.5040603@yahoo.com.cn>

On 07/19/2011 06:49 PM, Eric Germaneau wrote:
>
>
> On 07/18/2011 10:45 AM, Hongsheng Zhao wrote:
>> On 07/19/2011 09:23 AM, Eric Germaneau wrote:
>>> Hey Amin,
>>>
>>> The approach you proposed is ok but you should relax the cell as well.
>>> By keeping the cell fix the system does not feel the pressure you wish
>>> to apply.
>> Not so clear about the meaning of this sentence, could you please give
>> some more explanations? ;-(
> Under pressure keeping the unit cell fix is useless since the system
> won't feel it.
> It just makes sense.
> So, if you wish to see the effect of the pressure you have to perform
> vc-relax calculation.
> Take it that way, in thermodynamic you have 2 important ensembles,
> isochoric and isobaric.
> So either the volume is fix and you get out the corresponding pressure,
> or the pressure is fix and you get out the corresponding volume.
> Note that the volume of gas for instance decreases inversely
> proportionally to pressure.
> The pressure is the intensive variable related to the volume (extensive).
> You simply can not have both of them constant at the same time.

Yes, you're right.  I'm so sorry for my previous misleading posts on 
this thread.  Thanks again.

> Hope it helps.
>>
>>> You can also change the volume, relax the positions only and compute the
>>> pressure.
>>> The best is to compute the free energy as function of pressure ans so
>>> the QHA method is the best way to go.
>> I think this method cann't do the job of structure-searching-and-finding
>> for unknown phases when we changing the external pressure.
> Yes, it can but in the case of structure-searching it's very expensive.
> In that case you'd better generate random unit cell parameters, random
> positions and run vc-relax.
> Even this can be expensive since you have to do it a lot of times ....
> Just take a look to this papers, PRL 97 1 (2006)
> <http://link.aps.org/doi/10.1103/PhysRevLett.97.045504> and JPCM 23
> 053201 (2011)
> <http://stacks.iop.org/0953-8984/23/i=5/a=053201?key=crossref.44087776832bc9a0edd0dc492a67d376>.
> It is the main work of Professor Pickard
> <http://www.st-andrews.ac.uk/physics/condmat/pickard/Crystals%20ex%20nihilo.html>.
> Best.

Thanks a lot for this information ;-)

Regards
>
>>
>> Regards
>>
>>> Note that at first you can ignore the thermal effect and compute the
>>> free energy from a regular phonon calculations.
>>> I'm also very interested in such calculations but don't have experiences
>>> doing this by mean of first principal calculations.



-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From mtorabi at uwo.ca  Tue Jul 19 03:46:18 2011
From: mtorabi at uwo.ca (Amin Torabi)
Date: Mon, 18 Jul 2011 21:46:18 -0400
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <4E24DDD1.5040603@yahoo.com.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>
	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>
	<510975832.04103@test1.gucas.ac.cn> <4E24DCAA.7000709@gucas.ac.cn>
	<510999887.17934@test1.gucas.ac.cn> <4E25612D.4090704@gucas.ac.cn>
	<4E24DDD1.5040603@yahoo.com.cn>
Message-ID: <CAEXRF5ycO_UN1nMKvbEdBqL7dNv+rwDK0+tSG9LcFHkhpvLnfA@mail.gmail.com>

Thanks Eric and Hongsheng for the discussion!

Can I also have your comments on this "common tangent" concept in first
order phase transitions? Is it applicable for my case?


And how can I use phonon calculations to help me find the phase transition?
I've heard about some "mode softening", but I am not sure how it can be used
in this context? Could you refer me to some article explaining the theory
behind this

Thanks again
Amin





On Mon, Jul 18, 2011 at 9:28 PM, Hongsheng Zhao <zhaohscas at yahoo.com.cn>wrote:

> On 07/19/2011 06:49 PM, Eric Germaneau wrote:
> >
> >
> > On 07/18/2011 10:45 AM, Hongsheng Zhao wrote:
> >> On 07/19/2011 09:23 AM, Eric Germaneau wrote:
> >>> Hey Amin,
> >>>
> >>> The approach you proposed is ok but you should relax the cell as well.
> >>> By keeping the cell fix the system does not feel the pressure you wish
> >>> to apply.
> >> Not so clear about the meaning of this sentence, could you please give
> >> some more explanations? ;-(
> > Under pressure keeping the unit cell fix is useless since the system
> > won't feel it.
> > It just makes sense.
> > So, if you wish to see the effect of the pressure you have to perform
> > vc-relax calculation.
> > Take it that way, in thermodynamic you have 2 important ensembles,
> > isochoric and isobaric.
> > So either the volume is fix and you get out the corresponding pressure,
> > or the pressure is fix and you get out the corresponding volume.
> > Note that the volume of gas for instance decreases inversely
> > proportionally to pressure.
> > The pressure is the intensive variable related to the volume (extensive).
> > You simply can not have both of them constant at the same time.
>
> Yes, you're right.  I'm so sorry for my previous misleading posts on
> this thread.  Thanks again.
>
> > Hope it helps.
> >>
> >>> You can also change the volume, relax the positions only and compute
> the
> >>> pressure.
> >>> The best is to compute the free energy as function of pressure ans so
> >>> the QHA method is the best way to go.
> >> I think this method cann't do the job of structure-searching-and-finding
> >> for unknown phases when we changing the external pressure.
> > Yes, it can but in the case of structure-searching it's very expensive.
> > In that case you'd better generate random unit cell parameters, random
> > positions and run vc-relax.
> > Even this can be expensive since you have to do it a lot of times ....
> > Just take a look to this papers, PRL 97 1 (2006)
> > <http://link.aps.org/doi/10.1103/PhysRevLett.97.045504> and JPCM 23
> > 053201 (2011)
> > <
> http://stacks.iop.org/0953-8984/23/i=5/a=053201?key=crossref.44087776832bc9a0edd0dc492a67d376
> >.
> > It is the main work of Professor Pickard
> > <
> http://www.st-andrews.ac.uk/physics/condmat/pickard/Crystals%20ex%20nihilo.html
> >.
> > Best.
>
> Thanks a lot for this information ;-)
>
> Regards
> >
> >>
> >> Regards
> >>
> >>> Note that at first you can ignore the thermal effect and compute the
> >>> free energy from a regular phonon calculations.
> >>> I'm also very interested in such calculations but don't have
> experiences
> >>> doing this by mean of first principal calculations.
>
>
>
> --
> Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Amin Torabi
Ph.D. Student
Chemistry Department
*The* University *of* Western Ontario
London, On Canada, N6A 5B7
Phone: 519-661-2111 Ext: 87871
****************************************
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From zhaohscas at yahoo.com.cn  Tue Jul 19 06:27:28 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 19 Jul 2011 12:27:28 +0800
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <CAEXRF5ycO_UN1nMKvbEdBqL7dNv+rwDK0+tSG9LcFHkhpvLnfA@mail.gmail.com>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<510975832.04103@test1.gucas.ac.cn>
	<4E24DCAA.7000709@gucas.ac.cn>	<510999887.17934@test1.gucas.ac.cn>
	<4E25612D.4090704@gucas.ac.cn>	<4E24DDD1.5040603@yahoo.com.cn>
	<CAEXRF5ycO_UN1nMKvbEdBqL7dNv+rwDK0+tSG9LcFHkhpvLnfA@mail.gmail.com>
Message-ID: <4E2507B0.4000802@yahoo.com.cn>

On 07/19/2011 09:46 AM, Amin Torabi wrote:
> Thanks Eric and Hongsheng for the discussion!
>
> Can I also have your comments on this "common tangent" concept in first
> order phase transitions? Is it applicable for my case?

Of course, you can, but be sure this is refer to the E-V plot.

>
>
> And how can I use phonon calculations to help me find the phase
> transition? I've heard about some "mode softening", but I am not sure
> how it can be used in this context? Could you refer me to some article
> explaining the theory behind this

I don't have experience on such thing.  Perhaps others can help.

Regards
>
> Thanks again
> Amin
>
>
>
>
>
> On Mon, Jul 18, 2011 at 9:28 PM, Hongsheng Zhao <zhaohscas at yahoo.com.cn
> <mailto:zhaohscas at yahoo.com.cn>> wrote:
>
>     On 07/19/2011 06:49 PM, Eric Germaneau wrote:
>      >
>      >
>      > On 07/18/2011 10:45 AM, Hongsheng Zhao wrote:
>      >> On 07/19/2011 09:23 AM, Eric Germaneau wrote:
>      >>> Hey Amin,
>      >>>
>      >>> The approach you proposed is ok but you should relax the cell
>     as well.
>      >>> By keeping the cell fix the system does not feel the pressure
>     you wish
>      >>> to apply.
>      >> Not so clear about the meaning of this sentence, could you
>     please give
>      >> some more explanations? ;-(
>      > Under pressure keeping the unit cell fix is useless since the system
>      > won't feel it.
>      > It just makes sense.
>      > So, if you wish to see the effect of the pressure you have to perform
>      > vc-relax calculation.
>      > Take it that way, in thermodynamic you have 2 important ensembles,
>      > isochoric and isobaric.
>      > So either the volume is fix and you get out the corresponding
>     pressure,
>      > or the pressure is fix and you get out the corresponding volume.
>      > Note that the volume of gas for instance decreases inversely
>      > proportionally to pressure.
>      > The pressure is the intensive variable related to the volume
>     (extensive).
>      > You simply can not have both of them constant at the same time.
>
>     Yes, you're right.  I'm so sorry for my previous misleading posts on
>     this thread.  Thanks again.
>
>      > Hope it helps.
>      >>
>      >>> You can also change the volume, relax the positions only and
>     compute the
>      >>> pressure.
>      >>> The best is to compute the free energy as function of pressure
>     ans so
>      >>> the QHA method is the best way to go.
>      >> I think this method cann't do the job of
>     structure-searching-and-finding
>      >> for unknown phases when we changing the external pressure.
>      > Yes, it can but in the case of structure-searching it's very
>     expensive.
>      > In that case you'd better generate random unit cell parameters,
>     random
>      > positions and run vc-relax.
>      > Even this can be expensive since you have to do it a lot of times
>     ....
>      > Just take a look to this papers, PRL 97 1 (2006)
>      > <http://link.aps.org/doi/10.1103/PhysRevLett.97.045504> and JPCM 23
>      > 053201 (2011)
>      >
>     <http://stacks.iop.org/0953-8984/23/i=5/a=053201?key=crossref.44087776832bc9a0edd0dc492a67d376>.
>      > It is the main work of Professor Pickard
>      >
>     <http://www.st-andrews.ac.uk/physics/condmat/pickard/Crystals%20ex%20nihilo.html>.
>      > Best.
>
>     Thanks a lot for this information ;-)
>
>     Regards
>      >
>      >>
>      >> Regards
>      >>
>      >>> Note that at first you can ignore the thermal effect and
>     compute the
>      >>> free energy from a regular phonon calculations.
>      >>> I'm also very interested in such calculations but don't have
>     experiences
>      >>> doing this by mean of first principal calculations.
>
>
>
>     --
>     Hongsheng Zhao <zhaohscas at yahoo.com.cn <mailto:zhaohscas at yahoo.com.cn>>
>     School of Physics and Electrical Information Science,
>     Ningxia University, Yinchuan 750021, China
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
> Amin Torabi
> Ph.D. Student
> Chemistry Department
> /The/ University /of/ Western Ontario
> London, On Canada, N6A 5B7
> Phone: 519-661-2111 Ext: 87871
> ****************************************
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From sclauzer at sissa.it  Tue Jul 19 08:51:34 2011
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 19 Jul 2011 08:51:34 +0200
Subject: [Pw_forum] Opening .xml files on linux
In-Reply-To: <1311022214.3759.YahooMailNeo@web43408.mail.sp1.yahoo.com>
References: <CANxi7+O8VJ6He1JsH0jV06tWaLEangyW2g4g8JXzTk2JRWXg0g@mail.gmail.com>
	<1310493661.76035.YahooMailNeo@web43412.mail.sp1.yahoo.com>
	<4A6933F2-7335-42F5-83E4-6DDD81A9DE34@sissa.it>
	<1311013149.22516.YahooMailNeo@web43407.mail.sp1.yahoo.com>
	<1311022214.3759.YahooMailNeo@web43408.mail.sp1.yahoo.com>
Message-ID: <51BBBB32-7A41-4BD6-9422-424FB72E6F44@sissa.it>

I've just downloaded espresso-4.3.1 from here 
http://qe-forge.org/frs/?group_id=10
and I've found that both .html and .txt files are already present in the Doc/ folder as usual (what I said about "make doc" maybe applies to the CVS version, if I remember well).
So you should have no problem to get those files and I don't see why you want to display the .xml files, since you should have also the other formats.

GS


Il giorno 18/lug/2011, alle ore 22.50, Izaak Williamson ha scritto:

> After running ./configure I used the command "make all" and usually, the Doc file is created with the necessary .txt and .html files. With the newest version (4.3.1) however, instead of having INPUT_PW.txt for example, it has INPUT_PW.xml. There are no .txt or .html files anymore. I do not mind that the .txt files are not there, I just want to be able to open the .xml files properly.
> 
> Thanks for the help.
> 
> From: Gabriele Sclauzero <sclauzer at sissa.it>
> To: Izaak Williamson <izaakw89 at yahoo.com>; PWSCF Forum <pw_forum at pwscf.org>
> Sent: Monday, July 18, 2011 1:59 AM
> Subject: Re: [Pw_forum] Opening .xml files on linux
> 
> Have you tried with
>    make doc
> after running configure? The .txt and .html files should appear in the Doc directory.
> 
> HTH
> 
> GS
> 
> Il giorno 12/lug/2011, alle ore 20.01, Izaak Williamson ha scritto:
> 
>> Hello everyone,
>> 
>> I noticed the new version of QUANTUM ESPRESSO (4.3.1) has changed all of its documentation files to .xml (instead of the former .txt). The problem is, when I try to open these files through firefox, none of the formatting is kept. Everything is written as one continuous paragraph making it very difficult to read. How are these files meant to be opened? Is there an add-on or program that I will need to download?
>> 
>> Thanks in advance.
>> 
>> -- 
>> Izaak Williamson
>> Research Assistant
>> Physics Department
>> Boise State University
>> 
>> 
>> 
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>    PH H2 462, Station 3, CH-1015 Lausanne
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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

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From zhaohscas at yahoo.com.cn  Tue Jul 19 10:40:54 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 19 Jul 2011 16:40:54 +0800
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <4E257835.70409@gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<4E23E910.1050004@yahoo.com.cn>	<CAEXRF5z8Qzw9cy1D7=Dt-bumGwvjyZ0bQ1yQ=Ja1Zn8j7pD0Ww@mail.gmail.com>	<511034047.29551@test1.gucas.ac.cn>
	<4E257835.70409@gucas.ac.cn>
Message-ID: <4E254316.7000700@yahoo.com.cn>

On 07/19/2011 08:27 PM, Eric Germaneau wrote:
[snipped]
> The guy wanted our opening, I got it.

What's  the meaning of this sentence?  It's so incomprehensible to me.

Regards
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From zhaohscas at yahoo.com.cn  Tue Jul 19 10:43:49 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 19 Jul 2011 16:43:49 +0800
Subject: [Pw_forum] The issue confused me when calculating the elastic
	constants.
Message-ID: <4E2543C5.5030800@yahoo.com.cn>

Hi all,

You can find the following descriptions from this website: 
http://dft-blog.natanzon.eu/search/label/SIESTA,

--------------
?SIESTA calculates stress tensor and you know stress/strain relationship 
from the textbooks. You have to relax your system properly to have your 
stress tensor be close to zero. Then manually deform lattice vectors in 
selected directions and obtain the value of stress. For example, if you 
want to calculate C11, you have to deform lattice vector a (I suppose it 
is (a,0,0)) to a(1+e), where e is your value of strain. Then you make 
the calculation with relaxing atomic positions but NOT lattice vectors 
(VariableCell false) and obtain the value of stress tensor Sigma_ij and 
find C11:

C11 = Sigma11/e?
--------------

 From the above description, we can know that this method do a 
non-VariableCell calculation after manually deforming the lattice 
vector, in this case, changing a --> into a(1+e).  My issue is: due to 
the cell's shape been fixed, the cell's volume is also fixed.  But when 
we impose a strain along the direction of lattice vector a, I think the 
system should has a shrinking effect in the direction perpendicular to 
the strain's direction.  So I think, during the relaxing calculation, 
both the  atomic positions and the lattice vector perpendicular to 
lattice vector *a* should be changeable while keeping the   lattice 
vector *a* fixed after manually strained it.  Any hints on my confusion 
  will be highly appreciated.  Thanks in advance.

Best
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From victor.bermudez at nrl.navy.mil  Tue Jul 19 12:33:09 2011
From: victor.bermudez at nrl.navy.mil (Vic Bermudez)
Date: Tue, 19 Jul 2011 06:33:09 -0400
Subject: [Pw_forum] Restarting a NEB Calculation
Message-ID: <AKEFIBNCPJEJJMHNOPHIMEHKCHAA.victor.bermudez@nrl.navy.mil>

Hello,

	Can someone please tell me what is required to restart a NEB calculation
that has timed out ?  What files from the initial run are needed for the
restart ?  Are there any file naming conventions that must be followed ?
What modifications (other than restart_mode='restart') are needed in the
input file ?
	One final question ... does it make any difference whether I restart using
the latest .path file from the previous run or manually, using the latest
atom positions in the .crd file ?

	Thanks,
	Vic Bermudez

Victor M. Bermudez
Code 6876
U.S. Naval Research Laboratory
4555 Overlook Ave., S.W.
Washington, DC 20375-5347

Phone: 202-767-6728
FAX: 202-767-1165
E-mail: victor.bermudez at nrl.navy.mil


From gabriel.greene at tyndall.ie  Tue Jul 19 13:14:15 2011
From: gabriel.greene at tyndall.ie (Gabriel Greene)
Date: Tue, 19 Jul 2011 12:14:15 +0100
Subject: [Pw_forum] PBE Hybrid funcitonals and LDA pseudopotentials
Message-ID: <D4A761F73683694BBD69D634FF298015C03751@MAIL.tyndall.ie>

Hi,

I have been attempting to use the hybrid functional PBE0 to tune the bandgap of InGaAs, while using Virtual Crystal Approximation to obtain In(0.57)Ga(0.43)As. I initially tried mixing the PBE pseudos of Ga and In, but ran into a number of problems (unequal nqf mesh when mixing, and using ultrasoft pseudos with hybrid functionals).

I then tried the Norm-conserving LDA pseudos (which also have no nqf information to worry about) for mixing In and Ga (also using LDA for As pseudo, obviously). I then found I could tune the bandgap by specifying "PBE0" in the &SYSTEM card of the input file by changing the proportion of Fock exchange (alpha, or "exx_fraction" in funct.f90), while specifying LDA pseudos for each atomic species.

I am surprised this would work because my understanding is that LDA contains no exchange term, yet modifying the value of alpha has an effect on the bandgap just like if I had specified PBE pseudopotentials in the ATOMIC_SPECIES card. I initially set up this calculation as a test to just prove to myself that the results obtained using LDA pseudopotentials are independant of the amount of exchange, yet this is not so.

My understanding of hybrid functional implementation is obviously incomplete, so can someone help me understand these results?

Thank you very much for the help,

Gabriel Greene,
PhD student, Electronics Theory Group,
Tyndall National Institute,
Cork Ireland
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From pascal.boulet at univ-provence.fr  Tue Jul 19 15:47:13 2011
From: pascal.boulet at univ-provence.fr (pascal boulet)
Date: Tue, 19 Jul 2011 15:47:13 +0200
Subject: [Pw_forum]  Pressure-induced phase transition
Message-ID: <4E258AE1.4000609@univ-provence.fr>

Dear Amin,

Regarding your question:

And how can I use phonon calculations to help me find the phase transition?
I've heard about some "mode softening", but I am not sure how it can be used
in this context?


When pressure changes you may observe that one or several phonon modes
are softening, meaning, their frequencies are decreasing, eventually
becoming imaginary in values. To see this you have to calculate the
phonon dispersion band, that is, the phonon modes over the whole
Brillouin zone (BZ), not just at the gamma point. If for some pressure
you observe a negative (or more correctly imaginary) frequency at a
particular q-point of the BZ, it means that the system undergoes an
instability and is likely to transform into another structure.

This you can see in the following paper: Phys. Rev. B, 78, 100102(R),
2008 in Figure 3b where the phonon softening is observed at the X q-point.


Regards
Pascal




    * Anglais - d?tect?
    * Anglais
    * Fran?ais

    * Anglais
    * Fran?ais

<javascript:void(0);>

From abdulrafiuraji at gmail.com  Tue Jul 19 18:35:25 2011
From: abdulrafiuraji at gmail.com (Abdulrafiu Raji)
Date: Tue, 19 Jul 2011 18:35:25 +0200
Subject: [Pw_forum] Problem with XSPECTRA: file can't open
Message-ID: <CACJL2X4CDtJc9bvgkjTjk90NEbg3DzeNuUs7eY8hX-E_B+489w@mail.gmail.com>

Dear QE users,

I was trying to run the Xspectra.x code on a linux cluster machine. However,
the xspectra.x code stops just after it starts with some error messages
(please find below). I used the same version of the code for the 'scf' and
xanes-dipole calculations, i.e. version 4.2.1.   You will observed that I
have not done much modifications to the 'xanes-dipole'  input file given in
the examples, in the code. The present calculations are suppose to be dry
runs for more realistic calculations. You will also find below, input files
for the scf and 'xanes-dipole' used for the runs. I guarantee that the
relevant directories/files exist.
Thank you for your attention.

Abdulrafiu Raji,
ICTP, Trieste,
Italy.


==============

Program XSPECTRA v.4.2.1   starts on 19Jul2011 at 17:45: 8

     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
 bef

     Program XSPECTRA v.4.2.1   starts on 19Jul2011 at 17:45: 8

     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

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from input_xspectra : error #         1
     reading input_xspectra namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

     Program XSPECTRA v.4.2.1   starts on 19Jul2011 at 17:45: 8

     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

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from input_xspectra : error #         1
     reading input_xspectra namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

     Program XSPECTRA v.4.2.1   starts on 19Jul2011 at 17:45: 8

     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

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from input_xspectra : error #         1
     reading input_xspectra namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

     Program XSPECTRA v.4.2.1   starts on 19Jul2011 at 17:45: 8

     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

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from input_xspectra : error #         1
     reading input_xspectra namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

     Program XSPECTRA v.4.2.1   starts on 19Jul2011 at 17:45: 8

     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

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from input_xspectra : error #         1
     reading input_xspectra namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

     Program XSPECTRA v.4.2.1   starts on 19Jul2011 at 17:45: 8

     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

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from input_xspectra : error #         1
     reading input_xspectra namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

     Program XSPECTRA v.4.2.1   starts on 19Jul2011 at 17:45: 8

     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

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from input_xspectra : error #         1
     reading input_xspectra namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from read_rho_xml : error #         1
     cannot open
/home/araji/XAS_SiO2_scr.1/qtz_ar1SCF_kp2.save/charge-density.dat file for
reading
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

======================================================


&input_xspectra
    calculation='xanes_dipole'
    prefix='qtz_ar1SCF_kp2',
    outdir='/home/araji/XAS_SiO2_scr.1/',
    xonly_plot=.false.,
    xniter=2000,
    xcheck_conv=50,
    xepsilon(1)=1.0,
    xepsilon(2)=1.0,
    xepsilon(3)=0.0,
    xiabs=1,
    x_save_file='SiO2.XAS.pln.sav',
    xread_wf=.false.,
    ef_r=0.402521132,
    xerror=0.001,
    wf_collect=.true.,
 /
 &plot
    xnepoint=1000,
    xgamma=0.8,
    xemin=-10.0,
    xemax=100.0,
    terminator=.true.,
    cut_occ_states=.true.,
 &end
 &pseudos
    filecore='Si.wfc',
    r_paw(1)=2.4,
 &end
 &cut_occ
    cut_desmooth=0.1,
 &end
3 3 3 0 0 0

=============================================

 &control
    calculation='scf',
    restart_mode='from_scratch',
    pseudo_dir = '/home/araji/pseudo/',
    outdir =  '/home/araji/XAS_SiO2_scr.1/',
    prefix ='qtz_ar1SCF_kp2',
    verbosity = 'high',
    wf_collect = .true.,
    tstress = .true.
    tprnfor = .true.
 &end

 &system
    ibrav = 4 ,
    celldm(1) = 18.57259936,
    celldm(3) = 1.10010,
    nat = 72 ,
    ntyp = 3 ,
    nspin = 1,
    ecutwfc = 20.0,
    ecutrho = 150.0,
    nbnd    =  220
    smearing = 'mp',
    occupations ='smearing',
    degauss = 0.03,
 &end

 &electrons
    diagonalization ='david',
    conv_thr = 1.d-7,
    mixing_mode = 'local-TF',
    mixing_beta = 0.4,
 &end

ATOMIC_SPECIES
Sih 28.086   Si.pbe-n-van.UPF
Si 28.086    Si.pbe-n-van.UPF
O  15.9994   O.pbe-van_bm.UPF

ATOMIC_POSITIONS (angstrom)
Sih       2.285991646   0.000000000   0.000000000
Si      -1.143116139   1.979809724   3.604091561
Si      -1.143116068  -1.979809771   1.801907971
Si       2.285991634  -0.000000000   5.405999279
Si      -1.143116068   1.979809771   9.010090587
Si      -1.143116139  -1.979809724   7.207906997
Si      -0.170757339   4.255645987   0.000049498
Si      -3.600430710   6.235957125   3.604080320
Si      -3.600218341   2.275689888   1.801903273
Si      -0.170757352   4.255645987   5.406048778
Si      -3.600430638   6.235957173   9.010079346
...
....
....
.
.
.
.
.
.
K_POINTS (automatic)
2       2      2     0       0      0

=================================
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From giannozz at democritos.it  Tue Jul 19 19:08:32 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 19 Jul 2011 19:08:32 +0200
Subject: [Pw_forum] Problem with XSPECTRA: file can't open
In-Reply-To: <CACJL2X4CDtJc9bvgkjTjk90NEbg3DzeNuUs7eY8hX-E_B+489w@mail.gmail.com>
References: <CACJL2X4CDtJc9bvgkjTjk90NEbg3DzeNuUs7eY8hX-E_B+489w@mail.gmail.com>
Message-ID: <DA9BA2F3-B831-4DF7-A104-A3EA0B79356F@democritos.it>

Let me guess: you are running in parallel (with mpirun or
mpiexec) an executable compiled for serial execution

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 germaneau at gucas.ac.cn  Wed Jul 20 15:05:24 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Wed, 20 Jul 2011 09:05:24 -0400
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <511038476.25140@test1.gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<510975832.04103@test1.gucas.ac.cn>	<4E24DCAA.7000709@gucas.ac.cn>
	<510999887.17934@test1.gucas.ac.cn> <4E25612D.4090704@gucas.ac.cn>
	<511038476.25140@test1.gucas.ac.cn>
Message-ID: <4E26D294.1040001@gucas.ac.cn>



On 07/18/2011 09:28 PM, Hongsheng Zhao wrote:
> On 07/19/2011 06:49 PM, Eric Germaneau wrote:
>>
>> On 07/18/2011 10:45 AM, Hongsheng Zhao wrote:
>>> On 07/19/2011 09:23 AM, Eric Germaneau wrote:
>>>> Hey Amin,
>>>>
>>>> The approach you proposed is ok but you should relax the cell as well.
>>>> By keeping the cell fix the system does not feel the pressure you wish
>>>> to apply.
>>> Not so clear about the meaning of this sentence, could you please give
>>> some more explanations? ;-(
>> Under pressure keeping the unit cell fix is useless since the system
>> won't feel it.
>> It just makes sense.
>> So, if you wish to see the effect of the pressure you have to perform
>> vc-relax calculation.
>> Take it that way, in thermodynamic you have 2 important ensembles,
>> isochoric and isobaric.
>> So either the volume is fix and you get out the corresponding pressure,
>> or the pressure is fix and you get out the corresponding volume.
>> Note that the volume of gas for instance decreases inversely
>> proportionally to pressure.
>> The pressure is the intensive variable related to the volume (extensive).
>> You simply can not have both of them constant at the same time.
> Yes, you're right.  I'm so sorry for my previous misleading posts on
> this thread.  Thanks again.
No worries!
I'm glad to see that this discussion was useful.
Best,

         ?ric.
>
>> Hope it helps.
>>>> You can also change the volume, relax the positions only and compute the
>>>> pressure.
>>>> The best is to compute the free energy as function of pressure ans so
>>>> the QHA method is the best way to go.
>>> I think this method cann't do the job of structure-searching-and-finding
>>> for unknown phases when we changing the external pressure.
>> Yes, it can but in the case of structure-searching it's very expensive.
>> In that case you'd better generate random unit cell parameters, random
>> positions and run vc-relax.
>> Even this can be expensive since you have to do it a lot of times ....
>> Just take a look to this papers, PRL 97 1 (2006)
>> <http://link.aps.org/doi/10.1103/PhysRevLett.97.045504>  and JPCM 23
>> 053201 (2011)
>> <http://stacks.iop.org/0953-8984/23/i=5/a=053201?key=crossref.44087776832bc9a0edd0dc492a67d376>.
>> It is the main work of Professor Pickard
>> <http://www.st-andrews.ac.uk/physics/condmat/pickard/Crystals%20ex%20nihilo.html>.
>> Best.
> Thanks a lot for this information ;-)
>
> Regards
>>> Regards
>>>
>>>> Note that at first you can ignore the thermal effect and compute the
>>>> free energy from a regular phonon calculations.
>>>> I'm also very interested in such calculations but don't have experiences
>>>> doing this by mean of first principal calculations.
>
>

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html /

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From germaneau at gucas.ac.cn  Wed Jul 20 15:08:15 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Wed, 20 Jul 2011 09:08:15 -0400
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <511064387.08802@test1.gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<4E23E910.1050004@yahoo.com.cn>	<CAEXRF5z8Qzw9cy1D7=Dt-bumGwvjyZ0bQ1yQ=Ja1Zn8j7pD0Ww@mail.gmail.com>	<511034047.29551@test1.gucas.ac.cn>
	<4E257835.70409@gucas.ac.cn> <511064387.08802@test1.gucas.ac.cn>
Message-ID: <4E26D33F.7070003@gucas.ac.cn>

Sorry, I wanted to say opinion (point of view).
My mind gets stuck sometime :-)

On 07/19/2011 04:40 AM, Hongsheng Zhao wrote:
> On 07/19/2011 08:27 PM, Eric Germaneau wrote:
> [snipped]
>> The guy wanted our opening, I got it.
> What's  the meaning of this sentence?  It's so incomprehensible to me.
>
> Regards

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html /

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From germaneau at gucas.ac.cn  Wed Jul 20 15:24:20 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Wed, 20 Jul 2011 09:24:20 -0400
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <511040348.32013@test1.gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>
	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>
	<510975832.04103@test1.gucas.ac.cn> <4E24DCAA.7000709@gucas.ac.cn>
	<510999887.17934@test1.gucas.ac.cn>
	<4E25612D.4090704@gucas.ac.cn> <4E24DDD1.5040603@yahoo.com.cn>
	<511040348.32013@test1.gucas.ac.cn>
Message-ID: <4E26D704.20404@gucas.ac.cn>

Well, I don't know about "common tangent" concept.
You can study structure stability looking at phonon dispersion for instance.
An instability could mean that the structure undergoes a phase 
transition (or that it's not fully relaxed)
You can also compute the free energy of your system where phonons will 
give you the harmonic part (see PRL 64 045123 (2001) 
<http://link.aps.org/doi/10.1103/PhysRevB.64.045123>).
So you can look at several thing when changing the pressure, among them 
structure change, phonon, energy, free energy (not that easy).
Why not electronic density of sates?
Good luck,

           ?ric.

On 07/18/2011 09:46 PM, Amin Torabi wrote:
> Thanks Eric and Hongsheng for the discussion!
>
> Can I also have your comments on this "common tangent" concept in 
> first order phase transitions? Is it applicable for my case?
>
>
> And how can I use phonon calculations to help me find the phase 
> transition? I've heard about some "mode softening", but I am not sure 
> how it can be used in this context? Could you refer me to some article 
> explaining the theory behind this
>
> Thanks again
> Amin
>
>
>
>
>
> On Mon, Jul 18, 2011 at 9:28 PM, Hongsheng Zhao 
> <zhaohscas at yahoo.com.cn <mailto:zhaohscas at yahoo.com.cn>> wrote:
>
>     On 07/19/2011 06:49 PM, Eric Germaneau wrote:
>     >
>     >
>     > On 07/18/2011 10:45 AM, Hongsheng Zhao wrote:
>     >> On 07/19/2011 09:23 AM, Eric Germaneau wrote:
>     >>> Hey Amin,
>     >>>
>     >>> The approach you proposed is ok but you should relax the cell
>     as well.
>     >>> By keeping the cell fix the system does not feel the pressure
>     you wish
>     >>> to apply.
>     >> Not so clear about the meaning of this sentence, could you
>     please give
>     >> some more explanations? ;-(
>     > Under pressure keeping the unit cell fix is useless since the system
>     > won't feel it.
>     > It just makes sense.
>     > So, if you wish to see the effect of the pressure you have to
>     perform
>     > vc-relax calculation.
>     > Take it that way, in thermodynamic you have 2 important ensembles,
>     > isochoric and isobaric.
>     > So either the volume is fix and you get out the corresponding
>     pressure,
>     > or the pressure is fix and you get out the corresponding volume.
>     > Note that the volume of gas for instance decreases inversely
>     > proportionally to pressure.
>     > The pressure is the intensive variable related to the volume
>     (extensive).
>     > You simply can not have both of them constant at the same time.
>
>     Yes, you're right.  I'm so sorry for my previous misleading posts on
>     this thread.  Thanks again.
>
>     > Hope it helps.
>     >>
>     >>> You can also change the volume, relax the positions only and
>     compute the
>     >>> pressure.
>     >>> The best is to compute the free energy as function of pressure
>     ans so
>     >>> the QHA method is the best way to go.
>     >> I think this method cann't do the job of
>     structure-searching-and-finding
>     >> for unknown phases when we changing the external pressure.
>     > Yes, it can but in the case of structure-searching it's very
>     expensive.
>     > In that case you'd better generate random unit cell parameters,
>     random
>     > positions and run vc-relax.
>     > Even this can be expensive since you have to do it a lot of
>     times ....
>     > Just take a look to this papers, PRL 97 1 (2006)
>     > <http://link.aps.org/doi/10.1103/PhysRevLett.97.045504> and JPCM 23
>     > 053201 (2011)
>     >
>     <http://stacks.iop.org/0953-8984/23/i=5/a=053201?key=crossref.44087776832bc9a0edd0dc492a67d376>.
>     > It is the main work of Professor Pickard
>     >
>     <http://www.st-andrews.ac.uk/physics/condmat/pickard/Crystals%20ex%20nihilo.html>.
>     > Best.
>
>     Thanks a lot for this information ;-)
>
>     Regards
>     >
>     >>
>     >> Regards
>     >>
>     >>> Note that at first you can ignore the thermal effect and
>     compute the
>     >>> free energy from a regular phonon calculations.
>     >>> I'm also very interested in such calculations but don't have
>     experiences
>     >>> doing this by mean of first principal calculations.
>
>
>
>     --
>     Hongsheng Zhao <zhaohscas at yahoo.com.cn
>     <mailto:zhaohscas at yahoo.com.cn>>
>     School of Physics and Electrical Information Science,
>     Ningxia University, Yinchuan 750021, China
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> -- 
> Amin Torabi
> Ph.D. Student
> Chemistry Department
> /The/ University /of/ Western Ontario
> London, On Canada, N6A 5B7
> Phone: 519-661-2111 Ext: 87871
> ****************************************
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/Please, if possible, don't send me MS Word or PowerPoint attachments
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From zhaohscas at yahoo.com.cn  Wed Jul 20 04:21:47 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Wed, 20 Jul 2011 10:21:47 +0800
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <4E26D704.20404@gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<510975832.04103@test1.gucas.ac.cn>
	<4E24DCAA.7000709@gucas.ac.cn>	<510999887.17934@test1.gucas.ac.cn>	<4E25612D.4090704@gucas.ac.cn>
	<4E24DDD1.5040603@yahoo.com.cn>	<511040348.32013@test1.gucas.ac.cn>
	<4E26D704.20404@gucas.ac.cn>
Message-ID: <4E263BBB.5080705@yahoo.com.cn>

On 07/20/2011 09:24 PM, Eric Germaneau wrote:
> Well, I don't know about "common tangent" concept.

See the page 3 of this notes by Keith Refson:

http://www.castep.org/CASTEP_talks_07/refson2.pdf


> You can study structure stability looking at phonon dispersion for instance.
> An instability could mean that the structure undergoes a phase
> transition (or that it's not fully relaxed)

What's the characteristic of the phonon dispersion when phase transition 
occurs?  More hints?

> You can also compute the free energy of your system where phonons will
> give you the harmonic part (see PRL 64 045123 (2001)
> <http://link.aps.org/doi/10.1103/PhysRevB.64.045123>).
> So you can look at several thing when changing the pressure, among them
> structure change, phonon, energy, free energy (not that easy).
> Why not electronic density of sates?

Again, do you have experience in using DOS for judging phase transition? 
  Any hints on the  the characteristic of it when the phase transition 
occurs?

Regards
> Good luck,
>
> ?ric.
>
> On 07/18/2011 09:46 PM, Amin Torabi wrote:
>> Thanks Eric and Hongsheng for the discussion!
>>
>> Can I also have your comments on this "common tangent" concept in
>> first order phase transitions? Is it applicable for my case?
>>
>>
>> And how can I use phonon calculations to help me find the phase
>> transition? I've heard about some "mode softening", but I am not sure
>> how it can be used in this context? Could you refer me to some article
>> explaining the theory behind this
>>
>> Thanks again
>> Amin
>>
>>
>>
>>
>>
>> On Mon, Jul 18, 2011 at 9:28 PM, Hongsheng Zhao
>> <zhaohscas at yahoo.com.cn <mailto:zhaohscas at yahoo.com.cn>> wrote:
>>
>>     On 07/19/2011 06:49 PM, Eric Germaneau wrote:
>>     >
>>     >
>>     > On 07/18/2011 10:45 AM, Hongsheng Zhao wrote:
>>     >> On 07/19/2011 09:23 AM, Eric Germaneau wrote:
>>     >>> Hey Amin,
>>     >>>
>>     >>> The approach you proposed is ok but you should relax the cell
>>     as well.
>>     >>> By keeping the cell fix the system does not feel the pressure
>>     you wish
>>     >>> to apply.
>>     >> Not so clear about the meaning of this sentence, could you
>>     please give
>>     >> some more explanations? ;-(
>>     > Under pressure keeping the unit cell fix is useless since the system
>>     > won't feel it.
>>     > It just makes sense.
>>     > So, if you wish to see the effect of the pressure you have to
>>     perform
>>     > vc-relax calculation.
>>     > Take it that way, in thermodynamic you have 2 important ensembles,
>>     > isochoric and isobaric.
>>     > So either the volume is fix and you get out the corresponding
>>     pressure,
>>     > or the pressure is fix and you get out the corresponding volume.
>>     > Note that the volume of gas for instance decreases inversely
>>     > proportionally to pressure.
>>     > The pressure is the intensive variable related to the volume
>>     (extensive).
>>     > You simply can not have both of them constant at the same time.
>>
>>     Yes, you're right. I'm so sorry for my previous misleading posts on
>>     this thread. Thanks again.
>>
>>     > Hope it helps.
>>     >>
>>     >>> You can also change the volume, relax the positions only and
>>     compute the
>>     >>> pressure.
>>     >>> The best is to compute the free energy as function of pressure
>>     ans so
>>     >>> the QHA method is the best way to go.
>>     >> I think this method cann't do the job of
>>     structure-searching-and-finding
>>     >> for unknown phases when we changing the external pressure.
>>     > Yes, it can but in the case of structure-searching it's very
>>     expensive.
>>     > In that case you'd better generate random unit cell parameters,
>>     random
>>     > positions and run vc-relax.
>>     > Even this can be expensive since you have to do it a lot of
>>     times ....
>>     > Just take a look to this papers, PRL 97 1 (2006)
>>     > <http://link.aps.org/doi/10.1103/PhysRevLett.97.045504> and JPCM 23
>>     > 053201 (2011)
>>     >
>>     <http://stacks.iop.org/0953-8984/23/i=5/a=053201?key=crossref.44087776832bc9a0edd0dc492a67d376>.
>>     > It is the main work of Professor Pickard
>>     >
>>     <http://www.st-andrews.ac.uk/physics/condmat/pickard/Crystals%20ex%20nihilo.html>.
>>     > Best.
>>
>>     Thanks a lot for this information ;-)
>>
>>     Regards
>>     >
>>     >>
>>     >> Regards
>>     >>
>>     >>> Note that at first you can ignore the thermal effect and
>>     compute the
>>     >>> free energy from a regular phonon calculations.
>>     >>> I'm also very interested in such calculations but don't have
>>     experiences
>>     >>> doing this by mean of first principal calculations.
>>
>>
>>
>>     --
>>     Hongsheng Zhao <zhaohscas at yahoo.com.cn
>>     <mailto:zhaohscas at yahoo.com.cn>>
>>     School of Physics and Electrical Information Science,
>>     Ningxia University, Yinchuan 750021, China
>>     _______________________________________________
>>     Pw_forum mailing list
>>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>>     http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>>
>>
>> --
>> Amin Torabi
>> Ph.D. Student
>> Chemistry Department
>> /The/ University /of/ Western Ontario
>> London, On Canada, N6A 5B7
>> Phone: 519-661-2111 Ext: 87871
>> ****************************************
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
> --
> /Be the change you wish to see in the world
> / ? Mahatma Gandhi ?
>
> Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>
>
> College of Physical Sciences
> Graduate University of Chinese Academy of Sciences
> Yuquan Road 19A
> Beijing 100049
> China
>
> /Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html /
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From xjin.xmu at gmail.com  Wed Jul 20 04:27:05 2011
From: xjin.xmu at gmail.com (jinxi)
Date: Wed, 20 Jul 2011 10:27:05 +0800
Subject: [Pw_forum] compiling upftools meet error with pgi7.0
Message-ID: <4E263CF9.4010209@gmail.com>

Dear all:

When I ''make upf'' with pgi 7.0, I meet error with:

''PGF90-S-0038-Symbol, sizeof, has not been explicitly declared 
(casino_pp.F90)
   0 inform,   0 warnings,   1 severes, 0 fatal for write_casino_tab
make[1]: *** [casino_pp.o] Error 2''

How can I make upf ?
If possible, how to modify the code in file ''casino_pp.F90''?

Many thanks!

From germaneau at gucas.ac.cn  Wed Jul 20 16:45:29 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Wed, 20 Jul 2011 10:45:29 -0400
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <511128033.30830@test1.gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>	<510975832.04103@test1.gucas.ac.cn>
	<4E24DCAA.7000709@gucas.ac.cn>	<510999887.17934@test1.gucas.ac.cn>	<4E25612D.4090704@gucas.ac.cn>
	<4E24DDD1.5040603@yahoo.com.cn>	<511040348.32013@test1.gucas.ac.cn>
	<4E26D704.20404@gucas.ac.cn> <511128033.30830@test1.gucas.ac.cn>
Message-ID: <4E26EA09.9050406@gucas.ac.cn>



On 07/19/2011 10:21 PM, Hongsheng Zhao wrote:
> On 07/20/2011 09:24 PM, Eric Germaneau wrote:
>> Well, I don't know about "common tangent" concept.
> See the page 3 of this notes by Keith Refson:
>
> http://www.castep.org/CASTEP_talks_07/refson2.pdf
Thank you.
>
>
>> You can study structure stability looking at phonon dispersion for instance.
>> An instability could mean that the structure undergoes a phase
>> transition (or that it's not fully relaxed)
> What's the characteristic of the phonon dispersion when phase transition
> occurs?  More hints?
I noticed the reply of Pascal Boulet after I sent my post. He point it 
out very well.
>
>> You can also compute the free energy of your system where phonons will
>> give you the harmonic part (see PRL 64 045123 (2001)
>> <http://link.aps.org/doi/10.1103/PhysRevB.64.045123>).
>> So you can look at several thing when changing the pressure, among them
>> structure change, phonon, energy, free energy (not that easy).
>> Why not electronic density of sates?
> Again, do you have experience in using DOS for judging phase transition?
>    Any hints on the  the characteristic of it when the phase transition
> occurs?
I've no idea, that was just a suggestion.
I suppose some change may occur in the electronic structure ...
But the effect of the pressure on the electronic structure may be less 
significant than the temperature. I don't know.
An expert on /ab initio/ calculation would be able to give you an answer.
>
> Regards
>> Good luck,
>>
>> ?ric.
>>
>> On 07/18/2011 09:46 PM, Amin Torabi wrote:
>>> Thanks Eric and Hongsheng for the discussion!
>>>
>>> Can I also have your comments on this "common tangent" concept in
>>> first order phase transitions? Is it applicable for my case?
>>>
>>>
>>> And how can I use phonon calculations to help me find the phase
>>> transition? I've heard about some "mode softening", but I am not sure
>>> how it can be used in this context? Could you refer me to some article
>>> explaining the theory behind this
>>>
>>> Thanks again
>>> Amin
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Jul 18, 2011 at 9:28 PM, Hongsheng Zhao
>>> <zhaohscas at yahoo.com.cn<mailto:zhaohscas at yahoo.com.cn>>  wrote:
>>>
>>>      On 07/19/2011 06:49 PM, Eric Germaneau wrote:
>>>      >
>>>      >
>>>      >  On 07/18/2011 10:45 AM, Hongsheng Zhao wrote:
>>>      >>  On 07/19/2011 09:23 AM, Eric Germaneau wrote:
>>>      >>>  Hey Amin,
>>>      >>>
>>>      >>>  The approach you proposed is ok but you should relax the cell
>>>      as well.
>>>      >>>  By keeping the cell fix the system does not feel the pressure
>>>      you wish
>>>      >>>  to apply.
>>>      >>  Not so clear about the meaning of this sentence, could you
>>>      please give
>>>      >>  some more explanations? ;-(
>>>      >  Under pressure keeping the unit cell fix is useless since the system
>>>      >  won't feel it.
>>>      >  It just makes sense.
>>>      >  So, if you wish to see the effect of the pressure you have to
>>>      perform
>>>      >  vc-relax calculation.
>>>      >  Take it that way, in thermodynamic you have 2 important ensembles,
>>>      >  isochoric and isobaric.
>>>      >  So either the volume is fix and you get out the corresponding
>>>      pressure,
>>>      >  or the pressure is fix and you get out the corresponding volume.
>>>      >  Note that the volume of gas for instance decreases inversely
>>>      >  proportionally to pressure.
>>>      >  The pressure is the intensive variable related to the volume
>>>      (extensive).
>>>      >  You simply can not have both of them constant at the same time.
>>>
>>>      Yes, you're right. I'm so sorry for my previous misleading posts on
>>>      this thread. Thanks again.
>>>
>>>      >  Hope it helps.
>>>      >>
>>>      >>>  You can also change the volume, relax the positions only and
>>>      compute the
>>>      >>>  pressure.
>>>      >>>  The best is to compute the free energy as function of pressure
>>>      ans so
>>>      >>>  the QHA method is the best way to go.
>>>      >>  I think this method cann't do the job of
>>>      structure-searching-and-finding
>>>      >>  for unknown phases when we changing the external pressure.
>>>      >  Yes, it can but in the case of structure-searching it's very
>>>      expensive.
>>>      >  In that case you'd better generate random unit cell parameters,
>>>      random
>>>      >  positions and run vc-relax.
>>>      >  Even this can be expensive since you have to do it a lot of
>>>      times ....
>>>      >  Just take a look to this papers, PRL 97 1 (2006)
>>>      >  <http://link.aps.org/doi/10.1103/PhysRevLett.97.045504>  and JPCM 23
>>>      >  053201 (2011)
>>>      >
>>>      <http://stacks.iop.org/0953-8984/23/i=5/a=053201?key=crossref.44087776832bc9a0edd0dc492a67d376>.
>>>      >  It is the main work of Professor Pickard
>>>      >
>>>      <http://www.st-andrews.ac.uk/physics/condmat/pickard/Crystals%20ex%20nihilo.html>.
>>>      >  Best.
>>>
>>>      Thanks a lot for this information ;-)
>>>
>>>      Regards
>>>      >
>>>      >>
>>>      >>  Regards
>>>      >>
>>>      >>>  Note that at first you can ignore the thermal effect and
>>>      compute the
>>>      >>>  free energy from a regular phonon calculations.
>>>      >>>  I'm also very interested in such calculations but don't have
>>>      experiences
>>>      >>>  doing this by mean of first principal calculations.
>>>
>>>
>>>
>>>      --
>>>      Hongsheng Zhao<zhaohscas at yahoo.com.cn
>>>      <mailto:zhaohscas at yahoo.com.cn>>
>>>      School of Physics and Electrical Information Science,
>>>      Ningxia University, Yinchuan 750021, China
>>>      _______________________________________________
>>>      Pw_forum mailing list
>>>      Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org>
>>>      http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>>
>>>
>>> --
>>> Amin Torabi
>>> Ph.D. Student
>>> Chemistry Department
>>> /The/ University /of/ Western Ontario
>>> London, On Canada, N6A 5B7
>>> Phone: 519-661-2111 Ext: 87871
>>> ****************************************
>>>
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>> --
>> /Be the change you wish to see in the world
>> / ? Mahatma Gandhi ?
>>
>> Dr. ?ric Germaneau<mailto:germaneau at gucas.ac.cn>
>>
>> College of Physical Sciences
>> Graduate University of Chinese Academy of Sciences
>> Yuquan Road 19A
>> Beijing 100049
>> China
>>
>> /Please, if possible, don't send me MS Word or PowerPoint attachments
>> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html /
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
/Be the change you wish to see in the world
/ ? Mahatma Gandhi ?

Dr. ?ric Germaneau 
<http://www.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html /

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From psavita at crlindia.com  Wed Jul 20 06:51:45 2011
From: psavita at crlindia.com (psavita at crlindia.com)
Date: Wed, 20 Jul 2011 10:21:45 +0530
Subject: [Pw_forum] Restarting a NEB Calculation (Vic Bermudez)
In-Reply-To: <mailman.14266.1311093329.1814.pw_forum@pwscf.org>
References: <mailman.14266.1311093329.1814.pw_forum@pwscf.org>
Message-ID: <OFFD1D52AE.6AE38C18-ON652578D3.001AB5EE-652578D3.001AB5F5@crlindia.com>

An HTML attachment was scrubbed...
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From giannozz at democritos.it  Wed Jul 20 08:16:10 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 20 Jul 2011 08:16:10 +0200
Subject: [Pw_forum] compiling upftools meet error with pgi7.0
In-Reply-To: <4E263CF9.4010209@gmail.com>
References: <4E263CF9.4010209@gmail.com>
Message-ID: <95956499-BFEF-4B6C-9C48-D62C7FA19A23@democritos.it>


On Jul 20, 2011, at 4:27 , jinxi wrote:

> ''PGF90-S-0038-Symbol, sizeof, has not been explicitly declared
> (casino_pp.F90)

tis was fixed three months ago. See revision 7721,
http://qe-forge.org/scm/browser.php?group_id=10

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 20 08:28:42 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 20 Jul 2011 08:28:42 +0200
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <4E26D704.20404@gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>
	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>
	<510975832.04103@test1.gucas.ac.cn> <4E24DCAA.7000709@gucas.ac.cn>
	<510999887.17934@test1.gucas.ac.cn>
	<4E25612D.4090704@gucas.ac.cn> <4E24DDD1.5040603@yahoo.com.cn>
	<511040348.32013@test1.gucas.ac.cn> <4E26D704.20404@gucas.ac.cn>
Message-ID: <A74FB560-D810-4244-956C-D100C9E580C2@democritos.it>


On Jul 20, 2011, at 15:24 , Eric Germaneau wrote:

> Well, I don't know about "common tangent" concept.

you should: it is basic thermodynamics. Some time ago
I wrote something on phase transitions: pag.13-21 of
http://www.fisica.uniud.it/~giannozz/Corsi/sissa02.pdf
These lecture notes are not worth much, but given the
confusion of ideas that emerges from this thread, they
might be useful

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 wonvein at gmail.com  Wed Jul 20 11:26:58 2011
From: wonvein at gmail.com (WANG Wei)
Date: Wed, 20 Jul 2011 18:26:58 +0900
Subject: [Pw_forum] Problem with NEB.x in QE-4.3
In-Reply-To: <F3E9914B-A1E0-4CF6-AED8-A447B38AC4FE@democritos.it>
References: <CAOcD3SLHbygsNq_iYTwTDMgHy6_s-oAyYdGPPTvDv4X1CA+TRQ@mail.gmail.com>
	<F3E9914B-A1E0-4CF6-AED8-A447B38AC4FE@democritos.it>
Message-ID: <CAOcD3SJz=DOL2HROF+jHwcuGQcQ3qyV1qT9R7r5HqMzd21xJYw@mail.gmail.com>

Dear Layla and Prof. Giannozzi,

Thank you for your reply. I think this error which is related with PGI
fortran compiler. Because this error did not occur when I using intel
fortran. I will try to  remove it.

Sincerely,
WANG
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From giuseppe.mattioli at mlib.ism.cnr.it  Wed Jul 20 15:24:41 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Wed, 20 Jul 2011 15:24:41 +0200
Subject: [Pw_forum] Restarting a NEB Calculation
In-Reply-To: <AKEFIBNCPJEJJMHNOPHIMEHKCHAA.victor.bermudez@nrl.navy.mil>
References: <AKEFIBNCPJEJJMHNOPHIMEHKCHAA.victor.bermudez@nrl.navy.mil>
Message-ID: <201107201524.41765.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Vic
You should obtain a smooth restart pattern by adding both a flag in the neb.x 
input section,

BEGIN
BEGIN_PATH_INPUT
&PATH
  restart_mode='restart',
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT

and a flag in the pw.x input section

BEGIN_ENGINE_INPUT
 &CONTROL
    restart_mode='restart',
 /
END_ENGINE_INPUT

HTH

Giuseppe



On Tuesday 19 July 2011 12:33:09 Vic Bermudez wrote:
> Hello,
>
> 	Can someone please tell me what is required to restart a NEB calculation
> that has timed out ?  What files from the initial run are needed for the
> restart ?  Are there any file naming conventions that must be followed ?
> What modifications (other than restart_mode='restart') are needed in the
> input file ?
> 	One final question ... does it make any difference whether I restart using
> the latest .path file from the previous run or manually, using the latest
> atom positions in the .crd file ?
>
> 	Thanks,
> 	Vic Bermudez
>
> Victor M. Bermudez
> Code 6876
> U.S. Naval Research Laboratory
> 4555 Overlook Ave., S.W.
> Washington, DC 20375-5347
>
> Phone: 202-767-6728
> FAX: 202-767-1165
> E-mail: victor.bermudez at nrl.navy.mil
>
> _______________________________________________
> 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 guntram.schmidt at chemie.uni-halle.de  Wed Jul 20 16:01:46 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Wed, 20 Jul 2011 16:01:46 +0200
Subject: [Pw_forum] QHA and monoclinic/orthorhombic structures
In-Reply-To: <4E26EA09.9050406@gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>
	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>
	<510975832.04103@test1.gucas.ac.cn> <4E24DCAA.7000709@gucas.ac.cn>
	<510999887.17934@test1.gucas.ac.cn>
	<4E25612D.4090704@gucas.ac.cn> <4E24DDD1.5040603@yahoo.com.cn>
	<511040348.32013@test1.gucas.ac.cn> <4E26D704.20404@gucas.ac.cn>
	<511128033.30830@test1.gucas.ac.cn> <4E26EA09.9050406@gucas.ac.cn>
Message-ID: <4E26DFCA.3050405@chemie.uni-halle.de>

Dear All,

when trying to understand the Examples of QHA, I saw that the script 
stops execution, when monoclinic or orthorhombic structures are tried to 
be calculated.
Is there a way to get the gibb energy of a monoclinic structure at room 
temperature, anyway? Or is this "ttrinp" not neccesary to do such 
calculations? What is it for, anyways? I couldn't find any documentation 
on it...

Thanks a lot for input on this,
Guntram

From giannozz at democritos.it  Wed Jul 20 16:39:50 2011
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Wed, 20 Jul 2011 16:39:50 +0200
Subject: [Pw_forum] QHA and monoclinic/orthorhombic structures
In-Reply-To: <4E26DFCA.3050405@chemie.uni-halle.de>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>
	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>
	<510975832.04103@test1.gucas.ac.cn> <4E24DCAA.7000709@gucas.ac.cn>
	<510999887.17934@test1.gucas.ac.cn> <4E25612D.4090704@gucas.ac.cn>
	<4E24DDD1.5040603@yahoo.com.cn> <511040348.32013@test1.gucas.ac.cn>
	<4E26D704.20404@gucas.ac.cn> <511128033.30830@test1.gucas.ac.cn>
	<4E26EA09.9050406@gucas.ac.cn> <4E26DFCA.3050405@chemie.uni-halle.de>
Message-ID: <20110720163950.6pwyqa9g1wckc88k@mail.democritos.it>

Quoting Guntram Schmidt <guntram.schmidt at chemie.uni-halle.de>:

> Is there a way to get the gibb energy of a monoclinic structure at room
> temperature, anyway?

there is a simple code, PH/fqha.f90, that calculates the vibrational
contribution to the free energy in the quasi-harmonic approximation,
given the phonon DOS. It is far from sophisticated but works for all
structures

Paolo



----------------------------------------------------------------
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From eyvaz_isaev at yahoo.com  Wed Jul 20 16:46:15 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 20 Jul 2011 07:46:15 -0700 (PDT)
Subject: [Pw_forum] QHA and monoclinic/orthorhombic structures
In-Reply-To: <4E26DFCA.3050405@chemie.uni-halle.de>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>
	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>
	<510975832.04103@test1.gucas.ac.cn> <4E24DCAA.7000709@gucas.ac.cn>
	<510999887.17934@test1.gucas.ac.cn>
	<4E25612D.4090704@gucas.ac.cn> <4E24DDD1.5040603@yahoo.com.cn>
	<511040348.32013@test1.gucas.ac.cn> <4E26D704.20404@gucas.ac.cn>
	<511128033.30830@test1.gucas.ac.cn> <4E26EA09.9050406@gucas.ac.cn>
	<4E26DFCA.3050405@chemie.uni-halle.de>
Message-ID: <1311173175.23248.YahooMailNeo@web65712.mail.ac4.yahoo.com>

Hi,

In fact, these structures are not available yet for phonon DOS calculations via QHA. 

But I am working on orthorhombic structures and hopefully will fix it soon. For monoclinic structures I am not sure. The presence of? predefined ttrinp file is crucial? for the program as it uses the tetrahedra method for integration over the IBZ. 


Another way is calculating phonon DOS via matdyn.x and then use obtained phonon DOS? with F_QHA.x.

But keep in mind phonon DOS file name for F_QHA.x is PHDOS.out which contains 2 extra files in the beginning:

#
#? 1000? 320.4? 0.3207
?
The first line is empty
Then? 1000 is total step, 320.4 is the highest frequency in cm^{-1} and 0.3207 is the fequency step.

Hope this helps. Any questions, please.

Bests,
Eyvaz.


-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


________________________________
From: Guntram Schmidt <guntram.schmidt at chemie.uni-halle.de>
To: pw_forum at pwscf.org
Sent: Wednesday, July 20, 2011 6:01 PM
Subject: [Pw_forum] QHA and monoclinic/orthorhombic structures

Dear All,

when trying to understand the Examples of QHA, I saw that the script 
stops execution, when monoclinic or orthorhombic structures are tried to 
be calculated.
Is there a way to get the gibb energy of a monoclinic structure at room 
temperature, anyway? Or is this "ttrinp" not neccesary to do such 
calculations? What is it for, anyways? I couldn't find any documentation 
on it...

Thanks a lot for input on this,
Guntram
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From abdulrafiuraji at gmail.com  Wed Jul 20 18:52:36 2011
From: abdulrafiuraji at gmail.com (Abdulrafiu Raji)
Date: Wed, 20 Jul 2011 18:52:36 +0200
Subject: [Pw_forum] Pw_forum Digest, Vol 49, Issue 53
In-Reply-To: <mailman.14273.1311125069.1814.pw_forum@pwscf.org>
References: <mailman.14273.1311125069.1814.pw_forum@pwscf.org>
Message-ID: <CACJL2X6TxXLwmvybjs+AzmEjLsWgktjWFOLi3jGwwKqr4xKL-A@mail.gmail.com>

Thanks Paolo, you are absolutely right!...I was running the XANES script
with mpirun. However, I tried to run the script again, serially, by doing
the following:  I copied the QE version 4.2.1 to my home directory on a HPC,
and compiled Xspectra code using:    'make xspectra'. The resulting
'xspectra.x' was then copied into my home directory: 'home/araji/xspectra.x'
and the job was submitted using the script below. However, the code stopped
again, just after starting with the error message (please find below). The
shell script for submitting the job) is also appended. I repeat once again
that I used the same version of the code for both the 'scf' and 'xanes'
calculations.

Thank you very much.

.......................
A. T. Raji
ICTP,
Trieste. Italy.
===========

Program XSPECTRA v.4.2.1   starts on 20Jul2011 at 18:39:37

     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
 bef

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from read_rho_xml : error #         1
     cannot open
/home/araji/XAS_SiO2_scr.1/qtz_ar1SCF_kp2.save/charge-density.dat file for
reading
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

===================================
#PBS -N SiO2.XAS_pln_kpt_2.in
### Number and which of nodes as well as number of CPUs per node:
#####PBS -l nodes=1:ppn=8

### resource limits: amount of memory and CPU time ([[h:]m:]s).
### Queue name (default, ib, ...)
#PBS -q serial

#############
### This job's working directory
echo "Working directory is $PBS_O_WORKDIR"
cd /home/araji/XAS_SiO2
echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`
## Run your executable
######. /etc/profile.d/modules.sh
######## module load  espresso/4.2.1/openmpi/1.4.3/gnu

#######module load openmpi/1.4.3/gnu/4.4.0

/home/araji/xspectra.x < SiO2.XAS_pln_kpt_2.in  > SiO2.XAS_pln_kpt_2.out
=============================================

&control
    calculation='scf',
    restart_mode='from_scratch',
    pseudo_dir = '/home/araji/pseudo/',
    outdir =  '/home/araji/XAS_SiO2_scr.1/',
    prefix ='qtz_ar1SCF_kp2',
    verbosity = 'high',
    wf_collect = .true.,
    ----
....
.
.
.
K_POINTS (automatic)
2       2      2     0       0      0

=====================
 &input_xspectra
    calculation='xanes_dipole'
    prefix='qtz_ar1SCF_kp2',
    outdir='/home/araji/XAS_SiO2_scr.1/',
    xonly_plot=.false.,
    xniter=2000,
     xcheck_conv=50,
    xepsilon(1)=1.0,
    xepsilon(2)=1.0,
    xepsilon(3)=0.0,
    xiabs=1,
    x_save_file='SiO2.XAS.pln.sav',
    xread_wf=.false.,
    ef_r=0.402521132,
    xerror=0.001,
    wf_collect=.true.,

   .....
............
.
.
.
.
&cut_occ
    cut_desmooth=0.1,
 &end
3 3 3 0 0 0

>

===============


> . Re: Problem with XSPECTRA: file can't open (Paolo Giannozzi)
>
> Message: 1
> Date: Tue, 19 Jul 2011 19:08:32 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Problem with XSPECTRA: file can't open
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <DA9BA2F3-B831-4DF7-A104-A3EA0B79356F at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Let me guess: you are running in parallel (with mpirun or
> mpiexec) an executable compiled for serial execution
>
> 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
>
>
>
>
>
>
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From wibarrah at gmail.com  Wed Jul 20 19:12:06 2011
From: wibarrah at gmail.com (=?ISO-8859-1?Q?Wilfredo_Ibarra_Hern=E1ndez?=)
Date: Wed, 20 Jul 2011 12:12:06 -0500
Subject: [Pw_forum] more k-points
Message-ID: <CAF8R2aHDp_q0_JBM-FD3N6d=nML5+2Dw_-FFR=J6FAxT8RixMQ@mail.gmail.com>

Hello pwscf community

I'm calculating el-ph interaction with pwscf, and for this is necessary a
dense k-point grid

I put a 60X60X60 grid of k-points, but the code don't let me do this.

I'm looking for the npk variable for do it greater and neglect the error "to
dense k-point grid"

My question is, modifying npk, Is possible solve my problem? and if the
answer is yes,

Where is this variable?.

I know about another code which can do el-ph calculation using Wannier
functions (EPW)

but this code doesn't work with the trigonal structure, and this is the
reason which

I'm doing my calculations with pwscf.

Thanks for your help.

-- 
Ibarra Hern?ndez Wilfredo
Master student in materials sciences
Cinvestav Quer?taro M?xico
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From giannozz at democritos.it  Wed Jul 20 21:11:17 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 20 Jul 2011 21:11:17 +0200
Subject: [Pw_forum] more k-points
In-Reply-To: <CAF8R2aHDp_q0_JBM-FD3N6d=nML5+2Dw_-FFR=J6FAxT8RixMQ@mail.gmail.com>
References: <CAF8R2aHDp_q0_JBM-FD3N6d=nML5+2Dw_-FFR=J6FAxT8RixMQ@mail.gmail.com>
Message-ID: <AE9FD51F-108D-405F-80DC-D28FFA737707@democritos.it>


On Jul 20, 2011, at 19:12 , Wilfredo Ibarra Hern?ndez wrote:

> I'm looking for the npk variable [...] Where is this variable?

in Modules/parameters.f90

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 20 21:15:56 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 20 Jul 2011 21:15:56 +0200
Subject: [Pw_forum] Pw_forum Digest, Vol 49, Issue 53
In-Reply-To: <CACJL2X6TxXLwmvybjs+AzmEjLsWgktjWFOLi3jGwwKqr4xKL-A@mail.gmail.com>
References: <mailman.14273.1311125069.1814.pw_forum@pwscf.org>
	<CACJL2X6TxXLwmvybjs+AzmEjLsWgktjWFOLi3jGwwKqr4xKL-A@mail.gmail.com>
Message-ID: <7F4B01A5-0DC1-457A-9A67-A8A2F9D19D8D@democritos.it>


On Jul 20, 2011, at 18:52 , Abdulrafiu Raji wrote:

>      cannot open /home/araji/XAS_SiO2_scr.1/qtz_ar1SCF_kp2.save/ 
> charge-density.dat file

it is not there, or it is corrupted, or empty, or not in the right  
format.
Note that it is a binary file that should be written by and read by
executables compiled with the same compiler on th same machine,
as a rule

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 wibarrah at gmail.com  Wed Jul 20 22:03:01 2011
From: wibarrah at gmail.com (=?ISO-8859-1?Q?Wilfredo_Ibarra_Hern=E1ndez?=)
Date: Wed, 20 Jul 2011 15:03:01 -0500
Subject: [Pw_forum] more k-points
In-Reply-To: <AE9FD51F-108D-405F-80DC-D28FFA737707@democritos.it>
References: <CAF8R2aHDp_q0_JBM-FD3N6d=nML5+2Dw_-FFR=J6FAxT8RixMQ@mail.gmail.com>
	<AE9FD51F-108D-405F-80DC-D28FFA737707@democritos.it>
Message-ID: <CAF8R2aEyNvRyEJLGc5axdRd-ZuWGeCFOhc6hX+K5vdUa-30CSQ@mail.gmail.com>

Thanks,

I change it and now is works.


2011/7/20 Paolo Giannozzi <giannozz at democritos.it>

>
> On Jul 20, 2011, at 19:12 , Wilfredo Ibarra Hern?ndez wrote:
>
> > I'm looking for the npk variable [...] Where is this variable?
>
> in Modules/parameters.f90
>
> 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
>



-- 
Ibarra Hern?ndez Wilfredo
Master student in materials sciences
Cinvestav Quer?taro M?xico
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From germaneau at gucas.ac.cn  Thu Jul 21 15:01:16 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Thu, 21 Jul 2011 09:01:16 -0400
Subject: [Pw_forum] Pressure-induced phase transition
In-Reply-To: <511142894.04825@test1.gucas.ac.cn>
References: <CAEXRF5wCf3wQvSSjzFSBzybzbUdCSFx8gBOPUsKDHJs20PF1Lw@mail.gmail.com>
	<CAEXRF5wHESoRBzeQ-diDqdMC1m3cveryvSWDuU4UR7BceM5GJA@mail.gmail.com>
	<510975832.04103@test1.gucas.ac.cn> <4E24DCAA.7000709@gucas.ac.cn>
	<510999887.17934@test1.gucas.ac.cn>
	<4E25612D.4090704@gucas.ac.cn> <4E24DDD1.5040603@yahoo.com.cn>
	<511040348.32013@test1.gucas.ac.cn> <4E26D704.20404@gucas.ac.cn>
	<511142894.04825@test1.gucas.ac.cn>
Message-ID: <4E28231C.1050709@gucas.ac.cn>

Dear Professor Giannozzi,

I realized that was just a matter of name.
I got it, thank you,

       ?ric.

On 07/20/2011 02:28 AM, Paolo Giannozzi wrote:
> On Jul 20, 2011, at 15:24 , Eric Germaneau wrote:
>
>> Well, I don't know about "common tangent" concept.
> you should: it is basic thermodynamics. Some time ago
> I wrote something on phase transitions: pag.13-21 of
> http://www.fisica.uniud.it/~giannozz/Corsi/sissa02.pdf
> These lecture notes are not worth much, but given the
> confusion of ideas that emerges from this thread, they
> might be useful
>
> 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
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau 
<http://www.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html /

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From flux_ray12 at 163.com  Thu Jul 21 08:34:01 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 21 Jul 2011 14:34:01 +0800 (CST)
Subject: [Pw_forum] ph.x cannot reach convergence within 100 steps
In-Reply-To: <1310888353.20005.YahooMailNeo@web65703.mail.ac4.yahoo.com>
References: <1310888353.20005.YahooMailNeo@web65703.mail.ac4.yahoo.com>
	<1310805580.13329.YahooMailNeo@web65711.mail.ac4.yahoo.com>
	<4fe46835.f662.13131080d5a.Coremail.flux_ray12@163.com>
	<7c36558a.2c24.13137040a7b.Coremail.flux_ray12@163.com>
Message-ID: <1da3fd9.4162.1314b669eb0.Coremail.flux_ray12@163.com>

Dear Prof. Isaev:
Thank you for your suggestiong.
I have obtained the convergent result by decreasing alpha_mix(1) from 0.7 to 0.4. But the result has imaginary frequency (about -80 cm^-1) at X(100).
Further more, I also tried VCA (by virtual.x) +DFPT method for the same composition and strucutre, X(100) still had imaginary frequency (also about -80 cm^-1).
Then,  may I make a conclusion that this structure or composition is unstable?
Looking forward to your reply.
Best Regards.

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-17 15:39:13,"Eyvaz Isaev" <eyvaz_isaev at yahoo.com> wrote:

> I was not sure whether this problem caused by empty-band number, so I increase nbnd.
 
You should increase nbnd if you see "too few bands" message  in *.ph.out file.

Bests,
Eyvaz.
 

 

From: GAO Zhe <flux_ray12 at 163.com>
To: Eyvaz Isaev <eyvaz_isaev at yahoo.com>; PWSCF Forum <pw_forum at pwscf.org>
Sent: Sunday, July 17, 2011 11:33 AM
Subject: Re: [Pw_forum] ph.x cannot reach convergence within 100 steps


Thank you very much, Prof. Isaev.
I tried all of 'scf', 'relax' and 'vc-relax' before ph.x, but got the same problem in each case~
I was not sure whether this problem caused by empty-band number, so I increase nbnd. It may too large for my model~ Now, I am trying to change the values of alpha_mix(1) and nmix_ph for a better convergent.
Thank you, again ^_^

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-16 16:39:40?"Eyvaz Isaev" <eyvaz_isaev at yahoo.com> wrote:

Hi,



>Recently, I am trying to calculate phonon dispersion via ph.x. However, in some cases, ph.x cannot reach convergence within 100 steps and stop >automaticly.
 
1. You should  perform 'scf', not 'vc-relax' before phonon calculations.
2. You have a rather large system (nbnd=100), but used alpha_mix(1) by default (0.7). Try it around 0.1.
3. Try changing nmix_ph (by default 4).
4. If this does not help change 'maxter=100' in phcom.f90 and recompile.

Bests,
Eyvaz.


-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
isaev at ifm.liu.se,eyvaz_isaev at yahoo.com

From: GAO Zhe <flux_ray12 at 163.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Saturday, July 16, 2011 7:40 AM
Subject: [Pw_forum] ph.x cannot reach convergence within 100 steps


Dear QE developer and users:
Recently, I am trying to calculate phonon dispersion via ph.x. However, in some cases, ph.x cannot reach convergence within 100 steps and stop automaticly.
I have tested the convergent lattice parameter, cut-off energy and k-points (M-P grid), and the thresholds of force and stress were also very low. Even if I increase the tr2_ph from 1.0d-12 (default) to 1.0d-10, the |ddv_scf|^2  values was around 10^(-6) or 10^(-7) magnitude. The problem usually occurred at the second q-point, but sometimes, even if lucky enough, it would definitely occur at the third q-point (4 q-points in 3x3x3 case).
Are there any methods to solve this problem? Any suggestion will be welcome.
Calculations were used GGA-PBE USPP.
This is my input file:
cat >W25.relax.in <<EOF
&control
     calculation = 'vc-relax' ,
     disk_io = 'low' ,
     prefix = 'W' ,
     outdir = '$TempDIR/' ,
     pseudo_dir = '$PseudoDIR/' ,
     etot_conv_thr = 1.0d-12 ,
     forc_conv_thr = 1.0d-4 ,
/
&system
     ibrav = 1 ,
     celldm(1) = ******* ,
     nat = ** ,
     ntyp = 3 ,
     nbnd = 100 ,
     ecutwfc = 47.5 ,
     ecutrho = 450 ,
     occupations = 'smearing' ,
     smearing = 'mp' ,
     degauss = 0.003 ,
/
&electrons
     conv_thr = 1.0d-12 ,
     startingpot = 'atomic' ,
     startingwfc = 'atomic+random' ,
     diagonalization = 'cg' ,
     electron_maxstep = 150 ,
/
&ions
     ion_dynamics = 'bfgs' ,
/
&cell
     cell_dynamics = 'bfgs' ,
     press_conv_thr = 0.01 ,
/
ATOMIC_SPECIES
  V   50.9415   V.pbe-n-van.UPF
  W   183.800   W.pbe-nsp-van.UPF
  C   12.0110   C.pbe-van_ak.UPF
ATOMIC_POSITIONS crystal
  V   0.50  0.50  0.00
...........
  C   0.50  0.50  0.50
K_POINTS automatic
13  13  13   0  0  0
EOF
echo -e "  Relaxing Structure...\c"
$MPIBIN/mpirun -n 6 pw.x -npool 2 <W.relax.in >W.relax.out
echo -e " DONE"

cat >W.ph.in <<EOF
Phonon Calculation
&inputph
     outdir = '$TempDIR/' ,
     prefix = 'W' ,
     ldisp = .true. ,
     nq1 = 3 ,
     nq2 = 3 ,
     nq3 = 3 ,
     tr2_ph = 1.0d-10 ,
     fildyn = 'W.dyn' ,
/
EOF
echo -e "  Calculating Dynamic Matrix...\c"
$MPIBIN/mpirun -n 6 ph.x -npool 2 <W.ph.in >W.ph.out
echo -e " DONE"



--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea





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From eyvaz_isaev at yahoo.com  Thu Jul 21 10:10:10 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 21 Jul 2011 01:10:10 -0700 (PDT)
Subject: [Pw_forum] ph.x cannot reach convergence within 100 steps
In-Reply-To: <1da3fd9.4162.1314b669eb0.Coremail.flux_ray12@163.com>
References: <1310888353.20005.YahooMailNeo@web65703.mail.ac4.yahoo.com>
	<1310805580.13329.YahooMailNeo@web65711.mail.ac4.yahoo.com>
	<4fe46835.f662.13131080d5a.Coremail.flux_ray12@163.com>
	<7c36558a.2c24.13137040a7b.Coremail.flux_ray12@163.com>
	<1da3fd9.4162.1314b669eb0.Coremail.flux_ray12@163.com>
Message-ID: <1311235810.59290.YahooMailNeo@web65715.mail.ac4.yahoo.com>

>Then,? may I make a conclusion that this structure or composition is unstable?
?
If? you have imaginary frequency, yes. If the structure is a high temperature phase, it is another story. DFPT works at? low? temperatures (strongly speaking at T=0K).

Bests,
Eyvaz.

-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


________________________________
From: GAO Zhe <flux_ray12 at 163.com>
? .

I have obtained the convergent result by decreasing alpha_mix(1) from 0.7 to 0.4. But the result has imaginary frequency (about -80 cm^-1) at X(100).
Further more, I also tried VCA (by virtual.x) +DFPT method for the same composition and strucutre, X(100) still had imaginary frequency (also about -80 cm^-1).
Then,? may I make a conclusion that this structure or composition is unstable?
Looking forward to your reply.
Best Regards.

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea

At 2011-07-17 15:39:13,"Eyvaz?Isaev"?<eyvaz_isaev at yahoo.com> wrote:

> I was not sure whether this problem caused by empty-band number, so I increase nbnd.
>?
>You should increase nbnd if you see "too few bands" message? in *.ph.out file. 
>
>Bests,
>Eyvaz. 
>?
>
>?
>
>
>________________________________
>From: GAO Zhe <flux_ray12 at 163.com>
>To: Eyvaz Isaev <eyvaz_isaev at yahoo.com>; PWSCF Forum <pw_forum at pwscf.org>
>Sent: Sunday, July 17, 2011 11:33 AM
>Subject: Re: [Pw_forum] ph.x cannot reach convergence within 100 steps
>
>
>Thank you very much, Prof. Isaev.
>I tried all of 'scf', 'relax' and 'vc-relax' before ph.x, but got the same problem in each case~
>I was not sure whether this problem caused by empty-band number, so I increase nbnd. It may too large for my model~ Now, I am trying to change the values of alpha_mix(1) and nmix_ph for a better convergent.
>Thank you, again ^_^
>
>--
>GAO Zhe
>CMC Lab, MSE, SNU, Seoul, S.Korea
>
>At 2011-07-16 16:39:40?"Eyvaz?Isaev"?<eyvaz_isaev at yahoo.com> wrote:
>
>Hi, 
>>
>>
>>
>>>Recently, I am trying to calculate phonon dispersion via ph.x. However, 
in some cases, ph.x cannot reach convergence within 100 steps and stop 
>automaticly.
>>?
>>1. You should? perform 'scf', not 'vc-relax' before phonon calculations.
>>2. You have a rather large system (nbnd=100), but used alpha_mix(1) by default (0.7). Try it around 0.1.
>>3. Try changing nmix_ph (by default 4).
>>4. If this does not help change 'maxter=100' in phcom.f90 and recompile.
>>
>>Bests,
>>Eyvaz.
>>
>>
>>-------------------------------------------------------------------
>>Prof. Eyvaz Isaev, 
>>Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
>>Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
>>isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>>
>>
>>________________________________
>>From: GAO?Zhe <flux_ray12 at 163.com>
>>To: PWSCF Forum <pw_forum at pwscf.org>
>>Sent: Saturday, July 16, 2011 7:40 AM
>>Subject: [Pw_forum] ph.x cannot reach convergence within 100 steps
>>
>>
>>Dear QE developer and users:
>>Recently, I am trying to calculate phonon dispersion via ph.x. However, in some cases, ph.x cannot reach convergence within 100 steps and stop automaticly.
>>I have tested the convergent lattice parameter, cut-off energy and k-points (M-P grid), and the thresholds of force and stress were also very low. Even if I increase the tr2_ph from
 1.0d-12 (default) to 1.0d-10, the |ddv_scf|^2? values was around 10^(-6) or 10^(-7) magnitude. The problem usually occurred at the second q-point, but sometimes, even if lucky enough, it would definitely occur at
 the third q-point (4 q-points in 3x3x3 case).
>>Are there any methods to solve this problem? Any suggestion will be welcome.
>>Calculations were used GGA-PBE USPP.
>>This is my input file:
>>cat >W25.relax.in <<EOF
>>&control
>>???? calculation = 'vc-relax' ,
>>???? disk_io = 'low' ,
>>???? prefix = 'W' ,
>>???? outdir = '$TempDIR/' ,
>>???? pseudo_dir = '$PseudoDIR/' ,
>>???? etot_conv_thr = 1.0d-12 ,
>>???? forc_conv_thr = 1.0d-4 ,
>>/
>>&system
>>???? ibrav = 1 ,
>>???? celldm(1) = ******* ,
>>???? nat = ** ,
>>???? ntyp = 3 ,
>>???? nbnd = 100 ,
>>???? ecutwfc = 47.5 ,
>>???? ecutrho = 450 ,
>>???? occupations =
 'smearing' ,
>>???? smearing = 'mp' ,
>>???? degauss = 0.003 ,
>>/
>>&electrons
>>???? conv_thr = 1.0d-12 ,
>>???? startingpot = 'atomic' ,
>>???? startingwfc = 'atomic+random' ,
>>???? diagonalization = 'cg' ,
>>???? electron_maxstep = 150 ,
>>/
>>&ions
>>???? ion_dynamics = 'bfgs' ,
>>/
>>&cell
>>???? cell_dynamics = 'bfgs' ,
>>???? press_conv_thr = 0.01 ,
>>/
>>ATOMIC_SPECIES
>>? V?? 50.9415?? V.pbe-n-van.UPF
>>? W?? 183.800?? W.pbe-nsp-van.UPF
>>? C?? 12.0110?? C.pbe-van_ak.UPF
>>ATOMIC_POSITIONS crystal
>>? V?? 0.50? 0.50? 0.00
>>...........
>>? C?? 0.50? 0.50? 0.50
>>K_POINTS
 automatic
>>13? 13? 13?? 0? 0? 0
>>EOF
>>echo -e "? Relaxing Structure...\c"
>>$MPIBIN/mpirun -n 6 pw.x -npool 2 <W.relax.in >W.relax.out
>>echo -e " DONE"
>>
>>cat >W.ph.in <<EOF
>>Phonon Calculation
>>&inputph
>>???? outdir = '$TempDIR/' ,
>>???? prefix = 'W' ,
>>???? ldisp = .true. ,
>>???? nq1 = 3 ,
>>???? nq2 = 3 ,
>>???? nq3 = 3 ,
>>???? tr2_ph = 1.0d-10 ,
>>???? fildyn = 'W.dyn' ,
>>/
>>EOF
>>echo -e "? Calculating Dynamic Matrix...\c"
>>$MPIBIN/mpirun -n 6 ph.x -npool 2 <W.ph.in >W.ph.out
>>echo -e " DONE"
>>
>>
>>
>>--
>>GAO Zhe
>>CMC Lab, MSE, SNU, Seoul, S.Korea
>>
>>
>>
>>_______________________________________________
>>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 guntram.schmidt at chemie.uni-halle.de  Thu Jul 21 12:49:01 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Thu, 21 Jul 2011 12:49:01 +0200
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
Message-ID: <4E28041D.6050101@chemie.uni-halle.de>

Dear All,

after getting strange error-messages, which might be related to 
lapack/blas (
DSYGV : 2538-2015
The number of elements (ARG NO. 11) in a work array must be greater than
or equal to (2048).
)
I'd like to use "our own" lapack/blas.
Unfortunately QE won't find/accept them - what's the right way, to help it?

I tried:
  ./configure MPIF90=mpfort LIBDIRS="/gpfs/usrurz/lapack/lapack-3.2.1"
with

:/gpfs/usrurz/lapack/lapack-3.2.1> ls
BLAS               CCI_README     Makefile                   README
cci                ccisrc.tar     make.inc                   README_hh
cci.log            INSTALL        make.inc.example           SRC
CCI_NOTES          lapack_pwr6.a  make.inc.old               TESTING
CCI_QUICK_INSTALL  LICENSE        make.log_pwr6_xlf_q64_cci  tmglib_pwr6.a

yielding a quite promising directory of an installed lapack/blas?

But QE insists on its own libraries.

The system is an IBM 575 with Power-Linux=SLES11_on_Power and the only 
information I found is this here:
http://www2.fz-juelich.de/jsc/jump/usage/FAQ/essl/


Any ideas on this?
Thanks a lot,
Guntram

From mulwawinfred at yahoo.com  Thu Jul 21 15:12:14 2011
From: mulwawinfred at yahoo.com (Winfred Mulwa)
Date: Thu, 21 Jul 2011 06:12:14 -0700 (PDT)
Subject: [Pw_forum] Welcome to the "Pw_forum" mailing list (Digest mode)
In-Reply-To: <mailman.503.1311253228.1813.pw_forum@pwscf.org>
References: <mailman.503.1311253228.1813.pw_forum@pwscf.org>
Message-ID: <1311253934.20385.YahooMailNeo@web113213.mail.gq1.yahoo.com>

My email is mulwawinfred at yahoo.com



________________________________
From: "pw_forum-request at pwscf.org" <pw_forum-request at pwscf.org>
To: mulwawinfred at yahoo.com
Sent: Thursday, July 21, 2011 4:00 PM
Subject: Welcome to the "Pw_forum" mailing list (Digest mode)

Welcome to the Pw_forum at pwscf.org mailing list!
----------------------------------------------------------------------
Before posting, please read the guidelines:
http://www.quantum-espresso.org/wiki/index.php/Pw_users Please also
read how to report problems:
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From joerg.buchwald at iom-leipzig.de  Thu Jul 21 15:06:31 2011
From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald)
Date: Thu, 21 Jul 2011 15:06:31 +0200
Subject: [Pw_forum] problem in calculating the binding energies with pwscf
Message-ID: <20110721150631.4216eb09@PC-Mayr-Mitarb6.pc-flexi>

Hello,
I'm performing some first test-calculations with pwscf, where I try to
get the binding energy of bulk silicon. The problem is, that the
resulting energy, which should be the difference of the total
energy of silicon crystal structure and the a free atom, is about 3eV
too low. I used different pseudopotentials, different
lattice-parameters and I also tested the convergencies (with k and
the energy-cut-off) which worked, but I don't have a clue what a made
wrong.

Here are my Input files:

---
 &control
    prefix='silicon',
    pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
    outdir = '/home/joerg/scratch',
 /
 &system
    ibrav=  2, celldm(1) =10.263142, nat=  2, ntyp= 1,
    ecutwfc = 30.0,
 /
 &electrons
 /
ATOMIC_SPECIES
 Si  28.086  Si.pbe-n-van.UPF
ATOMIC_POSITIONS
 Si 0.00 0.00 0.00
 Si 0.25 0.25 0.25
K_POINTS automatic
 9 9 9 1 1 1
---

and for the free atom:

---
&control
    prefix='silicon',
    pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
    outdir = '/home/joerg/scratch',
 /
 &system
    ibrav=  0, celldm(1) =50.2, nat=  1, ntyp= 1,
    ecutwfc = 80.0,occupations='fixed',starting_magnetization(1)=10,
 /
 &electrons
 /
ATOMIC_SPECIES
 Si  28.086  Si.pbe-n-van.UPF
ATOMIC_POSITIONS
 Si 0.50 0.50 0.50
K_POINTS gamma

CELL_PARAMETERS {cubic}
    1.00 0.00 0.00
    0.00 1.00 0.00
    0.00 0.00 1.00
---

It would be nice if someone could help me.
Thx & regards,
J?rg Buchwald


Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
Permoserstrasse 15
04318 Leipzig
GERMANY


From giannozz at democritos.it  Thu Jul 21 15:38:04 2011
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Thu, 21 Jul 2011 15:38:04 +0200
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <4E28041D.6050101@chemie.uni-halle.de>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
Message-ID: <20110721153804.1lwfpxwr6gcccko4@mail.democritos.it>

Quoting Guntram Schmidt <guntram.schmidt at chemie.uni-halle.de>:

> DSYGV : 2538-2015
> The number of elements (ARG NO. 11) in a work array must be greater than
> or equal to (2048).

Verify a) if -D__ESSL present in your DFLAGS and FDFLAGS, and b ) if 
essl is loaded before lapack. If a).and.b), you may try to replace 
-D__ESSL with -D__LINUX_ESSL in DFLAGS and FDFLAGS, or to edit 
PW/rdiaghg.f90 .
See comments there, in make.sys, and in include/defs/h.README

> I tried:
>  ./configure MPIF90=mpfort LIBDIRS="/gpfs/usrurz/lapack/lapack-3.2.1"
> [...] But QE insists on its own libraries.

not all environment variables are treated in the same way by configure.
I think that a check for libraries is still performed in LIBDIRS. If
there is no liblapack.a there, nothing will be found.

P.

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.


From Michael at ihpc.a-star.edu.sg  Thu Jul 21 14:46:37 2011
From: Michael at ihpc.a-star.edu.sg (Michael Sullivan)
Date: Thu, 21 Jul 2011 20:46:37 +0800
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <4E28041D.6050101@chemie.uni-halle.de>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
Message-ID: <299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>

Guntram:

I've never seen this error message, but if you can try to edit the make.sys file directly. Replace the LAPACK_LIBS flag to point to your own LAPACK and probably change LAPACK_LIBS_SWITCH to external. That said, though, I've found that usually if it can't find it, there's a reason.

Good luck!

Mike
michael at ihpc.a-star.edu.sg
http://www.sullivan.sg/

On 21-Jul-2011, at 6:49 PM, Guntram Schmidt wrote:

> Dear All,
>
> after getting strange error-messages, which might be related to
> lapack/blas (
> DSYGV : 2538-2015
> The number of elements (ARG NO. 11) in a work array must be greater than
> or equal to (2048).
> )
> I'd like to use "our own" lapack/blas.
> Unfortunately QE won't find/accept them - what's the right way, to help it?
>
> I tried:
>  ./configure MPIF90=mpfort LIBDIRS="/gpfs/usrurz/lapack/lapack-3.2.1"
> with
>
> :/gpfs/usrurz/lapack/lapack-3.2.1> ls
> BLAS               CCI_README     Makefile                   README
> cci                ccisrc.tar     make.inc                   README_hh
> cci.log            INSTALL        make.inc.example           SRC
> CCI_NOTES          lapack_pwr6.a  make.inc.old               TESTING
> CCI_QUICK_INSTALL  LICENSE        make.log_pwr6_xlf_q64_cci  tmglib_pwr6.a
>
> yielding a quite promising directory of an installed lapack/blas?
>
> But QE insists on its own libraries.
>
> The system is an IBM 575 with Power-Linux=SLES11_on_Power and the only
> information I found is this here:
> http://www2.fz-juelich.de/jsc/jump/usage/FAQ/essl/
>
>
> Any ideas on this?
> Thanks a lot,
> Guntram
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.

From giuseppe.mattioli at mlib.ism.cnr.it  Thu Jul 21 16:16:15 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Thu, 21 Jul 2011 16:16:15 +0200
Subject: [Pw_forum] problem in calculating the binding energies with
	pwscf
In-Reply-To: <20110721150631.4216eb09@PC-Mayr-Mitarb6.pc-flexi>
References: <20110721150631.4216eb09@PC-Mayr-Mitarb6.pc-flexi>
Message-ID: <201107211616.16192.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Jorg
Calculations of isolated atoms may sometimes be tricky.
Try to have a look at

/yourespresso/examples/example11

HTH

Giuseppe


On Thursday 21 July 2011 15:06:31 J?rg Buchwald wrote:
> Hello,
> I'm performing some first test-calculations with pwscf, where I try to
> get the binding energy of bulk silicon. The problem is, that the
> resulting energy, which should be the difference of the total
> energy of silicon crystal structure and the a free atom, is about 3eV
> too low. I used different pseudopotentials, different
> lattice-parameters and I also tested the convergencies (with k and
> the energy-cut-off) which worked, but I don't have a clue what a made
> wrong.
>
> Here are my Input files:
>
> ---
>  &control
>     prefix='silicon',
>     pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
>     outdir = '/home/joerg/scratch',
>  /
>  &system
>     ibrav=  2, celldm(1) =10.263142, nat=  2, ntyp= 1,
>     ecutwfc = 30.0,
>  /
>  &electrons
>  /
> ATOMIC_SPECIES
>  Si  28.086  Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
>  Si 0.00 0.00 0.00
>  Si 0.25 0.25 0.25
> K_POINTS automatic
>  9 9 9 1 1 1
> ---
>
> and for the free atom:
>
> ---
> &control
>     prefix='silicon',
>     pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
>     outdir = '/home/joerg/scratch',
>  /
>  &system
>     ibrav=  0, celldm(1) =50.2, nat=  1, ntyp= 1,
>     ecutwfc = 80.0,occupations='fixed',starting_magnetization(1)=10,
>  /
>  &electrons
>  /
> ATOMIC_SPECIES
>  Si  28.086  Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
>  Si 0.50 0.50 0.50
> K_POINTS gamma
>
> CELL_PARAMETERS {cubic}
>     1.00 0.00 0.00
>     0.00 1.00 0.00
>     0.00 0.00 1.00
> ---
>
> It would be nice if someone could help me.
> Thx & regards,
> J?rg Buchwald
>
>
> Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
> Permoserstrasse 15
> 04318 Leipzig
> GERMANY
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



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? ?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 elbuesta at icqmail.com  Thu Jul 21 17:13:43 2011
From: elbuesta at icqmail.com (elbuesta at icqmail.com)
Date: Thu, 21 Jul 2011 11:13:43 -0400 (EDT)
Subject: [Pw_forum] problem in calculating the binding energies with
	pwscf
In-Reply-To: <20110721150631.4216eb09@PC-Mayr-Mitarb6.pc-flexi>
References: <20110721150631.4216eb09@PC-Mayr-Mitarb6.pc-flexi>
Message-ID: <8CE15CFE98D0BD6-1DF4-3C64@Webmail-m117.sysops.aol.com>

Hello Joerg Buchwald, 

a few comments. Starting magnetization should be between -1 and 1. 1 means that all available electrons from the PP have spin up. Also, if you want to do spin unrestricted calculations, you should set nspin=2. Only starting magnetization does not do anything. 

In addition, I wouldn't compare the energy of the bulk and the isolated atom this way because the cutoff on the WFC is quite different for each case: energy differences converge much faster than the total energy. But I don't think that is the problem here, only the magnetization is.

I slightly modified your inputs and got 4.5eV. If I remember well, this value is okay. I hope it helps. All best!

Free Si atom:

&control
    prefix='si_free',
    pseudo_dir='/home/alex/pseudo'
    outdir = '/scratch/alex',
 /
 &system
    ibrav=  1, celldm(1) =25, nat=  1, ntyp= 1,
    ecutwfc = 30.0,occupations='fixed',nspin=2,tot_magnetization=2.,nosym=.true.,
 /
 &electrons
 /
ATOMIC_SPECIES
 Si  28.086  Si.pbe-n-van.UPF
ATOMIC_POSITIONS
 Si 0.50 0.50 0.50
K_POINTS gamma
......................................

Bulk Si:

&control
    prefix='silicon',
    pseudo_dir='/home/alex/pseudo'
    outdir = '/scratch/alex',
 /
 &system
    ibrav=  2, celldm(1) =10.263142, nat=  2, ntyp= 1,
    ecutwfc = 40.0,
 /
 &electrons
 /
ATOMIC_SPECIES
 Si  28.086  Si.pbe-n-van.UPF
ATOMIC_POSITIONS
 Si 0.00 0.00 0.00
 Si 0.25 0.25 0.25
K_POINTS automatic
 9 9 9 1 1 1

................................................................


-----Original Message-----

From: J?rg Buchwald <joerg.buchwald at iom-leipzig.de>
To: pw_forum <pw_forum at pwscf.org>
Sent: Thu, Jul 21, 2011 3:15 pm
Subject: [Pw_forum] problem in calculating the binding energies with pwscf


Hello,
I'm performing some first test-calculations with pwscf, where I try to
get the binding energy of bulk silicon. The problem is, that the
resulting energy, which should be the difference of the total
energy of silicon crystal structure and the a free atom, is about 3eV
too low. I used different pseudopotentials, different
lattice-parameters and I also tested the convergencies (with k and
the energy-cut-off) which worked, but I don't have a clue what a made
wrong.

Here are my Input files:

---
 &control
    prefix='silicon',
    pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
    outdir = '/home/joerg/scratch',
 /
 &system
    ibrav=  2, celldm(1) =10.263142, nat=  2, ntyp= 1,
    ecutwfc = 30.0,
 /
 &electrons
 /
ATOMIC_SPECIES
 Si  28.086  Si.pbe-n-van.UPF
ATOMIC_POSITIONS
 Si 0.00 0.00 0.00
 Si 0.25 0.25 0.25
K_POINTS automatic
 9 9 9 1 1 1
---

and for the free atom:

---
&control
    prefix='silicon',
    pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
    outdir = '/home/joerg/scratch',
 /
 &system
    ibrav=  0, celldm(1) =50.2, nat=  1, ntyp= 1,
    ecutwfc = 80.0,occupations='fixed',starting_magnetization(1)=10,
 /
 &electrons
 /
ATOMIC_SPECIES
 Si  28.086  Si.pbe-n-van.UPF
ATOMIC_POSITIONS
 Si 0.50 0.50 0.50
K_POINTS gamma

CELL_PARAMETERS {cubic}
    1.00 0.00 0.00
    0.00 1.00 0.00
    0.00 0.00 1.00
---

It would be nice if someone could help me.
Thx & regards,
J?rg Buchwald


Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
Permoserstrasse 15
04318 Leipzig
GERMANY

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


 
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From zhaohscas at yahoo.com.cn  Fri Jul 22 02:11:15 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Fri, 22 Jul 2011 08:11:15 +0800
Subject: [Pw_forum] problem in calculating the binding energies
	with	pwscf
In-Reply-To: <8CE15CFE98D0BD6-1DF4-3C64@Webmail-m117.sysops.aol.com>
References: <20110721150631.4216eb09@PC-Mayr-Mitarb6.pc-flexi>
	<8CE15CFE98D0BD6-1DF4-3C64@Webmail-m117.sysops.aol.com>
Message-ID: <4E28C023.8000508@yahoo.com.cn>

On 07/21/2011 11:13 PM, elbuesta at icqmail.com wrote:
> Hello Joerg Buchwald,
>
> a few comments. Starting magnetization should be between -1 and 1. 1

Why not between -1 and 1?  Any hints?

> means that all available electrons from the PP have spin up. Also, if
> you want to do spin unrestricted calculations, you should set nspin=2.

What do you mean by saying "spin unrestricted calculations", I have 
little experience on magnetic calculations, could you please give me 
some hints?

> Only starting magnetization does not do anything.
>
> In addition, I wouldn't compare the energy of the bulk and the isolated
> atom this way

Then, what's you way for this issue, any hints?

> because the cutoff on the WFC is quite different for each
> case: energy differences converge much faster than the total energy. But
> I don't think that is the problem here, only the magnetization is.
>
> I slightly modified your inputs and got 4.5eV. If I remember well, this
> value is okay. I hope it helps. All best!
>
> Free Si atom:
>
> &control
>
>      prefix='si_free',
>
>      pseudo_dir='/home/alex/pseudo'
>
>      outdir = '/scratch/alex',
>
>   /
>
>   &system
>
>      ibrav=  1, celldm(1) =25, nat=  1, ntyp= 1,
>
>      ecutwfc = 30.0,occupations='fixed',nspin=2,tot_magnetization=2.,nosym=.true.,
>
>   /
>
>   &electrons
>
>   /
>
> ATOMIC_SPECIES
>
>   Si  28.086  Si.pbe-n-van.UPF
>
> ATOMIC_POSITIONS
>
>   Si 0.50 0.50 0.50
>
> K_POINTS gamma
>
> ......................................
>
>
>
> Bulk Si:
>
> &control
> prefix='silicon',
> pseudo_dir='/home/alex/pseudo'
> outdir = '/scratch/alex',
> /
> &system
> ibrav= 2, celldm(1) =10.263142, nat= 2, ntyp= 1,
> ecutwfc = 40.0,
> /
> &electrons
> /
> ATOMIC_SPECIES
> Si 28.086 Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
> Si 0.00 0.00 0.00
> Si 0.25 0.25 0.25
> K_POINTS automatic
> 9 9 9 1 1 1
>
> ................................................................
>
>
> -----Original Message-----
> From: J?rg Buchwald <joerg.buchwald at iom-leipzig.de>
> To: pw_forum <pw_forum at pwscf.org>
> Sent: Thu, Jul 21, 2011 3:15 pm
> Subject: [Pw_forum] problem in calculating the binding energies with pwscf
>
> Hello,
> I'm performing some first test-calculations with pwscf, where I try to
> get the binding energy of bulk silicon. The problem is, that the
> resulting energy, which should be the difference of the total
> energy of silicon crystal structure and the a free atom, is about 3eV
> too low. I used different pseudopotentials, different
> lattice-parameters and I also tested the convergencies (with k and
> the energy-cut-off) which worked, but I don't have a clue what a made
> wrong.
>
> Here are my Input files:
>
> ---
>   &control
>      prefix='silicon',
>      pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
>      outdir = '/home/joerg/scratch',
>   /
>   &system
>      ibrav=  2, celldm(1) =10.263142, nat=  2, ntyp= 1,
>      ecutwfc = 30.0,
>   /
>   &electrons
>   /
> ATOMIC_SPECIES
>   Si  28.086  Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
>   Si 0.00 0.00 0.00
>   Si 0.25 0.25 0.25
> K_POINTS automatic
>   9 9 9 1 1 1
> ---
>
> and for the free atom:
>
> ---
> &control
>      prefix='silicon',
>      pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
>      outdir = '/home/joerg/scratch',
>   /
>   &system
>      ibrav=  0, celldm(1) =50.2, nat=  1, ntyp= 1,
>      ecutwfc = 80.0,occupations='fixed',starting_magnetization(1)=10,
>   /
>   &electrons
>   /
> ATOMIC_SPECIES
>   Si  28.086  Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
>   Si 0.50 0.50 0.50
> K_POINTS gamma
>
> CELL_PARAMETERS {cubic}
>      1.00 0.00 0.00
>      0.00 1.00 0.00
>      0.00 0.00 1.00
> ---
>
> It would be nice if someone could help me.
> Thx&  regards,
> J?rg Buchwald
>
>
> Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
> Permoserstrasse 15
> 04318 Leipzig
> GERMANY
>
> _______________________________________________
> 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


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From zhaohscas at yahoo.com.cn  Fri Jul 22 06:07:54 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Fri, 22 Jul 2011 12:07:54 +0800
Subject: [Pw_forum] My vague understanding of internal degrees of freedom.
Message-ID: <4E28F79A.6040709@yahoo.com.cn>

Hi all,

I've learned that the single-point energy calculation 
(calculation='scf') can be used for the following purpose:

---------
It can be used to calculate an equation of state (i.e. a pressure-volume 
and/or energy-volume dependence) for high-symmetry systems with no 
internal degrees of freedom, as long as the Stress property is specified.
---------

But I've some puzzles on the meaning of internal degrees of freedom. 
Say, for a bcc structure, does it has internal degrees of freedom or 
not?   Furthermore, in the general case, how can I know whether a system 
has the internal degrees of freedom or not?

ps.  According to the paper J. Phys.: Condens. Matter 21 395502, the 
internal degrees of freedom, also can be called the microscopic degrees 
of freedom, is the atomic coordinates; and the macroscopic degrees of 
freedom are the shape and size of the unit
cell.
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From ustc.scgyer at gmail.com  Fri Jul 22 09:49:10 2011
From: ustc.scgyer at gmail.com (xiaochuan Ge)
Date: Fri, 22 Jul 2011 09:49:10 +0200
Subject: [Pw_forum] My vague understanding of internal degrees of freedom
Message-ID: <CAJQfR0SST-0Nx6q5WsPZkv-Gi=yoA5AM6JnDUyFU3+8e=22VYg@mail.gmail.com>

Dear Hongsheng Zhao,
I am not sure about what you want to ask. But I guess if what you mean
by "internal degrees" is what you have specified, a system having or
not having the internal degrees does not depend on the shape of of the
cell.  You may check the input description of pw.x, I think the "no
internal degrees of freedom" is mentioned for scf calculation is
because in "relax" the atomic coordinates are allowed to evolve during
the calculation, while when scf is specified only electronic
configurations have the freedom to evolve keeping all the atomic
coordinates fixed.
I hope that I have answered your question, excuse me if I have
misunderstood your real puzzle.
Best wishes,
Ge Xiaochuan

2011/7/22  <pw_forum-request at pwscf.org>:
> My vague understanding of internal degrees of freedom

From s.m.rezaeisani at gmail.com  Fri Jul 22 09:54:11 2011
From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani)
Date: Fri, 22 Jul 2011 12:24:11 +0430
Subject: [Pw_forum] Wrong niter_ph (error in ph.x run)
Message-ID: <CAADUHkk=D+UUBo=AAE+cQ95tAiVyEUHOaFTDix5SqSVWLyw-QA@mail.gmail.com>

Dear all
I tried to calculate phonon frequencies for a system that need more
iteration number than its default, so I add niter_ph into the namelist. But,
I got this error:

#ph.in %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     task #         0
     from phq_readin : error #         1
      Wrong niter_ph
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

This is my input file:

 &inputph
  amass(1)=*,
  amass(2)=*,
  amass(3)=*,
  tr2_ph=1.0d-14,
  prefix='*',
  niter_ph = 300,
  ldisp=.true.,
  nq1=4 , nq2=4 , nq3=4
  outdir='*',
  fildyn='*.dyn',
 /

Thanks
-- 
==========================================
Seyed Mojtaba Rezaei Sani
Computational Condensed Matter Research Lab
Physics Department, Isfahan University of Technology
84156-83111 Isfahan, Iran
Tel lab: +98 311 391 3731
Group page: http://cmsgroup.iut.ac.ir/
s.rezaeisani at ph.iut.ac.ir
===========================================
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From Lorenzo.Paulatto at impmc.upmc.fr  Fri Jul 22 10:21:31 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Fri, 22 Jul 2011 10:21:31 +0200
Subject: [Pw_forum] Wrong niter_ph (error in ph.x run)
In-Reply-To: <CAADUHkk=D+UUBo=AAE+cQ95tAiVyEUHOaFTDix5SqSVWLyw-QA@mail.gmail.com>
References: <CAADUHkk=D+UUBo=AAE+cQ95tAiVyEUHOaFTDix5SqSVWLyw-QA@mail.gmail.com>
Message-ID: <op.vy0hh5qpxuur8c@vanoxite.impmc.jussieu.fr>

On Fri, 22 Jul 2011 09:54:11 +0200, Seyed Mojtaba Rezaei Sani  
<s.m.rezaeisani at gmail.com> wrote:
>      from phq_readin : error #         1
>       Wrong niter_ph

Dear Seyed,
for some reason I don't know the maximum number of iteration of the ph  
solver is set to 100, to "fix" this just open PH/phcom.f90 and change
   INTEGER, PARAMETER :: maxter = 100
to something larger (at least 300 in your case). ***Then recompile the  
code***.

As a side note, if your system is not converging maybe you have made some  
mistake in the input, i.e. not using smearing where you should or the  
structure is badly optimized.

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

From zhaohscas at yahoo.com.cn  Fri Jul 22 11:51:29 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Fri, 22 Jul 2011 17:51:29 +0800
Subject: [Pw_forum] My vague understanding of internal degrees of freedom
In-Reply-To: <CAJQfR0SST-0Nx6q5WsPZkv-Gi=yoA5AM6JnDUyFU3+8e=22VYg@mail.gmail.com>
References: <CAJQfR0SST-0Nx6q5WsPZkv-Gi=yoA5AM6JnDUyFU3+8e=22VYg@mail.gmail.com>
Message-ID: <4E294821.5030703@yahoo.com.cn>

On 07/22/2011 03:49 PM, xiaochuan Ge wrote:
> Dear Hongsheng Zhao,
> I am not sure about what you want to ask. But I guess if what you mean
> by "internal degrees" is what you have specified, a system having or
> not having the internal degrees does not depend on the shape of of the
> cell.  You may check the input description of pw.x, I think the "no
> internal degrees of freedom" is mentioned for scf calculation is
> because in "relax" the atomic coordinates are allowed to evolve during
> the calculation, while when scf is specified only electronic
> configurations have the freedom to evolve keeping all the atomic
> coordinates fixed.
> I hope that I have answered your question, excuse me if I have
> misunderstood your real puzzle.

Let me give you more detailed descriptions.  Say, we can use the 
following method to calculate the elastic constant:

Imply a series of deformations on the cell. Then calculate the stress 
tensor for each strain step.  For this purpose, generally, we need to do 
non-variable relaxation calculations ater we manually applied each 
strain/deformation.  In order to  improve the computational efficiency. 
   We may want to keep the lattice vectors perpendicular to the strain's 
direction fixed and then obtain the stress tensor corresponding to the 
stretched/compressed direction.  Finally, we use this to derive the 
elastic constants.

In this case, for each strain step, if there are no  internal degrees of 
freedom for the system, the single-point energy calculations should be OK.

For example, if the unit cell of our system is a simple cubic one, 
there are no atoms in the internal of cell.  So I I think this should be 
the case we noted as: "no
internal degrees of freedom".  Another example is that the body centered 
  cubic unit cell, in this case, we have atom in the internal of cell, 
but the position of internal atom is resides at high-symmetry position 
which should be most stable position for that atom, so the relaxation 
for that atom after each  strain step is also unnecessary.  Of course, 
in all of these calculations,  we should use fractional coordinations 
for all of the atoms in the input file so that the atoms positions can 
be updated to its new deformation positons uniformly with each strain 
step.  In this case, I think  the single-point energy calculations  for 
each strain step should be OK.

But for a Wurtzite ZnO, this is not the case, when we impose a strain, 
say, along the z axis, considering that there are atoms in general 
positions  in the unit cell, so we must relax the atoms positions for 
each strain step, other than a single-point energy calculations  for 
each strain step.

Based on the above description,  let we back to my question again:  I 
want know for a specific system, how we know whether there are "internal 
degrees of freedom" or not.  How to judge it?

I hope I stated my issue clearly this time.

Regards

> Best wishes,
> Ge Xiaochuan
>
> 2011/7/22<pw_forum-request at pwscf.org>:
>> My vague understanding of internal degrees of freedom
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From hannu.komsa at epfl.ch  Fri Jul 22 11:51:46 2011
From: hannu.komsa at epfl.ch (hannu.komsa at epfl.ch)
Date: Fri, 22 Jul 2011 11:51:46 +0200
Subject: [Pw_forum] PBE Hybrid funcitonals and LDA pseudopotentials
In-Reply-To: <mailman.14266.1311093329.1814.pw_forum@pwscf.org>
References: <mailman.14266.1311093329.1814.pw_forum@pwscf.org>
Message-ID: <20110722115146.15322ocwmx3onacy@webmail.epfl.ch>

Dear Gabriel,

> I have been attempting to use the hybrid functional PBE0 to tune the  
> bandgap of InGaAs, while using Virtual Crystal Approximation to  
> obtain In(0.57)Ga(0.43)As. I initially tried mixing the PBE pseudos  
> of Ga and In, but ran into a number of problems (unequal nqf mesh  
> when mixing, and using ultrasoft pseudos with hybrid functionals).

When I tested VCA for InGaAs, it didn't look so good. At least the  
lattice constant dependence on Ga/In composition came out pretty bad  
as Ga and In are of quite different sizes. I used pseudos taken from  
the abinit page and converted to QE. VCA seemed to work fine for  
those, also at the PBE level.

> I then tried the Norm-conserving LDA pseudos (which also have no nqf  
> information to worry about) for mixing In and Ga (also using LDA for  
> As pseudo, obviously). I then found I could tune the bandgap by  
> specifying "PBE0" in the &SYSTEM card of the input file by changing  
> the proportion of Fock exchange (alpha, or "exx_fraction" in  
> funct.f90), while specifying LDA pseudos for each atomic species.

You can mix and mash pseudos and functionals, but if you are not  
absolutely sure of what you are doing, it will likely fall in the  
category of garbage-in-garbage-out. PW also warns you about this.

> I am surprised this would work because my understanding is that LDA  
> contains no exchange term, yet modifying the value of alpha has an  
> effect on the bandgap just like if I had specified PBE  
> pseudopotentials in the ATOMIC_SPECIES card. I initially set up this  
> calculation as a test to just prove to myself that the results  
> obtained using LDA pseudopotentials are independant of the amount of  
> exchange, yet this is not so.

You might want to read some more literature about DFT and functionals,  
as the above description is mostly wrong. All functionals have  
exchange term, but with different (level of) approximation.


Regards,
   Hannu-Pekka Komsa
   EPFL, Switzerland


From s.m.rezaeisani at gmail.com  Fri Jul 22 12:00:08 2011
From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani)
Date: Fri, 22 Jul 2011 14:30:08 +0430
Subject: [Pw_forum] Wrong niter_ph (error in ph.x run)
In-Reply-To: <op.vy0hh5qpxuur8c@vanoxite.impmc.jussieu.fr>
References: <CAADUHkk=D+UUBo=AAE+cQ95tAiVyEUHOaFTDix5SqSVWLyw-QA@mail.gmail.com>
	<op.vy0hh5qpxuur8c@vanoxite.impmc.jussieu.fr>
Message-ID: <CAADUHkmXwGnJW1wFV5_15jLLMwnBjanaba85n0E4RJxmtMRwRw@mail.gmail.com>

Thank you Lorenzo, good side note!

On Fri, Jul 22, 2011 at 12:51 PM, Lorenzo Paulatto <
Lorenzo.Paulatto at impmc.upmc.fr> wrote:

> On Fri, 22 Jul 2011 09:54:11 +0200, Seyed Mojtaba Rezaei Sani
> <s.m.rezaeisani at gmail.com> wrote:
> >      from phq_readin : error #         1
> >       Wrong niter_ph
>
> Dear Seyed,
> for some reason I don't know the maximum number of iteration of the ph
> solver is set to 100, to "fix" this just open PH/phcom.f90 and change
>   INTEGER, PARAMETER :: maxter = 100
> to something larger (at least 300 in your case). ***Then recompile the
> code***.
>
> As a side note, if your system is not converging maybe you have made some
> mistake in the input, i.e. not using smearing where you should or the
> structure is badly optimized.
>
> 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
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
==========================================
 Seyed Mojtaba Rezaei Sani
Computational Condensed Matter Research Lab
Physics Department, Isfahan University of Technology
84156-83111 Isfahan, Iran
Tel lab: +98 311 391 3731
Group page: http://cmsgroup.iut.ac.ir/
s.rezaeisani at ph.iut.ac.ir
===========================================
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From eyvaz_isaev at yahoo.com  Fri Jul 22 12:32:35 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 22 Jul 2011 03:32:35 -0700 (PDT)
Subject: [Pw_forum] Wrong niter_ph (error in ph.x run)
In-Reply-To: <CAADUHkk=D+UUBo=AAE+cQ95tAiVyEUHOaFTDix5SqSVWLyw-QA@mail.gmail.com>
References: <CAADUHkk=D+UUBo=AAE+cQ95tAiVyEUHOaFTDix5SqSVWLyw-QA@mail.gmail.com>
Message-ID: <1311330755.61878.YahooMailNeo@web65716.mail.ac4.yahoo.com>

Hi, 
I am sorry, but probably, you read the forum not so carefully.? Quite recently there was a query:

?Re: [Pw_forum] ph.x cannot reach convergence within 100 steps 

and followed replies on my side. Please find this thread in the forum archive.

Besides, the message you got just means that there is no niter_ph keyword in &inputph namelist.

Bests,
Eyvaz.
?


-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


________________________________
From: Seyed Mojtaba Rezaei Sani <s.m.rezaeisani at gmail.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Friday, July 22, 2011 11:54 AM
Subject: [Pw_forum] Wrong niter_ph (error in ph.x run)


Dear all
I tried to calculate phonon frequencies for a system that need more iteration number than its default, so I add niter_ph into the namelist. But, I got this error:
?
#ph.in %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
???? task #???????? 0
???? from phq_readin : error #???????? 1
????? Wrong niter_ph 
?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

This is my input file:

?&inputph
? amass(1)=*,
? amass(2)=*,
? amass(3)=*,
? tr2_ph=1.0d-14,
? prefix='*',
? niter_ph = 300,
? ldisp=.true.,
? nq1=4 , nq2=4 , nq3=4
? outdir='*',
? fildyn='*.dyn',
?/

Thanks
-- 
==========================================

Seyed Mojtaba Rezaei Sani
Computational Condensed Matter Research Lab
Physics Department, Isfahan University of Technology
84156-83111 Isfahan, 
Iran
Tel lab: +98 311 391 3731? 
Group page: http://cmsgroup.iut.ac.ir/
s.rezaeisani at ph.iut.ac.ir
===========================================


_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From abdulrafiuraji at gmail.com  Fri Jul 22 12:53:00 2011
From: abdulrafiuraji at gmail.com (Abdulrafiu Raji)
Date: Fri, 22 Jul 2011 12:53:00 +0200
Subject: [Pw_forum] "xspectra.x" crashed with segmentation fault
Message-ID: <CACJL2X7Y6s0eRk-Ji4TF_mSs46CnUZ6mxbjKUpZFCJgPzZcY7w@mail.gmail.com>

Thank you. I compiled the xspectra.x  and pw.x executables  with the same
compiler on the same machine. The program ran  for few seconds and the
initial error message :"cannot open
/home/araji/XAS_SiO2_scr.1/qtz_ar1SCF_kp2.save/charge-density.dat file" did
not appear anymore. However, the program stopped abruptly. I write below,
respectively, the output and the accompanying error messages.

Please note that the Xspectra examples in the code ran perfectly well on the
machine.

Thanks for your attention

Abdulrafiu Tunde Raji
ICTP, Trieste.
Italy.


============

     Program XSPECTRA v.4.2.1   starts on 22Jul2011 at 11:48:23

     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

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

     Planes per process (thick) : nr3 =  80 npp =   10 ncplane =  5625
     Planes per process (smooth): nr3s=  60 npps=    8 ncplanes=  2916

     Proc/  planes cols     G    planes cols    G      columns  G
     Pool       (dense grid)       (smooth grid)      (wavefct grid)
        1    10    447    23677    8    238     9232     73     1579
        2    10    446    23674    8    238     9228     73     1579
        3    10    446    23674    8    238     9222     73     1579
        4    10    446    23674    8    238     9216     73     1579
        5    10    446    23674    7    238     9210     73     1579
        6    10    446    23674    7    238     9200     73     1579
        7    10    446    23674    7    238     9202     73     1579
        8    10    448    23676    7    237     9199     72     1574
     tot     80   3571   189397   60   1903    73709    583    12627

 af
 k-points : nkstot=          27
 -------------- Crystal Structure ------------
 celldm(1:6)
   18.57259936    0.00000000    1.10010000
    0.00000000    0.00000000    0.00000000
 direct lattice vectors
    1.00000000   -0.50000000    0.00000000
    0.00000000    0.86602540    0.00000000
    0.00000000    0.00000000    1.10010000
 reciprocal lattice vectors
    1.00000000    0.00000000    0.00000000
    0.57735027    1.15470054   -0.00000000
   -0.00000000    0.00000000    0.90900827
 nks=          27  nkstot=          27
  ----k-point list [units 2*pi/celldm(1)], weight---------
     1    0.00000000    0.00000000    0.00000000    0.07407407
     2    0.00000000    0.00000000    0.30300276    0.07407407
     3    0.00000000    0.00000000    0.60600551    0.07407407
     4    0.00000000    0.38490018    0.00000000    0.07407407
     5    0.00000000    0.38490018    0.30300276    0.07407407
     6    0.00000000    0.38490018    0.60600551    0.07407407
     7    0.00000000    0.76980036    0.00000000    0.07407407
     8    0.00000000    0.76980036    0.30300276    0.07407407
     9    0.00000000    0.76980036    0.60600551    0.07407407
    10    0.33333333    0.19245009    0.00000000    0.07407407
    11    0.33333333    0.19245009    0.30300276    0.07407407
    12    0.33333333    0.19245009    0.60600551    0.07407407
    13    0.33333333    0.57735027    0.00000000    0.07407407
    14    0.33333333    0.57735027    0.30300276    0.07407407
    15    0.33333333    0.57735027    0.60600551    0.07407407
    16    0.33333333    0.96225045    0.00000000    0.07407407
    17    0.33333333    0.96225045    0.30300276    0.07407407
    18    0.33333333    0.96225045    0.60600551    0.07407407
    19    0.66666667    0.38490018    0.00000000    0.07407407
    20    0.66666667    0.38490018    0.30300276    0.07407407
    21    0.66666667    0.38490018    0.60600551    0.07407407
    22    0.66666667    0.76980036    0.00000000    0.07407407
    23    0.66666667    0.76980036    0.30300276    0.07407407
    24    0.66666667    0.76980036    0.60600551    0.07407407
    25    0.66666667    1.15470054    0.00000000    0.07407407
    26    0.66666667    1.15470054    0.30300276    0.07407407
    27    0.66666667    1.15470054    0.60600551    0.07407407
 -------------------------------------------------
 --- Polarisation and k vector [cartesian coordinates]----
xepsilon(:)= 0.50000000 0.86602540 0.00000000
xkvec(:)= 1.00000000 0.00000000 0.00000000
 xmesh=         899
====================================

[node26:10484] *** Process received signal ***
[node26:10485] *** Process received signal ***
[node26:10485] Signal: Segmentation fault (11)
[node26:10485] Signal code: Address not mapped (1)
[node26:10485] Failing at address: 0x111d00
[node26:10482] *** Process received signal ***
[node26:10482] Signal: Segmentation fault (11)
[node26:10482] Signal code: Address not mapped (1)
[node26:10482] Failing at address: 0x111d00
[node26:10484] Signal: Segmentation fault (11)
[node26:10484] Signal code: Address not mapped (1)
[node26:10484] Failing at address: 0x111d00
[node26:10481] *** Process received signal ***
[node26:10481] Signal: Segmentation fault (11)
[node26:10481] Signal code: Address not mapped (1)
[node26:10481] Failing at address: 0x111d00
[node26:10485] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10485] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10485] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10485] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10485] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10485] *** End of error message ***
[node26:10482] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10482] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10482] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10482] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10482] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10482] *** End of error message ***
[node26:10484] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10484] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10484] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10484] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10484] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10484] *** End of error message ***
[node26:10487] *** Process received signal ***
[node26:10487] Signal: Segmentation fault (11)
[node26:10487] Signal code: Address not mapped (1)
[node26:10487] Failing at address: 0x111d00
[node26:10487] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10487] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10487] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10487] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10487] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10487] *** End of error message ***
[node26:10481] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10481] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10481] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10481] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10481] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10481] *** End of error message ***
[node26:10480] *** Process received signal ***
[node26:10480] Signal: Segmentation fault (11)
[node26:10480] Signal code: Address not mapped (1)
[node26:10480] Failing at address: 0x111d00
[node26:10483] *** Process received signal ***
[node26:10483] Signal: Segmentation fault (11)
[node26:10483] Signal code: Address not mapped (1)
[node26:10483] Failing at address: 0x111d00
[node26:10486] *** Process received signal ***
[node26:10486] Signal: Segmentation fault (11)
[node26:10486] Signal code: Address not mapped (1)
[node26:10486] Failing at address: 0x111d00
[node26:10480] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10480] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10480] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10480] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10480] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10480] *** End of error message ***
[node26:10483] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10483] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10483] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10483] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10483] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10483] *** End of error message ***
[node26:10486] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10486] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10486] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10486] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10486] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10486] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 10482 on node node26.hpc exited
on signal 11 (Segmentation fault).
--------------------------------------------------------------------------



  3. Re: Pw_forum Digest, Vol 49, Issue 53 (Paolo Giannozzi)
>
> Message: 3
> Date: Wed, 20 Jul 2011 21:15:56 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Pw_forum Digest, Vol 49, Issue 53
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <7F4B01A5-0DC1-457A-9A67-A8A2F9D19D8D at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
>
> On Jul 20, 2011, at 18:52 , Abdulrafiu Raji wrote:
>
> >      cannot open /home/araji/XAS_SiO2_scr.1/qtz_ar1SCF_kp2.save/
> > charge-density.dat file
>
> it is not there, or it is corrupted, or empty, or not in the right
> format.
> Note that it is a binary file that should be written by and read by
> executables compiled with the same compiler on th same machine,
> as a rule
>
> 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
>
>
>
>
>
>
>
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From gabriel.greene at tyndall.ie  Fri Jul 22 13:24:25 2011
From: gabriel.greene at tyndall.ie (Gabriel Greene)
Date: Fri, 22 Jul 2011 12:24:25 +0100
Subject: [Pw_forum] PBE Hybrid funcitonals and LDA pseudopotentials
References: <mailman.14266.1311093329.1814.pw_forum@pwscf.org>
	<20110722115146.15322ocwmx3onacy@webmail.epfl.ch>
Message-ID: <D4A761F73683694BBD69D634FF298015C03775@MAIL.tyndall.ie>


> I am surprised this would work because my understanding is that LDA  
> contains no exchange term

My apologies, I meant LDA contains no HF-exchange, of course it contains slater exchange.

Thanks


-----Original Message-----
From: pw_forum-bounces at pwscf.org on behalf of hannu.komsa at epfl.ch
Sent: Fri 7/22/2011 10:51 AM
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] PBE Hybrid funcitonals and LDA pseudopotentials
 
Dear Gabriel,

> I have been attempting to use the hybrid functional PBE0 to tune the  
> bandgap of InGaAs, while using Virtual Crystal Approximation to  
> obtain In(0.57)Ga(0.43)As. I initially tried mixing the PBE pseudos  
> of Ga and In, but ran into a number of problems (unequal nqf mesh  
> when mixing, and using ultrasoft pseudos with hybrid functionals).

When I tested VCA for InGaAs, it didn't look so good. At least the  
lattice constant dependence on Ga/In composition came out pretty bad  
as Ga and In are of quite different sizes. I used pseudos taken from  
the abinit page and converted to QE. VCA seemed to work fine for  
those, also at the PBE level.

> I then tried the Norm-conserving LDA pseudos (which also have no nqf  
> information to worry about) for mixing In and Ga (also using LDA for  
> As pseudo, obviously). I then found I could tune the bandgap by  
> specifying "PBE0" in the &SYSTEM card of the input file by changing  
> the proportion of Fock exchange (alpha, or "exx_fraction" in  
> funct.f90), while specifying LDA pseudos for each atomic species.

You can mix and mash pseudos and functionals, but if you are not  
absolutely sure of what you are doing, it will likely fall in the  
category of garbage-in-garbage-out. PW also warns you about this.

> I am surprised this would work because my understanding is that LDA  
> contains no exchange term, yet modifying the value of alpha has an  
> effect on the bandgap just like if I had specified PBE  
> pseudopotentials in the ATOMIC_SPECIES card. I initially set up this  
> calculation as a test to just prove to myself that the results  
> obtained using LDA pseudopotentials are independant of the amount of  
> exchange, yet this is not so.

You might want to read some more literature about DFT and functionals,  
as the above description is mostly wrong. All functionals have  
exchange term, but with different (level of) approximation.


Regards,
   Hannu-Pekka Komsa
   EPFL, Switzerland

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

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From joerg.buchwald at iom-leipzig.de  Fri Jul 22 13:40:47 2011
From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald)
Date: Fri, 22 Jul 2011 13:40:47 +0200
Subject: [Pw_forum] problem in calculating the binding energies with
 pwscf
In-Reply-To: <8CE15CFE98D0BD6-1DF4-3C64@Webmail-m117.sysops.aol.com>
References: <20110721150631.4216eb09@PC-Mayr-Mitarb6.pc-flexi>
	<8CE15CFE98D0BD6-1DF4-3C64@Webmail-m117.sysops.aol.com>
Message-ID: <20110722134047.451e583a@PC-Mayr-Mitarb6.pc-flexi>

Hi,
Thx, now it looks much better. I set the starting_magnetization to 10
only for test reasons, but as you said, it was the wrong switch.
Regards,
J?rg

--
Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
Permoserstrasse 15
04318 Leipzig
GERMANY


Am Thu, 21 Jul 2011 11:13:43 -0400 (EDT)
schrieb elbuesta at icqmail.com:

> Hello Joerg Buchwald, 
> 
> a few comments. Starting magnetization should be between -1 and 1. 1
> means that all available electrons from the PP have spin up. Also, if
> you want to do spin unrestricted calculations, you should set
> nspin=2. Only starting magnetization does not do anything. 
> 
> In addition, I wouldn't compare the energy of the bulk and the
> isolated atom this way because the cutoff on the WFC is quite
> different for each case: energy differences converge much faster than
> the total energy. But I don't think that is the problem here, only
> the magnetization is.
> 
> I slightly modified your inputs and got 4.5eV. If I remember well,
> this value is okay. I hope it helps. All best!
> 
> Free Si atom:
> 
> &control
>     prefix='si_free',
>     pseudo_dir='/home/alex/pseudo'
>     outdir = '/scratch/alex',
>  /
>  &system
>     ibrav=  1, celldm(1) =25, nat=  1, ntyp= 1,
>     ecutwfc =
> 30.0,occupations='fixed',nspin=2,tot_magnetization=2.,nosym=.true., /
>  &electrons
>  /
> ATOMIC_SPECIES
>  Si  28.086  Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
>  Si 0.50 0.50 0.50
> K_POINTS gamma
> ......................................
> 
> Bulk Si:
> 
> &control
>     prefix='silicon',
>     pseudo_dir='/home/alex/pseudo'
>     outdir = '/scratch/alex',
>  /
>  &system
>     ibrav=  2, celldm(1) =10.263142, nat=  2, ntyp= 1,
>     ecutwfc = 40.0,
>  /
>  &electrons
>  /
> ATOMIC_SPECIES
>  Si  28.086  Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
>  Si 0.00 0.00 0.00
>  Si 0.25 0.25 0.25
> K_POINTS automatic
>  9 9 9 1 1 1
> 
> ................................................................
> 
> 
> -----Original Message-----
> 
> From: J?rg Buchwald <joerg.buchwald at iom-leipzig.de>
> To: pw_forum <pw_forum at pwscf.org>
> Sent: Thu, Jul 21, 2011 3:15 pm
> Subject: [Pw_forum] problem in calculating the binding energies with
> pwscf
> 
> 
> Hello,
> I'm performing some first test-calculations with pwscf, where I try to
> get the binding energy of bulk silicon. The problem is, that the
> resulting energy, which should be the difference of the total
> energy of silicon crystal structure and the a free atom, is about 3eV
> too low. I used different pseudopotentials, different
> lattice-parameters and I also tested the convergencies (with k and
> the energy-cut-off) which worked, but I don't have a clue what a made
> wrong.
> 
> Here are my Input files:
> 
> ---
>  &control
>     prefix='silicon',
>     pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
>     outdir = '/home/joerg/scratch',
>  /
>  &system
>     ibrav=  2, celldm(1) =10.263142, nat=  2, ntyp= 1,
>     ecutwfc = 30.0,
>  /
>  &electrons
>  /
> ATOMIC_SPECIES
>  Si  28.086  Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
>  Si 0.00 0.00 0.00
>  Si 0.25 0.25 0.25
> K_POINTS automatic
>  9 9 9 1 1 1
> ---
> 
> and for the free atom:
> 
> ---
> &control
>     prefix='silicon',
>     pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
>     outdir = '/home/joerg/scratch',
>  /
>  &system
>     ibrav=  0, celldm(1) =50.2, nat=  1, ntyp= 1,
>     ecutwfc = 80.0,occupations='fixed',starting_magnetization(1)=10,
>  /
>  &electrons
>  /
> ATOMIC_SPECIES
>  Si  28.086  Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
>  Si 0.50 0.50 0.50
> K_POINTS gamma
> 
> CELL_PARAMETERS {cubic}
>     1.00 0.00 0.00
>     0.00 1.00 0.00
>     0.00 0.00 1.00
> ---
> 
> It would be nice if someone could help me.
> Thx & regards,
> J?rg Buchwald
> 
> 
> Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
> Permoserstrasse 15
> 04318 Leipzig
> GERMANY
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
>  


From guntram.schmidt at chemie.uni-halle.de  Fri Jul 22 14:01:28 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Fri, 22 Jul 2011 14:01:28 +0200
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
Message-ID: <4E296698.8000702@chemie.uni-halle.de>

Dear Mike,

thanks for your comment.
I got it working now, using:

./configure LIBDIRS="/gpfs/usrurz/lapack/lapack-3.2.1 
/gpfs/usrurz/lib64" FC=xlf2003_r FCFLAGS="-qfree=f90 -C -g -qnosmp" 
MPIF90=mpfort LAPACK_LIBS="-L/gpfs/usrurz/lib64 -llapack"

However, I'm not quite sure on the meaning of all these parameters :-(.
I'm still wondering, wether the following lines are reasonable:
-----------------------------
The following libraries have been found:
   BLAS_LIBS=
   LAPACK_LIBS=-L/gpfs/usrurz/lib64 -llapack 
/gpfs/home/aasfu/espresso-4.3.1/lapack-3.2/lapack.a
   FFT_LIBS=-lessl
   MASS_LIBS= -lmassvp4_64 -lmass_64
--------------------------------

Woudn't the LAPACK_LIBS mean, that the quantum-espresso version 
overrides all commands/functions of the /gpfs/usrurz/lib64/llapack.a ?
Or is the priority the other way round?

Also I wonder, why BLAS_LIBS is empty - is it, because BLAS is included 
in LAPACK?

Thank you,
Guntram


Am 21.07.2011 14:46, schrieb Michael Sullivan:
> Guntram:
>
> I've never seen this error message, but if you can try to edit the make.sys file directly. Replace the LAPACK_LIBS flag to point to your own LAPACK and probably change LAPACK_LIBS_SWITCH to external. That said, though, I've found that usually if it can't find it, there's a reason.
>
> Good luck!
>
> Mike
> michael at ihpc.a-star.edu.sg
> http://www.sullivan.sg/
>
> On 21-Jul-2011, at 6:49 PM, Guntram Schmidt wrote:
>
>> Dear All,
>>
>> after getting strange error-messages, which might be related to
>> lapack/blas (
>> DSYGV : 2538-2015
>> The number of elements (ARG NO. 11) in a work array must be greater than
>> or equal to (2048).
>> )
>> I'd like to use "our own" lapack/blas.
>> Unfortunately QE won't find/accept them - what's the right way, to help it?
>>
>> I tried:
>>   ./configure MPIF90=mpfort LIBDIRS="/gpfs/usrurz/lapack/lapack-3.2.1"
>> with
>>
>> :/gpfs/usrurz/lapack/lapack-3.2.1>  ls
>> BLAS               CCI_README     Makefile                   README
>> cci                ccisrc.tar     make.inc                   README_hh
>> cci.log            INSTALL        make.inc.example           SRC
>> CCI_NOTES          lapack_pwr6.a  make.inc.old               TESTING
>> CCI_QUICK_INSTALL  LICENSE        make.log_pwr6_xlf_q64_cci  tmglib_pwr6.a
>>
>> yielding a quite promising directory of an installed lapack/blas?
>>
>> But QE insists on its own libraries.
>>
>> The system is an IBM 575 with Power-Linux=SLES11_on_Power and the only
>> information I found is this here:
>> http://www2.fz-juelich.de/jsc/jump/usage/FAQ/essl/
>>
>>
>> Any ideas on this?
>> Thanks a lot,
>> Guntram
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> "1991-2011 - Creating Growth, Enhancing Lives. Commemorating A*STAR's 20 Years of Science, Technology and Research in Singapore."
>
> IHPC Values  ::  Impact   ::   Honesty   ::   Performance   ::   Co-operation
> This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.
> _______________________________________________
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> http://www.democritos.it/mailman/listinfo/pw_forum

From giannozz at democritos.it  Fri Jul 22 15:40:03 2011
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Fri, 22 Jul 2011 15:40:03 +0200
Subject: [Pw_forum] "xspectra.x" crashed with segmentation fault
In-Reply-To: <CACJL2X7Y6s0eRk-Ji4TF_mSs46CnUZ6mxbjKUpZFCJgPzZcY7w@mail.gmail.com>
References: <CACJL2X7Y6s0eRk-Ji4TF_mSs46CnUZ6mxbjKUpZFCJgPzZcY7w@mail.gmail.com>
Message-ID: <20110722154003.lmtj2iyhb4gs0w4k@mail.democritos.it>

Quoting Abdulrafiu Raji <abdulrafiuraji at gmail.com>:

> However, the program stopped abruptly. I write below,
> respectively, the output and the accompanying error messages.

you should verify if this error is still present in a more recent version
of the code, if it is reproducible on other architectures or with other
compilers, if it happens in serial or in parallel or both, etc...

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



----------------------------------------------------------------
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From pasianot at cnea.gov.ar  Fri Jul 22 13:46:45 2011
From: pasianot at cnea.gov.ar (RCP)
Date: Fri, 22 Jul 2011 08:46:45 -0300
Subject: [Pw_forum] My vague understanding of internal degrees of freedom
In-Reply-To: <4E294821.5030703@yahoo.com.cn>
References: <CAJQfR0SST-0Nx6q5WsPZkv-Gi=yoA5AM6JnDUyFU3+8e=22VYg@mail.gmail.com>
	<4E294821.5030703@yahoo.com.cn>
Message-ID: <4E296325.2010501@cnea.gov.ar>


 Hello,


Hongsheng Zhao wrote:
> On 07/22/2011 03:49 PM, xiaochuan Ge wrote:
>   
...
> Based on the above description, let we back to my question again: I
> want know for a specific system, how we know whether there are "internal
> degrees of freedom" or not.  How to judge it?
>   

 By symmetry.
 As you said, in order to calculate the elastic constants, one applies 
an (infinitesimal) uniform
 strain. This will generally break the original symmetry of the cell. 
Now the question is: can one
 assure that forces on atoms are zero for this new (lower) symmetry ?. 
If the answer is YES, then
 do not worry about internal degrees of freedom. Contrarily, if it is 
NO, then you must account for
 internal degrees of freedom.

 Thus your best bet for a complex unit cell is that there are internal 
degrees of freedom, and the
 difference among the two situations, namely, with/without, just means 
an energy difference
 between the relaxed/unrelaxed atomic coordinates.

 HTH

 Roberto



From giannozz at democritos.it  Fri Jul 22 15:44:16 2011
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Fri, 22 Jul 2011 15:44:16 +0200
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <4E296698.8000702@chemie.uni-halle.de>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E296698.8000702@chemie.uni-halle.de>
Message-ID: <20110722154416.hcix64lq808kgw8s@mail.democritos.it>

Quoting Guntram Schmidt <guntram.schmidt at chemie.uni-halle.de>:

> FCFLAGS="-qfree=f90 -C -g -qnosmp"

options -C -g and no optimization? You have a big cpu grant.

> Or is the priority the other way round?

it is: libraries are loaded in the order they are listed

> Also I wonder, why BLAS_LIBS is empty

BLAS (and part of LAPACK) are contained in essl. ON IBM machines
you should use essl as much as you can

P.



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From zhaohscas at yahoo.com.cn  Fri Jul 22 16:16:22 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Fri, 22 Jul 2011 22:16:22 +0800
Subject: [Pw_forum] My vague understanding of internal degrees of freedom
In-Reply-To: <4E296325.2010501@cnea.gov.ar>
References: <CAJQfR0SST-0Nx6q5WsPZkv-Gi=yoA5AM6JnDUyFU3+8e=22VYg@mail.gmail.com>	<4E294821.5030703@yahoo.com.cn>
	<4E296325.2010501@cnea.gov.ar>
Message-ID: <4E298636.90507@yahoo.com.cn>

On 07/22/2011 07:46 PM, RCP wrote:
>
>   Hello,
>
>
> Hongsheng Zhao wrote:
>> On 07/22/2011 03:49 PM, xiaochuan Ge wrote:
>>
> ...
>> Based on the above description, let we back to my question again: I
>> want know for a specific system, how we know whether there are "internal
>> degrees of freedom" or not.  How to judge it?
>>
>
>   By symmetry.
>   As you said, in order to calculate the elastic constants, one applies
> an (infinitesimal) uniform
>   strain. This will generally break the original symmetry of the cell.
> Now the question is: can one
>   assure that forces on atoms are zero for this new (lower) symmetry ?.
> If the answer is YES, then
>   do not worry about internal degrees of freedom. Contrarily, if it is
> NO, then you must account for
>   internal degrees of freedom.
>
>   Thus your best bet for a complex unit cell is that there are internal
> degrees of freedom, and the
>   difference among the two situations, namely, with/without, just means
> an energy difference
>   between the relaxed/unrelaxed atomic coordinates.

Thanks a lot, I've got it.

Regards
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From guntram.schmidt at chemie.uni-halle.de  Fri Jul 22 16:40:20 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Fri, 22 Jul 2011 16:40:20 +0200
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <20110722154416.hcix64lq808kgw8s@mail.democritos.it>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E296698.8000702@chemie.uni-halle.de>
	<20110722154416.hcix64lq808kgw8s@mail.democritos.it>
Message-ID: <4E298BD4.4080201@chemie.uni-halle.de>

Dear Paolo,

>> FCFLAGS="-qfree=f90 -C -g -qnosmp"
>
> options -C -g and no optimization? You have a big cpu grant.

As I already wrote, I have no idea on these parameters, they are copied 
from various sources to get the compilation working without any errors...
Do you refer to cpu-usage when executing make or cpu-usage of the 
compiled quantum espresso?

>> Or is the priority the other way round?
>
> it is: libraries are loaded in the order they are listed

But this would mean, in
-L/gpfs/usrurz/lib64 -llapack 
/gpfs/home/aasfu/espresso-4.3.1/lapack-3.2/lapack.a
all (optimized) functions from /gpfs/usrurz/lib64/llapack.a would be 
overwritten by the functions from espresso/lapack?
Or is the implementation, that existing functions are not 
overwritten/redefined?

>> Also I wonder, why BLAS_LIBS is empty
>
> BLAS (and part of LAPACK) are contained in essl. ON IBM machines
> you should use essl as much as you can

What does this mean? That an empty BLAS_LIBS is fine?
Where/How can I suggest more usage of essl?

Thanks a lot,
Guntram

From Lorenzo.Paulatto at impmc.upmc.fr  Fri Jul 22 17:52:20 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Fri, 22 Jul 2011 17:52:20 +0200
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <4E298BD4.4080201@chemie.uni-halle.de>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E296698.8000702@chemie.uni-halle.de>
	<20110722154416.hcix64lq808kgw8s@mail.democritos.it>
	<4E298BD4.4080201@chemie.uni-halle.de>
Message-ID: <op.vy02dipwxuur8c@vanoxite.impmc.jussieu.fr>

On Fri, 22 Jul 2011 16:40:20 +0200, Guntram Schmidt  
<guntram.schmidt at chemie.uni-halle.de> wrote:
> What does this mean? That an empty BLAS_LIBS is fine?
> Where/How can I suggest more usage of essl?

I only want to point out that after having run configure you can edit  
make.sys directly by hand, it is way easier then passing a long string of  
parameters to configure. It is also one of the few files in the code which  
is extensively commented...

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

From robinshy at gmail.com  Sat Jul 23 10:45:13 2011
From: robinshy at gmail.com (Robin H)
Date: Sat, 23 Jul 2011 16:45:13 +0800
Subject: [Pw_forum] problem with creating the pseudopotential of Zn
Message-ID: <CALd2EAQizgOxcGy_q_zQx9Db2-20cNMFHQZZkgBjsRwO5zNMXA@mail.gmail.com>

Hi,everyone.I have tried many times to creat the PP of Zn,but the problems
come out everytime.Even if I correct the one,then there will be anthoer.Zn
is one of the transition iron atom,and I'm not sure  my input  items are all
proper for it.This is my input file for ld1.x .And the next is the wrong
information.I need some help.
 *input :*
     &input
    title='Zn'
    zed=30.
    rel=1,
    config='[Ar] 3d10.00 4s1.00 4p1.00',
    iswitch=3,
    dft='revPBE'
 /
 &inputp
   lloc=2,
   pseudotype=3,
   file_pseudopw='Zn.revPBE.UPF',
   author='ADC',
 /
6
3D  3  2  10.00  0.00  1.80  2.00
3D  3  2  0.00   0.05  1.80  2.00
4S  1  0  1.00   0.00  1.80  2.00
4S  1  0  0.00   0.05  1.80  2.00
4P  2  1  1.00   0.00  1.80  2.10
4P  2  1  0.00   0.05  1.80  2.10



*wrong information :*
* *Program LD1 v.4.3.1        starts on 23Jul2011 at 16:29: 5
     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     1 processors
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from ld1_readin : error #         1
     only one local channel
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0
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From baroni at sissa.it  Sat Jul 23 15:34:18 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Sat, 23 Jul 2011 15:34:18 +0200
Subject: [Pw_forum] problem with creating the pseudopotential of Zn
In-Reply-To: <CALd2EAQizgOxcGy_q_zQx9Db2-20cNMFHQZZkgBjsRwO5zNMXA@mail.gmail.com>
References: <CALd2EAQizgOxcGy_q_zQx9Db2-20cNMFHQZZkgBjsRwO5zNMXA@mail.gmail.com>
Message-ID: <0DF2E7C8-B2F6-4AB8-BE62-7A4D11F47824@sissa.it>

I am no expert here, but it looks like you are attempting to run on a parallel machine. Not a great idea. ld1 can run on cell phone, these days ... SB

On Jul 23, 2011, at 10:45 AM, Robin H wrote:

> Hi,everyone.I have tried many times to creat the PP of Zn,but the problems come out everytime.Even if I correct the one,then there will be anthoer.Zn is one of the transition iron atom,and I'm not sure  my input  items are all proper for it.This is my input file for ld1.x .And the next is the wrong information.I need some help.
>  input :
>      &input
>     title='Zn'
>     zed=30.
>     rel=1,
>     config='[Ar] 3d10.00 4s1.00 4p1.00',
>     iswitch=3,
>     dft='revPBE'
>  /
>  &inputp
>    lloc=2,
>    pseudotype=3,
>    file_pseudopw='Zn.revPBE.UPF',
>    author='ADC',
>  /
> 6
> 3D  3  2  10.00  0.00  1.80  2.00 
> 3D  3  2  0.00   0.05  1.80  2.00
> 4S  1  0  1.00   0.00  1.80  2.00
> 4S  1  0  0.00   0.05  1.80  2.00
> 4P  2  1  1.00   0.00  1.80  2.10
> 4P  2  1  0.00   0.05  1.80  2.10
>  
>  
> wrong information :
>  Program LD1 v.4.3.1        starts on 23Jul2011 at 16:29: 5
>      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     1 processors
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from ld1_readin : error #         1
>      only one local channel
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      stopping ...
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0
>  
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
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

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From lorenzo.paulatto at impmc.upmc.fr  Sat Jul 23 15:57:27 2011
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Sat, 23 Jul 2011 15:57:27 +0200
Subject: [Pw_forum] problem with creating the pseudopotential of Zn
In-Reply-To: <CALd2EAQizgOxcGy_q_zQx9Db2-20cNMFHQZZkgBjsRwO5zNMXA@mail.gmail.com>
References: <CALd2EAQizgOxcGy_q_zQx9Db2-20cNMFHQZZkgBjsRwO5zNMXA@mail.gmail.com>
Message-ID: <op.vy2rp1uv5jfbqb@paulax>

In data 23 luglio 2011 alle ore 10:45:13, Robin H <robinshy at gmail.com> ha
scritto:
>      from ld1_readin : error #         1
>      only one local channel

   From atomic_doc/INPUT_LD1.txt

      Variable:       lloc

      Type:           INTEGER
      Default:        -1
      Description:    Angular momentum of the local channel.
              * lloc=-1 or lloc=-2 pseudizes the all-electron potential
                if lloc=-2 the original recipe of Troullier-Martins
                is used (izero first and second derivatives at r=0)
              * lloc>-1 uses the corresponding channel as local PP
              NB: if lloc>-1, the corresponding channel must be the last in  
the
              list of wavefunctions appearing after the namelist &inputp
              In the relativistic case, if lloc > 0 both the j=lloc-1/2 and
              the j=lloc+1/2 wavefunctions must be at the end of the list.

best regards

-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From flux_ray12 at 163.com  Sat Jul 23 17:29:18 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Sat, 23 Jul 2011 23:29:18 +0800 (CST)
Subject: [Pw_forum] problem with creating the pseudopotential of Zn
In-Reply-To: <CALd2EAQizgOxcGy_q_zQx9Db2-20cNMFHQZZkgBjsRwO5zNMXA@mail.gmail.com>
References: <CALd2EAQizgOxcGy_q_zQx9Db2-20cNMFHQZZkgBjsRwO5zNMXA@mail.gmail.com>
Message-ID: <36f98ebe.3d22.131579d6572.Coremail.flux_ray12@163.com>

when lloc=2, d orbital should be the last one~
I am not good at PP generation and theory, but your problem can be fixed with such modifications ( I am not sure whether LD1 code supports Revised-PBE, and I met a negative rho problem if I used RRKJ method ):
&input
    zed = 30.
    rel = 1,
    config = '[Ar] 3d10 4s1 4p1' ,
    iswitch = 3,
    dft = 'PBE'
/
&inputp
   lloc = 1 ,
   pseudotype = 3 ,
   file_pseudopw = 'Zn.PBE.UPF' ,
   nlcc = .true. ,
   tm = .true. ,
/
5
3D  3  2  10.00  0.00  1.80  2.00
3D  3  2  0.00   0.05  1.80  2.00
4S  1  0  1.00   0.00  1.80  2.00
4S  1  0  0.00   0.05  1.80  2.00
4P  2  1  1.00   0.00  1.80  2.10

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-23 16:45:13,"Robin H" <robinshy at gmail.com> wrote:

Hi,everyone.I have tried many times to creat the PP of Zn,but the problems come out everytime.Even if I correct the one,then there will be anthoer.Zn is one of the transition iron atom,and I'm not sure  my input  items are all proper for it.This is my input file for ld1.x .And the next is the wrong information.I need some help.
 input :
     &input
    title='Zn'
    zed=30.
    rel=1,
    config='[Ar] 3d10.00 4s1.00 4p1.00',
    iswitch=3,
    dft='revPBE'
 /
 &inputp
   lloc=2,
   pseudotype=3,
   file_pseudopw='Zn.revPBE.UPF',
   author='ADC',
 /
6
3D  3  2  10.00  0.00  1.80  2.00
3D  3  2  0.00   0.05  1.80  2.00
4S  1  0  1.00   0.00  1.80  2.00
4S  1  0  0.00   0.05  1.80  2.00
4P  2  1  1.00   0.00  1.80  2.10
4P  2  1  0.00   0.05  1.80  2.10

 

 
wrong information :
 Program LD1 v.4.3.1        starts on 23Jul2011 at 16:29: 5
     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);
          URLhttp://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     1 processors
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from ld1_readin : error #         1
     only one local channel
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0

 

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From giannozz at democritos.it  Sat Jul 23 21:11:08 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 23 Jul 2011 21:11:08 +0200
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <4E298BD4.4080201@chemie.uni-halle.de>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E296698.8000702@chemie.uni-halle.de>
	<20110722154416.hcix64lq808kgw8s@mail.democritos.it>
	<4E298BD4.4080201@chemie.uni-halle.de>
Message-ID: <FDC80EA9-E83F-4222-9568-99BC425E3C5C@democritos.it>


On Jul 22, 2011, at 16:40 , Guntram Schmidt wrote:

> As I already wrote, I have no idea on these parameters

you shouldn't use options and parameters if you do not know what
they are doing. Use plain "configure" with no options, and if something
doesn't go right, try to figure out what and why.

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 zhaohscas at yahoo.com.cn  Sun Jul 24 12:55:11 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Sun, 24 Jul 2011 18:55:11 +0800
Subject: [Pw_forum] Can pwscf do the Superconductivity study?
Message-ID: <4E2BFA0F.6000101@yahoo.com.cn>

Hi all,

I want to know can pwscf be used to  study Superconductivity, say, based 
on bcs theory?

Regards
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From mohnish.iitk at gmail.com  Mon Jul 25 06:02:19 2011
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Mon, 25 Jul 2011 09:32:19 +0530
Subject: [Pw_forum] Nature of antiferomagnetism in thin films
Message-ID: <CAMhNW-cUpu-ZcB8p4T9JaAM+Aj753kK7YH3D1J4RJWxkbdvwXA@mail.gmail.com>

Dear QE users,

I want to do calculations of thin films of antiferromagnetic oxide like CoO.
The CoO has rocksalt structure and magnetization along (111) direction.
Suppose we take 3 layers and 4 layers for of CoO along (111), then my doubt
is that will the magnetization oscillate i.e. in even number of layers it
will be zero and odd number of layers will have some finite value? Or wil
the film will show antiferrromagnetism in plane i.e. every layers of CoO
will be antiferromagnetic? And what about other directions like (001) or
(10-10) in wurtzite structure.

Thanks a lot in advance for help..

-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
Senior Project Associate,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
-----------------------------------------------------------------
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From yjh9898 at postech.ac.kr  Mon Jul 25 07:20:19 2011
From: yjh9898 at postech.ac.kr (=?UTF-8?B?7Jyk7KCV7ZuI?=)
Date: Mon, 25 Jul 2011 14:20:19 +0900
Subject: [Pw_forum] =?utf-8?q?PHONON_error_with_trans=3D=2Efalse=2E_and_el?=
	=?utf-8?b?cGg9LnRydWUu?=
Message-ID: <1311571219392.95394.postech@postech.ac.kr>

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From yjh9898 at postech.ac.kr  Mon Jul 25 09:09:41 2011
From: yjh9898 at postech.ac.kr (=?UTF-8?B?SmVvbmdodW4gWXVu?=)
Date: Mon, 25 Jul 2011 16:09:41 +0900
Subject: [Pw_forum] =?utf-8?q?PHONON_error_with_elph=3D=2Etrue=2E_and_tran?=
	=?utf-8?b?cz0uZmFsc2Uu?=
Message-ID: <1311577781577.6843.postech@postech.ac.kr>

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From flux_ray12 at 163.com  Mon Jul 25 12:21:22 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Mon, 25 Jul 2011 18:21:22 +0800 (CST)
Subject: [Pw_forum] PHONON error with trans=.false. and elph=.true.
In-Reply-To: <1311571219392.95394.postech@postech.ac.kr>
References: <1311571219392.95394.postech@postech.ac.kr>
Message-ID: <7b80aea4.eaeb.13160d03348.Coremail.flux_ray12@163.com>

Were there any error report in your terminate, such like"Segment fault" ?

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-25 13:20:19,"???" <yjh9898 at postech.ac.kr> wrote:

I am trying to calculate the electron-phonon coupling with PHONON 4.2.1.
I modified the program to work with elph=.true. and trans=.false., referring PW_forum. (i.e I fixed the bug that known)
The previous PHONON calculation for mode frequencies were done earlier, but I found the problem.


The input is written below:
---------------------------------------------------


biGr_Ca


&inputph
    amass(1)=40.078
    amass(2)=12.011
    outdir='./'
    iverbosity=0
    prefix='CaGr131scf'
    niter_ph=100
    tr2_ph=1e-12
    fildyn='131.dyn'
    fildrho='rhoresp'
    fildvscf='potvar131'
    trans=.false.
    ldisp=.true.
    elph=.true.
    nq1=6, nq2=6, nq3=1
/
----------------------------------------------------


AND, I've found the problem: The program stops WITHOUT error message, just before the calculation.
-------------------------------------------------------------------------
.........
     site n.  atom      mass           positions (a_0 units)
        1        Ca  40.0780   tau( 1) = (    0.00000    0.00000    0.00000  )


     Computing dynamical matrix for
                    q = (   0.0000000   0.0000000   0.0000000 )


     25 Sym.Ops. (with q -> -q+G )




     G cutoff =  553.0542  (  14740 G-vectors)     FFT grid: ( 48, 48,240)
     G cutoff =  201.1106  (   3234 G-vectors)  smooth grid: ( 30, 30,144)
     number of k points=    19  gaussian broad. (Ry)=  0.0300     ngauss =   1


     PseudoPot. # 1 for Ca read from file Ca.pbe-nsp-van.UPF
     Pseudo is Ultrasoft + core correction, Zval = 10.0
     Generated by new atomic code, or converted to UPF format
     Using radial grid of  845 points,  6 beta functions with:
                l(1) =   0
                l(2) =   0
                l(3) =   1
                l(4) =   1
                l(5) =   2
                l(6) =   2
     Q(r) pseudized with  6 coefficients,  rinner =    1.200   1.200   1.200
                                                       1.200   1.200




     Atomic displacements:
     There are   2 irreducible representations


     Representation     1      2 modes -E_1u To be done


     Representation     2      1 modes -A_2u To be done




     PHONON       :     4.38s CPU time,        6.23s WALL time


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


Please help me for this unexpected error.


P.S I wonder the trans=.false. calculation with 16 cpus in a pool is compatible with phonon frequency calculation with 64 cpus in 4 pools. The fildvscf is splat in four files......
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From zafartariq2003 at yahoo.com  Mon Jul 25 13:05:33 2011
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Mon, 25 Jul 2011 04:05:33 -0700 (PDT)
Subject: [Pw_forum] Warnings And Errors in Compilation of QHA......
Message-ID: <1311591933.28899.YahooMailClassic@web65411.mail.ac4.yahoo.com>

Dear All

I try best to compile QHA but can not create *.x files. Now I have fedora core 14. Will any body help me. I think that QHA has some deleted routines. I have such type of warnings. If Some one has complete QHA then please send it to me. Thanking in anticipation


[zafar at localhost QHA]$ ./Compile
gfortran -O3 -ffast-math -fno-f2c -c? tetra.f
gfortran -O3 -ffast-math -fno-f2c -c? k_brillouin.f
gfortran -O3 -ffast-math -fno-f2c -c? generate_tetra.f
gfortran -O3 -ffast-math -fno-f2c -c? det3.f
gfortran -O3 -ffast-math -fno-f2c -c? det4.f
gfortran -static -o tetra.x tetra.o k_brillouin.o generate_tetra.o? det3.o det4.o?? 
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
make: *** [tetra] Error 1
gfortran -O3 -ffast-math -fno-f2c? -c? Debye.f90
Debye.f90:144.8:

???? do T = T_low_start, T_low, T_low_delta
??????? 1
Warning: Deleted feature: Loop variable at (1) must be integer
Debye.f90:144.11:

???? do T = T_low_start, T_low, T_low_delta
?????????? 1
Warning: Deleted feature: Start expression in DO loop at (1) must be integer
Debye.f90:144.24:

???? do T = T_low_start, T_low, T_low_delta
??????????????????????? 1
Warning: Deleted feature: End expression in DO loop at (1) must be integer
Debye.f90:144.31:

???? do T = T_low_start, T_low, T_low_delta
?????????????????????????????? 1
Warning: Deleted feature: Step expression in DO loop at (1) must be integer
Debye.f90:177.4:

?do T = T_low+5, T_high, T_high_delta
??? 1
Warning: Deleted feature: Loop variable at (1) must be integer
Debye.f90:177.7:

?do T = T_low+5, T_high, T_high_delta
?????? 1
Warning: Deleted feature: Start expression in DO loop at (1) must be integer
Debye.f90:177.16:

?do T = T_low+5, T_high, T_high_delta
??????????????? 1
Warning: Deleted feature: End expression in DO loop at (1) must be integer
Debye.f90:177.24:

?do T = T_low+5, T_high, T_high_delta
??????????????????????? 1
Warning: Deleted feature: Step expression in DO loop at (1) must be integer
gfortran -O3 -ffast-math -fno-f2c -c? Debye_T.f
gfortran -O3 -ffast-math -fno-f2c -c? debye3.f
gfortran -O3 -ffast-math -fno-f2c -c? cheval.f
gfortran -O3 -ffast-math -fno-f2c -c? d1mach.f
gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o 
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
make: *** [Debye_x] Error 1
gfortran -O3 -ffast-math -fno-f2c -c? Mean_square_displacement.f90
Mean_square_displacement.f90:162.7:

??? do T=T_start,T_end,T_delta
?????? 1
Warning: Deleted feature: Loop variable at (1) must be integer
gfortran -static -o Mean_square_displacement.x Mean_square_displacement.o?? 
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
make: *** [MSD] Error 1
ln: creating symbolic link `tetra.x': File exists
ln: creating symbolic link `phonon_dos.x': File exists
ln: creating symbolic link `Debye.x': File exists
ln: creating symbolic link `Atom_projected_properties.x': File exists
ln: creating symbolic link `F_QHA.x': File exists
ln: creating symbolic link `Ghost_DOS.x': File exists
ln: creating symbolic link `Partial_phonon_DOS.x': File exists
ln: creating symbolic link `Mean_square_displacement.x': File exists
ln: creating symbolic link `atom_info.x': File exists

Muhammad Zafar

PhD Scholar

Department of Physics

The Islamia University of Bahawalpur,Pakistan
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From flux_ray12 at 163.com  Mon Jul 25 14:07:37 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Mon, 25 Jul 2011 20:07:37 +0800 (CST)
Subject: [Pw_forum] Warnings And Errors in Compilation of QHA......
In-Reply-To: <1311591933.28899.YahooMailClassic@web65411.mail.ac4.yahoo.com>
References: <1311591933.28899.YahooMailClassic@web65411.mail.ac4.yahoo.com>
Message-ID: <3f7402f9.f9b4.13161317a25.Coremail.flux_ray12@163.com>

I think your problem is caused by the lack of libraries for compiling. You may not run the binary executable files before solving dependent problem, even others copy binary files to you.
Please check whether you have libm.so.? in your /usr/lib (32bit) or /usr/lib64 (64bit), or you can use command "yum install libm.so.*"(run it as root) in terminate.

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-25 19:05:33,"zafar rasheed" <zafartariq2003 at yahoo.com> wrote:

Dear All

I try best to compile QHA but can not create *.x files. Now I have fedora core 14. Will any body help me. I think that QHA has some deleted routines. I have such type of warnings. If Some one has complete QHA then please send it to me. Thanking in anticipation


[zafar at localhost QHA]$ ./Compile
gfortran -O3 -ffast-math -fno-f2c -c  tetra.f
gfortran -O3 -ffast-math -fno-f2c -c  k_brillouin.f
gfortran -O3 -ffast-math -fno-f2c -c  generate_tetra.f
gfortran -O3 -ffast-math -fno-f2c -c  det3.f
gfortran -O3 -ffast-math -fno-f2c -c  det4.f
gfortran -static -o tetra.x tetra.o k_brillouin.o generate_tetra.o  det3.o det4.o  
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
make: *** [tetra] Error 1
gfortran -O3 -ffast-math -fno-f2c  -c  Debye.f90
Debye.f90:144.8:

     do T = T_low_start, T_low, T_low_delta
        1
Warning: Deleted feature: Loop variable at (1) must be integer
Debye.f90:144.11:

     do T = T_low_start, T_low, T_low_delta
           1
Warning: Deleted feature: Start expression in DO loop at (1) must be integer
Debye.f90:144.24:

     do T = T_low_start, T_low, T_low_delta
                        1
Warning: Deleted feature: End expression in DO loop at (1) must be integer
Debye.f90:144.31:

     do T = T_low_start, T_low, T_low_delta
                               1
Warning: Deleted feature: Step expression in DO loop at (1) must be integer
Debye.f90:177.4:

 do T = T_low+5, T_high, T_high_delta
    1
Warning: Deleted feature: Loop variable at (1) must be integer
Debye.f90:177.7:

 do T = T_low+5, T_high, T_high_delta
       1
Warning: Deleted feature: Start expression in DO loop at (1) must be integer
Debye.f90:177.16:

 do T = T_low+5, T_high, T_high_delta
                1
Warning: Deleted feature: End expression in DO loop at (1) must be integer
Debye.f90:177.24:

 do T = T_low+5, T_high, T_high_delta
                        1
Warning: Deleted feature: Step expression in DO loop at (1) must be integer
gfortran -O3 -ffast-math -fno-f2c -c  Debye_T.f
gfortran -O3 -ffast-math -fno-f2c -c  debye3.f
gfortran -O3 -ffast-math -fno-f2c -c  cheval.f
gfortran -O3 -ffast-math -fno-f2c -c  d1mach.f
gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
make: *** [Debye_x] Error 1
gfortran -O3 -ffast-math -fno-f2c -c  Mean_square_displacement.f90
Mean_square_displacement.f90:162.7:

    do T=T_start,T_end,T_delta
       1
Warning: Deleted feature: Loop variable at (1) must be integer
gfortran -static -o Mean_square_displacement.x Mean_square_displacement.o  
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
make: *** [MSD] Error 1
ln: creating symbolic link `tetra.x': File exists
ln: creating symbolic link `phonon_dos.x': File exists
ln: creating symbolic link `Debye.x': File exists
ln: creating symbolic link `Atom_projected_properties.x': File exists
ln: creating symbolic link `F_QHA.x': File exists
ln: creating symbolic link `Ghost_DOS.x': File exists
ln: creating symbolic link `Partial_phonon_DOS.x': File exists
ln: creating symbolic link `Mean_square_displacement.x': File exists
ln: creating symbolic link `atom_info.x': File exists

Muhammad Zafar
PhD Scholar
Department of Physics
The Islamia University of Bahawalpur,Pakistan
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From trambui at u.boisestate.edu  Mon Jul 25 21:00:38 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Mon, 25 Jul 2011 13:00:38 -0600
Subject: [Pw_forum] occupancy of the state from PDOS calculation
Message-ID: <CANzxBn8TgpnptyLPSTnTZOq2v57aa1NNkX1qXGwSgsQ-Uj+VpQ@mail.gmail.com>

Dear Everyone,
    From the PDOS calculation (projwfc.x), can we find the occupancy of the
state? Also, can we run for ionization energy calculation from pdos?

Regards,

Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From vovi47 at yahoo.com  Tue Jul 26 01:31:57 2011
From: vovi47 at yahoo.com (Vi Vo)
Date: Mon, 25 Jul 2011 16:31:57 -0700 (PDT)
Subject: [Pw_forum] (no subject)
Message-ID: <1311636717.59460.YahooMailRC@web114512.mail.gq1.yahoo.com>

Dear All,

I was doing a test calculation for CuO and got a message: 
"     WARNING: atomic wfc #  6 for atom type 1 has zero norm
     WARNING: atomic wfc #  6 for atom type 2 has zero norm
     WARNING: atomic wfc #  2 for atom type 3 has zero norm
     WARNING: atomic wfc #  4 for atom type 3 has zero norm
     WARNING: atomic wfc #  5 for atom type 3 has zero norm

The norm of the wfc is zero.  Why does it happen?  Does it depend on the  pseudo 
potential used?  Can a gipaw pp be used with pw.x? (I download the pp from QE 
pps).

Thank you very much in advance,

Vi 
 University of Houston
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From bdslipun at gmail.com  Tue Jul 26 08:53:17 2011
From: bdslipun at gmail.com (bhabya sahoo)
Date: Tue, 26 Jul 2011 12:23:17 +0530
Subject: [Pw_forum] (no subject)
Message-ID: <CAJVAAvDJU=6q8QZk4g2cyOH=q2akf=CrpKQO5CyZgPuz9Yeajg@mail.gmail.com>

why xspectra.x is not coming in bin directory of quantum espresso code
but others are compiling fine .
version 4.3 of quantum espresso code
sothat the example is not running


























bd sahoo reserch scolar
mumbai
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From bdslipun at gmail.com  Tue Jul 26 09:05:43 2011
From: bdslipun at gmail.com (bhabya sahoo)
Date: Tue, 26 Jul 2011 12:35:43 +0530
Subject: [Pw_forum] (no subject)
In-Reply-To: <CAJVAAvDJU=6q8QZk4g2cyOH=q2akf=CrpKQO5CyZgPuz9Yeajg@mail.gmail.com>
References: <CAJVAAvDJU=6q8QZk4g2cyOH=q2akf=CrpKQO5CyZgPuz9Yeajg@mail.gmail.com>
Message-ID: <CAJVAAvByLoBjLg32mgu64tw_shrbFSU3fBe7RCxBWvEjryX=Sw@mail.gmail.com>

On Tue, Jul 26, 2011 at 12:23 PM, bhabya sahoo <bdslipun at gmail.com> wrote:

> why xspectra.x is not coming in bin directory of quantum espresso code
> but others are compiling fine .
> version 4.3 of quantum espresso code
> sothat the example is not running
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
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>
>
>
>
>
>
> bd sahoo reserch scolar
> mumbai
>
>
> _______________________________________________
> 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 26 09:16:40 2011
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Tue, 26 Jul 2011 09:16:40 +0200
Subject: [Pw_forum] (no subject)
In-Reply-To: <1311636717.59460.YahooMailRC@web114512.mail.gq1.yahoo.com>
References: <1311636717.59460.YahooMailRC@web114512.mail.gq1.yahoo.com>
Message-ID: <op.vy7s52ar5jfbqb@paulax>

In data 26 luglio 2011 alle ore 01:31:57, Vi Vo <vovi47 at yahoo.com> ha  
scritto:
> I was doing a test calculation for CuO and got a message:
> "     WARNING: atomic wfc #  6 for atom type 1 has zero norm
>      WARNING: atomic wfc #  6 for atom type 2 has zero norm
>      WARNING: atomic wfc #  2 for atom type 3 has zero norm
>      WARNING: atomic wfc #  4 for atom type 3 has zero norm
>      WARNING: atomic wfc #  5 for atom type 3 has zero norm
>
> The norm of the wfc is zero.  Why does it happen?  Does it depend on  
> the  pseudo

It is not the wfc, but the atomic wfc. Unless you are doing an lda+U  
calculation yo ucan safely ignore the warning.

best regards

-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From lorenzo.paulatto at impmc.upmc.fr  Tue Jul 26 09:19:09 2011
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Tue, 26 Jul 2011 09:19:09 +0200
Subject: [Pw_forum] (no subject)
In-Reply-To: <CAJVAAvDJU=6q8QZk4g2cyOH=q2akf=CrpKQO5CyZgPuz9Yeajg@mail.gmail.com>
References: <CAJVAAvDJU=6q8QZk4g2cyOH=q2akf=CrpKQO5CyZgPuz9Yeajg@mail.gmail.com>
Message-ID: <op.vy7s97uq5jfbqb@paulax>

In data 26 luglio 2011 alle ore 08:53:17, bhabya sahoo  
<bdslipun at gmail.com> ha scritto:
> why xspectra.x is not coming in bin directory of quantum espresso code
> but others are compiling fine .
> version 4.3 of quantum espresso code
> sothat the example is not running

Xspectra is not included in "make all", you need to type explicitly "make  
xspectra" in the QE root directory in order to compile it.

best regards


-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From zafartariq2003 at yahoo.com  Tue Jul 26 09:39:44 2011
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Tue, 26 Jul 2011 00:39:44 -0700 (PDT)
Subject: [Pw_forum] Pw_forum Digest, Vol 49, Issue 68
In-Reply-To: <mailman.14526.1311664803.1814.pw_forum@pwscf.org>
Message-ID: <1311665984.92529.YahooMailClassic@web65413.mail.ac4.yahoo.com>

Dear GAO Zhe

Thanks for the help. I apply some changes in FFFlags and FC and compiles succesfully. 

Muhammad Zafar

PhD Scholar

Department of Physics

The Islamia University of Bahawalpur,Pakistan

--- On Tue, 7/26/11, 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 49, Issue 68
To: pw_forum at pwscf.org
Date: Tuesday, July 26, 2011, 12:20 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. Re: Warnings And Errors in Compilation of QHA...... (GAO Zhe)
???2. occupancy of the state from PDOS calculation (Tram Bui)
???3. (no subject) (Vi Vo)
???4. (no subject) (bhabya sahoo)
???5. Re: (no subject) (bhabya sahoo)
???6. Re: (no subject) (Lorenzo Paulatto)
???7. Re: (no subject) (Lorenzo Paulatto)


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

Message: 1
Date: Mon, 25 Jul 2011 20:07:37 +0800 (CST)
From: "GAO Zhe" <flux_ray12 at 163.com>
Subject: Re: [Pw_forum] Warnings And Errors in Compilation of
??? QHA......
To: "PWSCF Forum" <pw_forum at pwscf.org>
Message-ID: <3f7402f9.f9b4.13161317a25.Coremail.flux_ray12 at 163.com>
Content-Type: text/plain; charset="gbk"

I think your problem is caused by the lack of libraries for compiling. You may not run the binary executable files before solving dependent problem, even others copy binary files to you.
Please check whether you have libm.so.? in your /usr/lib (32bit) or /usr/lib64 (64bit), or you can use command "yum install libm.so.*"(run it as root) in terminate.

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-25 19:05:33,"zafar rasheed" <zafartariq2003 at yahoo.com> wrote:

Dear All

I try best to compile QHA but can not create *.x files. Now I have fedora core 14. Will any body help me. I think that QHA has some deleted routines. I have such type of warnings. If Some one has complete QHA then please send it to me. Thanking in anticipation


[zafar at localhost QHA]$ ./Compile
gfortran -O3 -ffast-math -fno-f2c -c? tetra.f
gfortran -O3 -ffast-math -fno-f2c -c? k_brillouin.f
gfortran -O3 -ffast-math -fno-f2c -c? generate_tetra.f
gfortran -O3 -ffast-math -fno-f2c -c? det3.f
gfortran -O3 -ffast-math -fno-f2c -c? det4.f
gfortran -static -o tetra.x tetra.o k_brillouin.o generate_tetra.o? det3.o det4.o? 
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
make: *** [tetra] Error 1
gfortran -O3 -ffast-math -fno-f2c? -c? Debye.f90
Debye.f90:144.8:

? ???do T = T_low_start, T_low, T_low_delta
? ? ? ? 1
Warning: Deleted feature: Loop variable at (1) must be integer
Debye.f90:144.11:

? ???do T = T_low_start, T_low, T_low_delta
? ? ? ? ???1
Warning: Deleted feature: Start expression in DO loop at (1) must be integer
Debye.f90:144.24:

? ???do T = T_low_start, T_low, T_low_delta
? ? ? ? ? ? ? ? ? ? ? ? 1
Warning: Deleted feature: End expression in DO loop at (1) must be integer
Debye.f90:144.31:

? ???do T = T_low_start, T_low, T_low_delta
? ? ? ? ? ? ? ? ? ? ? ? ? ? ???1
Warning: Deleted feature: Step expression in DO loop at (1) must be integer
Debye.f90:177.4:

 do T = T_low+5, T_high, T_high_delta
? ? 1
Warning: Deleted feature: Loop variable at (1) must be integer
Debye.f90:177.7:

 do T = T_low+5, T_high, T_high_delta
? ? ???1
Warning: Deleted feature: Start expression in DO loop at (1) must be integer
Debye.f90:177.16:

 do T = T_low+5, T_high, T_high_delta
? ? ? ? ? ? ? ? 1
Warning: Deleted feature: End expression in DO loop at (1) must be integer
Debye.f90:177.24:

 do T = T_low+5, T_high, T_high_delta
? ? ? ? ? ? ? ? ? ? ? ? 1
Warning: Deleted feature: Step expression in DO loop at (1) must be integer
gfortran -O3 -ffast-math -fno-f2c -c? Debye_T.f
gfortran -O3 -ffast-math -fno-f2c -c? debye3.f
gfortran -O3 -ffast-math -fno-f2c -c? cheval.f
gfortran -O3 -ffast-math -fno-f2c -c? d1mach.f
gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
make: *** [Debye_x] Error 1
gfortran -O3 -ffast-math -fno-f2c -c? Mean_square_displacement.f90
Mean_square_displacement.f90:162.7:

? ? do T=T_start,T_end,T_delta
? ? ???1
Warning: Deleted feature: Loop variable at (1) must be integer
gfortran -static -o Mean_square_displacement.x Mean_square_displacement.o? 
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
make: *** [MSD] Error 1
ln: creating symbolic link `tetra.x': File exists
ln: creating symbolic link `phonon_dos.x': File exists
ln: creating symbolic link `Debye.x': File exists
ln: creating symbolic link `Atom_projected_properties.x': File exists
ln: creating symbolic link `F_QHA.x': File exists
ln: creating symbolic link `Ghost_DOS.x': File exists
ln: creating symbolic link `Partial_phonon_DOS.x': File exists
ln: creating symbolic link `Mean_square_displacement.x': File exists
ln: creating symbolic link `atom_info.x': File exists

Muhammad Zafar
PhD Scholar
Department of Physics
The Islamia University of Bahawalpur,Pakistan
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------------------------------

Message: 2
Date: Mon, 25 Jul 2011 13:00:38 -0600
From: Tram Bui <trambui at u.boisestate.edu>
Subject: [Pw_forum] occupancy of the state from PDOS calculation
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
??? <CANzxBn8TgpnptyLPSTnTZOq2v57aa1NNkX1qXGwSgsQ-Uj+VpQ at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Everyone,
? ? From the PDOS calculation (projwfc.x), can we find the occupancy of the
state? Also, can we run for ionization energy calculation from pdos?

Regards,

Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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Message: 3
Date: Mon, 25 Jul 2011 16:31:57 -0700 (PDT)
From: Vi Vo <vovi47 at yahoo.com>
Subject: [Pw_forum] (no subject)
To: pwscf <pw_forum at pwscf.org>
Message-ID:
??? <1311636717.59460.YahooMailRC at web114512.mail.gq1.yahoo.com>
Content-Type: text/plain; charset="us-ascii"

Dear All,

I was doing a test calculation for CuO and got a message: 
"? ???WARNING: atomic wfc #? 6 for atom type 1 has zero norm
? ???WARNING: atomic wfc #? 6 for atom type 2 has zero norm
? ???WARNING: atomic wfc #? 2 for atom type 3 has zero norm
? ???WARNING: atomic wfc #? 4 for atom type 3 has zero norm
? ???WARNING: atomic wfc #? 5 for atom type 3 has zero norm

The norm of the wfc is zero.? Why does it happen?? Does it depend on the? pseudo 
potential used?? Can a gipaw pp be used with pw.x? (I download the pp from QE 
pps).

Thank you very much in advance,

Vi 
 University of Houston
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Message: 4
Date: Tue, 26 Jul 2011 12:23:17 +0530
From: bhabya sahoo <bdslipun at gmail.com>
Subject: [Pw_forum] (no subject)
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
??? <CAJVAAvDJU=6q8QZk4g2cyOH=q2akf=CrpKQO5CyZgPuz9Yeajg at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

why xspectra.x is not coming in bin directory of quantum espresso code
but others are compiling fine .
version 4.3 of quantum espresso code
sothat the example is not running


























bd sahoo reserch scolar
mumbai
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Message: 5
Date: Tue, 26 Jul 2011 12:35:43 +0530
From: bhabya sahoo <bdslipun at gmail.com>
Subject: Re: [Pw_forum] (no subject)
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
??? <CAJVAAvByLoBjLg32mgu64tw_shrbFSU3fBe7RCxBWvEjryX=Sw at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

On Tue, Jul 26, 2011 at 12:23 PM, bhabya sahoo <bdslipun at gmail.com> wrote:

> why xspectra.x is not coming in bin directory of quantum espresso code
> but others are compiling fine .
> version 4.3 of quantum espresso code
> sothat the example is not running
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> bd sahoo reserch scolar
> mumbai
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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Message: 6
Date: Tue, 26 Jul 2011 09:16:40 +0200
From: "Lorenzo Paulatto" <lorenzo.paulatto at impmc.upmc.fr>
Subject: Re: [Pw_forum] (no subject)
To: "PWSCF Forum" <pw_forum at pwscf.org>
Message-ID: <op.vy7s52ar5jfbqb at paulax>
Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes

In data 26 luglio 2011 alle ore 01:31:57, Vi Vo <vovi47 at yahoo.com> ha? 
scritto:
> I was doing a test calculation for CuO and got a message:
> "? ???WARNING: atomic wfc #? 6 for atom type 1 has zero norm
>? ? ? WARNING: atomic wfc #? 6 for atom type 2 has zero norm
>? ? ? WARNING: atomic wfc #? 2 for atom type 3 has zero norm
>? ? ? WARNING: atomic wfc #? 4 for atom type 3 has zero norm
>? ? ? WARNING: atomic wfc #? 5 for atom type 3 has zero norm
>
> The norm of the wfc is zero.? Why does it happen?? Does it depend on? 
> the? pseudo

It is not the wfc, but the atomic wfc. Unless you are doing an lda+U? 
calculation yo ucan safely ignore the warning.

best regards

-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:???http://www-int.impmc.upmc.fr/~paulatto/
mail:? 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05


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

Message: 7
Date: Tue, 26 Jul 2011 09:19:09 +0200
From: "Lorenzo Paulatto" <lorenzo.paulatto at impmc.upmc.fr>
Subject: Re: [Pw_forum] (no subject)
To: "PWSCF Forum" <pw_forum at pwscf.org>
Message-ID: <op.vy7s97uq5jfbqb at paulax>
Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes

In data 26 luglio 2011 alle ore 08:53:17, bhabya sahoo? 
<bdslipun at gmail.com> ha scritto:
> why xspectra.x is not coming in bin directory of quantum espresso code
> but others are compiling fine .
> version 4.3 of quantum espresso code
> sothat the example is not running

Xspectra is not included in "make all", you need to type explicitly "make? 
xspectra" in the QE root directory in order to compile it.

best regards


-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:???http://www-int.impmc.upmc.fr/~paulatto/
mail:? 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05


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

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


End of Pw_forum Digest, Vol 49, Issue 68
****************************************
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From abmus007 at gmail.com  Tue Jul 26 09:56:33 2011
From: abmus007 at gmail.com (Abolore Musari)
Date: Tue, 26 Jul 2011 02:56:33 -0500
Subject: [Pw_forum] ibrav and celldm(4)
In-Reply-To: <A874817B-B61A-48DD-A969-3DD8E8E68013@democritos.it>
References: <BANLkTikUnUfQCzoxqHqtV7Vw0WJgscFumQ@mail.gmail.com>
	<BANLkTikcuPPcykvKcHM4Mo643RDoZLQtVg@mail.gmail.com>
	<A874817B-B61A-48DD-A969-3DD8E8E68013@democritos.it>
Message-ID: <CAOP21k+UyMVaOR-cL7Dmvz3z3DmFSZn9Da8ppavRytVu_4ibSg@mail.gmail.com>

Dear Paulo, I dont understand what u mean by svn version and also want
to ask that does it mean that l cant use the cell parameters given by
Emine if yes pls can u give me another cell parameters l could use.
pls i would appreciate ur quick response. Thanks Abolore

On 6/27/11, Paolo Giannozzi <giannozz at democritos.it> wrote:
>
> On Jun 25, 2011, at 23:39 , Abolore Musari wrote:
>
>> alpha equal beta equal 90 degree
>
> beta = 90 ...
>
>> beta was gotten from reitveld refinement to be 113.81
>
> ...or beta = 113.81?
>
>> i dont know if my celldm(4) which is equal to cos(ab) should
>> be cos90 or cos113.81 or tell me the appropriate way to get
>> celldm(4)=cos(ab).
>
> the monoclinic (P? ibrav=12?) lattice can be described with
> unique (i.e. orthogonal to a) axis c, b axis at angle gamma /= 90
> with a; or with unique axis b, c axis at angle beta /= 90 with a.
> QE uses the former description; apparently you have found
> the latter description in the literature, so you have to either
> convert the latter into the former, or write down explicitly the
> crystal axis, or to use the latest svn version that allows for
> the latter description as well (ibrav=-12)
>
> 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 sclauzer at sissa.it  Tue Jul 26 10:01:39 2011
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 26 Jul 2011 10:01:39 +0200
Subject: [Pw_forum] occupancy of the state from PDOS calculation
In-Reply-To: <CANzxBn8TgpnptyLPSTnTZOq2v57aa1NNkX1qXGwSgsQ-Uj+VpQ@mail.gmail.com>
References: <CANzxBn8TgpnptyLPSTnTZOq2v57aa1NNkX1qXGwSgsQ-Uj+VpQ@mail.gmail.com>
Message-ID: <9A14AA32-CD75-4ABC-B672-6CCBACCB7BA5@sissa.it>


Il giorno 25/lug/2011, alle ore 21.00, Tram Bui ha scritto:

> Dear Everyone,
>     From the PDOS calculation (projwfc.x), can we find the occupancy of the state?

Which state?

> Also, can we run for ionization energy calculation from pdos?

Never heard so. To compute ionization energies you need energies, not pdos.


GS

> 
> Regards,
> 
> Tram Bui
> 
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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

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From giuseppe.mattioli at mlib.ism.cnr.it  Tue Jul 26 11:27:46 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Tue, 26 Jul 2011 11:27:46 +0200
Subject: [Pw_forum] ibrav and celldm(4)
In-Reply-To: <CAOP21k+UyMVaOR-cL7Dmvz3z3DmFSZn9Da8ppavRytVu_4ibSg@mail.gmail.com>
References: <BANLkTikUnUfQCzoxqHqtV7Vw0WJgscFumQ@mail.gmail.com>
	<A874817B-B61A-48DD-A969-3DD8E8E68013@democritos.it>
	<CAOP21k+UyMVaOR-cL7Dmvz3z3DmFSZn9Da8ppavRytVu_4ibSg@mail.gmail.com>
Message-ID: <201107261127.47060.giuseppe.mattioli@mlib.ism.cnr.it>


> Dear Paulo, I dont understand what u mean by svn version

the "current (still not released) version" of QE that you can download by 
using the command

svn checkout svn://scm.qe-forge.org/scmrepos/svn/q-e/trunk

previous installation of the apache "subversion" tool (at least it works in a 
linux/unix environment)

Please do not ask this forum for quick responses. Nobody earns money for this 
service to the community...

HTH

Giuseppe


On Tuesday 26 July 2011 09:56:33 Abolore Musari wrote:
> Dear Paulo, I dont understand what u mean by svn version and also want
> to ask that does it mean that l cant use the cell parameters given by
> Emine if yes pls can u give me another cell parameters l could use.
> pls i would appreciate ur quick response. Thanks Abolore
>
> On 6/27/11, Paolo Giannozzi <giannozz at democritos.it> wrote:
> > On Jun 25, 2011, at 23:39 , Abolore Musari wrote:
> >> alpha equal beta equal 90 degree
> >
> > beta = 90 ...
> >
> >> beta was gotten from reitveld refinement to be 113.81
> >
> > ...or beta = 113.81?
> >
> >> i dont know if my celldm(4) which is equal to cos(ab) should
> >> be cos90 or cos113.81 or tell me the appropriate way to get
> >> celldm(4)=cos(ab).
> >
> > the monoclinic (P? ibrav=12?) lattice can be described with
> > unique (i.e. orthogonal to a) axis c, b axis at angle gamma /= 90
> > with a; or with unique axis b, c axis at angle beta /= 90 with a.
> > QE uses the former description; apparently you have found
> > the latter description in the literature, so you have to either
> > convert the latter into the former, or write down explicitly the
> > crystal axis, or to use the latest svn version that allows for
> > the latter description as well (ibrav=-12)
> >
> > 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
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> 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 mohnish.iitk at gmail.com  Tue Jul 26 12:03:57 2011
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Tue, 26 Jul 2011 15:33:57 +0530
Subject: [Pw_forum] antiferromagnetism in thin films
Message-ID: <CAMhNW-euy7y4sJXHaMvMeMRcG2-EMRzPv9a2zxQJjav_-urK-A@mail.gmail.com>

Dear QE users,

I want to do calculations of thin films of antiferromagnetic oxide like CoO.
The CoO has rocksalt structure and magnetization along (111) direction.
Suppose we take 3 layers and 4 layers for of CoO along (111), then my doubt
is that will the magnetization oscillate i.e. in even number of layers it
will be zero and odd number of layers will have some finite value? Or wil
the film will show antiferrromagnetism in plane i.e. every layers of CoO
will be antiferromagnetic? And what about other directions like (001) or
(10-10) in wurtzite structure.

Thanks a lot in advance for help..

-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
Senior Project Associate,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
-----------------------------------------------------------------
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From zucco at dipteris.unige.it  Tue Jul 26 13:50:02 2011
From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini)
Date: Tue, 26 Jul 2011 13:50:02 +0200
Subject: [Pw_forum] Segmentation fault on relaxed structure in vc-relax on
	QE4.3.1
Message-ID: <C44EC6BA-38DF-4536-B0C2-11215367C36E@dipteris.unige.it>

Hello to all,
I'm doing a cell relaxation on a structure with LDA+U (with openmpi-1.3.4 without -openmp flag, ifort 12).
Comparing the final structure obtained with QE 4.1.1 (same configuration) the result is absolutely similar but during the computation of the last SCF cycle *on relaxed structure* this segmentation fault error (repeated for each process) happens

....
nsum =  12.0000000
 exit write_ns
 Atomic wfc used for LDA+U Projector are NOT orthogonalized
     Starting wfc are   58 atomic +   32 random wfc
forrtl: severe (174): SIGSEGV, segmentation fault occurred
pw.x               000000000066D631  vhpsi_                     51  vhpsi.f90
pw.x               0000000000616146  h_psi_                     70  h_psi.f90
pw.x               000000000064D26A  protate_wfc_gamma         222  rotate_wfc_gamma.f90
pw.x               0000000000647F42  rotate_wfc_                50  rotate_wfc.f90
pw.x               00000000005580B8  wfcinit_                  124  wfcinit.f90
pw.x               00000000004593B4  init_run_                 103  init_run.f90
pw.x               0000000000477ABC  move_ions_                293  move_ions.f90
pw.x               000000000043CCDC  MAIN__                    176  pwscf.f90
pw.x               000000000043C87C  Unknown               Unknown  Unknown
libc.so.6          00002B78F09A2BFD  Unknown               Unknown  Unknown
pw.x               000000000043C779  Unknown               Unknown  Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
...

Making a similar computation on calcite (clearly without LDA+U), the computation is smooth til the end.

Have you some ideas about that?

Thank you very much for your help

m.


*******************************************************
Marino Vetuschi Zuccolini
zucco at dipteris.unige.it
Researcher / Geochemist
Laboratory of Geochemistry

DIPartimento per lo studio della TErra e delle sue RISorse - Universit?  di Genova
Tel. ++39 010 3538136 Fax. ++39 010 352169
Corso Europa 26, 16132 - Genova - Italy



From giuseppe.mattioli at mlib.ism.cnr.it  Tue Jul 26 15:31:57 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Tue, 26 Jul 2011 15:31:57 +0200
Subject: [Pw_forum] antiferromagnetism in thin films
In-Reply-To: <CAMhNW-euy7y4sJXHaMvMeMRcG2-EMRzPv9a2zxQJjav_-urK-A@mail.gmail.com>
References: <CAMhNW-euy7y4sJXHaMvMeMRcG2-EMRzPv9a2zxQJjav_-urK-A@mail.gmail.com>
Message-ID: <201107261531.58222.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Mohnish
changing the subject will not produce automatically an answer... I suspect 
that you are asking something that deserves itself a full investigation. Let 
us know the results.
Yours
Giuseppe

On Tuesday 26 July 2011 12:03:57 mohnish pandey wrote:
> Dear QE users,
>
> I want to do calculations of thin films of antiferromagnetic oxide like
> CoO. The CoO has rocksalt structure and magnetization along (111)
> direction. Suppose we take 3 layers and 4 layers for of CoO along (111),
> then my doubt is that will the magnetization oscillate i.e. in even number
> of layers it will be zero and odd number of layers will have some finite
> value? Or wil the film will show antiferrromagnetism in plane i.e. every
> layers of CoO will be antiferromagnetic? And what about other directions
> like (001) or (10-10) in wurtzite structure.
>
> Thanks a lot in advance for help..



-- 
********************************************************
- 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 vovi47 at yahoo.com  Tue Jul 26 21:29:11 2011
From: vovi47 at yahoo.com (Vi Vo)
Date: Tue, 26 Jul 2011 12:29:11 -0700 (PDT)
Subject: [Pw_forum] (no subject)
In-Reply-To: <op.vy7s52ar5jfbqb@paulax>
References: <1311636717.59460.YahooMailRC@web114512.mail.gq1.yahoo.com>
	<op.vy7s52ar5jfbqb@paulax>
Message-ID: <1311708551.91624.YahooMailRC@web114504.mail.gq1.yahoo.com>

Dear Lorenzo,

Thank you very much.
In LDA+U calculation I also see these warning, so what will be the risk or 
unreliability.

Vi





________________________________
From: Lorenzo Paulatto <lorenzo.paulatto at impmc.upmc.fr>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Tue, July 26, 2011 12:16:40 AM
Subject: Re: [Pw_forum] (no subject)

In data 26 luglio 2011 alle ore 01:31:57, Vi Vo <vovi47 at yahoo.com> ha  
scritto:
> I was doing a test calculation for CuO and got a message:
> "     WARNING: atomic wfc #  6 for atom type 1 has zero norm
>      WARNING: atomic wfc #  6 for atom type 2 has zero norm
>      WARNING: atomic wfc #  2 for atom type 3 has zero norm
>      WARNING: atomic wfc #  4 for atom type 3 has zero norm
>      WARNING: atomic wfc #  5 for atom type 3 has zero norm
>
> The norm of the wfc is zero.  Why does it happen?  Does it depend on  
> the  pseudo

It is not the wfc, but the atomic wfc. Unless you are doing an lda+U  
calculation yo ucan safely ignore the warning.

best regards

-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:  http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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From guntram.schmidt at chemie.uni-halle.de  Tue Jul 26 21:31:34 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Tue, 26 Jul 2011 21:31:34 +0200
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
Message-ID: <4E2F1616.8080905@chemie.uni-halle.de>

Heureka!

After several days of compiling and complaining I've found a possible 
solution!
In contrast to all warning regarding the loading of essl before lapack, 
it mustn't be loaded before lapack!
When I add lessl before lapack, I get the DSYGV : 2538-2015 error messages.
The following make.sys finally works regarding these problems on my 
system (IBM 575):

------------------------------------------
# make.sys.  Generated from make.sys.in by configure.

# compilation rules

.SUFFIXES :
.SUFFIXES : .o .c .f .f90

# most fortran compilers can directly preprocess c-like directives: use
# 	$(MPIF90) $(F90FLAGS) -c $<
# if explicit preprocessing by the C preprocessor is needed, use:
# 	$(CPP) $(CPPFLAGS) $< -o $*.F90
#	$(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
# remember the tabulator in the first column !!!

.f90.o:
	$(MPIF90) $(F90FLAGS) -c $<

# .f.o and .c.o: do not modify

.f.o:
	$(F77) $(FFLAGS) -c $<

.c.o:
	$(CC) $(CFLAGS)  -c $<


# DFLAGS  = precompilation options (possible arguments to -D and -U)
#           used by the C compiler and preprocessor
# FDFLAGS = as DFLAGS, for the f90 compiler
# See include/defs.h.README for a list of options and their meaning
# With the exception of IBM xlf, FDFLAGS = $(DFLAGS)
# For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas

DFLAGS         = -D__XLF -D__LINUX_ESSL -D__MASS -D__MPI -D__PARA
FDFLAGS        = -D__XLF,-D__LINUX_ESSL,-D__MASS,-D__MPI,-D__PARA

# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include

IFLAGS         = -I../include

# MOD_FLAGS = flag used by f90 compiler to locate modules
# Each Makefile defines the list of needed modules in MODFLAGS

MOD_FLAG      = -I

# Compilers: fortran-90, fortran-77, C
# If a parallel compilation is desired, MPIF90 should be a fortran-90
# compiler that produces executables for parallel execution using MPI
# (such as for instance mpif90, mpf90, mpxlf90,...);
# otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...)
# If you have a parallel machine but no suitable candidate for MPIF90,
# try to specify the directory containing "mpif.h" in IFLAGS
# and to specify the location of MPI libraries in MPI_LIBS

MPIF90         = mpfort -compiler xlf90_r
#F90           = mpfort -compiler xlf90_r
CC             = mpcc -compiler xlc_r
F77            = mpfort -compiler xlf_r

# C preprocessor and preprocessing flags - for explicit preprocessing,
# if needed (see the compilation rules above)
# preprocessing flags must include DFLAGS and IFLAGS

CPP            = cpp
CPPFLAGS       = -P -traditional $(DFLAGS) $(IFLAGS)

# compiler flags: C, F90, F77
# C flags must include DFLAGS and IFLAGS
# F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate 
syntax

CFLAGS         = -O3 -q64 -qthreaded $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) -qfree=f90 -WF,$(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS         = -q64 -qthreaded -O4 -qsuffix=cpp=f90 -qdpc 
-qalias=nointptr -Q

# compiler flags without optimization for fortran-77
# the latter is NEEDED to properly compile dlamch.f, used by lapack

FFLAGS_NOOPT   = -q64 -qthreaded -O0

# Linker, linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90, LD_LIBS is empty

LD             = mpfort
LDFLAGS        = -q64 -qthreaded
LD_LIBS        =

# External Libraries (if any) : blas, lapack, fft, MPI

# If you have nothing better, use the local copy :
# BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a
# BLAS_LIBS_SWITCH = internal

BLAS_LIBS      =
BLAS_LIBS_SWITCH = external

# If you have nothing better, use the local copy :
# LAPACK_LIBS = /your/path/to/espresso/lapack-3.2/lapack.a
# LAPACK_LIBS_SWITCH = internal
# For IBM machines with essl (-D__ESSL): load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order

LAPACK_LIBS    = -L/gpfs/usrurz/lib64 -llapack
LAPACK_LIBS_SWITCH = internal

SCALAPACK_LIBS =

# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW in DFLAGS)

FFT_LIBS       = -lessl

# For parallel execution, the correct path to MPI libraries must
# be specified in MPI_LIBS (except for IBM if you use mpxlf)

MPI_LIBS       =

# IBM-specific: MASS libraries, if available and if -D__MASS is defined 
in FDFLAGS

MASS_LIBS      =  -lmassvp4_64 -lmass_64

# ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv

AR             = ar
ARFLAGS        = ruv

# ranlib command. If ranlib is not needed (it isn't in most cases) use
# RANLIB = echo

RANLIB         = ranlib

# all internal and external libraries - do not modify

FLIB_TARGETS   = all

LIBOBJS        = ../flib/ptools.a ../flib/flib.a ../clib/clib.a 
../iotk/src/libiotk.a
LIBS           = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) 
$(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(LD_LIBS)

# topdir for linking espresso libs with plugins
TOPDIR = /gpfs/home/aasfu/espresso_16
-------------------------------------


Thank you nevertheless for your efforts, Michael and Paolo!



Am 21.07.2011 14:46, schrieb Michael Sullivan:
> Guntram:
>
> I've never seen this error message, but if you can try to edit the make.sys file directly. Replace the LAPACK_LIBS flag to point to your own LAPACK and probably change LAPACK_LIBS_SWITCH to external. That said, though, I've found that usually if it can't find it, there's a reason.
>
> Good luck!
>
> Mike
> michael at ihpc.a-star.edu.sg
> http://www.sullivan.sg/
>
> On 21-Jul-2011, at 6:49 PM, Guntram Schmidt wrote:
>
>> Dear All,
>>
>> after getting strange error-messages, which might be related to
>> lapack/blas (
>> DSYGV : 2538-2015
>> The number of elements (ARG NO. 11) in a work array must be greater than
>> or equal to (2048).
>> )
>> I'd like to use "our own" lapack/blas.
>> Unfortunately QE won't find/accept them - what's the right way, to help it?
>>
>> I tried:
>>   ./configure MPIF90=mpfort LIBDIRS="/gpfs/usrurz/lapack/lapack-3.2.1"
>> with
>>
>> :/gpfs/usrurz/lapack/lapack-3.2.1>  ls
>> BLAS               CCI_README     Makefile                   README
>> cci                ccisrc.tar     make.inc                   README_hh
>> cci.log            INSTALL        make.inc.example           SRC
>> CCI_NOTES          lapack_pwr6.a  make.inc.old               TESTING
>> CCI_QUICK_INSTALL  LICENSE        make.log_pwr6_xlf_q64_cci  tmglib_pwr6.a
>>
>> yielding a quite promising directory of an installed lapack/blas?
>>
>> But QE insists on its own libraries.
>>
>> The system is an IBM 575 with Power-Linux=SLES11_on_Power and the only
>> information I found is this here:
>> http://www2.fz-juelich.de/jsc/jump/usage/FAQ/essl/
>>
>>
>> Any ideas on this?
>> Thanks a lot,
>> Guntram
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> "1991-2011 - Creating Growth, Enhancing Lives. Commemorating A*STAR's 20 Years of Science, Technology and Research in Singapore."
>
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> This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.
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From guntram.schmidt at chemie.uni-halle.de  Tue Jul 26 21:50:47 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Tue, 26 Jul 2011 21:50:47 +0200
Subject: [Pw_forum] phcg.x segmentation fault
In-Reply-To: <4E28F79A.6040709@yahoo.com.cn>
References: <4E28F79A.6040709@yahoo.com.cn>
Message-ID: <4E2F1A97.6040106@chemie.uni-halle.de>

Dear All,

I'm trying to adopt the working SiH4-example for phonon calculations 
(http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_advph.html) 
to my molecular crystal.

phcg.x crashes with

ERROR: 0031-250  task 0: Segmentation fault

using differing compiled versions of QE (with and without 
essl/lapack-combinations)...

The input file is:
-----------------------------------
Normal modes for SiH4
  &inputph
   tr2_ph=1.0d-14,
   prefix='i2t0480.xyz.42.168',
   outdir='/gpfs/home/aasfu/tmp/i2t0480.xyz.42.168/',
  amass(1)=30.973762,
  amass(2)=15.9994,
  amass(3)=14.00679,
  amass(4)=12.011,
  amass(5)=1.00794,
   epsil=.true.,
   trans=.true.,
   asr=.true.
   fildyn='i2t0480.xyz.scf.42.rpb-nc.UPF.dyn'
  /
  0.0 0.0 0.0
-------------------------------------
having done a successful scf-calculation on the referenced system (what 
are the files needed as input by phcg.x?).

The output file finished abruptly after:
-------------------------------------
       Stick Mesh
       ----------
       nst =  3369,  nstw =   846, nsts =  3369
                   n.st   n.stw   n.sts    n.g    n.gw   n.gs
       min        6737    1691    6737  495721   61939  495721
       max        6737    1691    6737  495721   61939  495721
           6737    1691    6737  495721   61939  495721


         Check: negative/imaginary core charge=   -0.000007    0.000000


 
---------------------------------------------------------------------------------
    Carrying out vdW-DF run using the following parameters:

    Nqs =      20    Nr_points =    1024   r_max =   100.000
    q_mesh =       0.00001000
         0.04494208
         0.09755937
         0.15916263
         0.23128650
         0.31572767
         0.41458969
         0.53033537
         0.66584808
         0.82450364
         1.01025438
         1.22772762
         1.48234092
         1.78043706
         2.12944203
         2.53805004
         3.01644009
         3.57652955
         4.23227104
         5.00000000

    Gradients computed in Reciprocal space

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


Any ideas what's wrong?
I gave the calculation 12GB of memory for 196 atoms - this should be 
enough, shoudn't it be?

Thanks,
Guntram

From guntram.schmidt at chemie.uni-halle.de  Tue Jul 26 22:39:36 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Tue, 26 Jul 2011 22:39:36 +0200
Subject: [Pw_forum] phcg.x segmentation fault
In-Reply-To: <20110726215716.ndzigpum5cogcgcw@webmail.sissa.it>
References: <4E28F79A.6040709@yahoo.com.cn>
	<4E2F1A97.6040106@chemie.uni-halle.de>
	<20110726215716.ndzigpum5cogcgcw@webmail.sissa.it>
Message-ID: <4E2F2608.2030002@chemie.uni-halle.de>

:(

So there is no chance to get the free energy of molecular crystals 
calculated, as there is always some phonon-code needed for the 
vibrational contribution?

Or are there any detour ideas?

Thanks,
Guntram


Am 26.07.2011 21:57, schrieb Emine Kucukbenli:
> Guntram,
> Phonons with vdW-DF is not implemented yet.
> emine kucukbenli, phd student, sissa, italy
>
>
> Quoting Guntram Schmidt <guntram.schmidt at chemie.uni-halle.de>:
>
>> Dear All,
>>
>> I'm trying to adopt the working SiH4-example for phonon calculations
>> (http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_advph.html)
>> to my molecular crystal.
>>
>> phcg.x crashes with
>>
>> ERROR: 0031-250 task 0: Segmentation fault
>>
>> using differing compiled versions of QE (with and without
>> essl/lapack-combinations)...
>>
>> The input file is:
>> -----------------------------------
>> Normal modes for SiH4
>> &inputph
>> tr2_ph=1.0d-14,
>> prefix='i2t0480.xyz.42.168',
>> outdir='/gpfs/home/aasfu/tmp/i2t0480.xyz.42.168/',
>> amass(1)=30.973762,
>> amass(2)=15.9994,
>> amass(3)=14.00679,
>> amass(4)=12.011,
>> amass(5)=1.00794,
>> epsil=.true.,
>> trans=.true.,
>> asr=.true.
>> fildyn='i2t0480.xyz.scf.42.rpb-nc.UPF.dyn'
>> /
>> 0.0 0.0 0.0
>> -------------------------------------
>> having done a successful scf-calculation on the referenced system (what
>> are the files needed as input by phcg.x?).
>>
>> The output file finished abruptly after:
>> -------------------------------------
>> Stick Mesh
>> ----------
>> nst = 3369, nstw = 846, nsts = 3369
>> n.st n.stw n.sts n.g n.gw n.gs
>> min 6737 1691 6737 495721 61939 495721
>> max 6737 1691 6737 495721 61939 495721
>> 6737 1691 6737 495721 61939 495721
>>
>>
>> Check: negative/imaginary core charge= -0.000007 0.000000
>>
>>
>>
>> ---------------------------------------------------------------------------------
>>
>> Carrying out vdW-DF run using the following parameters:
>>
>> Nqs = 20 Nr_points = 1024 r_max = 100.000
>> q_mesh = 0.00001000
>> 0.04494208
>> 0.09755937
>> 0.15916263
>> 0.23128650
>> 0.31572767
>> 0.41458969
>> 0.53033537
>> 0.66584808
>> 0.82450364
>> 1.01025438
>> 1.22772762
>> 1.48234092
>> 1.78043706
>> 2.12944203
>> 2.53805004
>> 3.01644009
>> 3.57652955
>> 4.23227104
>> 5.00000000
>>
>> Gradients computed in Reciprocal space
>>
>>
>> ---------------------------------------------------------------------------------
>>
>>
>>
>> Any ideas what's wrong?
>> I gave the calculation 12GB of memory for 196 atoms - this should be
>> enough, shoudn't it be?
>>
>> Thanks,
>> Guntram
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
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>
>

From Michael at ihpc.a-star.edu.sg  Wed Jul 27 05:40:35 2011
From: Michael at ihpc.a-star.edu.sg (Michael Sullivan)
Date: Wed, 27 Jul 2011 11:40:35 +0800
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <4E2F1616.8080905@chemie.uni-halle.de>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E2F1616.8080905@chemie.uni-halle.de>
Message-ID: <0FA242DB-AA44-4B5C-BA79-992927CEBB5A@ihpc.a-star.edu.sg>

Guntram:

If I'm not wrong, that just means that you're not using ESSL.

Mike
michael at ihpc.a-star.edu.sg
http://www.sullivan.sg/

On 27-Jul-2011, at 3:31 AM, Guntram Schmidt wrote:

> Heureka!
>
> After several days of compiling and complaining I've found a possible
> solution!
> In contrast to all warning regarding the loading of essl before lapack,
> it mustn't be loaded before lapack!
> When I add lessl before lapack, I get the DSYGV : 2538-2015 error messages.
> The following make.sys finally works regarding these problems on my
> system (IBM 575):


"1991-2011 - Creating Growth, Enhancing Lives. Commemorating A*STAR's 20 Years of Science, Technology and Research in Singapore."

IHPC Values  ::  Impact   ::   Honesty   ::   Performance   ::   Co-operation
This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.

From kangbugy at lycos.co.kr  Wed Jul 27 06:02:36 2011
From: kangbugy at lycos.co.kr (=?UTF-8?B?a2FuZ2J1Z3lAbHljb3MuY28ua3I=?=)
Date: Wed, 27 Jul 2011 13:02:36 +0900
Subject: [Pw_forum] =?utf-8?q?ph=2Ex_segmentation_fault?=
Message-ID: <c0d6e1e9fe31f722ac727de6c4d71e43$5c6718fe@pcmail3.nate.com>

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From goodluck_1982 at 163.com  Wed Jul 27 07:04:47 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Wed, 27 Jul 2011 13:04:47 +0800
Subject: [Pw_forum] What files are needed when pw.x restarts? In what case
 the *.wfc files are need?
In-Reply-To: <4E2F1616.8080905@chemie.uni-halle.de>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>	<4E28041D.6050101@chemie.uni-halle.de>	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E2F1616.8080905@chemie.uni-halle.de>
Message-ID: <4E2F9C6F.9030009@163.com>

Dear all,

      Now I'm wondering what files are needed when pw.x restarts from a 
interrupted run. Is a single file outdir/prefix.save/charge-density.dat  
enough? Are *.wfc files needed?
      What's the function of the parameter "wf_collect = .true." ?  I 
set outdir='./work' , wfcdir='/tmp', restart_mode='restart'. Then *.wfc 
files exist  in /tmp.
      I note that, when I set *wf_collect = .false.*, there are files 
under ./work (case 1):
         xxx.UPF
         charge-density.dat
         data-file.xml
        K00001/eigenval.xml
        K.....
    and when I set *wf_collect = .true.*, there are files under ./work 
(case 2):
         xxx.UPF
         charge-density.dat
         data-file.xml
         gvectors.dat
        K00001/eigenval.xml
        K00001/evc.dat
        K00001/gkvectors.dat
       K .....
What's the use of gvectors.dat files?
  In case 1, because wf_collect=.false., *.wfc files keep existing in 
/tmp,  when pw.x restarts, it can read wfc from /tmp.
However, in case 2, *.wfc files are removed from /tmp after run and 
don't appear in ./work either, therefore when pw.x restarts, it cannot 
read wfc from anywhere. Now that wf_collect=.true., how are wfc files 
are collected and to where?
BTW:  in both cases, pw.x can read the existing charge density, is this 
enough for a restarted run even if  no wfc files found?

Best wishes
Liu Gui-Bin
Dept. of Physics
The Universit of Hong Kong
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From hashemifar at cc.iut.ac.ir  Wed Jul 27 08:13:24 2011
From: hashemifar at cc.iut.ac.ir (Seyed Javad Hashemifar)
Date: Wed, 27 Jul 2011 08:13:24 +0200
Subject: [Pw_forum] What files are needed when pw.x restarts? In what
 case the *.wfc files are need?
In-Reply-To: <4E2F9C6F.9030009@163.com>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E2F1616.8080905@chemie.uni-halle.de> <4E2F9C6F.9030009@163.com>
Message-ID: <CAKScr_rju9zXEqtjyu=Q8686xUkcyVup7P+Cmq5Wxh=qiLc+qg@mail.gmail.com>

Hello
As far as I know, since pw.x uses iterative diagonalization method, in
addition to the charge density files, it needs to wave function files also
to restart a calculation. If there is no wave function file, then you can
set some atomic wave functions in namelist ELECTRONS:

http://www.quantum-espresso.org/input-syntax/INPUT_PW.html#id2468572

to restart your job, but in this case it will not be restarted exactly from
the position of interruption.

If you set wf_collect=.true. then most likely you able to restart or
continue your parallel job with a different parallel setting (for example on
different number of processors).
SJ Hashemifar
======================================
Seyed Javad  Hashemifar
Department of Physics, Isfahan University of Technology
84156-83111 Isfahan, Iran
Tel: +98 311 391 2375     Fax:+98 311 3912376
Email:  hashemifar at cc.iut.ac.ir
Group Homepage:      http://cmsgroup.iut.ac.ir
Personal Homepage:  http://hashemifar.iut.ac.ir
---------------------------------------------------------------------------


On Wed, Jul 27, 2011 at 7:04 AM, gbliu <goodluck_1982 at 163.com> wrote:

> **
> Dear all,
>
>      Now I'm wondering what files are needed when pw.x restarts from a
> interrupted run. Is a single file outdir/prefix.save/charge-density.dat
> enough? Are *.wfc files needed?
>      What's the function of the parameter "wf_collect = .true." ?  I set
> outdir='./work' , wfcdir='/tmp', restart_mode='restart'. Then *.wfc files
> exist  in /tmp.
>      I note that, when I set *wf_collect = .false.*, there are files under
> ./work  (case 1):
>         xxx.UPF
>         charge-density.dat
>         data-file.xml
>        K00001/eigenval.xml
>        K.....
>    and when I set *wf_collect = .true.*, there are files under ./work (case
> 2):
>         xxx.UPF
>         charge-density.dat
>         data-file.xml
>         gvectors.dat
>        K00001/eigenval.xml
>        K00001/evc.dat
>        K00001/gkvectors.dat
>       K .....
> What's the use of gvectors.dat files?
>  In case 1, because wf_collect=.false., *.wfc files keep existing in /tmp,
> when pw.x restarts, it can read wfc from /tmp.
> However, in case 2, *.wfc files are removed from /tmp after run and don't
> appear in ./work either, therefore when pw.x restarts, it cannot read wfc
> from anywhere. Now that wf_collect=.true., how are wfc files are collected
> and to where?
> BTW:  in both cases, pw.x can read the existing charge density, is this
> enough for a restarted run even if  no wfc files found?
>
> Best wishes
> Liu Gui-Bin
> Dept. of Physics
> The Universit of Hong Kong
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From guntram.schmidt at chemie.uni-halle.de  Wed Jul 27 09:26:16 2011
From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt)
Date: Wed, 27 Jul 2011 09:26:16 +0200
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <0FA242DB-AA44-4B5C-BA79-992927CEBB5A@ihpc.a-star.edu.sg>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E2F1616.8080905@chemie.uni-halle.de>
	<0FA242DB-AA44-4B5C-BA79-992927CEBB5A@ihpc.a-star.edu.sg>
Message-ID: <4E2FBD98.4050006@chemie.uni-halle.de>

Dear Mike,

how could I confirm this?
Adding -lessl after the -llapack results in working executables, too.

Also essl is referenced for fft.

Or is essl mainly used to improve lapack?

Thanks,
Guntram


Am 27.07.2011 05:40, schrieb Michael Sullivan:
> Guntram:
>
> If I'm not wrong, that just means that you're not using ESSL.
>
> Mike
> michael at ihpc.a-star.edu.sg
> http://www.sullivan.sg/
>
> On 27-Jul-2011, at 3:31 AM, Guntram Schmidt wrote:
>
>> Heureka!
>>
>> After several days of compiling and complaining I've found a possible
>> solution!
>> In contrast to all warning regarding the loading of essl before lapack,
>> it mustn't be loaded before lapack!
>> When I add lessl before lapack, I get the DSYGV : 2538-2015 error messages.
>> The following make.sys finally works regarding these problems on my
>> system (IBM 575):
>
>
> "1991-2011 - Creating Growth, Enhancing Lives. Commemorating A*STAR's 20 Years of Science, Technology and Research in Singapore."
>
> IHPC Values  ::  Impact   ::   Honesty   ::   Performance   ::   Co-operation
> This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

From goodluck_1982 at 163.com  Wed Jul 27 09:28:55 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Wed, 27 Jul 2011 15:28:55 +0800
Subject: [Pw_forum] What files are needed when pw.x restarts? In what
 case the *.wfc files are need?
In-Reply-To: <CAKScr_rju9zXEqtjyu=Q8686xUkcyVup7P+Cmq5Wxh=qiLc+qg@mail.gmail.com>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>	<4E28041D.6050101@chemie.uni-halle.de>	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>	<4E2F1616.8080905@chemie.uni-halle.de>
	<4E2F9C6F.9030009@163.com>
	<CAKScr_rju9zXEqtjyu=Q8686xUkcyVup7P+Cmq5Wxh=qiLc+qg@mail.gmail.com>
Message-ID: <4E2FBE37.3050409@163.com>

Hi Hashemifar,

I just guess and expect that  wf_collect=.true. will collect *.wfc files 
from wfcdir to outdir after each iteration or at the end of run. Is this 
right? But it seems not.  As mentioned in last mail, *.wfc files don't 
appear in ourdir  anytime.

Best wishes
Liu Guibin


? 2011/7/27 14:13, Seyed Javad Hashemifar ??:
> Hello
> As far as I know, since pw.x uses iterative diagonalization method, in 
> addition to the charge density files, it needs to wave function files 
> also to restart a calculation. If there is no wave function file, then 
> you can set some atomic wave functions in namelist ELECTRONS:
>
> http://www.quantum-espresso.org/input-syntax/INPUT_PW.html#id2468572
>
> to restart your job, but in this case it will not be restarted exactly 
> from the position of interruption.
>
> If you set wf_collect=.true. then most likely you able to restart or 
> continue your parallel job with a different parallel setting (for 
> example on different number of processors).
> SJ Hashemifar
> ======================================
> Seyed Javad  Hashemifar
> Department of Physics, Isfahan University of Technology
> 84156-83111 Isfahan, Iran
> Tel: +98 311 391 2375     Fax:+98 311 3912376
> Email: hashemifar at cc.iut.ac.ir <mailto:hashemifar at cc.iut.ac.ir>
> Group Homepage: http://cmsgroup.iut.ac.ir
> Personal Homepage: http://hashemifar.iut.ac.ir
> ---------------------------------------------------------------------------
>
>
> On Wed, Jul 27, 2011 at 7:04 AM, gbliu <goodluck_1982 at 163.com 
> <mailto:goodluck_1982 at 163.com>> wrote:
>
>     Dear all,
>
>          Now I'm wondering what files are needed when pw.x restarts
>     from a interrupted run. Is a single file
>     outdir/prefix.save/charge-density.dat  enough? Are *.wfc files needed?
>          What's the function of the parameter "wf_collect = .true." ? 
>     I set outdir='./work' , wfcdir='/tmp', restart_mode='restart'.
>     Then *.wfc files exist  in /tmp.
>          I note that, when I set *wf_collect = .false.*, there are
>     files under ./work (case 1):
>             xxx.UPF
>             charge-density.dat
>             data-file.xml
>            K00001/eigenval.xml
>            K.....
>        and when I set *wf_collect = .true.*, there are files under
>     ./work (case 2):
>             xxx.UPF
>             charge-density.dat
>             data-file.xml
>             gvectors.dat
>            K00001/eigenval.xml
>            K00001/evc.dat
>            K00001/gkvectors.dat
>           K .....
>     What's the use of gvectors.dat files?
>      In case 1, because wf_collect=.false., *.wfc files keep existing
>     in /tmp,  when pw.x restarts, it can read wfc from /tmp.
>     However, in case 2, *.wfc files are removed from /tmp after run
>     and don't appear in ./work either, therefore when pw.x restarts,
>     it cannot read wfc from anywhere. Now that wf_collect=.true., how
>     are wfc files are collected and to where?
>     BTW:  in both cases, pw.x can read the existing charge density, is
>     this enough for a restarted run even if  no wfc files found?
>
>     Best wishes
>     Liu Gui-Bin
>     Dept. of Physics
>     The Universit of Hong Kong
>
>     _______________________________________________
>     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

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From hashemifar at cc.iut.ac.ir  Wed Jul 27 09:41:59 2011
From: hashemifar at cc.iut.ac.ir (Seyed Javad Hashemifar)
Date: Wed, 27 Jul 2011 09:41:59 +0200
Subject: [Pw_forum] What files are needed when pw.x restarts? In what
 case the *.wfc files are need?
In-Reply-To: <4E2FBE37.3050409@163.com>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E2F1616.8080905@chemie.uni-halle.de> <4E2F9C6F.9030009@163.com>
	<CAKScr_rju9zXEqtjyu=Q8686xUkcyVup7P+Cmq5Wxh=qiLc+qg@mail.gmail.com>
	<4E2FBE37.3050409@163.com>
Message-ID: <CAKScr_p22KHGBx_SiV1SAZkAP9xcOnLR4ZFm8L7wWv8nHyniFg@mail.gmail.com>

I guess if you set wf_collect=.true. the collection of *.wfc files is done
after reaching self consistency not after each iteration. Probably, the
evc.dat files are the collected *.wfc files (I am not sure). You may check
their sizes, if they are very big files, then most likely they are the
collected wave functions files.
SJ Hashemifar
======================================
Seyed Javad  Hashemifar
Department of Physics, Isfahan University of Technology
84156-83111 Isfahan, Iran
Tel: +98 311 391 2375     Fax:+98 311 3912376
Email:  hashemifar at cc.iut.ac.ir
Group Homepage:      http://cmsgroup.iut.ac.ir
Personal Homepage:  http://hashemifar.iut.ac.ir
---------------------------------------------------------------------------


On Wed, Jul 27, 2011 at 9:28 AM, gbliu <goodluck_1982 at 163.com> wrote:

> **
> Hi Hashemifar,
>
> I just guess and expect that  wf_collect=.true. will collect *.wfc files
> from wfcdir to outdir after each iteration or at the end of run. Is this
> right? But it seems not.  As mentioned in last mail, *.wfc files don't
> appear in ourdir  anytime.
>
> Best wishes
> Liu Guibin
>
>
> ? 2011/7/27 14:13, Seyed Javad Hashemifar ??:
>
> Hello
> As far as I know, since pw.x uses iterative diagonalization method, in
> addition to the charge density files, it needs to wave function files also
> to restart a calculation. If there is no wave function file, then you can
> set some atomic wave functions in namelist ELECTRONS:
>
>  http://www.quantum-espresso.org/input-syntax/INPUT_PW.html#id2468572
>
>  to restart your job, but in this case it will not be restarted exactly
> from the position of interruption.
>
>  If you set wf_collect=.true. then most likely you able to restart or
> continue your parallel job with a different parallel setting (for example on
> different number of processors).
> SJ Hashemifar
> ======================================
> Seyed Javad  Hashemifar
> Department of Physics, Isfahan University of Technology
> 84156-83111 Isfahan, Iran
> Tel: +98 311 391 2375     Fax:+98 311 3912376
> Email:  hashemifar at cc.iut.ac.ir
> Group Homepage:      http://cmsgroup.iut.ac.ir
> Personal Homepage:  http://hashemifar.iut.ac.ir
> ---------------------------------------------------------------------------
>
>
> On Wed, Jul 27, 2011 at 7:04 AM, gbliu <goodluck_1982 at 163.com> wrote:
>
>>  Dear all,
>>
>>      Now I'm wondering what files are needed when pw.x restarts from a
>> interrupted run. Is a single file outdir/prefix.save/charge-density.dat
>> enough? Are *.wfc files needed?
>>      What's the function of the parameter "wf_collect = .true." ?  I set
>> outdir='./work' , wfcdir='/tmp', restart_mode='restart'. Then *.wfc files
>> exist  in /tmp.
>>      I note that, when I set *wf_collect = .false.*, there are files
>> under ./work  (case 1):
>>         xxx.UPF
>>         charge-density.dat
>>         data-file.xml
>>        K00001/eigenval.xml
>>        K.....
>>    and when I set *wf_collect = .true.*, there are files under ./work (case
>> 2):
>>         xxx.UPF
>>         charge-density.dat
>>         data-file.xml
>>         gvectors.dat
>>        K00001/eigenval.xml
>>        K00001/evc.dat
>>        K00001/gkvectors.dat
>>       K .....
>> What's the use of gvectors.dat files?
>>  In case 1, because wf_collect=.false., *.wfc files keep existing in
>> /tmp,  when pw.x restarts, it can read wfc from /tmp.
>> However, in case 2, *.wfc files are removed from /tmp after run and don't
>> appear in ./work either, therefore when pw.x restarts, it cannot read wfc
>> from anywhere. Now that wf_collect=.true., how are wfc files are collected
>> and to where?
>> BTW:  in both cases, pw.x can read the existing charge density, is this
>> enough for a restarted run even if  no wfc files found?
>>
>> Best wishes
>> Liu Gui-Bin
>> Dept. of Physics
>> The Universit of Hong Kong
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
> _______________________________________________
> 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 giuseppe.mattioli at mlib.ism.cnr.it  Wed Jul 27 11:44:25 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Wed, 27 Jul 2011 11:44:25 +0200
Subject: [Pw_forum] What files are needed when pw.x restarts? In what
	case the *.wfc files are need?
In-Reply-To: <CAKScr_p22KHGBx_SiV1SAZkAP9xcOnLR4ZFm8L7wWv8nHyniFg@mail.gmail.com>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E2FBE37.3050409@163.com>
	<CAKScr_p22KHGBx_SiV1SAZkAP9xcOnLR4ZFm8L7wWv8nHyniFg@mail.gmail.com>
Message-ID: <201107271144.26452.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Liu
Only a couple of notes:
The wf_collect key collects indeed the wfc information (at the end of the scf 
cycle, I suppose, but I'm not sure) in order to restart the calculation with 
a different parallel scheme. It is particularly useful when you want to 
perform serial post-processing calculations (i.e., when using the pp.x code) 
after parallel pw.x ones.
However, pw.x tries to restart the calculation by looking for everything 
useful in a number of different possible schemes: for instance, when you 
perform a geometry optimisation and the .wfc* files are badly written or 
corrupted, you may restart from scratch the scf cycle, without affecting the 
bfgs history contained into the .bfgs binary file.
HTH
Giuseppe

On Wednesday 27 July 2011 09:41:59 Seyed Javad Hashemifar wrote:
> I guess if you set wf_collect=.true. the collection of *.wfc files is done
> after reaching self consistency not after each iteration. Probably, the
> evc.dat files are the collected *.wfc files (I am not sure). You may check
> their sizes, if they are very big files, then most likely they are the
> collected wave functions files.
> SJ Hashemifar
> ======================================
> Seyed Javad  Hashemifar
> Department of Physics, Isfahan University of Technology
> 84156-83111 Isfahan, Iran
> Tel: +98 311 391 2375     Fax:+98 311 3912376
> Email:  hashemifar at cc.iut.ac.ir
> Group Homepage:      http://cmsgroup.iut.ac.ir
> Personal Homepage:  http://hashemifar.iut.ac.ir
> ---------------------------------------------------------------------------
>
> On Wed, Jul 27, 2011 at 9:28 AM, gbliu <goodluck_1982 at 163.com> wrote:
> > **
> > Hi Hashemifar,
> >
> > I just guess and expect that  wf_collect=.true. will collect *.wfc files
> > from wfcdir to outdir after each iteration or at the end of run. Is this
> > right? But it seems not.  As mentioned in last mail, *.wfc files don't
> > appear in ourdir  anytime.
> >
> > Best wishes
> > Liu Guibin
> >
> >
> > ? 2011/7/27 14:13, Seyed Javad Hashemifar ??:
> >
> > Hello
> > As far as I know, since pw.x uses iterative diagonalization method, in
> > addition to the charge density files, it needs to wave function files
> > also to restart a calculation. If there is no wave function file, then
> > you can set some atomic wave functions in namelist ELECTRONS:
> >
> >  http://www.quantum-espresso.org/input-syntax/INPUT_PW.html#id2468572
> >
> >  to restart your job, but in this case it will not be restarted exactly
> > from the position of interruption.
> >
> >  If you set wf_collect=.true. then most likely you able to restart or
> > continue your parallel job with a different parallel setting (for example
> > on different number of processors).
> > SJ Hashemifar
> > ======================================
> > Seyed Javad  Hashemifar
> > Department of Physics, Isfahan University of Technology
> > 84156-83111 Isfahan, Iran
> > Tel: +98 311 391 2375     Fax:+98 311 3912376
> > Email:  hashemifar at cc.iut.ac.ir
> > Group Homepage:      http://cmsgroup.iut.ac.ir
> > Personal Homepage:  http://hashemifar.iut.ac.ir
> > -------------------------------------------------------------------------
> >--
> >
> > On Wed, Jul 27, 2011 at 7:04 AM, gbliu <goodluck_1982 at 163.com> wrote:
> >>  Dear all,
> >>
> >>      Now I'm wondering what files are needed when pw.x restarts from a
> >> interrupted run. Is a single file outdir/prefix.save/charge-density.dat
> >> enough? Are *.wfc files needed?
> >>      What's the function of the parameter "wf_collect = .true." ?  I set
> >> outdir='./work' , wfcdir='/tmp', restart_mode='restart'. Then *.wfc
> >> files exist  in /tmp.
> >>      I note that, when I set *wf_collect = .false.*, there are files
> >> under ./work  (case 1):
> >>         xxx.UPF
> >>         charge-density.dat
> >>         data-file.xml
> >>        K00001/eigenval.xml
> >>        K.....
> >>    and when I set *wf_collect = .true.*, there are files under ./work
> >> (case 2):
> >>         xxx.UPF
> >>         charge-density.dat
> >>         data-file.xml
> >>         gvectors.dat
> >>        K00001/eigenval.xml
> >>        K00001/evc.dat
> >>        K00001/gkvectors.dat
> >>       K .....
> >> What's the use of gvectors.dat files?
> >>  In case 1, because wf_collect=.false., *.wfc files keep existing in
> >> /tmp,  when pw.x restarts, it can read wfc from /tmp.
> >> However, in case 2, *.wfc files are removed from /tmp after run and
> >> don't appear in ./work either, therefore when pw.x restarts, it cannot
> >> read wfc from anywhere. Now that wf_collect=.true., how are wfc files
> >> are collected and to where?
> >> BTW:  in both cases, pw.x can read the existing charge density, is this
> >> enough for a restarted run even if  no wfc files found?
> >>
> >> Best wishes
> >> Liu Gui-Bin
> >> Dept. of Physics
> >> The Universit of Hong Kong
> >>
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >
> > _______________________________________________
> > 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



-- 
********************************************************
- 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 baroni at sissa.it  Wed Jul 27 12:45:57 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 27 Jul 2011 12:45:57 +0200
Subject: [Pw_forum] phcg.x segmentation fault
In-Reply-To: <4E2F2608.2030002@chemie.uni-halle.de>
References: <4E28F79A.6040709@yahoo.com.cn>
	<4E2F1A97.6040106@chemie.uni-halle.de>
	<20110726215716.ndzigpum5cogcgcw@webmail.sissa.it>
	<4E2F2608.2030002@chemie.uni-halle.de>
Message-ID: <DB88690B-F975-4430-8B61-7CACBCC630C3@sissa.it>

I understand the implementation of VdW functionals in the linear-response codes is presently under way. SB

On Jul 26, 2011, at 10:39 PM, Guntram Schmidt wrote:

> :(
> 
> So there is no chance to get the free energy of molecular crystals 
> calculated, as there is always some phonon-code needed for the 
> vibrational contribution?
> 
> Or are there any detour ideas?
> 
> Thanks,
> Guntram
> 
> 
> Am 26.07.2011 21:57, schrieb Emine Kucukbenli:
>> Guntram,
>> Phonons with vdW-DF is not implemented yet.
>> emine kucukbenli, phd student, sissa, italy
>> 
>> 
>> Quoting Guntram Schmidt <guntram.schmidt at chemie.uni-halle.de>:
>> 
>>> Dear All,
>>> 
>>> I'm trying to adopt the working SiH4-example for phonon calculations
>>> (http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_advph.html)
>>> to my molecular crystal.
>>> 
>>> phcg.x crashes with
>>> 
>>> ERROR: 0031-250 task 0: Segmentation fault
>>> 
>>> using differing compiled versions of QE (with and without
>>> essl/lapack-combinations)...
>>> 
>>> The input file is:
>>> -----------------------------------
>>> Normal modes for SiH4
>>> &inputph
>>> tr2_ph=1.0d-14,
>>> prefix='i2t0480.xyz.42.168',
>>> outdir='/gpfs/home/aasfu/tmp/i2t0480.xyz.42.168/',
>>> amass(1)=30.973762,
>>> amass(2)=15.9994,
>>> amass(3)=14.00679,
>>> amass(4)=12.011,
>>> amass(5)=1.00794,
>>> epsil=.true.,
>>> trans=.true.,
>>> asr=.true.
>>> fildyn='i2t0480.xyz.scf.42.rpb-nc.UPF.dyn'
>>> /
>>> 0.0 0.0 0.0
>>> -------------------------------------
>>> having done a successful scf-calculation on the referenced system (what
>>> are the files needed as input by phcg.x?).
>>> 
>>> The output file finished abruptly after:
>>> -------------------------------------
>>> Stick Mesh
>>> ----------
>>> nst = 3369, nstw = 846, nsts = 3369
>>> n.st n.stw n.sts n.g n.gw n.gs
>>> min 6737 1691 6737 495721 61939 495721
>>> max 6737 1691 6737 495721 61939 495721
>>> 6737 1691 6737 495721 61939 495721
>>> 
>>> 
>>> Check: negative/imaginary core charge= -0.000007 0.000000
>>> 
>>> 
>>> 
>>> ---------------------------------------------------------------------------------
>>> 
>>> Carrying out vdW-DF run using the following parameters:
>>> 
>>> Nqs = 20 Nr_points = 1024 r_max = 100.000
>>> q_mesh = 0.00001000
>>> 0.04494208
>>> 0.09755937
>>> 0.15916263
>>> 0.23128650
>>> 0.31572767
>>> 0.41458969
>>> 0.53033537
>>> 0.66584808
>>> 0.82450364
>>> 1.01025438
>>> 1.22772762
>>> 1.48234092
>>> 1.78043706
>>> 2.12944203
>>> 2.53805004
>>> 3.01644009
>>> 3.57652955
>>> 4.23227104
>>> 5.00000000
>>> 
>>> Gradients computed in Reciprocal space
>>> 
>>> 
>>> ---------------------------------------------------------------------------------
>>> 
>>> 
>>> 
>>> Any ideas what's wrong?
>>> I gave the calculation 12GB of memory for 196 atoms - this should be
>>> enough, shoudn't it be?
>>> 
>>> Thanks,
>>> Guntram
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>> 
>> 
>> 
>> 
>> ----------------------------------------------------------------
>> SISSA Webmail https://webmail.sissa.it/
>> Powered by Horde http://www.horde.org/
>> 
>> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
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

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From mohnish.iitk at gmail.com  Wed Jul 27 13:16:35 2011
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Wed, 27 Jul 2011 16:46:35 +0530
Subject: [Pw_forum] antiferromagnetism in thin films
In-Reply-To: <201107261531.58222.giuseppe.mattioli@mlib.ism.cnr.it>
References: <CAMhNW-euy7y4sJXHaMvMeMRcG2-EMRzPv9a2zxQJjav_-urK-A@mail.gmail.com>
	<201107261531.58222.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <CAMhNW-d3+UrEKWVYg_21fZZVSyTmRdUJFc3oo3GPvL9+uDQBXQ@mail.gmail.com>

Dear Dr. Mattioli,

I will do the calculation for different spin configurations and will let you
know as soon as I have the results. And regarding the "subject" I am sorry
to change that, I did that by mistake and did not realize.


On Tue, Jul 26, 2011 at 7:01 PM, Giuseppe Mattioli <
giuseppe.mattioli at mlib.ism.cnr.it> wrote:

>
> Dear Mohnish
> changing the subject will not produce automatically an answer... I suspect
> that you are asking something that deserves itself a full investigation.
> Let
> us know the results.
> Yours
> Giuseppe
>
> On Tuesday 26 July 2011 12:03:57 mohnish pandey wrote:
> > Dear QE users,
> >
> > I want to do calculations of thin films of antiferromagnetic oxide like
> > CoO. The CoO has rocksalt structure and magnetization along (111)
> > direction. Suppose we take 3 layers and 4 layers for of CoO along (111),
> > then my doubt is that will the magnetization oscillate i.e. in even
> number
> > of layers it will be zero and odd number of layers will have some finite
> > value? Or wil the film will show antiferrromagnetism in plane i.e. every
> > layers of CoO will be antiferromagnetic? And what about other directions
> > like (001) or (10-10) in wurtzite structure.
> >
> > Thanks a lot in advance for help..
>
>
>
> --
> ********************************************************
> - 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
>



-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
Senior Project Associate,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
-----------------------------------------------------------------
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From djulriya at mail.ru  Wed Jul 27 13:46:06 2011
From: djulriya at mail.ru (=?utf-8?Q?=D0=AE=D0=BB=D1=8F_=D0=A4=D0=B8=D0=BB=D0=B8=D1=87=D0=B5=D0=B2=D0=B0?=)
Date: Wed, 27 Jul 2011 15:46:06 +0400
Subject: [Pw_forum] Question about geometry relaxation
Message-ID: <E1Qm2Yw-0007KP-00.djulriya-mail-ru@f90.mail.ru>

Dear QE users,

I'm a new user of QE.
Now I try to provide the geometry relaxation of carbon diamond-like structure, but I'm not sure that I'm doing it right.
It would be kind of you, if you advise me what type of optimizer or some parameters which I don't use here should I use to achieve the best results?
Below I will give an example of my input file.

 &control
    calculation = 'vc-relax'
    restart_mode='from_scratch',
    prefix='carbon',
    tstress = .true.
    tprnfor = .true.
    pseudo_dir = './',
    outdir='./'
wf_collect=.true.,
etot_conv_thr = 1.0D-6,
forc_conv_thr = 1.0D-4,
nstep = 500,

 /
 &system
                     nosym = .false.,
                     ibrav = 1,
                     celldm(1) = 8.0907,
                     nat = 16,
                     ntyp = 1,
                     occupations = 'smearing',
             ecutwfc = 60,
             degauss = 0.05,
 /
 &ELECTRONS
               diagonalization = 'cg' ,
               electron_maxstep = 150,
 /
 &IONS
  ion_dynamics='bfgs',
  pot_extrapolation = "first_order",
 /
 &CELL
   cell_dynamics = 'bfgs' ,
   cell_factor = 1.6,
   press = 0 ,
   !cell_dofree = 'xyz',
press_conv_thr = 0.5D-1, 
 /
ATOMIC_SPECIES
 C    12    C.pbe-van_ak.UPF
ATOMIC_POSITIONS crystal
...
K_POINTS automatic 
 8 8 8  0 0 0


Thank you in advice.
Sincerely yours
Julia Filicheva


/First year of master degree study
Moscow Institute of Physics and Technology/

From rdong at ncsu.edu  Wed Jul 27 18:31:54 2011
From: rdong at ncsu.edu (DONG Rui)
Date: Wed, 27 Jul 2011 12:31:54 -0400
Subject: [Pw_forum] vdw-df2
Message-ID: <CAHLEWG1DYUWXVumB=VpvxHZnmbuVFVqwLg1h+HaVdo+D=V_mfw@mail.gmail.com>

Hi, all

I have something not clear about the vdw-df implementation.

It is mentioned in the example that we'd better use revised pbe when using
the vdw-df, but "revPBE" itself is another xc-functional? What do we do now?

Do we write the input_dft="revPBE+vdW-DF2"?

or we do "revPBE" first and use the result to restart a "vdW-DF2"
calculation?

Thank you very much for help!

-- 
Sincerely,

Rui DONG
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From i.kirker at ucl.ac.uk  Wed Jul 27 18:57:39 2011
From: i.kirker at ucl.ac.uk (Ian Kirker)
Date: Wed, 27 Jul 2011 17:57:39 +0100
Subject: [Pw_forum] allocate_radial_grid error: mesh>ndmx
Message-ID: <1311785859.3446.35.camel@OptiPlex>

I've been having a first try at using PWscf, after using CASTEP and
various molecular atom-centered codes, and I've managed to perform some
basic calculations with the supplied pseudopotentials. However, when
attempting to perform a test single-point calculation on Pu(OH)_4 with a
plutonium pseudopotential converted over from CASTEP's OTF generator
using the usp2upf tool from the ONETEP site, I get the following error:

     from allocate_radial_grid : error #         1
     mesh>ndmx

Looking at the source suggests that this might be something to do with
some size restriction on the logarithmic radial grids, but I'm really
not sure at all. Switching the plutonium for palladium (for no other
reason than that it seemed like it would fit and was in the PSP library)
produced a working calculation, so it seems like the problem might be
either with the pseudopotential conversion or with some quality of the
pseudopotential being too large/dense/etc for PWscf.

Does anyone have any suggestions for things I could try, either with
PWscf or to check in the pseudopotential to see what's not working or
make this work? 

(Alternatively/additionally, a source for a good plutonium PBE
pseudopotential that does work would be good too - I've had a try at
both generating my own and using atomic with parameters taken from the
CASTEP OTF one but have had various problems with that.)

Many thanks,
-Ian Kirker.



From ackaur at ucdavis.edu  Wed Jul 27 19:45:18 2011
From: ackaur at ucdavis.edu (Amandeep Kaur)
Date: Wed, 27 Jul 2011 10:45:18 -0700
Subject: [Pw_forum] allocate_radial_grid error: mesh>ndmx
In-Reply-To: <1311785859.3446.35.camel@OptiPlex>
References: <1311785859.3446.35.camel@OptiPlex>
Message-ID: <CAPB9MTwTvyc3Gbt2dGHeQGrsphyhhfnND4xcwSapF51DEqy7pQ@mail.gmail.com>

Your mesh size should not exceed ndmx which is probably 3500. I am not sure
about the exact number. Check the file radial_grids.f90 in the Module
directory for the size of ndmx.

Aman

On Wed, Jul 27, 2011 at 9:57 AM, Ian Kirker <i.kirker at ucl.ac.uk> wrote:

> I've been having a first try at using PWscf, after using CASTEP and
> various molecular atom-centered codes, and I've managed to perform some
> basic calculations with the supplied pseudopotentials. However, when
> attempting to perform a test single-point calculation on Pu(OH)_4 with a
> plutonium pseudopotential converted over from CASTEP's OTF generator
> using the usp2upf tool from the ONETEP site, I get the following error:
>
>     from allocate_radial_grid : error #         1
>     mesh>ndmx
>
> Looking at the source suggests that this might be something to do with
> some size restriction on the logarithmic radial grids, but I'm really
> not sure at all. Switching the plutonium for palladium (for no other
> reason than that it seemed like it would fit and was in the PSP library)
> produced a working calculation, so it seems like the problem might be
> either with the pseudopotential conversion or with some quality of the
> pseudopotential being too large/dense/etc for PWscf.
>
> Does anyone have any suggestions for things I could try, either with
> PWscf or to check in the pseudopotential to see what's not working or
> make this work?
>
> (Alternatively/additionally, a source for a good plutonium PBE
> pseudopotential that does work would be good too - I've had a try at
> both generating my own and using atomic with parameters taken from the
> CASTEP OTF one but have had various problems with that.)
>
> Many thanks,
> -Ian Kirker.
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Amandeep Kaur
Graduate Student
Department of Physics
University of California,Davis
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From kolbba5 at wfu.edu  Wed Jul 27 19:45:47 2011
From: kolbba5 at wfu.edu (Kolb, Brian)
Date: Wed, 27 Jul 2011 13:45:47 -0400
Subject: [Pw_forum] vdw-df2
In-Reply-To: <CAHLEWG1DYUWXVumB=VpvxHZnmbuVFVqwLg1h+HaVdo+D=V_mfw@mail.gmail.com>
References: <CAHLEWG1DYUWXVumB=VpvxHZnmbuVFVqwLg1h+HaVdo+D=V_mfw@mail.gmail.com>
Message-ID: <CA+vbgTEXjJkTqHSCdPO=UW5Jb042+mDYmk4Tp_iCXOrvBrwB3A@mail.gmail.com>

The revised PBE that should (perhaps) be used with vdW-DF is for exchange
only.  The vdW-DF functional is strictly a correlation functional.  So what
you really want is SLA (local exchange piece) PW (local correlation piece)
RPB (semi-local exchange piece) and VDW (non-local correlation piece).  If
you specify in your input file input_dft = "vdW-DF" this will all be set
automatically for you.

Hope this helps.

Brian Kolb
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From giannozz at democritos.it  Wed Jul 27 19:53:41 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 27 Jul 2011 19:53:41 +0200
Subject: [Pw_forum] allocate_radial_grid error: mesh>ndmx
In-Reply-To: <1311785859.3446.35.camel@OptiPlex>
References: <1311785859.3446.35.camel@OptiPlex>
Message-ID: <53440974-7DA2-410C-9C1B-C9AEFAC77B21@democritos.it>


On Jul 27, 2011, at 18:57 , Ian Kirker wrote:

>      from allocate_radial_grid : error #         1
>      mesh>ndmx

$ grep "mesh>ndmx" */*f90
Modules/radial_grids.f90:      if(mesh>ndmx) &
Modules/radial_grids.f90:         call errore('allocate_radial_grid',  
'mesh>ndmx',1)

$ grep ndmx Modules/radial_grids.f90
   ! - ndmx     : parameter definition max grid dimension
        ndmx=3500     ! the maximum mesh size
   PUBLIC :: ndmx, radial_grid_type, &
       if(mesh>ndmx) &
          call errore('allocate_radial_grid', 'mesh>ndmx',1)
       if(mesh+1 > ndmx) call errore('do_mesh','ndmx is too small',1)

Just increase it and recompile. Moving to dynamical allocation was  
not worth
the effort.

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 27 22:31:29 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 27 Jul 2011 22:31:29 +0200
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <0FA242DB-AA44-4B5C-BA79-992927CEBB5A@ihpc.a-star.edu.sg>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E2F1616.8080905@chemie.uni-halle.de>
	<0FA242DB-AA44-4B5C-BA79-992927CEBB5A@ihpc.a-star.edu.sg>
Message-ID: <61A00C8B-E1AF-4FAF-B140-238805CEF4F0@democritos.it>


On Jul 27, 2011, at 5:40 , Michael Sullivan wrote:

> If I'm not wrong, that just means that you're not using ESSL.

it is true that by linking lapack before essl, the lapack version
of lapack routines is linked, not the essl version. However
the fft and blas from essl are linked (unless there is a
copy of blas into lapack, which shouldn't be the case).
The resulting loss of performances should be minor.
If fft and blas from essl are not linked, the loss of
performances is much larger.

Final clarification:

-D__ESSL means that the fft routines of essl are used, and
that the calls of some lapack routines follow the essl syntax,
not the lapack syntax;

-D__LINUX_ESSL means that the fft routines of essl are used,
and that the calls of lapack routines follow the lapack syntax.

In all cases, it is convenient to link essl before lapack (essl does
not contain all lapack routines, just a subset, so not linking lapack
may result in missing symbols). If the lapack replacements in essl
do not follow the lapack syntax (IBM SP machines, typically),
-D__ESSL should be used. If they follow the lapack syntax, or if
they do not contain lapack replacements (IBM BlueGene and other
strange IBM machines), -D__LINUX_ESSL should be used.

Complicated? blame the geniuses who wrote lapack replacements
with the same names but called in a different way

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 i.kirker at ucl.ac.uk  Wed Jul 27 23:00:39 2011
From: i.kirker at ucl.ac.uk (Ian Kirker)
Date: Wed, 27 Jul 2011 22:00:39 +0100
Subject: [Pw_forum] allocate_radial_grid error: mesh>ndmx
Message-ID: <1311800439.3446.42.camel@OptiPlex>

On Wed, Jul 27, 2011, at 10:45, Amandeep Kaur <ackaur at ucdavis.edu>
wrote:
> Your mesh size should not exceed ndmx which is probably 3500. I am not
> sure about the exact number. Check the file radial_grids.f90 in 
> the Module directory for the size of ndmx.

On Wed, Jul 27, 2011 at 19:53, Paulo Giannozzi <> wrote: 

>        ndmx=3500     ! the maximum mesh size
>
> Just increase it and recompile. Moving to dynamical allocation was  
> not worth the effort.


Thank you for the help: I set it up to 10000, recompiled, and now the
calculation seems to be running happily.

-Ian Kirker.



From trambui at u.boisestate.edu  Wed Jul 27 23:34:38 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Wed, 27 Jul 2011 15:34:38 -0600
Subject: [Pw_forum] occupancy of the state from PDOS calculation
In-Reply-To: <9A14AA32-CD75-4ABC-B672-6CCBACCB7BA5@sissa.it>
References: <CANzxBn8TgpnptyLPSTnTZOq2v57aa1NNkX1qXGwSgsQ-Uj+VpQ@mail.gmail.com>
	<9A14AA32-CD75-4ABC-B672-6CCBACCB7BA5@sissa.it>
Message-ID: <CANzxBn_O19rHeEUFbuFL5RD-o=_uw2jC7tmmP8A4sV3Cnb2q5w@mail.gmail.com>

Dear Gabriele,
    Sorry for the unclear question. So let say if I found a "p" state from
the pdos calculation of my interstitial defected cell. Is it possible to
find the occupancy of that "p state"?

Regards,
Tram


On Tue, Jul 26, 2011 at 2:01 AM, Gabriele Sclauzero <sclauzer at sissa.it>wrote:

>
>  Il giorno 25/lug/2011, alle ore 21.00, Tram Bui ha scritto:
>
> Dear Everyone,
>     From the PDOS calculation (projwfc.x), can we find the occupancy of the
> state?
>
>
> Which state?
>
>  Also, can we run for ionization energy calculation from pdos?
>
>
> Never heard so. To compute ionization energies you need energies, not pdos.
>
>
> GS
>
>
> Regards,
>
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *   PH H2 462, Station 3, CH-1015 Lausanne*
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From lorenzo.paulatto at impmc.upmc.fr  Thu Jul 28 00:56:12 2011
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 28 Jul 2011 00:56:12 +0200
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <4E2FBD98.4050006@chemie.uni-halle.de>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E2F1616.8080905@chemie.uni-halle.de>
	<0FA242DB-AA44-4B5C-BA79-992927CEBB5A@ihpc.a-star.edu.sg>
	<4E2FBD98.4050006@chemie.uni-halle.de>
Message-ID: <op.vzavbyds5jfbqb@paulax>

In data 27 luglio 2011 alle ore 09:26:16, Guntram Schmidt  
<guntram.schmidt at chemie.uni-halle.de> ha scritto:
> how could I confirm this?

You have to check the compiler's manual, it will *probably* say that when  
you are loading symbols (e.g. subroutines, functions) with the same name  
the *last* one to be loaded will be used.

> Or is essl mainly used to improve lapack?

it contains an optimized (for ibm) implementation of lapack, and fftw as  
well, if I remember correctly.



-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From trambui at u.boisestate.edu  Thu Jul 28 01:07:36 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Wed, 27 Jul 2011 17:07:36 -0600
Subject: [Pw_forum] the issues with density of state vs. energy plot
Message-ID: <CANzxBn-gybz-XNy6tA8Ekc7G56um3FT7YkEjLZaWq0LaPwdR8g@mail.gmail.com>

Dear Everyone,
      I have done the DOS calculation for a bulk 3C-SiC (zinc-blend). and I
found the Fermi energy (Ef) level is =10.6381 (eV). so I plot the DOS vs.
Energy (eV) for my bulk system and also substract the energy to the Ef in
order to have Ef=0 at the top of the valence band. But the plot turned out
to be different. The top of the valence band is below 0. I have attached
some files here. Would please let me know what I might have done wrong in my
input? or what could have been wrong in my plot?

Best Regards,

Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From zhaohscas at yahoo.com.cn  Thu Jul 28 01:55:06 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Wed, 27 Jul 2011 19:55:06 -0400
Subject: [Pw_forum] Using a big box model to calculating the energy of
	isolated atom.
Message-ID: <4E30A55A.9080100@yahoo.com.cn>

Hi all,

I've learned that when using the a large-cell ( i.e., a big box ) to 
calculate the energy of isolated atom, it should be done without 
symmetry.   But I'm not sure what's the meaning of the  "without 
symmetry"  here and how to ensure this when we using a a big box model 
for this purpose.  Any hints on this issue?

Regards
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From karandeepster at gmail.com  Thu Jul 28 07:14:39 2011
From: karandeepster at gmail.com (karan deep)
Date: Thu, 28 Jul 2011 10:44:39 +0530
Subject: [Pw_forum] Confusion in choosing rlderiv
Message-ID: <CA+PV1XD5KjippU_msAwUD9sdshw6dqAH_20E2anuRfWxRf+UCw@mail.gmail.com>

Thanks sir
 sorry for late reply

>>  it is not a strict rule, as long as rd is not much smaller than rc

can u provide precisely  the amount of deviation

Karandeep
Research Scholar
Physics Department,
IIT,  Delhi
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From parwana.habibi at cea.fr  Thu Jul 28 08:52:39 2011
From: parwana.habibi at cea.fr (HABIBI Parwana)
Date: Thu, 28 Jul 2011 08:52:39 +0200
Subject: [Pw_forum] question about LDOS calculation within boxes using pp.x
References: <FEDCEEA1C7E5C14283E6AAE20D5DBB5C0248955F@DIODON.extra.cea.fr>
Message-ID: <FEDCEEA1C7E5C14283E6AAE20D5DBB5C02489562@DIODON.extra.cea.fr>

Dear QE users,

I have been trying to use pp.x on a Cr(001) slab, and I would like to calculate PDOS in a box above de surface.
As a matter of fact, I would like to see the decrease of the wavefunctions in the vacuum, by analysing the PDOS in boxes at different heights.
After a calculation on small boxes, I would like to have, now, an average type box, on the whole surface, so let's say a pavement-like box.

After a pp.x regular PDOS calculation, I have noticed that the segmentation along x and y direction is 30, I thought that regarding this information, I could take a box with a width of 30 on x and y direction for another pp.x calculation with the boxes to get the big box I need.

Hence, pp.x generates a .xsf file for visualizing the boxes. When I would calculate it with a small box (width=2 on x and y directions, ie irmin(1)=1, irmax(1)=3 in the pp.x input file), I could see the box with xcrysden. However, using the big values (30) for my boxes boundaries, I cannot visualize them. But I still get a result about ldos in the boxes.

My questions are the following : how can I be sure that the ldos calculation are actually done within my big boxes boundaries? Is it correct to use that big segmentation in the first place?

I've included the pp.x box input.

Thank you,


Parwana Habibi
PhD student
CEA-Saclay
DSM/IRAMIS/SPCSI/LNOSC
France
 




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From gabriele.sclauzero at epfl.ch  Thu Jul 28 10:10:11 2011
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Thu, 28 Jul 2011 10:10:11 +0200
Subject: [Pw_forum] the issues with density of state vs. energy plot
In-Reply-To: <CANzxBn-gybz-XNy6tA8Ekc7G56um3FT7YkEjLZaWq0LaPwdR8g@mail.gmail.com>
References: <CANzxBn-gybz-XNy6tA8Ekc7G56um3FT7YkEjLZaWq0LaPwdR8g@mail.gmail.com>
Message-ID: <C0632B95-7246-40D3-8981-94EC7CFB8BA8@epfl.ch>


Il giorno 28/lug/2011, alle ore 01.07, Tram Bui ha scritto:

> Dear Everyone,
>       I have done the DOS calculation for a bulk 3C-SiC (zinc-blend). and I found the Fermi energy (Ef) level is =10.6381 (eV).

3C-SiC is a semiconductor, thus speaking of Fermi Energy in this case does not make much sense because there is a bandgap. If for some reason you want to use smearing, then Ef is used and computed in the calculation. Ef should fall somewhere in the gap, not necessarily at the top of the valence band. In practice it could fall either at the top of the valence band or at the bottom of the conduction band, depending on the value of degauss and on the accuracy of the k-point sampling. In either case, you shouldn't attach much importance to it in the case of an insulator (unless it falls in some other place, then your calculation might have some troubles...).

> so I plot the DOS vs. Energy (eV) for my bulk system and also substract the energy to the Ef in order to have Ef=0 at the top of the valence band. But the plot turned out to be different. The top of the valence band is below 0. I have attached some files here. Would please let me know what I might have done wrong in my input? or what could have been wrong in my plot?

Your DOS looks perfectly reasonable to me. You may need to improve the BZ sampling or reduce the smearing used to plot the DOS. Better would be using the tetrahedra method (see used guide).

Regards,


GS

> 
> Best Regards,
>  
> Tram Bui
> 
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
> 
> <nscf.in><dos.in><sic-b.dos><plotdos.pdf>_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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







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From gabriele.sclauzero at epfl.ch  Thu Jul 28 10:12:56 2011
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Thu, 28 Jul 2011 10:12:56 +0200
Subject: [Pw_forum] Using a big box model to calculating the energy of
	isolated atom.
In-Reply-To: <4E30A55A.9080100@yahoo.com.cn>
References: <4E30A55A.9080100@yahoo.com.cn>
Message-ID: <4F3F69C4-E8A0-4386-B2AA-8A4FD2FEA531@epfl.ch>


Il giorno 28/lug/2011, alle ore 01.55, Hongsheng Zhao ha scritto:

> Hi all,
> 
> I've learned that when using the a large-cell ( i.e., a big box ) to 
> calculate the energy of isolated atom, it should be done without 
> symmetry.   But I'm not sure what's the meaning of the  "without 
> symmetry"  here and how to ensure this when we using a a big box model 
> for this purpose.  Any hints on this issue?

This is a FAQ on this forum: have you spent some time browsing the archives?

OK, I'll give you a hint: "nosym"... but use it with care!

HTH

GS

> 
> Regards
> -- 
> Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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







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From gabriele.sclauzero at epfl.ch  Thu Jul 28 10:30:23 2011
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Thu, 28 Jul 2011 10:30:23 +0200
Subject: [Pw_forum] occupancy of the state from PDOS calculation
In-Reply-To: <CANzxBn_O19rHeEUFbuFL5RD-o=_uw2jC7tmmP8A4sV3Cnb2q5w@mail.gmail.com>
References: <CANzxBn8TgpnptyLPSTnTZOq2v57aa1NNkX1qXGwSgsQ-Uj+VpQ@mail.gmail.com>
	<9A14AA32-CD75-4ABC-B672-6CCBACCB7BA5@sissa.it>
	<CANzxBn_O19rHeEUFbuFL5RD-o=_uw2jC7tmmP8A4sV3Cnb2q5w@mail.gmail.com>
Message-ID: <71FA7AD8-44A2-45D9-881A-002B4435BE6F@epfl.ch>



Il giorno 27/lug/2011, alle ore 23.34, Tram Bui ha scritto:

> Dear Gabriele,
>     Sorry for the unclear question. So let say if I found a "p" state from the pdos calculation of my interstitial defected cell.

Your question is still not completely clear to me. How can you speak of "p" state when the atom is in the solid. I guess that the p states could mix with s,d,... states, unless symmetry forbids it. Also, you should be sure that the state is localized on the interstitial.

> Is it possible to find the occupancy of that "p state"?

In principle you could just try to integrate the corresponding peak of the PDOS up to the Fermi energy. But I'm not sure this will give what you have in mind (which I cannot know, by the way).

I guess it would be easier and more precise by using Wannier functions, but I've got no experience with that technique so far.


GS


>  
> Regards,
> Tram
> 
>  
> On Tue, Jul 26, 2011 at 2:01 AM, Gabriele Sclauzero <sclauzer at sissa.it> wrote:
> 
> Il giorno 25/lug/2011, alle ore 21.00, Tram Bui ha scritto:
> 
>> Dear Everyone,
>>     From the PDOS calculation (projwfc.x), can we find the occupancy of the state?
> 
> Which state?
> 
>> Also, can we run for ionization energy calculation from pdos?
> 
> Never heard so. To compute ionization energies you need energies, not pdos.
> 
> 
> GS
> 
>> 
>> Regards,
>> 
>> Tram Bui
>> 
>> M.S. Materials Science & Engineering
>> trambui at u.boisestate.edu
>> 
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>    PH H2 462, Station 3, CH-1015 Lausanne
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> 
> -- 
> Tram Bui
> 
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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







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From pnyawere at gmail.com  Thu Jul 28 10:38:33 2011
From: pnyawere at gmail.com (Phillip Nyawere)
Date: Thu, 28 Jul 2011 10:38:33 +0200
Subject: [Pw_forum] Using a big box model to calculating the energy of
 isolated atom.
In-Reply-To: <4F3F69C4-E8A0-4386-B2AA-8A4FD2FEA531@epfl.ch>
References: <4E30A55A.9080100@yahoo.com.cn>
	<4F3F69C4-E8A0-4386-B2AA-8A4FD2FEA531@epfl.ch>
Message-ID: <CAB-NT9LrTqrcsbori8zAvqEwEaUVgSmtOH=kTjrewON1CDKAnw@mail.gmail.com>

To implement no symmetry use
nosym=.true. at the $system

On Thu, Jul 28, 2011 at 10:12 AM, Gabriele Sclauzero <
gabriele.sclauzero at epfl.ch> wrote:

>
> Il giorno 28/lug/2011, alle ore 01.55, Hongsheng Zhao ha scritto:
>
> Hi all,
>
> I've learned that when using the a large-cell ( i.e., a big box ) to
> calculate the energy of isolated atom, it should be done without
> symmetry.   But I'm not sure what's the meaning of the  "without
> symmetry"  here and how to ensure this when we using a a big box model
> for this purpose.  Any hints on this issue?
>
>
> This is a FAQ on this forum: have you spent some time browsing the
> archives?
>
> OK, I'll give you a hint: "nosym"... but use it with care!
>
> HTH
>
> GS
>
>
> Regards
> --
> Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *   PH H2 462, Station 3, CH-1015 Lausanne*
>
>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Phillip W. Otieno Nyawere,
The Abdus Salam International Center for Theoretical Physics,
Enrico Fermi Building Associate Office 18,
Strada Costiera 11,
34014 Trieste, Italy
Tel +393895378328, or +39 040 2240 567
pnyawere at gmail.com, pnyawere at ictp.it, <potieno at kabarak.ac.ke>

God raises the meek from the ground and sits them with Kings.
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From lmartinsamos at gmail.com  Thu Jul 28 12:18:00 2011
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Thu, 28 Jul 2011 12:18:00 +0200
Subject: [Pw_forum] Quantum ESPRESSO v.4.3.2 available for download
Message-ID: <CAGCSmJSnO2jQDMwKzWugpOHedDkKMz8PvXUiy1x01Hd7MLQf5Q@mail.gmail.com>

Version 4.3.2 of the Quantum ESPRESSO distribution is available
for download from the website http://www.quantum-espresso.org and
http://www.qe-forge.org. This release fixes several bugs and contains
the following improvements over version 4.3.1:

* A few crystal lattices can be specified using the traditional
  crystallography parameter (labelled with negative ibrav values)
* A few extensions to PP format converters, conversion to UPF v.2
* C09 GGA Exchange functional, courtesy of Ikutaro Hamada

For a list of bug fixes, see file Doc/release-notes.

Everybody who is using the Quantum ESPRESSO distribution is encouraged
to upgrade and to report problems to the mailing list.

The Quantum ESPRESSO group
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From eyvaz_isaev at yahoo.com  Thu Jul 28 13:47:25 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 28 Jul 2011 04:47:25 -0700 (PDT)
Subject: [Pw_forum] Pw_forum Digest, Vol 49, Issue 68
In-Reply-To: <1311665984.92529.YahooMailClassic@web65413.mail.ac4.yahoo.com>
References: <mailman.14526.1311664803.1814.pw_forum@pwscf.org>
	<1311665984.92529.YahooMailClassic@web65413.mail.ac4.yahoo.com>
Message-ID: <1311853645.75142.YahooMailNeo@web65716.mail.ac4.yahoo.com>

Dear Zafar,

I am happy that you got QHA compiled. And thanks Gao, too.

Please do not use a Digest for Subject, use more appropriate one.


Bests,
Eyvaz

?
-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


________________________________
From: zafar rasheed <zafartariq2003 at yahoo.com>
To: pw_forum at pwscf.org
Sent: Tuesday, July 26, 2011 11:39 AM
Subject: Re: [Pw_forum] Pw_forum Digest, Vol 49, Issue 68


Dear GAO Zhe

Thanks for the help. I apply some changes in FFFlags and FC and compiles succesfully. 

Muhammad Zafar
PhD Scholar
Department of Physics
The Islamia University of Bahawalpur,Pakistan

--- On Tue, 7/26/11, 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 49, Issue 68
>To: pw_forum at pwscf.org
>Date: Tuesday, July 26, 2011, 12:20 PM
>
>
>Send Pw_forum mailing list submissions to
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>
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>Today's Topics:
>
>???1. Re: Warnings And Errors in Compilation of QHA...... (GAO Zhe)
>???2. occupancy of the state from PDOS calculation (Tram Bui)
>???3. (no subject) (Vi Vo)
>???4. (no subject) (bhabya sahoo)
>???5. Re: (no subject) (bhabya sahoo)
>???6. Re: (no subject) (Lorenzo Paulatto)
>???7. Re: (no subject) (Lorenzo
 Paulatto)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Mon, 25 Jul 2011 20:07:37 +0800 (CST)
>From: "GAO Zhe" <flux_ray12 at 163.com>
>Subject: Re: [Pw_forum] Warnings And Errors in Compilation of
>??? QHA......
>To: "PWSCF Forum" <pw_forum at pwscf.org>
>Message-ID: <3f7402f9.f9b4.13161317a25.Coremail.flux_ray12 at 163.com>
>Content-Type: text/plain; charset="gbk"
>
>I think your problem is caused by the lack of libraries for compiling. You may not run the binary executable files before solving dependent problem, even others copy
 binary files to you.
>Please check whether you have libm.so.? in your /usr/lib (32bit) or /usr/lib64 (64bit), or you can use command "yum install libm.so.*"(run it as root) in terminate.
>
>--
>GAO Zhe
>CMC Lab, MSE, SNU, Seoul, S.Korea
>
>
>At 2011-07-25 19:05:33,"zafar rasheed" <zafartariq2003 at yahoo.com> wrote:
>
>Dear All
>
>I try best to compile QHA but can not create *.x files. Now I have fedora core 14. Will any body help me. I think that QHA has some deleted routines. I have such type of warnings. If Some one has complete QHA then please send it to me. Thanking in anticipation
>
>
>[zafar at localhost QHA]$ ./Compile
>gfortran -O3 -ffast-math -fno-f2c -c? tetra.f
>gfortran -O3 -ffast-math -fno-f2c -c? k_brillouin.f
>gfortran -O3 -ffast-math -fno-f2c -c? generate_tetra.f
>gfortran -O3 -ffast-math
 -fno-f2c -c? det3.f
>gfortran -O3 -ffast-math -fno-f2c -c? det4.f
>gfortran -static -o tetra.x tetra.o k_brillouin.o generate_tetra.o? det3.o det4.o? 
>/usr/bin/ld: cannot find -lm
>/usr/bin/ld: cannot find -lc
>collect2: ld returned 1 exit status
>make: *** [tetra] Error 1
>gfortran -O3 -ffast-math -fno-f2c? -c? Debye.f90
>Debye.f90:144.8:
>
>? ???do T = T_low_start, T_low, T_low_delta
>? ? ? ? 1
>Warning: Deleted feature: Loop variable at (1) must be integer
>Debye.f90:144.11:
>
>? ???do T = T_low_start, T_low, T_low_delta
>? ? ? ? ???1
>Warning: Deleted feature: Start expression in DO loop at (1) must be integer
>Debye.f90:144.24:
>
>? ???do T = T_low_start, T_low, T_low_delta
>? ? ? ? ? ? ? ? ? ? ? ?
 1
>Warning: Deleted feature: End expression in DO loop at (1) must be integer
>Debye.f90:144.31:
>
>? ???do T = T_low_start, T_low, T_low_delta
>? ? ? ? ? ? ? ? ? ? ? ? ? ? ???1
>Warning: Deleted feature: Step expression in DO loop at (1) must be integer
>Debye.f90:177.4:
>
>do T = T_low+5, T_high, T_high_delta
>? ? 1
>Warning: Deleted feature: Loop variable at (1) must be integer
>Debye.f90:177.7:
>
>do T = T_low+5, T_high, T_high_delta
>? ? ???1
>Warning: Deleted feature: Start expression in DO loop at (1) must be integer
>Debye.f90:177.16:
>
>do T = T_low+5, T_high, T_high_delta
>? ? ? ? ? ? ? ? 1
>Warning: Deleted feature: End expression in DO loop at (1) must be integer
>Debye.f90:177.24:
>
>do T = T_low+5, T_high,
 T_high_delta
>? ? ? ? ? ? ? ? ? ? ? ? 1
>Warning: Deleted feature: Step expression in DO loop at (1) must be integer
>gfortran -O3 -ffast-math -fno-f2c -c? Debye_T.f
>gfortran -O3 -ffast-math -fno-f2c -c? debye3.f
>gfortran -O3 -ffast-math -fno-f2c -c? cheval.f
>gfortran -O3 -ffast-math -fno-f2c -c? d1mach.f
>gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o
>/usr/bin/ld: cannot find -lm
>/usr/bin/ld: cannot find -lc
>collect2: ld returned 1 exit status
>make: *** [Debye_x] Error 1
>gfortran -O3 -ffast-math -fno-f2c -c? Mean_square_displacement.f90
>Mean_square_displacement.f90:162.7:
>
>? ? do T=T_start,T_end,T_delta
>? ? ???1
>Warning: Deleted feature: Loop variable at (1) must be integer
>gfortran -static -o Mean_square_displacement.x Mean_square_displacement.o? 
>/usr/bin/ld: cannot find -lm
>/usr/bin/ld: cannot find -lc
>collect2: ld returned 1 exit status
>make: *** [MSD] Error 1
>ln: creating symbolic link `tetra.x': File exists
>ln: creating symbolic link `phonon_dos.x': File exists
>ln: creating symbolic link `Debye.x': File exists
>ln: creating symbolic link `Atom_projected_properties.x': File exists
>ln: creating symbolic link `F_QHA.x': File exists
>ln: creating symbolic link `Ghost_DOS.x': File exists
>ln: creating symbolic link `Partial_phonon_DOS.x': File exists
>ln: creating symbolic link `Mean_square_displacement.x': File exists
>ln: creating symbolic link `atom_info.x': File exists
>
>Muhammad Zafar
>PhD Scholar
>Department of Physics
>The Islamia University of Bahawalpur,Pakistan
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>------------------------------
>
>Message: 2
>Date: Mon, 25 Jul 2011 13:00:38 -0600
>From: Tram Bui <trambui at u.boisestate.edu>
>Subject: [Pw_forum] occupancy of the state from PDOS calculation
>To: PWSCF Forum <pw_forum at pwscf.org>
>Message-ID:
>??? <CANzxBn8TgpnptyLPSTnTZOq2v57aa1NNkX1qXGwSgsQ-Uj+VpQ at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Dear Everyone,
>? ? From the PDOS
 calculation (projwfc.x), can we find the occupancy of the
>state? Also, can we run for ionization energy calculation from pdos?
>
>Regards,
>
>Tram Bui
>
>M.S. Materials Science & Engineering
>trambui at u.boisestate.edu
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>
>------------------------------
>
>Message: 3
>Date: Mon, 25 Jul 2011 16:31:57 -0700 (PDT)
>From: Vi Vo <vovi47 at yahoo.com>
>Subject: [Pw_forum] (no subject)
>To: pwscf <pw_forum at pwscf.org>
>Message-ID:
>??? <1311636717.59460.YahooMailRC at web114512.mail.gq1.yahoo.com>
>Content-Type: text/plain; charset="us-ascii"
>
>Dear All,
>
>I was doing a test calculation for CuO and got a message: 
>"? ???WARNING: atomic wfc #? 6 for atom type 1 has zero norm
>? ???WARNING: atomic wfc #? 6 for atom type 2 has zero norm
>? ???WARNING: atomic wfc #? 2 for atom type 3 has zero norm
>? ???WARNING: atomic wfc #? 4 for atom type 3 has zero norm
>? ???WARNING: atomic wfc #? 5 for atom type 3 has zero norm
>
>The norm of the wfc is zero.? Why does it
 happen?? Does it depend on the? pseudo 
>potential used?? Can a gipaw pp be used with pw.x? (I download the pp from QE 
>pps).
>
>Thank you very much in advance,
>
>Vi 
>University of Houston
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>------------------------------
>
>Message: 4
>Date: Tue, 26 Jul 2011 12:23:17 +0530
>From: bhabya sahoo <bdslipun at gmail.com>
>Subject: [Pw_forum] (no subject)
>To: PWSCF Forum <pw_forum at pwscf.org>
>Message-ID:
>???
 <CAJVAAvDJU=6q8QZk4g2cyOH=q2akf=CrpKQO5CyZgPuz9Yeajg at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>why xspectra.x is not coming in bin directory of quantum espresso code
>but others are compiling fine .
>version 4.3 of quantum espresso code
>sothat the example is not running
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
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>
>
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>
>
>
>
>
>bd sahoo reserch scolar
>mumbai
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>------------------------------
>
>Message: 5
>Date: Tue, 26 Jul 2011
 12:35:43 +0530
>From: bhabya sahoo <bdslipun at gmail.com>
>Subject: Re: [Pw_forum] (no subject)
>To: PWSCF Forum <pw_forum at pwscf.org>
>Message-ID:
>??? <CAJVAAvByLoBjLg32mgu64tw_shrbFSU3fBe7RCxBWvEjryX=Sw at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>On Tue, Jul 26, 2011 at 12:23 PM, bhabya sahoo <bdslipun at gmail.com> wrote:
>
>> why xspectra.x is not coming in bin directory of quantum espresso code
>> but others are compiling fine .
>> version 4.3 of quantum espresso code
>> sothat the example is not
 running
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> bd sahoo reserch scolar
>> mumbai
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
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>>
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>------------------------------
>
>Message: 6
>Date: Tue, 26 Jul 2011 09:16:40 +0200
>From: "Lorenzo Paulatto" <lorenzo.paulatto at impmc.upmc.fr>
>Subject: Re: [Pw_forum] (no subject)
>To: "PWSCF Forum" <pw_forum at pwscf.org>
>Message-ID: <op.vy7s52ar5jfbqb at paulax>
>Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes
>
>In data 26 luglio 2011 alle ore 01:31:57, Vi Vo <vovi47 at yahoo.com> ha? 
>scritto:
>> I was doing a test calculation for CuO and got a message:
>> "? ???WARNING: atomic wfc #? 6 for atom type 1 has zero norm
>>? ? ? WARNING: atomic wfc #? 6 for
 atom type 2 has zero norm
>>? ? ? WARNING: atomic wfc #? 2 for atom type 3 has zero norm
>>? ? ? WARNING: atomic wfc #? 4 for atom type 3 has zero norm
>>? ? ? WARNING: atomic wfc #? 5 for atom type 3 has zero norm
>>
>> The norm of the wfc is zero.? Why does it happen?? Does it depend on? 
>> the? pseudo
>
>It is not the wfc, but the atomic wfc. Unless you are doing an lda+U? 
>calculation yo ucan safely ignore the warning.
>
>best regards
>
>-- 
>Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
>phone: +33 (0)1 44275 084 / skype: paulatz
>www:???http://www-int.impmc.upmc.fr/~paulatto/
>mail:? 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex
 05
>
>
>------------------------------
>
>Message: 7
>Date: Tue, 26 Jul 2011 09:19:09 +0200
>From: "Lorenzo Paulatto" <lorenzo.paulatto at impmc.upmc.fr>
>Subject: Re: [Pw_forum] (no subject)
>To: "PWSCF Forum" <pw_forum at pwscf.org>
>Message-ID: <op.vy7s97uq5jfbqb at paulax>
>Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes
>
>In data 26 luglio 2011 alle ore 08:53:17, bhabya sahoo? 
><bdslipun at gmail.com> ha scritto:
>> why xspectra.x is not coming in bin directory of quantum espresso code
>> but others are compiling fine .
>> version 4.3 of quantum espresso code
>> sothat the example is not
 running
>
>Xspectra is not included in "make all", you need to type explicitly "make? 
>xspectra" in the QE root directory in order to compile it.
>
>best regards
>
>
>-- 
>Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
>phone: +33 (0)1 44275 084 / skype: paulatz
>www:???http://www-int.impmc.upmc.fr/~paulatto/
>mail:? 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
>
>
>------------------------------
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>End of Pw_forum Digest, Vol 49, Issue
 68
>****************************************
> 
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From eyvaz_isaev at yahoo.com  Thu Jul 28 14:49:28 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 28 Jul 2011 05:49:28 -0700 (PDT)
Subject: [Pw_forum] the issues with density of state vs. energy plot
In-Reply-To: <CANzxBn-gybz-XNy6tA8Ekc7G56um3FT7YkEjLZaWq0LaPwdR8g@mail.gmail.com>
References: <CANzxBn-gybz-XNy6tA8Ekc7G56um3FT7YkEjLZaWq0LaPwdR8g@mail.gmail.com>
Message-ID: <1311857368.88398.YahooMailNeo@web65716.mail.ac4.yahoo.com>

Hi,

You deal with a semiconductor with a band gap. In this case the Fermi level can be placed in any place inside the gap. The correct way in this case is taking the highest occupied state as the Fermi level. Calculate number of valence electrons in your system and keep in mind the Pauli excluding principle.? ??

Bests,
Eyvaz.

?

-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


________________________________
From: Tram Bui <trambui at u.boisestate.edu>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Thursday, July 28, 2011 3:07 AM
Subject: [Pw_forum] the issues with density of state vs. energy plot


Dear Everyone,
????? I have done the DOS calculation for a bulk 3C-SiC (zinc-blend). and I found the Fermi energy (Ef) level is =10.6381 (eV). so I plot the DOS vs. Energy (eV) for my bulk system and also substract the energy to the Ef in order to have Ef=0 at the top of the valence band. But the plot turned out to be different. The top of the valence band is below 0. I have attached some files here. Would please let me know what I might have done wrong in my input? or what could have been wrong in my plot?

Best Regards,
?
Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu


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From eyvaz_isaev at yahoo.com  Thu Jul 28 14:59:08 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 28 Jul 2011 05:59:08 -0700 (PDT)
Subject: [Pw_forum] Can pwscf do the Superconductivity study?
In-Reply-To: <4E2BFA0F.6000101@yahoo.com.cn>
References: <4E2BFA0F.6000101@yahoo.com.cn>
Message-ID: <1311857948.10988.YahooMailNeo@web65716.mail.ac4.yahoo.com>

You can calculate electron-phonon coupling constant using ph.x (first you should do a scf calculation), then evaluate T_c by means of the McMillan or Allen-Dynes type equation. 

?
You can try find the paper? "Electron-phonon coupling in metallic solids from density functional theory"? by Shyamal K. Bose and Jens Kortus.? 


Good luck,
Eyvaz.


-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


________________________________
From: Hongsheng Zhao <zhaohscas at yahoo.com.cn>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Sunday, July 24, 2011 2:55 PM
Subject: [Pw_forum] Can pwscf do the Superconductivity study?

Hi all,

I want to know can pwscf be used to? study Superconductivity, say, based 
on bcs theory?

Regards
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China
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From eyvaz_isaev at yahoo.com  Thu Jul 28 15:21:37 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 28 Jul 2011 06:21:37 -0700 (PDT)
Subject: [Pw_forum] PHONON error with elph=.true. and trans=.false.
In-Reply-To: <1311577781577.6843.postech@postech.ac.kr>
References: <1311577781577.6843.postech@postech.ac.kr>
Message-ID: <1311859297.37988.YahooMailNeo@web65712.mail.ac4.yahoo.com>

As far as I know (may be obsolete info) "npool" was not implemented for electron-phonon calculations.

Bests,
Eyvaz.

?
-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


________________________________
From: Jeonghun Yun <yjh9898 at postech.ac.kr>
To: pw_forum at pwscf.org
Sent: Monday, July 25, 2011 11:09 AM
Subject: [Pw_forum] PHONON error with elph=.true. and trans=.false.


 
I am trying to calculate the electron-phonon coupling with PHONON 4.2.1.
I modified the program to work with elph=.true. and trans=.false., referring PW_forum. (i.e I fixed the bug that known)
The previous PHONON calculation for mode frequencies were done earlier, but I found the problem.

The input is written below:
---------------------------------------------------

biGr_Ca

&inputph
? ? amass(1)=40.078
? ? amass(2)=12.011
? ? outdir='./'
? ? iverbosity=0
? ? prefix='CaGr131scf'
? ? niter_ph=100
? ? tr2_ph=1e-12
? ? fildyn='131.dyn'
? ? fildrho='rhoresp'
? ? fildvscf='potvar131'
? ? trans=.false.
? ? ldisp=.true.
? ? elph=.true.
? ? nq1=6, nq2=6, nq3=1
/
----------------------------------------------------

AND, I've found the problem: The program stops?WITHOUT error message, just before the calculation.
-------------------------------------------------------------------------
.........
? ? ?site n. ?atom ? ? ?mass ? ? ? ? ? positions (a_0 units)
? ? ? ? 1 ? ? ? ?Ca ?40.0780 ? tau( 1) = ( ? ?0.00000 ? ?0.00000 ? ?0.00000 ?)

? ? ?Computing dynamical matrix for
? ? ? ? ? ? ? ? ? ? q = ( ? 0.0000000 ? 0.0000000 ? 0.0000000 )

? ? ?25 Sym.Ops. (with q -> -q+G )


? ? ?G cutoff = ?553.0542 ?( ?14740 G-vectors) ? ? FFT grid: ( 48, 48,240)
? ? ?G cutoff = ?201.1106 ?( ? 3234 G-vectors) ?smooth grid: ( 30, 30,144)
? ? ?number of k points= ? ?19 ?gaussian broad. (Ry)= ?0.0300 ? ? ngauss = ? 1

? ? ?PseudoPot. # 1 for Ca read from file Ca.pbe-nsp-van.UPF
? ? ?Pseudo is Ultrasoft + core correction, Zval = 10.0
? ? ?Generated by new atomic code, or converted to UPF format
? ? ?Using radial grid of ?845 points, ?6 beta functions with:
? ? ? ? ? ? ? ? l(1) = ? 0
? ? ? ? ? ? ? ? l(2) = ? 0
? ? ? ? ? ? ? ? l(3) = ? 1
? ? ? ? ? ? ? ? l(4) = ? 1
? ? ? ? ? ? ? ? l(5) = ? 2
? ? ? ? ? ? ? ? l(6) = ? 2
? ? ?Q(r) pseudized with ?6 coefficients, ?rinner = ? ?1.200 ? 1.200 ? 1.200
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?1.200 ? 1.200


? ? ?Atomic displacements:
? ? ?There are ? 2 irreducible representations

? ? ?Representation ? ? 1 ? ? ?2 modes -E_1u To be done

? ? ?Representation ? ? 2 ? ? ?1 modes -A_2u To be done


? ? ?PHONON ? ? ? : ? ? 4.38s CPU time, ? ? ? ?6.23s WALL time

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

Please help me for this unexpected error.

P.S I wonder the trans=.false. calculation with 16 cpus in a pool is compatible with phonon frequency calculation with 64 cpus in 4 pools. The fildvscf is splat in four files...... 
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From joerg.buchwald at iom-leipzig.de  Thu Jul 28 17:04:05 2011
From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald)
Date: Thu, 28 Jul 2011 17:04:05 +0200
Subject: [Pw_forum] strange error with monoclinic structure
Message-ID: <20110728170405.0c0d3902@PC-Mayr-Mitarb6.pc-flexi>

Hi,
to get the shear modulus i performed some simulations with a monoclinic
silicon lattice. I simulated with different angles.
For celldm(4)=0.004 or celldm(4)=0.002 it works, but if i set
celldm(4)=0.003 i get the following error

--
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from davcio : error #        99
     error while reading from file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from davcio : error #        99
     error while reading from file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
--
an here is my input file:
--
&control
    calculation='scf'
    prefix='silicon',
    pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
    outdir = '/home/joerg/scratch',
    tstress=.true.
    disk_io='none'
 /
 &system
    ibrav=  12, celldm(1) =10.334309, celldm(2)=1.0, celldm(3)=1.00,
     celldm(4)=0.003, nat=  8, ntyp= 1, ecutwfc = 50.0,ecutrho=500.0
 /
 &electrons
    diagonalization='cg'
    mixing_mode='plain'
 /
 &ions
 /
 &cell
 /
ATOMIC_SPECIES
 Si  28.086  Si.pbe-n-van.UPF
ATOMIC_POSITIONS
 Si 0.00 0.00 0.00
 Si 0.25 0.25 0.25
 Si 0.50 0.50 0.00
 Si 0.75 0.75 0.25
 Si 0.50 0.00 0.50
 Si 0.75 0.25 0.75
 Si 0.00 0.50 0.50
 Si 0.25 0.75 0.75
K_POINTS automatic
 15 15 15 0 0 0
--
Do you have any idea what the problem could be?
Thx,
J?rg 

--
J?rg Buchwald
Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
Permoserstrasse 15
04318 Leipzig
GERMANY

From giannozz at democritos.it  Thu Jul 28 17:30:44 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 28 Jul 2011 17:30:44 +0200
Subject: [Pw_forum] What files are needed when pw.x restarts? In what
	case the *.wfc files are need?
In-Reply-To: <CAKScr_p22KHGBx_SiV1SAZkAP9xcOnLR4ZFm8L7wWv8nHyniFg@mail.gmail.com>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E2F1616.8080905@chemie.uni-halle.de> <4E2F9C6F.9030009@163.com>
	<CAKScr_rju9zXEqtjyu=Q8686xUkcyVup7P+Cmq5Wxh=qiLc+qg@mail.gmail.com>
	<4E2FBE37.3050409@163.com>
	<CAKScr_p22KHGBx_SiV1SAZkAP9xcOnLR4ZFm8L7wWv8nHyniFg@mail.gmail.com>
Message-ID: <CBC4DC5E-EE0C-44B0-8E26-6625B82E9A1D@democritos.it>


On Jul 27, 2011, at 9:41 , Seyed Javad Hashemifar wrote:

> I guess if you set wf_collect=.true. the collection of *.wfc files  
> is done after
> reaching self consistency not after each iteration. Probably, the  
> evc.dat files
> are the collected *.wfc files

I can confirm 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 giannozz at democritos.it  Thu Jul 28 17:33:51 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 28 Jul 2011 17:33:51 +0200
Subject: [Pw_forum] (no subject)
In-Reply-To: <1311708551.91624.YahooMailRC@web114504.mail.gq1.yahoo.com>
References: <1311636717.59460.YahooMailRC@web114512.mail.gq1.yahoo.com>
	<op.vy7s52ar5jfbqb@paulax>
	<1311708551.91624.YahooMailRC@web114504.mail.gq1.yahoo.com>
Message-ID: <4C143759-687E-4E1E-BD84-2F3A9B2D33F4@democritos.it>


On Jul 26, 2011, at 21:29 , Vi Vo wrote:

> In LDA+U calculation I also see these warning, so what will be the  
> risk or unreliability.

there is no risk, as long as bound atomic states are present in the  
PP files.
I guess that the "zero-norm" states that are still present in some PP  
files are
unbound states used uring thr generation of the PP. They do not  
affect the
final results in any way.

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 28 17:38:04 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 28 Jul 2011 17:38:04 +0200
Subject: [Pw_forum] Segmentation fault on relaxed structure in vc-relax
	on QE4.3.1
In-Reply-To: <C44EC6BA-38DF-4536-B0C2-11215367C36E@dipteris.unige.it>
References: <C44EC6BA-38DF-4536-B0C2-11215367C36E@dipteris.unige.it>
Message-ID: <5DCDB2A2-4C90-4B12-BF41-66420303C182@democritos.it>


On Jul 26, 2011, at 13:50 , Marino Vetuschi Zuccolini wrote:

> during the computation of the last SCF cycle *on relaxed structure*
> this segmentation fault error (repeated for each process) happens

a problem in the last step of a variable-cell optimization was fixed
in v.4.3.2. Please file a bug report on qe-forge if still present.

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 zucco at dipteris.unige.it  Thu Jul 28 18:14:52 2011
From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini)
Date: Thu, 28 Jul 2011 18:14:52 +0200
Subject: [Pw_forum] Segmentation fault on relaxed structure in vc-relax
	on QE4.3.1
In-Reply-To: <5DCDB2A2-4C90-4B12-BF41-66420303C182@democritos.it>
References: <C44EC6BA-38DF-4536-B0C2-11215367C36E@dipteris.unige.it>
	<5DCDB2A2-4C90-4B12-BF41-66420303C182@democritos.it>
Message-ID: <D94C979F-FF09-41E5-A72F-03A9963B9EB0@dipteris.unige.it>

I've compiled the 4.3.2 version of QE and the bug it is not present apparently on some tests I did.
I will follow your suggestion if it will still present.

Thank you very much.

m.
On 28 Jul 2011, at 17:38, Paolo Giannozzi wrote:

> 
> On Jul 26, 2011, at 13:50 , Marino Vetuschi Zuccolini wrote:
> 
>> during the computation of the last SCF cycle *on relaxed structure*
>> this segmentation fault error (repeated for each process) happens
> 
> a problem in the last step of a variable-cell optimization was fixed
> in v.4.3.2. Please file a bug report on qe-forge if still present.
> 
> 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



*******************************************************
Marino Vetuschi Zuccolini
zucco at dipteris.unige.it
Researcher / Geochemist
Laboratory of Geochemistry

DIPartimento per lo studio della TErra e delle sue RISorse - Universit?  di Genova
Tel. ++39 010 3538136 Fax. ++39 010 352169
Corso Europa 26, 16132 - Genova - Italy



From eyvaz_isaev at yahoo.com  Thu Jul 28 22:20:15 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 28 Jul 2011 13:20:15 -0700 (PDT)
Subject: [Pw_forum] Question about geometry relaxation
In-Reply-To: <E1Qm2Yw-0007KP-00.djulriya-mail-ru@f90.mail.ru>
References: <E1Qm2Yw-0007KP-00.djulriya-mail-ru@f90.mail.ru>
Message-ID: <1311884415.52633.YahooMailNeo@web65714.mail.ac4.yahoo.com>

Dear Julia,

Welcome to the QE community!

In order to understand that? you are doing something in the right way first you should do simple tests. Download examples files and explore them. 

If you feel? that you understand what you got then you can try more? advanced jobs.

Nevertheless, you can contact me directly, but no guarantee that I will reply immediately.

Bests,
Eyvaz.

?
-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


________________________________
From: ??? ???????? <djulriya at mail.ru>
To: pw_forum at pwscf.org
Sent: Wednesday, July 27, 2011 3:46 PM
Subject: [Pw_forum] Question about geometry relaxation

Dear QE users,

I'm a new user of QE.
Now I try to provide the geometry relaxation of carbon diamond-like structure, but I'm not sure that I'm doing it right.
It would be kind of you, if you advise me what type of optimizer or some parameters which I don't use here should I use to achieve the best results?
Below I will give an example of my input file.

&control
? ? calculation = 'vc-relax'
? ? restart_mode='from_scratch',
? ? prefix='carbon',
? ? tstress = .true.
? ? tprnfor = .true.
? ? pseudo_dir = './',
? ? outdir='./'
wf_collect=.true.,
etot_conv_thr = 1.0D-6,
forc_conv_thr = 1.0D-4,
nstep = 500,

/
&system
? ? ? ? ? ? ? ? ? ?  nosym = .false.,
? ? ? ? ? ? ? ? ? ?  ibrav = 1,
? ? ? ? ? ? ? ? ? ?  celldm(1) = 8.0907,
? ? ? ? ? ? ? ? ? ?  nat = 16,
? ? ? ? ? ? ? ? ? ?  ntyp = 1,
? ? ? ? ? ? ? ? ? ?  occupations = 'smearing',
? ? ? ? ? ?  ecutwfc = 60,
? ? ? ? ? ?  degauss = 0.05,
/
&ELECTRONS
? ? ? ? ? ? ?  diagonalization = 'cg' ,
? ? ? ? ? ? ?  electron_maxstep = 150,
/
&IONS
? ion_dynamics='bfgs',
? pot_extrapolation = "first_order",
/
&CELL
?  cell_dynamics = 'bfgs' ,
?  cell_factor = 1.6,
?  press = 0 ,
?  !cell_dofree = 'xyz',
press_conv_thr = 0.5D-1, 
/
ATOMIC_SPECIES
C? ? 12? ? C.pbe-van_ak.UPF
ATOMIC_POSITIONS crystal
...
K_POINTS automatic 
8 8 8? 0 0 0


Thank you in advice.
Sincerely yours
Julia Filicheva


/First year of master degree study
Moscow Institute of Physics and Technology/
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From chengyu.young at gmail.com  Thu Jul 28 23:03:52 2011
From: chengyu.young at gmail.com (chengyu yang)
Date: Thu, 28 Jul 2011 17:03:52 -0400
Subject: [Pw_forum] Slow calculation of (5,
	5) CNT transmission and complex bands.
Message-ID: <CAOk-W=GMvgBKO3McU5tO2x_eBtCmUM7QsA1EVDzKkWcEeB_9=A@mail.gmail.com>

Dear All,
         I am trying to calculate the complex bands and the transmission of
a (5,5) defectless carbon nanotube using PWCOND.x, however, the calculation
process is very slow and I can see it kind of stopped at the point:  ngper,
shell number =         2809         299.
         My input files are like this:


##################################################################################
scf input file:

&CONTROL
                 calculation = 'scf' ,
                restart_mode = 'from_scratch' ,
                       prefix = '55' ,
 /
 &SYSTEM
                       ibrav = 6,
                   celldm(1) = 21.764541128,celldm(3)=0.213765379
                         nat = 20,
                        ntyp = 1,
                     ecutwfc = 75 ,
 /
 &ELECTRONS
                    conv_thr = 1.0d-8 ,
                 mixing_beta = 0.7 ,
 /
ATOMIC_SPECIES
    C   12.01100  C.pz-vbc.UPF

ATOMIC_POSITIONS angstrom

  C        3.409595     0.000000    -1.231179
  C        3.113484     1.389805    -1.231179
  C        2.758420     2.004110    -0.000000
  C        1.701954     2.954436    -0.000000
  C        1.053623     3.242718    -1.231179
  C       -0.359664     3.390572    -1.231179
  C       -1.053623     3.242718    -0.000000
  C       -2.283903     2.531625    -0.000000
  C       -2.758420     2.004110    -1.231179
  C       -3.335768     0.705684    -1.231179
  C       -3.409595     0.000000    -0.000000
  C       -3.113484    -1.389805    -0.000000
  C       -2.758420    -2.004110    -1.231179
  C       -1.701954    -2.954436    -1.231179
  C       -1.053623    -3.242718     0.000000
  C        0.359664    -3.390572     0.000000
  C        1.053623    -3.242718    -1.231179
  C        2.283903    -2.531625    -1.231179
  C        2.758420    -2.004110     0.000000
  C        3.335768    -0.705684     0.000000




K_POINTS automatic
 1 1 5 0 0 0


###############################################################################

pwcond.in file:


&inputcond
    prefixl='55'
    band_file ='bands.cnt55'
    ikind=0
    energy0=4.d0
    denergy=-0.1d0
    ewind=3.d0
    epsproj=1.d-4
    delgep = 1.d-9
    cutplot = 3.d0
 /
    1
    0.0 0.0 1.0
    5

###########################################################
and the output file:

     GEOMETRY:

     lattice parameter (a_0)   =      21.7645  a.u.
     the volume                =    2203.8697 (a.u.)^3
     the cross section         =     473.6953 (a.u.)^2
     l of the unit cell        =       0.2138 (a_0)
     number of atoms/cell      =           20
     number of atomic types    =            1

     crystal axes: (cart. coord. in units of a_0)
               a(1) = (  1.0000  0.0000  0.0000 )
               a(2) = (  0.0000  1.0000  0.0000 )
               a(3) = (  0.0000  0.0000  0.2138 )


   Cartesian axes

     site n.     atom                  positions (a_0 units)
          1           C   tau(  1)=(  0.2960  0.0000  0.1069  )
          2           C   tau(  2)=(  0.2703  0.1207  0.1069  )
          3           C   tau(  3)=(  0.2395  0.1740  0.2138  )
          4           C   tau(  4)=(  0.1478  0.2565  0.2138  )
          5           C   tau(  5)=(  0.0915  0.2816  0.1069  )
          6           C   tau(  6)=( -0.0312  0.2944  0.1069  )
          7           C   tau(  7)=( -0.0915  0.2816  0.2138  )
          8           C   tau(  8)=( -0.1983  0.2198  0.2138  )
          9           C   tau(  9)=( -0.2395  0.1740  0.1069  )
         10           C   tau( 10)=( -0.2896  0.0613  0.1069  )
         11           C   tau( 11)=( -0.2960  0.0000  0.2138  )
         12           C   tau( 12)=( -0.2703 -0.1207  0.2138  )
         13           C   tau( 13)=( -0.2395 -0.1740  0.1069  )
         14           C   tau( 14)=( -0.1478 -0.2565  0.1069  )
         15           C   tau( 15)=( -0.0915 -0.2816  0.2138  )
         16           C   tau( 16)=(  0.0312 -0.2944  0.2138  )
         17           C   tau( 17)=(  0.0915 -0.2816  0.1069  )
         18           C   tau( 18)=(  0.1983 -0.2198  0.1069  )
         19           C   tau( 19)=(  0.2395 -0.1740  0.2138  )
         20           C   tau( 20)=(  0.2896 -0.0613  0.2138  )

     nr1s                      =          120
     nr2s                      =          120
     nr3s                      =           27
     nrx1s                     =          120
     nrx2s                     =          120
     nrx3s                     =           27
     nr1                       =          120
     nr2                       =          120
     nr3                       =           27
     nrx1                      =          120
     nrx2                      =          120
     nrx3                      =           27

 _______________________________
  Radii of nonlocal spheres:

     type       ibeta     ang. mom.          radius (a_0 units)
          C       1         0                    0.0593
----- General information -----

----- Complex band structure calculation -----

     nrx                       =          120
     nry                       =          120
     nz1                       =           11


     energy0               =         4.0E+00
     denergy               =        -1.0E-01
     nenergy               =          5
     ecut2d                =         7.5E+01
     ewind                 =         3.0E+00
     epsproj               =         1.0E-04


     number of k_|| points=    1
                       cryst. coord.
        k(    1) = (   0.0000000   0.0000000), wk =   1.0000000
----- Information about left lead -----

     nocros                   =           10
     noins                    =           10
     norb                     =           30
     norbf                    =           30
     nrz                      =           27

      iorb      type   ibeta   ang. mom.   m       position (a_0)
        1        1       1        0        1   taunew(   1)=(  0.2395
0.1740  0.0000)
        2        1       1        0        1   taunew(   2)=(  0.1478
0.2565  0.0000)
        3        1       1        0        1   taunew(   3)=( -0.0915
0.2816  0.0000)
        4        1       1        0        1   taunew(   4)=( -0.1983
0.2198  0.0000)
        5        1       1        0        1   taunew(   5)=( -0.2960
0.0000  0.0000)
        6        1       1        0        1   taunew(   6)=( -0.2703
-0.1207  0.0000)
        7        1       1        0        1   taunew(   7)=( -0.0915
-0.2816  0.0000)
        8        1       1        0        1   taunew(   8)=(  0.0312
-0.2944  0.0000)
        9        1       1        0        1   taunew(   9)=(  0.2395
-0.1740  0.0000)
       10        1       1        0        1   taunew(  10)=(  0.2896
-0.0613  0.0000)
       11        1       1        0        1   taunew(  11)=(  0.2960
0.0000  0.1069)
       12        1       1        0        1   taunew(  12)=(  0.2703
0.1207  0.1069)
       13        1       1        0        1   taunew(  13)=(  0.0915
0.2816  0.1069)
       14        1       1        0        1   taunew(  14)=( -0.0312
0.2944  0.1069)
       15        1       1        0        1   taunew(  15)=( -0.2395
0.1740  0.1069)
       16        1       1        0        1   taunew(  16)=( -0.2896
0.0613  0.1069)
       17        1       1        0        1   taunew(  17)=( -0.2395
-0.1740  0.1069)
       18        1       1        0        1   taunew(  18)=( -0.1478
-0.2565  0.1069)
       19        1       1        0        1   taunew(  19)=(  0.0915
-0.2816  0.1069)
       20        1       1        0        1   taunew(  20)=(  0.1983
-0.2198  0.1069)
       21        1       1        0        1   taunew(  21)=(  0.2395
0.1740  0.2138)
       22        1       1        0        1   taunew(  22)=(  0.1478
0.2565  0.2138)
       23        1       1        0        1   taunew(  23)=( -0.0915
0.2816  0.2138)
       24        1       1        0        1   taunew(  24)=( -0.1983
0.2198  0.2138)
       25        1       1        0        1   taunew(  25)=( -0.2960
0.0000  0.2138)
       26        1       1        0        1   taunew(  26)=( -0.2703
-0.1207  0.2138)
       27        1       1        0        1   taunew(  27)=( -0.0915
-0.2816  0.2138)
       28        1       1        0        1   taunew(  28)=(  0.0312
-0.2944  0.2138)
       29        1       1        0        1   taunew(  29)=(  0.2395
-0.1740  0.2138)
       30        1       1        0        1   taunew(  30)=(  0.2896
-0.0613  0.2138)
    k slab    z(k)  z(k+1)     crossing(iorb=1,norb)
    1   0.0000 0.0079 0.0079   111111111100000000000000000000
    2   0.0079 0.0158 0.0079   111111111100000000000000000000
    3   0.0158 0.0238 0.0079   111111111100000000000000000000
    4   0.0238 0.0317 0.0079   111111111100000000000000000000
    5   0.0317 0.0396 0.0079   111111111100000000000000000000
    6   0.0396 0.0475 0.0079   111111111100000000000000000000
    7   0.0475 0.0554 0.0079   111111111111111111110000000000
    8   0.0554 0.0633 0.0079   111111111111111111110000000000
    9   0.0633 0.0713 0.0079   000000000011111111110000000000
   10   0.0713 0.0792 0.0079   000000000011111111110000000000
   11   0.0792 0.0871 0.0079   000000000011111111110000000000
   12   0.0871 0.0950 0.0079   000000000011111111110000000000
   13   0.0950 0.1029 0.0079   000000000011111111110000000000
   14   0.1029 0.1108 0.0079   000000000011111111110000000000
   15   0.1108 0.1188 0.0079   000000000011111111110000000000
   16   0.1188 0.1267 0.0079   000000000011111111110000000000
   17   0.1267 0.1346 0.0079   000000000011111111110000000000
   18   0.1346 0.1425 0.0079   000000000011111111110000000000
   19   0.1425 0.1504 0.0079   000000000011111111110000000000
   20   0.1504 0.1583 0.0079   000000000011111111111111111111
   21   0.1583 0.1663 0.0079   000000000011111111111111111111
   22   0.1663 0.1742 0.0079   000000000000000000001111111111
   23   0.1742 0.1821 0.0079   000000000000000000001111111111
   24   0.1821 0.1900 0.0079   000000000000000000001111111111
   25   0.1900 0.1979 0.0079   000000000000000000001111111111
   26   0.1979 0.2058 0.0079   000000000000000000001111111111
   27   0.2058 0.2138 0.0079   000000000000000000001111111111

        k(    1) = (   0.0000000   0.0000000), wk =   1.0000000

 ngper, shell number =         2809         299
####################################################################################
the output file stopped  there, and I couldn't see the process. Maybe it
takes long time cause I found it took 1 hour to calculate a transmission.
I don't quite understand the parameters setting, I have adjusted the ewind,
epsproj, nzl, according to the postings on this forum. However,
the result seemed not change.

I appreciate everyone who could give me some advice.
Thank you!

Regards.

Chengyu Yang
Material Science and Engineering,
 University of Central Florida, USA
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From vovi47 at yahoo.com  Thu Jul 28 23:05:33 2011
From: vovi47 at yahoo.com (Vi Vo)
Date: Thu, 28 Jul 2011 14:05:33 -0700 (PDT)
Subject: [Pw_forum] (no subject)
In-Reply-To: <4C143759-687E-4E1E-BD84-2F3A9B2D33F4@democritos.it>
References: <1311636717.59460.YahooMailRC@web114512.mail.gq1.yahoo.com>
	<op.vy7s52ar5jfbqb@paulax>
	<1311708551.91624.YahooMailRC@web114504.mail.gq1.yahoo.com>
	<4C143759-687E-4E1E-BD84-2F3A9B2D33F4@democritos.it>
Message-ID: <1311887133.43053.YahooMailRC@web114517.mail.gq1.yahoo.com>

Dear Paolo,

Thank you very much.


Vi





________________________________
From: Paolo Giannozzi <giannozz at democritos.it>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Thu, July 28, 2011 8:33:51 AM
Subject: Re: [Pw_forum] (no subject)


On Jul 26, 2011, at 21:29 , Vi Vo wrote:

> In LDA+U calculation I also see these warning, so what will be the  
> risk or unreliability.

there is no risk, as long as bound atomic states are present in the  
PP files.
I guess that the "zero-norm" states that are still present in some PP  
files are
unbound states used uring thr generation of the PP. They do not  
affect the
final results in any way.

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




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From Michael at ihpc.a-star.edu.sg  Thu Jul 28 23:28:59 2011
From: Michael at ihpc.a-star.edu.sg (Michael Sullivan)
Date: Fri, 29 Jul 2011 05:28:59 +0800
Subject: [Pw_forum] How to convince QE from local lapack/blas?
In-Reply-To: <61A00C8B-E1AF-4FAF-B140-238805CEF4F0@democritos.it>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>
	<4E28041D.6050101@chemie.uni-halle.de>
	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>
	<4E2F1616.8080905@chemie.uni-halle.de>
	<0FA242DB-AA44-4B5C-BA79-992927CEBB5A@ihpc.a-star.edu.sg>
	<61A00C8B-E1AF-4FAF-B140-238805CEF4F0@democritos.it>
Message-ID: <BD569A5C-6EA5-4D20-AB80-5B51B2FFB028@ihpc.a-star.edu.sg>

Thanks, Paolo, for the clarification.

Mike
michael at ihpc.a-star.edu.sg
http://www.sullivan.sg/

On 27-Jul-2011, at 3:31 PM, Paolo Giannozzi wrote:

>
> On Jul 27, 2011, at 5:40 , Michael Sullivan wrote:
>
>> If I'm not wrong, that just means that you're not using ESSL.
>
> it is true that by linking lapack before essl, the lapack version
> of lapack routines is linked, not the essl version. However
> the fft and blas from essl are linked (unless there is a
> copy of blas into lapack, which shouldn't be the case).
> The resulting loss of performances should be minor.
> If fft and blas from essl are not linked, the loss of
> performances is much larger.
>
> Final clarification:
>
> -D__ESSL means that the fft routines of essl are used, and
> that the calls of some lapack routines follow the essl syntax,
> not the lapack syntax;
>
> -D__LINUX_ESSL means that the fft routines of essl are used,
> and that the calls of lapack routines follow the lapack syntax.
>
> In all cases, it is convenient to link essl before lapack (essl does
> not contain all lapack routines, just a subset, so not linking lapack
> may result in missing symbols). If the lapack replacements in essl
> do not follow the lapack syntax (IBM SP machines, typically),
> -D__ESSL should be used. If they follow the lapack syntax, or if
> they do not contain lapack replacements (IBM BlueGene and other
> strange IBM machines), -D__LINUX_ESSL should be used.
>
> Complicated? blame the geniuses who wrote lapack replacements
> with the same names but called in a different way
>
> 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 flux_ray12 at 163.com  Fri Jul 29 01:38:09 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Fri, 29 Jul 2011 07:38:09 +0800 (CST)
Subject: [Pw_forum] strange error with monoclinic structure
In-Reply-To: <20110728170405.0c0d3902@PC-Mayr-Mitarb6.pc-flexi>
References: <20110728170405.0c0d3902@PC-Mayr-Mitarb6.pc-flexi>
Message-ID: <4aeb0627.872.131731cc1a1.Coremail.flux_ray12@163.com>

How about changing your "prefix", in &control, or clean "outdir", in &control, too, before a new calculation?

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea




At 2011-07-28 23:04:05,"J?rg Buchwald" <joerg.buchwald at iom-leipzig.de> wrote:
>Hi,
>to get the shear modulus i performed some simulations with a monoclinic
>silicon lattice. I simulated with different angles.
>For celldm(4)=0.004 or celldm(4)=0.002 it works, but if i set
>celldm(4)=0.003 i get the following error
>
>--
>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     from davcio : error #        99
>     error while reading from file
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>     stopping ...
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     from davcio : error #        99
>     error while reading from file
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>     stopping ...
>--
>an here is my input file:
>--
>&control
>    calculation='scf'
>    prefix='silicon',
>    pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
>    outdir = '/home/joerg/scratch',
>    tstress=.true.
>    disk_io='none'
> /
> &system
>    ibrav=  12, celldm(1) =10.334309, celldm(2)=1.0, celldm(3)=1.00,
>     celldm(4)=0.003, nat=  8, ntyp= 1, ecutwfc = 50.0,ecutrho=500.0
> /
> &electrons
>    diagonalization='cg'
>    mixing_mode='plain'
> /
> &ions
> /
> &cell
> /
>ATOMIC_SPECIES
> Si  28.086  Si.pbe-n-van.UPF
>ATOMIC_POSITIONS
> Si 0.00 0.00 0.00
> Si 0.25 0.25 0.25
> Si 0.50 0.50 0.00
> Si 0.75 0.75 0.25
> Si 0.50 0.00 0.50
> Si 0.75 0.25 0.75
> Si 0.00 0.50 0.50
> Si 0.25 0.75 0.75
>K_POINTS automatic
> 15 15 15 0 0 0
>--
>Do you have any idea what the problem could be?
>Thx,
>J?rg 
>
>--
>J?rg Buchwald
>Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
>Permoserstrasse 15
>04318 Leipzig
>GERMANY
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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From chengyu.young at gmail.com  Fri Jul 29 03:32:27 2011
From: chengyu.young at gmail.com (chengyu yang)
Date: Thu, 28 Jul 2011 21:32:27 -0400
Subject: [Pw_forum] Slow calculation of (5,
	5) CNT transmission and complex bands.
In-Reply-To: <CAOk-W=GMvgBKO3McU5tO2x_eBtCmUM7QsA1EVDzKkWcEeB_9=A@mail.gmail.com>
References: <CAOk-W=GMvgBKO3McU5tO2x_eBtCmUM7QsA1EVDzKkWcEeB_9=A@mail.gmail.com>
Message-ID: <CAOk-W=EzzLoJy_K8ZKTdFhe7pbRjSCKAP=9Wu_MSNOEahXFgAQ@mail.gmail.com>

Sorry every one, my posting may be too long. May anyone have a look at my
parameters and point out the problem?
It took me almost 2 hours to get a band output file.

Chengyu Yang
MMAE, University of Central Florida,USA


2011/7/28 chengyu yang <chengyu.young at gmail.com>

> Dear All,
>          I am trying to calculate the complex bands and the transmission of
> a (5,5) defectless carbon nanotube using PWCOND.x, however, the calculation
> process is very slow and I can see it kind of stopped at the point:  ngper,
> shell number =         2809         299.
>          My input files are like this:
>
>
> ##################################################################################
> scf input file:
>
> &CONTROL
>                  calculation = 'scf' ,
>                 restart_mode = 'from_scratch' ,
>                        prefix = '55' ,
>  /
>  &SYSTEM
>                        ibrav = 6,
>                    celldm(1) = 21.764541128,celldm(3)=0.213765379
>                          nat = 20,
>                         ntyp = 1,
>                      ecutwfc = 75 ,
>  /
>  &ELECTRONS
>                     conv_thr = 1.0d-8 ,
>                  mixing_beta = 0.7 ,
>  /
> ATOMIC_SPECIES
>     C   12.01100  C.pz-vbc.UPF
>
> ATOMIC_POSITIONS angstrom
>
>   C        3.409595     0.000000    -1.231179
>   C        3.113484     1.389805    -1.231179
>   C        2.758420     2.004110    -0.000000
>   C        1.701954     2.954436    -0.000000
>   C        1.053623     3.242718    -1.231179
>   C       -0.359664     3.390572    -1.231179
>   C       -1.053623     3.242718    -0.000000
>   C       -2.283903     2.531625    -0.000000
>   C       -2.758420     2.004110    -1.231179
>   C       -3.335768     0.705684    -1.231179
>   C       -3.409595     0.000000    -0.000000
>   C       -3.113484    -1.389805    -0.000000
>   C       -2.758420    -2.004110    -1.231179
>   C       -1.701954    -2.954436    -1.231179
>   C       -1.053623    -3.242718     0.000000
>   C        0.359664    -3.390572     0.000000
>   C        1.053623    -3.242718    -1.231179
>   C        2.283903    -2.531625    -1.231179
>   C        2.758420    -2.004110     0.000000
>   C        3.335768    -0.705684     0.000000
>
>
>
>
> K_POINTS automatic
>  1 1 5 0 0 0
>
>
>
> ###############################################################################
>
> pwcond.in file:
>
>
> &inputcond
>     prefixl='55'
>     band_file ='bands.cnt55'
>     ikind=0
>     energy0=4.d0
>     denergy=-0.1d0
>     ewind=3.d0
>     epsproj=1.d-4
>     delgep = 1.d-9
>     cutplot = 3.d0
>  /
>     1
>     0.0 0.0 1.0
>     5
>
> ###########################################################
> and the output file:
>
>      GEOMETRY:
>
>      lattice parameter (a_0)   =      21.7645  a.u.
>      the volume                =    2203.8697 (a.u.)^3
>      the cross section         =     473.6953 (a.u.)^2
>      l of the unit cell        =       0.2138 (a_0)
>      number of atoms/cell      =           20
>      number of atomic types    =            1
>
>      crystal axes: (cart. coord. in units of a_0)
>                a(1) = (  1.0000  0.0000  0.0000 )
>                a(2) = (  0.0000  1.0000  0.0000 )
>                a(3) = (  0.0000  0.0000  0.2138 )
>
>
>    Cartesian axes
>
>      site n.     atom                  positions (a_0 units)
>           1           C   tau(  1)=(  0.2960  0.0000  0.1069  )
>           2           C   tau(  2)=(  0.2703  0.1207  0.1069  )
>           3           C   tau(  3)=(  0.2395  0.1740  0.2138  )
>           4           C   tau(  4)=(  0.1478  0.2565  0.2138  )
>           5           C   tau(  5)=(  0.0915  0.2816  0.1069  )
>           6           C   tau(  6)=( -0.0312  0.2944  0.1069  )
>           7           C   tau(  7)=( -0.0915  0.2816  0.2138  )
>           8           C   tau(  8)=( -0.1983  0.2198  0.2138  )
>           9           C   tau(  9)=( -0.2395  0.1740  0.1069  )
>          10           C   tau( 10)=( -0.2896  0.0613  0.1069  )
>          11           C   tau( 11)=( -0.2960  0.0000  0.2138  )
>          12           C   tau( 12)=( -0.2703 -0.1207  0.2138  )
>          13           C   tau( 13)=( -0.2395 -0.1740  0.1069  )
>          14           C   tau( 14)=( -0.1478 -0.2565  0.1069  )
>          15           C   tau( 15)=( -0.0915 -0.2816  0.2138  )
>          16           C   tau( 16)=(  0.0312 -0.2944  0.2138  )
>          17           C   tau( 17)=(  0.0915 -0.2816  0.1069  )
>          18           C   tau( 18)=(  0.1983 -0.2198  0.1069  )
>          19           C   tau( 19)=(  0.2395 -0.1740  0.2138  )
>          20           C   tau( 20)=(  0.2896 -0.0613  0.2138  )
>
>      nr1s                      =          120
>      nr2s                      =          120
>      nr3s                      =           27
>      nrx1s                     =          120
>      nrx2s                     =          120
>      nrx3s                     =           27
>      nr1                       =          120
>      nr2                       =          120
>      nr3                       =           27
>      nrx1                      =          120
>      nrx2                      =          120
>      nrx3                      =           27
>
>  _______________________________
>   Radii of nonlocal spheres:
>
>      type       ibeta     ang. mom.          radius (a_0 units)
>           C       1         0                    0.0593
> ----- General information -----
>
> ----- Complex band structure calculation -----
>
>      nrx                       =          120
>      nry                       =          120
>      nz1                       =           11
>
>
>      energy0               =         4.0E+00
>      denergy               =        -1.0E-01
>      nenergy               =          5
>      ecut2d                =         7.5E+01
>      ewind                 =         3.0E+00
>      epsproj               =         1.0E-04
>
>
>      number of k_|| points=    1
>                        cryst. coord.
>         k(    1) = (   0.0000000   0.0000000), wk =   1.0000000
> ----- Information about left lead -----
>
>      nocros                   =           10
>      noins                    =           10
>      norb                     =           30
>      norbf                    =           30
>      nrz                      =           27
>
>       iorb      type   ibeta   ang. mom.   m       position (a_0)
>         1        1       1        0        1   taunew(   1)=(  0.2395
> 0.1740  0.0000)
>         2        1       1        0        1   taunew(   2)=(  0.1478
> 0.2565  0.0000)
>         3        1       1        0        1   taunew(   3)=( -0.0915
> 0.2816  0.0000)
>         4        1       1        0        1   taunew(   4)=( -0.1983
> 0.2198  0.0000)
>         5        1       1        0        1   taunew(   5)=( -0.2960
> 0.0000  0.0000)
>         6        1       1        0        1   taunew(   6)=( -0.2703
> -0.1207  0.0000)
>         7        1       1        0        1   taunew(   7)=( -0.0915
> -0.2816  0.0000)
>         8        1       1        0        1   taunew(   8)=(  0.0312
> -0.2944  0.0000)
>         9        1       1        0        1   taunew(   9)=(  0.2395
> -0.1740  0.0000)
>        10        1       1        0        1   taunew(  10)=(  0.2896
> -0.0613  0.0000)
>        11        1       1        0        1   taunew(  11)=(  0.2960
> 0.0000  0.1069)
>        12        1       1        0        1   taunew(  12)=(  0.2703
> 0.1207  0.1069)
>        13        1       1        0        1   taunew(  13)=(  0.0915
> 0.2816  0.1069)
>        14        1       1        0        1   taunew(  14)=( -0.0312
> 0.2944  0.1069)
>        15        1       1        0        1   taunew(  15)=( -0.2395
> 0.1740  0.1069)
>        16        1       1        0        1   taunew(  16)=( -0.2896
> 0.0613  0.1069)
>        17        1       1        0        1   taunew(  17)=( -0.2395
> -0.1740  0.1069)
>        18        1       1        0        1   taunew(  18)=( -0.1478
> -0.2565  0.1069)
>        19        1       1        0        1   taunew(  19)=(  0.0915
> -0.2816  0.1069)
>        20        1       1        0        1   taunew(  20)=(  0.1983
> -0.2198  0.1069)
>        21        1       1        0        1   taunew(  21)=(  0.2395
> 0.1740  0.2138)
>        22        1       1        0        1   taunew(  22)=(  0.1478
> 0.2565  0.2138)
>        23        1       1        0        1   taunew(  23)=( -0.0915
> 0.2816  0.2138)
>        24        1       1        0        1   taunew(  24)=( -0.1983
> 0.2198  0.2138)
>        25        1       1        0        1   taunew(  25)=( -0.2960
> 0.0000  0.2138)
>        26        1       1        0        1   taunew(  26)=( -0.2703
> -0.1207  0.2138)
>        27        1       1        0        1   taunew(  27)=( -0.0915
> -0.2816  0.2138)
>        28        1       1        0        1   taunew(  28)=(  0.0312
> -0.2944  0.2138)
>        29        1       1        0        1   taunew(  29)=(  0.2395
> -0.1740  0.2138)
>        30        1       1        0        1   taunew(  30)=(  0.2896
> -0.0613  0.2138)
>     k slab    z(k)  z(k+1)     crossing(iorb=1,norb)
>     1   0.0000 0.0079 0.0079   111111111100000000000000000000
>     2   0.0079 0.0158 0.0079   111111111100000000000000000000
>     3   0.0158 0.0238 0.0079   111111111100000000000000000000
>     4   0.0238 0.0317 0.0079   111111111100000000000000000000
>     5   0.0317 0.0396 0.0079   111111111100000000000000000000
>     6   0.0396 0.0475 0.0079   111111111100000000000000000000
>     7   0.0475 0.0554 0.0079   111111111111111111110000000000
>     8   0.0554 0.0633 0.0079   111111111111111111110000000000
>     9   0.0633 0.0713 0.0079   000000000011111111110000000000
>    10   0.0713 0.0792 0.0079   000000000011111111110000000000
>    11   0.0792 0.0871 0.0079   000000000011111111110000000000
>    12   0.0871 0.0950 0.0079   000000000011111111110000000000
>    13   0.0950 0.1029 0.0079   000000000011111111110000000000
>    14   0.1029 0.1108 0.0079   000000000011111111110000000000
>    15   0.1108 0.1188 0.0079   000000000011111111110000000000
>    16   0.1188 0.1267 0.0079   000000000011111111110000000000
>    17   0.1267 0.1346 0.0079   000000000011111111110000000000
>    18   0.1346 0.1425 0.0079   000000000011111111110000000000
>    19   0.1425 0.1504 0.0079   000000000011111111110000000000
>    20   0.1504 0.1583 0.0079   000000000011111111111111111111
>    21   0.1583 0.1663 0.0079   000000000011111111111111111111
>    22   0.1663 0.1742 0.0079   000000000000000000001111111111
>    23   0.1742 0.1821 0.0079   000000000000000000001111111111
>    24   0.1821 0.1900 0.0079   000000000000000000001111111111
>    25   0.1900 0.1979 0.0079   000000000000000000001111111111
>    26   0.1979 0.2058 0.0079   000000000000000000001111111111
>    27   0.2058 0.2138 0.0079   000000000000000000001111111111
>
>         k(    1) = (   0.0000000   0.0000000), wk =   1.0000000
>
>  ngper, shell number =         2809         299
>
> ####################################################################################
> the output file stopped  there, and I couldn't see the process. Maybe it
> takes long time cause I found it took 1 hour to calculate a transmission.
> I don't quite understand the parameters setting, I have adjusted the ewind,
> epsproj, nzl, according to the postings on this forum. However,
> the result seemed not change.
>
> I appreciate everyone who could give me some advice.
> Thank you!
>
> Regards.
>
> Chengyu Yang
> Material Science and Engineering,
>  University of Central Florida, USA
>
>
>
>
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From giannozz at democritos.it  Fri Jul 29 08:09:59 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 29 Jul 2011 08:09:59 +0200
Subject: [Pw_forum] strange error with monoclinic structure
In-Reply-To: <20110728170405.0c0d3902@PC-Mayr-Mitarb6.pc-flexi>
References: <20110728170405.0c0d3902@PC-Mayr-Mitarb6.pc-flexi>
Message-ID: <AB112421-2818-4E2D-BD86-93E198841A9C@democritos.it>


On Jul 28, 2011, at 17:04 , J?rg Buchwald wrote:

>      from davcio : error #        99
>      error while reading from file

if this happens at the beginning of the calculation, there may
be corrupted or inconsistent restart file in the scratch directory.
Your input works fine for me :
   http://www.fisica.uniud.it/~giannozz/public/boh.out
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 samuel.pon at gmail.com  Fri Jul 29 11:27:27 2011
From: samuel.pon at gmail.com (=?ISO-8859-1?Q?Samuel_Ponc=E9?=)
Date: Fri, 29 Jul 2011 11:27:27 +0200
Subject: [Pw_forum] Change of occupation number and cut3d
Message-ID: <CAESzT+7mGrm60sUFknrJj0E87eq0YyNiJzMP7HSEiFbxpgJJig@mail.gmail.com>

Dear Quantum espresso user/developers,

I have two questions:

1) Is it possible in pwscf to change "by hand" the occupation number ( and
impose a charge compensation accordingly) and if so how to do it?
I would like to do so because the sum over the different mode of the partial
derivative of the phonon frequency with respect of the occupation number
gives the zero point motion renormalization using Brooks theorem. I would
like to do this by finite difference (hence doing by hand some calculation
at different occupation number).

 2) Is it possible to extract informations in text format form the
wavefunctions? What is the right post processing tool to do so? Like having
the value of the wavefunction for a defined k points and band index?

Thanks you!

Samuel Ponc?.
(phD student, Universit? Catholique de Louvain, Belgium).
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From joerg.buchwald at iom-leipzig.de  Fri Jul 29 11:46:02 2011
From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald)
Date: Fri, 29 Jul 2011 11:46:02 +0200
Subject: [Pw_forum] strange error with monoclinic structure
In-Reply-To: <AB112421-2818-4E2D-BD86-93E198841A9C@democritos.it>
References: <20110728170405.0c0d3902@PC-Mayr-Mitarb6.pc-flexi>
	<AB112421-2818-4E2D-BD86-93E198841A9C@democritos.it>
Message-ID: <20110729114602.6c795e8e@PC-Mayr-Mitarb6.pc-flexi>

Am Fri, 29 Jul 2011 08:09:59 +0200
schrieb Paolo Giannozzi <giannozz at democritos.it>:

> 
> On Jul 28, 2011, at 17:04 , J?rg Buchwald wrote:
> 
> >      from davcio : error #        99
> >      error while reading from file
> 
> if this happens at the beginning of the calculation, there may
> be corrupted or inconsistent restart file in the scratch directory.
> Your input works fine for me :
>    http://www.fisica.uniud.it/~giannozz/public/boh.out
> 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

ok sorry for that question, i thought the state is saved by the
identifier prefix only, and mainly because of the disk_io switch turned
off, i didn't thought that it would have any influence...
Thx,
J?rg

--
J?rg Buchwald
Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
Permoserstrasse 15
04318 Leipzig
GERMANY

From zhaohscas at yahoo.com.cn  Fri Jul 29 12:02:45 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Fri, 29 Jul 2011 18:02:45 +0800
Subject: [Pw_forum] Using a big box model to calculating the energy of
 isolated atom.
In-Reply-To: <CAB-NT9LrTqrcsbori8zAvqEwEaUVgSmtOH=kTjrewON1CDKAnw@mail.gmail.com>
References: <4E30A55A.9080100@yahoo.com.cn>
	<4F3F69C4-E8A0-4386-B2AA-8A4FD2FEA531@epfl.ch>
	<CAB-NT9LrTqrcsbori8zAvqEwEaUVgSmtOH=kTjrewON1CDKAnw@mail.gmail.com>
Message-ID: <4E328545.7070000@yahoo.com.cn>

On 07/28/2011 04:38 PM, Phillip Nyawere wrote:
> To implement no symmetry use
> nosym=.true. at the $system

Thanks a lot for all of the helps on this topic.  I've checked and read 
most the topics on this ML which are related to "calculating the energy 
of isolated atom".  It seems this is  a tricky thing based on most of 
the replies on this similar topics on this ML.

Based on my understanding, till now, there are still some issues 
puzzling me on this topic:

1- On the manual of pwscf (p37), we can find the following descriptions:

--------
...
Specify nosym=.true. to avoid generation of additional k-points in low 
symmetry
...
-----------

I want to know, by using nosym=.true., what's the different on the 
k-points set obtained with the ones without using this option?  For 
example, when using a bcc box with a atom at its center,  what's the 
corresponding   k-points set when using nosym=.true.?

Furthermore, when we say a isolated atom, we mean a zero dimension 
system.  So the corresponding BZ  sampling by using gamma only should be 
OK.  If so,  there is no k-points issues at all - there only one k point 
should be considered.  Hence I'm confused on the description given by 
the manual *avoid generation of additional k-points in low symmetry*. 
Any hints?

2- From this ML, I found the following notes:

---------
while doing calculations for any zero dimensions you should always set 
nosym =.true.
-----------

Does this mean: when I do the  calculations for isolated 
atom/molecule/nanocluster and so on, I should always set nosym =.true.?

3-  Prof. Paolo Giannozzi given the following descriptions on some 
similar topic in this ML:

---------
calculations on isolated atoms with plane waves are tricky.
Compare your results with what you get with the atomic code,
in which you can fix occupancies at will
------------

My issue: how to fix the occupancies based on the results?  Any examples?

What do you mean by saying *at will*?  If really is a thing *at will*, 
why should we do it?

Regards

>
> On Thu, Jul 28, 2011 at 10:12 AM, Gabriele Sclauzero
> <gabriele.sclauzero at epfl.ch <mailto:gabriele.sclauzero at epfl.ch>> wrote:
>
>
>     Il giorno 28/lug/2011, alle ore 01.55, Hongsheng Zhao ha scritto:
>
>>     Hi all,
>>
>>     I've learned that when using the a large-cell ( i.e., a big box ) to
>>     calculate the energy of isolated atom, it should be done without
>>     symmetry.   But I'm not sure what's the meaning of the "without
>>     symmetry"  here and how to ensure this when we using a a big box
>>     model
>>     for this purpose.  Any hints on this issue?
>
>     This is a FAQ on this forum: have you spent some time browsing the
>     archives?
>
>     OK, I'll give you a hint: "nosym"... but use it with care!
>
>     HTH
>
>     GS
>
>>
>>     Regards
>>     --
>>     Hongsheng Zhao <zhaohscas at yahoo.com.cn
>>     <mailto:zhaohscas at yahoo.com.cn>>
>>     School of Physics and Electrical Information Science,
>>     Ningxia University, Yinchuan 750021, China
>>     _______________________________________________
>>     Pw_forum mailing list
>>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>     ? Gabriele Sclauzero, EPFL SB ITP CSEA
>     /   PH H2 462, Station 3, CH-1015 Lausanne/
>
>
>
>
>
>
>
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
> Phillip W. Otieno Nyawere,
> The Abdus Salam International Center for Theoretical Physics,
> Enrico Fermi Building Associate Office 18,
> Strada Costiera 11,
> 34014 Trieste, Italy
> Tel +393895378328, or +39 040 2240 567
> pnyawere at gmail.com <mailto:pnyawere at gmail.com>, pnyawere at ictp.it,
> <mailto:potieno at kabarak.ac.ke>
>
> God raises the meek from the ground and sits them with Kings.
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From goodluck_1982 at 163.com  Fri Jul 29 12:07:21 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Fri, 29 Jul 2011 18:07:21 +0800
Subject: [Pw_forum] What files are needed when pw.x restarts? In what
 case the *.wfc files are need?
In-Reply-To: <CBC4DC5E-EE0C-44B0-8E26-6625B82E9A1D@democritos.it>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>	<4E28041D.6050101@chemie.uni-halle.de>	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>	<4E2F1616.8080905@chemie.uni-halle.de>
	<4E2F9C6F.9030009@163.com>	<CAKScr_rju9zXEqtjyu=Q8686xUkcyVup7P+Cmq5Wxh=qiLc+qg@mail.gmail.com>	<4E2FBE37.3050409@163.com>	<CAKScr_p22KHGBx_SiV1SAZkAP9xcOnLR4ZFm8L7wWv8nHyniFg@mail.gmail.com>
	<CBC4DC5E-EE0C-44B0-8E26-6625B82E9A1D@democritos.it>
Message-ID: <4E328659.8040200@163.com>

? 2011/7/28 23:30, Paolo Giannozzi ??:
> On Jul 27, 2011, at 9:41 , Seyed Javad Hashemifar wrote:
>
>> I guess if you set wf_collect=.true. the collection of *.wfc files
>> is done after
>> reaching self consistency not after each iteration. Probably, the
>> evc.dat files
>> are the collected *.wfc files
> I can confirm this
>
Now that *.wfc are collected only after consistency is reached and 
appear as evc.dat, a restarted pw.x scf run can not use them and only 
charge density available. Is this right, for parallel jobs?

> 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 zucco at dipteris.unige.it  Fri Jul 29 12:51:03 2011
From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini)
Date: Fri, 29 Jul 2011 12:51:03 +0200
Subject: [Pw_forum] Segmentation fault on relaxed structure in vc-relax
	on QE4.3.1
In-Reply-To: <D94C979F-FF09-41E5-A72F-03A9963B9EB0@dipteris.unige.it>
References: <C44EC6BA-38DF-4536-B0C2-11215367C36E@dipteris.unige.it>
	<5DCDB2A2-4C90-4B12-BF41-66420303C182@democritos.it>
	<D94C979F-FF09-41E5-A72F-03A9963B9EB0@dipteris.unige.it>
Message-ID: <1FA8802D-1DFE-48E5-8DA6-678001203DE5@dipteris.unige.it>

Paolo,
the problem is still there. How can I report the bug on qe-forge. I've already an account.

Thank you 

m.

On 28 Jul 2011, at 18:14, Marino Vetuschi Zuccolini wrote:

> I've compiled the 4.3.2 version of QE and the bug it is not present apparently on some tests I did.
> I will follow your suggestion if it will still present.
> 
> Thank you very much.
> 
> m.
> On 28 Jul 2011, at 17:38, Paolo Giannozzi wrote:
> 
>> 
>> On Jul 26, 2011, at 13:50 , Marino Vetuschi Zuccolini wrote:
>> 
>>> during the computation of the last SCF cycle *on relaxed structure*
>>> this segmentation fault error (repeated for each process) happens
>> 
>> a problem in the last step of a variable-cell optimization was fixed
>> in v.4.3.2. Please file a bug report on qe-forge if still present.
>> 
>> 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
> 
> 
> 
> *******************************************************
> Marino Vetuschi Zuccolini
> zucco at dipteris.unige.it
> Researcher / Geochemist
> Laboratory of Geochemistry
> 
> DIPartimento per lo studio della TErra e delle sue RISorse - Universit?  di Genova
> Tel. ++39 010 3538136 Fax. ++39 010 352169
> Corso Europa 26, 16132 - Genova - Italy
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



*******************************************************
Marino Vetuschi Zuccolini
zucco at dipteris.unige.it
Researcher / Geochemist
Laboratory of Geochemistry

DIPartimento per lo studio della TErra e delle sue RISorse - Universit?  di Genova
Tel. ++39 010 3538136 Fax. ++39 010 352169
Corso Europa 26, 16132 - Genova - Italy



From chengyu.young at gmail.com  Fri Jul 29 17:42:58 2011
From: chengyu.young at gmail.com (chengyu yang)
Date: Fri, 29 Jul 2011 11:42:58 -0400
Subject: [Pw_forum] Slow calculation of (5,
 5) CNT transmission and complex bands.
In-Reply-To: <4E327A29.2010400@materials.ox.ac.uk>
References: <CAOk-W=GMvgBKO3McU5tO2x_eBtCmUM7QsA1EVDzKkWcEeB_9=A@mail.gmail.com>
	<CAOk-W=EzzLoJy_K8ZKTdFhe7pbRjSCKAP=9Wu_MSNOEahXFgAQ@mail.gmail.com>
	<4E327A29.2010400@materials.ox.ac.uk>
Message-ID: <CAOk-W=FRZrM3kFMa8eVKySkQFBJPBoKMwQSYBFFQF1nZqnaR_g@mail.gmail.com>

Dear Dr. Marzari and all,
         Thanks very much. I will try wannier . Here are some other
questions,
          1.If I want to do research on the properties of carbon
nanotube/metal system, I saw them using NEGF , but I didn't see NEGF package
in Quantum Espresso, does this mean I should try other codes like SIESTA?
          2.If I want to research the conductivity properties of carbon
nanotube/metal system under magnetic field, which code should I use?Can
Quantum Espresso handle this? I learned a little about the quantum
transport, but I still didn't find the right code to deal with such a
complicated proplem.
          Sorry I am a newie in this field, and I don't have quite a strong
physics background.
          Thank you again.

Chengyu Yang
Materials Science and Engineering,University of Central Florida
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From giannozz at democritos.it  Fri Jul 29 18:04:01 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 29 Jul 2011 18:04:01 +0200
Subject: [Pw_forum] What files are needed when pw.x restarts? In what
	case the *.wfc files are need?
In-Reply-To: <4E328659.8040200@163.com>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>	<4E28041D.6050101@chemie.uni-halle.de>	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>	<4E2F1616.8080905@chemie.uni-halle.de>
	<4E2F9C6F.9030009@163.com>	<CAKScr_rju9zXEqtjyu=Q8686xUkcyVup7P+Cmq5Wxh=qiLc+qg@mail.gmail.com>	<4E2FBE37.3050409@163.com>	<CAKScr_p22KHGBx_SiV1SAZkAP9xcOnLR4ZFm8L7wWv8nHyniFg@mail.gmail.com>
	<CBC4DC5E-EE0C-44B0-8E26-6625B82E9A1D@democritos.it>
	<4E328659.8040200@163.com>
Message-ID: <F025D39B-82B7-42D7-8DEE-078A51C35530@democritos.it>


On Jul 29, 2011, at 12:07 , gbliu wrote:

> Now that *.wfc are collected only after consistency is reached and
> appear as evc.dat, a restarted pw.x scf run can not use them and
> only charge density available.

it cannot use them to "restart", i.e. to continue an incomplete  
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 chengyu.young at gmail.com  Fri Jul 29 21:16:18 2011
From: chengyu.young at gmail.com (chengyu yang)
Date: Fri, 29 Jul 2011 15:16:18 -0400
Subject: [Pw_forum] Slow calculation of (5,
 5) CNT transmission and complex bands.
In-Reply-To: <CAOk-W=FRZrM3kFMa8eVKySkQFBJPBoKMwQSYBFFQF1nZqnaR_g@mail.gmail.com>
References: <CAOk-W=GMvgBKO3McU5tO2x_eBtCmUM7QsA1EVDzKkWcEeB_9=A@mail.gmail.com>
	<CAOk-W=EzzLoJy_K8ZKTdFhe7pbRjSCKAP=9Wu_MSNOEahXFgAQ@mail.gmail.com>
	<4E327A29.2010400@materials.ox.ac.uk>
	<CAOk-W=FRZrM3kFMa8eVKySkQFBJPBoKMwQSYBFFQF1nZqnaR_g@mail.gmail.com>
Message-ID: <CAOk-W=FqEKChn22yxiboP2wULt1cERHAm5estb-DzmfSQ3XPtw@mail.gmail.com>

Dear All,
         After two hours , my transmission calculation comes out a result.
But I thought it may be not converged and didn't get the final result.
May anybody have a look at my output file? I attached in this email.
       My input file is like this:
       &inputcond
    prefixl='55'
    tran_file='trans.cnt55',
    ikind=0
    energy0=4.d0
    denergy=-0.1d0
    ewind=3.d0
    epsproj=1.d-4
    delgep = 1.d-9
    cutplot = 3.d0
 /
    1
    0.0 0.0 1.0
    5


Is there somebody that can give me an advice?
I really appreciate it.

Chengyu Yang
Materials Science and Engineering,
University of Central Florida, USA
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From masoudnahali at gmail.com  Fri Jul 29 22:55:55 2011
From: masoudnahali at gmail.com (Masoud Nahali)
Date: Sat, 30 Jul 2011 01:25:55 +0430
Subject: [Pw_forum] Using a big box model to calculating the energy of
	isolated atom
Message-ID: <CAM-1hStYs2wyZLihhcvRgXFtSTDXDEK9im5OrVfU9YjX+sBT0Q@mail.gmail.com>

Dear Hongsheng

In this case I think that the more important issue to be noticed is
considering spin polarization for most of atoms.  Many mistakes in this
issue arise from not considering spin polarization.
I guess Considering "Symmetry" may symmetrize the charge density and causes
some changes in electronic structure of atom (population of orbitals) or may
do reversely with nosym='true'.
Also, it is impossible for me to describe this issue based on DFT and the
exchange-correlation parts in details.

In quantum chemistry software based on Gaussian type orbitals basis set (not
plane wave basis set) we compare energy of an atom with considering
different spin multiplicities then find the lowest energy and call it
"ground state". I can do it for some atoms (whatever you select) by Firefly
software (former PC-GAMESS) and then you can compare it with the
corresponding calculation by QE.
These days I am very busy and going on a journey so let me do it in a due
course; contact me :)

Best Wishes

 Masoud



--------------
Masoud Nahali, Sharif University of Technology
masoud.nahali at gmail.com; a <http://alum.sharif.edu/%7Em_nahali>
lum.sharif.edu/~m_nahali

P Save a Tree . . . Please don't print this e-mail unless you really need
to.


Hongsheng Zhao Wrote :

 Thanks a lot for all of the helps on this topic.  I've checked and read
> most the topics on this ML which are related to "calculating the energy
> of isolated atom".  It seems this is  a tricky thing based on most of
> the replies on this similar topics on this ML.
>
> Based on my understanding, till now, there are still some issues
> puzzling me on this topic:
>
> 1- On the manual of pwscf (p37), we can find the following descriptions:
>
> --------
> ...
> Specify nosym=.true. to avoid generation of additional k-points in low
> symmetry
> ...
> -----------
>
> I want to know, by using nosym=.true., what's the different on the
> k-points set obtained with the ones without using this option?  For
> example, when using a bcc box with a atom at its center,  what's the
> corresponding   k-points set when using nosym=.true.?
>
> Furthermore, when we say a isolated atom, we mean a zero dimension
> system.  So the corresponding BZ  sampling by using gamma only should be
> OK.  If so,  there is no k-points issues at all - there only one k point
> should be considered.  Hence I'm confused on the description given by
> the manual *avoid generation of additional k-points in low symmetry*.
> Any hints?
>
> 2- From this ML, I found the following notes:
>
> ---------
> while doing calculations for any zero dimensions you should always set
> nosym =.true.
> -----------
>
> Does this mean: when I do the  calculations for isolated
> atom/molecule/nanocluster and so on, I should always set nosym =.true.?
>
> 3-  Prof. Paolo Giannozzi given the following descriptions on some
> similar topic in this ML:
>
> ---------
> calculations on isolated atoms with plane waves are tricky.
> Compare your results with what you get with the atomic code,
> in which you can fix occupancies at will
> ------------
>
> My issue: how to fix the occupancies based on the results?  Any examples?
>
> What do you mean by saying *at will*?  If really is a thing *at will*,
> why should we do it?
>
> Regards
>
> >
> > On Thu, Jul 28, 2011 at 10:12 AM, Gabriele Sclauzero
> > <gabriele.sclauzero at epfl.ch <mailto:gabriele.sclauzero at epfl.ch>> wrote:
> >
> >
> >     Il giorno 28/lug/2011, alle ore 01.55, Hongsheng Zhao ha scritto:
> >
> >>     Hi all,
> >>
> >>     I've learned that when using the a large-cell ( i.e., a big box ) to
> >>     calculate the energy of isolated atom, it should be done without
> >>     symmetry.   But I'm not sure what's the meaning of the "without
> >>     symmetry"  here and how to ensure this when we using a a big box
> >>     model
> >>     for this purpose.  Any hints on this issue?
> >
> >     This is a FAQ on this forum: have you spent some time browsing the
> >     archives?
> >
> >     OK, I'll give you a hint: "nosym"... but use it with care!
> >
> >     HTH
> >
> >     GS
> >
> >>
> >>     Regards
> >>     --
> >>     Hongsheng Zhao <zhaohscas at yahoo.com.cn
> >>     <mailto:zhaohscas at yahoo.com.cn>>
> >>     School of Physics and Electrical Information Science,
> >>     Ningxia University, Yinchuan 750021, China
> >>     _______________________________________________
> >>     Pw_forum mailing list
> >>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >>     http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >     ? Gabriele Sclauzero, EPFL SB ITP CSEA
> >     /   PH H2 462, Station 3, CH-1015 Lausanne/
> >
>
>
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From zhaohscas at yahoo.com.cn  Sat Jul 30 02:23:56 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Sat, 30 Jul 2011 08:23:56 +0800
Subject: [Pw_forum] Using a big box model to calculating the energy of
 isolated atom
In-Reply-To: <CAM-1hStYs2wyZLihhcvRgXFtSTDXDEK9im5OrVfU9YjX+sBT0Q@mail.gmail.com>
References: <CAM-1hStYs2wyZLihhcvRgXFtSTDXDEK9im5OrVfU9YjX+sBT0Q@mail.gmail.com>
Message-ID: <4E334F1C.8030404@yahoo.com.cn>

On 07/30/2011 04:55 AM, Masoud Nahali wrote:
>
> Dear Hongsheng
>
> In this case I think that the more important issue to be noticed is
> considering spin polarization for most of atoms.  Many mistakes in this
> issue arise from not considering spin polarization.
> I guess Considering "Symmetry" may symmetrize the charge density and
> causes some changes in electronic structure of atom (population of
> orbitals) or may do reversely with nosym='true'.
> Also, it is impossible for me to describe this issue based on DFT and
> the exchange-correlation parts in details.
>
> In quantum chemistry software based on Gaussian type orbitals basis set
> (not plane wave basis set)

When using plane wave basis set, say, pwcsf/vasp/castep and so on, what 
will happen in that case?

> we compare energy of an atom with considering
> different spin multiplicities then find the lowest energy and call it
> "ground state".

In plane-wave-basis-set based codes, we also can find the "ground 
state", what's the differences between these two "ground state" obtained 
by different  basis sets?

> I can do it for some atoms (whatever you select) by
> Firefly software (former PC-GAMESS) and then you can compare it with the
> corresponding calculation by QE.

I want to know: does this comparison make sense?

> These days I am very busy and going on a journey so let me do it in a
> due course; contact me :)

Thanks a lot for your kindly help and reply ;-)

>
> Best Wishes
>
>   Masoud
>
>
>
> --------------
> Masoud Nahali, Sharif University of Technology
> masoud.nahali at gmail.com <mailto:masoud.nahali at gmail.com>; a
> <http://alum.sharif.edu/%7Em_nahali>lum.sharif.edu/~m_nahali
> <http://lum.sharif.edu/~m_nahali>
>
> PSave a Tree . . . Please don't print this e-mail unless you really need to.
>
>
>
> Hongsheng Zhao Wrote :
>
>       Thanks a lot for all of the helps on this topic.  I've checked and
>     read
>     most the topics on this ML which are related to "calculating the energy
>     of isolated atom".  It seems this is  a tricky thing based on most of
>     the replies on this similar topics on this ML.
>
>     Based on my understanding, till now, there are still some issues
>     puzzling me on this topic:
>
>     1- On the manual of pwscf (p37), we can find the following descriptions:
>
>     --------
>     ...
>     Specify nosym=.true. to avoid generation of additional k-points in low
>     symmetry
>     ...
>     -----------
>
>     I want to know, by using nosym=.true., what's the different on the
>     k-points set obtained with the ones without using this option?  For
>     example, when using a bcc box with a atom at its center,  what's the
>     corresponding   k-points set when using nosym=.true.?
>
>     Furthermore, when we say a isolated atom, we mean a zero dimension
>     system.  So the corresponding BZ  sampling by using gamma only should be
>     OK.  If so,  there is no k-points issues at all - there only one k point
>     should be considered.  Hence I'm confused on the description given by
>     the manual *avoid generation of additional k-points in low symmetry*.
>     Any hints?
>
>     2- From this ML, I found the following notes:
>
>     ---------
>     while doing calculations for any zero dimensions you should always set
>     nosym =.true.
>     -----------
>
>     Does this mean: when I do the  calculations for isolated
>     atom/molecule/nanocluster and so on, I should always set nosym =.true.?
>
>     3-  Prof. Paolo Giannozzi given the following descriptions on some
>     similar topic in this ML:
>
>     ---------
>     calculations on isolated atoms with plane waves are tricky.
>     Compare your results with what you get with the atomic code,
>     in which you can fix occupancies at will
>     ------------
>
>     My issue: how to fix the occupancies based on the results?  Any
>     examples?
>
>     What do you mean by saying *at will*?  If really is a thing *at will*,
>     why should we do it?
>
>     Regards
>
>      >
>      > On Thu, Jul 28, 2011 at 10:12 AM, Gabriele Sclauzero
>      > <gabriele.sclauzero at epfl.ch <mailto:gabriele.sclauzero at epfl.ch>
>     <mailto:gabriele.sclauzero at epfl.ch
>     <mailto:gabriele.sclauzero at epfl.ch>>> wrote:
>      >
>      >
>      >     Il giorno 28/lug/2011, alle ore 01.55, Hongsheng Zhao ha scritto:
>      >
>      >>     Hi all,
>      >>
>      >>     I've learned that when using the a large-cell ( i.e., a big
>     box ) to
>      >>     calculate the energy of isolated atom, it should be done without
>      >>     symmetry.   But I'm not sure what's the meaning of the "without
>      >>     symmetry"  here and how to ensure this when we using a a big box
>      >>     model
>      >>     for this purpose.  Any hints on this issue?
>      >
>      >     This is a FAQ on this forum: have you spent some time
>     browsing the
>      >     archives?
>      >
>      >     OK, I'll give you a hint: "nosym"... but use it with care!
>      >
>      >     HTH
>      >
>      >     GS
>      >
>      >>
>      >>     Regards
>      >>     --
>      >>     Hongsheng Zhao <zhaohscas at yahoo.com.cn
>     <mailto:zhaohscas at yahoo.com.cn>
>      >> <mailto:zhaohscas at yahoo.com.cn <mailto:zhaohscas at yahoo.com.cn>>>
>      >>     School of Physics and Electrical Information Science,
>      >>     Ningxia University, Yinchuan 750021, China
>      >>     _______________________________________________
>      >>     Pw_forum mailing list
>      >> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     <mailto:Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>>
>      >> http://www.democritos.it/mailman/listinfo/pw_forum
>      >
>      >
>      >     ? Gabriele Sclauzero, EPFL SB ITP CSEA
>      >     /   PH H2 462, Station 3, CH-1015 Lausanne/
>      >
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

From chengyu.young at gmail.com  Sat Jul 30 04:16:08 2011
From: chengyu.young at gmail.com (chengyu yang)
Date: Fri, 29 Jul 2011 22:16:08 -0400
Subject: [Pw_forum] Slow calculation of (5,
 5) CNT transmission and complex bands.
In-Reply-To: <CAOk-W=FqEKChn22yxiboP2wULt1cERHAm5estb-DzmfSQ3XPtw@mail.gmail.com>
References: <CAOk-W=GMvgBKO3McU5tO2x_eBtCmUM7QsA1EVDzKkWcEeB_9=A@mail.gmail.com>
	<CAOk-W=EzzLoJy_K8ZKTdFhe7pbRjSCKAP=9Wu_MSNOEahXFgAQ@mail.gmail.com>
	<4E327A29.2010400@materials.ox.ac.uk>
	<CAOk-W=FRZrM3kFMa8eVKySkQFBJPBoKMwQSYBFFQF1nZqnaR_g@mail.gmail.com>
	<CAOk-W=FqEKChn22yxiboP2wULt1cERHAm5estb-DzmfSQ3XPtw@mail.gmail.com>
Message-ID: <CAOk-W=EkMgbKGUrTkvmakd6S+taB0V8=pgMa4YCWQkPejRRm3A@mail.gmail.com>

Can anybody have a look at what's going on?
Thanks.

Chengyu
MMAE,University of Central Florida


2011/7/29 chengyu yang <chengyu.young at gmail.com>

> Dear All,
>          After two hours , my transmission calculation comes out a result.
> But I thought it may be not converged and didn't get the final result.
> May anybody have a look at my output file? I attached in this email.
>        My input file is like this:
>        &inputcond
>     prefixl='55'
>     tran_file='trans.cnt55',
>
>     ikind=0
>     energy0=4.d0
>     denergy=-0.1d0
>     ewind=3.d0
>     epsproj=1.d-4
>     delgep = 1.d-9
>     cutplot = 3.d0
>  /
>     1
>     0.0 0.0 1.0
>     5
>
>
> Is there somebody that can give me an advice?
> I really appreciate it.
>
>
> Chengyu Yang
> Materials Science and Engineering,
> University of Central Florida, USA
>
>
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From flux_ray12 at 163.com  Sat Jul 30 14:54:02 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Sat, 30 Jul 2011 20:54:02 +0800 (CST)
Subject: [Pw_forum] Change of occupation number and cut3d
In-Reply-To: <CAESzT+7mGrm60sUFknrJj0E87eq0YyNiJzMP7HSEiFbxpgJJig@mail.gmail.com>
References: <CAESzT+7mGrm60sUFknrJj0E87eq0YyNiJzMP7HSEiFbxpgJJig@mail.gmail.com>
Message-ID: <43a1d5aa.ba4e.1317b1bc2fd.Coremail.flux_ray12@163.com>

Dear Ponce:
I am sorry that I may not catch the right meaning of your first question. If you mean how to make extra or less charge for a model, you can use "total_charge" in &system namelist.
If you wanna get information of wavefunction, you'd better read Doc/INPUT_PP. For the charge density at specified k-point and band, you can calculate |psi|^2 through pp.x. Moreover, if you want to obtain the charge density for all k-points on specified bands, you can summary them by pp.x, too. P.S.: the original code of pp.x can just allow 7 filepp, but you can change the variable, nfilemax, in PP/chdens.f90, then make pp.x.
Good Luck.

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-07-29 17:27:27,"Samuel Ponc?" <samuel.pon at gmail.com> wrote:
Dear Quantum espresso user/developers,

I have two questions:

1) Is it possible in pwscf to change "by hand" the occupation number ( and impose a charge compensation accordingly) and if so how to do it?
I would like to do so because the sum over the different mode of the partial derivative of the phonon frequency with respect of the occupation number gives the zero point motion renormalization using Brooks theorem. I would like to do this by finite difference (hence doing by hand some calculation at different occupation number).

 2) Is it possible to extract informations in text format form the wavefunctions? What is the right post processing tool to do so? Like having the value of the wavefunction for a defined k points and band index?

Thanks you!

Samuel Ponc?.
(phD student, Universit? Catholique de Louvain, Belgium).
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From flux_ray12 at 163.com  Sat Jul 30 15:17:14 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Sat, 30 Jul 2011 21:17:14 +0800 (CST)
Subject: [Pw_forum] Does not disk_io='low' work with calculation='bands'?
Message-ID: <203411d1.bb79.1317b31035d.Coremail.flux_ray12@163.com>

Dear QE Developer and Users:
I met a problem while calculating band structure. My in put file is like this:
cat >XXX.scf.in <<EOF
&control
     calculation = 'scf' ,
     prefix = 'XXX' ,
     outdir= '$TempDIR/' ,
     pseudo_dir = '$PseudoDIR/' ,
     etot_conv_thr = 1.0d-9 ,
     restart_mode = 'from_scratch' ,
     disk_io = 'low' ,
/
&system
     ibrav = 2 ,
     celldm(1) = *** ,
     nat = 2 ,
     ntyp = 2 ,
     ecutwfc = 42.5 ,
     ecutrho = 400 ,
     occupations = 'smearing' ,
     smearing = 'mp' ,
     degauss = 0.015 ,
/
&electrons
     conv_thr = 1.0d-9 ,
     startingpot = 'atomic' ,
     startingwfc = 'atomic+random' ,
     diagonalization = 'david' ,
     mixing_mode = 'plain' ,
     mixing_beta = 0.7 ,
/
ATOMIC_SPECIES
 *******
ATOMIC_POSITIONS crystal
  *******
K_POINTS
 10
  0.0000000   0.0000000   0.0000000  0.0160000
***********
  0.6000000  -0.2000000   1.0000000  0.3840000
EOF
pw.x <XXX.scf.in >XXX.scf.out
cat >XXX.band.in <<EOF
&control
     calculation = 'bands' ,
     prefix = 'XXX' ,
     outdir= '$TempDIR/' ,
     pseudo_dir = '$PseudoDIR/' ,
     etot_conv_thr = 1.0d-9 ,
     disk_io = 'low' ,
/
&system
     ibrav = 2 ,
     celldm(1) = *** ,
     nat = 2 ,
     ntyp = 2 ,
     ecutwfc = 42.5 ,
     ecutrho = 400 ,
     nbnd = 12 ,
/
&electrons
     diagonalization = 'david' ,
/
ATOMIC_SPECIES
 ******
ATOMIC_POSITIONS crystal
  ******
K_POINTS
 28
   0.0 0.0 0.0 1.0
*******
   0.5 0.5 0.5 1.0
EOF
pw.x <XXX.band.in >XXX.band.out
Then, I got an error frompw.x and process stopped. The error was:
        Each <psi_i|beta_j> matrix      0.01 Mb     (     52,  12)
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from davcio : error #        99
     error while reading from file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
However, after I removeddisk_io = 'low' in SCF calculation, non-SCF calculation can run without any problem.
I checkedXXX.save/charge-density.dat, the files' size seemed same when disk_io equal to 'low' and 'default'. Is this phenomenon meansdisk_io = 'low' cannot be used duringcalculation='bands' and 'nscf'? I am afraiddisk_io = 'default' would lower speed when model was huge~

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea
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From elie.moujaes at hotmail.co.uk  Sat Jul 30 15:28:01 2011
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Sat, 30 Jul 2011 14:28:01 +0100
Subject: [Pw_forum] DOS of a 60 carbon grain boundary system
Message-ID: <DUB110-W165F2A88A05CF64BD6ADAAD3360@phx.gbl>


Dear all,
I am trying to reproduce calculations done on the electronic DOS of a 60 carbon system. I have got that the DOS is around 0.2 at the Fermi level whereas the calculations done previously got that it is exactly zero. In addition their curve seems sharper than mine. I used degauss=0.01 in nscf and scf calculations. the grid for scf was  4 4 1 whilst it was 9 9 1 for nscf. You will find attached the ps file of the DOS. Can anyone advise me on that?
Thanks
Eie Moukaes
University of NottinghamNG7 2RDUK 		 	   		  
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From rdong at ncsu.edu  Sat Jul 30 17:06:29 2011
From: rdong at ncsu.edu (DONG Rui)
Date: Sat, 30 Jul 2011 11:06:29 -0400
Subject: [Pw_forum] vdw2
Message-ID: <CAHLEWG3yzR6bJN8TL8BGSb8TMuhv+jd7ANoa3xjuX=2QbEW0+w@mail.gmail.com>

Hi, all

Thanks for last reply.
Now I am wondering, what is the difference between vdw1 and vdw2?
In the short name definition, vdw-df=".........+vdw", I guess, it is vdw1
because in the output is shows,
  Exchange-correlation      = SLA+PW+RPB+VDW ( 1 4 4 0 1)
But, when I define the input_dft=" SLA+PW+RPB+VDW2", output says "conflict",

Now, Can anyone tell me the difference?
Are the 1 and 2 from the two references consequently?

Thank you!

Rui
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From rdong at ncsu.edu  Sat Jul 30 17:16:26 2011
From: rdong at ncsu.edu (DONG Rui)
Date: Sat, 30 Jul 2011 11:16:26 -0400
Subject: [Pw_forum] vdw-df2
Message-ID: <CAHLEWG3c5QxftNR=b+LmU-hjMC=3bqvYj_dA2J=tS-LfYARXGg@mail.gmail.com>

Never mind, I got it. Someone can delete the previous message.
Thank you!

Rui
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From giannozz at democritos.it  Sat Jul 30 17:22:49 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 30 Jul 2011 17:22:49 +0200
Subject: [Pw_forum] Does not disk_io='low' work with calculation='bands'?
In-Reply-To: <203411d1.bb79.1317b31035d.Coremail.flux_ray12@163.com>
References: <203411d1.bb79.1317b31035d.Coremail.flux_ray12@163.com>
Message-ID: <CC5CEAD2-AF60-4613-A8DB-C4FDE4C448A5@democritos.it>


On Jul 30, 2011, at 15:17 , GAO Zhe wrote:

>      from davcio : error #        99
>      error while reading from file

> Is this phenomenon means disk_io = 'low' cannot be used during
> calculation='bands' and 'nscf'?

there is actually some problem with disk_io option in non-scf  
calculations.
It will be fixed sooner or later. The entire logic (or lack of it) of  
this option
has to be reviewed.

> I am afraid disk_io = 'default' would lower speed when model was huge

it will cause more disk I/O and use more disk space, but less RAM space

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 ttduyle at gmail.com  Sat Jul 30 17:24:14 2011
From: ttduyle at gmail.com (Duy Le)
Date: Sat, 30 Jul 2011 11:24:14 -0400
Subject: [Pw_forum] vdw2
In-Reply-To: <CAHLEWG3yzR6bJN8TL8BGSb8TMuhv+jd7ANoa3xjuX=2QbEW0+w@mail.gmail.com>
References: <CAHLEWG3yzR6bJN8TL8BGSb8TMuhv+jd7ANoa3xjuX=2QbEW0+w@mail.gmail.com>
Message-ID: <CAF-j6z9YHem982M1S48Br_H4OKx0bf1H2+hVxMW1KoEpaU3Sxg@mail.gmail.com>

One thing you should do is to read at least 2 papers:
vdW-DF: PRL 92, 246401 (2004)
vdW-DF2: Phys. Rev. B 82, 081101 (2010)
They will tell you what are the differences between vdW-DF and vdW-DF2.

In short, they differ in the exchange part, gradient coefficient etc...
--------------------------------------------------
Duy Le
PhD Candidate
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Sat, Jul 30, 2011 at 11:06 AM, DONG Rui <rdong at ncsu.edu> wrote:
> Hi, all
>
> Thanks for last reply.
> Now I am wondering, what is the difference between vdw1 and vdw2?
> In the short name definition, vdw-df=".........+vdw", I guess, it is vdw1
> because in the output is shows,
> ? Exchange-correlation????? = SLA+PW+RPB+VDW ( 1 4 4 0 1)
> But, when I define the input_dft=" SLA+PW+RPB+VDW2", output says "conflict",
>
> Now, Can anyone tell me the difference?
> Are the 1 and 2 from the two references consequently?
>
> Thank you!
>
> Rui
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From giannozz at democritos.it  Sat Jul 30 17:27:28 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 30 Jul 2011 17:27:28 +0200
Subject: [Pw_forum] Slow calculation of (5,
	5) CNT transmission and complex bands.
In-Reply-To: <CAOk-W=EkMgbKGUrTkvmakd6S+taB0V8=pgMa4YCWQkPejRRm3A@mail.gmail.com>
References: <CAOk-W=GMvgBKO3McU5tO2x_eBtCmUM7QsA1EVDzKkWcEeB_9=A@mail.gmail.com>
	<CAOk-W=EzzLoJy_K8ZKTdFhe7pbRjSCKAP=9Wu_MSNOEahXFgAQ@mail.gmail.com>
	<4E327A29.2010400@materials.ox.ac.uk>
	<CAOk-W=FRZrM3kFMa8eVKySkQFBJPBoKMwQSYBFFQF1nZqnaR_g@mail.gmail.com>
	<CAOk-W=FqEKChn22yxiboP2wULt1cERHAm5estb-DzmfSQ3XPtw@mail.gmail.com>
	<CAOk-W=EkMgbKGUrTkvmakd6S+taB0V8=pgMa4YCWQkPejRRm3A@mail.gmail.com>
Message-ID: <D78E3CCE-0CB7-4778-9CE4-1B3ADA59C172@democritos.it>


On Jul 30, 2011, at 4:16 , chengyu yang wrote:

> Can anybody have a look at what's going on?

you didn't have a look at this document:
    http://www.quantum-espresso.org/wiki/index.php/Pw_users
especially the following part:
* Remember that the mailing list is a voluntary endeavour:
   nobody is entitled to an answer, even less to an immediate answer.
did you?

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 samuel.pon at gmail.com  Sat Jul 30 17:37:30 2011
From: samuel.pon at gmail.com (=?ISO-8859-1?Q?Samuel_Ponc=E9?=)
Date: Sat, 30 Jul 2011 17:37:30 +0200
Subject: [Pw_forum] Change of occupation number and cut3d
In-Reply-To: <43a1d5aa.ba4e.1317b1bc2fd.Coremail.flux_ray12@163.com>
References: <CAESzT+7mGrm60sUFknrJj0E87eq0YyNiJzMP7HSEiFbxpgJJig@mail.gmail.com>
	<43a1d5aa.ba4e.1317b1bc2fd.Coremail.flux_ray12@163.com>
Message-ID: <CAESzT+6sB_+NZKXhEBC+hR9BV18HogVGrDmfWy0houAtcuan3A@mail.gmail.com>

Dear Mr. Zhe,

Thank you for your answer!

I did try to add the variable tot_charge = +0.00046875 because I have 64 k
points and 4 valences band ( 4-(63*4+3.97)/64)

However if I add the variable 'occupations = "fixed"' then I get the
following WARNING:
     WARNING: integrated charge=     8.00000000, expected=     7.99953125

I off course get the exact same total energy as with tot_charge = 0 (this is
not the expected behaviour).

I did try without the variable 'occupation' (by the way what is the default
value for occupation?) and also get the exact same total energy.

I also do not understand why I don't have an occupation of 2.0 for all my
valence states?

 k = 0.0000 0.0000 0.0000 (  1243 PWs)   bands (ev):

    -7.9264  13.7887  13.7887  13.7887

     occupation numbers
     0.0312   0.0312   0.0312   0.0312

Best regards,

Samuel Ponc?.


2011/7/30 GAO Zhe <flux_ray12 at 163.com>

> Dear Ponce:
> I am sorry that I may not catch the right meaning of your first question.
> If you mean how to make extra or less charge for a model, you can use
> "total_charge" in &system namelist.
> If you wanna get information of wavefunction, you'd better read
> Doc/INPUT_PP. For the charge density at specified k-point and band, you can
> calculate |psi|^2 through pp.x. Moreover, if you want to obtain the charge
> density for all k-points on specified bands, you can summary them by pp.x,
> too. P.S.: the original code of pp.x can just allow 7 filepp, but you can
> change the variable, nfilemax, in PP/chdens.f90, then make pp.x.
> Good Luck.
> --
> GAO Zhe
> CMC Lab, MSE, SNU, Seoul, S.Korea
>
> At 2011-07-29 17:27:27,"Samuel Ponc?" <samuel.pon at gmail.com> wrote:
>
> Dear Quantum espresso user/developers,
>
> I have two questions:
>
> 1) Is it possible in pwscf to change "by hand" the occupation number ( and
> impose a charge compensation accordingly) and if so how to do it?
> I would like to do so because the sum over the different mode of the
> partial derivative of the phonon frequency with respect of the occupation
> number gives the zero point motion renormalization using Brooks theorem. I
> would like to do this by finite difference (hence doing by hand some
> calculation at different occupation number).
>
>  2) Is it possible to extract informations in text format form the
> wavefunctions? What is the right post processing tool to do so? Like having
> the value of the wavefunction for a defined k points and band index?
>
> Thanks you!
>
> Samuel Ponc?.
> (phD student, Universit? Catholique de Louvain, Belgium).
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From ttduyle at gmail.com  Sat Jul 30 18:31:01 2011
From: ttduyle at gmail.com (Duy Le)
Date: Sat, 30 Jul 2011 12:31:01 -0400
Subject: [Pw_forum] Change of occupation number and cut3d
In-Reply-To: <CAESzT+6sB_+NZKXhEBC+hR9BV18HogVGrDmfWy0houAtcuan3A@mail.gmail.com>
References: <CAESzT+7mGrm60sUFknrJj0E87eq0YyNiJzMP7HSEiFbxpgJJig@mail.gmail.com>
	<43a1d5aa.ba4e.1317b1bc2fd.Coremail.flux_ray12@163.com>
	<CAESzT+6sB_+NZKXhEBC+hR9BV18HogVGrDmfWy0houAtcuan3A@mail.gmail.com>
Message-ID: <CAF-j6z-c6np-C_CcaX=X8UKeHZUndUn9=pYXE9VCp6MAvcmL+w@mail.gmail.com>

2011/7/30 Samuel Ponc? <samuel.pon at gmail.com>:
> I did try to add the variable tot_charge = +0.00046875 because I have 64 k
> points and 4 valences band ( 4-(63*4+3.97)/64)

Not sure what you were calculating. tot_charge is additional charge
you add to your system.
For example, if you have a system with 8 electron, and if you define
tot_charge = +1, you will have 8-1=7 electron in the system.

> However if I add the variable 'occupations = "fixed"' then I get the
> following WARNING:
> ???? WARNING: integrated charge=???? 8.00000000, expected=???? 7.99953125
>
> I off course get the exact same total energy as with tot_charge = 0 (this is
> not the expected behaviour).
>
> I did try without the variable 'occupation' (by the way what is the default
> value for occupation?) and also get the exact same total energy.

This does not depend on occupation. Read manual about occupation for
more details.
If you do a simple math: 7.99953125+0.00046875 you will see a "magic" number.


> I also do not understand why I don't have an occupation of 2.0 for all my
> valence states?
>
> ?k = 0.0000 0.0000 0.0000 (? 1243 PWs)?? bands (ev):
>
> ??? -7.9264? 13.7887? 13.7887? 13.7887
>
> ???? occupation numbers
> ???? 0.0312?? 0.0312?? 0.0312?? 0.0312
you should post your input for further advice.
--------------------------------------------------
Duy Le
PhD Candidate
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


>
>
> 2011/7/30 GAO Zhe <flux_ray12 at 163.com>
>>
>> Dear Ponce:
>> I am sorry that I may not catch the right meaning of your first question.
>> If you mean how to make extra or less charge for a model, you can use
>> "total_charge" in &system namelist.
>> If you wanna get information of wavefunction, you'd better read
>> Doc/INPUT_PP. For the charge density at specified k-point and band, you can
>> calculate |psi|^2 through pp.x. Moreover, if you want to obtain the charge
>> density for all k-points on specified bands, you can summary them by pp.x,
>> too. P.S.: the original code of pp.x can just allow 7 filepp, but you can
>> change the variable, nfilemax, in PP/chdens.f90, then make pp.x.
>> Good Luck.
>> --
>> GAO Zhe
>> CMC Lab, MSE, SNU, Seoul, S.Korea
>>
>> At 2011-07-29 17:27:27,"Samuel?Ponc?"?<samuel.pon at gmail.com> wrote:
>>
>> Dear Quantum espresso user/developers,
>>
>> I have two questions:
>>
>> 1) Is it possible in pwscf to change "by hand" the occupation number ( and
>> impose a charge compensation accordingly) and if so how to do it?
>> I would like to do so because the sum over the different mode of the
>> partial derivative of the phonon frequency with respect of the occupation
>> number gives the zero point motion renormalization using Brooks theorem. I
>> would like to do this by finite difference (hence doing by hand some
>> calculation at different occupation number).
>>
>> ?2) Is it possible to extract informations in text format form the
>> wavefunctions? What is the right post processing tool to do so? Like having
>> the value of the wavefunction for a defined k points and band index?
>>
>> Thanks you!
>>
>> Samuel Ponc?.
>> (phD student, Universit? Catholique de Louvain, Belgium).
>>
>>
>>
>> _______________________________________________
>> 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
>
>

From foursea at 163.com  Sun Jul 31 11:27:36 2011
From: foursea at 163.com (lilonghua)
Date: Sun, 31 Jul 2011 17:27:36 +0800
Subject: [Pw_forum] Example08 stop at Fermi surface calculation
Message-ID: <201107311727358753332@163.com>

Dear all,

I have searched the forum, but I didn't find any information that could help me. Therefore, I send my question.

In the case of Example08, I found the calculation always stop at the "running the Fermi Surface calculation ..."?I use "top" to watch and only "mpirun" command is runing, not "pw.x"! Further, I found that both the serial calculation with the default number of k-point(4913 in the example08) and the parallel calculation with less k-points for  FS are OK! 

So, I am very confused. Can anyone solve this problem? Thanks!
 
  Best regards,
Longhua Li
2011-07-31 				
----------------------------------------
lilonghua

From goodluck_1982 at 163.com  Sun Jul 31 11:55:38 2011
From: goodluck_1982 at 163.com (gbliu)
Date: Sun, 31 Jul 2011 17:55:38 +0800
Subject: [Pw_forum] What files are needed when pw.x restarts? In what
 case the *.wfc files are need?
In-Reply-To: <F025D39B-82B7-42D7-8DEE-078A51C35530@democritos.it>
References: <CAPoAzqppLx5mqJX-2oY3eex_B+h-GP=r017xd1FFHwNJtePb2A@mail.gmail.com>	<4E28041D.6050101@chemie.uni-halle.de>	<299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg>	<4E2F1616.8080905@chemie.uni-halle.de>	<4E2F9C6F.9030009@163.com>	<CAKScr_rju9zXEqtjyu=Q8686xUkcyVup7P+Cmq5Wxh=qiLc+qg@mail.gmail.com>	<4E2FBE37.3050409@163.com>	<CAKScr_p22KHGBx_SiV1SAZkAP9xcOnLR4ZFm8L7wWv8nHyniFg@mail.gmail.com>	<CBC4DC5E-EE0C-44B0-8E26-6625B82E9A1D@democritos.it>	<4E328659.8040200@163.com>
	<F025D39B-82B7-42D7-8DEE-078A51C35530@democritos.it>
Message-ID: <4E35269A.6010906@163.com>


>> Now that *.wfc are collected only after consistency is reached and
>> appear as evc.dat, a restarted pw.x scf run can not use them and
>> only charge density available.
> it cannot use them to "restart", i.e. to continue an incomplete
> calculation.
>

Thanks!

Liu

> 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 samuel.pon at gmail.com  Sun Jul 31 15:49:43 2011
From: samuel.pon at gmail.com (=?ISO-8859-1?Q?Samuel_Ponc=E9?=)
Date: Sun, 31 Jul 2011 15:49:43 +0200
Subject: [Pw_forum] Change of occupation number and cut3d
In-Reply-To: <CAF-j6z-c6np-C_CcaX=X8UKeHZUndUn9=pYXE9VCp6MAvcmL+w@mail.gmail.com>
References: <CAESzT+7mGrm60sUFknrJj0E87eq0YyNiJzMP7HSEiFbxpgJJig@mail.gmail.com>
	<43a1d5aa.ba4e.1317b1bc2fd.Coremail.flux_ray12@163.com>
	<CAESzT+6sB_+NZKXhEBC+hR9BV18HogVGrDmfWy0houAtcuan3A@mail.gmail.com>
	<CAF-j6z-c6np-C_CcaX=X8UKeHZUndUn9=pYXE9VCp6MAvcmL+w@mail.gmail.com>
Message-ID: <CAESzT+4=JgJe3sgcupGDwd1aeKFQFS1QiZFXfXkynuUXvMzpBg@mail.gmail.com>

Dear Le,

I have normally 8 electrons in my system and define a charge of tot_charge =
+0.00046875. I then have 7.99953125 electrons in my system. I want to do
than so that I can make a finite difference calculation with respect to the
occupation number of my HOMO. As I'm only considering the gamma point of
diamond and as the HOMO is 3X degenerate at that point I decrease the
occupation number of the last 3 valences bands from 2.0 electrons per bands
to 1.99 electrons per bands.

The numbers that occupation numbers gives in the output file of PWSCF is the
occupation number (theoretically 2.0 for the valence band) weighted by the
symmetries of the k point grid.

*Actual behaviour:*
     number of k points=    8
                       cart. coord. in units 2pi/a_0
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0312500
        k(    2) = (  -0.2500000   0.2500000  -0.2500000), wk =   0.2500000
        k(    3) = (   0.5000000  -0.5000000   0.5000000), wk =   0.1250000
        k(    4) = (   0.0000000   0.5000000   0.0000000), wk =   0.1875000
        k(    5) = (   0.7500000  -0.2500000   0.7500000), wk =   0.7500000
        k(    6) = (   0.5000000   0.0000000   0.5000000), wk =   0.3750000
        k(    7) = (   0.0000000  -1.0000000   0.0000000), wk =   0.0937500
        k(    8) = (  -0.5000000  -1.0000000   0.0000000), wk =   0.1875000

And for the gamma point:

 k = 0.0000 0.0000 0.0000 (  1243 PWs)   bands (ev):

    -7.9264  13.7887  13.7887  13.7887  19.5000  19.5000  19.5000  27.9310

     occupation numbers
     0.0312   0.0312   0.0312   0.0312   0.0000   0.0000   0.0000   0.0000

*Expected behaviour*
     number of k points=    8
                       cart. coord. in units 2pi/a_0
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0312500
        k(    2) = (  -0.2500000   0.2500000  -0.2500000), wk =   0.2500000
        k(    3) = (   0.5000000  -0.5000000   0.5000000), wk =   0.1250000
        k(    4) = (   0.0000000   0.5000000   0.0000000), wk =   0.1875000
        k(    5) = (   0.7500000  -0.2500000   0.7500000), wk =   0.7500000
        k(    6) = (   0.5000000   0.0000000   0.5000000), wk =   0.3750000
        k(    7) = (   0.0000000  -1.0000000   0.0000000), wk =   0.0937500
        k(    8) = (  -0.5000000  -1.0000000   0.0000000), wk =   0.1875000

And for the gamma point:

 k = 0.0000 0.0000 0.0000 (  1243 PWs)   bands (ev):

    -7.9264  13.7887  13.7887  13.7887  19.5000  19.5000  19.5000  27.9310

     occupation numbers
     0.0312   *0.03109375*   *0.03109375    **0.03109375   *0.0000
0.0000   0.0000   0.0000

( The bold number corresponds to 1.99/64 )

Here is my input file:

&CONTROL
  calculation  = "scf"                     ! scf run
  restart_mode = "from_scratch"            ! "restart" form an interrupted
run
  prefix       = "Diamond"                 ! Basename for all binary files
  verbosity    = "high"                    ! Output more informations
  wf_collect   = .true.                    ! Collect wf in one single file

  pseudo_dir   = '$PSEUDO_DIR/'
  outdir       = '$TMP_DIR/'

  tstress      = .true.                    ! If true, print stress
  tprnfor      = .true.                    ! If true, print forces
/
&SYSTEM
  nbnd      = 8                            ! 4 valence and 4 cond.
  ibrav     = 2                            ! Correspond to fcc lattice
  celldm(1) = 6.66491891                   ! Lattice spacing in Bohr
  nat       = 2                            ! Number of atoms
  ntyp      = 1                            ! Number of different atomic type
  ecutwfc   = 100                          ! Wf cutoff in Ry
  ecutrho   = 400                          ! Density cutoff (4*ecutwfc for
nc psp and 9-10 for ultrasoft)
  tot_charge = +0.00046875                 ! 4-(63*4+3.97)/64
  occupations = "fixed"
/
&ELECTRONS
  diagonalization = "david"                ! Diagonalization method: "david"
or "cg"
  conv_thr        = 1e-16                  ! Energy accuracy threshold in Ry
  mixing_beta     = 0.5                    ! Charge mixing, reduce it if SCF
is unstable
/

ATOMIC_SPECIES
C  12.011  C.pz-vbc.UPF                        ! Label  |  mass  |
pseudopotential

ATOMIC_POSITIONS {bohr}
C  0.00  0.00  00.00
C  1.66622973 1.66622973 1.66622973

K_POINTS automatic
4 4 4 0 0 0

Best regards,

Samuel Ponc?

2011/7/30 Duy Le <ttduyle at gmail.com>

> 2011/7/30 Samuel Ponc? <samuel.pon at gmail.com>:
> > I did try to add the variable tot_charge = +0.00046875 because I have 64
> k
> > points and 4 valences band ( 4-(63*4+3.97)/64)
>
> Not sure what you were calculating. tot_charge is additional charge
> you add to your system.
> For example, if you have a system with 8 electron, and if you define
> tot_charge = +1, you will have 8-1=7 electron in the system.
>
> > However if I add the variable 'occupations = "fixed"' then I get the
> > following WARNING:
> >      WARNING: integrated charge=     8.00000000, expected=     7.99953125
> >
> > I off course get the exact same total energy as with tot_charge = 0 (this
> is
> > not the expected behaviour).
> >
> > I did try without the variable 'occupation' (by the way what is the
> default
> > value for occupation?) and also get the exact same total energy.
>
> This does not depend on occupation. Read manual about occupation for
> more details.
> If you do a simple math: 7.99953125+0.00046875 you will see a "magic"
> number.
>
>
> > I also do not understand why I don't have an occupation of 2.0 for all my
> > valence states?
> >
> >  k = 0.0000 0.0000 0.0000 (  1243 PWs)   bands (ev):
> >
> >     -7.9264  13.7887  13.7887  13.7887
> >
> >      occupation numbers
> >      0.0312   0.0312   0.0312   0.0312
> you should post your input for further advice.
> --------------------------------------------------
> Duy Le
> PhD Candidate
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
> >
> >
> > 2011/7/30 GAO Zhe <flux_ray12 at 163.com>
> >>
> >> Dear Ponce:
> >> I am sorry that I may not catch the right meaning of your first
> question.
> >> If you mean how to make extra or less charge for a model, you can use
> >> "total_charge" in &system namelist.
> >> If you wanna get information of wavefunction, you'd better read
> >> Doc/INPUT_PP. For the charge density at specified k-point and band, you
> can
> >> calculate |psi|^2 through pp.x. Moreover, if you want to obtain the
> charge
> >> density for all k-points on specified bands, you can summary them by
> pp.x,
> >> too. P.S.: the original code of pp.x can just allow 7 filepp, but you
> can
> >> change the variable, nfilemax, in PP/chdens.f90, then make pp.x.
> >> Good Luck.
> >> --
> >> GAO Zhe
> >> CMC Lab, MSE, SNU, Seoul, S.Korea
> >>
> >> At 2011-07-29 17:27:27,"Samuel Ponc?" <samuel.pon at gmail.com> wrote:
> >>
> >> Dear Quantum espresso user/developers,
> >>
> >> I have two questions:
> >>
> >> 1) Is it possible in pwscf to change "by hand" the occupation number (
> and
> >> impose a charge compensation accordingly) and if so how to do it?
> >> I would like to do so because the sum over the different mode of the
> >> partial derivative of the phonon frequency with respect of the
> occupation
> >> number gives the zero point motion renormalization using Brooks theorem.
> I
> >> would like to do this by finite difference (hence doing by hand some
> >> calculation at different occupation number).
> >>
> >>  2) Is it possible to extract informations in text format form the
> >> wavefunctions? What is the right post processing tool to do so? Like
> having
> >> the value of the wavefunction for a defined k points and band index?
> >>
> >> Thanks you!
> >>
> >> Samuel Ponc?.
> >> (phD student, Universit? Catholique de Louvain, Belgium).
> >>
> >>
> >>
> >> _______________________________________________
> >> 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
>
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