From ptao10b at imr.ac.cn  Tue Nov  1 03:03:41 2011
From: ptao10b at imr.ac.cn (=?GBK?B?zNXF9A==?=)
Date: Tue, 1 Nov 2011 10:03:41 +0800 (CST)
Subject: [Pw_forum] Please help me
Message-ID: <1e03fc3.2947.1335cde2419.Coremail.ptao10b@imr.ac.cn>

Dear all,

I just met a strange problem when using "dynmat.x" at K point. The supercell of graphene contains 6 carbon atoms which have 18 vibrating modes. All of them are available in the file "gg.dynK".

However, if I apply the "dynmat.x" on "gg.dynK", the screen displayed like this:

forrtl: severe (24): end-of-file during read, unit 5, file stdin, line 442, position 0
Image              PC                Routine            Line        Source             
dynmat.x           0000000000A865AD  Unknown               Unknown  Unknown
dynmat.x           0000000000A850B5  Unknown               Unknown  Unknown
dynmat.x           0000000000A1B719  Unknown               Unknown  Unknown
dynmat.x           00000000009B45CF  Unknown               Unknown  Unknown
dynmat.x           00000000009B3E02  Unknown               Unknown  Unknown
dynmat.x           00000000009E6B66  Unknown               Unknown  Unknown
dynmat.x           000000000043ADC1  Unknown               Unknown  Unknown
dynmat.x           000000000043AA6C  Unknown               Unknown  Unknown
libc.so.6          00002AD76A9EE184  Unknown               Unknown  Unknown
dynmat.x           000000000043A999  Unknown               Unknown  Unknown

Could someone tell me how to do? Thanks.

Yours,
Plato





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From akohlmey at gmail.com  Tue Nov  1 03:16:34 2011
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Mon, 31 Oct 2011 22:16:34 -0400
Subject: [Pw_forum] Please help me
In-Reply-To: <1e03fc3.2947.1335cde2419.Coremail.ptao10b@imr.ac.cn>
References: <1e03fc3.2947.1335cde2419.Coremail.ptao10b@imr.ac.cn>
Message-ID: <CADTmJ6GD9WkNWCATrOVymC6B9F3Aq3=T+waNtgxSmgvXeJ6ogQ@mail.gmail.com>

2011/10/31 ?? <ptao10b at imr.ac.cn>:
> Dear all,
>
> I just met a strange problem when using "dynmat.x" at K point. The supercell of graphene contains 6 carbon atoms which have 18 vibrating modes. All of them are available in the file "gg.dynK".
>
> However, if I apply the "dynmat.x" on "gg.dynK", the screen displayed like this:

as it should. this is not how you use dynmat.x
please read the documentation.

axel.

>
> forrtl: severe (24): end-of-file during read, unit 5, file stdin, line 442, position 0
> Image ? ? ? ? ? ? ?PC ? ? ? ? ? ? ? ?Routine ? ? ? ? ? ?Line ? ? ? ?Source
> dynmat.x ? ? ? ? ? 0000000000A865AD ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> dynmat.x ? ? ? ? ? 0000000000A850B5 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> dynmat.x ? ? ? ? ? 0000000000A1B719 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> dynmat.x ? ? ? ? ? 00000000009B45CF ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> dynmat.x ? ? ? ? ? 00000000009B3E02 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> dynmat.x ? ? ? ? ? 00000000009E6B66 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> dynmat.x ? ? ? ? ? 000000000043ADC1 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> dynmat.x ? ? ? ? ? 000000000043AA6C ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> libc.so.6 ? ? ? ? ?00002AD76A9EE184 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> dynmat.x ? ? ? ? ? 000000000043A999 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
>
> Could someone tell me how to do? Thanks.
>
> Yours,
> Plato
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From ptao10b at imr.ac.cn  Tue Nov  1 03:51:06 2011
From: ptao10b at imr.ac.cn (=?GBK?B?zNXF9A==?=)
Date: Tue, 1 Nov 2011 10:51:06 +0800 (CST)
Subject: [Pw_forum] Please help me
In-Reply-To: <1e03fc3.2947.1335cde2419.Coremail.ptao10b@imr.ac.cn>
References: <1e03fc3.2947.1335cde2419.Coremail.ptao10b@imr.ac.cn>
Message-ID: <11cab42.2cbe.1335d098c97.Coremail.ptao10b@imr.ac.cn>

The problem is solved. It's my fault. Thank you for your help!


> -----????-----
> ???: "??" <ptao10b at imr.ac.cn>
> ????: 2011?11?1? ???
> ???: pw_forum <pw_forum at pwscf.org>
> ??: 
> ??: [Pw_forum] Please help me
> 
> Dear all,
> 
> I just met a strange problem when using "dynmat.x" at K point. The supercell of graphene contains 6 carbon atoms which have 18 vibrating modes. All of them are available in the file "gg.dynK".
> 
> However, if I apply the "dynmat.x" on "gg.dynK", the screen displayed like this:
> 
> forrtl: severe (24): end-of-file during read, unit 5, file stdin, line 442, position 0
> Image              PC                Routine            Line        Source             
> dynmat.x           0000000000A865AD  Unknown               Unknown  Unknown
> dynmat.x           0000000000A850B5  Unknown               Unknown  Unknown
> dynmat.x           0000000000A1B719  Unknown               Unknown  Unknown
> dynmat.x           00000000009B45CF  Unknown               Unknown  Unknown
> dynmat.x           00000000009B3E02  Unknown               Unknown  Unknown
> dynmat.x           00000000009E6B66  Unknown               Unknown  Unknown
> dynmat.x           000000000043ADC1  Unknown               Unknown  Unknown
> dynmat.x           000000000043AA6C  Unknown               Unknown  Unknown
> libc.so.6          00002AD76A9EE184  Unknown               Unknown  Unknown
> dynmat.x           000000000043A999  Unknown               Unknown  Unknown
> 
> Could someone tell me how to do? Thanks.
> 
> Yours,
> Plato
> 
> 
> 
> 
> 






From bdslipun at gmail.com  Tue Nov  1 05:26:16 2011
From: bdslipun at gmail.com (bhabya sahoo)
Date: Tue, 1 Nov 2011 09:56:16 +0530
Subject: [Pw_forum] Raman spectra calculation using QE
In-Reply-To: <WFTUAYMVQBBBAXTPUNGCUDRGSKSB.wumindt2@zju.edu.cn>
References: <WFTUAYMVQBBBAXTPUNGCUDRGSKSB.wumindt2@zju.edu.cn>
Message-ID: <CAJVAAvDEN38fXOq6oXWWmvM+79os0PwRsT_qWdjn-ormAjJm_g@mail.gmail.com>

can u explain me the procedure for calculating ramman spectra in esp[resso

i am a new user






b d sahoo
mumbai barc


On Tue, Nov 1, 2011 at 2:10 AM, wumindt2 <wumindt2 at zju.edu.cn> wrote:

> Dear All,
>
> I calculated the Raman intensity of quartz and got the result shown below.
> To plot the Raman spectra, colume [cm-1] should be the x axis, is colume
> [Raman]
> exactly the y axis?  And what's the meaning of the [depol] colume?
>
> By the way, since epsil can only be calculated at q=0, does it mean there
> is no convergence test of Raman spectra with respect to q point?
>
> Thanks for any help!
> "
>     IR cross sections are in (D/A)^2/amu units
>     Raman cross sections are in A^4/amu units
>     multiply Raman by 0.435857 for Clausius-Mossotti correction
>
> #  mode   [cm-1]     [THz]      IR           Raman     depol
>    1      0.00    0.0000    0.0000    117648.2478    0.0796
>    2      0.00    0.0000    0.0000     54851.8779    0.0878
>    3      0.00    0.0000    0.0000      5721.3899    0.1088
>    4      0.00    0.0000    0.0000     27197.6383    0.0792
>    5      0.00    0.0000    0.0000    147366.7743    0.0728
>    6      0.00    0.0000    0.0000     79591.1052    0.0839
>    7    134.34    4.0273    0.0005     11088.3162    0.6209
>    8    240.10    7.1981    0.1622     16185.7766    0.1558
>    9    241.21    7.2313    0.2024     24875.8773    0.1058
>   10    314.53    9.4293    3.0075      5175.3355    0.2916
>   11    328.75    9.8557    0.1138     17701.2140    0.6847
>   12    346.33   10.3827    3.1900     13146.6141    0.1307
>   13    390.34   11.7020    0.1564     53220.0070    0.0658
>   14    405.27   12.1496    9.5614      5754.0126    0.2673
>   15    434.56   13.0277    5.7052    303619.7884    0.0609
>   16    470.12   14.0938    5.8666      2135.0450    0.5859
>   17    551.14   16.5227    5.7194      5307.8446    0.7482
>   18    663.69   19.8969    2.9906     11422.0326    0.7170
>   19    664.81   19.9304    0.5153     14523.9240    0.4764
>   20    679.62   20.3742   16.2637      2261.0076    0.2333
>   21    745.02   22.3351    8.9307    157046.7356    0.1277
>   22    835.16   25.0373   11.9576      5478.4532    0.6700
>   23    924.96   27.7294   18.0245     18670.7483    0.2741
>   24    985.40   29.5415   40.4317     10913.6235    0.3922
>   25    996.49   29.8738   20.1984     46086.8553    0.5930
>   26   1052.71   31.5592   13.6824     14469.3320    0.4908
>   27   1069.38   32.0591    0.0030     39309.3312    0.7484
>
> Min WU
> University of Saskachewan, Cananda
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From giannozz at democritos.it  Tue Nov  1 09:18:31 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 1 Nov 2011 09:18:31 +0100
Subject: [Pw_forum] Raman spectra calculation  using QE
In-Reply-To: <WFTUAYMVQBBBAXTPUNGCUDRGSKSB.wumindt2@zju.edu.cn>
References: <WFTUAYMVQBBBAXTPUNGCUDRGSKSB.wumindt2@zju.edu.cn>
Message-ID: <DA761E1C-94D1-442D-8F12-501E872CBD13@democritos.it>


On Oct 31, 2011, at 21:40 , wumindt2 wrote:

> And what's the meaning of the [depol] column?

depolarization ratio

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 nbruno014 at gmail.com  Tue Nov  1 13:07:21 2011
From: nbruno014 at gmail.com (nicolas bruno)
Date: Tue, 1 Nov 2011 13:07:21 +0100
Subject: [Pw_forum] Structural properties
Message-ID: <CAL81bo1__vZ0T6+6GZjYB+f03drN3eA7-6_WXBNaX5oNNQw=rw@mail.gmail.com>

Dear all,

I am a new user of  QE and I want to calculate the structural
properties for AlN, could someone direct me for this in particular how
interpret the output to get the lattice parameter?
Thanks in advance.

From arvifis at gmail.com  Tue Nov  1 13:19:55 2011
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Tue, 1 Nov 2011 10:19:55 -0200
Subject: [Pw_forum] Structural properties
In-Reply-To: <CAL81bo1__vZ0T6+6GZjYB+f03drN3eA7-6_WXBNaX5oNNQw=rw@mail.gmail.com>
References: <CAL81bo1__vZ0T6+6GZjYB+f03drN3eA7-6_WXBNaX5oNNQw=rw@mail.gmail.com>
Message-ID: <CABEdBFMWP7D+Gvj3p-JPh128f_Gmig0=fQ7aaRA3YcVd4moo6A@mail.gmail.com>

Dear Nicolar, what kind of calculate are you doing..?? relax or vc-relax
..??

Please write your affiliation

PhD std Arles V. Gil Rebaza
IFLP - Argentina

2011/11/1 nicolas bruno <nbruno014 at gmail.com>

> Dear all,
>
> I am a new user of  QE and I want to calculate the structural
> properties for AlN, could someone direct me for this in particular how
> interpret the output to get the lattice parameter?
> Thanks in advance.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
###--------->   Arles V.   <---------###
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From Alexander.Urban at chemie.uni-erlangen.de  Tue Nov  1 14:38:54 2011
From: Alexander.Urban at chemie.uni-erlangen.de (Alexander Urban)
Date: Tue, 01 Nov 2011 14:38:54 +0100
Subject: [Pw_forum] Berry phase electric field calculations with empty bands
Message-ID: <4EAFF66E.6040004@chemie.uni-erlangen.de>

Dear Quantum Espresso users,

is it possible to perform Berry phase electric field calculations for a 
periodic insulator including empty bands (1) in principle and (2) using 
PWSCF?

I know how to do Berry phase electric field calculations with PWSCF 
(using the `lelfield' keyword) and I also verified the polarizations of 
a number of isolated systems with the results of the sawtooth potential 
(using the `tefield' keyword).  But when I include unoccupied bands, by 
setting `nbnd' to a value larger than nelec/2, the polarization in the 
output does not look reasonable anymore and does not converge.  However, 
the SCF loop converges and also the eigenvalues (i.e. the band 
structures) look fine.

In the PWSCF source code (QE version 4.3.2), namely in 
`c_phase_field.f90', I found the following lines of code:

!  --- Check that we are working with an insulator with no empty bands ---
    IF ((degauss > 0.01d0) .OR. (nbnd /= nelec/2)) &
         WRITE (stdout,*) 'PAY ATTENTION: EL FIELD AND OCCUPATIONS'
    !  CALL errore('c_phase', &
    !        'Polarization only for insulators and no empty bands',1)

The call to the `errore' subroutine is commented out, how do I have to 
interpret this?  Does not the electric polarization only depend on the 
occupied bands, anyway?  Can I trust the SCF wavefunctions?

Sorry for the long e-mail,

Alex


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

Alexander Urban (PhD student)
Interdisciplinary Center for Molecular Materials (ICMM)
Computer Chemistry Center (CCC)
University of Erlangen-Nuremberg
Germany


From giannozz at democritos.it  Tue Nov  1 16:11:27 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 1 Nov 2011 16:11:27 +0100
Subject: [Pw_forum] Berry phase electric field calculations with empty
	bands
In-Reply-To: <4EAFF66E.6040004@chemie.uni-erlangen.de>
References: <4EAFF66E.6040004@chemie.uni-erlangen.de>
Message-ID: <8164764A-E03E-4407-9496-899DA8ABBE7C@democritos.it>


On Nov 1, 2011, at 14:38 , Alexander Urban wrote:

> is it possible to perform Berry phase electric field calculations  
> for a
> periodic insulator including empty bands (1) in principle and (2)  
> using
> PWSCF?

based on my little knowledge of the subject, I would say (1) yes,
(2) likely no. It should be relatively straightforward to generalized
the current algorithms to work even in presence of unoccupied
bands (it is sufficient to consider the correct weight), but
i) it hasn't been done (or it hasn't been completed), and
ii) it must be done in a proper way, avoiding to increase
the complexity of the code.

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 Alexander.Urban at chemie.uni-erlangen.de  Tue Nov  1 16:43:04 2011
From: Alexander.Urban at chemie.uni-erlangen.de (Alexander Urban)
Date: Tue, 01 Nov 2011 16:43:04 +0100
Subject: [Pw_forum] Berry phase electric field calculations with empty
 bands
In-Reply-To: <8164764A-E03E-4407-9496-899DA8ABBE7C@democritos.it>
References: <4EAFF66E.6040004@chemie.uni-erlangen.de>
	<8164764A-E03E-4407-9496-899DA8ABBE7C@democritos.it>
Message-ID: <4EB01388.1050109@chemie.uni-erlangen.de>

Thank you for your response, Paolo Giannozzi.


On 11/01/2011 04:11 PM, Paolo Giannozzi wrote:
> based on my little knowledge of the subject, I would say (1) yes,
> (2) likely no.
That is what I thought...

> It should be relatively straightforward to generalized
> the current algorithms to work even in presence of unoccupied
> bands (it is sufficient to consider the correct weight), but
> i) it hasn't been done (or it hasn't been completed), and
> ii) it must be done in a proper way, avoiding to increase
> the complexity of the code.
I do consider to introduce the necessary modifications.

Maybe someone more familiar with the PWSCF code could point me into the 
right direction?

My thoughts:

- The electric enthalpy SCF wavefunctions are wrong (with empty bands)
   because the electric polarization P is wrong.
- The reason for the error in P is that the sums in the computation
   of P in `c_phase_field()' run over all nbnd bands where it should
   only be the occupied ones (i.e. the occupation numbers have to be used
   as weights).
- The only subroutine that has to be modified is `c_phase_field()'.

If this reasoning is correct, I would take a closer look at 
`c_phase_field()' and estimate the effort to introduce the changes.

Thanks,

Alex

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

Alexander Urban (PhD student)
Interdisciplinary Center for Molecular Materials (ICMM)
Computer Chemistry Center (CCC)
University of Erlangen-Nuremberg
Germany


From naromero at gmail.com  Tue Nov  1 17:27:18 2011
From: naromero at gmail.com (Nichols A. Romero)
Date: Tue, 1 Nov 2011 11:27:18 -0500
Subject: [Pw_forum] Zn NC_PP from qe-forge
In-Reply-To: <8EC42FD1-AADF-4368-91EB-34008CD7DB1C@anl.gov>
References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com>
	<6669DB08-98EE-4E1B-B471-0CC2F167E2DA@anl.gov>
	<CAOb2PV1U_zWhuDkxpdd8Yi9dtpiEAx4PZtGcWMSx1hjqCk0LDA@mail.gmail.com>
	<4E9F83B4.10609@wm.edu>
	<8EC42FD1-AADF-4368-91EB-34008CD7DB1C@anl.gov>
Message-ID: <CAOb2PV2=Jwo3nrvFjnKpB7bNeU=4_bAP0evPNJqcjk8KXL6XJg@mail.gmail.com>

Sorry for replying to this old thread. I still don't quite understand
the behavior for the energy as a function E_{cut,psi} for the
case of E_{cut,rho}=4*E_{cut,psi}. You would expect for a
norm-conserving pseudopotential that the total energy be monotonically
decreasing (Rayleigh-Ritz principle) as it achieves convergence. But
adding the non-linear core correction (nlcc) seems to negate
this behavior. I am assuming that the nlcc can be evaluated exactly in
real-space. Perhaps the FFT is leading to some aliasing
effect?

On Thu, Oct 20, 2011 at 11:05 AM, William Parker <wparker at anl.gov> wrote:
> Thanks, Eric, for the insight. ?That core correction can be vicious. ?Turning up the density cutoff does help. ?There is still oscillation in the total energy at the 100 micro-Ry (meV) level for density cutoff 16 times the wave function cutoff, but I guess one shouldn't expect too much stability at that level.
>
> https://wiki.alcf.anl.gov/wparker/images/6/68/ZnO_ecut_convergence_rho4_10_16_lda_ncpp.png
>
> --William
>
> On Oct 19, 2011, at 9:13 PM, Eric J. Walter wrote:
>
>>
>> Hi,
>>
>>> Just to double-check. Is charge density cutoff 4 times that planewave cutoff?
>>
>> I think that this hits on the issue... ?The Zn.pz-nc.UPF has a sharp
>> core correction. ?The FFT/Density grid
>> needs to be increased significantly, here is a plot of from 4x to 20x
>> ecutwfc for the case with and without
>> a core correction in Zn. I think this is the cause of the odd *ecutwfc*
>> shown by William Parker.
>>
>> http://dl.dropbox.com/u/8094696/Znplot.pdf
>>
>> So, in this case, no, the density cutoff needs to be higher:
>>
>>
>> Eric
>>
>>
>>
>>
>> On 10/19/2011 08:47 PM, Nichols A. Romero wrote:
>>> The behavior here is what I might expect for a real-space DFT code,
>>> but V_NL is evaluated in reciprocal space right (we don't have
>>> real-space projectors)?
>>>
>>> Just to double-check. Is charge density cutoff 4 times that planewave cutoff?
>>>
>>>
>>> On Wed, Oct 19, 2011 at 2:51 PM, William Parker<wparker at anl.gov> ?wrote:
>>>> Dear Yun Song and interested parties,
>>>>
>>>> The possibility of a phonon test case in ZnO piqued my curiosity so I decided to have a go at it. ?I find a very odd convergence pattern with these two pseudopotentials in this system--the total energy has a damped sinusoidal decay with increasing cutoff:
>>>> (selecting the maxima and minima at 10 Ry sampling)
>>>>
>>>> E_cutoff (Ry) ? E_total (Ry)
>>>> 100 ? ? ? ? ? ? -338.741
>>>> 160 ? ? ? ? ? ? -338.660
>>>> 210 ? ? ? ? ? ? -338.675
>>>> 290 ? ? ? ? ? ? -338.665
>>>> 370 ? ? ? ? ? ? -338.668
>>>> 400 ? ? ? ? ? ? -338.667
>>>>
>>>> Figure here: https://wiki.alcf.anl.gov/wparker/images/b/b5/ZnO_ecut_convergence_lda_ncpp.png
>>>> Details here: https://wiki.alcf.anl.gov/wparker/index.php/Zinc_Oxide_Parameter_Convergence
>>>>
>>>> I have never encountered this kind of behavior with norm-conserving pseudopotentials before. ?At worst, I've seen little steps in an otherwise smooth convergence to a value. ?The eigenvalues at the various k-points don't appear to have any ghost states that come and go with cutoff. ?Has anyone observed this kind of oscillation in the total energy with increasing plane-wave cutoff before? ?What gives rise to it?
>>>>
>>>> --William
>>>>
>>>> *********************************************************
>>>> ?William D. Parker
>>>> ?Computational Postdoctoral Fellow ? fax: (630) 252-4798
>>>> ?MSD-212, Rm. C-215
>>>> ?Argonne National Laboratory
>>>> ?9700 S. Cass Ave.
>>>> ?Argonne, IL 60439
>>>> *********************************************************
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Pw_forum mailing list
>>>> Pw_forum at pwscf.org
>>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>>
>>>
>>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
> *********************************************************
> ?William D. Parker
> ?Computational Postdoctoral Fellow ? fax: (630) 252-4798
> ?MSD-212, Rm. C-215
> ?Argonne National Laboratory
> ?9700 S. Cass Ave.
> ?Argonne, IL 60439
> *********************************************************
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Nichols A. Romero, Ph.D.
Argonne Leadership Computing Facility
Argonne, IL 60490
(630) 447-9793

From joerg.buchwald at iom-leipzig.de  Tue Nov  1 17:34:54 2011
From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald)
Date: Tue, 1 Nov 2011 17:34:54 +0100
Subject: [Pw_forum] conflicting values icorr /igcx
Message-ID: <20111101173454.31fcfb63@PC-Mayr-Mitarb6.pc-flexi>

Hi,
I'm trying to model bulk sapphire with norm conserving potentials for O
respectively for Al and O and I get the following error:
--
  stopping ...
     from set_dft_from_name : error #         1
      conflicting values for icorr
--
The same input file worked with ultrasoft and gradient corrected
ultrasoft potentials, but with any of the ncpp (which
I got also from the quantum espresso website) it didn't.
I can't figure out what the sourcecode really does at that point and
the error seems to be quite undocumented.
Thanks for hints,
J?rg


-- 
Leibniz-Institut fuer Oberflaechenmodifizierung e.V.

Permoserstrasse 15
04318 Leipzig
GERMANY

Phone: +49 341 / 235-3367
Web: http://www.uni-leipzig.de/~agmayr
     

From bahaartv at gmail.com  Tue Nov  1 18:37:59 2011
From: bahaartv at gmail.com (bahaareh tavakoli nejad)
Date: Tue, 1 Nov 2011 10:37:59 -0700
Subject: [Pw_forum] Pw_forum Digest, Vol 53, Issue 1
In-Reply-To: <mailman.16728.1320113033.1814.pw_forum@pwscf.org>
References: <mailman.16728.1320113033.1814.pw_forum@pwscf.org>
Message-ID: <CAGMO+LarRZSO+uvFb4Peb2D8ghQ28_un-fvu8U4FBgiB0CBiYA@mail.gmail.com>

subject:Conversion pseudopotential file with fhi or hgh format to upf
format for using in quantum espresso package in suse 11 linux.
Hi.
I am performing the following steps:
1.open terminal
2.run executable file such as fhi2upf.x
3.input file:
4.type name of input file such as 80.Hg.LDA.fhi
5.error:
read-fhi: assuming abinit format
at line 100 of file fhi2upf.f90(unit=1, file='80.Hg.LDA.fhi')
Fortran runtime error:Bad real number in item 1 of list input

please help me for error reason.
thanks
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From f.anis45 at yahoo.com  Tue Nov  1 18:48:54 2011
From: f.anis45 at yahoo.com (F Anis)
Date: Tue, 1 Nov 2011 10:48:54 -0700 (PDT)
Subject: [Pw_forum] (no subject)
Message-ID: <1320169734.75286.YahooMailNeo@web120303.mail.ne1.yahoo.com>

subject:Conversion pseudopotential file with fhi or hgh format to upf format for using in quantum espresso package in suse 11 linux.
I am performing the following steps:
1.open terminal
2.run executable file such as fhi2upf.x
3.input file:
4.type name of input file such as 80.Hg.LDA.fhi
5.error:
read-fhi: assuming abinit format
at line 100 of file fhi2upf.f90(unit=1, file='80.Hg.LDA.fhi')
Fortran runtime error:Bad real number in item 1 of list input

please help me for error reason.
thanks 
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From giannozz at democritos.it  Tue Nov  1 19:12:20 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 1 Nov 2011 19:12:20 +0100
Subject: [Pw_forum] conflicting values icorr /igcx
In-Reply-To: <20111101173454.31fcfb63@PC-Mayr-Mitarb6.pc-flexi>
References: <20111101173454.31fcfb63@PC-Mayr-Mitarb6.pc-flexi>
Message-ID: <CA9078C3-2B32-4A3D-A434-E030FC544592@democritos.it>


On Nov 1, 2011, at 17:34 , J?rg Buchwald wrote:

>      from set_dft_from_name : error #         1
>       conflicting values for icorr
> [...] the error seems to be quite undocumented.

as undocumented as your report is. Which QE version
and which pseudopotentials?

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





From giannozz at democritos.it  Tue Nov  1 19:16:29 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 1 Nov 2011 19:16:29 +0100
Subject: [Pw_forum] Zn NC_PP from qe-forge
In-Reply-To: <CAOb2PV2=Jwo3nrvFjnKpB7bNeU=4_bAP0evPNJqcjk8KXL6XJg@mail.gmail.com>
References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com>
	<6669DB08-98EE-4E1B-B471-0CC2F167E2DA@anl.gov>
	<CAOb2PV1U_zWhuDkxpdd8Yi9dtpiEAx4PZtGcWMSx1hjqCk0LDA@mail.gmail.com>
	<4E9F83B4.10609@wm.edu>
	<8EC42FD1-AADF-4368-91EB-34008CD7DB1C@anl.gov>
	<CAOb2PV2=Jwo3nrvFjnKpB7bNeU=4_bAP0evPNJqcjk8KXL6XJg@mail.gmail.com>
Message-ID: <029705A5-A6F3-4215-BC19-F28DBD059BE7@democritos.it>


On Nov 1, 2011, at 17:27 , Nichols A. Romero wrote:

> I am assuming that the nlcc can be evaluated exactly in real-space.

it could, but it isn't: it is brought to G-space, translated,
brought back to real 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 joerg.buchwald at iom-leipzig.de  Tue Nov  1 20:19:43 2011
From: joerg.buchwald at iom-leipzig.de (joerg.buchwald at iom-leipzig.de)
Date: Tue, 1 Nov 2011 20:19:43 +0100
Subject: [Pw_forum] conflicting values icorr /igcx
Message-ID: <43397.1320175183@iom-leipzig.de>

  BODY { font-family:Arial, Helvetica, sans-serif;font-size:12px; }
 sorry,
 I'm using QE 4.3.2 and as pseudopotentials, i tried nearly all ncpp
which are in the pseudo package from the QE site: e.g.
Al.pbe-rrkj.UPF, Al.pz-vbc.UPF, O.blyp-mt.UPF,
  O.pz-mt.UPF.
  J?rg
 On Tue 01/11/11  7:12 PM , Paolo Giannozzi giannozz at democritos.it
sent:
 On Nov 1, 2011, at 17:34 , J?rg Buchwald wrote:
 >      from set_dft_from_name : error #         1
 >       conflicting values for icorr
 > [...] the error seems to be quite undocumented.
 as undocumented as your report is. Which QE version
 and which pseudopotentials?
 P.
 ---
 Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222
 _______________________________________________
 Pw_forum mailing list
 Pw_forum at pwscf.org [1]
 http://www.democritos.it/mailman/listinfo/pw_forum
 

Links:
------
[1] mailto:Pw_forum at pwscf.org
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From giannozz at democritos.it  Tue Nov  1 21:16:44 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 1 Nov 2011 21:16:44 +0100
Subject: [Pw_forum] Berry phase electric field calculations with empty
	bands
In-Reply-To: <4EB01388.1050109@chemie.uni-erlangen.de>
References: <4EAFF66E.6040004@chemie.uni-erlangen.de>
	<8164764A-E03E-4407-9496-899DA8ABBE7C@democritos.it>
	<4EB01388.1050109@chemie.uni-erlangen.de>
Message-ID: <FD60E719-B3B5-4EA1-8EB3-3847138C9F65@democritos.it>


On Nov 1, 2011, at 16:43 , Alexander Urban wrote:

> If this reasoning is correct, I would take a closer look at
> `c_phase_field()' and estimate the effort to introduce the changes.

it might actually be sufficient, as a quick-and-dirty fix, to replace
the line
                      l_cal=.true.
with
                      l_cal= (nb <= nelec/2) .and. (mb <= nelec/2)

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  Tue Nov  1 22:04:42 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 1 Nov 2011 22:04:42 +0100
Subject: [Pw_forum] conflicting values icorr /igcx
In-Reply-To: <43397.1320175183@iom-leipzig.de>
References: <43397.1320175183@iom-leipzig.de>
Message-ID: <42BC2B1F-7AD0-49A1-82C8-B765A18EACFA@democritos.it>


On Nov 1, 2011, at 20:19 , joerg.buchwald at iom-leipzig.de wrote:

> I'm using QE 4.3.2 and as pseudopotentials, i tried nearly all ncpp
> which are in the pseudo package from the QE site: e.g. Al.pbe- 
> rrkj.UPF,
> Al.pz-vbc.UPF, O.blyp-mt.UPF, O.pz-mt.UPF.

if you use PP generated with different XC, you need to specify which XC
you want with input variable "input_dft". It works for me (see attached)
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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  Tue Nov  1 22:27:32 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 1 Nov 2011 22:27:32 +0100
Subject: [Pw_forum] (no subject)
In-Reply-To: <1320169734.75286.YahooMailNeo@web120303.mail.ne1.yahoo.com>
References: <1320169734.75286.YahooMailNeo@web120303.mail.ne1.yahoo.com>
Message-ID: <DD089B24-8364-44F1-94E1-2A51195C7199@democritos.it>


On Nov 1, 2011, at 18:48 , F Anis wrote:
    the same message as
On Nov 1, 2011, at 18:37 , bahaareh tavakoli nejad wrote:
    So, who is who?

> subject:Conversion pseudopotential file with fhi or hgh format to  
> upf format for using in quantum espresso package in suse 11 linux.

subject must be written in the Subject: field. Please read the  
posting guidelines.

> I am performing the following steps:
> 1.open terminal
> 2.run executable file such as fhi2upf.x
> 3.input file:
> 4.type name of input file such as 80.Hg.LDA.fhi
> 5.error:
> read-fhi: assuming abinit format
> at line 100 of file fhi2upf.f90(unit=1, file='80.Hg.LDA.fhi')
> Fortran runtime error:Bad real number in item 1 of list input

there is no such error with the current version of QE:

giannozz at fe12lx:~$ trunk/espresso-4.3.2/upftools/fhi2upf.x 80-Hg.LDA.fhi
Assuming abinit format. First line:
mercury, fhi98PP : Trouiller-Martins-type, LDA Ceperley/Alder Perdew/ 
Wang (1992), l= 1 local
Pseudopotential with NLCC successfully read
Confirm or modify l max, l loc (read:  3  1) > 3 1
PPs in FHI format do not contain information on atomic valence  
(pseudo-)wavefunctions
Provide the label and the occupancy for each atomic wavefunction used  
in the PP generation
If unknown: list valence wfcts and occupancies for the atomic ground  
state in increasing l order: s,p,d,f
Wavefunction # 1: label (e.g. 4s), occupancy > 6s 2.0
Wavefunction # 2: label (e.g. 4s), occupancy > 6p 0.0
Wavefunction # 3: label (e.g. 4s), occupancy > 5d 10.0
Wavefunction # 4: label (e.g. 4s), occupancy > 4f 0.0
Pseudopotential successfully converted
Output PP file in UPF format :  80-Hg.LDA.fhi.UPF
Pseudopotential successfully written
Please review the content of the PP_INFO fields
*** Please TEST BEFORE USING !!! ***
---
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 joerg.buchwald at iom-leipzig.de  Wed Nov  2 00:20:26 2011
From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald)
Date: Wed, 2 Nov 2011 00:20:26 +0100
Subject: [Pw_forum] conflicting values icorr /igcx
In-Reply-To: <42BC2B1F-7AD0-49A1-82C8-B765A18EACFA@democritos.it>
References: <43397.1320175183@iom-leipzig.de>
	<42BC2B1F-7AD0-49A1-82C8-B765A18EACFA@democritos.it>
Message-ID: <20111102002026.776f1b2f@debian>

Am Tue, 1 Nov 2011 22:04:42 +0100
schrieb Paolo Giannozzi <giannozz at democritos.it>:

> 
> On Nov 1, 2011, at 20:19 , joerg.buchwald at iom-leipzig.de wrote:
> 
> > I'm using QE 4.3.2 and as pseudopotentials, i tried nearly all ncpp
> > which are in the pseudo package from the QE site: e.g. Al.pbe- 
> > rrkj.UPF,
> > Al.pz-vbc.UPF, O.blyp-mt.UPF, O.pz-mt.UPF.
> 
> if you use PP generated with different XC, you need to specify which
> XC you want with input variable "input_dft". It works for me (see
> attached)

Thanks,
that's actually logical.
cheers,
j?rg

From germaneau at gucas.ac.cn  Wed Nov  2 14:04:42 2011
From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=)
Date: Wed, 02 Nov 2011 09:04:42 -0400
Subject: [Pw_forum] Question regarding stars in postscript band plots
Message-ID: <4EB13FEA.7030909@gucas.ac.cn>

Dear all,

When I generate postscript band plots I noticed that above a certain 
value energies (y axis) are replacedd by "*****".
So, I'm just wondering whether there is a way to get ride of them and 
actually print the numerical values.
Thank you,

                        ?ric.

-- 
/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>

Graduate University of Chinese Academy of Sciences
College of Physical 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 physics.skgupta at gmail.com  Wed Nov  2 08:36:31 2011
From: physics.skgupta at gmail.com (Sanjeev Gupta)
Date: Wed, 2 Nov 2011 13:06:31 +0530
Subject: [Pw_forum] Raman spectra calculation using QE
In-Reply-To: <CAJVAAvDEN38fXOq6oXWWmvM+79os0PwRsT_qWdjn-ormAjJm_g@mail.gmail.com>
References: <WFTUAYMVQBBBAXTPUNGCUDRGSKSB.wumindt2@zju.edu.cn>
	<CAJVAAvDEN38fXOq6oXWWmvM+79os0PwRsT_qWdjn-ormAjJm_g@mail.gmail.com>
Message-ID: <CAB4TLP+AMgtajFb-5APiQtg4Ockz5T6Ce4k+BznBaWg=StZN4g@mail.gmail.com>

see the examples of espresso. there u can find the answer of your question.

wishes
SKG

On Tue, Nov 1, 2011 at 9:56 AM, bhabya sahoo <bdslipun at gmail.com> wrote:

> can u explain me the procedure for calculating ramman spectra in esp[resso
>
> i am a new user
>
>
>
>
>
>
> b d sahoo
> mumbai barc
>
>
> On Tue, Nov 1, 2011 at 2:10 AM, wumindt2 <wumindt2 at zju.edu.cn> wrote:
>
>> Dear All,
>>
>> I calculated the Raman intensity of quartz and got the result shown below.
>> To plot the Raman spectra, colume [cm-1] should be the x axis, is colume
>> [Raman]
>> exactly the y axis?  And what's the meaning of the [depol] colume?
>>
>> By the way, since epsil can only be calculated at q=0, does it mean there
>> is no convergence test of Raman spectra with respect to q point?
>>
>> Thanks for any help!
>> "
>>     IR cross sections are in (D/A)^2/amu units
>>     Raman cross sections are in A^4/amu units
>>     multiply Raman by 0.435857 for Clausius-Mossotti correction
>>
>> #  mode   [cm-1]     [THz]      IR           Raman     depol
>>    1      0.00    0.0000    0.0000    117648.2478    0.0796
>>    2      0.00    0.0000    0.0000     54851.8779    0.0878
>>    3      0.00    0.0000    0.0000      5721.3899    0.1088
>>    4      0.00    0.0000    0.0000     27197.6383    0.0792
>>    5      0.00    0.0000    0.0000    147366.7743    0.0728
>>    6      0.00    0.0000    0.0000     79591.1052    0.0839
>>    7    134.34    4.0273    0.0005     11088.3162    0.6209
>>    8    240.10    7.1981    0.1622     16185.7766    0.1558
>>    9    241.21    7.2313    0.2024     24875.8773    0.1058
>>   10    314.53    9.4293    3.0075      5175.3355    0.2916
>>   11    328.75    9.8557    0.1138     17701.2140    0.6847
>>   12    346.33   10.3827    3.1900     13146.6141    0.1307
>>   13    390.34   11.7020    0.1564     53220.0070    0.0658
>>   14    405.27   12.1496    9.5614      5754.0126    0.2673
>>   15    434.56   13.0277    5.7052    303619.7884    0.0609
>>   16    470.12   14.0938    5.8666      2135.0450    0.5859
>>   17    551.14   16.5227    5.7194      5307.8446    0.7482
>>   18    663.69   19.8969    2.9906     11422.0326    0.7170
>>   19    664.81   19.9304    0.5153     14523.9240    0.4764
>>   20    679.62   20.3742   16.2637      2261.0076    0.2333
>>   21    745.02   22.3351    8.9307    157046.7356    0.1277
>>   22    835.16   25.0373   11.9576      5478.4532    0.6700
>>   23    924.96   27.7294   18.0245     18670.7483    0.2741
>>   24    985.40   29.5415   40.4317     10913.6235    0.3922
>>   25    996.49   29.8738   20.1984     46086.8553    0.5930
>>   26   1052.71   31.5592   13.6824     14469.3320    0.4908
>>   27   1069.38   32.0591    0.0030     39309.3312    0.7484
>>
>> Min WU
>> University of Saskachewan, Cananda
>> _______________________________________________
>> 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
>
>


-- 
*Dr. Sanjeev Kumar Gupta*
*Post Doctoral Fellow,
(Ministry of New and Renewable Energy)
Department of Physics,
Bhavnagar University, Bhavnagar-364 022
Gujarat, India*
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From bdslipun at gmail.com  Wed Nov  2 09:47:02 2011
From: bdslipun at gmail.com (bhabya sahoo)
Date: Wed, 2 Nov 2011 14:17:02 +0530
Subject: [Pw_forum] Raman spectra calculation using QE
In-Reply-To: <WFTUAYMVQBBBAXTPUNGCUDRGSKSB.wumindt2@zju.edu.cn>
References: <WFTUAYMVQBBBAXTPUNGCUDRGSKSB.wumindt2@zju.edu.cn>
Message-ID: <CAJVAAvCTAaCkYZh5aGEhBTmYLF1oQ7qYdMEA10RCGzH8gQipDQ@mail.gmail.com>

can u tell me how raman intensity is calculated
because in example IR intensity is given in example 9

On Tue, Nov 1, 2011 at 2:10 AM, wumindt2 <wumindt2 at zju.edu.cn> wrote:

> Dear All,
>
> I calculated the Raman intensity of quartz and got the result shown below.
> To plot the Raman spectra, colume [cm-1] should be the x axis, is colume
> [Raman]
> exactly the y axis?  And what's the meaning of the [depol] colume?
>
> By the way, since epsil can only be calculated at q=0, does it mean there
> is no convergence test of Raman spectra with respect to q point?
>
> Thanks for any help!
> "
>     IR cross sections are in (D/A)^2/amu units
>     Raman cross sections are in A^4/amu units
>     multiply Raman by 0.435857 for Clausius-Mossotti correction
>
> #  mode   [cm-1]     [THz]      IR           Raman     depol
>    1      0.00    0.0000    0.0000    117648.2478    0.0796
>    2      0.00    0.0000    0.0000     54851.8779    0.0878
>    3      0.00    0.0000    0.0000      5721.3899    0.1088
>    4      0.00    0.0000    0.0000     27197.6383    0.0792
>    5      0.00    0.0000    0.0000    147366.7743    0.0728
>    6      0.00    0.0000    0.0000     79591.1052    0.0839
>    7    134.34    4.0273    0.0005     11088.3162    0.6209
>    8    240.10    7.1981    0.1622     16185.7766    0.1558
>    9    241.21    7.2313    0.2024     24875.8773    0.1058
>   10    314.53    9.4293    3.0075      5175.3355    0.2916
>   11    328.75    9.8557    0.1138     17701.2140    0.6847
>   12    346.33   10.3827    3.1900     13146.6141    0.1307
>   13    390.34   11.7020    0.1564     53220.0070    0.0658
>   14    405.27   12.1496    9.5614      5754.0126    0.2673
>   15    434.56   13.0277    5.7052    303619.7884    0.0609
>   16    470.12   14.0938    5.8666      2135.0450    0.5859
>   17    551.14   16.5227    5.7194      5307.8446    0.7482
>   18    663.69   19.8969    2.9906     11422.0326    0.7170
>   19    664.81   19.9304    0.5153     14523.9240    0.4764
>   20    679.62   20.3742   16.2637      2261.0076    0.2333
>   21    745.02   22.3351    8.9307    157046.7356    0.1277
>   22    835.16   25.0373   11.9576      5478.4532    0.6700
>   23    924.96   27.7294   18.0245     18670.7483    0.2741
>   24    985.40   29.5415   40.4317     10913.6235    0.3922
>   25    996.49   29.8738   20.1984     46086.8553    0.5930
>   26   1052.71   31.5592   13.6824     14469.3320    0.4908
>   27   1069.38   32.0591    0.0030     39309.3312    0.7484
>
> Min WU
> University of Saskachewan, Cananda
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From giannozz at democritos.it  Wed Nov  2 09:54:18 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 02 Nov 2011 09:54:18 +0100
Subject: [Pw_forum] Question regarding stars in postscript band plots
In-Reply-To: <4EB13FEA.7030909@gucas.ac.cn>
References: <4EB13FEA.7030909@gucas.ac.cn>
Message-ID: <1320224058.20583.0.camel@fe12lx.fisica.uniud.it>

On Wed, 2011-11-02 at 09:04 -0400, ?ric Germaneau wrote:

> When I generate postscript band plots I noticed that above a certain
> value energies (y axis) are replaced by "*****".
> So, I'm just wondering whether there is a way to get rid of them
>  and actually print the numerical values.

modify the format

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



From nbruno014 at gmail.com  Wed Nov  2 13:04:37 2011
From: nbruno014 at gmail.com (nicolas bruno)
Date: Wed, 2 Nov 2011 13:04:37 +0100
Subject: [Pw_forum] Pw_forum Digest, Vol 53, Issue 3
In-Reply-To: <mailman.16744.1320169737.1814.pw_forum@pwscf.org>
References: <mailman.16744.1320169737.1814.pw_forum@pwscf.org>
Message-ID: <CAL81bo1upLBw5moE4Pc4M5LuLr6YP6icr5nyU1pwmXdzRwjPsg@mail.gmail.com>

Dear Arles,

I do a relax calculations
N. Bruno PhD student

2011/11/1 <pw_forum-request at pwscf.org>

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> Today's Topics:
>
>   1. Structural properties (nicolas bruno)
>   2. Re: Structural properties (Arles V. Gil Rebaza)
>   3. Berry phase electric field calculations with empty bands
>      (Alexander Urban)
>   4. Re: Berry phase electric field calculations with empty    bands
>      (Paolo Giannozzi)
>   5. Re: Berry phase electric field calculations with empty bands
>      (Alexander Urban)
>   6. Re: Zn NC_PP from qe-forge (Nichols A. Romero)
>   7. conflicting values icorr /igcx (J?rg Buchwald)
>   8. Re: Pw_forum Digest, Vol 53, Issue 1 (bahaareh tavakoli nejad)
>   9. (no subject) (F Anis)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 1 Nov 2011 13:07:21 +0100
> From: nicolas bruno <nbruno014 at gmail.com>
> Subject: [Pw_forum] Structural properties
> To: pw_forum at pwscf.org
> Message-ID:
>        <CAL81bo1__vZ0T6+6GZjYB+f03drN3eA7-6_WXBNaX5oNNQw=rw at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear all,
>
> I am a new user of  QE and I want to calculate the structural
> properties for AlN, could someone direct me for this in particular how
> interpret the output to get the lattice parameter?
> Thanks in advance.
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 1 Nov 2011 10:19:55 -0200
> From: "Arles V. Gil Rebaza" <arvifis at gmail.com>
> Subject: Re: [Pw_forum] Structural properties
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>        <CABEdBFMWP7D+Gvj3p-JPh128f_Gmig0=fQ7aaRA3YcVd4moo6A at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Nicolar, what kind of calculate are you doing..?? relax or vc-relax
> ..??
>
> Please write your affiliation
>
> PhD std Arles V. Gil Rebaza
> IFLP - Argentina
>
> 2011/11/1 nicolas bruno <nbruno014 at gmail.com>
>
> > Dear all,
> >
> > I am a new user of  QE and I want to calculate the structural
> > properties for AlN, could someone direct me for this in particular how
> > interpret the output to get the lattice parameter?
> > Thanks in advance.
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> ###--------->   Arles V.   <---------###
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>
> ------------------------------
>
> Message: 3
> Date: Tue, 01 Nov 2011 14:38:54 +0100
> From: Alexander Urban <Alexander.Urban at chemie.uni-erlangen.de>
> Subject: [Pw_forum] Berry phase electric field calculations with empty
>        bands
> To: Pw_forum at pwscf.org
> Message-ID: <4EAFF66E.6040004 at chemie.uni-erlangen.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear Quantum Espresso users,
>
> is it possible to perform Berry phase electric field calculations for a
> periodic insulator including empty bands (1) in principle and (2) using
> PWSCF?
>
> I know how to do Berry phase electric field calculations with PWSCF
> (using the `lelfield' keyword) and I also verified the polarizations of
> a number of isolated systems with the results of the sawtooth potential
> (using the `tefield' keyword).  But when I include unoccupied bands, by
> setting `nbnd' to a value larger than nelec/2, the polarization in the
> output does not look reasonable anymore and does not converge.  However,
> the SCF loop converges and also the eigenvalues (i.e. the band
> structures) look fine.
>
> In the PWSCF source code (QE version 4.3.2), namely in
> `c_phase_field.f90', I found the following lines of code:
>
> !  --- Check that we are working with an insulator with no empty bands ---
>    IF ((degauss > 0.01d0) .OR. (nbnd /= nelec/2)) &
>         WRITE (stdout,*) 'PAY ATTENTION: EL FIELD AND OCCUPATIONS'
>    !  CALL errore('c_phase', &
>    !        'Polarization only for insulators and no empty bands',1)
>
> The call to the `errore' subroutine is commented out, how do I have to
> interpret this?  Does not the electric polarization only depend on the
> occupied bands, anyway?  Can I trust the SCF wavefunctions?
>
> Sorry for the long e-mail,
>
> Alex
>
>
> ----------------------
>
> Alexander Urban (PhD student)
> Interdisciplinary Center for Molecular Materials (ICMM)
> Computer Chemistry Center (CCC)
> University of Erlangen-Nuremberg
> Germany
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 1 Nov 2011 16:11:27 +0100
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Berry phase electric field calculations with
>        empty   bands
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <8164764A-E03E-4407-9496-899DA8ABBE7C at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
>
> On Nov 1, 2011, at 14:38 , Alexander Urban wrote:
>
> > is it possible to perform Berry phase electric field calculations
> > for a
> > periodic insulator including empty bands (1) in principle and (2)
> > using
> > PWSCF?
>
> based on my little knowledge of the subject, I would say (1) yes,
> (2) likely no. It should be relatively straightforward to generalized
> the current algorithms to work even in presence of unoccupied
> bands (it is sufficient to consider the correct weight), but
> i) it hasn't been done (or it hasn't been completed), and
> ii) it must be done in a proper way, avoiding to increase
> the complexity of the code.
>
> 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
>
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 01 Nov 2011 16:43:04 +0100
> From: Alexander Urban <Alexander.Urban at chemie.uni-erlangen.de>
> Subject: Re: [Pw_forum] Berry phase electric field calculations with
>        empty bands
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4EB01388.1050109 at chemie.uni-erlangen.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Thank you for your response, Paolo Giannozzi.
>
>
> On 11/01/2011 04:11 PM, Paolo Giannozzi wrote:
> > based on my little knowledge of the subject, I would say (1) yes,
> > (2) likely no.
> That is what I thought...
>
> > It should be relatively straightforward to generalized
> > the current algorithms to work even in presence of unoccupied
> > bands (it is sufficient to consider the correct weight), but
> > i) it hasn't been done (or it hasn't been completed), and
> > ii) it must be done in a proper way, avoiding to increase
> > the complexity of the code.
> I do consider to introduce the necessary modifications.
>
> Maybe someone more familiar with the PWSCF code could point me into the
> right direction?
>
> My thoughts:
>
> - The electric enthalpy SCF wavefunctions are wrong (with empty bands)
>   because the electric polarization P is wrong.
> - The reason for the error in P is that the sums in the computation
>   of P in `c_phase_field()' run over all nbnd bands where it should
>   only be the occupied ones (i.e. the occupation numbers have to be used
>   as weights).
> - The only subroutine that has to be modified is `c_phase_field()'.
>
> If this reasoning is correct, I would take a closer look at
> `c_phase_field()' and estimate the effort to introduce the changes.
>
> Thanks,
>
> Alex
>
> ----------------------
>
> Alexander Urban (PhD student)
> Interdisciplinary Center for Molecular Materials (ICMM)
> Computer Chemistry Center (CCC)
> University of Erlangen-Nuremberg
> Germany
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 1 Nov 2011 11:27:18 -0500
> From: "Nichols A. Romero" <naromero at gmail.com>
> Subject: Re: [Pw_forum] Zn NC_PP from qe-forge
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>        <CAOb2PV2=Jwo3nrvFjnKpB7bNeU=4_bAP0evPNJqcjk8KXL6XJg at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Sorry for replying to this old thread. I still don't quite understand
> the behavior for the energy as a function E_{cut,psi} for the
> case of E_{cut,rho}=4*E_{cut,psi}. You would expect for a
> norm-conserving pseudopotential that the total energy be monotonically
> decreasing (Rayleigh-Ritz principle) as it achieves convergence. But
> adding the non-linear core correction (nlcc) seems to negate
> this behavior. I am assuming that the nlcc can be evaluated exactly in
> real-space. Perhaps the FFT is leading to some aliasing
> effect?
>
> On Thu, Oct 20, 2011 at 11:05 AM, William Parker <wparker at anl.gov> wrote:
> > Thanks, Eric, for the insight. ?That core correction can be vicious.
> ?Turning up the density cutoff does help. ?There is still oscillation in
> the total energy at the 100 micro-Ry (meV) level for density cutoff 16
> times the wave function cutoff, but I guess one shouldn't expect too much
> stability at that level.
> >
> >
> https://wiki.alcf.anl.gov/wparker/images/6/68/ZnO_ecut_convergence_rho4_10_16_lda_ncpp.png
> >
> > --William
> >
> > On Oct 19, 2011, at 9:13 PM, Eric J. Walter wrote:
> >
> >>
> >> Hi,
> >>
> >>> Just to double-check. Is charge density cutoff 4 times that planewave
> cutoff?
> >>
> >> I think that this hits on the issue... ?The Zn.pz-nc.UPF has a sharp
> >> core correction. ?The FFT/Density grid
> >> needs to be increased significantly, here is a plot of from 4x to 20x
> >> ecutwfc for the case with and without
> >> a core correction in Zn. I think this is the cause of the odd *ecutwfc*
> >> shown by William Parker.
> >>
> >> http://dl.dropbox.com/u/8094696/Znplot.pdf
> >>
> >> So, in this case, no, the density cutoff needs to be higher:
> >>
> >>
> >> Eric
> >>
> >>
> >>
> >>
> >> On 10/19/2011 08:47 PM, Nichols A. Romero wrote:
> >>> The behavior here is what I might expect for a real-space DFT code,
> >>> but V_NL is evaluated in reciprocal space right (we don't have
> >>> real-space projectors)?
> >>>
> >>> Just to double-check. Is charge density cutoff 4 times that planewave
> cutoff?
> >>>
> >>>
> >>> On Wed, Oct 19, 2011 at 2:51 PM, William Parker<wparker at anl.gov>
> ?wrote:
> >>>> Dear Yun Song and interested parties,
> >>>>
> >>>> The possibility of a phonon test case in ZnO piqued my curiosity so I
> decided to have a go at it. ?I find a very odd convergence pattern with
> these two pseudopotentials in this system--the total energy has a damped
> sinusoidal decay with increasing cutoff:
> >>>> (selecting the maxima and minima at 10 Ry sampling)
> >>>>
> >>>> E_cutoff (Ry) ? E_total (Ry)
> >>>> 100 ? ? ? ? ? ? -338.741
> >>>> 160 ? ? ? ? ? ? -338.660
> >>>> 210 ? ? ? ? ? ? -338.675
> >>>> 290 ? ? ? ? ? ? -338.665
> >>>> 370 ? ? ? ? ? ? -338.668
> >>>> 400 ? ? ? ? ? ? -338.667
> >>>>
> >>>> Figure here:
> https://wiki.alcf.anl.gov/wparker/images/b/b5/ZnO_ecut_convergence_lda_ncpp.png
> >>>> Details here:
> https://wiki.alcf.anl.gov/wparker/index.php/Zinc_Oxide_Parameter_Convergence
> >>>>
> >>>> I have never encountered this kind of behavior with norm-conserving
> pseudopotentials before. ?At worst, I've seen little steps in an otherwise
> smooth convergence to a value. ?The eigenvalues at the various k-points
> don't appear to have any ghost states that come and go with cutoff. ?Has
> anyone observed this kind of oscillation in the total energy with
> increasing plane-wave cutoff before? ?What gives rise to it?
> >>>>
> >>>> --William
> >>>>
> >>>> *********************************************************
> >>>> ?William D. Parker
> >>>> ?Computational Postdoctoral Fellow ? fax: (630) 252-4798
> >>>> ?MSD-212, Rm. C-215
> >>>> ?Argonne National Laboratory
> >>>> ?9700 S. Cass Ave.
> >>>> ?Argonne, IL 60439
> >>>> *********************************************************
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Pw_forum mailing list
> >>>> Pw_forum at pwscf.org
> >>>> http://www.democritos.it/mailman/listinfo/pw_forum
> >>>>
> >>>
> >>>
> >>
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >
> > *********************************************************
> > ?William D. Parker
> > ?Computational Postdoctoral Fellow ? fax: (630) 252-4798
> > ?MSD-212, Rm. C-215
> > ?Argonne National Laboratory
> > ?9700 S. Cass Ave.
> > ?Argonne, IL 60439
> > *********************************************************
> >
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Nichols A. Romero, Ph.D.
> Argonne Leadership Computing Facility
> Argonne, IL 60490
> (630) 447-9793
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 1 Nov 2011 17:34:54 +0100
> From: J?rg Buchwald <joerg.buchwald at iom-leipzig.de>
> Subject: [Pw_forum] conflicting values icorr /igcx
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <20111101173454.31fcfb63 at PC-Mayr-Mitarb6.pc-flexi>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
> I'm trying to model bulk sapphire with norm conserving potentials for O
> respectively for Al and O and I get the following error:
> --
>  stopping ...
>     from set_dft_from_name : error #         1
>      conflicting values for icorr
> --
> The same input file worked with ultrasoft and gradient corrected
> ultrasoft potentials, but with any of the ncpp (which
> I got also from the quantum espresso website) it didn't.
> I can't figure out what the sourcecode really does at that point and
> the error seems to be quite undocumented.
> Thanks for hints,
> J?rg
>
>
> --
> Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
>
> Permoserstrasse 15
> 04318 Leipzig
> GERMANY
>
> Phone: +49 341 / 235-3367
> Web: http://www.uni-leipzig.de/~agmayr
>
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 1 Nov 2011 10:37:59 -0700
> From: bahaareh tavakoli nejad <bahaartv at gmail.com>
> Subject: Re: [Pw_forum] Pw_forum Digest, Vol 53, Issue 1
> To: pw_forum at pwscf.org
> Message-ID:
>        <CAGMO+LarRZSO+uvFb4Peb2D8ghQ28_un-fvu8U4FBgiB0CBiYA at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> subject:Conversion pseudopotential file with fhi or hgh format to upf
> format for using in quantum espresso package in suse 11 linux.
> Hi.
> I am performing the following steps:
> 1.open terminal
> 2.run executable file such as fhi2upf.x
> 3.input file:
> 4.type name of input file such as 80.Hg.LDA.fhi
> 5.error:
> read-fhi: assuming abinit format
> at line 100 of file fhi2upf.f90(unit=1, file='80.Hg.LDA.fhi')
> Fortran runtime error:Bad real number in item 1 of list input
>
> please help me for error reason.
> thanks
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>
> ------------------------------
>
> Message: 9
> Date: Tue, 1 Nov 2011 10:48:54 -0700 (PDT)
> From: F Anis <f.anis45 at yahoo.com>
> Subject: [Pw_forum] (no subject)
> To: "Pw_forum at pwscf.org" <Pw_forum at pwscf.org>
> Message-ID:
>        <1320169734.75286.YahooMailNeo at web120303.mail.ne1.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> subject:Conversion pseudopotential file with fhi or hgh format to upf
> format for using in quantum espresso package in suse 11 linux.
> I am performing the following steps:
> 1.open terminal
> 2.run executable file such as fhi2upf.x
> 3.input file:
> 4.type name of input file such as 80.Hg.LDA.fhi
> 5.error:
> read-fhi: assuming abinit format
> at line 100 of file fhi2upf.f90(unit=1, file='80.Hg.LDA.fhi')
> Fortran runtime error:Bad real number in item 1 of list input
>
> please help me for error reason.
> thanks
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>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 53, Issue 3
> ***************************************
>
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From elie.moujaes at hotmail.co.uk  Wed Nov  2 13:49:52 2011
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Wed, 2 Nov 2011 12:49:52 +0000
Subject: [Pw_forum] electron-phonon calculations
Message-ID: <DUB110-W270CF40762AEDC0D97C4E0D3D40@phx.gbl>


Dear all,

I have relaxed the system I am working on with 8 points using shifted x and y axes, namely :

K_POINTS {AUTOMATIC}

2 8 1  1 1 0

with a pressure =0.06 Kbars.

My aim is to do electron phonon calculations; however here, we need to use unshifted axes with denser points; I used

K_POINTS {AUTOMATIC}

2 16 1  1 1 0

The pressure on the system in this case was 0.1 Kbars (shifting a bit from the 0.06 Kbars in the first case). My question is is it ok to do that and will the forces have severe changes (I forgot to print the forces) or should I have relaxed the system in the first place with unshifted axes?

Regards

Elie Moukaes
University of Nottingham
UK

 		 	   		  
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From yunpengwang85 at gmail.com  Wed Nov  2 23:49:33 2011
From: yunpengwang85 at gmail.com (Yun-Peng Wang)
Date: Thu, 03 Nov 2011 06:49:33 +0800
Subject: [Pw_forum] V_loc |psi> in h_psi
In-Reply-To: <mailman.1.1320136044.26364.pw_forum@pwscf.org>
References: <mailman.1.1320136044.26364.pw_forum@pwscf.org>
Message-ID: <4EB1C8FD.5070809@gmail.com>

Hi,

I am looking at the pwscf code. When computing H|psi>, the kinetic part 
and nonlocal part are performed in k-space, however the local part 
V_local|psi> is performed in real space. I think calculation of local 
part V_local|psi> in k-space is more convenient if V_local can be 
transformed into k-space. What is the problem forbidding k-space 
calculation of V_local|psi> ?

best wishes,
Yun-Peng

From germaneau at gucas.ac.cn  Thu Nov  3 11:58:16 2011
From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=)
Date: Thu, 03 Nov 2011 06:58:16 -0400
Subject: [Pw_forum] k-path for phonon
Message-ID: <4EB273C8.4030407@gucas.ac.cn>

Dear all,

I got confused about how to generate k-path for matdyn.in file.
I just realized that xcrysgen does not have option to write k-vectors in 
2pi/a unit ....
Would you please tell me hoe you proceed?
Thank you,

                         ?ric.

-- 
/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>

Graduate University of Chinese Academy of Sciences
College of Physical 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 Nov  3 01:48:42 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 3 Nov 2011 08:48:42 +0800 (CST)
Subject: [Pw_forum] k-path for phonon
In-Reply-To: <4EB273C8.4030407@gucas.ac.cn>
References: <4EB273C8.4030407@gucas.ac.cn>
Message-ID: <1ced53a3.ab2.13366e632a6.Coremail.flux_ray12@163.com>

In my opinion, having chosen the k-path by xcrysden, you can modify the k-path file in QE/PlotPhon/Include, then the full k-path can be generated by QE/PlotPhon/bin/k_for_bands.x


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


At 2011-11-03 18:58:16,"?ric Germaneau" <germaneau at gucas.ac.cn> wrote:
Dear all,

I got confused about how to generate k-path for matdyn.in file.
I just realized that xcrysgen does not have option to write k-vectors in 2pi/a unit ....
Would you please tell me hoe you proceed?
Thank you,

                        ?ric.


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

Dr. ?ric Germaneau

Graduate University of Chinese Academy of Sciences
College of Physical 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 tribhuwan.physics at gmail.com  Thu Nov  3 10:40:09 2011
From: tribhuwan.physics at gmail.com (Tribhuwan Pandey)
Date: Thu, 3 Nov 2011 15:10:09 +0530
Subject: [Pw_forum]  Phonon eigenvector calculation
Message-ID: <CACKvTSMuOX0BUvWeGGZV8U9BZBXnPg3to10oLosv9i97yh8ifw@mail.gmail.com>

Dear all

I am working on  a project related to thermal conductivity calculation by
solving Boltzmann  transport equation.For this i need to calculate phonon
eigenvectors corresponding to anharmonic force constant .Can some body help
me in this matter.


*
 Regards
Tribhuwan Pandey
*
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From f.anis45 at yahoo.com  Thu Nov  3 10:51:36 2011
From: f.anis45 at yahoo.com (F Anis)
Date: Thu, 3 Nov 2011 02:51:36 -0700 (PDT)
Subject: [Pw_forum] fortran 90 for suse 11 linux
Message-ID: <1320313896.30403.YahooMailNeo@web120305.mail.ne1.yahoo.com>

Hi
I am need to fortran compiler for suse 11 linux.
thanks
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From Lorenzo.Paulatto at impmc.upmc.fr  Thu Nov  3 10:55:05 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 03 Nov 2011 10:55:05 +0100
Subject: [Pw_forum] fortran 90 for suse 11 linux
In-Reply-To: <1320313896.30403.YahooMailNeo@web120305.mail.ne1.yahoo.com>
References: <1320313896.30403.YahooMailNeo@web120305.mail.ne1.yahoo.com>
Message-ID: <op.v4c653qixuur8c@vanoxite.impmc.jussieu.fr>

Dear Anis,
I think you wrote to the wrong mailing list! This mailing list is dedicate  
to the Quantum-ESPRESSO code for electronic-structure calculations.

Anyway, g95 and gfortran are free/open source; there also exist some free  
non-commercial version of the intel fortran compiler.

best regards

On Thu, 03 Nov 2011 10:51:36 +0100, F Anis <f.anis45 at yahoo.com> wrote:

> Hi
> I am need to fortran compiler for suse 11 linux.
> thanks


-- 
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 f.anis45 at yahoo.com  Thu Nov  3 11:03:11 2011
From: f.anis45 at yahoo.com (F Anis)
Date: Thu, 3 Nov 2011 03:03:11 -0700 (PDT)
Subject: [Pw_forum] fortran compiler
Message-ID: <1320314591.45397.YahooMailNeo@web120301.mail.ne1.yahoo.com>

Hi? 
I am need to fortran compiler for suse 11 linux to Conversion pseudopotential file with fhi or hgh format to upf format for using in quantum espresso package.because:
I am performing the following steps:
1.open terminal
2.run executable file such as fhi2upf.x
3.input file:
4.type name of input file such as 80.Hg.LDA.fhi
5.error:
read-fhi: assuming abinit format
at line 100 of file fhi2upf.f90(unit=1, file='80.Hg.LDA.fhi')
Fortran runtime error:Bad real number in item 1 of list input

The error reason is: fortran compiler for my suse 11 linux is destroyed.
thanks 
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From Lorenzo.Paulatto at impmc.upmc.fr  Thu Nov  3 11:57:06 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 03 Nov 2011 11:57:06 +0100
Subject: [Pw_forum] V_loc |psi> in h_psi
In-Reply-To: <4EB1C8FD.5070809@gmail.com>
References: <mailman.1.1320136044.26364.pw_forum@pwscf.org>
	<4EB1C8FD.5070809@gmail.com>
Message-ID: <op.v4c91gowxuur8c@vanoxite.impmc.jussieu.fr>

On Wed, 02 Nov 2011 23:49:33 +0100, Yun-Peng Wang  
<yunpengwang85 at gmail.com> wrote:
> I think calculation of local
> part V_local|psi> in k-space is more convenient if V_local can be
> transformed into k-space.

Why do you think it would be more convenient?

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 pankaj.espresso at gmail.com  Thu Nov  3 13:50:18 2011
From: pankaj.espresso at gmail.com (Pankaj Pankaj)
Date: Thu, 3 Nov 2011 18:20:18 +0530
Subject: [Pw_forum] problem in scf run
Message-ID: <CAA6iE10ET_Dh1q_HdbEA-YbZ1RHVBgSYvQrZJXDOOEAAd5cr9w@mail.gmail.com>

Dear All,

  When i tried to run my scf cal, i got following message

At line 155 of file read_cards.f90
Fortran runtime error: End of file
At line 155 of file read_cards.f90
Fortran runtime error: End of file
At line 155 of file read_cards.f90
Fortran runtime error: End of file
At line 155 of file read_cards.f90
Fortran runtime error: End of file
--------------------------------------------------------------------------
mpirun has exited due to process rank 1 with PID 1914 on
node shiva exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).

Whereas for VERY SIMILAR file do not give any error. Where can be problem.

Thank you so much.

Kind Regards
Pankaj
Research Assistant
AU India
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From baroni at sissa.it  Thu Nov  3 15:05:46 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 3 Nov 2011 15:05:46 +0100
Subject: [Pw_forum] V_loc |psi> in h_psi
In-Reply-To: <4EB1C8FD.5070809@gmail.com>
References: <mailman.1.1320136044.26364.pw_forum@pwscf.org>
	<4EB1C8FD.5070809@gmail.com>
Message-ID: <87BFD584-FB13-4E2F-AB6E-439371A1E7F5@sissa.it>

Youn-Peng: V_local is diagonal in the coordinate representation, that's why it is conveniently calculated in real space (in pw.x, as well as in any sensible modern plane-wave electronic-structure code). SB

On Nov 2, 2011, at 11:49 PM, Yun-Peng Wang wrote:

> Hi,
> 
> I am looking at the pwscf code. When computing H|psi>, the kinetic part 
> and nonlocal part are performed in k-space, however the local part 
> V_local|psi> is performed in real space. I think calculation of local 
> part V_local|psi> in k-space is more convenient if V_local can be 
> transformed into k-space. What is the problem forbidding k-space 
> calculation of V_local|psi> ?
> 
> best wishes,
> Yun-Peng
> _______________________________________________
> 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

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From akohlmey at gmail.com  Thu Nov  3 15:18:08 2011
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Thu, 3 Nov 2011 10:18:08 -0400
Subject: [Pw_forum] fortran compiler
In-Reply-To: <1320314591.45397.YahooMailNeo@web120301.mail.ne1.yahoo.com>
References: <1320314591.45397.YahooMailNeo@web120301.mail.ne1.yahoo.com>
Message-ID: <CADTmJ6EtetqGnJO8UD8x2TyLK2CLiiVjmtge7KDOjrnY3F8QFA@mail.gmail.com>

On Thu, Nov 3, 2011 at 6:03 AM, F Anis <f.anis45 at yahoo.com> wrote:

> Hi
>     I am need to fortran compiler for suse 11 linux to Conversion
> pseudopotential file with fhi or hgh format to upf format for using in
> quantum espresso package.because:
> I am performing the following steps:
> 1.open terminal
> 2.run executable file such as fhi2upf.x
> 3.input file:
> 4.type name of input file such as 80.Hg.LDA.fhi
> 5.error:
> read-fhi: assuming abinit format
> at line 100 of file fhi2upf.f90(unit=1, file='80.Hg.LDA.fhi')
> Fortran runtime error:Bad real number in item 1 of list input
>
> The error reason is: fortran compiler for my suse 11 linux is destroyed.
>

no, it is not. the reason is that you have a bad input,
as the executable is telling you. PEBCAC.

axel.


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


-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com  http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
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From akohlmey at gmail.com  Thu Nov  3 15:19:57 2011
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Thu, 3 Nov 2011 10:19:57 -0400
Subject: [Pw_forum] problem in scf run
In-Reply-To: <CAA6iE10ET_Dh1q_HdbEA-YbZ1RHVBgSYvQrZJXDOOEAAd5cr9w@mail.gmail.com>
References: <CAA6iE10ET_Dh1q_HdbEA-YbZ1RHVBgSYvQrZJXDOOEAAd5cr9w@mail.gmail.com>
Message-ID: <CADTmJ6EmDG8o7_qs3nofgCxSUJU4Fd3sF=9uSFmvTHQokQrXfA@mail.gmail.com>

On Thu, Nov 3, 2011 at 8:50 AM, Pankaj Pankaj <pankaj.espresso at gmail.com>wrote:

> Dear All,
>
>   When i tried to run my scf cal, i got following message
>
> At line 155 of file read_cards.f90
> Fortran runtime error: End of file
> At line 155 of file read_cards.f90
> Fortran runtime error: End of file
> At line 155 of file read_cards.f90
> Fortran runtime error: End of file
> At line 155 of file read_cards.f90
> Fortran runtime error: End of file
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 1 with PID 1914 on
> node shiva exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
>
> Whereas for VERY SIMILAR file do not give any error. Where can be problem.
>

your input is missing an essential part.
and "end of file" error means, that the
code is trying to read something, but
it is not there.

axel.


>
> Thank you so much.
>
> Kind Regards
> Pankaj
> Research Assistant
> AU India
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com  http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
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From baroni at sissa.it  Thu Nov  3 16:49:18 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 3 Nov 2011 16:49:18 +0100
Subject: [Pw_forum] problem in scf run
In-Reply-To: <CADTmJ6EmDG8o7_qs3nofgCxSUJU4Fd3sF=9uSFmvTHQokQrXfA@mail.gmail.com>
References: <CAA6iE10ET_Dh1q_HdbEA-YbZ1RHVBgSYvQrZJXDOOEAAd5cr9w@mail.gmail.com>
	<CADTmJ6EmDG8o7_qs3nofgCxSUJU4Fd3sF=9uSFmvTHQokQrXfA@mail.gmail.com>
Message-ID: <14119DAC-136A-450C-B413-9A7D30A4001A@sissa.it>

Welcome back, Axel.
I am very glad to read from you back (and very sorry that you did not make it to Trieste).
Stefano

On Nov 3, 2011, at 3:19 PM, Axel Kohlmeyer wrote:

> 
> 
> On Thu, Nov 3, 2011 at 8:50 AM, Pankaj Pankaj <pankaj.espresso at gmail.com> wrote:
> Dear All,
> 
>   When i tried to run my scf cal, i got following message
> 
> At line 155 of file read_cards.f90
> Fortran runtime error: End of file
> At line 155 of file read_cards.f90
> Fortran runtime error: End of file
> At line 155 of file read_cards.f90
> Fortran runtime error: End of file
> At line 155 of file read_cards.f90
> Fortran runtime error: End of file
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 1 with PID 1914 on
> node shiva exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> 
> Whereas for VERY SIMILAR file do not give any error. Where can be problem.
> 
> your input is missing an essential part.
> and "end of file" error means, that the
> code is trying to read something, but
> it is not there.
> 
> axel.
>  
> 
> Thank you so much.
> 
> Kind Regards
> Pankaj
> Research Assistant
> AU India
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> 
> -- 
> Dr. Axel Kohlmeyer   
> akohlmey at gmail.com  http://goo.gl/1wk0
> 
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
> _______________________________________________
> 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

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From dceresoli at gmail.com  Thu Nov  3 21:06:16 2011
From: dceresoli at gmail.com (Davide Ceresoli)
Date: Thu, 03 Nov 2011 21:06:16 +0100
Subject: [Pw_forum] GIPAW: error in output
In-Reply-To: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it>
References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it>
Message-ID: <4EB2F438.5070406@gmail.com>

On 01/-10/-28163 08:59 PM, Carlo Nervi wrote:
> The gipaw calculations proceed, apparently ends normally,
> but the output contains several NotaNumber (NaN). Anuone
> have an idea qhat's wrong or could please give some hints
> how to solve the problem?
> Thank you,
>    Carlo
Problem found! Change line 356 of qe-gipaw/src/nmr_routines.f90 from:
     call greenfunction(ik,aux1, aux2 , 0.d0)
to:
     call greenfunction(ik,aux1, aux2 , (/0.d0,0.d0,0.d0/))

I've found that the Intel compiler is anyway filling the q array with
zeros, but other compilers don't. As a result q(2) and q(3) contained
random values from the RAM.

I've tested with gfortran and I hope that now it will work with
every compiler.

Best,
     Davide

From payam.norouzzadeh at gmail.com  Thu Nov  3 21:46:56 2011
From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh)
Date: Thu, 3 Nov 2011 15:46:56 -0500
Subject: [Pw_forum] mean square displacement amplitude for an atom
Message-ID: <CAND4gJGVToC63q2mZ89cB9-zFN+i5w_QiUxmHzGDrf775bBS9w@mail.gmail.com>

Hello QE users

Does anyone know how to calculate mean square displacement amplitude for an
atom in unit cell using pwscf?

Best regards,Payam Norouzzadeh
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From akohlmey at gmail.com  Thu Nov  3 22:09:17 2011
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Thu, 3 Nov 2011 17:09:17 -0400
Subject: [Pw_forum] problem in scf run
In-Reply-To: <14119DAC-136A-450C-B413-9A7D30A4001A@sissa.it>
References: <CAA6iE10ET_Dh1q_HdbEA-YbZ1RHVBgSYvQrZJXDOOEAAd5cr9w@mail.gmail.com>
	<CADTmJ6EmDG8o7_qs3nofgCxSUJU4Fd3sF=9uSFmvTHQokQrXfA@mail.gmail.com>
	<14119DAC-136A-450C-B413-9A7D30A4001A@sissa.it>
Message-ID: <CADTmJ6H=RG8KXquQ9VaT5_+vcnTL2AhHqzbtbSjyGVcq_XCLLQ@mail.gmail.com>

ciao stefano,

On Thu, Nov 3, 2011 at 11:49 AM, Stefano Baroni <baroni at sissa.it> wrote:

> Welcome back, Axel.
>

glad to be back. i have acquired a couple of "customers" on
Temple's HPC facility that use quantum espresso, so
it'll be helpful for me to have a hand on the Q-E pulse again. ;-)


> I am very glad to read from you back (and very sorry that you did not make
> it to Trieste).
>

i can assure you it is not because of trieste or the people there.
in this particular case, it was an extremely difficult decision
between two equally appealing opportunities, where no side
deserved to be turned down. i guess, sometimes your life can
be made difficult by giving you what you want, but too much of it.

cheers,
    axel.

Stefano
>
> On Nov 3, 2011, at 3:19 PM, Axel Kohlmeyer wrote:
>
>
>
> On Thu, Nov 3, 2011 at 8:50 AM, Pankaj Pankaj <pankaj.espresso at gmail.com>wrote:
>
>> Dear All,
>>
>>   When i tried to run my scf cal, i got following message
>>
>> At line 155 of file read_cards.f90
>> Fortran runtime error: End of file
>> At line 155 of file read_cards.f90
>> Fortran runtime error: End of file
>> At line 155 of file read_cards.f90
>> Fortran runtime error: End of file
>> At line 155 of file read_cards.f90
>> Fortran runtime error: End of file
>> --------------------------------------------------------------------------
>> mpirun has exited due to process rank 1 with PID 1914 on
>> node shiva exiting without calling "finalize". This may
>> have caused other processes in the application to be
>> terminated by signals sent by mpirun (as reported here).
>>
>> Whereas for VERY SIMILAR file do not give any error. Where can be problem.
>>
>
> your input is missing an essential part.
> and "end of file" error means, that the
> code is trying to read something, but
> it is not there.
>
> axel.
>
>
>>
>> Thank you so much.
>>
>> Kind Regards
>> Pankaj
>> Research Assistant
>> AU India
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey at gmail.com  http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
> _______________________________________________
> 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
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com  http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
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From carlo.nervi at unito.it  Fri Nov  4 00:21:35 2011
From: carlo.nervi at unito.it (Carlo Nervi)
Date: Fri, 4 Nov 2011 00:21:35 +0100 (CET)
Subject: [Pw_forum] GIPAW: error in output
In-Reply-To: <4EB2F438.5070406@gmail.com>
References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it>
	<4EB2F438.5070406@gmail.com>
Message-ID: <60091.130.192.119.45.1320362495.squirrel@mail.unito.it>

Thanks Davide,
this is really great!
Please note that a similar error (IMHO) is also present in
the epr_routines.f90

Many many thanks,
  Carlo

>
> On 01/-10/-28163 08:59 PM, Carlo Nervi wrote:
>> The gipaw calculations proceed, apparently ends
>> normally,
>> but the output contains several NotaNumber (NaN). Anuone
>> have an idea qhat's wrong or could please give some
>> hints
>> how to solve the problem?
>> Thank you,
>>    Carlo
> Problem found! Change line 356 of
> qe-gipaw/src/nmr_routines.f90 from:
>      call greenfunction(ik,aux1, aux2 , 0.d0)
> to:
>      call greenfunction(ik,aux1, aux2 ,
> (/0.d0,0.d0,0.d0/))
>
> I've found that the Intel compiler is anyway filling the q
> array with
> zeros, but other compilers don't. As a result q(2) and
> q(3) contained
> random values from the RAM.
>
> I've tested with gfortran and I hope that now it will work
> with
> every compiler.
>
> Best,
>      Davide
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


From songsong19840614 at hotmail.com  Fri Nov  4 02:15:56 2011
From: songsong19840614 at hotmail.com (KangYun Song)
Date: Fri, 4 Nov 2011 01:15:56 +0000
Subject: [Pw_forum] GIPAW: error in output
In-Reply-To: <4EA66C9D.6060800@gmail.com>
References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it>,
	<4EA66C9D.6060800@gmail.com>
Message-ID: <COL113-W197C68AADAD2D36500CEC6C8DA0@phx.gbl>


Dear Carlo and Davide:
         Gfortran is really for pwscf.Last year I use gfortran to Compile(ubuntu,Dell computer).Although I am successfully ,the result from example is not match to the reference.So the Intel Compile is good for pwscf with Red hat enterprise 5.0.

Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.
 

> Date: Tue, 25 Oct 2011 10:00:29 +0200
> From: dceresoli at gmail.com
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] GIPAW: error in output
> 
> Dear Carlo,
> if I must guess, 90% that it is a problem of the gfortran
> compiler. I recognize that the situation of fortran compilers
> and of the floating-point behavior of CPUs is very annoying.
> 
> I'm using the Intel compiler with MKL and FFTW3 and I've run
> most calculations of x86_64 CPUs. If I will have time, I'll
> give a try to gfortran 4.6.
> 
> Best,
> Davide
> 
> 
> On 01/-10/-28163 08:59 PM, Carlo Nervi wrote:
> > Hello,
> > I succesfully compiled QE 4.3.2 and the corresponding
> > GIPAW module on a Opteron 6168 linux using gfortran 4.6,
> > acml 5.0.0 and amdlibm 3.0.1.
> >
> > I did the benzene-scf.in job in the
> > GIPAW/examples/benzene-USPP/ directory. The scf energy is
> > the same as the reference output, which is in the same
> > directory (apparently all is okay).
> > I've compiled the gipaw module by the common way 'make
> > gipaw' from the source QE dir. - I hope this was okay...
> >
> > The gipaw calculations proceed, apparently ends normally,
> > but the output contains several NotaNumber (NaN). Anuone
> > have an idea qhat's wrong or could please give some hints
> > how to solve the problem?
> > Thank you,
> > Carlo
> >
> > ...
> > negative rho (up, down): 0.103E-03 0.000E+00
> > init_paw_1: ntyp= 1 rc= 1.4000 rs= 0.9333
> > init_paw_1: ntyp= 1 rc= 1.4000 rs= 0.9333
> > init_paw_1: ntyp= 1 rc= 1.4000 rs= 0.9333
> > init_paw_1: ntyp= 1 rc= 1.4000 rs= 0.9333
> >
> > init_gipaw_1: projectors nearly linearly dependent:
> > ntyp = 1, l/n1/n2 = 0 2 1 0.99622328
> > init_gipaw_1: projectors nearly linearly dependent:
> > ntyp = 1, l/n1/n2 = 1 2 1 0.99789339
> > init_paw_1: ntyp= 2 rc= 0.8000 rs= 0.5333
> > init_paw_1: ntyp= 2 rc= 0.8000 rs= 0.5333
> > init_gipaw_1: projectors nearly linearly dependent:
> > ntyp = 2, l/n1/n2 = 0 2 1 0.99987400
> >
> > GIPAW : 4.81s CPU 10.71s WALL
> >
> > Computing the magnetic susceptibility isolve=0
> > ethr=0.1000E-13
> > k-point # 1 of 1 pool # 1
> > ik 1 ibnd 16 linter: root not converged 0.305E+07
> > ik 1 ibnd 16 linter: root not converged 0.139E+31
> > ik 1 ibnd 16 linter: root not converged 0.122E+27
> > End of magnetic susceptibility calculation
> >
> > f-sum rule (1st term):
> > ************** 0.0000 0.0000
> > 0.0000 -29.8546 0.0000
> > 0.0000 0.0000 -29.9120
> >
> > f-sum rule (2nd term):
> > -0.3248 0.0000 0.0000
> > 0.0000 -0.3248 0.0000
> >
> > ...
> >
> > Contributions to the NMR chemical shifts:
> > -------------------------------
> >
> > Core contribution in ppm:
> >
> > Atom 1 C pos: ( 0.000000 0.107679 0.000000)
> > sigma: 200.51
> > Atom 2 C pos: ( 0.093253 0.053840 0.000000)
> > sigma: 200.51
> > Atom 3 C pos: ( 0.093253 -0.053840 0.000000)
> > sigma: 200.51
> > Atom 4 C pos: ( 0.000000 -0.107679 0.000000)
> > sigma: 200.51
> > Atom 5 C pos: ( -0.093253 -0.053840 0.000000)
> > sigma: 200.51
> > Atom 6 C pos: ( -0.093253 0.053840 0.000000)
> > sigma: 200.51
> > Atom 7 H pos: ( 0.000000 0.191523 0.000000)
> > sigma: 0.00
> > Atom 8 H pos: ( 0.165864 0.095761 0.000000)
> > sigma: 0.00
> > Atom 9 H pos: ( 0.165864 -0.095761 0.000000)
> > sigma: 0.00
> > Atom 10 H pos: ( 0.000000 -0.191523 0.000000)
> > sigma: 0.00
> > Atom 11 H pos: ( -0.165864 -0.095761 0.000000)
> > sigma: 0.00
> > Atom 12 H pos: ( -0.165864 0.095761 0.000000)
> > sigma: 0.00
> >
> > Bare contribution in ppm:
> >
> > Atom 1 C pos: ( 0.000000 0.107679 0.000000)
> > sigma: NaN
> > NaN NaN NaN
> > NaN NaN NaN
> > NaN NaN NaN
> >
> > Atom 2 C pos: ( 0.093253 0.053840 0.000000)
> > sigma: NaN
> > NaN NaN NaN
> > NaN NaN NaN
> > NaN NaN NaN
> >
> > ...
> > Total NMR chemical shifts in ppm:
> > ---------------------------------------
> >
> > Atom 1 C pos: ( 0.000000 0.107679 0.000000)
> > sigma: NaN
> > C 1 anisotropy: NaN eta: 0.0000
> > C 1 sigma_xx= NaN axis=( NaN
> > NaN 0.000000)
> > C 1 sigma_yy= NaN axis=( NaN
> > NaN 0.000000)
> > C 1 sigma_zz= NaN axis=( 0.000000
> > 0.000000 1.000000)
> >
> > Atom 2 C pos: ( 0.093253 0.053840 0.000000)
> > sigma: NaN
> > C 2 anisotropy: NaN eta: 0.0000
> > C 2 sigma_xx= NaN axis=( NaN
> > NaN 0.000000)
> > C 2 sigma_yy= NaN axis=( NaN
> > NaN 0.000000)
> > C 2 sigma_zz= NaN axis=( 0.000000
> > 0.000000 1.000000)
> >
> >
> >
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
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From songsong19840614 at hotmail.com  Fri Nov  4 04:02:27 2011
From: songsong19840614 at hotmail.com (KangYun Song)
Date: Fri, 4 Nov 2011 03:02:27 +0000
Subject: [Pw_forum] Structural properties
In-Reply-To: <CABEdBFMWP7D+Gvj3p-JPh128f_Gmig0=fQ7aaRA3YcVd4moo6A@mail.gmail.com>
References: <CAL81bo1__vZ0T6+6GZjYB+f03drN3eA7-6_WXBNaX5oNNQw=rw@mail.gmail.com>,
	<CABEdBFMWP7D+Gvj3p-JPh128f_Gmig0=fQ7aaRA3YcVd4moo6A@mail.gmail.com>
Message-ID: <COL113-W24AD5C0C396BCC8B60795DC8DA0@phx.gbl>


Dear Nicola:
        The lattice parameter from output is:
CELL_PARAMETERS (alat=  5.07500000)
   1.000458212   0.000000000   0.000000000
  -0.500229106   0.866422227   0.000000000
   0.000000000   0.000000000   1.636876279
It means 
   acosx/5.075   acosy/5.075   acosz/5.075
   bcosx/5.075   bcosy/5.075   bcosz/5.075
   cosx/5.075    ccosy/5.075   ccosz/5.075
 
Last example is:
   a=1.000458212*5.075,
   c=1.636876279*5.075

Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.
 



Date: Tue, 1 Nov 2011 10:19:55 -0200
From: arvifis at gmail.com
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] Structural properties

Dear Nicolar, what kind of calculate are you doing..?? relax or vc-relax ..??

Please write your affiliation 

PhD std Arles V. Gil Rebaza
IFLP - Argentina


2011/11/1 nicolas bruno <nbruno014 at gmail.com>

Dear all,

I am a new user of  QE and I want to calculate the structural
properties for AlN, could someone direct me for this in particular how
interpret the output to get the lattice parameter?
Thanks in advance.
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


-- 
###--------->   Arles V.   <---------###

_______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum 		 	   		  
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From germaneau at gucas.ac.cn  Fri Nov  4 16:43:14 2011
From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=)
Date: Fri, 04 Nov 2011 11:43:14 -0400
Subject: [Pw_forum] Structural properties
In-Reply-To: <520373911.26062@gscas.net.cn>
References: <CAL81bo1__vZ0T6+6GZjYB+f03drN3eA7-6_WXBNaX5oNNQw=rw@mail.gmail.com>,
	<CABEdBFMWP7D+Gvj3p-JPh128f_Gmig0=fQ7aaRA3YcVd4moo6A@mail.gmail.com>
	<520373911.26062@gscas.net.cn>
Message-ID: <4EB40812.5030108@gucas.ac.cn>

Dear Yun Song,

I'm sorry but that does not seem to right.
If H is the cell description in Cartesian coordinates, meaning H = 
CELL_PARAMETERS * alat, we have :

    V1(1) = H(1,1)
    V1(2) = H(2,1)
    V1(3) = H(3,1)

    V2(1) = H(1,2)
    V2(2) = H(2,2)
    V2(3) = H(3,2)

    V3(1) = H(1,3)
    V3(2) = H(2,3)
    V3(3) = H(3,3)

    a = sqrt(dot_product(V1,V1))
    b = sqrt(dot_product(V2,V2))
    c = sqrt(dot_product(V3,V3))

    alpha = acos( dot_product(V2,V3) / ( b * c ) ) /  RAD
    beta  = acos( dot_product(V1,V3) / ( c * a ) ) /  RAD
    gamma = acos( dot_product(V1,V2) / ( a * b ) ) /  RAD

Best,

                            ?ric.

On 11/03/2011 11:02 PM, KangYun Song wrote:
> Dear Nicola:
>         The lattice parameter from output is:
>
> CELL_PARAMETERS (alat=5.07500000)
> 1.0004582120.0000000000.000000000
> -0.5002291060.8664222270.000000000
> 0.0000000000.0000000001.636876279
>
> It means
>
>    acosx/5.075   acosy/5.075   acosz/5.075
>
>    bcosx/5.075   bcosy/5.075   bcosz/5.075
>
>    cosx/5.075    ccosy/5.075   ccosz/5.075
>
> Last example is:
>
>    a=1.000458212*5.075,
>
>    c=1.636876279*5.075
>
> Yun Song,Kang
> Department Physical Science and Technology of  Inner Mongolia University.
>
> ------------------------------------------------------------------------
> Date: Tue, 1 Nov 2011 10:19:55 -0200
> From: arvifis at gmail.com
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Structural properties
>
> Dear Nicolar, what kind of calculate are you doing..?? relax or 
> vc-relax ..??
>
> Please write your affiliation
>
> PhD std Arles V. Gil Rebaza
> IFLP - Argentina
>
> 2011/11/1 nicolas bruno <nbruno014 at gmail.com <mailto:nbruno014 at gmail.com>>
>
>     Dear all,
>
>     I am a new user of  QE and I want to calculate the structural
>     properties for AlN, could someone direct me for this in particular how
>     interpret the output to get the lattice parameter?
>     Thanks in advance.
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> -- 
> ###--------->   Arles V. <---------###
>
> _______________________________________________ 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

-- 
/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>

Graduate University of Chinese Academy of Sciences
College of Physical 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 tribhuwan.physics at gmail.com  Fri Nov  4 05:39:41 2011
From: tribhuwan.physics at gmail.com (Tribhuwan Pandey)
Date: Fri, 4 Nov 2011 10:09:41 +0530
Subject: [Pw_forum] Fwd:  Phonon eigenvector calculation
In-Reply-To: <CACKvTSMuOX0BUvWeGGZV8U9BZBXnPg3to10oLosv9i97yh8ifw@mail.gmail.com>
References: <CACKvTSMuOX0BUvWeGGZV8U9BZBXnPg3to10oLosv9i97yh8ifw@mail.gmail.com>
Message-ID: <CACKvTSNCPMn8_Ci69kxqWckfHUr6g71pfqS9cDJjc5wpkNGbaw@mail.gmail.com>

Dear all

I am working on  a project related to thermal conductivity calculation by
solving Boltzmann  transport equation.For this i need to calculate phonon
eigenvectors corresponding to anharmonic force constant .Can some body help
me in this matter.


*
 Regards
Tribhuwan Pandey
*



-- 
*

*
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From hqzhou at nju.edu.cn  Fri Nov  4 05:53:52 2011
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Fri, 4 Nov 2011 12:53:52 +0800
Subject: [Pw_forum] problem in scf run
References: <CAA6iE10ET_Dh1q_HdbEA-YbZ1RHVBgSYvQrZJXDOOEAAd5cr9w@mail.gmail.com>
	<CADTmJ6EmDG8o7_qs3nofgCxSUJU4Fd3sF=9uSFmvTHQokQrXfA@mail.gmail.com>
Message-ID: <DE466F54C96445EAB03DCD0C91F69EBD@solarflare>

Axel,

I noticed recently that you have come back to qe mailing list, warm welcome!

You are always a very valuable person at every forum you had and have been taking care of!

zhou huiqun
@earth sciences, nanjing university, china
  ----- Original Message ----- 
  From: Axel Kohlmeyer 
  To: PWSCF Forum 
  Sent: Thursday, November 03, 2011 10:19 PM
  Subject: Re: [Pw_forum] problem in scf run





  On Thu, Nov 3, 2011 at 8:50 AM, Pankaj Pankaj <pankaj.espresso at gmail.com> wrote:

    Dear All,

      When i tried to run my scf cal, i got following message

    At line 155 of file read_cards.f90
    Fortran runtime error: End of file
    At line 155 of file read_cards.f90
    Fortran runtime error: End of file
    At line 155 of file read_cards.f90
    Fortran runtime error: End of file
    At line 155 of file read_cards.f90
    Fortran runtime error: End of file
    --------------------------------------------------------------------------
    mpirun has exited due to process rank 1 with PID 1914 on
    node shiva exiting without calling "finalize". This may
    have caused other processes in the application to be
    terminated by signals sent by mpirun (as reported here).

    Whereas for VERY SIMILAR file do not give any error. Where can be problem.



  your input is missing an essential part.
  and "end of file" error means, that the
  code is trying to read something, but
  it is not there.


  axel.


    Thank you so much.

    Kind Regards
    Pankaj
    Research Assistant
    AU India

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







  -- 
  Dr. Axel Kohlmeyer   
  akohlmey at gmail.com  http://goo.gl/1wk0

  College of Science and Technology
  Temple University, Philadelphia PA, USA.



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


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From mpayami at aeoi.org.ir  Fri Nov  4 09:01:58 2011
From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari)
Date: Fri, 04 Nov 2011 11:31:58 +0330
Subject: [Pw_forum] Error in pseudopotential generation
In-Reply-To: <60091.130.192.119.45.1320362495.squirrel@mail.unito.it>
References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it>
	<4EB2F438.5070406@gmail.com>
	<60091.130.192.119.45.1320362495.squirrel@mail.unito.it>
Message-ID: <WC20111104080158.0300EB@aeoi.org.ir>

Dear QE Users and Developers,

I am trying to generate a pseudopotential for Al. I am using the following 
input:
---
&input
        iswitch=3,

        rlderiv=2.1,
        eminld=-11.0,
        emaxld=2.0,
        deld=0.01d0,
        nld=5,

        rel=0,
        zed=14.0,
        config="[He] 2s2 2p6 3s2 3p1 3d-1"
        dft='LDA',
 /
 &inputp
   lloc=2,
   pseudotype=1,
   file_pseudopw='Al.rrkj3_plus_core.UPF',
   zval=11.0,
 /
5
2S  1  0  2.00  0.00  2.40  2.40
2P  2  1  6.00  0.00  2.40  2.40    
3S  3  0  2.00  0.00  2.40  2.40
3P  4  1  1.00  0.00  2.40  2.40
3D  5  2  0.00 -0.10  2.40  2.40
---

But I receive the error message:

......
task # 0
from ld1_readin :error # 1
Two wavefunctions for the same l
......

I would be grateful for any hints.
Best regards,
Mahmoud Payami
Physics Group, AEOI,Tehran-Iran
E-mail: mpayami at aeoi.org.ir

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From m.abbasnejad at gmail.com  Fri Nov  4 09:42:04 2011
From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad)
Date: Fri, 4 Nov 2011 17:42:04 +0900
Subject: [Pw_forum] Error in pseudopotential generation
In-Reply-To: <WC20111104080158.0300EB@aeoi.org.ir>
References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it>
	<4EB2F438.5070406@gmail.com>
	<60091.130.192.119.45.1320362495.squirrel@mail.unito.it>
	<WC20111104080158.0300EB@aeoi.org.ir>
Message-ID: <CAF3mdWOBWJJ1w2ondwdp=3W_5oZWr_2jdMFj-WxRyD45dZ-fpQ@mail.gmail.com>

Dear Payami,

I think, the error is related to the type of pseudo potential you are using.
pseudotype=1 is single-projector PP. So you can not define both 2S and 3S
or 2P and 3P simultaneously.

Yours,
Mohaddeseh,
University of Tehran
.


On Fri, Nov 4, 2011 at 5:01 PM, Mahmoud Payami Shabestari <
mpayami at aeoi.org.ir> wrote:

>  Dear QE Users and Developers,
>
> I am trying to generate a pseudopotential for Al. I am using the following
> input:
> ---
>   &input
>         iswitch=3,
>
>         rlderiv=2.1,
>         eminld=-11.0,
>         emaxld=2.0,
>         deld=0.01d0,
>         nld=5,
>
>         rel=0,
>         zed=14.0,
>         config="[He] 2s2 2p6 3s2 3p1 3d-1"
>         dft='LDA',
>  /
>  &inputp
>    lloc=2,
>    pseudotype=1,
>    file_pseudopw='Al.rrkj3_plus_core.UPF',
>    zval=11.0,
>  /
> 5
> 2S  1  0  2.00  0.00  2.40  2.40
> 2P  2  1  6.00  0.00  2.40  2.40
> 3S  3  0  2.00  0.00  2.40  2.40
> 3P  4  1  1.00  0.00  2.40  2.40
> 3D  5  2  0.00 -0.10  2.40  2.40
> ---
>
> But I receive the error message:
>
> ......
> task # 0
> from ld1_readin :error # 1
> Two wavefunctions for the same l
> ......
>
> I would be grateful for any hints.
> Best regards,
>                         Mahmoud Payami
>
> Physics Group, AEOI,Tehran-Iran
> E-mail: mpayami at aeoi.org.ir
> --------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From mpayami at aeoi.org.ir  Fri Nov  4 10:59:40 2011
From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari)
Date: Fri, 04 Nov 2011 13:29:40 +0330
Subject: [Pw_forum] Error in pseudopotential generation
In-Reply-To: <CAF3mdWOBWJJ1w2ondwdp=3W_5oZWr_2jdMFj-WxRyD45dZ-fpQ@mail.gmail.com>
References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it>
	<4EB2F438.5070406@gmail.com>
	<60091.130.192.119.45.1320362495.squirrel@mail.unito.it>
	<WC20111104080158.0300EB@aeoi.org.ir>
	<CAF3mdWOBWJJ1w2ondwdp=3W_5oZWr_2jdMFj-WxRyD45dZ-fpQ@mail.gmail.com>
Message-ID: <WC20111104095940.7400EE@aeoi.org.ir>

Dear Mohaddeseh,



Thank you very much for your answer.

As you suggested, I changed to "pseudotype=2", and the new 
error appeared:

Supplied (11.0) and calculated (12.0) valence charge do not match.


I included "dx=0.008" in the namelist &INPUT, but no new 
result.

So densing the radial mesh did not cure it. Where does the extra charge 
come from?

Best regards,

Mahmoud Payami

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

Mahmoud Payami

Physics Group, AEOI, Tehran-Iran

E-mail : mpayami at aeoi.org.ir

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

Dear Payami,

I think, the error is related to the type of pseudo potential you are using.
pseudotype=1 is single-projector PP. So you can not define both 2S and 3S or 
2P and 3P simultaneously.



Yours,
Mohaddeseh,


University of Tehran
.


On Fri, Nov 4, 2011 at 5:01 PM, Mahmoud Payami Shabestari 
<mpayami at aeoi.org.ir [mailto:mpayami at aeoi.org.ir]> wrote:



Dear QE Users and Developers,



I am trying to generate a pseudopotential for Al. I am using the 
following input:

---

&input

        iswitch=3,



        rlderiv=2.1,

        eminld=-11.0,

        emaxld=2.0,

        deld=0.01d0,

        nld=5,



        rel=0,

        zed=14.0,

        config="[He] 2s2 2p6 3s2 3p1 
3d-1"

        dft='LDA',

 /

 &inputp

   lloc=2,

   pseudotype=1,

   file_pseudopw='Al.rrkj3_plus_core.UPF',

   zval=11.0,

 /

5

2S  1  0  2.00  0.00  2.40  2.40

2P  2  1  6.00  0.00  2.40  2.40   
 

3S  3  0  2.00  0.00  2.40  2.40

3P  4  1  1.00  0.00  2.40  2.40

3D  5  2  0.00 -0.10  2.40  2.40

---



But I receive the error message:



......

task # 0

from ld1_readin :error # 1

Two wavefunctions for the same l

......



I would be grateful for any hints.

Best regards,

Mahmoud Payami

Physics Group, AEOI,Tehran-Iran

E-mail: mpayami at aeoi.org.ir [mailto:mpayami at aeoi.org.ir]

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


_______________________________________________

Pw_forum mailing list

Pw_forum at pwscf.org [mailto:Pw_forum at pwscf.org]

http://www.democritos.it/mailman/listinfo/pw_forum 
[http://www.democritos.it/mailman/listinfo/pw_forum]
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From mpayami at aeoi.org.ir  Fri Nov  4 15:10:45 2011
From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari)
Date: Fri, 04 Nov 2011 17:40:45 +0330
Subject: [Pw_forum] correct values for "nns"
In-Reply-To: <4EB2F438.5070406@gmail.com>
References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it>
	<4EB2F438.5070406@gmail.com>
Message-ID: <WC20111104141045.3500F1@aeoi.org.ir>

Dear QE users,

I am using the following input for a test pseudopotential generation:
--- &input
        iswitch=3,
        rlderiv=2.1,
        eminld=-11.0,
        emaxld=2.0,
        deld=0.01d0,
        nld=5,

        rel=0,
        zed=13.0,
        config="[He] 2s2 2p6 3s2 3p1 3d-1"
        dft='LDA',
 /
 &inputp
   lloc=2,
   pseudotype=2,
   file_pseudopw='Al.rrkj3_plus_core.UPF',
   zval=11.0,
 /
5
2S  1  0  2.00  0.00  2.40  2.40
2P  2  1  6.00  0.00  2.40  2.40    
3S  2  0  2.00  0.00  2.40  2.40
3P  3  1  1.00  0.00  2.40  2.40
3D  3  2  0.00 -0.10  2.40  2.40
---

I am not sure if I am using correct "nns" values. So, the following error 
message appears:
-----

Computing logarithmic derivative in   2.09870

       WARNING! Expected number of nodes:   1=     2-  0-  1, number of 
nodes found:  0.
       Setting wfc to zero for this iteration.
       (This warning will only be printed once per wavefunction)


       WARNING! Expected number of nodes:   1=     3-  1-  1, number of 
nodes found:  0.
       Setting wfc to zero for this iteration.
       (This warning will only be printed once per wavefunction)


 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from run_pseudo : error #         1
     Errors in PS-KS equation
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
----

Any comments is highly appreciated.

Cheers,
Mahmoud

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

Mahmoud Payami

Physics Group, AEOI, Tehran-Iran

E-mail : mpayami at aeoi.org.ir

--------------------------------------------------
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From hariomcosmos at gmail.com  Fri Nov  4 15:16:20 2011
From: hariomcosmos at gmail.com (hariom jani)
Date: Fri, 4 Nov 2011 15:16:20 +0100
Subject: [Pw_forum] Defining spin states in PWscf
Message-ID: <CAAq=-GZksLicDYQj6hYHh85R-e41Q-www_J=zMXBvGvX55KJbg@mail.gmail.com>

Dear fellow QE users,

I am currently using fully relativistic pseudo-potentials to compute
certain spin-orbit based properties in solids.
Given a silicon system, there are 4 valence and 4 conduction bands (each
doubly degenerate in the spin components)  in total.

When i perform PWscf calculations, I set 'lspinorb' and 'noncolin' (in the
system namelist) to .true.

I desire that the 2 degenerate spin states of every band be defined as
uniquely up and down (and not merely their linear combinations).

1. To achieve this I am currently using 'starting_spin_angle'=true, but is
the correct command to use? If not, what should be done?
2. Can this done, in spite of using the 'noncolin' command?

Thanks
Hariom Jani
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From m.abbasnejad at gmail.com  Fri Nov  4 16:15:38 2011
From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad)
Date: Sat, 5 Nov 2011 00:15:38 +0900
Subject: [Pw_forum] correct values for "nns"
In-Reply-To: <WC20111104141045.3500F1@aeoi.org.ir>
References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it>
	<4EB2F438.5070406@gmail.com> <WC20111104141045.3500F1@aeoi.org.ir>
Message-ID: <CAF3mdWPPOUafRD6-m00uuVA9Wddm2c6aKppmgdytUYmoKrWnYA@mail.gmail.com>

Dear Payami,

Actually, I don't have too much experience about generating pseudo
potential.
However, you may change the rcut in order to generate the desired PP.
E.g. you can run the code by choosing :
5
2S  1  0  2.00  0.00  5.0  5.0
2P  2  1  6.00  0.00  4.50  4.50
3S  3  0  2.00  0.00  4.50  4.50
3P  4  1  1.00  0.00  4.50  4.50
3D  5  2  0.00 -0.10  4.0  4.0

Although, they do not give any reliable results and still you also have to
get rid of warning in the out file:
"WARNING! Expected number of nodes:   0=     2-  1-  1, number of nodes fou
nd:  1.
       Setting wfc to zero for this iteration.
       (This warning will only be printed once per wave function)"

Of course, the professionals will give you more comments!

Yours,
Mohaddeseh
University of Tehran


On Fri, Nov 4, 2011 at 11:10 PM, Mahmoud Payami Shabestari <
mpayami at aeoi.org.ir> wrote:

> Dear QE users,
>
> I am using the following input for a test pseudopotential generation:
> ---
>  &input
>         iswitch=3,
>         rlderiv=2.1,
>         eminld=-11.0,
>         emaxld=2.0,
>         deld=0.01d0,
>         nld=5,
>
>         rel=0,
>         zed=13.0,
>         config="[He] 2s2 2p6 3s2 3p1 3d-1"
>         dft='LDA',
>  /
>  &inputp
>    lloc=2,
>    pseudotype=2,
>    file_pseudopw='Al.rrkj3_plus_core.UPF',
>    zval=11.0,
>  /
> 5
> 2S  1  0  2.00  0.00  2.40  2.40
> 2P  2  1  6.00  0.00  2.40  2.40
> 3S  2  0  2.00  0.00  2.40  2.40
> 3P  3  1  1.00  0.00  2.40  2.40
> 3D  3  2  0.00 -0.10  2.40  2.40
> ---
>
> I am not sure if I am using correct "nns" values. So, the following error
> message appears:
> -----
>
>       Computing logarithmic derivative in   2.09870
>
>        WARNING! Expected number of nodes:   1=     2-  0-  1, number of
> nodes found:  0.
>        Setting wfc to zero for this iteration.
>        (This warning will only be printed once per wavefunction)
>
>
>        WARNING! Expected number of nodes:   1=     3-  1-  1, number of
> nodes found:  0.
>        Setting wfc to zero for this iteration.
>        (This warning will only be printed once per wavefunction)
>
>
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from run_pseudo : error #         1
>      Errors in PS-KS equation
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>      stopping ...
> ----
>
> Any comments is highly appreciated.
>
> Cheers,
>             Mahmoud
>
> --------------------------------------------------
> Mahmoud Payami
> Physics Group, AEOI, Tehran-Iran
> E-mail : mpayami at aeoi.org.ir
> --------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From dalcorso at sissa.it  Fri Nov  4 16:21:45 2011
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Fri, 04 Nov 2011 16:21:45 +0100
Subject: [Pw_forum] Defining spin states in PWscf
In-Reply-To: <CAAq=-GZksLicDYQj6hYHh85R-e41Q-www_J=zMXBvGvX55KJbg@mail.gmail.com>
References: <CAAq=-GZksLicDYQj6hYHh85R-e41Q-www_J=zMXBvGvX55KJbg@mail.gmail.com>
Message-ID: <1320420105.20806.11.camel@ulisse.cm.sissa.it>


On Fri, 2011-11-04 at 15:16 +0100, hariom jani wrote:
> Dear fellow QE users,
> 
> I am currently using fully relativistic pseudo-potentials to compute
> certain spin-orbit based properties in solids. 
> Given a silicon system, there are 4 valence and 4 conduction bands
> (each doubly degenerate in the spin components)  in total.
> 
> When i perform PWscf calculations, I set 'lspinorb' and 'noncolin' (in
> the system namelist) to .true. 
> 
> I desire that the 2 degenerate spin states of every band be defined as
> uniquely up and down (and not merely their linear combinations). 
> 
> 1. To achieve this I am currently using 'starting_spin_angle'=true,
> but is the correct command to use? If not, what should be done? 
> 2. Can this done, in spite of using the 'noncolin' command?
> 

It cannot be done.
When there is spin-orbit, the Hamiltonian does not commute with S_z so
you cannot divide the bands into up or down. If there is a strong
magnetization (much larger than spin-orbit) than the real bands do not
differ too much from up or down bands and it might be convenient to
start with wavefunctions that are much closer to spin-up and spin-down
states than to spin-angle states. In any case at self-consistency the
states are no more completely up or completely down. 

Andrea

> Thanks
> Hariom Jani
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Bonomea 265              Fax. 0039-040-3787249
I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it



From mpayami at aeoi.org.ir  Fri Nov  4 18:41:11 2011
From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari)
Date: Fri, 04 Nov 2011 21:11:11 +0330
Subject: [Pw_forum] correct values for "nns"
In-Reply-To: <CAF3mdWPPOUafRD6-m00uuVA9Wddm2c6aKppmgdytUYmoKrWnYA@mail.gmail.com>
References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it>
	<4EB2F438.5070406@gmail.com> <WC20111104141045.3500F1@aeoi.org.ir>
	<CAF3mdWPPOUafRD6-m00uuVA9Wddm2c6aKppmgdytUYmoKrWnYA@mail.gmail.com>
Message-ID: <WC20111104174111.8700F2@aeoi.org.ir>

Dear Mohaddeseh,

The r_cut s  you chose seem to be too large and I think for 2S and 2P they 
are quite irrelevant.
In fact, the problem is that still I DO_NOT understand the meaning of "nns" 
parameter.
Thank you so much for your kind contributions.
Any hints from Paolo and Andrea is highly appreciated.
Bests,
mahmoud

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

Mahmoud Payami

Physics Group, AEOI, Tehran-Iran

E-mail : mpayami at aeoi.org.ir

--------------------------------------------------Dear Payami,
Actually, I don't have too much experience about generating pseudo 
potential.
However, you may change the rcut in order to generate the desired PP.
E.g. you can run the code by choosing :


5
2S  1  0  2.00  0.00  5.0  5.0
2P  2  1  6.00  0.00  4.50  4.50
3S  3  0  2.00  0.00  4.50  4.50
3P  4  1  1.00  0.00  4.50  4.50
3D  5  2  0.00 -0.10  4.0  4.0

Although, they do not give any reliable results and still you also have to 
get rid of warning in the out file:
"WARNING! Expected number of nodes:   0=     2-  1-  1, number of nodes fou


nd:  1.
Setting wfc to zero for this iteration.
(This warning will only be printed once per wave function)"

Of course, the professionals will give you more comments!



Yours,
Mohaddeseh
University of Tehran

On Fri, Nov 4, 2011 at 11:10 PM, Mahmoud Payami Shabestari 
<mpayami at aeoi.org.ir [mailto:mpayami at aeoi.org.ir]> wrote:



Dear QE users,



I am using the following input for a test pseudopotential 
generation:

---

&input

        iswitch=3,

        rlderiv=2.1,

        eminld=-11.0,

        emaxld=2.0,

        deld=0.01d0,

        nld=5,



        rel=0,

        zed=13.0,

        config="[He] 2s2 2p6 3s2 3p1 
3d-1"

        dft='LDA',

 /

 &inputp

   lloc=2,

   pseudotype=2,

   file_pseudopw='Al.rrkj3_plus_core.UPF',

   zval=11.0,

 /

5

2S  1  0  2.00  0.00  2.40  2.40

2P  2  1  6.00  0.00  2.40  2.40   
 

3S  2  0  2.00  0.00  2.40  2.40

3P  3  1  1.00  0.00  2.40  2.40

3D  3  2  0.00 -0.10  2.40  2.40

---



I am not sure if I am using correct "nns" values. So, the 
following error message appears:

-----



Computing logarithmic derivative in   
2.09870



       WARNING! Expected number of 
nodes:   1=     2-  0-  1, number of 
nodes found:  0.

       Setting wfc to zero for this 
iteration.

       (This warning will only be printed once 
per wavefunction)





       WARNING! Expected number of 
nodes:   1=     3-  1-  1, number of 
nodes found:  0.

       Setting wfc to zero for this 
iteration.

       (This warning will only be printed once 
per wavefunction)





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

     from run_pseudo : error 
#         1

     Errors in PS-KS equation

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



     stopping ...

----



Any comments is highly appreciated.



Cheers,

Mahmoud



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

Mahmoud Payami

Physics Group, AEOI, Tehran-Iran

E-mail : mpayami at aeoi.org.ir [mailto:mpayami at aeoi.org.ir]

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


_______________________________________________

Pw_forum mailing list

Pw_forum at pwscf.org [mailto:Pw_forum at pwscf.org]

http://www.democritos.it/mailman/listinfo/pw_forum 
[http://www.democritos.it/mailman/listinfo/pw_forum]
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From mpayami at aeoi.org.ir  Fri Nov  4 19:32:33 2011
From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari)
Date: Fri, 04 Nov 2011 22:02:33 +0330
Subject: [Pw_forum] "nns"
In-Reply-To: <WC20111104174111.8700F2@aeoi.org.ir>
References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it>
	<4EB2F438.5070406@gmail.com> <WC20111104141045.3500F1@aeoi.org.ir>
	<CAF3mdWPPOUafRD6-m00uuVA9Wddm2c6aKppmgdytUYmoKrWnYA@mail.gmail.com>
	<WC20111104174111.8700F2@aeoi.org.ir>
Message-ID: <WC20111104183233.8600F3@aeoi.org.ir>

Hi Andrea and Paolo,

If nns=1 for lowest s, nns=2 for lowest p, and so on; what values assume nns 
for the corresponding next_to_lowest states?
Thanks in advance.
mahmoud

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

Mahmoud Payami

Physics Group, AEOI, Tehran-Iran

E-mail : mpayami at aeoi.org.ir

--------------------------------------------------
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From agkvashnin at gmail.com  Fri Nov  4 19:57:47 2011
From: agkvashnin at gmail.com (Alexander G. Kvashnin)
Date: Fri, 4 Nov 2011 11:57:47 -0700
Subject: [Pw_forum] Question about work function
Message-ID: <CAFWb5iL6Hs+0Nkf2gd2ZoX4aVHd9q1h=qbznv2P9=xnNchfTxg@mail.gmail.com>

Dear espresso users!

I'll try to calculate work function under the finite electric field using
tefield flag.
But I didn't obtain any differences with the case without electric field, I
didn't notice any inluence of sawlike potential.
I attached my input file. Could anybody told me, what's wrong?

&CONTROL
  calculation = "scf",
  pseudo_dir  = "./",
  outdir      = "./",
  restart_mode = "from_scratch",
  prefix = "ex1",
  tefield = .true.
  dipfield = .true.
/
&SYSTEM
  ibrav       = 0,
  nat         = 9,
  ntyp        = 2,
  ecutwfc     = 30.D0,
  occupations = "smearing",
  smearing    = "m-v",
  degauss     = 0.05D0,
  nr3         = 144,
  edir = 2,
  eamp = 0.002  ,
  emaxpos = 0.9,
  eopreg = 0.2,
/
&ELECTRONS
  conv_thr    = 1.D-10,
  mixing_beta = 0.7D0,

/

&IONS
  ion_dynamics='bfgs',
  pot_extrapolation = "first_order",
 /
&CELL
   cell_dynamics = 'bfgs' ,
   cell_factor = 1.6,
   press = 0 ,
   !cell_dofree = 'xyz',
/


ATOMIC_SPECIES
H  1.0079   H.pz-vbc.UPF
C  12.0107  C.pz-vbc.UPF

ATOMIC_POSITIONS angstrom
C       -0.009799755      3.916644416     -0.001504366
***
***
H        0.000000000      0.000000000      0.000000000


CELL_PARAMETERS
4.669187146 0 0
0 16.10277883 0
0 0 18.90359168


K_POINTS {automatic}
10 1 1 0 0 0


Thank you!

-- 
Sincerely yours
*Alexander G. Kvashnin*
--------------------------------------------------------------------------------------------------------------------------------
Second year of master degree study
Moscow Institute of Physics and Technology          http://mipt.ru/
141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia

Junior research scientist
Technological Institute for Superhard
and Novel Carbon Materials
http://www.ntcstm.troitsk.ru/
142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia
================================================================
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From henod2001 at yahoo.com  Sat Nov  5 08:41:50 2011
From: henod2001 at yahoo.com (henry odhiambo)
Date: Sat, 5 Nov 2011 00:41:50 -0700 (PDT)
Subject: [Pw_forum] Elastic Constants
Message-ID: <1320478910.30765.YahooMailClassic@web121018.mail.ne1.yahoo.com>

Hello everyone!
?
This may be trivial but just try, please.
?
Can anyone give me direction on how to calculate elastic constants using Quantum ESPRESSO codes.
?
Thank you.
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From giannozz at democritos.it  Sat Nov  5 09:58:31 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 5 Nov 2011 09:58:31 +0100
Subject: [Pw_forum] "nns"
In-Reply-To: <WC20111104183233.8600F3@aeoi.org.ir>
References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it>
	<4EB2F438.5070406@gmail.com> <WC20111104141045.3500F1@aeoi.org.ir>
	<CAF3mdWPPOUafRD6-m00uuVA9Wddm2c6aKppmgdytUYmoKrWnYA@mail.gmail.com>
	<WC20111104174111.8700F2@aeoi.org.ir>
	<WC20111104183233.8600F3@aeoi.org.ir>
Message-ID: <891879D7-BE36-4E8E-BE4D-01DCD5830551@democritos.it>


On Nov 4, 2011, at 19:32 , Mahmoud Payami Shabestari wrote:

>  If nns=1 for lowest s, nns=2 for lowest p, and so on; what values  
> assume nns for the corresponding next_to_lowest states?

nns=2 for s, nns=3 for p, etc

Note that there are some serious limitations in the current
algorithm for multiple-channel pseudopotentials: all pseudo-orbitals
are required to be nodeless, so you cannot generate a pseudopotential
using the 2s and 3s bound states, for instance: 3s cannot be nodeless.

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 mpayami at aeoi.org.ir  Sat Nov  5 10:51:03 2011
From: mpayami at aeoi.org.ir (Mahmoud Payami)
Date: Sat, 5 Nov 2011 13:21:03 +0330
Subject: [Pw_forum] "nns"
References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it><4EB2F438.5070406@gmail.com>
	<WC20111104141045.3500F1@aeoi.org.ir><CAF3mdWPPOUafRD6-m00uuVA9Wddm2c6aKppmgdytUYmoKrWnYA@mail.gmail.com><WC20111104174111.8700F2@aeoi.org.ir><WC20111104183233.8600F3@aeoi.org.ir>
	<891879D7-BE36-4E8E-BE4D-01DCD5830551@democritos.it>
Message-ID: <B5E802CAF7994733980BE33117387DBA@b>

Dear Paolo,

Thank you very much. I was looking for nodeless pseudo-orbitals for both 2S 
and 3S.
Best regards,
mahmoud




>
> On Nov 4, 2011, at 19:32 , Mahmoud Payami Shabestari wrote:
>
>>  If nns=1 for lowest s, nns=2 for lowest p, and so on; what values
>> assume nns for the corresponding next_to_lowest states?
>
> nns=2 for s, nns=3 for p, etc
>
> Note that there are some serious limitations in the current
> algorithm for multiple-channel pseudopotentials: all pseudo-orbitals
> are required to be nodeless, so you cannot generate a pseudopotential
> using the 2s and 3s bound states, for instance: 3s cannot be nodeless.
>
> 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 kalamaillist at gmail.com  Sat Nov  5 11:53:28 2011
From: kalamaillist at gmail.com (WF)
Date: Sat, 5 Nov 2011 18:53:28 +0800
Subject: [Pw_forum] How to show bands above fermi level in PDOS?
Message-ID: <000501cc9ba9$29991ba0$7ccb52e0$@gmail.com>

Hello everyone,

         I am calculating PDOS of an insulator. In the initial SCF, keyword
'nbnd' is not specified. A NSCF calculation, still without 'nbnd' keyword,
is done to get Fermi level. And in the later PDOS calculation, no band above
Fermi level is showed. If I need to show some bands above Fermi level, from
where should I restart my calculation? Is it necessary to rerun SCF with a
large 'nbnd' or there are some quicker way to do it ?

         Thanks.

 

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

Wu F,

College of Chemistry and Molecular Engineering,

Peking University.

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

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From songsong19840614 at hotmail.com  Sat Nov  5 12:25:42 2011
From: songsong19840614 at hotmail.com (KangYun Song)
Date: Sat, 5 Nov 2011 11:25:42 +0000
Subject: [Pw_forum] How to show bands above fermi level in PDOS?
In-Reply-To: <000501cc9ba9$29991ba0$7ccb52e0$@gmail.com>
References: <000501cc9ba9$29991ba0$7ccb52e0$@gmail.com>
Message-ID: <COL113-W6158A9BBB2E7B3D00D9EF4C8DB0@phx.gbl>


Dear Wu F:
        You can try to increase the value of nbnd of scf and nscf.

Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.
 



From: kalamaillist at gmail.com
To: pw_forum at pwscf.org
Date: Sat, 5 Nov 2011 18:53:28 +0800
Subject: [Pw_forum] How to show bands above fermi level in PDOS?






Hello everyone,
         I am calculating PDOS of an insulator. In the initial SCF, keyword ?nbnd? is not specified. A NSCF calculation, still without ?nbnd? keyword, is done to get Fermi level. And in the later PDOS calculation, no band above Fermi level is showed. If I need to show some bands above Fermi level, from where should I restart my calculation? Is it necessary to rerun SCF with a large ?nbnd? or there are some quicker way to do it ?
         Thanks.
 
------------------------------------
Wu F,
College of Chemistry and Molecular Engineering,
Peking University.
------------------------------------
_______________________________________________ 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 Nov  5 12:31:15 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 5 Nov 2011 12:31:15 +0100
Subject: [Pw_forum] How to show bands above fermi level in PDOS?
In-Reply-To: <000501cc9ba9$29991ba0$7ccb52e0$@gmail.com>
References: <000501cc9ba9$29991ba0$7ccb52e0$@gmail.com>
Message-ID: <64FE9E01-BB61-4C21-9045-0F4E2F3EB263@democritos.it>


On Nov 5, 2011, at 11:53 , WF wrote:
> Is it necessary to rerun SCF with a large ?nbnd?
>

no: you may increase nbnd in the non-scf step
and re-run the non-scf 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 mohnish.iitk at gmail.com  Sat Nov  5 15:05:28 2011
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Sat, 5 Nov 2011 19:35:28 +0530
Subject: [Pw_forum] Elastic Constants
In-Reply-To: <1320478910.30765.YahooMailClassic@web121018.mail.ne1.yahoo.com>
References: <1320478910.30765.YahooMailClassic@web121018.mail.ne1.yahoo.com>
Message-ID: <CAMhNW-ex2BYjtyuQfBFXKL3oFzmOCgEyFp7Z-c_Dm-V2+YjReg@mail.gmail.com>

Search archives. And provide your affiliation in future.

On Sat, Nov 5, 2011 at 1:11 PM, henry odhiambo <henod2001 at yahoo.com> wrote:

> Hello everyone!
>
> This may be trivial but just try, please.
>
> Can anyone give me direction on how to calculate elastic constants using
> Quantum ESPRESSO codes.
>
> Thank you.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
BTech-Mtech, IIT Kanpur
Senior Project Associate,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
-----------------------------------------------------------------
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From w2agz at w2agz.com  Sun Nov  6 01:46:28 2011
From: w2agz at w2agz.com (W2AGZ)
Date: Sat, 5 Nov 2011 17:46:28 -0700
Subject: [Pw_forum] XCrysDen & Animation Capture
Message-ID: <5ddd01cc9c1d$8626dbe0$927493a0$@w2agz.com>

It seems that the mpeg_encode and whirlgif packages are no longer available
for XCrysDen, and their old source codes are "un-make-able," at least within
the current release of Ubuntu.  Any advice on how to "capture" the animation
sequence of, e.g., structure relaxation, for use in an presentation format
such as Powerpoint or Impress?

 

-Paul Grant

W2AGZ Technologies (www.w2agz.com)

Staff Associate, JPL-NASA

 

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From arvifis at gmail.com  Sun Nov  6 02:27:10 2011
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Sat, 5 Nov 2011 23:27:10 -0200
Subject: [Pw_forum] XCrysDen & Animation Capture
In-Reply-To: <5ddd01cc9c1d$8626dbe0$927493a0$@w2agz.com>
References: <5ddd01cc9c1d$8626dbe0$927493a0$@w2agz.com>
Message-ID: <CABEdBFN+duifTAHnpBXW2Lb5nsdOXL7OX6e9bWiVWbWNO2M8PA@mail.gmail.com>

You can use Jmol, this program read a XYZ file..

Best

PhD stud. Arles V. Gil Rebaza
IFLP - Argentina

2011/11/5 W2AGZ <w2agz at w2agz.com>

> It seems that the mpeg_encode and whirlgif packages are no longer
> available for XCrysDen, and their old source codes are ?un-make-able,? at
> least within the current release of Ubuntu.  Any advice on how to ?capture?
> the animation sequence of, e.g., structure relaxation, for use in an
> presentation format such as Powerpoint or Impress?****
>
> ** **
>
> -Paul Grant****
>
> W2AGZ Technologies (www.w2agz.com)****
>
> Staff Associate, JPL-NASA****
>
> ** **
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
###--------->   Arles V.   <---------###
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From akohlmey at gmail.com  Sun Nov  6 17:50:43 2011
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Sun, 6 Nov 2011 11:50:43 -0500
Subject: [Pw_forum] XCrysDen & Animation Capture
In-Reply-To: <5ddd01cc9c1d$8626dbe0$927493a0$@w2agz.com>
References: <5ddd01cc9c1d$8626dbe0$927493a0$@w2agz.com>
Message-ID: <CADTmJ6GJUibUg-eYSMyFCZceC3niW1Ymr-bWnwdu_7mPCoF46g@mail.gmail.com>

hi paul,

On Sat, Nov 5, 2011 at 8:46 PM, W2AGZ <w2agz at w2agz.com> wrote:

> It seems that the mpeg_encode and whirlgif packages are no longer
> available for XCrysDen, and their old source codes are ?un-make-able,? at
> least within the current release of Ubuntu.  Any advice on how to ?capture?
> the animation sequence of, e.g., structure relaxation, for use in an
> presentation format such as Powerpoint or Impress?
>

have you checked out one of the following programs?
- ppmtompeg (part of the netpbm package)
- mencoder (part of the mplayer suite)
- gifsicle (best gif encoder i know)
- convert (part of the ImageMagik package, worst gif encoder i know)

all of those were already supported by XCrySDen many years ago,
so i would assume they still are.

cheers,
    axel.

****
>
> ** **
>
> -Paul Grant****
>
> W2AGZ Technologies (www.w2agz.com)****
>
> Staff Associate, JPL-NASA****
>
> ** **
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com  http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
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From nicola.marzari at epfl.ch  Sun Nov  6 21:23:08 2011
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Sun, 06 Nov 2011 21:23:08 +0100
Subject: [Pw_forum] Elastic Constants
In-Reply-To: <1320478910.30765.YahooMailClassic@web121018.mail.ne1.yahoo.com>
References: <1320478910.30765.YahooMailClassic@web121018.mail.ne1.yahoo.com>
Message-ID: <4EB6ECAC.4040106@epfl.ch>

On 11/5/11 8:41 AM, henry odhiambo wrote:
> Hello everyone!
> This may be trivial but just try, please.
> Can anyone give me direction on how to calculate elastic constants using
> Quantum ESPRESSO codes.
> Thank you.
>
>


Dear Henry,

indeed, please sign with name *and* affiliation.

You can find some notes here (for Quantum-ESPRESSO), and
references to more general discussions:

http://ocw.mit.edu/courses/materials-science-and-engineering/3-320-atomistic-computer-modeling-of-materials-sma-5107-spring-2005/labs/lab_assignment2.pdf

In particular look at the URL reported:
http://cst-www.nrl.navy.mil/bind/static/example15/index.html
that links to this paper:
http://cst-www.nrl.navy.mil/users/mehl/papers/cij452.ps.gz

			nicola


-- 

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

From w2agz at w2agz.com  Sun Nov  6 22:47:44 2011
From: w2agz at w2agz.com (W2AGZ)
Date: Sun, 6 Nov 2011 13:47:44 -0800
Subject: [Pw_forum] XCrysDen & Animation Capture
Message-ID: <713a01cc9ccd$b8a06590$29e130b0$@w2agz.com>

Thanks, Arles and Axel.  I'll check out your suggestions.

 

Axel, maybe you should consider publishing a review of all tools available
for use on Quantum-Espresso ;-)

 

Cheers, -Paul

 

Paul Grant

W2AGZ Technologies (www.w2agz.com)

Staff Associate, JPL-NASA

 

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From victor.bermudez at nrl.navy.mil  Mon Nov  7 00:33:01 2011
From: victor.bermudez at nrl.navy.mil (Vic Bermudez)
Date: Sun, 6 Nov 2011 18:33:01 -0500
Subject: [Pw_forum] NEB Convergence Problem
Message-ID: <AKEFIBNCPJEJJMHNOPHIGEEKCIAA.victor.bermudez@nrl.navy.mil>

Greetings All,

	I'm struggling with a NEB calculation, and I wonder if someone can advise
me. I first converged the path using NEB without CI. This took many
iterations (810 to be exact), but it got there in the end. I then restarted
with the optimized path and CI set to 'auto'. As you can see from the
attached output, the convergence is extremely slow. In this case I know what
the "right" answer is because I'm reproducing results in the literature. The
forward activation energy should be about 1.65 eV, and at the current rate
at which the activation energy is increasing it will take many thousands of
iterations to get there. As a further comment, I originally had a problem
with erratic behavior (activation energies and NEB errors) because the SCF
convergence criterion was set too low, at the default of 10^-6. Increasing
to 10^-7 fixed that, and I've now increased it 10^-9, but that doesn't
improve the NEB behavior. Does anyone have an idea what the problem might be
?
	Also on the subject of NEB, I have a few further questions:

(1) The default values of k-min and k-max are 0.1. However, the program
prints out suggested values of about 0.6, as can be seen in the output. How
important is it to use the suggested values rather than the defaults ?  I've
tried varying k-min and k-max from 0.1 to 0.6 but with no effect on the rate
of convergence

(2) What are the pros and cons of using "broyden2" vs. "broyden" as the
opt_scheme. I've tried "broyden", "broyden2" and "quick-min", and none seems
to improve the rate of convergence. Is there any documentation describing
what "broyden2" actually does ?

(3) What is the meaning of the "ds" parameter, and what factors should one
consider in choosing the correct value ?

(4) What is the meaning of the "error" that NEB prints for each image at
each iteration ? Is this a measure of the force in a direction orthogonal to
the path ?

	Thanks in advance for whatever help can be provided !

_____________________   NEB Output  _________________________

	Program NEB v.4.3.2        starts on  5Nov2011 at  5: 1: 0

     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    64 processors
     R & G space division:  proc/pool =   64

     reading file 'pwscf.path'


     string_method                 =  neb
     restart_mode                  =  restart
     opt_scheme                    =  quick-min
     num_of_images                 =  15
     nstep_path                    =  4000
     CI_scheme                     =  auto
     first_last_opt                =  T
     use_freezing                  =  T
     ds                            =  1.0000 a.u.
     k_max                         =  0.2000 a.u.
     k_min                         =  0.2000 a.u.
     suggested k_max               =  0.6169 a.u.
     suggested k_min               =  0.6169 a.u.
     path_thr                      =  0.0500 eV / A

     ------------------------------ iteration
810 ------------------------------

     tcpu =      1.2    self-consistency for image   1
     tcpu =    558.0    self-consistency for image   2
     tcpu =   1121.5    self-consistency for image   3
     tcpu =   1648.4    self-consistency for image   4
     tcpu =   2200.4    self-consistency for image   5
     tcpu =   2758.9    self-consistency for image   6
     tcpu =   3371.4    self-consistency for image   7
     tcpu =   4029.8    self-consistency for image   8
     tcpu =   4737.3    self-consistency for image   9
     tcpu =   5287.6    self-consistency for image  10
     tcpu =   5838.6    self-consistency for image  11
     tcpu =   6379.0    self-consistency for image  12
     tcpu =   6924.0    self-consistency for image  13
     tcpu =   7472.4    self-consistency for image  14
     tcpu =   8028.7    self-consistency for image  15

     activation energy (->) =   1.223842 eV
     activation energy (<-) =   1.107219 eV

     image        energy (eV)        error (eV/A)        frozen

         1      -7731.9672919            0.034178            T
         2      -7732.0316501            0.042825            T
         3      -7732.2443631            0.048145            T
         4      -7732.1803814            0.048816            T
         5      -7731.1579038            0.046879            T
         6      -7731.2953554            0.048145            T
         7      -7731.1814917            0.045566            T
         8      -7730.7434498            0.078176            F
         9      -7731.4285103            0.049557            T
        10      -7731.9250436            0.048245            T
        11      -7731.9095723            0.040402            T
        12      -7731.9057520            0.048858            T
        13      -7731.9594729            0.049773            T
        14      -7731.9442331            0.049314            T
        15      -7731.8506693            0.043831            T

     climbing image =  8

     path length          = 35.365 bohr
     inter-image distance =  2.526 bohr

--
--
--
--
------------------------------ iteration 879 ------------------------------

     tcpu = 107190.5    self-consistency for image   3
     tcpu = 107381.2    self-consistency for image   4
     tcpu = 107567.5    self-consistency for image   5
     tcpu = 107836.9    self-consistency for image   6
     tcpu = 108077.7    self-consistency for image   7
     tcpu = 108322.3    self-consistency for image   8
     tcpu = 108536.7    self-consistency for image  10

     activation energy (->) =   1.242763 eV
     activation energy (<-) =   1.126140 eV

     image        energy (eV)        error (eV/A)        frozen

         1      -7731.9672919            0.034178            T
         2      -7732.0362516            0.061682            F
         3      -7732.2539800            0.064196            F
         4      -7732.1603886            0.073400            F
         5      -7730.8743402            0.058702            F
         6      -7731.3502431            0.082296            F
         7      -7731.1086585            0.039573            T
         8      -7730.7245292            0.069207            F
         9      -7731.5495175            0.058737            F
        10      -7731.9427494            0.042724            T
        11      -7731.9100248            0.035621            T
        12      -7731.9057520            0.042466            T
        13      -7731.9594729            0.049773            T
        14      -7731.9442331            0.049314            T
        15      -7731.8506693            0.043831            T

     climbing image =  8

     path length          = 35.706 bohr
     inter-image distance =  2.550 bohr

____________________________________________________________

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 tone.kokalj at ijs.si  Mon Nov  7 01:58:01 2011
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 07 Nov 2011 01:58:01 +0100
Subject: [Pw_forum] XCrysDen & Animation Capture
In-Reply-To: <CADTmJ6GJUibUg-eYSMyFCZceC3niW1Ymr-bWnwdu_7mPCoF46g@mail.gmail.com>
References: <5ddd01cc9c1d$8626dbe0$927493a0$@w2agz.com>
	<CADTmJ6GJUibUg-eYSMyFCZceC3niW1Ymr-bWnwdu_7mPCoF46g@mail.gmail.com>
Message-ID: <1320627481.3704.2.camel@catalyst.ijs.si>

On Sun, 2011-11-06 at 11:50 -0500, Axel Kohlmeyer wrote:
> hi paul,
> 
> On Sat, Nov 5, 2011 at 8:46 PM, W2AGZ <w2agz at w2agz.com> wrote:
>         It seems that the mpeg_encode and whirlgif packages are no
>         longer available for XCrysDen, and their old source codes are
>         ?un-make-able,? at least within the current release of Ubuntu.
>         Any advice on how to ?capture? the animation sequence of,
>         e.g., structure relaxation, for use in an presentation format
>         such as Powerpoint or Impress?
>         
>         
> 
> 
> have you checked out one of the following programs?
> - ppmtompeg (part of the netpbm package)
> - mencoder (part of the mplayer suite)
> - gifsicle (best gif encoder i know)
> - convert (part of the ImageMagik package, worst gif encoder i know)
> 
> 
> all of those were already supported by XCrySDen many years ago,
> so i would assume they still are.

Which, indeed, they still are. The mpeg_encode and whirlgif are not used
anymore for years.

It is true that sometimes making a movie can be tricky, but xcrysden
gives you a possibility to edit the movie encoding script before the
encoding, which can be useful when and if the default route fails.

Regards, Tone

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html


From tone.kokalj at ijs.si  Mon Nov  7 02:23:11 2011
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 07 Nov 2011 02:23:11 +0100
Subject: [Pw_forum] NEB Convergence Problem
In-Reply-To: <AKEFIBNCPJEJJMHNOPHIGEEKCIAA.victor.bermudez@nrl.navy.mil>
References: <AKEFIBNCPJEJJMHNOPHIGEEKCIAA.victor.bermudez@nrl.navy.mil>
Message-ID: <1320628991.3704.21.camel@catalyst.ijs.si>

On Sun, 2011-11-06 at 18:33 -0500, Vic Bermudez wrote:
> Greetings All,
> 
> 	I'm struggling with a NEB calculation, and I wonder if someone can advise
> me. I first converged the path using NEB without CI. This took many
> iterations (810 to be exact), but it got there in the end. I then restarted
> with the optimized path and CI set to 'auto'.

No don't do that. First use the no-CI, just to "stabilize" the path
trajectory to some extent, and to get a rough idea on the reaction path.

So there is a question: "how do I know when it is stabilized enough". At
the beginning of NEB run, the highest energy image can change from
iteration to iteration, but when this gets stable, i.e., a particular
image displays the highest energy over several number of iterations, say
10-15, then you can stop the no-CI run, and start with the CI run.

Just as a rough guide, from my experience, I would say that when the
error is on the order of 0.5 eV/A, this is already good enough to plug
in the CI.


>  As you can see from the
> attached output, the convergence is extremely slow. In this case I know what
> the "right" answer is because I'm reproducing results in the literature. The
> forward activation energy should be about 1.65 eV, and at the current rate
> at which the activation energy is increasing it will take many thousands of
> iterations to get there. 

Well I don't think this is the reason. Your convergence is already quite
good, with almost all the images below 0.05 eV/A. Hence I don't think it
will ever climb to 1.65 eV. There must be some difference with respect
to what you are comparing to: either the initial state (IS) is different
or you located a new TS with lower energy.

However in your energy path, I see a lot of problems. As for
intermediate images, two of them appear as minima (3 and 6) and two of
them as TS (5 and 8). Hence your IS is not really the best minimum (if
you calculate the barrier wrt image 3, you get a value of 1.50 eV, which
is already closer to your reference value). 

This is also the primary reason for bad convergence: the NEB convergence
is best at describing only one elementary reaction, i.e., IS-->TS-->FS,
involving only one saddle point. Please decompose your path into several
separate calculations:

1. first do two optimizations by taking the structure 3 and 6.
Structure-3 will definitely result in lower energy structure than your
IS.

2. when you understand #1, then construct a new NEB run so that it
consists of only one elementary step (i.e. one saddle point).

Regards, Tone
-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html


From pascal.boulet at univ-provence.fr  Mon Nov  7 09:07:48 2011
From: pascal.boulet at univ-provence.fr (pascal boulet)
Date: Mon, 07 Nov 2011 09:07:48 +0100
Subject: [Pw_forum] general question on materials physics
Message-ID: <4EB791D4.40403@univ-provence.fr>

Dear all,

Sorry to bother you with this silly question but it puzzles me a bit!

In a recent article, I have seen a DOS in which the Fermi level is
located in the conduction band. So, it seems to me that the materials is
metallic. But there is clearly a band gap of about 2 eV. I always
thought that for metals the gap was closed. Is there a contradiction in
the paper or am I wrong?

Thank you for your answer.

Best
Pascal

-- 
Dr. pascal Boulet, computational chemist
University of Aix-Marseille I 
Laboratoire Chimie Provence, UMR 6264
Group of Theoretical Chemistry
Avenue Normandie-Niemen
13397 Marseille Cedex 20
France
**********
Tel. (+33) (0)413.55.18.10
Fax. (+33) (0)491.55.18.50
**********
http://www.lc-provence.fr
https://sites.google.com/a/univ-provence.fr/pb-comput-chem
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


From pascal.boulet at univ-provence.fr  Mon Nov  7 09:22:10 2011
From: pascal.boulet at univ-provence.fr (pascal boulet)
Date: Mon, 07 Nov 2011 09:22:10 +0100
Subject: [Pw_forum]  general question on materials physics
Message-ID: <4EB79532.10505@univ-provence.fr>

I think that I've just found the answer: the SC is heavily doped!

P.

-- 
Dr. pascal Boulet, computational chemist
University of Aix-Marseille I 
Laboratoire Chimie Provence, UMR 6264
Group of Theoretical Chemistry
Avenue Normandie-Niemen
13397 Marseille Cedex 20
France
**********
Tel. (+33) (0)413.55.18.10
Fax. (+33) (0)491.55.18.50
**********
http://www.lc-provence.fr
https://sites.google.com/a/univ-provence.fr/pb-comput-chem
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


From degironc at sissa.it  Mon Nov  7 09:24:58 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 07 Nov 2011 09:24:58 +0100
Subject: [Pw_forum] general question on materials physics
In-Reply-To: <4EB791D4.40403@univ-provence.fr>
References: <4EB791D4.40403@univ-provence.fr>
Message-ID: <4EB795DA.7080605@sissa.it>

Dear Pascal
     the density of state of a material can have several gaps.
     for instance the core levels of all materials are well separated 
from the valence bands by large gaps, in many polar III-V or II-VI 
semiconductor the lower part of the valence band is separated by a gap 
from its upper part, etc.

     what matters to determine whether a material is a band insulator or 
a band metal is whether a gap separates the occupied from the empty 
levels. If in your case the Fermi energy is located within a partially 
filled group of bands it is a metal, even if somewhere nearby these 
bands are isolated from the others by energy gaps.

     beware that if the partially filled set of bands determines a 
rather narrow peak in the DOS you need to explore the possibility that 
the material is actually a Mott insulator where the independent-particle 
band picture is actually insufficient.

     best rtegards

stefano de Gironcoli - SISSA and DEMOCRITOS

On 11/07/2011 09:07 AM, pascal boulet wrote:
> Dear all,
>
> Sorry to bother you with this silly question but it puzzles me a bit!
>
> In a recent article, I have seen a DOS in which the Fermi level is
> located in the conduction band. So, it seems to me that the materials is
> metallic. But there is clearly a band gap of about 2 eV. I always
> thought that for metals the gap was closed. Is there a contradiction in
> the paper or am I wrong?
>
> Thank you for your answer.
>
> Best
> Pascal
>


From pascal.boulet at univ-provence.fr  Mon Nov  7 09:32:12 2011
From: pascal.boulet at univ-provence.fr (pascal boulet)
Date: Mon, 07 Nov 2011 09:32:12 +0100
Subject: [Pw_forum]  general question on materials physics
References: 4EB791D4.40403@univ-provence.fr
Message-ID: <4EB7978C.9020904@univ-provence.fr>

Thank you Stefano for your precisions.

Best regards
Pascal

-- 
Dr. pascal Boulet, computational chemist
University of Aix-Marseille I 
Laboratoire Chimie Provence, UMR 6264
Group of Theoretical Chemistry
Avenue Normandie-Niemen
13397 Marseille Cedex 20
France
**********
Tel. (+33) (0)413.55.18.10
Fax. (+33) (0)491.55.18.50
**********
http://www.lc-provence.fr
https://sites.google.com/a/univ-provence.fr/pb-comput-chem
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


From avallabh at purdue.edu  Mon Nov  7 14:30:51 2011
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Mon, 7 Nov 2011 08:30:51 -0500 (EST)
Subject: [Pw_forum] Query on Xcrysden
In-Reply-To: <157734259.92533.1320671322916.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <615177880.92612.1320672651869.JavaMail.root@mailhub016.itcs.purdue.edu>

Dear users,
 
            I am a new user of QE. I installed QE 4.3.1 and trying to repeat the simulations shown in the tutorials (http://www.fisica.uniud.it/~giannozz/QE-Tutorial/). Also i had some compatibility issues with my Linux environment and i cannot install the latest version of xcrysden for visualisation. I can only use the older version (V1.4). I want to know whether this older version is totally compatible with the QE version or not. Because i am not able to see the output files of the PWSCF calculations. Like for the file si.scf.in i am able to see the initial structure but not the output file si.scf.out.

 ERROR: while executing exec sh
 ERROR INFO: Child process exited abnormally


Thanks
Ajit

From renpj at dicp.ac.cn  Mon Nov  7 15:50:24 2011
From: renpj at dicp.ac.cn (Ren PJ)
Date: Mon, 7 Nov 2011 22:50:24 +0800
Subject: [Pw_forum] Query on Xcrysden
In-Reply-To: <615177880.92612.1320672651869.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <157734259.92533.1320671322916.JavaMail.root@mailhub016.itcs.purdue.edu>
	<615177880.92612.1320672651869.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <20111107225024.6a4bc925@ren-desktop>


There is a executable file which need not to install. The latest version
is 4.3. The url is: http://www-k3.ijs.si/kokalj/pwgui/




Pengju Ren
renpj at dicp.ac.cn
State  Key Laboratory of Catalysis, 
Dalian Institute of Chemical Physics, 
Chinese Academy of Sciences 
457 zhongshan Road, Dalian, 116023, P.R. China  

From victor.bermudez at nrl.navy.mil  Mon Nov  7 17:28:44 2011
From: victor.bermudez at nrl.navy.mil (Vic Bermudez)
Date: Mon, 7 Nov 2011 11:28:44 -0500
Subject: [Pw_forum] NEB Convergence Problem
In-Reply-To: <1320628991.3704.21.camel@catalyst.ijs.si>
Message-ID: <LEEKKBMDPAJFIINCBCGIIEGDDPAA.victor.bermudez@nrl.navy.mil>

Hi Tone,

	Thanks for your very helpful comments. I think that there may be a fundamental problem
with what I'm trying to do. What I'm looking at is a "simple" surface reaction where an HF
molecule reacts with an Si-OH on the surface of hexagonal SiC to form an Si-F site and
release H2O.  In other words, HF + Si-OH --> Si-F + H2O, where Si-OH is a surface species.
	Beginning with the IS, which is a free HF molecule a few Angstroms from the surface, the
HF first goes through a weakly-physisorbed state and then the TS. Once the reaction has
occurred the H2O goes through a weakly-physisorbed state before leaving as a free molecule
(the FS). There may also be more than one physisorbed state for the HF and the H2O. These
are very likely real (not artifacts of the calculation) and produce the structure that you
noticed to either side of the TS in the reaction path I sent earlier. The potential energy
surface I'm faced with can't really be modeled as a simple IS --> TS --> FS progression. I
don't think that it would be acceptable to force it to fit such a simple scheme, even if
that were possible.
	In my initial runs, my IS was a guess for the first physisorbed state of HF, and my FS
was a guess for the last physisorbed state of the H2O product. This was done to avoid
exactly the problems that you've described. The problem is that, if these are not good
guesses then, even if these are optimized, the reaction path is forced to begin and/or
terminate incorrectly. Choosing the IS and FS as the free molecules avoids this.
	So, at this point, my question is how can I deal with this complex energy surface in the
context of NEB, as implemented in QE ?  If I understand correctly, the only solution is to
"zero in" on the TS. This means using as the IS the last physisorbed state before  the TS
and for the FS the first physisorbed state after the TS. I would obtain these using the
appropriate images in my present reaction path, so they should be good guesses. This would
in effect isolate an IS --> TS --> FS segment centered on the true (highest-energy) TS in
the path. Is this the correct thing to do ?  My activation energy would then be the
difference between this TS and a system consisting of isolated free HF and bare
OH-terminated SiC (which I can easily compute).

	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 ptao10b at imr.ac.cn  Tue Nov  8 13:36:39 2011
From: ptao10b at imr.ac.cn (=?GBK?B?zNXF9A==?=)
Date: Tue, 8 Nov 2011 20:36:39 +0800 (CST)
Subject: [Pw_forum] I need LDA pseudopotential of Mo
Message-ID: <11219b7.4fa92.133832e26a3.Coremail.ptao10b@imr.ac.cn>

Dear all,
I browsed the internet, and the QE offical site only gave the Perdew-Wang 91 gradient-corrected functional of Mo. However, only the LDA pseudopotential is suitable for my calculation. Could someone nice guy give me a LDA pseudopotential of Mo or show me a website to download it?

Thank you very much!

Yours,
Plato Tao







From giannozz at democritos.it  Tue Nov  8 13:55:10 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 8 Nov 2011 13:55:10 +0100
Subject: [Pw_forum] I need LDA pseudopotential of Mo
In-Reply-To: <11219b7.4fa92.133832e26a3.Coremail.ptao10b@imr.ac.cn>
References: <11219b7.4fa92.133832e26a3.Coremail.ptao10b@imr.ac.cn>
Message-ID: <47B3DC10-EC49-4989-851E-27F6E9E73E1A@democritos.it>


On Nov 8, 2011, at 13:36 , ?? wrote:

> Could someone nice guy give me a LDA pseudopotential of Mo
> or show me a website to download it?

was it too hard to read here:
"For more info on pseudopotentials, follow the About link on the left"
do what is suggested, and look here:
http://www.quantum-espresso.org/pseudo-notes.php?
---
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 tone.kokalj at ijs.si  Tue Nov  8 14:22:58 2011
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 08 Nov 2011 14:22:58 +0100
Subject: [Pw_forum] NEB Convergence Problem
In-Reply-To: <LEEKKBMDPAJFIINCBCGIIEGDDPAA.victor.bermudez@nrl.navy.mil>
References: <LEEKKBMDPAJFIINCBCGIIEGDDPAA.victor.bermudez@nrl.navy.mil>
Message-ID: <20111108142258.20762jfdw0uh8w1e@nabiralnik.ijs.si>

Quoting Vic Bermudez <victor.bermudez at nrl.navy.mil>:
> The potential energy
> surface I'm faced with can't really be modeled as a simple IS --> TS  
> --> FS progression. I
> don't think that it would be acceptable to force it to fit such a  
> simple scheme, even if that were possible.

Nothing is forcing you to adopt a too simple scheme. Your reaction may  
appear very simple on the paper, but this does not mean it consists of  
single elementary step. This means you have to decompose it to a  
several elementary steps. If a step is nonactivated (e.g., adsorption)  
than model it with geometry optimization. If a given step is activated  
(e.g. diffusion or elementary chemical reaction) then model it with  
NEB. Hence your overall reaction may consists of, say, an adsorption,  
a few activated processes (surface diffusion, elementary reactions),  
and desorption. Model each of it with a separate calculation.

Hope this clarifies the issue.

Regards, Tone


From ptao10b at imr.ac.cn  Tue Nov  8 14:29:01 2011
From: ptao10b at imr.ac.cn (=?utf-8?B?6Zm26bmP?=)
Date: Tue, 8 Nov 2011 21:29:01 +0800 (CST)
Subject: [Pw_forum] I need LDA pseudopotential of Mo
In-Reply-To: <47B3DC10-EC49-4989-851E-27F6E9E73E1A@democritos.it>
References: <47B3DC10-EC49-4989-851E-27F6E9E73E1A@democritos.it>
	<11219b7.4fa92.133832e26a3.Coremail.ptao10b@imr.ac.cn>
Message-ID: <1d604dc.4fc5c.133835e17ac.Coremail.ptao10b@imr.ac.cn>

Thank you very much. I'll learn to generate it by myself.


> -----????-----
> ???: "Paolo Giannozzi" <giannozz at democritos.it>
> ????: 2011?11?8? ???
> ???: "PWSCF Forum" <pw_forum at pwscf.org>
> ??: 
> ??: Re: [Pw_forum] I need LDA pseudopotential of Mo
> 
> 
> On Nov 8, 2011, at 13:36 , ?? wrote:
> 
> > Could someone nice guy give me a LDA pseudopotential of Mo
> > or show me a website to download it?
> 
> was it too hard to read here:
> "For more info on pseudopotentials, follow the About link on the left"
> do what is suggested, and look here:
> http://www.quantum-espresso.org/pseudo-notes.php?
> ---
> 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 avallabh at purdue.edu  Tue Nov  8 18:06:00 2011
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Tue, 8 Nov 2011 12:06:00 -0500 (EST)
Subject: [Pw_forum] Query on "e-ph coupling"
In-Reply-To: <343445582.98252.1320771911774.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <1730348110.98262.1320771960562.JavaMail.root@mailhub016.itcs.purdue.edu>

Dear users,

          I had recently gone through the tutorials on e-ph coupling for Al. I am able to get the values of lambda and gamma from the program but it was not clear to me how to get the value of the matrix element "g" from that. Can someone please help me with this?

Thanks
Ajit


From romeda_8 at yahoo.com  Wed Nov  9 07:24:20 2011
From: romeda_8 at yahoo.com (r s)
Date: Tue, 8 Nov 2011 22:24:20 -0800 (PST)
Subject: [Pw_forum] What is the total energy content of a compound?
Message-ID: <1320819860.36401.YahooMailNeo@web120401.mail.ne1.yahoo.com>

Dear PW Forum,
I try to calculate the total energy of a compound by two packages?
a) PWscf Code (Pseudopotential)? ???b) Wien2k Code (Full-Potential)
The values that obtained for the total energy are: 
PWscf: ?- 5706.6313 eV/cell 
Wien2k: ?- 45633.14 eV/Cell
Why are different amounts of this quantity (Total Energy)? 
?Thanks,
--
Romeda
Bhavnagar University Bhavnagar 364002 Gujarat India.
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From baroni at sissa.it  Wed Nov  9 07:27:59 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 9 Nov 2011 07:27:59 +0100
Subject: [Pw_forum] What is the total energy content of a compound?
In-Reply-To: <1320819860.36401.YahooMailNeo@web120401.mail.ne1.yahoo.com>
References: <1320819860.36401.YahooMailNeo@web120401.mail.ne1.yahoo.com>
Message-ID: <718CE453-5B29-451F-A678-C38299DED86A@sissa.it>

because wien2k is an all-electron code, whereas pw.x is a pseudopotential one.
I think it would take (far) less to read the first few lines of documentation of the codes than actually running them.
SB

On Nov 9, 2011, at 7:24 AM, r s wrote:

> Dear PW Forum,
> I try to calculate the total energy of a compound by two packages?
> a) PWscf Code (Pseudopotential)     b) Wien2k Code (Full-Potential)
> The values that obtained for the total energy are:
> PWscf:  - 5706.6313 eV/cell
> Wien2k:  - 45633.14 eV/Cell
> Why are different amounts of this quantity (Total Energy)?
>  Thanks,
> --
> Romeda
> Bhavnagar University Bhavnagar 364002 Gujarat 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

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From baroni at sissa.it  Wed Nov  9 07:30:57 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 9 Nov 2011 07:30:57 +0100
Subject: [Pw_forum] What is the total energy content of a compound?
In-Reply-To: <1320819860.36401.YahooMailNeo@web120401.mail.ne1.yahoo.com>
References: <1320819860.36401.YahooMailNeo@web120401.mail.ne1.yahoo.com>
Message-ID: <8286C6B5-D603-45B8-AE71-CC7A41E47872@sissa.it>

On Nov 9, 2011, at 7:24 AM, r s wrote:

> Dear PW Forum,
> I try to calculate the total energy of a compound by two packages?
> a) PWscf Code (Pseudopotential)     b) Wien2k Code (Full-Potential)
ah! I did not notice that you knew the answer already!
how about investing some time in reading books, rather than blindly running codes? 
You may want to start with Ashcroft and Mermin's solid state, and continue with Martin's electronic structure
SB

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

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

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From giannozz at democritos.it  Wed Nov  9 10:42:40 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 09 Nov 2011 10:42:40 +0100
Subject: [Pw_forum] Query on "e-ph coupling"
In-Reply-To: <1730348110.98262.1320771960562.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <1730348110.98262.1320771960562.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <1320831760.10071.45.camel@fe12lx.fisica.uniud.it>

On Tue, 2011-11-08 at 12:06 -0500, Ajit Vallabhaneni wrote:

> I had recently gone through the tutorials on e-ph coupling for Al.
>  I am able to get the values of lambda and gamma from the program 
> but it was not clear to me how to get the value of the matrix element
>  "g" from that.

if you are referring to the matrix element of the electron-phonon
coupling, <\psi|dV/du|\psi>, you have to go inside the code to get it

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



From chengyu.young at gmail.com  Wed Nov  9 21:46:01 2011
From: chengyu.young at gmail.com (chengyu yang)
Date: Wed, 9 Nov 2011 15:46:01 -0500
Subject: [Pw_forum] PAW potential for C
Message-ID: <CAOk-W=EXSJ8CNW2Tzx3NQcv2pGSoN5xC8yFy_b=UMQssaopZVw@mail.gmail.com>

Dear Everyone,
         I am looking for the paw potential for C atom with the PBE as
XC function, can anyone tell me how can I get such a potential?
         On the other hand, I googled the forum and somebody said the
choice of potential has no react to the result of binding energy, does
that mean whether I choose paw or normal potential, the result is the
same?
        Third problem, is the K point's setting has influence on the
calculation of binding energy? I found on this forum Dr. Nicola said
he would set the k point as gamma for all the calculations, but in all
the paper I read they use settings as 1*1*13 or something like that.
        Thank you. Best regards.

Chengyu Yang
MMAE,University of Central Florida, US

From degironc at sissa.it  Wed Nov  9 23:32:44 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 09 Nov 2011 23:32:44 +0100
Subject: [Pw_forum] PAW potential for C
In-Reply-To: <CAOk-W=EXSJ8CNW2Tzx3NQcv2pGSoN5xC8yFy_b=UMQssaopZVw@mail.gmail.com>
References: <CAOk-W=EXSJ8CNW2Tzx3NQcv2pGSoN5xC8yFy_b=UMQssaopZVw@mail.gmail.com>
Message-ID: <4EBAFF8C.3050408@sissa.it>

Dear Chengyu Yang,
    Andrea Dal Corso is working on an extensive library of 
pseudopotentials and paw datasets .
    The project hosted by the QE-forge portal (http://qe-forge.org/) is 
named PSlibrary and can be reached directly at 
http://qe-forge.org/projects/pslibrary/ .
    It contains US and PAW input files for many elements including C.
best regards,
stefano de Gironcoli - SISSA and DEMOCRITOS

On 11/09/2011 09:46 PM, chengyu yang wrote:
> Dear Everyone,
>           I am looking for the paw potential for C atom with the PBE as
> XC function, can anyone tell me how can I get such a potential?
>           On the other hand, I googled the forum and somebody said the
> choice of potential has no react to the result of binding energy, does
> that mean whether I choose paw or normal potential, the result is the
> same?
>          Third problem, is the K point's setting has influence on the
> calculation of binding energy? I found on this forum Dr. Nicola said
> he would set the k point as gamma for all the calculations, but in all
> the paper I read they use settings as 1*1*13 or something like that.
>          Thank you. Best regards.
>
> Chengyu Yang
> MMAE,University of Central Florida, US
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From chengyu.young at gmail.com  Wed Nov  9 23:51:55 2011
From: chengyu.young at gmail.com (chengyu yang)
Date: Wed, 9 Nov 2011 17:51:55 -0500
Subject: [Pw_forum] PAW potential for C
In-Reply-To: <4EBAFF8C.3050408@sissa.it>
References: <CAOk-W=EXSJ8CNW2Tzx3NQcv2pGSoN5xC8yFy_b=UMQssaopZVw@mail.gmail.com>
	<4EBAFF8C.3050408@sissa.it>
Message-ID: <CAOk-W=HfnXQ3F4SN8Gx3sNSGP2cCVU4QGhi4HMktFjr5_AvL9g@mail.gmail.com>

Dear Dr. Gironcoli,
        I downloaded the folder and extracted files from it.  What do
you mean by  input file? Does that mean I should generate pseudo
potential by myself? If so can you teach me what code should I use?
        Thank you.
        Best regards.

Chengyu Yang
MMAE,University of Central Florida,US

2011/11/9 Stefano de Gironcoli <degironc at sissa.it>:
> Dear Chengyu Yang,
> ? ?Andrea Dal Corso is working on an extensive library of
> pseudopotentials and paw datasets .
> ? ?The project hosted by the QE-forge portal (http://qe-forge.org/) is
> named PSlibrary and can be reached directly at
> http://qe-forge.org/projects/pslibrary/ .
> ? ?It contains US and PAW input files for many elements including C.
> best regards,
> stefano de Gironcoli - SISSA and DEMOCRITOS
>
> On 11/09/2011 09:46 PM, chengyu yang wrote:
>> Dear Everyone,
>> ? ? ? ? ? I am looking for the paw potential for C atom with the PBE as
>> XC function, can anyone tell me how can I get such a potential?
>> ? ? ? ? ? On the other hand, I googled the forum and somebody said the
>> choice of potential has no react to the result of binding energy, does
>> that mean whether I choose paw or normal potential, the result is the
>> same?
>> ? ? ? ? ?Third problem, is the K point's setting has influence on the
>> calculation of binding energy? I found on this forum Dr. Nicola said
>> he would set the k point as gamma for all the calculations, but in all
>> the paper I read they use settings as 1*1*13 or something like that.
>> ? ? ? ? ?Thank you. Best regards.
>>
>> Chengyu Yang
>> MMAE,University of Central Florida, US
>> _______________________________________________
>> 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 chengyu.young at gmail.com  Wed Nov  9 23:55:58 2011
From: chengyu.young at gmail.com (chengyu yang)
Date: Wed, 9 Nov 2011 17:55:58 -0500
Subject: [Pw_forum] PAW potential for C
In-Reply-To: <CAOk-W=HfnXQ3F4SN8Gx3sNSGP2cCVU4QGhi4HMktFjr5_AvL9g@mail.gmail.com>
References: <CAOk-W=EXSJ8CNW2Tzx3NQcv2pGSoN5xC8yFy_b=UMQssaopZVw@mail.gmail.com>
	<4EBAFF8C.3050408@sissa.it>
	<CAOk-W=HfnXQ3F4SN8Gx3sNSGP2cCVU4QGhi4HMktFjr5_AvL9g@mail.gmail.com>
Message-ID: <CAOk-W=EXZVh3XJiKab4EiQMpUWi-kV+wp-WZU5SRsobcxPfSAQ@mail.gmail.com>

Dear Dr. Gironcoli and others,
        I think I got it in readme file.Thank you. Can you plz also
explain my other two questions, like: if the choice of potential and k
point change the final binding energy of two systems.  Thank you.
          Best regards.

Chengyu Yang
MMAE,University of Central Florida
US

From ttduyle at gmail.com  Thu Nov 10 00:04:14 2011
From: ttduyle at gmail.com (Duy Le)
Date: Wed, 9 Nov 2011 18:04:14 -0500
Subject: [Pw_forum] PAW potential for C
In-Reply-To: <CAOk-W=EXZVh3XJiKab4EiQMpUWi-kV+wp-WZU5SRsobcxPfSAQ@mail.gmail.com>
References: <CAOk-W=EXSJ8CNW2Tzx3NQcv2pGSoN5xC8yFy_b=UMQssaopZVw@mail.gmail.com>
	<4EBAFF8C.3050408@sissa.it>
	<CAOk-W=HfnXQ3F4SN8Gx3sNSGP2cCVU4QGhi4HMktFjr5_AvL9g@mail.gmail.com>
	<CAOk-W=EXZVh3XJiKab4EiQMpUWi-kV+wp-WZU5SRsobcxPfSAQ@mail.gmail.com>
Message-ID: <CAF-j6z97SYV-mXg68asuoRkSy26tPFvY=WtASUHz3H2iXQ2eKg@mail.gmail.com>

On Wed, Nov 9, 2011 at 5:55 PM, chengyu yang <chengyu.young at gmail.com>wrote:

> explain my other two questions, like: if the choice of potential and k
> point change the final binding energy of two systems.  Thank you.
>           Best regards.
>
>
The best way to answer these two questions is to test them. The tests are
very simple and easy to perform:

1. Use different potential to calculate the quantity in question.

2. Use different k-point set to calculate the quantity in question.

--------------------------------------------------
Duy Le
PhD Candidate
Department of Physics
University of Central Florida.

"Men don't need hand to do things"
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From chengyu.young at gmail.com  Thu Nov 10 00:12:56 2011
From: chengyu.young at gmail.com (chengyu yang)
Date: Wed, 9 Nov 2011 18:12:56 -0500
Subject: [Pw_forum] PAW potential for C
In-Reply-To: <CAF-j6z97SYV-mXg68asuoRkSy26tPFvY=WtASUHz3H2iXQ2eKg@mail.gmail.com>
References: <CAOk-W=EXSJ8CNW2Tzx3NQcv2pGSoN5xC8yFy_b=UMQssaopZVw@mail.gmail.com>
	<4EBAFF8C.3050408@sissa.it>
	<CAOk-W=HfnXQ3F4SN8Gx3sNSGP2cCVU4QGhi4HMktFjr5_AvL9g@mail.gmail.com>
	<CAOk-W=EXZVh3XJiKab4EiQMpUWi-kV+wp-WZU5SRsobcxPfSAQ@mail.gmail.com>
	<CAF-j6z97SYV-mXg68asuoRkSy26tPFvY=WtASUHz3H2iXQ2eKg@mail.gmail.com>
Message-ID: <CAOk-W=Go95a8dtSLFNot_Cf5PRfbNzFij1yd_U_vFmKcf_wf2g@mail.gmail.com>

Dear Duy Le,
         Thank you. Yes I understand that procedure, but my question
is about the concept: since the binding energy= E(1 at 2)-E(1)-E(2), than
should the choice of pseudopotential and k point doesn't matter
because they cancel each other in the process of subtraction.
      I know for total energy the result should be certainly different.

Chengyu Yang
MMAE,University of Central Florida
US

2011/11/9 Duy Le <ttduyle at gmail.com>:
> On Wed, Nov 9, 2011 at 5:55 PM, chengyu yang <chengyu.young at gmail.com>
> wrote:
>>
>> explain my other two questions, like: if the choice of potential and k
>> point change the final binding energy of two systems. ?Thank you.
>> ? ? ? ? ?Best regards.
>>
>
> The best way to answer these two questions is to test them. The tests are
> very simple and easy to perform:
> 1. Use different potential to calculate the quantity in question.
> 2. Use different k-point set to calculate the quantity in question.
> --------------------------------------------------
> Duy Le
> PhD Candidate
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From padmaja_patnaik at yahoo.co.uk  Thu Nov 10 06:21:18 2011
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Thu, 10 Nov 2011 05:21:18 +0000 (GMT)
Subject: [Pw_forum] LDA scheme used in QE
Message-ID: <1320902478.53447.YahooMailNeo@web28507.mail.ukl.yahoo.com>

Hi All

The pseudopotentials in QE are obtained using PZ /PW91/PBE etc schemes. When one pseudopotential is using PZ scheme that means one is referring to Perdew Zunger paper?? 'Self-interaction correction to density functional approximation for many electron system', in PRB, volume 23, 1981. That paper is for self-interaction corrected formalism. But in many posts in this forum I saw the answer as SIC is not implemented in PWSCF except the case of CP. Now I am confused about the pseudopotentials I am using. Are they SIC or not? Whenever I am using a pseudopotential with the name? *.pz-vbc.UPF I thought its referring to the above said paper and hence SIC.? Am I wrong? Is there any other Perdew Zunger paper for LDA which is referred? Please clarify. 


Thanking in advance
Regards

?
Padmaja Patnaik
Research Scholar
Dept of Physics
IIT Bombay
Mumbai, India
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From degironc at sissa.it  Thu Nov 10 06:42:14 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 10 Nov 2011 06:42:14 +0100
Subject: [Pw_forum] LDA scheme used in QE
In-Reply-To: <1320902478.53447.YahooMailNeo@web28507.mail.ukl.yahoo.com>
References: <1320902478.53447.YahooMailNeo@web28507.mail.ukl.yahoo.com>
Message-ID: <20111110064214.Horde.FlLwUh8V4mxOu2Q2iwfjf4A@webmail.sissa.it>

Dear Padmaja Patnaik,
   In that paper devoted to SIC there is an appendix where the PZ  
parametrization of Ceperley-Alder QMC data for the homogeneous  
electron gas is given to be used in LDA.
   this is what is meant for functional PZ: LDA using PZ parametrization.
   that paper is probably much more quoted for its appendix than for  
the, also very important, discussion of SIC error.
   best,
stefano



Quoting Padmaja Patnaik <padmaja_patnaik at yahoo.co.uk>:

> Hi All
>
> The pseudopotentials in QE are obtained using PZ /PW91/PBE etc  
> schemes. When one pseudopotential is using PZ scheme that means one  
> is referring to Perdew Zunger paper?? 'Self-interaction correction  
> to density functional approximation for many electron system', in  
> PRB, volume 23, 1981. That paper is for self-interaction corrected  
> formalism. But in many posts in this forum I saw the answer as SIC  
> is not implemented in PWSCF except the case of CP. Now I am confused  
> about the pseudopotentials I am using. Are they SIC or not? Whenever  
> I am using a pseudopotential with the name? *.pz-vbc.UPF I thought  
> its referring to the above said paper and hence SIC.? Am I wrong? Is  
> there any other Perdew Zunger paper for LDA which is referred?  
> Please clarify.
>
>
> Thanking in advance
> Regards
>
> ?
> Padmaja Patnaik
> Research Scholar
> Dept of Physics
> IIT Bombay
> Mumbai, India



From songsong19840614 at hotmail.com  Thu Nov 10 13:15:50 2011
From: songsong19840614 at hotmail.com (KangYun Song)
Date: Thu, 10 Nov 2011 12:15:50 +0000
Subject: [Pw_forum] QHA frequency is higher than *.freq
Message-ID: <COL113-W60CEBD49552B277D2F7BC8C8DC0@phx.gbl>


Hi,
         Recently,I calculated the phonon dispersion.And I use the *.fc from matdyn q2r.x to calculate frequecy and pdos.But this is a problem the freqency from matdyn.x of QHA is higher than *.freq from matdyn.x of phonon dispersion calculation.Why?Could anyone help me?The other material I use this method did not meet this problem.
         The matdyn.in of QHA is:
&input
    amass(1)=*,
    amass(2)=*,
    asr='crystal',
    flfrc=*.fc,
    flfrq='frequency'
&end
1183
     -0.33333   0.57735   0.81850   1.00000
     -0.30555   0.52924   0.75029   1.00000
     -0.30555   0.57735   0.75029   1.00000

??????
 
       The matdyn.in of phonon dispersion calculating is :          
&input
    asr='simple',  amass(1)=*, amass(2)=*, 
    flfrc='*.fc', flfrq='*.freq' ,la2F=.false. , 
 /
85
  0.0000000   0.0000000   0.3092146, wk =   0.0235294
  0.0555560   0.0000000   0.3092146, wk =   0.0235294
  0.1111110  -0.0000006   0.3092146, wk =   0.0235294
  0.1666670   0.0000006   0.3092146, wk =   0.0235294
  0.2222220   0.0000000   0.3092146, wk =   0.0235294
  0.2777780   0.0000000   0.3092146, wk =   0.0235294
????


Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University. 		 	   		  
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From giacsport at libero.it  Fri Nov 11 04:39:53 2011
From: giacsport at libero.it (giacsport at libero.it)
Date: Fri, 11 Nov 2011 04:39:53 +0100 (CET)
Subject: [Pw_forum] from 4.1 to 4.2 and 4.3.1 versions of QE in IBM sp6
Message-ID: <23106092.3389831320982793106.JavaMail.defaultUser@defaultHost>

Dear All,
              I am trying to plot my band for a Magnetic semiconductor, MnO2 
in some.
I am running the 4.1 version of QE at the CINECA IBM Sp6 machine.
I got this message.

  
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     task #         0
     from bands : error #         1
     The bands code with constrained magnetization has not been tested
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Ok. I looked in the forum and I saw the reason for it. 
Now, I was wondering  if more updated versions (4.2 and 4.3.1) could perform 
this kind of calculations.

I started testing it, and I simply replaced in my script for launching the 
job, the older version with the upgraded one (I tested both 4.2 and 4.3.1).
The same input which perfectly converged before, now gives me troubles and the 
message I got immediately is

  
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     task #         1
     from  read_namelists  : error #        88
      reading namelist system
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Where am i failing?  Ichjecked the forum once more and I think that it should 
not be mis-spelling (exactly the same Input). 
I checked the example file in the directory of the installed version of QE 4.2 
without finding macroscopic differences with my one (that I attach below)
A problem of parallel libraries? But this one too seems to me the real reason 
( I also tested the launching script in the same directory, getting the same 
message, and after loading the proper module xlf/12-1)

Maybe I am using some obsolete features....

May someone give me a hint to fix my doubt?
(well, if 4.2 and 4.3.1 can do band calculation for constrained magnetic 
systems, and also the reason of the difference for the old and new versions)
Many thanks,
Giacomo


&CONTROL
  calculation = "scf"
  pseudo_dir = './'
  outdir='./',
  restart_mode= "from_scratch",
  prefix      = "MnO2",
  tprnfor     = .true.,
  tstress     = .true.,
  wf_collect=.true.,
/
&SYSTEM
    ibrav=  4, celldm(1) = 5.462171712, celldm(3) = 3.7856422, nat=  3, ntyp= 
2,
    ecutwfc =100.0, nbnd=100, force_symmorphic=.true., nspin=2,
    occupations='smearing'
    smearing='gauss',
    degauss=0.01,
    starting_magnetization(1) = 1.,
    nelup=14,
    neldw=11,
    nelec=25,
/
&ELECTRONS
    diagonalization='david'
    mixing_mode = 'plain'
    mixing_beta = 0.7
    conv_thr =  1.0d-8
/
K_POINTS (automatic)
9 9 1 0 0 0

ATOMIC_SPECIES
 Mn  54.938  Mn_HSCV_LDA-1.0.UPF
  O  15.999  O.pz-mt.UPF

ATOMIC_POSITIONS (crystal)
Mn  0.0000000000000000  0.0000000000000000  0.5000000000000000
O   0.3403727063099424  0.6596272936900647  0.5876622657201906
O   0.6596272936900647  0.3403727063099424  0.4123377342797880


----------------------------------------------------
Giacomo Giorgi, PhD.
The University of Tokyo, Todai, Japan

From kucukben at sissa.it  Fri Nov 11 09:36:29 2011
From: kucukben at sissa.it (Emine Kucukbenli)
Date: Fri, 11 Nov 2011 09:36:29 +0100
Subject: [Pw_forum] from 4.1 to 4.2 and 4.3.1 versions of QE in IBM sp6
In-Reply-To: <23106092.3389831320982793106.JavaMail.defaultUser@defaultHost>
References: <23106092.3389831320982793106.JavaMail.defaultUser@defaultHost>
Message-ID: <20111111093629.Horde.HijlYh8V4mxOvN6Nk4r1RHA@webmail.sissa.it>


Dear Giacomo
The following error message

> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      task #         1
>      from  read_namelists  : error #        88
>       reading namelist system
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

means that there is a problem with parameters in the &system namelist  
of the input file.
So you need to look here:

> &SYSTEM
>     ibrav=  4, celldm(1) = 5.462171712, celldm(3) = 3.7856422, nat=  3, ntyp=
> 2,
>     ecutwfc =100.0, nbnd=100, force_symmorphic=.true., nspin=2,
>     occupations='smearing'
>     smearing='gauss',
>     degauss=0.01,
>     starting_magnetization(1) = 1.,
>     nelup=14,
>     neldw=11,
>     nelec=25,
> /

Apparently something has changed between versions.
 From the description of the input file in the following link:
http://www.quantum-espresso.org/input-syntax/INPUT_PW.html
I think the parameters that are no longer in use are nelec, neldw, and nelup.
look for the tot_charge and tot_magnetization etc.
cheers
emine kucukbenli, sissa, italy

From giannozz at democritos.it  Fri Nov 11 09:48:14 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 11 Nov 2011 09:48:14 +0100
Subject: [Pw_forum] from 4.1 to 4.2 and 4.3.1 versions of QE in IBM sp6
In-Reply-To: <23106092.3389831320982793106.JavaMail.defaultUser@defaultHost>
References: <23106092.3389831320982793106.JavaMail.defaultUser@defaultHost>
Message-ID: <1321001294.17550.1.camel@fe12lx.fisica.uniud.it>

On Fri, 2011-11-11 at 04:39 +0100, giacsport at libero.it wrote:

>     nelup=14,
>     neldw=11,
>     nelec=25,

from file Doc/release-notes that nobody ever reads:
===
Incompatible changes in version 4.2:

[...]
* nelec, nelup, neldw, multiplicity variables removed from input:
  use tot_charge and tot_magnetization instead
[...]
===

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



From songsong19840614 at hotmail.com  Fri Nov 11 13:55:14 2011
From: songsong19840614 at hotmail.com (KangYun Song)
Date: Fri, 11 Nov 2011 12:55:14 +0000
Subject: [Pw_forum] QHA frequency is higher than *.freq
In-Reply-To: <COL113-W60CEBD49552B277D2F7BC8C8DC0@phx.gbl>
References: <COL113-W60CEBD49552B277D2F7BC8C8DC0@phx.gbl>
Message-ID: <COL113-W6531F4056497CDE2F640E1C8DD0@phx.gbl>


Hi,
    The pdos is not similar to phonon dispersion and the frequency is not negative from ph.x.

Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.
 



From: songsong19840614 at hotmail.com
To: pw_forum at pwscf.org
Date: Thu, 10 Nov 2011 12:15:50 +0000
Subject: [Pw_forum] QHA frequency is higher than *.freq





Hi,
         Recently,I calculated the phonon dispersion.And I use the *.fc from matdyn q2r.x to calculate frequecy and pdos.But this is a problem the freqency from matdyn.x of QHA is higher than *.freq from matdyn.x of phonon dispersion calculation.Why?Could anyone help me?The other material I use this method did not meet this problem.
         The matdyn.in of QHA is:

&input
    amass(1)=*,
    amass(2)=*,
    asr='crystal',
    flfrc=*.fc,
    flfrq='frequency'
&end
1183
     -0.33333   0.57735   0.81850   1.00000
     -0.30555   0.52924   0.75029   1.00000
     -0.30555   0.57735   0.75029   1.00000
??????
 
       The matdyn.in of phonon dispersion calculating is :          

&input
    asr='simple',  amass(1)=*, amass(2)=*, 
    flfrc='*.fc', flfrq='*.freq' ,la2F=.false. , 
 /
85
  0.0000000   0.0000000   0.3092146, wk =   0.0235294
  0.0555560   0.0000000   0.3092146, wk =   0.0235294
  0.1111110  -0.0000006   0.3092146, wk =   0.0235294
  0.1666670   0.0000006   0.3092146, wk =   0.0235294
  0.2222220   0.0000000   0.3092146, wk =   0.0235294
  0.2777780   0.0000000   0.3092146, wk =   0.0235294
????

Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.

_______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum 		 	   		  
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From iyad.ne at gmail.com  Fri Nov 11 23:22:00 2011
From: iyad.ne at gmail.com (IYAD AL-QASIR)
Date: Fri, 11 Nov 2011 17:22:00 -0500
Subject: [Pw_forum] image parallelization for phonon calculations
Message-ID: <CAJMDj40PowftE2Khegug69KSKGXZP-cJpCO5BxBHQ8F-rJF+zw@mail.gmail.com>

Hello All,
I am trying to perform in parallel phonon calculations  using ph.x.

I used the command
mpiexec -np 12 ./ph.x -nimage 3 -npool 2 <input.in> input.ph.out

but I got the message the "*image parallelization is not permitted*"

Any Hint?

Thanks
_______________________________
IYAD I. AL-QASIR, PhD
Research Associate

Department of Nuclear Engineering
North Carolina State University
Campus Box 7909
2500 Stinson Dr.
Raleigh, NC 27695-7909
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From giannozz at democritos.it  Sat Nov 12 09:35:06 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 12 Nov 2011 09:35:06 +0100
Subject: [Pw_forum] image parallelization for phonon calculations
In-Reply-To: <CAJMDj40PowftE2Khegug69KSKGXZP-cJpCO5BxBHQ8F-rJF+zw@mail.gmail.com>
References: <CAJMDj40PowftE2Khegug69KSKGXZP-cJpCO5BxBHQ8F-rJF+zw@mail.gmail.com>
Message-ID: <FB88B8DD-DD40-4F5A-A21E-C8CB2DA092C3@democritos.it>


On Nov 11, 2011, at 23:22 , IYAD AL-QASIR wrote:

> Hello All,
> I am trying to perform in parallel phonon calculations  using ph.x.
>
> I used the command
> mpiexec -np 12 ./ph.x -nimage 3 -npool 2 <input.in> input.ph.out
>
> but I got the message the "image parallelization is not permitted"

$ grep 'image parallelization is not permitted' ~/CVS/espresso/*/*f90
(nothing found)

$ grep 'image parallelization' ~/CVS/espresso/*/*f90
(...)
/home/giannozz/CVS/espresso/PH/phq_readin.f90:     'elph with image  
parallelization is not yet available',1)

Is the above one the exact message you get?

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 mpayami at aeoi.org.ir  Sat Nov 12 10:48:25 2011
From: mpayami at aeoi.org.ir (Mahmoud Payami)
Date: Sat, 12 Nov 2011 13:18:25 +0330
Subject: [Pw_forum] Different mesh for pseudopotential
References: <CAJMDj40PowftE2Khegug69KSKGXZP-cJpCO5BxBHQ8F-rJF+zw@mail.gmail.com>
	<FB88B8DD-DD40-4F5A-A21E-C8CB2DA092C3@democritos.it>
Message-ID: <0DC3C6597EFC45FCA09C3C07BF5DB24F@b>

Dear QE users,

I am trying to test a given pseudopotential, which is generated by 
Vanderbilt's code, using the atomic code (ld1.x). I encounter the message:
------
%%%%%%%%%%%%%%%%%%%%
from read_pseudoup  :  error  #1
mesh not supported
%%%%%%%%%%%%%%%%%%

Googling, I found a post by Stefano 
(http://www.democritos.it/pipermail/pw_forum/2010-November.txt) explaining 
how the former code uses the "xmin" point as r=0. It was suggested to use 
the "virtual.x" to make an interpolation.
Is there an easy way in the upf tools?
Besr regards,
                       mahmoud

------------------------------------
Mahmoud Payami
Physics Group, AEOI, Tehran, Iran
Email : mpayami at aeoi.org.ir
-------------------------------------------------




From lorenzo.paulatto at impmc.upmc.fr  Sat Nov 12 11:50:56 2011
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Sat, 12 Nov 2011 11:50:56 +0100
Subject: [Pw_forum] image parallelization for phonon calculations
In-Reply-To: <CAJMDj40PowftE2Khegug69KSKGXZP-cJpCO5BxBHQ8F-rJF+zw@mail.gmail.com>
References: <CAJMDj40PowftE2Khegug69KSKGXZP-cJpCO5BxBHQ8F-rJF+zw@mail.gmail.com>
Message-ID: <op.v4txq6wg5jfbqb@paulax>

In data 11 novembre 2011 alle ore 23:22:00, IYAD AL-QASIR  
<iyad.ne at gmail.com> ha scritto:
> Any Hint?


Please provide a proper input/output and as many details as possible when  
reporting a problem, not just a riddle.

best regards


-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From giannozz at democritos.it  Sat Nov 12 14:09:22 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 12 Nov 2011 14:09:22 +0100
Subject: [Pw_forum] Different mesh for pseudopotential
In-Reply-To: <0DC3C6597EFC45FCA09C3C07BF5DB24F@b>
References: <CAJMDj40PowftE2Khegug69KSKGXZP-cJpCO5BxBHQ8F-rJF+zw@mail.gmail.com>
	<FB88B8DD-DD40-4F5A-A21E-C8CB2DA092C3@democritos.it>
	<0DC3C6597EFC45FCA09C3C07BF5DB24F@b>
Message-ID: <5487A736-9FD4-4069-BCF9-AD77CD170475@democritos.it>


On Nov 12, 2011, at 10:48 , Mahmoud Payami wrote:

> I am trying to test a given pseudopotential, which is generated by
> Vanderbilt's code, using the atomic code (ld1.x). I encounter the  
> message:
> ------
> %%%%%%%%%%%%%%%%%%%%
> from read_pseudoup  :  error  #1
> mesh not supported
> %%%%%%%%%%%%%%%%%%

this is an old problem. The atomic code uses as radial grid:
   r(i) = r_0 exp(i*dx) . The Vanderbilt code uses instead:
   r(i) = r_0 (exp(i*dx)-1). Some time ago I tried to convince
the atomic code to accept the latter grid, but it turned out
not to be an easy task. A straightforward but boring
solution is to interpolate all quantities from grids of type 2.

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  Sat Nov 12 14:11:11 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 12 Nov 2011 14:11:11 +0100
Subject: [Pw_forum] Different mesh for pseudopotential
In-Reply-To: <5487A736-9FD4-4069-BCF9-AD77CD170475@democritos.it>
References: <CAJMDj40PowftE2Khegug69KSKGXZP-cJpCO5BxBHQ8F-rJF+zw@mail.gmail.com>
	<FB88B8DD-DD40-4F5A-A21E-C8CB2DA092C3@democritos.it>
	<0DC3C6597EFC45FCA09C3C07BF5DB24F@b>
	<5487A736-9FD4-4069-BCF9-AD77CD170475@democritos.it>
Message-ID: <4088E57F-5970-4475-98FE-81442CE2AB11@democritos.it>


On Nov 12, 2011, at 14:09 , Paolo Giannozzi wrote:

> this is an old problem. The atomic code uses as radial grid:
>    r(i) = r_0 exp(i*dx) . The Vanderbilt code uses instead:
>    r(i) = r_0 (exp(i*dx)-1). Some time ago I tried to convince
> the atomic code to accept the latter grid, but it turned out
> not to be an easy task. A straightforward but boring
> solution is to interpolate all quantities from grids of type 2

...to grids of type 1 (sorry for the incomplete message)

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 mpayami at aeoi.org.ir  Sat Nov 12 14:49:27 2011
From: mpayami at aeoi.org.ir (Mahmoud Payami)
Date: Sat, 12 Nov 2011 17:19:27 +0330
Subject: [Pw_forum] Different mesh for pseudopotential
References: <CAJMDj40PowftE2Khegug69KSKGXZP-cJpCO5BxBHQ8F-rJF+zw@mail.gmail.com><FB88B8DD-DD40-4F5A-A21E-C8CB2DA092C3@democritos.it><0DC3C6597EFC45FCA09C3C07BF5DB24F@b><5487A736-9FD4-4069-BCF9-AD77CD170475@democritos.it>
	<4088E57F-5970-4475-98FE-81442CE2AB11@democritos.it>
Message-ID: <C20D873CFE7E4B55A37036DE52FD5C70@b>

Dear Paolo,

It is understandable that including the point "r=0" in a mesh demands 
special care, and so needs revision of some subroutines. Of course this 
is(?!) needless and more boring than that of just writing a small code to do 
the interpolations.
Thank you very much for your comments.

Best regards,
mahmoud

>
> On Nov 12, 2011, at 14:09 , Paolo Giannozzi wrote:
>
>> this is an old problem. The atomic code uses as radial grid:
>>    r(i) = r_0 exp(i*dx) . The Vanderbilt code uses instead:
>>    r(i) = r_0 (exp(i*dx)-1). Some time ago I tried to convince
>> the atomic code to accept the latter grid, but it turned out
>> not to be an easy task. A straightforward but boring
>> solution is to interpolate all quantities from grids of type 2
>
> ...to grids of type 1 (sorry for the incomplete message)
>
> 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 iyad.ne at gmail.com  Sat Nov 12 18:20:21 2011
From: iyad.ne at gmail.com (IYAD AL-QASIR)
Date: Sat, 12 Nov 2011 12:20:21 -0500
Subject: [Pw_forum] image parallelization for phonon calculations
In-Reply-To: <FB88B8DD-DD40-4F5A-A21E-C8CB2DA092C3@democritos.it>
References: <CAJMDj40PowftE2Khegug69KSKGXZP-cJpCO5BxBHQ8F-rJF+zw@mail.gmail.com>
	<FB88B8DD-DD40-4F5A-A21E-C8CB2DA092C3@democritos.it>
Message-ID: <CAJMDj40YiiYfQpDcpba2ntLvWUPG1US9_mWb-XmD_s_QxBxs2g@mail.gmail.com>

Thank you Prof. Giannozzi,

Actually, the message "*image parallelization is not permitted*" appeared
when I run pw.x ( sorry for the confusion in the last email)
mpiexec -np 12 ./pw.x -nimage 2 -npool 3 <scf.in> scf.out

So After i ran pw.x with niamge=1, I tried to run ph.x but using nimage >1
,
mpiexec -np 12 ./ph.x -nimage 2 -npool 3 <ph.in> ph.out

but I got

from d_&_i : error #         1
      some nodes have no k-points

Thanks
IYAD

On Sat, Nov 12, 2011 at 3:35 AM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Nov 11, 2011, at 23:22 , IYAD AL-QASIR wrote:
>
> > Hello All,
> > I am trying to perform in parallel phonon calculations  using ph.x.
> >
> > I used the command
> > mpiexec -np 12 ./ph.x -nimage 3 -npool 2 <input.in> input.ph.out
> >
> > but I got the message the "image parallelization is not permitted"
>
> $ grep 'image parallelization is not permitted' ~/CVS/espresso/*/*f90
> (nothing found)
>
> $ grep 'image parallelization' ~/CVS/espresso/*/*f90
> (...)
> /home/giannozz/CVS/espresso/PH/phq_readin.f90:     'elph with image
> parallelization is not yet available',1)
>
> Is the above one the exact message you get?
>
> 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  Sat Nov 12 19:33:10 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 12 Nov 2011 19:33:10 +0100
Subject: [Pw_forum] image parallelization for phonon calculations
In-Reply-To: <CAJMDj40YiiYfQpDcpba2ntLvWUPG1US9_mWb-XmD_s_QxBxs2g@mail.gmail.com>
References: <CAJMDj40PowftE2Khegug69KSKGXZP-cJpCO5BxBHQ8F-rJF+zw@mail.gmail.com>
	<FB88B8DD-DD40-4F5A-A21E-C8CB2DA092C3@democritos.it>
	<CAJMDj40YiiYfQpDcpba2ntLvWUPG1US9_mWb-XmD_s_QxBxs2g@mail.gmail.com>
Message-ID: <1DFC100D-F462-45B3-BA81-D9588A8E6E1D@democritos.it>


On Nov 12, 2011, at 18:20 , IYAD AL-QASIR wrote:

> Actually, the message "image parallelization is not permitted"
> appeared when I run pw.x ( sorry for the confusion in the last email)

there is no "image" parallization in pw.x. Only NEB has image  
parallelization.

> So After i ran pw.x with niamge=1, I tried to run ph.x but using  
> nimage >1 ,
> mpiexec -np 12 ./ph.x -nimage 2 -npool 3 <ph.in> ph.out
>
> but I got
>
> from d_&_i : error #         1
>       some nodes have no k-points


YOu have more pools than k-points. You need to understand the meaning
of the various parallelization levels before using them

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 songsong19840614 at hotmail.com  Sun Nov 13 12:18:45 2011
From: songsong19840614 at hotmail.com (KangYun Song)
Date: Sun, 13 Nov 2011 11:18:45 +0000
Subject: [Pw_forum] QHA frequency is higher than *.freq
In-Reply-To: <COL113-W6531F4056497CDE2F640E1C8DD0@phx.gbl>
References: <COL113-W60CEBD49552B277D2F7BC8C8DC0@phx.gbl>,
	<COL113-W6531F4056497CDE2F640E1C8DD0@phx.gbl>
Message-ID: <COL113-W29A4F4173D14BAEB988022C8C30@phx.gbl>




Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.
 



From: songsong19840614 at hotmail.com
To: pw_forum at pwscf.org
Date: Fri, 11 Nov 2011 12:55:14 +0000
Subject: Re: [Pw_forum] QHA frequency is higher than *.freq





Hi,
    The pdos is not similar to phonon dispersion and the frequency is not negative from ph.x.

Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.
 



From: songsong19840614 at hotmail.com
To: pw_forum at pwscf.org
Date: Thu, 10 Nov 2011 12:15:50 +0000
Subject: [Pw_forum] QHA frequency is higher than *.freq




Hi,
         Recently,I calculated the phonon dispersion.And I use the *.fc from matdyn q2r.x to calculate frequecy and pdos.But this is a problem the freqency from matdyn.x of QHA is higher than *.freq from matdyn.x of phonon dispersion calculation.Why?Could anyone help me?The other material I use this method did not meet this problem.
         The matdyn.in of QHA is:

&input
    amass(1)=*,
    amass(2)=*,
    asr='crystal',
    flfrc=*.fc,
    flfrq='frequency'
&end
1183
     -0.33333   0.57735   0.81850   1.00000
     -0.30555   0.52924   0.75029   1.00000
     -0.30555   0.57735   0.75029   1.00000
??????
 
       The matdyn.in of phonon dispersion calculating is :          

&input
    asr='simple',  amass(1)=*, amass(2)=*, 
    flfrc='*.fc', flfrq='*.freq' ,la2F=.false. , 
 /
85
  0.0000000   0.0000000   0.3092146, wk =   0.0235294
  0.0555560   0.0000000   0.3092146, wk =   0.0235294
  0.1111110  -0.0000006   0.3092146, wk =   0.0235294
  0.1666670   0.0000006   0.3092146, wk =   0.0235294
  0.2222220   0.0000000   0.3092146, wk =   0.0235294
  0.2777780   0.0000000   0.3092146, wk =   0.0235294
????

Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.

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From hqzhou at nju.edu.cn  Mon Nov 14 04:41:41 2011
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Mon, 14 Nov 2011 11:41:41 +0800
Subject: [Pw_forum] Query on Xcrysden
References: <157734259.92533.1320671322916.JavaMail.root@mailhub016.itcs.purdue.edu><615177880.92612.1320672651869.JavaMail.root@mailhub016.itcs.purdue.edu>
	<20111107225024.6a4bc925@ren-desktop>
Message-ID: <9049400A0E124656AC9501EECC6E6451@solarflare>

When you try to use XCrysden from PWgui, you still need to have a copy of
XCrysden to be installed in advance.


dr. zhou huiqun
@earth sciences, nanjing university, china

----- Original Message ----- 
From: "Ren PJ" <renpj at dicp.ac.cn>
To: <pw_forum at pwscf.org>
Sent: Monday, November 07, 2011 10:50 PM
Subject: Re: [Pw_forum] Query on Xcrysden


> 
> There is a executable file which need not to install. The latest version
> is 4.3. The url is: http://www-k3.ijs.si/kokalj/pwgui/
> 
> 
> 
> 
> Pengju Ren
> renpj at dicp.ac.cn
> State  Key Laboratory of Catalysis, 
> Dalian Institute of Chemical Physics, 
> Chinese Academy of Sciences 
> 457 zhongshan Road, Dalian, 116023, P.R. China  
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


From jianglai at sas.upenn.edu  Mon Nov 14 05:31:49 2011
From: jianglai at sas.upenn.edu (Lai Jiang)
Date: Sun, 13 Nov 2011 23:31:49 -0500
Subject: [Pw_forum] Problem with DFT + U calculations
Message-ID: <BLU0-SMTP246E9EC22BDF1927DE0943C80C00@phx.gbl>

Greetings all,

I'm having some problem getting convergence in my DFT +U calculations. My
system is anti-ferromagnetic double perovskite Sr2FeWO6. It is
experimentally an insulator but there are reports that state one needs
Hubbard U on Fe 3d orbital to account for the on site repulsion. However
after adding an U value it doesn't converge after 500 iterations and
sometimes the job got killed by the batch system (not walltime, something
like buffer overflow), typical pbs output looks like this (varies
on different platform):


Rank 16 [Wed Nov  9 23:21:11 2011] [c0-0c0s4n1] Fatal error in PMPI_Bcast:
Message truncated, error stack:
PMPI_Bcast(1308)......................: MPI_Bcast(buf=0x3e0def0,
count=26208, MPI_DOUBLE_PRECISION, root=1, comm=0xc4000000) failed
MPIR_Bcast(998).......................:
MPIR_Bcast_scatter_ring_allgather(842):
MPIR_Bcast_binomial(157)..............:
MPID_nem_gni_lmt_start_recv(920)......: Message from rank 0 and tag 2
truncated; 213408 bytes received but buffer size is 209664
[0] ERROR - nem_gni_error_handler(): a transaction error was detected,error
category 0x4 error code 0xb2e
Rank 0 [Wed Nov  9 23:21:11 2011] [c0-0c0s4n0] GNI transaction error
detected
[NID 00009] 2011-11-09 23:21:11 Apid 1944384: initiated application
termination


And the pw.x output ends like this:


atom   24   Tr[ns(na)]=   6.1782057
atom   24   spin  1
eigenvalues:  0.9740685 0.9841342 0.9842280 0.9899863 0.9914280
 eigenvectors
 1   0.0332876  0.0801355 -0.2854709  0.9362259 -0.1856276
 2   0.0172615  0.0589306  0.8879786  0.1822775 -0.4177297
 3   0.4670136  0.8765271 -0.0107306 -0.0778135  0.0861883
 4  -0.0557289 -0.0272157  0.3597350  0.2894423  0.8848545
 5   0.8816953 -0.4701756  0.0218145  0.0205958  0.0254629
 occupations
 0.990 -0.003  0.000  0.000  0.000
-0.003  0.986  0.000 -0.001  0.000
 0.000  0.000  0.984  0.003  0.001
 0.000 -0.001  0.003  0.976  0.003
 0.000  0.000  0.001  0.003  0.988
atom   24   spin  2
eigenvalues:  0.0394193 0.0400804 0.1166033 0.1376013 0.9206564
 eigenvectors
 1  -0.0457703 -0.2123040 -0.9448844 -0.2058039  0.1329300
 2   0.1857246  0.9542619 -0.1868327 -0.1235578  0.0686851
 3  -0.0675780 -0.0156072  0.1108752  0.1546050  0.9792822
 4  -0.9788987  0.1940608 -0.0050595 -0.0004723 -0.0638113
 5  -0.0245350 -0.0800506  0.2448840 -0.9583712  0.1206087
 occupations
 0.134 -0.017 -0.005  0.020 -0.002
-0.017  0.049 -0.018  0.067 -0.011
-0.005 -0.018  0.093 -0.205  0.034
 0.020  0.067 -0.205  0.851 -0.090
-0.002 -0.011  0.034 -0.090  0.127
nsum =  49.3436516
 exit write_ns

     total cpu time spent up to now is     4234.0 secs

     total energy              =   -5515.60273544 Ry
     Harris-Foulkes estimate   =   -5515.60272792 Ry
     estimated scf accuracy    <       0.00001279 Ry

     total magnetization       =     0.00 Bohr mag/cell
     absolute magnetization    =    32.50 Bohr mag/cell

     iteration #102     ecut=    50.00 Ry     beta=0.20
     Davidson diagonalization with overlap
Application 1944384 exit codes: 1
Application 1944384 exit signals: Killed
Application 1944384 resources: utime ~4162s, stime ~88s


My input file is:


&control
    calculation        =  'scf'
    title              =  'Sr2FeWO6'
    verbosity          =  'high'
    restart_mode       =  'from_scratch'
    pseudo_dir         =  '/workdir/jianglai/psp/gga'
    etot_conv_thr      =  1.D-6
    forc_conv_thr      =  2.D-4
    disk_io            =  'low'
    tstress            =  .true.
    tprnfor            =  .true.
    wf_collect         =  .true.
    nstep              =  5000
/
&system
    ibrav              =   -12
    A                  =   11.301600
    B                  =   5.613600
    C                  =   15.885000
    cosAC              =   -0.000366588948
    nat                =   80
    ntyp               =   5
    nbnd               =   351
    ecutwfc            =   50
    occupations        =   'smearing'
    degauss            =   2.D-3
    nspin              =   2
    starting_magnetization(2)    =0.5
    starting_magnetization(3)    =-0.5
    lda_plus_u         =   .true.
    hubbard_U(2)       =   4
    hubbard_U(3)       =   4
/
&electrons
    electron_maxstep   =   500
    startingwfc        =   'random'
    diagonalization    =   'david'
    mixing_mode        =   'plain'
    mixing_beta        =   2.D-1
    mixing_ndim        =   8
    conv_thr           =   1.0D-8
 /
&IONS
    bfgs_ndim          =   4
    upscale            =   25
    pot_extrapolation  =   'second_order'
    wfc_extrapolation  =   'second_order'
/
&CELL
    cell_dynamics      =   'bfgs'
    press_conv_thr     =   5.D-1
/
ATOMIC_SPECIES
    Sr    87.62   Sr.upf
    Fe1   55.847  Fe.semi.upf
    Fe2   55.847  Fe.semi.upf
    W     183.85  W.fhi.UPF
    O     15.999  O.upf

ATOMIC_POSITIONS {crystal}
Sr           0.499500   0.012900   0.124550
Sr           0.500500   0.987100   0.875450
Sr           0.750500   0.512900   0.125450
Sr           0.749500   0.487100   0.374550
Sr           0.499500   0.012900   0.624550
Sr           0.500500   0.987100   0.375450
Sr           0.750500   0.512900   0.625450
Sr           0.749500   0.487100   0.874550
Sr           0.999500   0.012900   0.124550
Sr           0.000500   0.987100   0.875450
Sr           0.250500   0.512900   0.125450
Sr           0.249500   0.487100   0.374550
Sr           0.250500   0.512900   0.625450
Sr           0.249500   0.487100   0.874550
Fe1           0.250000  -0.000000   0.250000
Fe1           0.750000  -0.000000   0.750000
Fe2           0.000000   0.500000   0.000000
Fe2           0.500000   0.500000   0.500000
Fe2           0.250000  -0.000000   0.750000
Fe2           0.750000  -0.000000   0.250000
Fe1          -0.000000   0.500000   0.500000
Fe1           0.500000   0.500000   0.000000
W            0.250000   0.000000   0.000000
W            0.750000   0.000000   0.000000
W           -0.000000   0.500000   0.250000
W            0.500000   0.500000   0.250000
W            0.250000  -0.000000   0.500000
W            0.750000  -0.000000   0.500000
W            0.000000   0.500000   0.750000
W            0.500000   0.500000   0.750000
O            0.023650   0.496000   0.129500
O            0.976350   0.504000   0.870500
O            0.226350   0.996000   0.120500
O            0.273650   0.004000   0.379500
O            0.023650   0.496000   0.629500
O            0.976350   0.504000   0.370500
O            0.226350   0.996000   0.620500
O            0.273650   0.004000   0.879500
O            0.523650   0.496000   0.129500
O            0.476350   0.504000   0.870500
O            0.726350   0.996000   0.120500
O            0.773650   0.004000   0.379500
O            0.523650   0.496000   0.629500
O            0.476350   0.504000   0.370500
O            0.726350   0.996000   0.620500
O            0.773650   0.004000   0.879500
O            0.359500   0.261000   0.012500
O            0.640500   0.739000   0.987500
O            0.890500   0.761000   0.237500
O            0.609500   0.239000   0.262500
O            0.359500   0.261000   0.512500
O            0.640500   0.739000   0.487500
O            0.890500   0.761000   0.737500
O            0.609500   0.239000   0.762500
O            0.859500   0.261000   0.012500
O            0.140500   0.739000   0.987500
O            0.390500   0.761000   0.237500
O            0.109500   0.239000   0.262500
O            0.859500   0.261000   0.512500
O            0.140500   0.739000   0.487500
O            0.390500   0.761000   0.737500
O            0.109500   0.239000   0.762500
O            0.121000   0.224000   0.488000
O            0.879000   0.776000   0.512000
O            0.129000   0.724000   0.762000
O            0.371000   0.276000   0.738000
O            0.121000   0.224000   0.988000
O            0.879000   0.776000   0.012000
O            0.129000   0.724000   0.262000
O            0.371000   0.276000   0.238000
O            0.621000   0.224000   0.488000
O            0.379000   0.776000   0.512000
O            0.629000   0.724000   0.762000
O            0.871000   0.276000   0.738000
O            0.621000   0.224000   0.988000
O            0.379000   0.776000   0.012000
O            0.629000   0.724000   0.262000
O            0.871000   0.276000   0.238000

K_POINTS (automatic)
2 4 1 1 1 1

I checked quantum espresso example files 25 and in README it says one needs
to set starting_ns_eigenvalues sometimes. I'm not sure whether it's the
case here but I'm gonna try. Still I don't quite understand the eigenvalues
and eigenvectors in write_ns routine. Are eigenvalues the energy of each of
the five d orbitals? The what are the eigenvectors?

That all said, if someone has experienced problems like this or knows why
convergence is so slow here, please let me know.

Thanks!

Lai Jiang
*********************************
Department of Chemistry
School of Arts and Sciences
University of Pennsylvania
*********************************
231 South 34th Street, Box 46
Philadelphia, PA 19104
Tel: 215-573-4241
Fax: 215-573-2112
Email: jianglai at sas.upenn.edu
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From guptasanjay.56 at gmail.com  Mon Nov 14 08:10:03 2011
From: guptasanjay.56 at gmail.com (Sanjay D. Gupta)
Date: Mon, 14 Nov 2011 12:40:03 +0530
Subject: [Pw_forum] Pw_forum Digest, Vol 53, Issue 23
In-Reply-To: <mailman.16994.1321245437.1814.pw_forum@pwscf.org>
References: <mailman.16994.1321245437.1814.pw_forum@pwscf.org>
Message-ID: <CAOPqkQaKPKVoEQ2OvBWha-FRA7Zt4sF=MZkgHhG012u454gURw@mail.gmail.com>

~Best Regards
...........................................................
Sanjay D. Gupta
Research Fellow
Department of Physics,
Bhavnagar University, Bhavnagar-364 022
Gujarat, Mobile-9879666643
email:guptasanjay_56 at yahoo.co.in
...........................................................


On Mon, Nov 14, 2011 at 10:07 AM, <pw_forum-request at pwscf.org> wrote:

> Send Pw_forum mailing list submissions to
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> Today's Topics:
>
>   1. Re: QHA frequency is higher than *.freq (KangYun Song)
>   2. Re: Query on Xcrysden (Huiqun Zhou)
>   3. Problem with DFT + U calculations (Lai Jiang)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 13 Nov 2011 11:18:45 +0000
> From: KangYun Song <songsong19840614 at hotmail.com>
> Subject: Re: [Pw_forum] QHA frequency is higher than *.freq
> To: pwscf <pw_forum at pwscf.org>
> Message-ID: <COL113-W29A4F4173D14BAEB988022C8C30 at phx.gbl>
> Content-Type: text/plain; charset="gb2312"
>
>
>
>
> Yun Song,Kang
> Department Physical Science and Technology of  Inner Mongolia University.
>
>
>
>
> From: songsong19840614 at hotmail.com
> To: pw_forum at pwscf.org
> Date: Fri, 11 Nov 2011 12:55:14 +0000
> Subject: Re: [Pw_forum] QHA frequency is higher than *.freq
>
>
>
>
>
> Hi,
>    The pdos is not similar to phonon dispersion and the frequency is not
> negative from ph.x.
>
> Yun Song,Kang
> Department Physical Science and Technology of  Inner Mongolia University.
>
>
>
>
> From: songsong19840614 at hotmail.com
> To: pw_forum at pwscf.org
> Date: Thu, 10 Nov 2011 12:15:50 +0000
> Subject: [Pw_forum] QHA frequency is higher than *.freq
>
>
>
>
> Hi,
>         Recently,I calculated the phonon dispersion.And I use the *.fc
> from matdyn q2r.x to calculate frequecy and pdos.But this is a problem the
> freqency from matdyn.x of QHA is higher than *.freq from matdyn.x of phonon
> dispersion calculation.Why?Could anyone help me?The other material I use
> this method did not meet this problem.
>         The matdyn.in of QHA is:
>
> &input
>    amass(1)=*,
>    amass(2)=*,
>    asr='crystal',
>    flfrc=*.fc,
>    flfrq='frequency'
> &end
> 1183
>     -0.33333   0.57735   0.81850   1.00000
>     -0.30555   0.52924   0.75029   1.00000
>     -0.30555   0.57735   0.75029   1.00000
> ??????
>
>       The matdyn.in of phonon dispersion calculating is :
>
> &input
>    asr='simple',  amass(1)=*, amass(2)=*,
>    flfrc='*.fc', flfrq='*.freq' ,la2F=.false. ,
>  /
> 85
>  0.0000000   0.0000000   0.3092146, wk =   0.0235294
>  0.0555560   0.0000000   0.3092146, wk =   0.0235294
>  0.1111110  -0.0000006   0.3092146, wk =   0.0235294
>  0.1666670   0.0000006   0.3092146, wk =   0.0235294
>  0.2222220   0.0000000   0.3092146, wk =   0.0235294
>  0.2777780   0.0000000   0.3092146, wk =   0.0235294
> ????
>
>
Dear
Yun Song,Kang,
you should have to correct your Edit.me file
as for example u have 4 atoms per unir cell then write like this
"ibrav=1
atoms="Cd1 Cd2 N1  N2"
mass="112.411 112.411  14.0067 14.0067"

Cheers...!!!!






> Yun Song,Kang
> Department Physical Science and Technology of  Inner Mongolia University.
>
> _______________________________________________ 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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> ------------------------------
>
> Message: 2
> Date: Mon, 14 Nov 2011 11:41:41 +0800
> From: "Huiqun Zhou" <hqzhou at nju.edu.cn>
> Subject: Re: [Pw_forum] Query on Xcrysden
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <9049400A0E124656AC9501EECC6E6451 at solarflare>
> Content-Type: text/plain; format=flowed; charset="iso-8859-1";
>        reply-type=original
>
> When you try to use XCrysden from PWgui, you still need to have a copy of
> XCrysden to be installed in advance.
>
>
> dr. zhou huiqun
> @earth sciences, nanjing university, china
>
> ----- Original Message -----
> From: "Ren PJ" <renpj at dicp.ac.cn>
> To: <pw_forum at pwscf.org>
> Sent: Monday, November 07, 2011 10:50 PM
> Subject: Re: [Pw_forum] Query on Xcrysden
>
>
> >
> > There is a executable file which need not to install. The latest version
> > is 4.3. The url is: http://www-k3.ijs.si/kokalj/pwgui/
> >
> >
> >
> >
> > Pengju Ren
> > renpj at dicp.ac.cn
> > State  Key Laboratory of Catalysis,
> > Dalian Institute of Chemical Physics,
> > Chinese Academy of Sciences
> > 457 zhongshan Road, Dalian, 116023, P.R. China
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 13 Nov 2011 23:31:49 -0500
> From: Lai Jiang <jianglai at sas.upenn.edu>
> Subject: [Pw_forum] Problem with DFT + U calculations
> To: pw_forum at pwscf.org
> Message-ID: <BLU0-SMTP246E9EC22BDF1927DE0943C80C00 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Greetings all,
>
> I'm having some problem getting convergence in my DFT +U calculations. My
> system is anti-ferromagnetic double perovskite Sr2FeWO6. It is
> experimentally an insulator but there are reports that state one needs
> Hubbard U on Fe 3d orbital to account for the on site repulsion. However
> after adding an U value it doesn't converge after 500 iterations and
> sometimes the job got killed by the batch system (not walltime, something
> like buffer overflow), typical pbs output looks like this (varies
> on different platform):
>
>
> Rank 16 [Wed Nov  9 23:21:11 2011] [c0-0c0s4n1] Fatal error in PMPI_Bcast:
> Message truncated, error stack:
> PMPI_Bcast(1308)......................: MPI_Bcast(buf=0x3e0def0,
> count=26208, MPI_DOUBLE_PRECISION, root=1, comm=0xc4000000) failed
> MPIR_Bcast(998).......................:
> MPIR_Bcast_scatter_ring_allgather(842):
> MPIR_Bcast_binomial(157)..............:
> MPID_nem_gni_lmt_start_recv(920)......: Message from rank 0 and tag 2
> truncated; 213408 bytes received but buffer size is 209664
> [0] ERROR - nem_gni_error_handler(): a transaction error was detected,error
> category 0x4 error code 0xb2e
> Rank 0 [Wed Nov  9 23:21:11 2011] [c0-0c0s4n0] GNI transaction error
> detected
> [NID 00009] 2011-11-09 23:21:11 Apid 1944384: initiated application
> termination
>
>
> And the pw.x output ends like this:
>
>
> atom   24   Tr[ns(na)]=   6.1782057
> atom   24   spin  1
> eigenvalues:  0.9740685 0.9841342 0.9842280 0.9899863 0.9914280
>  eigenvectors
>  1   0.0332876  0.0801355 -0.2854709  0.9362259 -0.1856276
>  2   0.0172615  0.0589306  0.8879786  0.1822775 -0.4177297
>  3   0.4670136  0.8765271 -0.0107306 -0.0778135  0.0861883
>  4  -0.0557289 -0.0272157  0.3597350  0.2894423  0.8848545
>  5   0.8816953 -0.4701756  0.0218145  0.0205958  0.0254629
>  occupations
>  0.990 -0.003  0.000  0.000  0.000
> -0.003  0.986  0.000 -0.001  0.000
>  0.000  0.000  0.984  0.003  0.001
>  0.000 -0.001  0.003  0.976  0.003
>  0.000  0.000  0.001  0.003  0.988
> atom   24   spin  2
> eigenvalues:  0.0394193 0.0400804 0.1166033 0.1376013 0.9206564
>  eigenvectors
>  1  -0.0457703 -0.2123040 -0.9448844 -0.2058039  0.1329300
>  2   0.1857246  0.9542619 -0.1868327 -0.1235578  0.0686851
>  3  -0.0675780 -0.0156072  0.1108752  0.1546050  0.9792822
>  4  -0.9788987  0.1940608 -0.0050595 -0.0004723 -0.0638113
>  5  -0.0245350 -0.0800506  0.2448840 -0.9583712  0.1206087
>  occupations
>  0.134 -0.017 -0.005  0.020 -0.002
> -0.017  0.049 -0.018  0.067 -0.011
> -0.005 -0.018  0.093 -0.205  0.034
>  0.020  0.067 -0.205  0.851 -0.090
> -0.002 -0.011  0.034 -0.090  0.127
> nsum =  49.3436516
>  exit write_ns
>
>     total cpu time spent up to now is     4234.0 secs
>
>     total energy              =   -5515.60273544 Ry
>     Harris-Foulkes estimate   =   -5515.60272792 Ry
>     estimated scf accuracy    <       0.00001279 Ry
>
>     total magnetization       =     0.00 Bohr mag/cell
>     absolute magnetization    =    32.50 Bohr mag/cell
>
>     iteration #102     ecut=    50.00 Ry     beta=0.20
>     Davidson diagonalization with overlap
> Application 1944384 exit codes: 1
> Application 1944384 exit signals: Killed
> Application 1944384 resources: utime ~4162s, stime ~88s
>
>
> My input file is:
>
>
> &control
>    calculation        =  'scf'
>    title              =  'Sr2FeWO6'
>    verbosity          =  'high'
>    restart_mode       =  'from_scratch'
>    pseudo_dir         =  '/workdir/jianglai/psp/gga'
>    etot_conv_thr      =  1.D-6
>    forc_conv_thr      =  2.D-4
>    disk_io            =  'low'
>    tstress            =  .true.
>    tprnfor            =  .true.
>    wf_collect         =  .true.
>    nstep              =  5000
> /
> &system
>    ibrav              =   -12
>    A                  =   11.301600
>    B                  =   5.613600
>    C                  =   15.885000
>    cosAC              =   -0.000366588948
>    nat                =   80
>    ntyp               =   5
>    nbnd               =   351
>    ecutwfc            =   50
>    occupations        =   'smearing'
>    degauss            =   2.D-3
>    nspin              =   2
>    starting_magnetization(2)    =0.5
>    starting_magnetization(3)    =-0.5
>    lda_plus_u         =   .true.
>    hubbard_U(2)       =   4
>    hubbard_U(3)       =   4
> /
> &electrons
>    electron_maxstep   =   500
>    startingwfc        =   'random'
>    diagonalization    =   'david'
>    mixing_mode        =   'plain'
>    mixing_beta        =   2.D-1
>    mixing_ndim        =   8
>    conv_thr           =   1.0D-8
>  /
> &IONS
>    bfgs_ndim          =   4
>    upscale            =   25
>    pot_extrapolation  =   'second_order'
>    wfc_extrapolation  =   'second_order'
> /
> &CELL
>    cell_dynamics      =   'bfgs'
>    press_conv_thr     =   5.D-1
> /
> ATOMIC_SPECIES
>    Sr    87.62   Sr.upf
>    Fe1   55.847  Fe.semi.upf
>    Fe2   55.847  Fe.semi.upf
>    W     183.85  W.fhi.UPF
>    O     15.999  O.upf
>
> ATOMIC_POSITIONS {crystal}
> Sr           0.499500   0.012900   0.124550
> Sr           0.500500   0.987100   0.875450
> Sr           0.750500   0.512900   0.125450
> Sr           0.749500   0.487100   0.374550
> Sr           0.499500   0.012900   0.624550
> Sr           0.500500   0.987100   0.375450
> Sr           0.750500   0.512900   0.625450
> Sr           0.749500   0.487100   0.874550
> Sr           0.999500   0.012900   0.124550
> Sr           0.000500   0.987100   0.875450
> Sr           0.250500   0.512900   0.125450
> Sr           0.249500   0.487100   0.374550
> Sr           0.250500   0.512900   0.625450
> Sr           0.249500   0.487100   0.874550
> Fe1           0.250000  -0.000000   0.250000
> Fe1           0.750000  -0.000000   0.750000
> Fe2           0.000000   0.500000   0.000000
> Fe2           0.500000   0.500000   0.500000
> Fe2           0.250000  -0.000000   0.750000
> Fe2           0.750000  -0.000000   0.250000
> Fe1          -0.000000   0.500000   0.500000
> Fe1           0.500000   0.500000   0.000000
> W            0.250000   0.000000   0.000000
> W            0.750000   0.000000   0.000000
> W           -0.000000   0.500000   0.250000
> W            0.500000   0.500000   0.250000
> W            0.250000  -0.000000   0.500000
> W            0.750000  -0.000000   0.500000
> W            0.000000   0.500000   0.750000
> W            0.500000   0.500000   0.750000
> O            0.023650   0.496000   0.129500
> O            0.976350   0.504000   0.870500
> O            0.226350   0.996000   0.120500
> O            0.273650   0.004000   0.379500
> O            0.023650   0.496000   0.629500
> O            0.976350   0.504000   0.370500
> O            0.226350   0.996000   0.620500
> O            0.273650   0.004000   0.879500
> O            0.523650   0.496000   0.129500
> O            0.476350   0.504000   0.870500
> O            0.726350   0.996000   0.120500
> O            0.773650   0.004000   0.379500
> O            0.523650   0.496000   0.629500
> O            0.476350   0.504000   0.370500
> O            0.726350   0.996000   0.620500
> O            0.773650   0.004000   0.879500
> O            0.359500   0.261000   0.012500
> O            0.640500   0.739000   0.987500
> O            0.890500   0.761000   0.237500
> O            0.609500   0.239000   0.262500
> O            0.359500   0.261000   0.512500
> O            0.640500   0.739000   0.487500
> O            0.890500   0.761000   0.737500
> O            0.609500   0.239000   0.762500
> O            0.859500   0.261000   0.012500
> O            0.140500   0.739000   0.987500
> O            0.390500   0.761000   0.237500
> O            0.109500   0.239000   0.262500
> O            0.859500   0.261000   0.512500
> O            0.140500   0.739000   0.487500
> O            0.390500   0.761000   0.737500
> O            0.109500   0.239000   0.762500
> O            0.121000   0.224000   0.488000
> O            0.879000   0.776000   0.512000
> O            0.129000   0.724000   0.762000
> O            0.371000   0.276000   0.738000
> O            0.121000   0.224000   0.988000
> O            0.879000   0.776000   0.012000
> O            0.129000   0.724000   0.262000
> O            0.371000   0.276000   0.238000
> O            0.621000   0.224000   0.488000
> O            0.379000   0.776000   0.512000
> O            0.629000   0.724000   0.762000
> O            0.871000   0.276000   0.738000
> O            0.621000   0.224000   0.988000
> O            0.379000   0.776000   0.012000
> O            0.629000   0.724000   0.262000
> O            0.871000   0.276000   0.238000
>
> K_POINTS (automatic)
> 2 4 1 1 1 1
>
> I checked quantum espresso example files 25 and in README it says one needs
> to set starting_ns_eigenvalues sometimes. I'm not sure whether it's the
> case here but I'm gonna try. Still I don't quite understand the eigenvalues
> and eigenvectors in write_ns routine. Are eigenvalues the energy of each of
> the five d orbitals? The what are the eigenvectors?
>
> That all said, if someone has experienced problems like this or knows why
> convergence is so slow here, please let me know.
>
> Thanks!
>
> Lai Jiang
> *********************************
> Department of Chemistry
> School of Arts and Sciences
> University of Pennsylvania
> *********************************
> 231 South 34th Street, Box 46
> Philadelphia, PA 19104
> Tel: 215-573-4241
> Fax: 215-573-2112
> Email: jianglai at sas.upenn.edu
> -------------- next part --------------
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>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 53, Issue 23
> ****************************************
>
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From helen at fh.huji.ac.il  Mon Nov 14 10:25:13 2011
From: helen at fh.huji.ac.il (helen at fh.huji.ac.il)
Date: Mon, 14 Nov 2011 11:25:13 +0200
Subject: [Pw_forum] jellium background
Message-ID: <20111114112513.16041wuixssynuzo@webmail.huji.ac.il>

Dear All,
I am looking at partially charged systems (tot_charge=non-integer).  I
want to know how the compensating Jellium background is implemented in
pwscf, as I need to know how it effects the calculated energy-values. I
saw a similar question from 2005 but unfortunately the links included in
the replies no longer work,
Thank you
Dr. Helen Eisenberg,
Post-doctoral researcher,
Fritz-Haber Center for Molecular Dynamics,
Hebrew University.


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From giannozz at democritos.it  Mon Nov 14 11:07:46 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 14 Nov 2011 11:07:46 +0100
Subject: [Pw_forum] jellium background
In-Reply-To: <20111114112513.16041wuixssynuzo@webmail.huji.ac.il>
References: <20111114112513.16041wuixssynuzo@webmail.huji.ac.il>
Message-ID: <1321265266.30225.2.camel@fe12lx.fisica.uniud.it>

On Mon, 2011-11-14 at 11:25 +0200, helen at fh.huji.ac.il wrote:

> I am looking at partially charged systems (tot_charge=non-integer).  I
> want to know how the compensating Jellium background is implemented in
> pwscf, as I need to know how it effects the calculated energy-values. I
> saw a similar question from 2005 but unfortunately the links included in
> the replies no longer work

attached. The other mentioned link (not very relevant in this specific
case, though) is
   http://www.theochem.ruhr-uni-bochum.de/research/marx/marx.pdf
P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy

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From giannozz at democritos.it  Mon Nov 14 11:10:35 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 14 Nov 2011 11:10:35 +0100
Subject: [Pw_forum] jellium background
In-Reply-To: <1321265266.30225.2.camel@fe12lx.fisica.uniud.it>
References: <20111114112513.16041wuixssynuzo@webmail.huji.ac.il>
	<1321265266.30225.2.camel@fe12lx.fisica.uniud.it>
Message-ID: <1321265435.30225.5.camel@fe12lx.fisica.uniud.it>

Actually, all this (pag.4-8) is for the neutral case. For the
charged case, the divergent terms are treated as for the neutral
case

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



From nicola.marzari at epfl.ch  Mon Nov 14 12:18:32 2011
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Mon, 14 Nov 2011 12:18:32 +0100
Subject: [Pw_forum] jellium background
In-Reply-To: <20111114112513.16041wuixssynuzo@webmail.huji.ac.il>
References: <20111114112513.16041wuixssynuzo@webmail.huji.ac.il>
Message-ID: <4EC0F908.6010407@epfl.ch>

On 11/14/11 10:25 AM, helen at fh.huji.ac.il wrote:
> Dear All,
> I am looking at partially charged systems (tot_charge=non-integer).  I
> want to know how the compensating Jellium background is implemented in
> pwscf, as I need to know how it effects the calculated energy-values. I
> saw a similar question from 2005 but unfortunately the links included in
> the replies no longer work,
> Thank you
> Dr. Helen Eisenberg


Dear Helen,


you could also look at this for a general discussion of the problem
(note also the erratum, re the makov-payne correction).

http://prb.aps.org/abstract/PRB/v77/i11/e115139

			nicola

> Post-doctoral researcher,
> Fritz-Haber Center for Molecular Dynamics,
> Hebrew University.
>
>
> ----------------------------------------------------------------
> 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


-- 

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

From kalamaillist at gmail.com  Mon Nov 14 16:49:32 2011
From: kalamaillist at gmail.com (WF)
Date: Mon, 14 Nov 2011 23:49:32 +0800
Subject: [Pw_forum] What kind of calculation needs wavefunction files
	created by pw.x ?
Message-ID: <001901cca2e5$038b19c0$0aa14d40$@gmail.com>

Hello everyone,

         From what I haved learned, pw.x generates wavefunction files under
temporary directory, and can be collected to output directory by options
wf_collect = .true. . It can be controlled by disk_io option to decrease the
I/O. However I don't really know whether should I keep this files to do
later calculation like DOS and bands or not. What kind of calculation needs
wavefunction files created by pw.x ?

         Thanks.

 

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

Wu F,

College of Chemistry and Molecular Engineering,

Peking University.

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

 

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From degliesposti at bo.imm.cnr.it  Mon Nov 14 16:53:30 2011
From: degliesposti at bo.imm.cnr.it (Cristian Degli Esposti Boschi)
Date: Mon, 14 Nov 2011 16:53:30 +0100
Subject: [Pw_forum] Compilation of QE 4.3.2 on (grid) cluster with OpenMPI /
	OpenMP
Message-ID: <4EC1397A.8030006@bo.imm.cnr.it>

Dear all,

together with Roberto Alfieri in Parma we are trying to install QE 4.3.2 
on a new cluster to be used also in a Grid environment.

We are experiencing two types of problems:

1) if one selects compilation with OpenMP (--enable-openmp) the 
following error is reported:

################################################################
# sum_band.f90:121: internal compiler error: in make_decl_rtl, at
# varasm.c:893
################################################################


2) if OpenMP is not selected compilation seems to be ok,
but then the following errors are reported when one tries to
run examples involving executables other than pw.x

running the band-structure calculation for Si...
###############################################################
# FROM IOTK LIBRARY, VERSION 1.2.0
# UNRECOVERABLE ERROR (ierr=1)
# ERROR IN: iotk_scan_end (iotk_scan.f90:241)
# CVS Revision: 1.23
# foundl
# ERROR IN: iotk_close_read (iotk_files.f90:746)
# CVS Revision: 1.20
###############################################################

  running the phonon calculation at X for Si...
###############################################################
# FROM IOTK LIBRARY, VERSION 1.2.0
# UNRECOVERABLE ERROR (ierr=1)
# ERROR IN: iotk_scan_end (iotk_scan.f90:241)
# CVS Revision: 1.23
# foundl
# ERROR IN: iotk_close_read (iotk_files.f90:746)
# CVS Revision: 1.20
###############################################################


The Linux environment essentially is
Scientific Linux 5.4 x86_64 with gcc 4.1.2 and openmpi-1.4-4

Does anyone have suggestions on how to fix these errors?

Thanks for your time.

Cristian Degli Esposti Boschi
CNR-IMM, Sezione di Bologna,
via Gobetti, 101, 40129, Bologna, Italia
tel. ++39 051 6399152, fax ++39 051 6399216
degliesposti -AT- bo.imm.cnr.it

From akohlmey at gmail.com  Mon Nov 14 17:01:25 2011
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Mon, 14 Nov 2011 11:01:25 -0500
Subject: [Pw_forum] Compilation of QE 4.3.2 on (grid) cluster with
 OpenMPI / OpenMP
In-Reply-To: <4EC1397A.8030006@bo.imm.cnr.it>
References: <4EC1397A.8030006@bo.imm.cnr.it>
Message-ID: <CADTmJ6H6-PZK1uJM+8hgKdrXCX9zJVGyR3Lzmogwj7FSZQ5yRQ@mail.gmail.com>

On Mon, Nov 14, 2011 at 10:53 AM, Cristian Degli Esposti Boschi
<degliesposti at bo.imm.cnr.it> wrote:
> Dear all,

dear cristian,

> together with Roberto Alfieri in Parma we are trying to install QE 4.3.2
> on a new cluster to be used also in a Grid environment.
>
> We are experiencing two types of problems:
>
> 1) if one selects compilation with OpenMP (--enable-openmp) the
> following error is reported:
>
> ################################################################
> # sum_band.f90:121: internal compiler error: in make_decl_rtl, at
> # varasm.c:893
> ################################################################

internal compiler error is _always_ a bug in the compiler.
in this case it likely means, that OpenMP support is not
working well.

>
> 2) if OpenMP is not selected compilation seems to be ok,
> but then the following errors are reported when one tries to
> run examples involving executables other than pw.x
>
> running the band-structure calculation for Si...
> ###############################################################
> # FROM IOTK LIBRARY, VERSION 1.2.0
> # UNRECOVERABLE ERROR (ierr=1)
> # ERROR IN: iotk_scan_end (iotk_scan.f90:241)
> # CVS Revision: 1.23
> # foundl
> # ERROR IN: iotk_close_read (iotk_files.f90:746)
> # CVS Revision: 1.20
> ###############################################################
>
> ?running the phonon calculation at X for Si...
> ###############################################################
> # FROM IOTK LIBRARY, VERSION 1.2.0
> # UNRECOVERABLE ERROR (ierr=1)
> # ERROR IN: iotk_scan_end (iotk_scan.f90:241)
> # CVS Revision: 1.23
> # foundl
> # ERROR IN: iotk_close_read (iotk_files.f90:746)
> # CVS Revision: 1.20
> ###############################################################

those are likely also due to the compiler.

>
> The Linux environment essentially is
> Scientific Linux 5.4 x86_64 with gcc 4.1.2 and openmpi-1.4-4

there you go. if you have gcc-4.1.x and particularly the gfortran
compiler bundled with it, you will have a hell of a time compiling
Q-E with it. gfortran-4.1.x has been a "work in progress".
you should upgrade to at least version 4.4.x and better 4.5.x.

axel.

> Does anyone have suggestions on how to fix these errors?
>
> Thanks for your time.
>
> Cristian Degli Esposti Boschi
> CNR-IMM, Sezione di Bologna,
> via Gobetti, 101, 40129, Bologna, Italia
> tel. ++39 051 6399152, fax ++39 051 6399216
> degliesposti -AT- bo.imm.cnr.it
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From giannozz at democritos.it  Mon Nov 14 17:04:06 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 14 Nov 2011 17:04:06 +0100
Subject: [Pw_forum] Compilation of QE 4.3.2 on (grid) cluster
	with	OpenMPI / OpenMP
In-Reply-To: <4EC1397A.8030006@bo.imm.cnr.it>
References: <4EC1397A.8030006@bo.imm.cnr.it>
Message-ID: <1321286646.3381.43.camel@fe12lx.fisica.uniud.it>

On Mon, 2011-11-14 at 16:53 +0100, Cristian Degli Esposti Boschi wrote:

> Scientific Linux 5.4 x86_64 with gcc 4.1.2 and openmpi-1.4-4
> Does anyone have suggestions on how to fix these errors?

1) update your gfortran to a recent version (almost impossible 
    with your linux version, I guess), or
2) install the Intel fortran compiler 

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



From tfcao at theory.issp.ac.cn  Tue Nov 15 09:14:45 2011
From: tfcao at theory.issp.ac.cn (=?utf-8?B?Q2FvIFRG?=)
Date: Tue, 15 Nov 2011 16:14:45 +0800
Subject: [Pw_forum] =?utf-8?q?_Davidson_diagonalization_with_overlap?=
Message-ID: <20111115081445.23202.qmail@ms.hfcas.ac.cn>

Dear QE users
         I am relaxing the structure of graphene with hydrogen adsorbed on it. But in iteration there is " Davidson diagonalization with overlap".  What can be the reasons?  And how to solve it . Any suggestions will be appreciated.
Here is part of the  out file:
 Writing output data file graphene.save
     NEW-OLD atomic charge density approx. for the potential

     total cpu time spent up to now is 127989.94 secs

     per-process dynamical memory:   116.7 Mb

     Self-consistent Calculation

     iteration #  1     ecut=    30.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-06,  avg # of iterations =  4.0

     total cpu time spent up to now is 129567.23 secs

     total energy              =   -1141.65432551 Ry
     Harris-Foulkes estimate   =   -1141.65612583 Ry
     estimated scf accuracy    <       0.00636573 Ry

     iteration #  2     ecut=    30.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.58E-06,  avg # of iterations =  2.0

     total cpu time spent up to now is 130246.48 secs

     total energy              =   -1141.65417045 Ry
     Harris-Foulkes estimate   =   -1141.65465073 Ry
     estimated scf accuracy    <       0.00113580 Ry

     iteration #  3     ecut=    30.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.83E-07,  avg # of iterations =  2.7

     total cpu time spent up to now is 131108.66 secs

     total energy              =   -1141.65435750 Ry
     Harris-Foulkes estimate   =   -1141.65436350 Ry
     estimated scf accuracy    <       0.00002145 Ry

     iteration #  4     ecut=    30.00 Ry     beta=0.70
     Davidson diagonalization with overlap
------
======================================================================
T.F.Cao  DFT and phonon physics
======================================================================
Add: Research Laboratory for Computational Materials Sciences,
Instutue of Solid State Physics,the Chinese Academy of Sciences,
P.O.Box 1129, Hefei 230031, P.R.China
Tel: 86-551-5591464-326(office)
Fax: 86-551-5591434

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From gabriele.sclauzero at epfl.ch  Tue Nov 15 09:22:50 2011
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Tue, 15 Nov 2011 09:22:50 +0100
Subject: [Pw_forum] What kind of calculation needs wavefunction files
	created by pw.x ?
In-Reply-To: <001901cca2e5$038b19c0$0aa14d40$@gmail.com>
References: <001901cca2e5$038b19c0$0aa14d40$@gmail.com>
Message-ID: <792FE4FA-53CD-49E2-A1C8-46C7E6708411@epfl.ch>

Dear Wu F, 

    I think you have already almost replied to your question...

Il giorno 14/nov/2011, alle ore 16.49, WF ha scritto:

> Hello everyone,
>          From what I haved learned, pw.x generates wavefunction files under temporary directory, and can be collected to output directory by options wf_collect = .true. . It can be controlled by disk_io option to decrease the I/O. However I don?t really know whether should I keep this files to do later calculation like DOS and bands or not.

Will you probably need to perform these calculations (only you can reply)? If yes, then keep the files.

> What kind of calculation needs wavefunction files created by pw.x ?

Actually, wavefunctions are not needed for DOS calculations, but they are for projected-DOS ones. For calculations with bands.x, you will need wavefunctions only in conjunction with the lsym=.TRUE. option.
Other standard calculations that require wavefunctions are, for instance, LDOS (and STM images), Wannier function analysis and maybe others. Also, sometimes you may want to use the final charge and wavefunctions as a starting guess for a successive calculation with pw.x.


HTH

GS

>          Thanks.
>  
> ------------------------------------
> Wu F,
> College of Chemistry and Molecular Engineering,
> Peking 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 gabriele.sclauzero at epfl.ch  Tue Nov 15 09:26:14 2011
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Tue, 15 Nov 2011 09:26:14 +0100
Subject: [Pw_forum] What kind of calculation needs wavefunction files
	created by pw.x ?
In-Reply-To: <792FE4FA-53CD-49E2-A1C8-46C7E6708411@epfl.ch>
References: <001901cca2e5$038b19c0$0aa14d40$@gmail.com>
	<792FE4FA-53CD-49E2-A1C8-46C7E6708411@epfl.ch>
Message-ID: <8DC345F4-CA0F-45F6-843F-45CA5821256E@epfl.ch>


Il giorno 15/nov/2011, alle ore 09.22, Gabriele Sclauzero ha scritto:

> Dear Wu F, 
> 
>     I think you have already almost replied to your question...
> 
> Il giorno 14/nov/2011, alle ore 16.49, WF ha scritto:
> 
>> Hello everyone,
>>          From what I haved learned, pw.x generates wavefunction files under temporary directory, and can be collected to output directory by options wf_collect = .true. . It can be controlled by disk_io option to decrease the I/O. However I don?t really know whether should I keep this files to do later calculation like DOS and bands or not.
> 
> Will you probably need to perform these calculations (only you can reply)? If yes, then keep the files.
> 
>> What kind of calculation needs wavefunction files created by pw.x ?
> 
> Actually, wavefunctions are not needed for DOS calculations, but they are for projected-DOS ones. For calculations with bands.x, you will need wavefunctions only in conjunction with the lsym=.TRUE. option.

Sorry, a small mistake here: also the old algorithm for ordering bands needs wavefunctions (but uses overlaps between wavefunctions instead of symmetry).


GS

> Other standard calculations that require wavefunctions are, for instance, LDOS (and STM images), Wannier function analysis and maybe others. Also, sometimes you may want to use the final charge and wavefunctions as a starting guess for a successive calculation with pw.x.
> 
> 
> HTH
> 
> GS
> 
>>          Thanks.
>>  
>> ------------------------------------
>> Wu F,
>> College of Chemistry and Molecular Engineering,
>> Peking 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 tribhuwan.physics at gmail.com  Tue Nov 15 10:42:35 2011
From: tribhuwan.physics at gmail.com (Tribhuwan Pandey)
Date: Tue, 15 Nov 2011 15:12:35 +0530
Subject: [Pw_forum] Phonon life time calculation
Message-ID: <CACKvTSNi1-kJ8os021UiaVk0s+g68Lyh2rEzxMsLcyPjRWJ_YA@mail.gmail.com>

Hi all

      I am calculating Inter atomic an-harmonic force constants ( phonon
life time )   using Quantum espresso 4.3.2, for my problem I need to
calculate Inter atomic an-harmonic force constants by considering
interaction up to seventh nearest neighbor.So i wants to know that whether
this interaction is included in Quantum espresso code ,or we need to modify
the code according to our problem.

-- 
*
With Regards
Tribhuwan Pandey


*
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From giuseppe.mattioli at mlib.ism.cnr.it  Tue Nov 15 11:22:38 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Tue, 15 Nov 2011 11:22:38 +0100
Subject: [Pw_forum] Davidson diagonalization with overlap
In-Reply-To: <20111115081445.23202.qmail@ms.hfcas.ac.cn>
References: <20111115081445.23202.qmail@ms.hfcas.ac.cn>
Message-ID: <201111151122.38807.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Cao
Why do you think that this is a problem? "Davidson" is the standard diagonalization algorithm of 
electronic degrees of freedom...
I suggest accurate reading of the QE manual...
HTH
Giuseppe

On Tuesday 15 November 2011 09:14:45 Cao TF wrote:
> Dear QE users
>          I am relaxing the structure of graphene with hydrogen adsorbed on
> it. But in iteration there is " Davidson diagonalization with overlap". 
> What can be the reasons?  And how to solve it . Any suggestions will be
> appreciated. Here is part of the  out file:
>  Writing output data file graphene.save
>      NEW-OLD atomic charge density approx. for the potential
>
>      total cpu time spent up to now is 127989.94 secs
>
>      per-process dynamical memory:   116.7 Mb
>
>      Self-consistent Calculation
>
>      iteration #  1     ecut=    30.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  1.00E-06,  avg # of iterations =  4.0
>
>      total cpu time spent up to now is 129567.23 secs
>
>      total energy              =   -1141.65432551 Ry
>      Harris-Foulkes estimate   =   -1141.65612583 Ry
>      estimated scf accuracy    <       0.00636573 Ry
>
>      iteration #  2     ecut=    30.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  1.58E-06,  avg # of iterations =  2.0
>
>      total cpu time spent up to now is 130246.48 secs
>
>      total energy              =   -1141.65417045 Ry
>      Harris-Foulkes estimate   =   -1141.65465073 Ry
>      estimated scf accuracy    <       0.00113580 Ry
>
>      iteration #  3     ecut=    30.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  2.83E-07,  avg # of iterations =  2.7
>
>      total cpu time spent up to now is 131108.66 secs
>
>      total energy              =   -1141.65435750 Ry
>      Harris-Foulkes estimate   =   -1141.65436350 Ry
>      estimated scf accuracy    <       0.00002145 Ry
>
>      iteration #  4     ecut=    30.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
> ------
> ======================================================================
> T.F.Cao  DFT and phonon physics
> ======================================================================
> Add: Research Laboratory for Computational Materials Sciences,
> Instutue of Solid State Physics,the Chinese Academy of Sciences,
> P.O.Box 1129, Hefei 230031, P.R.China
> Tel: 86-551-5591464-326(office)
> Fax: 86-551-5591434



-- 
********************************************************
- 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 flux_ray12 at 163.com  Tue Nov 15 12:29:46 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Tue, 15 Nov 2011 19:29:46 +0800 (CST)
Subject: [Pw_forum] problem about pp.x: namelist plot not found or invalid
Message-ID: <4c6b108e.10d34.133a6fd6dcc.Coremail.flux_ray12@163.com>

 Dear QE developer and users:
Hi
I am using pp.x to generate the charge density file on certain surface. The work for namelist, &inputpp, worked very well.
However, when I wanna summary the results from &inputpp to xcrysden file, the error occurred:
      chdens, namelist plot not found or invalid, exiting
Actually, I changed chdens.f90 a little bit on   INTEGER, PARAMETER :: nfilemax = 30, but I do not think this is the reason to meet such a problem~ Since if I create a short input file by PWGUI, then it works well. However, even if the short one created by myself, the same error happened.
Now, I need to summary more than 20 |psi|^2 files due to the density k-points mesh, so it is impossible to build the input file via PWGUI's help.
I checked chdens.f90, again, but I cannot understand the meaning of error~
Any suggetstion will be welcome.
P.S.: This is my input file (the &inputpp file have generated in the previous steps) :
 &inputpp
 /
 &plot
                       nfile = 27 ,
                    filpp(1) = 'CD_1.dat' ,
                   weight(1) = 0.0160000 ,
                    filpp(2) = 'CD_2.dat' ,
                   weight(2) = 0.0320000 ,
                    filpp(3) = 'CD_3.dat' ,
                   weight(3) = 0.0320000 ,
                    filpp(4) = 'CD_4.dat' ,
                   weight(4) = 0.0320000 ,
                    filpp(5) = 'CD_5.dat' ,
                   weight(5) = 0.0640000 ,
                    filpp(6) = 'CD_6.dat' ,
                   weight(6) = 0.0640000 ,
                    filpp(7) = 'CD_7.dat' ,
                   weight(7) = 0.0320000 ,
                    filpp(8) = 'CD_8.dat' ,
                   weight(8) = 0.0640000 ,
                    filpp(9) = 'CD_9.dat' ,
                   weight(9) = 0.0640000 ,
                   filpp(10) = 'CD_10.dat' ,
                  weight(10) = 0.0320000 ,
                   filpp(11) = 'CD_11.dat' ,
                  weight(11) = 0.0640000 ,
                   filpp(12) = 'CD_12.dat' ,
                  weight(12) = 0.0640000 ,
                   filpp(13) = 'CD_13.dat' ,
                  weight(13) = 0.0640000 ,
                   filpp(14) = 'CD_14.dat' ,
                  weight(14) = 0.1280000 ,
                   filpp(15) = 'CD_15.dat' ,
                  weight(15) = 0.1280000 ,
                   filpp(16) = 'CD_16.dat' ,
                  weight(16) = 0.0640000 ,
                   filpp(17) = 'CD_17.dat' ,
                  weight(17) = 0.1280000 ,
                   filpp(18) = 'CD_18.dat' ,
                  weight(18) = 0.1280000 ,
                   filpp(19) = 'CD_19.dat' ,
                  weight(19) = 0.0320000 ,
                   filpp(20) = 'CD_20.dat' ,
                  weight(20) = 0.0640000 ,
                   filpp(21) = 'CD_21.dat' ,
                  weight(21) = 0.0640000 ,
                   filpp(22) = 'CD_22.dat' ,
                  weight(22) = 0.0640000 ,
                   filpp(23) = 'CD_23.dat' ,
                  weight(23) = 0.1280000 ,
                   filpp(24) = 'CD_24.dat' ,
                  weight(24) = 0.1280000 ,
                   filpp(25) = 'CD_25.dat' ,
                  weight(25) = 0.0640000 ,
                   filpp(26) = 'CD_26.dat' ,
                  weight(26) = 0.1280000 ,
                   filpp(27) = 'CD_27.dat' ,
                  weight(27) = 0.1280000 ,
                     fileout = 'CDresult.xsf' ,
                       iflag = 2 ,
               output_format = 3 ,
                       e1(1) = 2.0,
                       e1(2) = 0.0,
                       e1(3) = 0.0,
                       e2(1) = 0.0,
                       e2(2) = 2.0,
                       e2(3) = 0.0,
                       x0(1) = 0.0,
                       x0(2) = 0.0,
                       x0(3) = 0.0,
                          nx = 45 ,
                          ny = 45 ,
 /




--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea
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From fratesi at mater.unimib.it  Tue Nov 15 12:44:40 2011
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Tue, 15 Nov 2011 12:44:40 +0100
Subject: [Pw_forum] problem about pp.x: namelist plot not found or
	invalid
In-Reply-To: <4c6b108e.10d34.133a6fd6dcc.Coremail.flux_ray12@163.com>
References: <4c6b108e.10d34.133a6fd6dcc.Coremail.flux_ray12@163.com>
Message-ID: <4EC250A8.2030208@mater.unimib.it>

Dear Gao Zhe,
"filpp" should be "filepp", at least.
Guido

Il 11/15/2011 12:29 PM, GAO Zhe ha scritto:
> Dear QE developer and users:
> Hi
> I am using pp.x to generate the charge density file on certain surface.
> The work for namelist, &inputpp, worked very well.
> However, when I wanna summary the results from &inputpp to xcrysden
> file, the error occurred:
> chdens, namelist plot not found or invalid, exiting
> Actually, I changed chdens.f90 a little bit on INTEGER, PARAMETER ::
> nfilemax = 30, but I do not think this is the reason to meet such a
> problem~ Since if I create a short input file by PWGUI, then it works
> well. However, even if the short one created by myself, the same error
> happened.
> Now, I need to summary more than 20 |psi|^2files due to the density
> k-points mesh, so it is impossible to build the input file via PWGUI's help.
> I checked chdens.f90, again, but I cannot understand the meaning of error~
> Any suggetstion will be welcome.
> P.S.: This is my input file (the &inputpp file have generated in the
> previous steps) :
> &inputpp
> /
> &plot
> nfile = 27 ,
> filpp(1) = 'CD_1.dat' ,
> weight(1) = 0.0160000 ,
> filpp(2) = 'CD_2.dat' ,
> weight(2) = 0.0320000 ,
> filpp(3) = 'CD_3.dat' ,
> weight(3) = 0.0320000 ,
> filpp(4) = 'CD_4.dat' ,
> weight(4) = 0.0320000 ,
> filpp(5) = 'CD_5.dat' ,
> weight(5) = 0.0640000 ,
> filpp(6) = 'CD_6.dat' ,
> weight(6) = 0.0640000 ,
> filpp(7) = 'CD_7.dat' ,
> weight(7) = 0.0320000 ,
> filpp(8) = 'CD_8.dat' ,
> weight(8) = 0.0640000 ,
> filpp(9) = 'CD_9.dat' ,
> weight(9) = 0.0640000 ,
> filpp(10) = 'CD_10.dat' ,
> weight(10) = 0.0320000 ,
> filpp(11) = 'CD_11.dat' ,
> weight(11) = 0.0640000 ,
> filpp(12) = 'CD_12.dat' ,
> weight(12) = 0.0640000 ,
> filpp(13) = 'CD_13.dat' ,
> weight(13) = 0.0640000 ,
> filpp(14) = 'CD_14.dat' ,
> weight(14) = 0.1280000 ,
> filpp(15) = 'CD_15.dat' ,
> weight(15) = 0.1280000 ,
> filpp(16) = 'CD_16.dat' ,
> weight(16) = 0.0640000 ,
> filpp(17) = 'CD_17.dat' ,
> weight(17) = 0.1280000 ,
> filpp(18) = 'CD_18.dat' ,
> weight(18) = 0.1280000 ,
> filpp(19) = 'CD_19.dat' ,
> weight(19) = 0.0320000 ,
> filpp(20) = 'CD_20.dat' ,
> weight(20) = 0.0640000 ,
> filpp(21) = 'CD_21.dat' ,
> weight(21) = 0.0640000 ,
> filpp(22) = 'CD_22.dat' ,
> weight(22) = 0.0640000 ,
> filpp(23) = 'CD_23.dat' ,
> weight(23) = 0.1280000 ,
> filpp(24) = 'CD_24.dat' ,
> weight(24) = 0.1280000 ,
> filpp(25) = 'CD_25.dat' ,
> weight(25) = 0.0640000 ,
> filpp(26) = 'CD_26.dat' ,
> weight(26) = 0.1280000 ,
> filpp(27) = 'CD_27.dat' ,
> weight(27) = 0.1280000 ,
> fileout = 'CDresult.xsf' ,
> iflag = 2 ,
> output_format = 3 ,
> e1(1) = 2.0,
> e1(2) = 0.0,
> e1(3) = 0.0,
> e2(1) = 0.0,
> e2(2) = 2.0,
> e2(3) = 0.0,
> x0(1) = 0.0,
> x0(2) = 0.0,
> x0(3) = 0.0,
> nx = 45 ,
> ny = 45 ,
> /
>
>
>
> --
> 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

-- 
Guido Fratesi

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

From flux_ray12 at 163.com  Tue Nov 15 12:47:26 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Tue, 15 Nov 2011 19:47:26 +0800 (CST)
Subject: [Pw_forum] problem about pp.x: namelist plot not found or
 invalid
In-Reply-To: <4c6b108e.10d34.133a6fd6dcc.Coremail.flux_ray12@163.com>
References: <4c6b108e.10d34.133a6fd6dcc.Coremail.flux_ray12@163.com>
Message-ID: <3848d128.110df.133a70d9bef.Coremail.flux_ray12@163.com>

Oh, I am sorry to bother~ I have found the problem.
This problem occurred when filepp(i) have not been written together, i.e.:
filepp(1)
filepp(2)
....
filepp(max)
weight(1)
weight(2)
....
weight(max)
is the only right way to create the input file.



At 2011-11-15 19:29:46,"GAO Zhe" <flux_ray12 at 163.com> wrote:

 Dear QE developer and users:
Hi
I am using pp.x to generate the charge density file on certain surface. The work for namelist, &inputpp, worked very well.
However, when I wanna summary the results from &inputpp to xcrysden file, the error occurred:
      chdens, namelist plot not found or invalid, exiting
Actually, I changed chdens.f90 a little bit on   INTEGER, PARAMETER :: nfilemax = 30, but I do not think this is the reason to meet such a problem~ Since if I create a short input file by PWGUI, then it works well. However, even if the short one created by myself, the same error happened.
Now, I need to summary more than 20 |psi|^2 files due to the density k-points mesh, so it is impossible to build the input file via PWGUI's help.
I checked chdens.f90, again, but I cannot understand the meaning of error~
Any suggetstion will be welcome.
P.S.: This is my input file (the &inputpp file have generated in the previous steps) :
 &inputpp
 /
 &plot
                       nfile = 27 ,
                    filpp(1) = 'CD_1.dat' ,
                   weight(1) = 0.0160000 ,
                    filpp(2) = 'CD_2.dat' ,
                   weight(2) = 0.0320000 ,
                    filpp(3) = 'CD_3.dat' ,
                   weight(3) = 0.0320000 ,
                    filpp(4) = 'CD_4.dat' ,
                   weight(4) = 0.0320000 ,
                    filpp(5) = 'CD_5.dat' ,
                   weight(5) = 0.0640000 ,
                    filpp(6) = 'CD_6.dat' ,
                   weight(6) = 0.0640000 ,
                    filpp(7) = 'CD_7.dat' ,
                   weight(7) = 0.0320000 ,
                    filpp(8) = 'CD_8.dat' ,
                   weight(8) = 0.0640000 ,
                    filpp(9) = 'CD_9.dat' ,
                   weight(9) = 0.0640000 ,
                   filpp(10) = 'CD_10.dat' ,
                  weight(10) = 0.0320000 ,
                   filpp(11) = 'CD_11.dat' ,
                  weight(11) = 0.0640000 ,
                   filpp(12) = 'CD_12.dat' ,
                  weight(12) = 0.0640000 ,
                   filpp(13) = 'CD_13.dat' ,
                  weight(13) = 0.0640000 ,
                   filpp(14) = 'CD_14.dat' ,
                  weight(14) = 0.1280000 ,
                   filpp(15) = 'CD_15.dat' ,
                  weight(15) = 0.1280000 ,
                   filpp(16) = 'CD_16.dat' ,
                  weight(16) = 0.0640000 ,
                   filpp(17) = 'CD_17.dat' ,
                  weight(17) = 0.1280000 ,
                   filpp(18) = 'CD_18.dat' ,
                  weight(18) = 0.1280000 ,
                   filpp(19) = 'CD_19.dat' ,
                  weight(19) = 0.0320000 ,
                   filpp(20) = 'CD_20.dat' ,
                  weight(20) = 0.0640000 ,
                   filpp(21) = 'CD_21.dat' ,
                  weight(21) = 0.0640000 ,
                   filpp(22) = 'CD_22.dat' ,
                  weight(22) = 0.0640000 ,
                   filpp(23) = 'CD_23.dat' ,
                  weight(23) = 0.1280000 ,
                   filpp(24) = 'CD_24.dat' ,
                  weight(24) = 0.1280000 ,
                   filpp(25) = 'CD_25.dat' ,
                  weight(25) = 0.0640000 ,
                   filpp(26) = 'CD_26.dat' ,
                  weight(26) = 0.1280000 ,
                   filpp(27) = 'CD_27.dat' ,
                  weight(27) = 0.1280000 ,
                     fileout = 'CDresult.xsf' ,
                       iflag = 2 ,
               output_format = 3 ,
                       e1(1) = 2.0,
                       e1(2) = 0.0,
                       e1(3) = 0.0,
                       e2(1) = 0.0,
                       e2(2) = 2.0,
                       e2(3) = 0.0,
                       x0(1) = 0.0,
                       x0(2) = 0.0,
                       x0(3) = 0.0,
                          nx = 45 ,
                          ny = 45 ,
 /




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



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From flux_ray12 at 163.com  Tue Nov 15 12:48:27 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Tue, 15 Nov 2011 19:48:27 +0800 (CST)
Subject: [Pw_forum] problem about pp.x: namelist plot not found or
 invalid
In-Reply-To: <4EC250A8.2030208@mater.unimib.it>
References: <4EC250A8.2030208@mater.unimib.it>
	<4c6b108e.10d34.133a6fd6dcc.Coremail.flux_ray12@163.com>
Message-ID: <11062da8.11110.133a70e8914.Coremail.flux_ray12@163.com>

I am sorry, this is my mistake, but I thing the order of filepp(i) and weight(i) could be another problem.





At 2011-11-15 19:44:40,"Guido Fratesi" <fratesi at mater.unimib.it> wrote:
>Dear Gao Zhe,
>"filpp" should be "filepp", at least.
>Guido
>
>Il 11/15/2011 12:29 PM, GAO Zhe ha scritto:
>> Dear QE developer and users:
>> Hi
>> I am using pp.x to generate the charge density file on certain surface.
>> The work for namelist, &inputpp, worked very well.
>> However, when I wanna summary the results from &inputpp to xcrysden
>> file, the error occurred:
>> chdens, namelist plot not found or invalid, exiting
>> Actually, I changed chdens.f90 a little bit on INTEGER, PARAMETER ::
>> nfilemax = 30, but I do not think this is the reason to meet such a
>> problem~ Since if I create a short input file by PWGUI, then it works
>> well. However, even if the short one created by myself, the same error
>> happened.
>> Now, I need to summary more than 20 |psi|^2files due to the density
>> k-points mesh, so it is impossible to build the input file via PWGUI's help.
>> I checked chdens.f90, again, but I cannot understand the meaning of error~
>> Any suggetstion will be welcome.
>> P.S.: This is my input file (the &inputpp file have generated in the
>> previous steps) :
>> &inputpp
>> /
>> &plot
>> nfile = 27 ,
>> filpp(1) = 'CD_1.dat' ,
>> weight(1) = 0.0160000 ,
>> filpp(2) = 'CD_2.dat' ,
>> weight(2) = 0.0320000 ,
>> filpp(3) = 'CD_3.dat' ,
>> weight(3) = 0.0320000 ,
>> filpp(4) = 'CD_4.dat' ,
>> weight(4) = 0.0320000 ,
>> filpp(5) = 'CD_5.dat' ,
>> weight(5) = 0.0640000 ,
>> filpp(6) = 'CD_6.dat' ,
>> weight(6) = 0.0640000 ,
>> filpp(7) = 'CD_7.dat' ,
>> weight(7) = 0.0320000 ,
>> filpp(8) = 'CD_8.dat' ,
>> weight(8) = 0.0640000 ,
>> filpp(9) = 'CD_9.dat' ,
>> weight(9) = 0.0640000 ,
>> filpp(10) = 'CD_10.dat' ,
>> weight(10) = 0.0320000 ,
>> filpp(11) = 'CD_11.dat' ,
>> weight(11) = 0.0640000 ,
>> filpp(12) = 'CD_12.dat' ,
>> weight(12) = 0.0640000 ,
>> filpp(13) = 'CD_13.dat' ,
>> weight(13) = 0.0640000 ,
>> filpp(14) = 'CD_14.dat' ,
>> weight(14) = 0.1280000 ,
>> filpp(15) = 'CD_15.dat' ,
>> weight(15) = 0.1280000 ,
>> filpp(16) = 'CD_16.dat' ,
>> weight(16) = 0.0640000 ,
>> filpp(17) = 'CD_17.dat' ,
>> weight(17) = 0.1280000 ,
>> filpp(18) = 'CD_18.dat' ,
>> weight(18) = 0.1280000 ,
>> filpp(19) = 'CD_19.dat' ,
>> weight(19) = 0.0320000 ,
>> filpp(20) = 'CD_20.dat' ,
>> weight(20) = 0.0640000 ,
>> filpp(21) = 'CD_21.dat' ,
>> weight(21) = 0.0640000 ,
>> filpp(22) = 'CD_22.dat' ,
>> weight(22) = 0.0640000 ,
>> filpp(23) = 'CD_23.dat' ,
>> weight(23) = 0.1280000 ,
>> filpp(24) = 'CD_24.dat' ,
>> weight(24) = 0.1280000 ,
>> filpp(25) = 'CD_25.dat' ,
>> weight(25) = 0.0640000 ,
>> filpp(26) = 'CD_26.dat' ,
>> weight(26) = 0.1280000 ,
>> filpp(27) = 'CD_27.dat' ,
>> weight(27) = 0.1280000 ,
>> fileout = 'CDresult.xsf' ,
>> iflag = 2 ,
>> output_format = 3 ,
>> e1(1) = 2.0,
>> e1(2) = 0.0,
>> e1(3) = 0.0,
>> e2(1) = 0.0,
>> e2(2) = 2.0,
>> e2(3) = 0.0,
>> x0(1) = 0.0,
>> x0(2) = 0.0,
>> x0(3) = 0.0,
>> nx = 45 ,
>> ny = 45 ,
>> /
>>
>>
>>
>> --
>> 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
>
>-- 
>Guido Fratesi
>
>Dipartimento di Scienza dei Materiali
>Universita` degli Studi di Milano-Bicocca
>via Cozzi 53, 20125 Milano, Italy
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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From fratesi at mater.unimib.it  Tue Nov 15 12:50:18 2011
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Tue, 15 Nov 2011 12:50:18 +0100
Subject: [Pw_forum] problem about pp.x: namelist plot not found or
	invalid
In-Reply-To: <3848d128.110df.133a70d9bef.Coremail.flux_ray12@163.com>
References: <4c6b108e.10d34.133a6fd6dcc.Coremail.flux_ray12@163.com>
	<3848d128.110df.133a70d9bef.Coremail.flux_ray12@163.com>
Message-ID: <4EC251FA.5080708@mater.unimib.it>

No, the order within the namelist is not important, but you solved the 
problem by correctly typing the variable names.
GF

Il 11/15/2011 12:47 PM, GAO Zhe ha scritto:
> Oh, I am sorry to bother~ I have found the problem.
> This problem occurred when filepp(i) have not been written together, i.e.:
> filepp(1)
> filepp(2)
> ....
> filepp(max)
> weight(1)
> weight(2)
> ....
> weight(max)
> is the only right way to create the input file.
>
>
> At 2011-11-15 19:29:46,"GAO Zhe" <flux_ray12 at 163.com> wrote:
>
>     Dear QE developer and users:
>     Hi
>     I am using pp.x to generate the charge density file on certain
>     surface. The work for namelist, &inputpp, worked very well.
>     However, when I wanna summary the results from &inputpp to xcrysden
>     file, the error occurred:
>     chdens, namelist plot not found or invalid, exiting
>     Actually, I changed chdens.f90 a little bit on INTEGER, PARAMETER ::
>     nfilemax = 30, but I do not think this is the reason to meet such a
>     problem~ Since if I create a short input file by PWGUI, then it
>     works well. However, even if the short one created by myself, the
>     same error happened.
>     Now, I need to summary more than 20 |psi|^2files due to the density
>     k-points mesh, so it is impossible to build the input file via
>     PWGUI's help.
>     I checked chdens.f90, again, but I cannot understand the meaning of
>     error~
>     Any suggetstion will be welcome.
>     P.S.: This is my input file (the &inputpp file have generated in the
>     previous steps) :
>     &inputpp
>     /
>     &plot
>     nfile = 27 ,
>     filpp(1) = 'CD_1.dat' ,
>     weight(1) = 0.0160000 ,
>     filpp(2) = 'CD_2.dat' ,
>     weight(2) = 0.0320000 ,
>     filpp(3) = 'CD_3.dat' ,
>     weight(3) = 0.0320000 ,
>     filpp(4) = 'CD_4.dat' ,
>     weight(4) = 0.0320000 ,
>     filpp(5) = 'CD_5.dat' ,
>     weight(5) = 0.0640000 ,
>     filpp(6) = 'CD_6.dat' ,
>     weight(6) = 0.0640000 ,
>     filpp(7) = 'CD_7.dat' ,
>     weight(7) = 0.0320000 ,
>     filpp(8) = 'CD_8.dat' ,
>     weight(8) = 0.0640000 ,
>     filpp(9) = 'CD_9.dat' ,
>     weight(9) = 0.0640000 ,
>     filpp(10) = 'CD_10.dat' ,
>     weight(10) = 0.0320000 ,
>     filpp(11) = 'CD_11.dat' ,
>     weight(11) = 0.0640000 ,
>     filpp(12) = 'CD_12.dat' ,
>     weight(12) = 0.0640000 ,
>     filpp(13) = 'CD_13.dat' ,
>     weight(13) = 0.0640000 ,
>     filpp(14) = 'CD_14.dat' ,
>     weight(14) = 0.1280000 ,
>     filpp(15) = 'CD_15.dat' ,
>     weight(15) = 0.1280000 ,
>     filpp(16) = 'CD_16.dat' ,
>     weight(16) = 0.0640000 ,
>     filpp(17) = 'CD_17.dat' ,
>     weight(17) = 0.1280000 ,
>     filpp(18) = 'CD_18.dat' ,
>     weight(18) = 0.1280000 ,
>     filpp(19) = 'CD_19.dat' ,
>     weight(19) = 0.0320000 ,
>     filpp(20) = 'CD_20.dat' ,
>     weight(20) = 0.0640000 ,
>     filpp(21) = 'CD_21.dat' ,
>     weight(21) = 0.0640000 ,
>     filpp(22) = 'CD_22.dat' ,
>     weight(22) = 0.0640000 ,
>     filpp(23) = 'CD_23.dat' ,
>     weight(23) = 0.1280000 ,
>     filpp(24) = 'CD_24.dat' ,
>     weight(24) = 0.1280000 ,
>     filpp(25) = 'CD_25.dat' ,
>     weight(25) = 0.0640000 ,
>     filpp(26) = 'CD_26.dat' ,
>     weight(26) = 0.1280000 ,
>     filpp(27) = 'CD_27.dat' ,
>     weight(27) = 0.1280000 ,
>     fileout = 'CDresult.xsf' ,
>     iflag = 2 ,
>     output_format = 3 ,
>     e1(1) = 2.0,
>     e1(2) = 0.0,
>     e1(3) = 0.0,
>     e2(1) = 0.0,
>     e2(2) = 2.0,
>     e2(3) = 0.0,
>     x0(1) = 0.0,
>     x0(2) = 0.0,
>     x0(3) = 0.0,
>     nx = 45 ,
>     ny = 45 ,
>     /
>
>
>
>     --
>     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

-- 
Guido Fratesi

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

From flux_ray12 at 163.com  Tue Nov 15 12:55:42 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Tue, 15 Nov 2011 19:55:42 +0800 (CST)
Subject: [Pw_forum] problem about pp.x: namelist plot not found or
 invalid
In-Reply-To: <4EC251FA.5080708@mater.unimib.it>
References: <4EC251FA.5080708@mater.unimib.it>
	<4c6b108e.10d34.133a6fd6dcc.Coremail.flux_ray12@163.com>
	<3848d128.110df.133a70d9bef.Coremail.flux_ray12@163.com>
Message-ID: <77dc1f84.11273.133a7152d2c.Coremail.flux_ray12@163.com>

Thank you very much for your patient.
since the bash script was a little bit complex, the careless and low level error occurred. Next time, I will check my input more carefully.


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




At 2011-11-15 19:50:18,"Guido Fratesi" <fratesi at mater.unimib.it> wrote:
>No, the order within the namelist is not important, but you solved the 
>problem by correctly typing the variable names.
>GF
>
>Il 11/15/2011 12:47 PM, GAO Zhe ha scritto:
>> Oh, I am sorry to bother~ I have found the problem.
>> This problem occurred when filepp(i) have not been written together, i.e.:
>> filepp(1)
>> filepp(2)
>> ....
>> filepp(max)
>> weight(1)
>> weight(2)
>> ....
>> weight(max)
>> is the only right way to create the input file.
>>
>>
>> At 2011-11-15 19:29:46,"GAO Zhe" <flux_ray12 at 163.com> wrote:
>>
>>     Dear QE developer and users:
>>     Hi
>>     I am using pp.x to generate the charge density file on certain
>>     surface. The work for namelist, &inputpp, worked very well.
>>     However, when I wanna summary the results from &inputpp to xcrysden
>>     file, the error occurred:
>>     chdens, namelist plot not found or invalid, exiting
>>     Actually, I changed chdens.f90 a little bit on INTEGER, PARAMETER ::
>>     nfilemax = 30, but I do not think this is the reason to meet such a
>>     problem~ Since if I create a short input file by PWGUI, then it
>>     works well. However, even if the short one created by myself, the
>>     same error happened.
>>     Now, I need to summary more than 20 |psi|^2files due to the density
>>     k-points mesh, so it is impossible to build the input file via
>>     PWGUI's help.
>>     I checked chdens.f90, again, but I cannot understand the meaning of
>>     error~
>>     Any suggetstion will be welcome.
>>     P.S.: This is my input file (the &inputpp file have generated in the
>>     previous steps) :
>>     &inputpp
>>     /
>>     &plot
>>     nfile = 27 ,
>>     filpp(1) = 'CD_1.dat' ,
>>     weight(1) = 0.0160000 ,
>>     filpp(2) = 'CD_2.dat' ,
>>     weight(2) = 0.0320000 ,
>>     filpp(3) = 'CD_3.dat' ,
>>     weight(3) = 0.0320000 ,
>>     filpp(4) = 'CD_4.dat' ,
>>     weight(4) = 0.0320000 ,
>>     filpp(5) = 'CD_5.dat' ,
>>     weight(5) = 0.0640000 ,
>>     filpp(6) = 'CD_6.dat' ,
>>     weight(6) = 0.0640000 ,
>>     filpp(7) = 'CD_7.dat' ,
>>     weight(7) = 0.0320000 ,
>>     filpp(8) = 'CD_8.dat' ,
>>     weight(8) = 0.0640000 ,
>>     filpp(9) = 'CD_9.dat' ,
>>     weight(9) = 0.0640000 ,
>>     filpp(10) = 'CD_10.dat' ,
>>     weight(10) = 0.0320000 ,
>>     filpp(11) = 'CD_11.dat' ,
>>     weight(11) = 0.0640000 ,
>>     filpp(12) = 'CD_12.dat' ,
>>     weight(12) = 0.0640000 ,
>>     filpp(13) = 'CD_13.dat' ,
>>     weight(13) = 0.0640000 ,
>>     filpp(14) = 'CD_14.dat' ,
>>     weight(14) = 0.1280000 ,
>>     filpp(15) = 'CD_15.dat' ,
>>     weight(15) = 0.1280000 ,
>>     filpp(16) = 'CD_16.dat' ,
>>     weight(16) = 0.0640000 ,
>>     filpp(17) = 'CD_17.dat' ,
>>     weight(17) = 0.1280000 ,
>>     filpp(18) = 'CD_18.dat' ,
>>     weight(18) = 0.1280000 ,
>>     filpp(19) = 'CD_19.dat' ,
>>     weight(19) = 0.0320000 ,
>>     filpp(20) = 'CD_20.dat' ,
>>     weight(20) = 0.0640000 ,
>>     filpp(21) = 'CD_21.dat' ,
>>     weight(21) = 0.0640000 ,
>>     filpp(22) = 'CD_22.dat' ,
>>     weight(22) = 0.0640000 ,
>>     filpp(23) = 'CD_23.dat' ,
>>     weight(23) = 0.1280000 ,
>>     filpp(24) = 'CD_24.dat' ,
>>     weight(24) = 0.1280000 ,
>>     filpp(25) = 'CD_25.dat' ,
>>     weight(25) = 0.0640000 ,
>>     filpp(26) = 'CD_26.dat' ,
>>     weight(26) = 0.1280000 ,
>>     filpp(27) = 'CD_27.dat' ,
>>     weight(27) = 0.1280000 ,
>>     fileout = 'CDresult.xsf' ,
>>     iflag = 2 ,
>>     output_format = 3 ,
>>     e1(1) = 2.0,
>>     e1(2) = 0.0,
>>     e1(3) = 0.0,
>>     e2(1) = 0.0,
>>     e2(2) = 2.0,
>>     e2(3) = 0.0,
>>     x0(1) = 0.0,
>>     x0(2) = 0.0,
>>     x0(3) = 0.0,
>>     nx = 45 ,
>>     ny = 45 ,
>>     /
>>
>>
>>
>>     --
>>     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
>
>-- 
>Guido Fratesi
>
>Dipartimento di Scienza dei Materiali
>Universita` degli Studi di Milano-Bicocca
>via Cozzi 53, 20125 Milano, Italy
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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From kalamaillist at gmail.com  Tue Nov 15 14:52:40 2011
From: kalamaillist at gmail.com (WF)
Date: Tue, 15 Nov 2011 21:52:40 +0800
Subject: [Pw_forum] What kind of calculation needs wavefunction files
	created by pw.x ?
Message-ID: <000301cca39d$db2b4220$9181c660$@gmail.com>

> Actually, wavefunctions are not needed for DOS calculations, but they are
for projected-DOS ones. For calculations with bands.x, you will need
wavefunctions only in conjunction with the lsym=.TRUE. option.
Other standard calculations that require wavefunctions are, for instance,
LDOS (and STM images), Wannier function analysis and maybe others. Also,
sometimes you may want to use the final charge and wavefunctions as a
starting guess for a successive calculation with pw.x.

Thank you very much for these detailed explanation. 

> ? 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

------------------------------------
Wu F,
College of Chemistry and Molecular Engineering, Peking University.
------------------------------------


From avallabh at purdue.edu  Tue Nov 15 15:09:05 2011
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Tue, 15 Nov 2011 09:09:05 -0500 (EST)
Subject: [Pw_forum] Query on "e-ph coupling"
In-Reply-To: <1320831760.10071.45.camel@fe12lx.fisica.uniud.it>
Message-ID: <523137433.122417.1321366145497.JavaMail.root@mailhub016.itcs.purdue.edu>



     From the tutorials, i have seen that "g" is needed for the calculation of " gamma". I just want to know whether the term "g" is internally being calculated or not. So do i just have to make changes to the code to print it or write code separately?

Thanks
Ajit

From tfcao at theory.issp.ac.cn  Tue Nov 15 15:24:24 2011
From: tfcao at theory.issp.ac.cn (=?utf-8?B?Q2FvIFRG?=)
Date: Tue, 15 Nov 2011 22:24:24 +0800
Subject: [Pw_forum] =?utf-8?q?Davidson_diagonalization_with_overlap?=
Message-ID: <20111115142424.28487.qmail@ms.hfcas.ac.cn>

Dear Giuseppe Mattioli
            Thank you very much for your kind replay .   When I  relax the structure, the calculation process stops here iteration #  4     ecut=    30.00 Ry     beta=0.70
  Davidson diagonalization with overlap. And I google it and have found this http://www.democritos.it/pipermail/pw_forum/2003-June/000374.html.
I can not fully understand it, so it appears to me that there in a problem in my calculation.

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From chenhanghuipwscf at gmail.com  Tue Nov 15 23:01:19 2011
From: chenhanghuipwscf at gmail.com (Hanghui Chen)
Date: Tue, 15 Nov 2011 17:01:19 -0500
Subject: [Pw_forum] vc-relax in QE 4.3.2
Message-ID: <CAOE2MOzNCrqUH+PqGEFtsSvY3=0hKddxfaARGQyAztmZAt0pEg@mail.gmail.com>

To the QE developers,
    In the new version of 4.3.2 Quantum Espresso, if I use 'vc-relax', I
find that at the end of relaxation, the code does a new self-consistent
calculation. However, if I turn on Hubbard U, the code crashes at the last
self-consistent calculation due to some segmentation fault. If no Hubbard U
is used, then everything is fine. I am wondering whether any one else on
the forum has similar experiences and whether this might be a bug in the
code or due to some compilation problems.
    Thank you.

Hanghui Chen
Department of Physics
Yale University
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From avallabh at purdue.edu  Wed Nov 16 03:53:24 2011
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Tue, 15 Nov 2011 21:53:24 -0500 (EST)
Subject: [Pw_forum] Query on "e-ph coupling"
In-Reply-To: <523137433.122417.1321366145497.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <1980394525.125821.1321412004803.JavaMail.root@mailhub016.itcs.purdue.edu>


Never mind, i figured that out myself. 


Thanks
Ajit

From giannozz at democritos.it  Wed Nov 16 11:04:31 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 16 Nov 2011 11:04:31 +0100
Subject: [Pw_forum] vc-relax in QE 4.3.2
In-Reply-To: <CAOE2MOzNCrqUH+PqGEFtsSvY3=0hKddxfaARGQyAztmZAt0pEg@mail.gmail.com>
References: <CAOE2MOzNCrqUH+PqGEFtsSvY3=0hKddxfaARGQyAztmZAt0pEg@mail.gmail.com>
Message-ID: <1321437871.5792.31.camel@fe12lx.fisica.uniud.it>

On Tue, 2011-11-15 at 17:01 -0500, Hanghui Chen wrote:

> I find that at the end of relaxation, the code does a new
> self-consistent calculation. However, if I turn on Hubbard U, 
> the code crashes at the last self-consistent calculation due 
> to some segmentation fault. If no Hubbard U is used, then 
> everything is fine. 

I vaguely remember something like this, but nobody has posted 
a sample input that exhibits such behavior, can be run in a 
reasonable time (i.e. few minutes) on a reasonable machine (i.e. 
a PC). If you have such an example, please post it, or even better, 
file a bug report on qe-forge:
   http://qe-forge.org/tracker/?atid=133&group_id=10&func=browse

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



From giannozz at democritos.it  Wed Nov 16 11:13:25 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 16 Nov 2011 11:13:25 +0100
Subject: [Pw_forum] Problem with DFT + U calculations
In-Reply-To: <BLU0-SMTP246E9EC22BDF1927DE0943C80C00@phx.gbl>
References: <BLU0-SMTP246E9EC22BDF1927DE0943C80C00@phx.gbl>
Message-ID: <1321438405.5792.41.camel@fe12lx.fisica.uniud.it>

On Sun, 2011-11-13 at 23:31 -0500, Lai Jiang wrote:


> I'm having some problem getting convergence in my DFT +U calculations.

there are two different problems here:

Bad convergence is one, and it is unfortunately a quite common problem
with DFT+U. I offer no suggestions for this, except the following: the
smearing (degauss) seems to me rather small, and this could lead to 
socillations and instabilities.

The crash is a different problem, which may or may not be related to
bad convergence. Unless a case is found for which the error can be
reproduced (again: in a reasonable time, on a resonable machine), it
is hard to say anything about it

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



From songsong19840614 at hotmail.com  Wed Nov 16 11:49:29 2011
From: songsong19840614 at hotmail.com (KangYun Song)
Date: Wed, 16 Nov 2011 10:49:29 +0000
Subject: [Pw_forum] QHA frequency is higher than *.freq
In-Reply-To: <COL113-W29A4F4173D14BAEB988022C8C30@phx.gbl>
References: <COL113-W60CEBD49552B277D2F7BC8C8DC0@phx.gbl>, ,
	<COL113-W6531F4056497CDE2F640E1C8DD0@phx.gbl>,
	<COL113-W29A4F4173D14BAEB988022C8C30@phx.gbl>
Message-ID: <COL113-W37056841977DF615C85DE4C8C60@phx.gbl>




Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.
 



From: songsong19840614 at hotmail.com
To: pw_forum at pwscf.org
Date: Sun, 13 Nov 2011 11:18:45 +0000
Subject: Re: [Pw_forum] QHA frequency is higher than *.freq







Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.
 



From: songsong19840614 at hotmail.com
To: pw_forum at pwscf.org
Date: Fri, 11 Nov 2011 12:55:14 +0000
Subject: Re: [Pw_forum] QHA frequency is higher than *.freq




Hi,
    The pdos is not similar to phonon dispersion and the frequency is not negative from ph.x.

Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.
 



From: songsong19840614 at hotmail.com
To: pw_forum at pwscf.org
Date: Thu, 10 Nov 2011 12:15:50 +0000
Subject: [Pw_forum] QHA frequency is higher than *.freq




Hi,
         Recently,I calculated the phonon dispersion.And I use the *.fc from matdyn q2r.x to calculate frequecy and pdos.But this is a problem the freqency from matdyn.x of QHA is higher than *.freq from matdyn.x of phonon dispersion calculation.Why?Could anyone help me?The other material I use this method did not meet this problem.
         The matdyn.in of QHA is:

&input
    amass(1)=*,
    amass(2)=*,
    asr='crystal',
    flfrc=*.fc,
    flfrq='frequency'
&end
1183
     -0.33333   0.57735   0.81850   1.00000
     -0.30555   0.52924   0.75029   1.00000
     -0.30555   0.57735   0.75029   1.00000
??????
 
       The matdyn.in of phonon dispersion calculating is :          

&input
    asr='simple',  amass(1)=*, amass(2)=*, 
    flfrc='*.fc', flfrq='*.freq' ,la2F=.false. , 
 /
85
  0.0000000   0.0000000   0.3092146, wk =   0.0235294
  0.0555560   0.0000000   0.3092146, wk =   0.0235294
  0.1111110  -0.0000006   0.3092146, wk =   0.0235294
  0.1666670   0.0000006   0.3092146, wk =   0.0235294
  0.2222220   0.0000000   0.3092146, wk =   0.0235294
  0.2777780   0.0000000   0.3092146, wk =   0.0235294
????

Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.

_______________________________________________ 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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From giannozz at democritos.it  Wed Nov 16 11:55:19 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 16 Nov 2011 11:55:19 +0100
Subject: [Pw_forum] QHA frequency is higher than *.freq
In-Reply-To: <COL113-W37056841977DF615C85DE4C8C60@phx.gbl>
References: <COL113-W60CEBD49552B277D2F7BC8C8DC0@phx.gbl>
	, , <COL113-W6531F4056497CDE2F640E1C8DD0@phx.gbl>
	, <COL113-W29A4F4173D14BAEB988022C8C30@phx.gbl>
	<COL113-W37056841977DF615C85DE4C8C60@phx.gbl>
Message-ID: <1321440919.6762.8.camel@fe12lx.fisica.uniud.it>

Repeating an ill-formulated question is unlikely to attract answers

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



From giuseppe.mattioli at mlib.ism.cnr.it  Wed Nov 16 12:52:24 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Wed, 16 Nov 2011 12:52:24 +0100
Subject: [Pw_forum] Davidson diagonalization with overlap
In-Reply-To: <20111115142424.28487.qmail@ms.hfcas.ac.cn>
References: <20111115142424.28487.qmail@ms.hfcas.ac.cn>
Message-ID: <201111161252.24905.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Cao
The link refers to a prehistoric version of pw and seems to have nothing to do with your problem...
I cannot say more without looking at your input file.

Giuseppe


On Tuesday 15 November 2011 15:24:24 Cao TF wrote:
> Dear Giuseppe Mattioli
>             Thank you very much for your kind replay .   When I  relax the
> structure, the calculation process stops here iteration #  4     ecut=   
> 30.00 Ry     beta=0.70 Davidson diagonalization with overlap. And I google
> it and have found this
> http://www.democritos.it/pipermail/pw_forum/2003-June/000374.html. I can
> not fully understand it, so it appears to me that there in a problem in my
> calculation.



-- 
********************************************************
- 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 nykondalu at gmail.com  Wed Nov 16 13:14:38 2011
From: nykondalu at gmail.com (yedu kondalu)
Date: Wed, 16 Nov 2011 17:44:38 +0530
Subject: [Pw_forum] calculation of lattice parameter and angle of
	rhombohedral structure
Message-ID: <CABJwmWfQ7NsBtZW1hmHwSrA9MyzAmSs6Uz-JjYHk2SNHZABcpQ@mail.gmail.com>

Dear users,

    I did the optimization for a compound using variable cell approximation
using PWSCF, which belongs to the space group R3m(160) Rhombohedral
representation.  The primitive vectors in terms of lattice parameter a =
8.25791360 a.u.
               a(1) = (   0.619505  -0.357671   0.698774 )
               a(2) = (   0.000000   0.715343   0.698774 )
               a(3) = (  -0.619505  -0.357671   0.698774 )

after completion of optimization step, the primitive vectors

CELL_PARAMETERS (alat=  8.25791360)
   0.636439417  -0.367448469   0.640642896
   0.000000000   0.734896938   0.640642896
  -0.636439417  -0.367448469   0.640642896

can u please explain me

how can I calculate the lattice parameter *a* and the *angle (alpha)*  ???

Thanks in advance

         Regards
     Yedukondalu
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From flux_ray12 at 163.com  Wed Nov 16 13:53:59 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Wed, 16 Nov 2011 20:53:59 +0800 (CST)
Subject: [Pw_forum] calculation of lattice parameter and angle of
 rhombohedral structure
In-Reply-To: <CABJwmWfQ7NsBtZW1hmHwSrA9MyzAmSs6Uz-JjYHk2SNHZABcpQ@mail.gmail.com>
References: <CABJwmWfQ7NsBtZW1hmHwSrA9MyzAmSs6Uz-JjYHk2SNHZABcpQ@mail.gmail.com>
Message-ID: <cd9065.18118.133ac70e351.Coremail.flux_ray12@163.com>

the three basis vectors of rhombohedral are (after relaxation) :
a = ( 0.636439417  -0.367448469   0.640642896 )
b = ( 0.000000000   0.734896938   0.640642896 )
c = ( -0.636439417  -0.367448469   0.640642896 )
then the lattice paremeter should be: A = sqrt (a1^2+a2^2+a3^2) * alat = 8.05092296 a.u. .
The angle between two vectors can be calculated by:
cosA = a (*) b / |a (*) b|,
where a and b are basis vectors, (*) represents the dot product.


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


At 2011-11-16 20:14:38,"yedu kondalu" <nykondalu at gmail.com> wrote:
Dear users,

    I did the optimization for a compound using variable cell approximation using PWSCF, which belongs to the space group R3m(160) Rhombohedral representation.  The primitive vectors in terms of lattice parameter a = 8.25791360 a.u. 
               a(1) = (   0.619505  -0.357671   0.698774 ) 
               a(2) = (   0.000000   0.715343   0.698774 ) 
               a(3) = (  -0.619505  -0.357671   0.698774 )

after completion of optimization step, the primitive vectors

CELL_PARAMETERS (alat=  8.25791360)
   0.636439417  -0.367448469   0.640642896
   0.000000000   0.734896938   0.640642896
  -0.636439417  -0.367448469   0.640642896

can u please explain me

how can I calculate the lattice parameter a and the angle (alpha)  ???

Thanks in advance

         Regards
     Yedukondalu


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From elie.moujaes at hotmail.co.uk  Wed Nov 16 14:51:34 2011
From: elie.moujaes at hotmail.co.uk (Elie M)
Date: Wed, 16 Nov 2011 13:51:34 +0000
Subject: [Pw_forum] parallel computing for phonon calculations
Message-ID: <DUB110-W1008678C0D46C001DD89DAD3C60@phx.gbl>


Dear all,
I am doing phonon calculations for a 60 Carbon atom Grain boundary system and I have got in total 180 irreducible representations which in fact take a lot of time and memory (this is if it was completed). Is it efficient to use parallel computing in QE for doing the phonon calculations? Any information on this is highly appreciated..
Thanks
Elie MoujaesUniversity of nottinghamNG7 2RDUK 		 	   		  
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From mrozikphd at gmail.com  Wed Nov 16 16:14:15 2011
From: mrozikphd at gmail.com (Michael Mrozik)
Date: Wed, 16 Nov 2011 10:14:15 -0500
Subject: [Pw_forum] Obtaining SCF convergence for Relax Calculation
Message-ID: <CALf5jvosz7dCn5-q2b57ED5eO6rxdUcdRRdKgXG7xG=kYBB83g@mail.gmail.com>

Hello to the PW_Forum:

I've been attempting to use QE for a period of time and I have run into
several issues, but I think they are all connected.  In my reading of the
forum and other tutorials, I have been able to put together the input file
below.  First off, I am using some scripts to run these jobs in a series so
I have set up a few control variables that I replace prior to the jobs
being submitted. (AAA = ecutwfc set to be 25, 30, 35, 40, 45...;  BBB = 4x,
6x, 8x, 10x, 12x; and CCC = ecutrho set to be the product of BBB and AAA.)
 I know the values for ecutwfc and ecutrho need fine tuning so this was my
way of solving for their values at once.  I am aware of the attached log
file not being run to completion, which is a queue time limit issue, but I
still have some questions. I am running this system, and a couple others,
with other pseudo-potentials because I want to not only test the program
but functionals as well.

1).  Since including a starting_magnetization (a requirement for iron-oxide
systems) I can no longer the any calculations to converge.  Is there a way
to ensure a magnetic ordering to the system and still get the calculation
to converge?

2).  I've read the information about the inclusion of the Hubbard U
correction and it would appear that the value of this parameter is system
dependent. (which makes sense)  But for someone who is trying to get a
system to converge, I feel that I should include this lda_plus_u = .true.,
but I want to know if there is a place/table/listing where the actual
determined/calculated values for U are maintained apart from just buried in
the literature? The input description of pwscf indicates that I need to
include values for all atoms in  my system, but as with the previous part
of this question, what is the U value for O and H? I don't think their
values should be included but I want to be sure.

Thanks for any insights/help into this,  I hope i've provided sufficient
information about my problems to be helpful.
- Mike

----
Michael K. Mrozik, Ph. D.
Post-Doc in the Department of Geosciences
Penn State University, University Park, PA

*********
Input File:
*********
 &CONTROL
                       title = 'GRLXLSCF',
                 calculation = 'relax',
                restart_mode = 'from_scratch',
                      outdir = '/MADEUPDIRECTORY/AAA/BBB/',
                  pseudo_dir = '/MADEUPDIRECTORY/QE/pseudo/',
                      prefix = 'GRLXBLYPAAABBB',
                   verbosity = 'high',
                     tprnfor = .true.,
 /
 &SYSTEM
                       ibrav = 12,
                           A = 9.296,
                           B = 20.035,
                           C = 6.028,
                       cosAB = -1.0472E-4,
                         nat = 128,
                        ntyp = 4,
                     ecutwfc = AAA.0,
                     ecutrho = CCC.0,
                  tot_charge = 0.000000,
   starting_magnetization(1) = 1,
   starting_magnetization(2) = -1,
                 occupations = 'fixed',
/
 &ELECTRONS
                 mixing_beta = 0.1,
                 mixing_mode = 'local-TF',
             diagonalization = 'cg',
                    conv_thr = 1D-6,
                 startingpot = 'random' ,
                 startingwfc = 'random',
 /
 &IONS
                ion_dynamics = 'bfgs',
 /
ATOMIC_SPECIES
   Feu   55.84500  Fe.blyp-sp-van_ak.UPF
   Fed   55.84500  Fe.blyp-sp-van_ak.UPF
    O   15.99900  O.blyp-van_ak.UPF
    H    1.00790  H.blyp-van_ak.UPF
ATOMIC_POSITIONS Angstrom
 Feu  0.190319598    8.516924949    0.753499153  1 1 1
 Fed  2.514515302    6.508932037    2.260501765  1 1 1
 Fed  4.456588263    1.500267943    2.260484695  1 1 1
 Feu  2.132402339    3.508295629    0.753481173  1 1 1
 Feu  0.190307315    8.516942024    3.767499722  1 1 1
 Fed  2.514514955    6.508837690    5.274494906  1 1 1
 Fed  4.456583802    1.500354418    5.274512120  1 1 1
 Feu  2.132426310    3.508304415    3.767515428  1 1 1
 Feu  0.189280389   18.534259350    0.753500442  1 1 1
 Fed  2.513728029   16.526431096    2.260501702  1 1 1
 Fed  4.455569428   11.517804725    2.260476166  1 1 1
 Feu  2.131575245   13.525709388    0.753499017  1 1 1
 Feu  0.189285836   18.534263562    3.767500089  1 1 1
 Fed  2.513737279   16.526421637    5.274499557  1 1 1
 Fed  4.455569646   11.517812353    5.274522033  1 1 1
 Feu  2.131559299   13.525638343    3.767499481  1 1 1
 Feu  4.838291318    8.516884684    0.753503120  1 1 1
 Fed  7.162584207    6.508834660    2.260501140  1 1 1
 Fed  9.104522850    1.500353290    2.260508414  1 1 1
 Feu  6.780443116    3.508216285    0.753501922  1 1 1
 Feu  4.838291966    8.516850814    3.767496432  1 1 1
 Fed  7.162581640    6.508885559    5.274499691  1 1 1
 Fed  9.104531389    1.500271872    5.274485423  1 1 1
 Feu  6.780435302    3.508209889    3.767490849  1 1 1
 Feu  4.837478473   18.534302371    0.753515700  1 1 1
 Fed  7.161657474   16.526405308    2.260502285  1 1 1
 Fed  9.103666222   11.517947683    2.260503119  1 1 1
 Feu  6.779490559   13.525653855    0.753478321  1 1 1
 Feu  4.837453218   18.534253816    3.767481644  1 1 1
 Fed  7.161656304   16.526415449    5.274499608  1 1 1
 Fed  9.103690931   11.517893530    5.274495373  1 1 1
 Feu  6.779478037   13.525656306    3.767521205  1 1 1
 O    0.926335986    0.516667864    0.753467363  1 1 1
 O    3.249818014    4.491780721    2.260521090  1 1 1
 O    3.720574435    9.500818106    2.260507179  1 1 1
 O    1.397070297    5.525472106    0.753458776  1 1 1
 O    3.300486519    2.030231637    0.753511916  1 1 1
 O    0.976343098    2.977948424    2.260494087  1 1 1
 O    1.346565334    7.987031437    2.260512471  1 1 1
 O    3.670455179    7.039369111    0.753479425  1 1 1
 O    0.926311558    0.516664842    3.767531665  1 1 1
 O    3.249816199    4.491860476    5.274475026  1 1 1
 O    3.720581555    9.500832693    5.274491125  1 1 1
 O    1.397073780    5.525459623    3.767535556  1 1 1
 O    3.300483684    2.030249225    3.767479128  1 1 1
 O    0.976293264    2.977933718    5.274504376  1 1 1
 O    1.346621615    7.986996610    5.274483520  1 1 1
 O    3.670430276    7.039348958    3.767521696  1 1 1
 O    0.925344158   10.534238098    0.753447840  1 1 1
 O    3.248954982   14.509538681    2.260448833  1 1 1
 O    3.719701045   19.518312023    2.260518515  1 1 1
 O    1.396462316   15.542862161    0.753516589  1 1 1
 O    3.299585736   12.047817307    0.753501133  1 1 1
 O    0.975360407   12.995621430    2.260487852  1 1 1
 O    1.345540981   18.004489632    2.260505259  1 1 1
 O    3.669521652   17.056860458    0.753493600  1 1 1
 O    0.925323885   10.534166385    3.767552202  1 1 1
 O    3.249008313   14.509508553    5.274551999  1 1 1
 O    3.719664181   19.518262882    5.274475916  1 1 1
 O    1.396261825   15.543015876    3.767482690  1 1 1
 O    3.299633087   12.047783242    3.767499312  1 1 1
 O    0.975324158   12.995571696    5.274510965  1 1 1
 O    1.345575546   18.004502683    5.274490697  1 1 1
 O    3.669505916   17.056871864    3.767506975  1 1 1
 O    5.574302275    0.516690427    0.753506149  1 1 1
 O    7.897860092    4.491880742    2.260505810  1 1 1
 O    8.368593895    9.500712544    2.260521640  1 1 1
 O    6.045098204    5.525519766    0.753501520  1 1 1
 O    7.948497721    2.030262278    0.753465152  1 1 1
 O    5.624271770    2.977927798    2.260483893  1 1 1
 O    5.994624051    7.987003954    2.260489634  1 1 1
 O    8.318483850    7.039422241    0.753493769  1 1 1
 O    5.574414290    0.516720048    3.767488110  1 1 1
 O    7.897856081    4.491842625    5.274490861  1 1 1
 O    8.368603339    9.500798024    5.274478736  1 1 1
 O    6.045076247    5.525497959    3.767494221  1 1 1
 O    7.948486425    2.030251522    3.767534743  1 1 1
 O    5.624322258    2.977938251    5.274513508  1 1 1
 O    5.994597106    7.987021696    5.274510325  1 1 1
 O    8.318500878    7.039432716    3.767501172  1 1 1
 O    5.573285648   10.534210651    0.753473176  1 1 1
 O    7.896919398   14.509698365    2.260475215  1 1 1
 O    8.367600401   19.518248324    2.260500011  1 1 1
 O    6.044312261   15.543050827    0.753538915  1 1 1
 O    7.947568421   12.047854552    0.753494944  1 1 1
 O    5.623268546   12.995381350    2.260512171  1 1 1
 O    5.993562421   18.004444850    2.260504188  1 1 1
 O    8.317422504   17.056816644    0.753508228  1 1 1
 O    5.573313427   10.534239139    3.767526712  1 1 1
 O    7.896960080   14.509617545    5.274521945  1 1 1
 O    8.367715235   19.518362224    5.274496758  1 1 1
 O    6.044221723   15.543095109    3.767458127  1 1 1
 O    7.947562497   12.047842725    3.767503800  1 1 1
 O    5.623283874   12.995376733    5.274485551  1 1 1
 O    5.993525717   18.004455868    5.274492044  1 1 1
 O    8.317461384   17.056772653    3.767486772  1 1 1
 H    1.870905429    0.814153528    0.753521517  1 1 1
 H    4.194583904    4.194548426    2.260493973  1 1 1
 H    2.776032151    9.203157376    2.260492109  1 1 1
 H    0.452334234    5.822627727    0.753501247  1 1 1
 H    1.870862429    0.814181973    3.767476488  1 1 1
 H    4.194568454    4.194538748    5.274501384  1 1 1
 H    2.776063900    9.203160161    5.274507802  1 1 1
 H    0.452357238    5.822612605    3.767493500  1 1 1
 H    1.869792910   10.831584655    0.753516714  1 1 1
 H    4.194159018   14.211982665    2.260524877  1 1 1
 H    2.775199651   19.220786322    2.260487780  1 1 1
 H    0.451612695   15.840194412    0.753501524  1 1 1
 H    1.869731850   10.831556319    3.767483887  1 1 1
 H    4.194281518   14.211967892    5.274475409  1 1 1
 H    2.775112585   19.220798862    5.274507909  1 1 1
 H    0.451593928   15.840178658    3.767498163  1 1 1
 H    6.518922048    0.814204617    0.753498312  1 1 1
 H    8.842541851    4.194524057    2.260495074  1 1 1
 H    7.424074390    9.203226451    2.260486428  1 1 1
 H    5.100361703    5.822631475    0.753493034  1 1 1
 H    6.519133851    0.814284768    3.767494916  1 1 1
 H    8.842574976    4.194534596    5.274503173  1 1 1
 H    7.424109508    9.203237429    5.274512036  1 1 1
 H    5.100337024    5.822659459    3.767507361  1 1 1
 H    6.517771718   10.831445568    0.753510895  1 1 1
 H    8.841713653   14.212166155    2.260519512  1 1 1
 H    7.422992747   19.220752655    2.260508677  1 1 1
 H    5.099584539   15.840088128    0.753466022  1 1 1
 H    6.517839937   10.831455916    3.767489843  1 1 1
 H    8.841869110   14.212073647    5.274479452  1 1 1
 H    7.423237889   19.220827446    5.274488671  1 1 1
 H    5.099503033   15.840118378    3.767533284  1 1 1
K_POINTS automatic
4 6 4  0 0 0
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From bamideleibrahim at yahoo.com  Wed Nov 16 18:19:22 2011
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Wed, 16 Nov 2011 09:19:22 -0800 (PST)
Subject: [Pw_forum] help on atomic position
Message-ID: <1321463962.28618.YahooMailNeo@web39422.mail.mud.yahoo.com>

Dear all, 

? I am working on Li15Si4 compound and i could not get the correct atomic positions for each of the 

elements in this compound. I will be delighted if anybody can give me the atomic positions for this compound.

?
Adetunji Bamidele Ibrahim
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.
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From omipet2000 at yahoo.com  Wed Nov 16 18:45:48 2011
From: omipet2000 at yahoo.com (Omileke Peter)
Date: Wed, 16 Nov 2011 09:45:48 -0800 (PST)
Subject: [Pw_forum] atomic position of Li15Si4
Message-ID: <1321465548.14855.YahooMailNeo@web120004.mail.ne1.yahoo.com>

Dear all,
???????? please I need assistance from anybody in the forum who
???????? have an idea on how to get atomic position of Li15Si4 compound.
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From arvifis at gmail.com  Wed Nov 16 19:15:08 2011
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Wed, 16 Nov 2011 16:15:08 -0200
Subject: [Pw_forum] help on atomic position
In-Reply-To: <1321463962.28618.YahooMailNeo@web39422.mail.mud.yahoo.com>
References: <1321463962.28618.YahooMailNeo@web39422.mail.mud.yahoo.com>
Message-ID: <CABEdBFPg-C+Yvb9Jg+NTmQ-zVgQWTCjvmKxUqQOQZW9=Td7_5Q@mail.gmail.com>

Dear Adetunji, these are some information, you should use google, is a
useful tool

http://jap.aip.org/resource/1/japiau/v102/i5/p053704_s1
http://cst-www.nrl.navy.mil/lattice/struk/d5_c.html

Best.
PhD. std Arles V. Gil Rebaza
La Plata - Argentine

2011/11/16 bamidele ibrahim <bamideleibrahim at yahoo.com>

> Dear all,
>   I am working on Li15Si4 compound and i could not get the correct atomic
> positions for each of the
> elements in this compound. I will be delighted if anybody can give me the
> atomic positions for this compound.
>
> 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
>
>


-- 
###--------->   Arles V.   <---------###
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From jianglai at sas.upenn.edu  Wed Nov 16 20:43:12 2011
From: jianglai at sas.upenn.edu (Lai Jiang)
Date: Wed, 16 Nov 2011 14:43:12 -0500
Subject: [Pw_forum] 'wf_collect' question
Message-ID: <BLU0-SMTP428343E575FD80758E699B380C60@phx.gbl>

Hello everyone,

When setting startingwfc = 'file' the program is supposed to read wfc files
from a previous run. But if the previous run uses 'wf_collect' =  .ture.
the wfc are deleted after scf and converted to evc.dat files at each k
point and can not be used as startingwfc. It is really confusing to me that
wf_collect does the opposite of what it is supposed to do. Is there any
reason behind it?

Thanks!

Lai Jiang
*********************************
Department of Chemistry
School of Arts and Sciences
University of Pennsylvania
*********************************
231 South 34th Street, Box 46
Philadelphia, PA 19104
Tel: 215-573-4241
Fax: 215-573-2112
Email: jianglai at sas.upenn.edu
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From trambui at u.boisestate.edu  Wed Nov 16 23:07:54 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Wed, 16 Nov 2011 15:07:54 -0700
Subject: [Pw_forum] relax calculation for some atoms in the structure
Message-ID: <CANzxBn86cezRwfH4-UQpsj9WTLxkC5v8RdkciuwTewuqS0LBrA@mail.gmail.com>

Dear QE users,
    I'd like to do a relax calculation for only certain atoms in my
structrure while keeping some other ones fixed, but I have not been able to
find out how to do so. Would you give me some suggestions? anything would
be appreciated.
Regards,
Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From songsong19840614 at hotmail.com  Thu Nov 17 02:41:18 2011
From: songsong19840614 at hotmail.com (KangYun Song)
Date: Thu, 17 Nov 2011 01:41:18 +0000
Subject: [Pw_forum] QHA frequency is higher than *.freq
In-Reply-To: <1321440919.6762.8.camel@fe12lx.fisica.uniud.it>
References: <COL113-W60CEBD49552B277D2F7BC8C8DC0@phx.gbl>,, ,
	<COL113-W6531F4056497CDE2F640E1C8DD0@phx.gbl>,,
	<COL113-W29A4F4173D14BAEB988022C8C30@phx.gbl>,
	<COL113-W37056841977DF615C85DE4C8C60@phx.gbl>,
	<1321440919.6762.8.camel@fe12lx.fisica.uniud.it>
Message-ID: <COL113-W27BB0510F96FED4C05D0BC8C70@phx.gbl>


Dear Paolo:
        Hi, if it is any question I cannot state clearly I am sorry for this. The main problem is the frequency of matdyn.x (asr=crystal)which the k-point is from tetra.x is very higher the matdyn.x(asr=simple) which the k-point is get it from xcrysden.And I calculate other structure is not met this problem.So it really bewilder me.
 
Best Regards.


Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.
 

> From: giannozz at democritos.it
> To: pw_forum at pwscf.org
> Date: Wed, 16 Nov 2011 11:55:19 +0100
> Subject: Re: [Pw_forum] QHA frequency is higher than *.freq
> 
> Repeating an ill-formulated question is unlikely to attract answers
> 
> -- 
> 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
 		 	   		  
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From songsong19840614 at hotmail.com  Thu Nov 17 02:43:34 2011
From: songsong19840614 at hotmail.com (KangYun Song)
Date: Thu, 17 Nov 2011 01:43:34 +0000
Subject: [Pw_forum] relax calculation for some atoms in the structure
In-Reply-To: <CANzxBn86cezRwfH4-UQpsj9WTLxkC5v8RdkciuwTewuqS0LBrA@mail.gmail.com>
References: <CANzxBn86cezRwfH4-UQpsj9WTLxkC5v8RdkciuwTewuqS0LBrA@mail.gmail.com>
Message-ID: <COL113-W3178CB8CBC6A1CBAF64F47C8C70@phx.gbl>


Dear Tram:
         You can see the example03, it will help for you.

Yun Song,Kang
Department Physical Science and Technology of  Inner Mongolia University.
 



Date: Wed, 16 Nov 2011 15:07:54 -0700
From: trambui at u.boisestate.edu
To: pw_forum at pwscf.org
Subject: [Pw_forum] relax calculation for some atoms in the structure

Dear QE users,
    I'd like to do a relax calculation for only certain atoms in my structrure while keeping some other ones fixed, but I have not been able to find out how to do so. Would you give me some suggestions? anything would be appreciated.
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 		 	   		  
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From hqzhou at nju.edu.cn  Thu Nov 17 06:49:25 2011
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Thu, 17 Nov 2011 13:49:25 +0800
Subject: [Pw_forum] calculation of lattice parameter and angle of
	rhombohedral structure
References: <CABJwmWfQ7NsBtZW1hmHwSrA9MyzAmSs6Uz-JjYHk2SNHZABcpQ@mail.gmail.com>
	<cd9065.18118.133ac70e351.Coremail.flux_ray12@163.com>
Message-ID: <333916570C304FBE95176B9CEF256B1F@solarflare>

I'm afraid the formula for calculating cosA should be
cosA = b (*) c / (|b| | c|)

dr. zhou huiqun
@earth sciences, nanjing university, china

  ----- Original Message ----- 
  From: GAO Zhe 
  To: PWSCF Forum 
  Sent: Wednesday, November 16, 2011 8:53 PM
  Subject: Re: [Pw_forum] calculation of lattice parameter and angle of rhombohedral structure


  the three basis vectors of rhombohedral are (after relaxation) :
  a = ( 0.636439417  -0.367448469   0.640642896 )
  b = ( 0.000000000   0.734896938   0.640642896 )
  c = ( -0.636439417  -0.367448469   0.640642896 )
  then the lattice paremeter should be: A = sqrt (a1^2+a2^2+a3^2) * alat = 8.05092296 a.u. .
  The angle between two vectors can be calculated by:
  cosA = a (*) b / |a (*) b|,
  where a and b are basis vectors, (*) represents the dot product.


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


  At 2011-11-16 20:14:38,"yedu kondalu" <nykondalu at gmail.com> wrote:

    Dear users,

        I did the optimization for a compound using variable cell approximation using PWSCF, which belongs to the space group R3m(160) Rhombohedral representation.  The primitive vectors in terms of lattice parameter a = 8.25791360 a.u.  
                   a(1) = (   0.619505  -0.357671   0.698774 )  
                   a(2) = (   0.000000   0.715343   0.698774 )  
                   a(3) = (  -0.619505  -0.357671   0.698774 ) 

    after completion of optimization step, the primitive vectors

    CELL_PARAMETERS (alat=  8.25791360)
       0.636439417  -0.367448469   0.640642896
       0.000000000   0.734896938   0.640642896
      -0.636439417  -0.367448469   0.640642896

    can u please explain me 

    how can I calculate the lattice parameter a and the angle (alpha)  ???

    Thanks in advance

             Regards
         Yedukondalu








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From germaneau at gucas.ac.cn  Thu Nov 17 20:02:19 2011
From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=)
Date: Thu, 17 Nov 2011 14:02:19 -0500
Subject: [Pw_forum] calculation of lattice parameter and angle of
 rhombohedral structure
In-Reply-To: <521506971.04431@gscas.net.cn>
References: <CABJwmWfQ7NsBtZW1hmHwSrA9MyzAmSs6Uz-JjYHk2SNHZABcpQ@mail.gmail.com>
	<cd9065.18118.133ac70e351.Coremail.flux_ray12@163.com>
	<521506971.04431@gscas.net.cn>
Message-ID: <4EC55A3B.8070303@gucas.ac.cn>

Actually it's

    cos(alpha) = *b* . *c* / ( |*b*||*c*| )

                                                                  ?ric.

On 11/17/2011 12:49 AM, Huiqun Zhou wrote:
> I'm afraid the formula for calculating cosA should be
> cosA = b (*) c / (|b| | c|)
> dr. zhou huiqun
> @earth sciences, nanjing university, china
>
>     ----- Original Message -----
>     *From:* GAO Zhe <mailto:flux_ray12 at 163.com>
>     *To:* PWSCF Forum <mailto:pw_forum at pwscf.org>
>     *Sent:* Wednesday, November 16, 2011 8:53 PM
>     *Subject:* Re: [Pw_forum] calculation of lattice parameter and
>     angle of rhombohedral structure
>
>     the three basis vectors of rhombohedral are (after relaxation) :
>     a = ( 0.636439417  -0.367448469   0.640642896 )
>     b = ( 0.000000000   0.734896938   0.640642896 )
>     c = ( -0.636439417  -0.367448469   0.640642896 )
>     then the lattice paremeter should be: A = sqrt (a1^2+a2^2+a3^2) *
>     alat = 8.05092296 a.u. .
>     The angle between two vectors can be calculated by:
>     cosA = a (*) b / |a (*) b|,
>     where a and b are basis vectors, (*) represents the dot product.
>
>     --
>     GAO Zhe
>     CMC Lab, MSE, SNU, Seoul, S.Korea
>
>     At 2011-11-16 20:14:38,"yedu kondalu" <nykondalu at gmail.com> wrote:
>
>         Dear users,
>
>             I did the optimization for a compound using variable cell
>         approximation using PWSCF, which belongs to the space group
>         R3m(160) Rhombohedral representation.  The primitive vectors
>         in terms of lattice parameter a = 8.25791360 a.u.
>                        a(1) = (   0.619505  -0.357671   0.698774 )
>                        a(2) = (   0.000000   0.715343   0.698774 )
>                        a(3) = (  -0.619505  -0.357671   0.698774 )
>
>         after completion of optimization step, the primitive vectors
>
>         CELL_PARAMETERS (alat=  8.25791360)
>            0.636439417  -0.367448469   0.640642896
>            0.000000000   0.734896938   0.640642896
>           -0.636439417  -0.367448469   0.640642896
>
>         can u please explain me
>
>         how can I calculate the lattice parameter *a* and the *angle
>         (alpha)*  ???
>
>         Thanks in advance
>
>                  Regards
>              Yedukondalu
>
>
>
>
>     ------------------------------------------------------------------------
>     _______________________________________________
>     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

-- 
/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>

Graduate University of Chinese Academy of Sciences
College of Physical 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 gabriele.sclauzero at epfl.ch  Thu Nov 17 11:15:17 2011
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Thu, 17 Nov 2011 11:15:17 +0100
Subject: [Pw_forum] calculation of lattice parameter and angle
 of	rhombohedral structure
In-Reply-To: <333916570C304FBE95176B9CEF256B1F@solarflare>
References: <CABJwmWfQ7NsBtZW1hmHwSrA9MyzAmSs6Uz-JjYHk2SNHZABcpQ@mail.gmail.com>	<cd9065.18118.133ac70e351.Coremail.flux_ray12@163.com>
	<333916570C304FBE95176B9CEF256B1F@solarflare>
Message-ID: <4EC4DEB5.7040304@epfl.ch>

Dear all,

I think that (using GAO Zhe's notation) both
b (*) c / (|b| |c|)
and
a (*) b / (|a| |b|)
should give the same result, because in the rhombohedral lattice the
three basis vectors form equal angles with each other.
Obviously, a (*) b / (|a (*) b|) is not correct because it would always
give 1 or -1 (and I believe it was just a typo).


HTH

GS


On 11/17/2011 06:49 AM, Huiqun Zhou wrote:
> I'm afraid the formula for calculating cosA should be
> cosA = b (*) c / (|b| | c|)
> dr. zhou huiqun
> @earth sciences, nanjing university, china
>
>     ----- Original Message -----
>     *From:* GAO Zhe <mailto:flux_ray12 at 163.com>
>     *To:* PWSCF Forum <mailto:pw_forum at pwscf.org>
>     *Sent:* Wednesday, November 16, 2011 8:53 PM
>     *Subject:* Re: [Pw_forum] calculation of lattice parameter and
>     angle of rhombohedral structure
>
>     the three basis vectors of rhombohedral are (after relaxation) :
>     a = ( 0.636439417 -0.367448469 0.640642896 )
>     b = ( 0.000000000 0.734896938 0.640642896 )
>     c = ( -0.636439417 -0.367448469 0.640642896 )
>     then the lattice paremeter should be: A = sqrt (a1^2+a2^2+a3^2) *
>     alat = 8.05092296 a.u. .
>     The angle between two vectors can be calculated by:
>     cosA = a (*) b / |a (*) b|,
>     where a and b are basis vectors, (*) represents the dot product.
>
>     --
>     GAO Zhe
>     CMC Lab, MSE, SNU, Seoul, S.Korea
>
>     At 2011-11-16 20:14:38,"yedu kondalu" <nykondalu at gmail.com> wrote:
>
>         Dear users,
>
>         I did the optimization for a compound using variable cell
>         approximation using PWSCF, which belongs to the space group
>         R3m(160) Rhombohedral representation. The primitive vectors in
>         terms of lattice parameter a = 8.25791360 a.u.
>         a(1) = ( 0.619505 -0.357671 0.698774 )
>         a(2) = ( 0.000000 0.715343 0.698774 )
>         a(3) = ( -0.619505 -0.357671 0.698774 )
>
>         after completion of optimization step, the primitive vectors
>
>         CELL_PARAMETERS (alat= 8.25791360)
>         0.636439417 -0.367448469 0.640642896
>         0.000000000 0.734896938 0.640642896
>         -0.636439417 -0.367448469 0.640642896
>
>         can u please explain me
>
>         how can I calculate the lattice parameter *a* and the *angle
>         (alpha)* ???
>
>         Thanks in advance
>
>         Regards
>         Yedukondalu
>


-- 

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

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From flux_ray12 at 163.com  Thu Nov 17 11:34:40 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 17 Nov 2011 18:34:40 +0800 (CST)
Subject: [Pw_forum] calculation of lattice parameter and angle
	of	rhombohedral structure
In-Reply-To: <4EC4DEB5.7040304@epfl.ch>
References: <4EC4DEB5.7040304@epfl.ch>
	<CABJwmWfQ7NsBtZW1hmHwSrA9MyzAmSs6Uz-JjYHk2SNHZABcpQ@mail.gmail.com>
	<cd9065.18118.133ac70e351.Coremail.flux_ray12@163.com>
	<333916570C304FBE95176B9CEF256B1F@solarflare>
Message-ID: <54776db5.c8d8.133b117b558.Coremail.flux_ray12@163.com>

Yes, that is my mistake. The denominator should be (|a| |b|).
Furthermore, I just wanted to say A as the angle between vector a and b~~~ Definitely, in rhombohedral structure, alpha = beta = gamma~


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


At 2011-11-17 18:15:17,"Gabriele Sclauzero" <gabriele.sclauzero at epfl.ch> wrote:
Dear all,

   I think that (using GAO Zhe's notation) both
b (*) c / (|b| |c|)
and
a (*) b / (|a| |b|)
should give the same result, because in the rhombohedral lattice the three basis vectors form equal angles with each other.
Obviously, a (*) b / (|a (*) b|) is not correct because it would always give 1 or -1 (and I believe it was just a typo).


HTH

GS


On 11/17/2011 06:49 AM, Huiqun Zhou wrote:
I'm afraid the formula for calculating cosA should be
cosA = b (*) c / (|b| | c|)
 
dr. zhou huiqun
@earth sciences, nanjing university, china
 
----- Original Message -----
From:GAO Zhe
To:PWSCF Forum
Sent: Wednesday, November 16, 2011 8:53 PM
Subject: Re: [Pw_forum] calculation of lattice parameter and angle of rhombohedral structure


the three basis vectors of rhombohedral are (after relaxation) :
a = ( 0.636439417  -0.367448469   0.640642896 )
b = ( 0.000000000   0.734896938   0.640642896 )
c = ( -0.636439417  -0.367448469   0.640642896 )
then the lattice paremeter should be: A = sqrt (a1^2+a2^2+a3^2) * alat = 8.05092296 a.u. .
The angle between two vectors can be calculated by:
cosA = a (*) b / |a (*) b|,
where a and b are basis vectors, (*) represents the dot product.


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


At 2011-11-16 20:14:38,"yedu kondalu" <nykondalu at gmail.com> wrote:
Dear users,

    I did the optimization for a compound using variable cell approximation using PWSCF, which belongs to the space group R3m(160) Rhombohedral representation.  The primitive vectors in terms of lattice parameter a = 8.25791360 a.u. 
               a(1) = (   0.619505  -0.357671   0.698774 ) 
               a(2) = (   0.000000   0.715343   0.698774 ) 
               a(3) = (  -0.619505  -0.357671   0.698774 )

after completion of optimization step, the primitive vectors

CELL_PARAMETERS (alat=  8.25791360)
   0.636439417  -0.367448469   0.640642896
   0.000000000   0.734896938   0.640642896
  -0.636439417  -0.367448469   0.640642896

can u please explain me

how can I calculate the lattice parameter a and the angle (alpha)  ???

Thanks in advance

         Regards
     Yedukondalu




-- 

Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne
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From hariomcosmos at gmail.com  Thu Nov 17 18:23:54 2011
From: hariomcosmos at gmail.com (hariom jani)
Date: Thu, 17 Nov 2011 18:23:54 +0100
Subject: [Pw_forum]  Defining spin states in PWscf
Message-ID: <CAAq=-GYpr95zi2eAfyNo=gdj2AVWoFyCWjbGLj0V4RtS+B+D8g@mail.gmail.com>

Dear Andrea,

Thanks for your reply.
I am aware of the physics that you have pointed out.

Nevertheless, what i desire to obtain the 'j' states which are defined
clearly

for example in the silicon system, after considering the spin-orbit
coupling, the 1st and 2nd valence band are degenerate:
prepared by taking the linear superposition of:  j = 1/2, j = -1/2.

Is there any command in QE, which i can use to obtain these exact states,
rather than their superposition?

Thanks
Hariom Jani
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From padmaja_patnaik at yahoo.co.uk  Thu Nov 17 18:47:11 2011
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Thu, 17 Nov 2011 17:47:11 +0000 (GMT)
Subject: [Pw_forum] k point value
Message-ID: <1321552031.2565.YahooMailNeo@web28515.mail.ukl.yahoo.com>

Dear all
I am using QE since last few yeras but still could not answer few questions a new student in my lab asked me. When we are doing band plot its a curve between k~E.? In the input file we give ka values as,
? 
?? 0.0? 0.0? 0.0? 
?? 0.0? 0.0? 0.1? 
?? 0.0? 0.0? 0.2? 
?? 0.0? 0.0? 0.3? 
?? 0.0? 0.0? 0.4? 

then what how are we getting the k values to plot the band structure. The values in the data file looks different from these values. 

Another question is, which unit is followed in QE? 
a.u. (hbar = e^2 = m_e = 1, energy? in Hartree)? or Rydberg unit ( hbar=1, e^2=2, m_e=1/2, energy in rydberg).

Sometimes the output energy is given in eV and sometimes in Rydberg. This is confusing that which unit is followed in QE.

please suggest on these two points. 
Regards


Padmaja Patnaik
Research Scholar
Dept of Physics
IIT Bombay
Mumbai, India
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From jiachenchem at gmail.com  Thu Nov 17 22:21:01 2011
From: jiachenchem at gmail.com (Jia Chen)
Date: Thu, 17 Nov 2011 16:21:01 -0500
Subject: [Pw_forum] question about input files in pseudopotential library
Message-ID: <CADa2diYB_ONiAtiOJZ5t=xyJxw3ucsG6fNs4FBAHZd1o=A_q4w@mail.gmail.com>

Dear All,

I was really happy to find the input file of pseudopotential we need in
pseudopotential library. After looking into the file, there is one thing I
don't quite understand. For example, the USPP of Bi in
pslibrary.0.2.2/us_ps_collection.job
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&input
  title='Br',
  zed=35.,
  rel=$nrel,
  config='[Ar] 3d10.0 4s2.0 4p5.0 4d-2.0',
  iswitch=3,
  dft='$gfun'
/
&inputp
  pseudotype=3,
  file_pseudopw='Br.$fct-rrkjus.UPF',
  author='ADC',
  lloc=2,
  which_augfun='PSQ',
  rmatch_augfun=1.6,
  nlcc=.true.,
  new_core_ps=.true.,
  rcore=1.4,
  tm=.true.
/
5
4S  1  0  2.00  0.00  1.70  1.90  0.0
...
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
As far as I know,  tm=.true. means the pseudopotential is in
*Troullier-Martins form.
But I guess the intention of this input file is to make USPP in RRKJ form,
and I havn't seen many USPP in **Troullier-Martins form. I wonder it is my
misunderstanding or a small mistake in the input file. Thank you very much.*
-- 
Jia Chen
Graduate Student
Dept of Chemistry
Princeton University
Princeton, NJ 08544
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From giannozz at democritos.it  Thu Nov 17 22:49:19 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 17 Nov 2011 22:49:19 +0100
Subject: [Pw_forum] question about input files in pseudopotential library
In-Reply-To: <CADa2diYB_ONiAtiOJZ5t=xyJxw3ucsG6fNs4FBAHZd1o=A_q4w@mail.gmail.com>
References: <CADa2diYB_ONiAtiOJZ5t=xyJxw3ucsG6fNs4FBAHZd1o=A_q4w@mail.gmail.com>
Message-ID: <175FE3A3-BB05-4472-83C7-53A7AF474935@democritos.it>


On Nov 17, 2011, at 22:21 , Jia Chen wrote:
>   tm=.true.
> [...] As far as I know,  tm=.true. means the pseudopotential
> is in Troullier-Martins form.

no, it means that the Troullier-Martins pseudization is used
(instead of the Rabe-Rappe-Kaxiras-Joannopoulos pseudization)
but not that the pseudopotential is generatedin the semi-local
form (pseudotype=1)

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 jiachenchem at gmail.com  Thu Nov 17 23:01:57 2011
From: jiachenchem at gmail.com (Jia Chen)
Date: Thu, 17 Nov 2011 17:01:57 -0500
Subject: [Pw_forum] question about input files in pseudopotential library
In-Reply-To: <175FE3A3-BB05-4472-83C7-53A7AF474935@democritos.it>
References: <CADa2diYB_ONiAtiOJZ5t=xyJxw3ucsG6fNs4FBAHZd1o=A_q4w@mail.gmail.com>
	<175FE3A3-BB05-4472-83C7-53A7AF474935@democritos.it>
Message-ID: <CADa2diYKHX69CbAxfsB-xHu9sAw+kuCOqKVmFE+q+=u9FamqKQ@mail.gmail.com>

Thank you very much for your answer. For me, the
file_pseudopw='Br.$fct-rrkjus.UPF' is still a little bit confusing, what do
you think?

On Thu, Nov 17, 2011 at 4:49 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Nov 17, 2011, at 22:21 , Jia Chen wrote:
> >   tm=.true.
> > [...] As far as I know,  tm=.true. means the pseudopotential
> > is in Troullier-Martins form.
>
> no, it means that the Troullier-Martins pseudization is used
> (instead of the Rabe-Rappe-Kaxiras-Joannopoulos pseudization)
> but not that the pseudopotential is generatedin the semi-local
> form (pseudotype=1)
>
> 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
>



-- 
Jia Chen

Dept of Chemistry
Princeton University
Princeton, NJ 08544
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From lorenzo.paulatto at impmc.upmc.fr  Thu Nov 17 23:05:41 2011
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 17 Nov 2011 23:05:41 +0100
Subject: [Pw_forum] question about input files in pseudopotential library
In-Reply-To: <CADa2diYB_ONiAtiOJZ5t=xyJxw3ucsG6fNs4FBAHZd1o=A_q4w@mail.gmail.com>
References: <CADa2diYB_ONiAtiOJZ5t=xyJxw3ucsG6fNs4FBAHZd1o=A_q4w@mail.gmail.com>
Message-ID: <op.v432bruu5jfbqb@paulax>

In data 17 novembre 2011 alle ore 22:21:01, Jia Chen  
<jiachenchem at gmail.com> ha scritto:
> As far as I know,  tm=.true. means the pseudopotential is in
> *Troullier-Martins form.
> But I guess the intention of this input file is to make USPP in RRKJ  
> form, and I havn't seen many USPP in **Troullier-Martins form. I wonder  
> it is my misunderstanding or a small mistake in the input file. Thank  
> you very much.*

Ultra-soft pesudopotentials are build on top of a very hard  
norm-conserving pseupotential; this is not the original formulation by  
Vanderbilt, but as far as I know, widely used and accepted nowadays.

In this specific case, the norm-conserving pseudo uses the  
Troullier-Martins formulation.

best regards


-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From jiachenchem at gmail.com  Thu Nov 17 23:15:52 2011
From: jiachenchem at gmail.com (Jia Chen)
Date: Thu, 17 Nov 2011 17:15:52 -0500
Subject: [Pw_forum] question about input files in pseudopotential library
In-Reply-To: <op.v432bruu5jfbqb@paulax>
References: <CADa2diYB_ONiAtiOJZ5t=xyJxw3ucsG6fNs4FBAHZd1o=A_q4w@mail.gmail.com>
	<op.v432bruu5jfbqb@paulax>
Message-ID: <CADa2diZNeOmv08y9jwci4BEJ2TSOd3KALNPxamrGbmB15ETdpA@mail.gmail.com>

I see, really appreciate it.

On Thu, Nov 17, 2011 at 5:05 PM, Lorenzo Paulatto <
lorenzo.paulatto at impmc.upmc.fr> wrote:

> In data 17 novembre 2011 alle ore 22:21:01, Jia Chen
> <jiachenchem at gmail.com> ha scritto:
> > As far as I know,  tm=.true. means the pseudopotential is in
> > *Troullier-Martins form.
> > But I guess the intention of this input file is to make USPP in RRKJ
> > form, and I havn't seen many USPP in **Troullier-Martins form. I wonder
> > it is my misunderstanding or a small mistake in the input file. Thank
> > you very much.*
>
> Ultra-soft pesudopotentials are build on top of a very hard
> norm-conserving pseupotential; this is not the original formulation by
> Vanderbilt, but as far as I know, widely used and accepted nowadays.
>
> In this specific case, the norm-conserving pseudo uses the
> Troullier-Martins formulation.
>
> best regards
>
>
> --
> Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www.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
>



-- 
Jia Chen

Dept of Chemistry
Princeton University
Princeton, NJ 08544
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From vranjan at ncsu.edu  Thu Nov 17 23:11:27 2011
From: vranjan at ncsu.edu (Vivek Ranjan)
Date: Thu, 17 Nov 2011 17:11:27 -0500
Subject: [Pw_forum] n_diag
Message-ID: <CAGwtzADk2MgBFSFDpL0pekFNLOVyKfVfPFPO_WVjdE0D4siTgg@mail.gmail.com>

To Paolo,

In the following paper:
http://www.fisica.uniud.it/~giannozz/Papers/rimini08.pdf
you write n^2_diag <= n_pw

However, the example given in the user guide (
http://quantum-espresso.org/user_guide/node18.html) is
ndiag = 144 and n_pw = 256

In this example ndiag^2 > n_pw

Is the intent here simple ndiag <= n_pw where ndiag = n**2

Thanks,

Vivek Ranjan
Physics, NCSU
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From 1009ukumar at gmail.com  Fri Nov 18 04:47:31 2011
From: 1009ukumar at gmail.com (Sonu Kumar)
Date: Fri, 18 Nov 2011 09:17:31 +0530
Subject: [Pw_forum] Re :question about input files in pseudopotential library
Message-ID: <CAHePdfDECHNNTz1Byb5dkr38j0Pt4+zZcdFP77NLe2qd_wnEJQ@mail.gmail.com>

Hi Jia Chen,

tm = true, means

.true. for Troullier-Martins pseudization [PRB 43, 1993 (1991)]

.false. for Rabe-Rappe-Kaxiras-Joannopoulos pseudization
  [PRB 41, 1227 (1990), erratum PRB 44, 13175 (1991)]

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

From 1009ukumar at gmail.com  Fri Nov 18 05:03:37 2011
From: 1009ukumar at gmail.com (Sonu Kumar)
Date: Fri, 18 Nov 2011 09:33:37 +0530
Subject: [Pw_forum] units in QE (thread renamed from k point value)
Message-ID: <CAHePdfCiCosEzm6Bv+F8=LhHoC3fvzVor0RwV9B2bGkTjnO8Ug@mail.gmail.com>

Hi Padmaja,

>Another question is, which unit is followed in QE?
>a.u. (hbar = e^2 = m_e = 1, energy? in Hartree)? or Rydberg unit ( hbar=1, e^2=2, m_e=1/2, energy in rydberg).

QE uses atomic rydberg units, so units of  angular momentum is  h bar,
the unit for mass is 2m_e ,unit for charge is e/sqrt(2), and unit of energy is
rydberg. wheras abinit uses hartree atomic units.

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

From renpj at dicp.ac.cn  Fri Nov 18 06:44:47 2011
From: renpj at dicp.ac.cn (Ren PJ)
Date: Fri, 18 Nov 2011 13:44:47 +0800
Subject: [Pw_forum] gipaw parallel run is too slow
Message-ID: <20111118134447.2b8cc28b@ren-desktop>


Dear QE users,
The kpoint of my job is set to 1*1*10, so I run gipaw.x in parallel mode
by :
mpirun -np 160 gipaw.x -npool 5 <input>output
The calculation was done on cluster, each node contain 8 processors.
It can't finished after 20 hours.
But when I run it on single node by:
mpirun -np 8 gipaw.x <input>output
Each kpoint calculation only need 4h30min and takes 24h in total.
Is there any thing wrong?

Thank you.
 
================================================
Pengju Ren
renpj at dicp.ac.cn
State  Key Laboratory of Catalysis, 
Dalian Institute of Chemical Physics, 
Chinese Academy of Sciences 
457 zhongshan Road, Dalian, 116023, P.R. China  

From mohnish.iitk at gmail.com  Fri Nov 18 07:32:36 2011
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Fri, 18 Nov 2011 12:02:36 +0530
Subject: [Pw_forum] k point value
In-Reply-To: <1321552031.2565.YahooMailNeo@web28515.mail.ukl.yahoo.com>
References: <1321552031.2565.YahooMailNeo@web28515.mail.ukl.yahoo.com>
Message-ID: <CAMhNW-cN+GNSDua2ErhEr5Y=-E4gLU-RJbAcoZoxp7_rNtcwww@mail.gmail.com>

Dear Padmaja,

These k-values are the k-points in high symmetry direction which you choose
to plot the band structure. Automatic grid generated for "scf" calculation
if often not suitable for band-structure plot so we choose a high symmetry
direction and discretize the reciprocal space in that direction. These are
called special k-points for band structure plot. You can write a small code
to generate a mesh with given high symmetry special k-points. And regarding
the answer to your second question the unit of the total energy is always
in Ryd. Its not a very big issue to figure out. Generally the fermi energy
and in few more cases the energy could be in eV. Hope this helps.

On Thu, Nov 17, 2011 at 11:17 PM, Padmaja Patnaik <
padmaja_patnaik at yahoo.co.uk> wrote:

> Dear all
> I am using QE since last few yeras but still could not answer few
> questions a new student in my lab asked me. When we are doing band plot its
> a curve between k~E.  In the input file we give ka values as,
>
>    0.0  0.0  0.0
>    0.0  0.0  0.1
>    0.0  0.0  0.2
>    0.0  0.0  0.3
>    0.0  0.0  0.4
>
> then what how are we getting the k values to plot the band structure. The
> values in the data file looks different from these values.
>
> Another question is, which unit is followed in QE?
> a.u. (hbar = e^2 = m_e = 1, energy  in Hartree)  or Rydberg unit ( hbar=1,
> e^2=2, m_e=1/2, energy in rydberg).
>
> Sometimes the output energy is given in eV and sometimes in Rydberg. This
> is confusing that which unit is followed in QE.
>
> please suggest on these two points.
> Regards
>
> Padmaja Patnaik
> Research Scholar
> Dept of Physics
> IIT Bombay
> Mumbai, India
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
BTech-Mtech, IIT Kanpur
Senior Project Associate,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
-----------------------------------------------------------------
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From swapnil.chandratre at gmail.com  Fri Nov 18 07:56:50 2011
From: swapnil.chandratre at gmail.com (swapnil chandratre)
Date: Fri, 18 Nov 2011 00:56:50 -0600
Subject: [Pw_forum] error in berry phase calculation
Message-ID: <CAJTZp8dbM_0Rz5xSmcus4QMzHjxsS0DgO9+2kqQ2dSOfdjJv+g@mail.gmail.com>

Hello,


 I am trying to implement berry phase calculation in my system. I perform
the scf calculation, but when I perform the nscf berry phase calculation,
 I receive the following error


     Program PWSCF v.4.3        starts on 17Nov2011 at  4:30:26

     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    24 processors
     R & G space division:  proc/pool =   24

     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...
Warning: card   C   5.000000E+00  2.062549E+01  1.458701E+01 ignored
Warning: card   C   5.000000E+00  1.996076E+01  1.584846E+01 ignored
Warning: card   C   5.000000E+00  1.851058E+01  1.843571E+01 ignored
Warning: card   C   5.000000E+00  1.778213E+01  1.965974E+01 ignored
Warning: card   C   5.000000E+00  2.062377E+01  1.710620E+01 ignored
Warning: card   C   5.000000E+00  1.989944E+01  1.839861E+01 ignored
Warning: card   C   5.000000E+00  1.848278E+01  2.092890E+01 ignored
Warning: card   C   5.000000E+00  1.776496E+01  2.219382E+01 ignored
Warning: card   C   5.000000E+00  2.061447E+01  1.966058E+01 ignored
Warning: card   C   5.000000E+00  1.990127E+01  2.092352E+01 ignored
Warning: card   C   5.000000E+00  1.847370E+01  2.345806E+01 ignored
Warning: card   C   5.000000E+00  1.776142E+01  2.472063E+01 ignored



basically the same error is repeated for the each atom defined. After this
the simulation stops ?

Has anyone met such problem before ?


-- 
Regards,
Swapnil Chandratre
Graduate Student
Dept. of Mechanical Engineering,
University of Houston,
Houston, TX
(M)-713-294-9546
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From Lorenzo.Paulatto at impmc.upmc.fr  Fri Nov 18 10:54:56 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Fri, 18 Nov 2011 10:54:56 +0100
Subject: [Pw_forum] gipaw parallel run is too slow
In-Reply-To: <20111118134447.2b8cc28b@ren-desktop>
References: <20111118134447.2b8cc28b@ren-desktop>
Message-ID: <op.v44y5uqlxuur8c@vanoxite.impmc.jussieu.fr>

On Fri, 18 Nov 2011 06:44:47 +0100, Ren PJ <renpj at dicp.ac.cn> wrote:
> mpirun -np 160 gipaw.x -npool 5 <input>output
> It can't finished after 20 hours.
> ...
> mpirun -np 8 gipaw.x <input>output
> Each kpoint calculation only need 4h30min and takes 24h in total.

Dear Pengju Ren,
when you increase the numebr of processors you increase the available  
computing power, but also the amount of communications on the network  
connectign those nodes. As the network has a finite speed, there will be a  
point where the code looses more time exchanging information between the  
cpus than doing any calculation.

Possible solutions:
1. use fewer cpus (between 8 and 160 there is plenty of space)
2. try with a different number of pools (you could try  
nkpoints*ncores_per_node)
3. buy some faster network hardware

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 renpj at dicp.ac.cn  Fri Nov 18 12:34:42 2011
From: renpj at dicp.ac.cn (Ren PJ)
Date: Fri, 18 Nov 2011 19:34:42 +0800
Subject: [Pw_forum] gipaw parallel run is too slow
In-Reply-To: <op.v44y5uqlxuur8c@vanoxite.impmc.jussieu.fr>
References: <20111118134447.2b8cc28b@ren-desktop>
	<op.v44y5uqlxuur8c@vanoxite.impmc.jussieu.fr>
Message-ID: <20111118193442.3a4c205e@ren-desktop>

On Fri, 18 Nov 2011 10:54:56 +0100

> Dear Pengju Ren,
> when you increase the numebr of processors you increase the
> available computing power, but also the amount of communications on
> the network connectign those nodes. As the network has a finite
> speed, there will be a point where the code looses more time
> exchanging information between the cpus than doing any calculation.
> 
> Possible solutions:
> 1. use fewer cpus (between 8 and 160 there is plenty of space)
> 2. try with a different number of pools (you could try  
> nkpoints*ncores_per_node)
> 3. buy some faster network hardware
> 
> best regards
> 

Dear Lorenzo Paulatto,
Thanks for your kind answer.
When I ran pw.x with 160 cpus it was about 10 times faster than with 8
cpus, I think the parallel efficiency is reasonable. So does gipaw.x
need more communications between nodes than pw.x? Maybe the gipaw code
could be improved by reducing the communication frequency.

Best Wishes

================================================
???
Pengju Ren
renpj at dicp.ac.cn
State  Key Laboratory of Catalysis, 
Dalian Institute of Chemical Physics, 
Chinese Academy of Sciences 
457 zhongshan Road, Dalian, 116023, P.R. China  

From lmartinsamos at gmail.com  Fri Nov 18 12:31:05 2011
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Fri, 18 Nov 2011 12:31:05 +0100
Subject: [Pw_forum] gipaw parallel run is too slow
In-Reply-To: <20111118193442.3a4c205e@ren-desktop>
References: <20111118134447.2b8cc28b@ren-desktop>
	<op.v44y5uqlxuur8c@vanoxite.impmc.jussieu.fr>
	<20111118193442.3a4c205e@ren-desktop>
Message-ID: <CAGCSmJTXxwwHkcm+j_h4rR8a03JZ5bbcRnUwgDdbpgRaFJmnzw@mail.gmail.com>

Dear Ren, there is at moment a big effort done in this direction from the
computational center in Irland (ICHEC) and the developers of QE-GIPAW (see
http://qe-forge.org/projects/qe-gipaw/).

bests

Layla

2011/11/18 Ren PJ <renpj at dicp.ac.cn>

> On Fri, 18 Nov 2011 10:54:56 +0100
>
> > Dear Pengju Ren,
> > when you increase the numebr of processors you increase the
> > available computing power, but also the amount of communications on
> > the network connectign those nodes. As the network has a finite
> > speed, there will be a point where the code looses more time
> > exchanging information between the cpus than doing any calculation.
> >
> > Possible solutions:
> > 1. use fewer cpus (between 8 and 160 there is plenty of space)
> > 2. try with a different number of pools (you could try
> > nkpoints*ncores_per_node)
> > 3. buy some faster network hardware
> >
> > best regards
> >
>
> Dear Lorenzo Paulatto,
> Thanks for your kind answer.
> When I ran pw.x with 160 cpus it was about 10 times faster than with 8
> cpus, I think the parallel efficiency is reasonable. So does gipaw.x
> need more communications between nodes than pw.x? Maybe the gipaw code
> could be improved by reducing the communication frequency.
>
> Best Wishes
>
> ================================================
> ???
> Pengju Ren
> renpj at dicp.ac.cn
> State  Key Laboratory of Catalysis,
> Dalian Institute of Chemical Physics,
> Chinese Academy of Sciences
> 457 zhongshan Road, Dalian, 116023, P.R. China
> _______________________________________________
> 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 Nov 18 12:43:14 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 18 Nov 2011 12:43:14 +0100
Subject: [Pw_forum] error in berry phase calculation
In-Reply-To: <CAJTZp8dbM_0Rz5xSmcus4QMzHjxsS0DgO9+2kqQ2dSOfdjJv+g@mail.gmail.com>
References: <CAJTZp8dbM_0Rz5xSmcus4QMzHjxsS0DgO9+2kqQ2dSOfdjJv+g@mail.gmail.com>
Message-ID: <1321616594.4401.3.camel@fe12lx.fisica.uniud.it>

On Fri, 2011-11-18 at 00:56 -0600, swapnil chandratre wrote:


> Warning: card   C   5.000000E+00  2.062549E+01  1.458701E+01 ignored
> Warning: card   C   5.000000E+00  1.996076E+01  1.584846E+01 ignored
> Warning: card   C   5.000000E+00  1.851058E+01  1.843571E+01 ignored
> Warning: card   C   5.000000E+00  1.778213E+01  1.965974E+01 ignored
> Warning: card   C   5.000000E+00  2.062377E+01  1.710620E+01 ignored
> Warning: card   C   5.000000E+00  1.989944E+01  1.839861E+01 ignored
> Warning: card   C   5.000000E+00  1.848278E+01  2.092890E+01 ignored
> Warning: card   C   5.000000E+00  1.776496E+01  2.219382E+01 ignored
> Warning: card   C   5.000000E+00  2.061447E+01  1.966058E+01 ignored
> Warning: card   C   5.000000E+00  1.990127E+01  2.092352E+01 ignored
> Warning: card   C   5.000000E+00  1.847370E+01  2.345806E+01 ignored
> Warning: card   C   5.000000E+00  1.776142E+01  2.472063E+01 ignored

you have more atom cards than atoms (or a wrong "nat")

P.

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



From giannozz at democritos.it  Fri Nov 18 12:53:55 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 18 Nov 2011 12:53:55 +0100
Subject: [Pw_forum] n_diag
In-Reply-To: <CAGwtzADk2MgBFSFDpL0pekFNLOVyKfVfPFPO_WVjdE0D4siTgg@mail.gmail.com>
References: <CAGwtzADk2MgBFSFDpL0pekFNLOVyKfVfPFPO_WVjdE0D4siTgg@mail.gmail.com>
Message-ID: <1321617235.4401.10.camel@fe12lx.fisica.uniud.it>

On Thu, 2011-11-17 at 17:11 -0500, Vivek Ranjan wrote:

> However, the example given in the user guide
> (http://quantum-espresso.org/user_guide/node18.html) is
> ndiag = 144 and n_pw = 256
> 
> In this example ndiag^2 > n_pw 

the example given in the user guide is consistent with how
the code works (i.e. you specify -ndiag N^2 to use N^2 
processors in scalapck diagonalization). The paper you mention 
(not a memorable one, by the way) uses a different convention
(ndiag=N, not N^2) . Thank you for remarking this

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



From giannozz at democritos.it  Fri Nov 18 13:05:07 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 18 Nov 2011 13:05:07 +0100
Subject: [Pw_forum] k point value
In-Reply-To: <1321552031.2565.YahooMailNeo@web28515.mail.ukl.yahoo.com>
References: <1321552031.2565.YahooMailNeo@web28515.mail.ukl.yahoo.com>
Message-ID: <1321617907.4401.17.camel@fe12lx.fisica.uniud.it>

On Thu, 2011-11-17 at 17:47 +0000, Padmaja Patnaik wrote:

> then what how are we getting the k values to plot the band structure.
> The values in the data file looks different from these values. 

if you are referring to the x axis in the plot: it is the distance 
from the first k-point, calculated along the provided k-point path.
It's what you need to get a band plot the looks like a band plot.

> Another question is, which unit is followed in QE? 
> a.u. (hbar = e^2 = m_e = 1, energy  in Hartree)  or Rydberg unit
> ( hbar=1, e^2=2, m_e=1/2, energy in rydberg).

CP uses Hartree, all other codes use Ry. Occasional usage of other 
units is typicalluy clearly stated.

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



From giannozz at democritos.it  Fri Nov 18 13:09:35 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 18 Nov 2011 13:09:35 +0100
Subject: [Pw_forum] QHA frequency is higher than *.freq
In-Reply-To: <COL113-W27BB0510F96FED4C05D0BC8C70@phx.gbl>
References: <COL113-W60CEBD49552B277D2F7BC8C8DC0@phx.gbl>
	,, , <COL113-W6531F4056497CDE2F640E1C8DD0@phx.gbl>
	,, <COL113-W29A4F4173D14BAEB988022C8C30@phx.gbl>
	, <COL113-W37056841977DF615C85DE4C8C60@phx.gbl>
	, <1321440919.6762.8.camel@fe12lx.fisica.uniud.it>
	<COL113-W27BB0510F96FED4C05D0BC8C70@phx.gbl>
Message-ID: <1321618175.4401.23.camel@fe12lx.fisica.uniud.it>

On Thu, 2011-11-17 at 01:41 +0000, KangYun Song wrote:

> The main problem is the frequency of matdyn.x (asr=crystal)which the
> k-point is from tetra.x

what is tetra.x?

> is very higher the matdyn.x(asr=simple) which the k-point is get it 
> from xcrysden. And I calculate other structure is not met this problem.

it is hard to say anything on the basis of such information (or lack of
it)

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



From giannozz at democritos.it  Fri Nov 18 13:54:38 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 18 Nov 2011 13:54:38 +0100
Subject: [Pw_forum] 'wf_collect' question
In-Reply-To: <BLU0-SMTP428343E575FD80758E699B380C60@phx.gbl>
References: <BLU0-SMTP428343E575FD80758E699B380C60@phx.gbl>
Message-ID: <1321620878.4401.38.camel@fe12lx.fisica.uniud.it>

On Wed, 2011-11-16 at 14:43 -0500, Lai Jiang wrote:

> When setting startingwfc = 'file' the program is supposed to read
>  wfc files from a previous run. But if the previous run uses
> 'wf_collect' =  .true. the wfc are deleted after scf and converted to
> evc.dat files at each k point and can not be used as startingwfc. It
> is really confusing to me that wf_collect does the opposite of what it
> is supposed to do.

wf_collect does what it is supposed to do: collect the various pieces
of wavefunctions, scattered across processors, into a single file (per
k-point) whose format does not depend upon the number of processors.
This is the file to be used for further processing (e.g. PDOS, phonons).

startingwfc = 'file' was introduced to restart from a previous 
interrupted run.  It may be used for other purposes as well, but
apparently this case has never been updated to read the "collected" 
file format, because nobody has ever felt the need for it. 

As a quick and dirty solution, you may just edit the part of the
code that removes the wavefunction files at the end. In 
PW/close_files.f90 remove "twfcollect" from the IF:

  !  ... close buffer/file containing wavefunctions: discard if
  !  ... wavefunctions are written in xml format, save otherwise
  !
  IF ( lflag .AND. (twfcollect .OR. io_level < 0 )) THEN
     CALL close_buffer ( iunwfc, 'DELETE' )
  ELSE
     CALL close_buffer ( iunwfc, 'KEEP' )
  END IF

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



From giannozz at democritos.it  Fri Nov 18 14:11:44 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 18 Nov 2011 14:11:44 +0100
Subject: [Pw_forum] Obtaining SCF convergence for Relax Calculation
In-Reply-To: <CALf5jvosz7dCn5-q2b57ED5eO6rxdUcdRRdKgXG7xG=kYBB83g@mail.gmail.com>
References: <CALf5jvosz7dCn5-q2b57ED5eO6rxdUcdRRdKgXG7xG=kYBB83g@mail.gmail.com>
Message-ID: <1321621904.4401.48.camel@fe12lx.fisica.uniud.it>

On Wed, 2011-11-16 at 10:14 -0500, Michael Mrozik wrote:

> is there a place/table/listing where the actual determined/calculated
> values for U are maintained apart from just buried in the literature?

not that I know

>  The input description of pwscf indicates that I need to include
> values for all atoms in  my system

where is this written? You have to include U for all atoms that need it,
typically only transition metals (but not always)

>    starting_magnetization(1) = 1,
>    starting_magnetization(2) = -1,

too much: this will assume that all Fe states are fully polarized.
Not that it will make any difference though

>                  occupations = 'fixed',

you should use smearing: with fixed occupancies you may easily
run into convergence problems if you system is not an insulator
(sometimes, even if it is)

>                  mixing_mode = 'local-TF',

this is mostly useful for surface. Is this one?

>              diagonalization = 'cg',

typically much slower than the default ('david')

>                  startingpot = 'random' ,
>                  startingwfc = 'random', 

I would leave the default values for these two

P.

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



From giannozz at democritos.it  Fri Nov 18 14:16:35 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 18 Nov 2011 14:16:35 +0100
Subject: [Pw_forum] parallel computing for phonon calculations
In-Reply-To: <DUB110-W1008678C0D46C001DD89DAD3C60@phx.gbl>
References: <DUB110-W1008678C0D46C001DD89DAD3C60@phx.gbl>
Message-ID: <1321622195.4401.51.camel@fe12lx.fisica.uniud.it>

On Wed, 2011-11-16 at 13:51 +0000, Elie M wrote:

>  Is it efficient to use parallel computing in QE for doing the phonon
> calculations? 

it is, or more exactly: it can be, but you have to understand how 
parallelism works and what you are doing 

P.

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



From swapnil.chandratre at gmail.com  Fri Nov 18 15:44:07 2011
From: swapnil.chandratre at gmail.com (swapnil chandratre)
Date: Fri, 18 Nov 2011 08:44:07 -0600
Subject: [Pw_forum] error in berry phase calculation
In-Reply-To: <1321616594.4401.3.camel@fe12lx.fisica.uniud.it>
References: <CAJTZp8dbM_0Rz5xSmcus4QMzHjxsS0DgO9+2kqQ2dSOfdjJv+g@mail.gmail.com>
	<1321616594.4401.3.camel@fe12lx.fisica.uniud.it>
Message-ID: <CAJTZp8d80K4mN=VBDMOXz9fN_LtDwT3OPAjeBjUma-OcjnAh4w@mail.gmail.com>

Thank you, Paolo.
On Nov 18, 2011 5:43 AM, "Paolo Giannozzi" <giannozz at democritos.it> wrote:

> On Fri, 2011-11-18 at 00:56 -0600, swapnil chandratre wrote:
>
>
> > Warning: card   C   5.000000E+00  2.062549E+01  1.458701E+01 ignored
> > Warning: card   C   5.000000E+00  1.996076E+01  1.584846E+01 ignored
> > Warning: card   C   5.000000E+00  1.851058E+01  1.843571E+01 ignored
> > Warning: card   C   5.000000E+00  1.778213E+01  1.965974E+01 ignored
> > Warning: card   C   5.000000E+00  2.062377E+01  1.710620E+01 ignored
> > Warning: card   C   5.000000E+00  1.989944E+01  1.839861E+01 ignored
> > Warning: card   C   5.000000E+00  1.848278E+01  2.092890E+01 ignored
> > Warning: card   C   5.000000E+00  1.776496E+01  2.219382E+01 ignored
> > Warning: card   C   5.000000E+00  2.061447E+01  1.966058E+01 ignored
> > Warning: card   C   5.000000E+00  1.990127E+01  2.092352E+01 ignored
> > Warning: card   C   5.000000E+00  1.847370E+01  2.345806E+01 ignored
> > Warning: card   C   5.000000E+00  1.776142E+01  2.472063E+01 ignored
>
> you have more atom cards than atoms (or a wrong "nat")
>
> 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
>
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From trambui at u.boisestate.edu  Fri Nov 18 23:18:45 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Fri, 18 Nov 2011 15:18:45 -0700
Subject: [Pw_forum] US pseudopotential generation
Message-ID: <CANzxBn8v1mV0Ccy_ecuswdA=eCAsBYN0LWHPcG5t1awepX48Bw@mail.gmail.com>

Dear Everyone,
     I have tried to generate a USPP of Cs with electron configuration of
[Xe]6s1, but now if I want to include the 5s and 5p states in the valence.
How should I write the new configuration for the input file? i.e. now [Xe]
can't be used as the core anymore, and I remember that the core has to be a
noble gas, so if I include 5s 5p 6s states for the valence, then what will
be done for the core? I really appreciate for all your help!

Regards,

Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From dstrubbe at berkeley.edu  Sat Nov 19 00:25:07 2011
From: dstrubbe at berkeley.edu (David Strubbe)
Date: Fri, 18 Nov 2011 15:25:07 -0800
Subject: [Pw_forum] crash in pslibrary.0.2.2
Message-ID: <CAENVOuXuCztDJzE-mQn8+AdRo+095g_TvZ0ZdW8KtEesPV8gPw@mail.gmail.com>

Dear QE developers,

I would like to report some problems with pslibrary.0.2.2. Everything works
fine for me when I do make_all_ps, except the input files below which cause
ld1 to crash with the respective error messages, which occur consistently.

David Strubbe
UC Berkeley


Bi.pbe-rrkjus.in, Bi.pz-rrkjus.in, Bi.rel-pz-rrkjus.in, Bi.rel-pbe-rrkjus.in

     from compute_q_3bess : error #         1
     problem with the q_i coefficients

Ti.pbe-nc.in

     from run_pseudo : error #         1
     Errors in PS-KS equation
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From nicola.marzari at epfl.ch  Sat Nov 19 00:29:50 2011
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Sat, 19 Nov 2011 00:29:50 +0100
Subject: [Pw_forum] crash in pslibrary.0.2.2
In-Reply-To: <CAENVOuXuCztDJzE-mQn8+AdRo+095g_TvZ0ZdW8KtEesPV8gPw@mail.gmail.com>
References: <CAENVOuXuCztDJzE-mQn8+AdRo+095g_TvZ0ZdW8KtEesPV8gPw@mail.gmail.com>
Message-ID: <4EC6EA6E.4090706@epfl.ch>



Hi David,


it worked for me a couple of days ago, with gfortran/gcc on a Macbook
Air. Can you try a couple of different compilers, or platforms, to see 
if that solves it?

			nicola



On 11/19/11 12:25 AM, David Strubbe wrote:
> Dear QE developers,
>
> I would like to report some problems with pslibrary.0.2.2. Everything
> works fine for me when I do make_all_ps, except the input files below
> which cause ld1 to crash with the respective error messages, which occur
> consistently.
>
> David Strubbe
> UC Berkeley
>
>
> Bi.pbe-rrkjus.in <http://Bi.pbe-rrkjus.in>, Bi.pz-rrkjus.in
> <http://Bi.pz-rrkjus.in>, Bi.rel-pz-rrkjus.in
> <http://Bi.rel-pz-rrkjus.in>, Bi.rel-pbe-rrkjus.in
> <http://Bi.rel-pbe-rrkjus.in>
>
> from compute_q_3bess : error # 1
> problem with the q_i coefficients
>
> Ti.pbe-nc.in <http://Ti.pbe-nc.in>
>
> from run_pseudo : error # 1
> Errors in PS-KS equation
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 

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

From dstrubbe at berkeley.edu  Sun Nov 20 08:32:22 2011
From: dstrubbe at berkeley.edu (David Strubbe)
Date: Sat, 19 Nov 2011 23:32:22 -0800
Subject: [Pw_forum] crash in pslibrary.0.2.2
In-Reply-To: <4EC6EA6E.4090706@epfl.ch>
References: <CAENVOuXuCztDJzE-mQn8+AdRo+095g_TvZ0ZdW8KtEesPV8gPw@mail.gmail.com>
	<4EC6EA6E.4090706@epfl.ch>
Message-ID: <CAENVOuWbF=ae_K+3nxa0v1_j-QSrbYVp5buH_965VXFziCoPew@mail.gmail.com>

Hi Nicola,

This was with ifort 11.1 -O3, running in parallel. In serial only the Ti
pseudo failed. I tried again with PGI on a Cray machine and everything
succeeded. So this is certainly a compiler-dependent issue. Just wanted to
bring it to the developers' attention.

David

2011/11/18 Nicola Marzari <nicola.marzari at epfl.ch>

>
>
> Hi David,
>
>
> it worked for me a couple of days ago, with gfortran/gcc on a Macbook
> Air. Can you try a couple of different compilers, or platforms, to see if
> that solves it?
>
>                        nicola
>
>
>
>
> On 11/19/11 12:25 AM, David Strubbe wrote:
>
>> Dear QE developers,
>>
>> I would like to report some problems with pslibrary.0.2.2. Everything
>> works fine for me when I do make_all_ps, except the input files below
>> which cause ld1 to crash with the respective error messages, which occur
>> consistently.
>>
>> David Strubbe
>> UC Berkeley
>>
>>
>> Bi.pbe-rrkjus.in <http://Bi.pbe-rrkjus.in>, Bi.pz-rrkjus.in
>> <http://Bi.pz-rrkjus.in>, Bi.rel-pz-rrkjus.in
>> <http://Bi.rel-pz-rrkjus.in>, Bi.rel-pbe-rrkjus.in
>> <http://Bi.rel-pbe-rrkjus.in>
>>
>>
>> from compute_q_3bess : error # 1
>> problem with the q_i coefficients
>>
>> Ti.pbe-nc.in <http://Ti.pbe-nc.in>
>>
>>
>> from run_pseudo : error # 1
>> Errors in PS-KS equation
>>
>>
>>
>> ______________________________**_________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/**mailman/listinfo/pw_forum<http://www.democritos.it/mailman/listinfo/pw_forum>
>>
>
>
> --
>
> ------------------------------**------------------------------**----------
> Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
>
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From avallabh at purdue.edu  Sun Nov 20 18:56:27 2011
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Sun, 20 Nov 2011 12:56:27 -0500 (EST)
Subject: [Pw_forum] Query on phonon dispersion
Message-ID: <978001911.140069.1321811787235.JavaMail.root@mailhub016.itcs.purdue.edu>

Dear users,

          I am trying to calculate phonon dispersion and DOS of graphene. I followed the procedure used for silicon in the tutorial with the necessary changes. But the phonon dispersion i obtained is not exactly the same as the one in literature. The ZO branch is particularly distorted and for one of the acoustic branches, the frequencies are slightly -ve near the gamma point. 
Any suggestions or thoughts in this regard are welcome. 

I want to know the answer for the following questions as well

i) Is "16x16x1" MP-grid size dense enough to obtain accurate result for graphene or do i need to increase it further? 
ii) What should be the value for "nbnds" for graphene? I used 8; but i read that for metals you may have to use a higher number. I tried 12 as well but i didnot see much difference in the end result. 
iii) In specifying the k-space coordinates to obtain frequencies at a point in the file "*.matdyn.in", what are the units for the co-ordinates? are they just (2*pi/alat) or crystal (in terms of reciprocal lattice vectors)? 

Thanks
Ajit

From lorenzo.paulatto at impmc.upmc.fr  Sun Nov 20 19:14:15 2011
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Sun, 20 Nov 2011 19:14:15 +0100
Subject: [Pw_forum] Query on phonon dispersion
In-Reply-To: <978001911.140069.1321811787235.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <978001911.140069.1321811787235.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <op.v49bl1ca5jfbqb@paulax>

In data 20 novembre 2011 alle ore 18:56:27, Ajit Vallabhaneni  
<avallabh at purdue.edu> ha scritto:
> I want to know the answer for the following questions as well

There is a lot of literature on the subject, please have a look at:
Phys. Rev. B 71, 205214
Phys. Rev. Lett. 93, 185503
Phys. Rev. Lett. 99, 176802


where all your question are answered (if I forgot something, feel free to  
come back to us)

best regards

-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From avallabh at purdue.edu  Sun Nov 20 21:51:12 2011
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Sun, 20 Nov 2011 15:51:12 -0500 (EST)
Subject: [Pw_forum] Query on phonon dispersion
In-Reply-To: <op.v49bl1ca5jfbqb@paulax>
Message-ID: <1662800490.140551.1321822272080.JavaMail.root@mailhub016.itcs.purdue.edu>

Paulatto,

            Thanks for your quick reply. But i still have doubts on my third question. It's more of a programming question which cannot be found in journal papers.

" iii) In specifying the k-space coordinates to obtain frequencies at a point in the file "*.matdyn.in", what are the units for the co-ordinates? are they just (2*pi/alat) or crystal (in terms of reciprocal lattice vectors)? "

 Also do you have experience on graphene? 

Thanks
Ajit

From giannozz at democritos.it  Sun Nov 20 22:14:17 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 20 Nov 2011 22:14:17 +0100
Subject: [Pw_forum] Query on phonon dispersion
In-Reply-To: <1662800490.140551.1321822272080.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <1662800490.140551.1321822272080.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <4FEF7A74-ACFE-4D5F-BB96-8EA75C69D056@democritos.it>


On Nov 20, 2011, at 21:51 , Ajit Vallabhaneni wrote:

> " iii) In specifying the k-space coordinates to obtain frequencies
> at a point in the file "*.matdyn.in", what are the units for the co- 
> ordinates?

2pi/a (it is written in the header of file matdyn.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 mtorabi at uwo.ca  Mon Nov 21 01:07:27 2011
From: mtorabi at uwo.ca (Amin Torabi)
Date: Sun, 20 Nov 2011 19:07:27 -0500
Subject: [Pw_forum] paw pp for Boron?
Message-ID: <CAEXRF5y1kA3wJhWMjqZDsJuBDY6QYFhS+bCToR=iY1eRjaQ0qg@mail.gmail.com>

Has anyone generated a paw pseudopotential for Boron? and willing to share
the UPF file?

Many thanks

-- 
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 w2agz at w2agz.com  Mon Nov 21 08:32:17 2011
From: w2agz at w2agz.com (W2AGZ)
Date: Sun, 20 Nov 2011 23:32:17 -0800
Subject: [Pw_forum] PlotPhon Examples
Message-ID: <a6b601cca81f$b3600a10$1a201e30$@w2agz.com>

To All (especially Eyvas),

 

Are the input scripts used to generate the .fc files for the two Al examples
and Fe from pw.x and ph.x available?

 

Thanks, -Paul

 

Paul Michael Grant, PhD

Physicist and Science Writer

Senior Life Fellow, American Physical Society

Fellow, Institute of Physics, United Kingdom

Staff Associate, Jet Propulsion Laboratory, NASA (2011)

Visiting Scholar, Applied Physics, Stanford (2005-2008)

EPRI Science Fellow (Retired)

IBM Research Staff Member Emeritus

Principal, W2AGZ Technologies

 <mailto:w2agz at w2agz.com> w2agz at w2agz.com

 <http://www.w2agz.com/> http://www.w2agz.com

 

 

 

 

 

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From w2agz at w2agz.com  Mon Nov 21 08:48:46 2011
From: w2agz at w2agz.com (W2AGZ)
Date: Sun, 20 Nov 2011 23:48:46 -0800
Subject: [Pw_forum] Segmentation Faults - Running QE-4.3.2 under Kubutu
	11.10 within Latest Oracle Virtualbox
Message-ID: <a70801cca822$012220b0$03666210$@w2agz.com>

To All,

 

I know segmentation faults are a constant nuisance given the multitude of
platforms on which we ask QE to perform, but I'm having consistent failures
trying to run the examples on a new Windows box I've built based on the
latest Win7 and Oracle VB (Yeah, Yeah.I know.just switch to Linux,
period.but I need to run antediluvian tasks from time to time).

 

The Forum blames most segmentation issues on virtual memory limitations.but
I have 100 gigs.

 

Thanks, -Paul

 

Paul Michael Grant, PhD

Physicist and Science Writer

Senior Life Fellow, American Physical Society

Fellow, Institute of Physics, United Kingdom

Staff Associate, Jet Propulsion Laboratory, NASA (2011)

Visiting Scholar, Applied Physics, Stanford (2005-2008)

EPRI Science Fellow (Retired)

IBM Research Staff Member Emeritus

Principal, W2AGZ Technologies

 <mailto:w2agz at w2agz.com> w2agz at w2agz.com

 <http://www.w2agz.com/> http://www.w2agz.com

 

 

 

 

 

 

 

 

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From flux_ray12 at 163.com  Mon Nov 21 09:29:40 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Mon, 21 Nov 2011 16:29:40 +0800 (CST)
Subject: [Pw_forum] PlotPhon Examples
In-Reply-To: <a6b601cca81f$b3600a10$1a201e30$@w2agz.com>
References: <a6b601cca81f$b3600a10$1a201e30$@w2agz.com>
Message-ID: <179a592.b148.133c53eb37a.Coremail.flux_ray12@163.com>

*.fc is generated from dynamics matrics by q2r.x.
The script in examples just organizes several programs, matdyn.x, k_for_bands.x, bands_to_gnuplot.x and E_min_max.x, working one by one with certain data exchanging.
Through pw.x and ph.x, you can just obtain dynamics matrics.


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


At 2011-11-21 15:32:17,W2AGZ <w2agz at w2agz.com> wrote:


To All (especially Eyvas),

 

Are the input scripts used to generate the .fc files for the two Al examples and Fe from pw.x and ph.x available?

 

Thanks, -Paul

 

Paul Michael Grant, PhD

Physicist and Science Writer

Senior Life Fellow, American Physical Society

Fellow, Institute of Physics, United Kingdom

Staff Associate, Jet Propulsion Laboratory, NASA (2011)

Visiting Scholar, Applied Physics, Stanford (2005-2008)

EPRI Science Fellow (Retired)

IBM Research Staff Member Emeritus

Principal, W2AGZ Technologies

w2agz at w2agz.com

http://www.w2agz.com

 

 

 

 

 
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From giannozz at democritos.it  Mon Nov 21 09:53:18 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 21 Nov 2011 09:53:18 +0100
Subject: [Pw_forum] Segmentation Faults - Running QE-4.3.2 under
	Kubutu	11.10 within Latest Oracle Virtualbox
In-Reply-To: <a70801cca822$012220b0$03666210$@w2agz.com>
References: <a70801cca822$012220b0$03666210$@w2agz.com>
Message-ID: <1321865598.18606.1.camel@fe12lx.fisica.uniud.it>

On Sun, 2011-11-20 at 23:48 -0800, W2AGZ wrote:

> The Forum blames most segmentation issues on virtual memory
> limitations?but I have 100 gigs.

not sure about whom the Forum blames; I tend to blame (unless 
there is evidence of the opposite) bad compilers for most 
"segmentation faults" 

P.

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



From kirtinandan07 at gmail.com  Mon Nov 21 10:24:58 2011
From: kirtinandan07 at gmail.com (vicky singh)
Date: Mon, 21 Nov 2011 14:54:58 +0530
Subject: [Pw_forum] ploting difference in charge density
Message-ID: <CANug7OwLrNb=TSqiNzurLCeUQg-7_w-Aug+c+qyKTsSM+p4fHQ@mail.gmail.com>

Dear PWSCF community,

I am comparing the effect of alloying on Ni system. I have ploted the
charge density with various alloying element. I wish to plot the difference
in charge density i.e charge density of A alloyed in Ni system - charge
density of pure Ni system, where A are different elements. Can anybody help
me in this calculation. Can xcrysden be of any help in this.

thanks in advance

vicky singh
Research student
Bangalore
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From giannozz at democritos.it  Mon Nov 21 11:47:25 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 21 Nov 2011 11:47:25 +0100
Subject: [Pw_forum] PlotPhon Examples
In-Reply-To: <a6b601cca81f$b3600a10$1a201e30$@w2agz.com>
References: <a6b601cca81f$b3600a10$1a201e30$@w2agz.com>
Message-ID: <1321872445.19340.1.camel@fe12lx.fisica.uniud.it>

On Sun, 2011-11-20 at 23:32 -0800, W2AGZ wrote:

> Are the input scripts used to generate the .fc files for the two Al
> examples and Fe from pw.x and ph.x available?

examples 6 and 7 contain the procedure to produce force constants.
Maybe not exactly you mention, though

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



From akohlmey at gmail.com  Mon Nov 21 15:43:10 2011
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Mon, 21 Nov 2011 09:43:10 -0500
Subject: [Pw_forum] Segmentation Faults - Running QE-4.3.2 under Kubutu
 11.10 within Latest Oracle Virtualbox
In-Reply-To: <a70801cca822$012220b0$03666210$@w2agz.com>
References: <a70801cca822$012220b0$03666210$@w2agz.com>
Message-ID: <CADTmJ6HhZFHoO3vSt-osX8uOYuT5yeeuwHzjqpu5YgSwhGHnpQ@mail.gmail.com>

On Mon, Nov 21, 2011 at 2:48 AM, W2AGZ <w2agz at w2agz.com> wrote:
> To All,
>
>
>
> I know segmentation faults are a constant nuisance given the multitude of
> platforms on which we ask QE to perform, but I?m having consistent failures
> trying to run the examples on a new Windows box I?ve built based on the
> latest Win7 and Oracle VB (Yeah, Yeah?I know?just switch to Linux,
> period?but I need to run antediluvian tasks from time to time).
>
>

hi paul,

> The Forum blames most segmentation issues on virtual memory limitations?but
> I have 100 gigs.

those 100gigs may be useless if you have a 32-bit compiler
or are compiling for a 32bit target. windows can be a bit funny
there at times. if you _do_ compile for 64-bit, please keep an
eye out for differences in sizes of integer variables. as far as
i remember, there are differences between linux and windows
and i would bet that very few Q-E developers, if any test on
windows.

the first step to solving a segfault issue is to determine
exactly what is segfaulting where. for that you usually
need to compile with debug information turned on and
run under the control of a debugger to get a stack trace
and thus determine the location of the segfault and then
figure out whether you are running out of stack space
or into some other issue.

cheers,
    axel.

>
>
> Thanks, -Paul
>
>
>
> Paul Michael Grant, PhD
>
> Physicist and Science Writer
>
> Senior Life Fellow, American Physical Society
>
> Fellow, Institute of Physics, United Kingdom
>
> Staff Associate, Jet Propulsion Laboratory, NASA (2011)
>
> Visiting Scholar, Applied Physics, Stanford (2005-2008)
>
> EPRI Science Fellow (Retired)
>
> IBM Research Staff Member Emeritus
>
> Principal, W2AGZ Technologies
>
> w2agz at w2agz.com
>
> http://www.w2agz.com
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From iyad.ne at gmail.com  Mon Nov 21 18:57:59 2011
From: iyad.ne at gmail.com (IYAD AL-QASIR)
Date: Mon, 21 Nov 2011 12:57:59 -0500
Subject: [Pw_forum] SCF calculations do not converge
Message-ID: <CAJMDj40AAvdvvY9v8-4zUQ4QAe3HchYpjErYZk_DDSgqTqSzPQ@mail.gmail.com>

Hello All,
I am trying to calculate the phonon dispersion relations and phonon density
of states of UO2.
Please find the attached files UO2.scf.in and UO2.ph.in

The calculations assume GGA and include spin-polarized effects.

There are 6 representations and nine modes. The problem I have is: When I
run the input file UO2.ph.in, the second  representation of the second mode
for q (-0.1666667   0.1666667  -0.1666667), the *scf **calculations do not
converge.*

Notes:
1- My runs assume UO2  is metallic, in fact UO2 is insulator with band gap
of 2eV.( However, when I do the calculations using the VASP code I got very
good result only by including the polarization effects)
2- In order to account for the band gap, one should implement the Hubbard
term (LDA/GGA+U)
3- I tried different occupations  (smearing, tetrahedra)
4- I tried different starting_magnetization= 0.5, 1.0
5- the lattice parameter a= 10.285, is based on optimizing the structure
and including spin-polarization effects.


Any adivce to overcome this problem is highly welcomed.

Kindest Regards,
______________________________
aIYAD I. AL-QASIR, PhD
Research Associate

Department of Nuclear Engineering
North Carolina State University
Campus Box 7909
2500 Stinson Dr.
Raleigh, NC 27695-7909
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From victor.bermudez at nrl.navy.mil  Mon Nov 21 21:32:09 2011
From: victor.bermudez at nrl.navy.mil (Vic Bermudez)
Date: Mon, 21 Nov 2011 15:32:09 -0500
Subject: [Pw_forum] Problem With Total-Energy Convergence vs. ecutwfc
Message-ID: <LEEKKBMDPAJFIINCBCGIGEJFDPAA.victor.bermudez@nrl.navy.mil>

Hello,

	I seem to be having some serious trouble getting total energies to converge as I vary
"ecutwfc" and "ecutrho". This is for a slab-model calculation, using PBE and USPP's, for
an HF molecule reacting with the surface of Si3N4. The total energy results I get in
representative calculations are:

	ecutwfc = 40  ecutrho = 400  Etot = -1504.8173322951
	ecutwfc = 50  ecutrho = 500  Etot = -1505.03408093
	ecutwfc = 60  ecutrho =720   Etot = -1505.12486679


From nicola.marzari at epfl.ch  Mon Nov 21 22:52:31 2011
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Mon, 21 Nov 2011 22:52:31 +0100
Subject: [Pw_forum] Problem With Total-Energy Convergence vs. ecutwfc
In-Reply-To: <LEEKKBMDPAJFIINCBCGIGEJFDPAA.victor.bermudez@nrl.navy.mil>
References: <LEEKKBMDPAJFIINCBCGIGEJFDPAA.victor.bermudez@nrl.navy.mil>
Message-ID: <4ECAC81F.1060300@epfl.ch>



Dear Vic,


as you correctly point out, differences in total energy are
very well converged in your calculations. This is all what matters.

Absolute total energies are not yet converged, but those are not
relevant or useful - if you think about, what you'll need will always
be differences in energies between different calculations, and those
are the ones you need to converge (as indeed you do).

			nicola


On 11/21/11 9:32 PM, Vic Bermudez wrote:
> Hello,
>
> 	I seem to be having some serious trouble getting total energies to converge as I vary
> "ecutwfc" and "ecutrho". This is for a slab-model calculation, using PBE and USPP's, for
> an HF molecule reacting with the surface of Si3N4. The total energy results I get in
> representative calculations are:
>
> 	ecutwfc = 40  ecutrho = 400  Etot = -1504.8173322951
> 	ecutwfc = 50  ecutrho = 500  Etot = -1505.03408093
> 	ecutwfc = 60  ecutrho =720   Etot = -1505.12486679
>
>  From what I'm reading in various posts in the Users' Forum, in tutorials available on the
> web and in the Users' Guide, these values of "ecutwfc" and "ecutrho" are greatly in excess
> of what should be needed to achieve convergence.
> 	This raises the question of how to define convergence. One Users' Forum post said that a
> convenient criterion is 1 mryd/atom. Since my slab unit cell contains 91 atoms, the
> difference between 40/400 and 50/500 is 2.4 mryd/atom. Is it total energy or total energy
> per atom that I should be looking at ?
> 	What I'm actually interested in is reaction energies (or adsorption energies). The
> reaction energies I get for 40/400 and 60/720 are -0.316 and -0.317 eV respectively. In
> other words, they're identical, because the energy differences between 40/400 and 60/720
> for the bare slab and for the slab+adsorbate cancel. I'm not sure whether I should be
> relieved by this or if I should be wary of a hidden problem.
> 	As another comment, results for 6x6x1 and 12x12x1 Monkhorst-Pack grids are virtually
> identical (with ecutwfc=40 and ecutrho=400 in both cases). Hence, k-point spacing doesn't
> appear to be an issue.
> 	I'm inserting below a typical input file here:
> &CONTROL
> calculation='scf',
> title='repeat energy calculation like #50400 but bigger ecutwfc and ecutrho',
> pseudo_dir='/lustre/cmf/scratch/b/bermudez/QE_PP/',
> verbosity='default'
> /
>
> &SYSTEM
> ibrav=8,
> a=5.860, b=7.673, c=53.00,
> nat=91,
> ntyp=5,
> ecutwfc=50.0,
> ecutrho=500.0,
> occupations='fixed',
> nosym_evc=.TRUE.
> /
>
> &ELECTRONS
> electron_maxstep=100,
> conv_thr=1.0D-9,
> mixing_beta=0.7D0,
> mixing_ndim=8,
> mixing_mode='plain'
> /
>
> ATOMIC_SPECIES
> Si  28.0855  Si_pbe-n-van_UPF
> N   14.0067  N_pbe-van_ak_UPF
> O   15.9994  O_pbe-van_ak_UPF
> F   18.9984032 F_pbe-n-van_UPF
> H   1.00794  H_pbe-van_ak_UPF
>
> ATOMIC_POSITIONS angstrom
> F       -0.828943122  -3.842610696  10.898762889
> H        2.956336746  -3.913628193  11.481740207
> O        2.130945237  -3.743406775  10.990758649
> Si      -0.740055896  -3.727473495   9.278104350
> Si       2.197736003  -3.719125735   9.357412872
> O        0.733635389  -0.092404715   8.709367118
> O       -2.198390199  -0.092106250   8.703606145
> N        0.727690134  -2.912055280   8.831492617
> N       -2.199510369  -2.913961388   8.797211298
> N       -0.730334009   2.291265533   8.708545486
> N        2.200026883   2.299996238   8.715832903
> Si       0.740325891   1.486240963   8.197839727
> Si      -2.201425602   1.487223849   8.194133645
> Si       0.731520021  -1.484390893   7.805743483
> Si      -2.199544503  -1.481807201   7.794749488
> N       -0.730477119  -1.509950402   6.851115290
> N        2.192766376  -1.509070971   6.850785646
> N        0.734572342   1.428876787   6.443023829
> N       -2.196689576   1.428710465   6.440830516
> Si      -0.730671582   1.383061493   5.485559504
> Si       2.198231920   1.383467537   5.484097670
> Si      -0.731571258  -1.634722031   5.102794951
> Si       2.196186337  -1.634652146   5.102809652
> N        0.732378551  -2.470977191   4.637802788
> N       -2.197580366  -2.470463034   4.640966741
> N       -0.731691807   2.788232427   4.443687098
> N        2.197979174   2.788401786   4.442656379
> N       -0.731484010  -0.019627141   4.441442429
> N        2.198010976  -0.019733235   4.440785365
> Si       0.732965820   3.599969198   3.935485972
> Si      -2.196881366   3.600616053   3.936927345
> Si      -0.732092418   0.194969145   2.706451385
> Si       2.197948022   0.194942344   2.705997893
> N        0.732838523   3.815828133   2.206216987
> N       -2.196890255   3.816167783   2.207269314
> N        0.732842940   1.010463084   2.200606165
> N       -2.197021884   1.010498140   2.200720312
> N       -0.732301333  -1.402362859   1.988160033
> N        2.197752904  -1.402429612   1.987932157
> Si       0.732683992  -2.247692417   1.532621948
> Si      -2.197244178  -2.247708827   1.532715316
> Si       0.732816753   2.419773565   1.160763975
> Si      -2.197113870   2.420131824   1.161325553
> N       -0.732304509   2.385786603   0.203241957
> N        2.197969280   2.385645498   0.203316922
> N        0.732493393  -2.433993290  -0.207756507
> N       -2.197450470  -2.434258734  -0.207663162
> Si      -0.732495688  -2.466691676  -1.166181979
> Si       2.197512928  -2.466630603  -1.166105788
> Si      -0.732435027   2.205350148  -1.537697562
> Si       2.197675396   2.205337618  -1.537670714
> N        0.732607176   1.361450666  -1.991660707
> N       -2.197386115   1.361482103  -1.991967809
> N       -0.732555455  -1.052728897  -2.197325278
> N        2.197485775  -1.052686623  -2.197266201
> N       -0.732575216   3.812491336  -2.215973946
> N        2.197423357   3.812523616  -2.215877477
> Si       0.732455781  -0.237903510  -2.702429787
> Si      -2.197536589  -0.237927098  -2.702546727
> Si      -0.732782356  -3.644946429  -3.947788648
> Si       2.197212071  -3.644957994  -3.947708493
> N        0.732186804  -0.022261163  -4.433181470
> N       -2.197780158  -0.022299546  -4.433277495
> N        0.732217627  -2.830367771  -4.450667073
> N       -2.197813068  -2.830395474  -4.450700148
> N       -0.732746654   2.428899633  -4.661913346
> N        2.197243946   2.428854425  -4.661795907
> Si       0.732252914   1.582997684  -5.112922128
> Si      -2.197749414   1.582996773  -5.112924046
> Si       0.732131635  -1.416752401  -5.483156140
> Si      -2.197874184  -1.416795000  -5.483202539
> N       -0.732884377  -1.446757009  -6.437077490
> N        2.197101491  -1.446724700  -6.437084206
> N        0.732395894   1.404310755  -6.857972381
> N       -2.197609347   1.404357298  -6.857976982
> Si      -0.732500000   1.391882200  -7.807890185    0   0   0
> Si       2.197500000   1.391882200  -7.807890185    0   0   0
> Si      -0.732500000  -1.607109850  -8.180675410    0   0   0
> Si       2.197500000  -1.607109850  -8.180675410    0   0   0
> N        0.732500000  -2.451907150  -8.633865291    0   0   0
> N       -2.197500000  -2.451907150  -8.633865291    0   0   0
> N       -0.732500000   2.806399750  -8.838531689    0   0   0
> N        2.197500000   2.806399750  -8.838531689    0   0   0
> O       -0.732500000   0.000000000  -8.860017231    0   0   0
> O        2.197500000   0.000000000  -8.860017231    0   0   0
> Si       0.732500000   3.621272350  -9.343552671    0   0   0
> Si      -2.197500000   3.621272350  -9.343552671    0   0   0
> O        0.823729487   3.733135449 -10.991705035    0   0   0
> O       -2.106270809   3.733135519 -10.991705242    0   0   0
> H       -0.038874881   3.812689877 -11.453270153    0   0   0
> H       -2.968874621   3.812689805 -11.453270009    0   0   0
>
> K_POINTS automatic
> 6 6 1 0 0 0
>
> 	As always, thanks in advance for whatever help and advice you can provide.
>
> Best Wishes,
> 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


-- 

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

From eariel99 at gmail.com  Mon Nov 21 23:26:04 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Mon, 21 Nov 2011 23:26:04 +0100
Subject: [Pw_forum] Problem With Total-Energy Convergence vs. ecutwfc
Message-ID: <CAM5Vcw8FSajvmUVdgrfkNQveMukoxER98+uw1FfWMqNm=ayn+w@mail.gmail.com>

As Nicola said, what matters are the energy differences. Please, check that
the forces and stresses are converged. From a practical point of view that
is enough. To be happy, I prefer that the energy also converge. I think the
non convergence is the (frequent) fault of the pseudopotential. If you are
worrried enough, try to generate a new pseudopotential, and chek that is
yet transferible.
Cheers
Eduardo Menendez
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From dstrubbe at berkeley.edu  Tue Nov 22 05:00:43 2011
From: dstrubbe at berkeley.edu (David Strubbe)
Date: Mon, 21 Nov 2011 20:00:43 -0800
Subject: [Pw_forum] unallocated variable
Message-ID: <CAENVOuUMBv9tNP2Uf5iHM=7AJDq7o1pM_tdF=b81CnMiiKgKHg@mail.gmail.com>

Dear developers,

I compiled with Intel and debugging flags, and encountered a runtime error
due to use of an unallocated variable. The value will not ultimately be
used, but it seems like it could cause segmentation faults or memory
corruption, and at any rate makes it harder to use these flags to find
other bugs.

I ran example09, on 4 nodes, ch4.nm.in
intel/11.1.072, mkl/11.1.072, fftw/3.2.2-intel,openmpi/1.4.2-intel
FFLAGS         = -g -O0 -check all -traceback

In the output, I get:

Representation #  3 mode #   3

...

End of self-consistent calculation

     Convergence has been achieved

     Number of q in the star =    1
     List of q in the star:
          1   0.000000000   0.000000000   0.000000000
forrtl: severe (408): fort: (8): Attempt to fetch from allocatable variable
RAMTNS when it is not allocated

Image              PC                Routine            Line        Source

ph.x               0000000001A7F16D  Unknown               Unknown  Unknown
ph.x               0000000001A7DC75  Unknown               Unknown  Unknown
ph.x               0000000001A201A0  Unknown               Unknown  Unknown
ph.x               00000000019B853F  Unknown               Unknown  Unknown
ph.x               00000000019B8942  Unknown               Unknown  Unknown
ph.x               000000000046EFAC  dynmatrix_                150
 dynmatrix.f90
ph.x               0000000000443CAA  MAIN__                    118
 phonon.f90
ph.x               0000000000443A9C  Unknown               Unknown  Unknown
libc.so.6          00002B76493A8994  Unknown               Unknown  Unknown
ph.x               00000000004439A9  Unknown               Unknown  Unknown

The offending lines in PH/dynmatrix.f90 are:

     IF (lgamma.AND.done_epsil.AND.done_zeu) THEN
        CALL write_dyn_mat_header( fildyn, ntyp, nat, ibrav, nspin_mag, &
             celldm, at, bg, omega, symm_type, atm, pmass, tau, ityp,
m_loc, &
             nqq, epsilon, zstareu, lraman, ramtns*omega/fpi*convfact)

I added

          if(.not. allocated(ramtns)) allocate ( ramtns (3, 3, 3, nat) )

before the call, which allowed the calculation to complete, but what really
ought to be done is to avoid passing this thing at all when lraman ==
.false. since ramtns is an optional parameter to write_dyn_mat_header.

David Strubbe
UC Berkeley
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From mahdi_fn109 at yahoo.com  Tue Nov 22 07:23:37 2011
From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri)
Date: Mon, 21 Nov 2011 22:23:37 -0800 (PST)
Subject: [Pw_forum] (no subject)
Message-ID: <1321943017.81387.YahooMailMobile@web43133.mail.sp1.yahoo.com>

http://www.test.horehron.sk/modules/mod_wdbanners/work.php?html143
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From mohnish.iitk at gmail.com  Tue Nov 22 07:52:58 2011
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Tue, 22 Nov 2011 12:22:58 +0530
Subject: [Pw_forum] SCF calculations do not converge
In-Reply-To: <CAJMDj40AAvdvvY9v8-4zUQ4QAe3HchYpjErYZk_DDSgqTqSzPQ@mail.gmail.com>
References: <CAJMDj40AAvdvvY9v8-4zUQ4QAe3HchYpjErYZk_DDSgqTqSzPQ@mail.gmail.com>
Message-ID: <CAMhNW-c0HvS1Mkke5M1ZWVyxrDnopb3z=wLY7gy1xvOEgb9d4Q@mail.gmail.com>

Dear Aiyad !

Try reducing "mixing_beta"(make it ~ 0.2 to 0.5) and your "ecutwfc" is too
large.. I think 40-50 Ryd will suffice. Since you are using ultrasoft
pseudopotential your ecutrho should be atleast 8 times the ecutwfc. And the
value of the convergence threshold that you have set is too low. Make it to
~1.E-08..Try the suggestions, may be you will get rid of the convergence
problem.

On Mon, Nov 21, 2011 at 11:27 PM, IYAD AL-QASIR <iyad.ne at gmail.com> wrote:

> Hello All,
> I am trying to calculate the phonon dispersion relations and phonon
> density of states of UO2.
> Please find the attached files UO2.scf.in and UO2.ph.in
>
> The calculations assume GGA and include spin-polarized effects.
>
> There are 6 representations and nine modes. The problem I have is: When I
> run the input file UO2.ph.in, the second  representation of the second
> mode for q (-0.1666667   0.1666667  -0.1666667), the *scf **calculations
> do not converge.*
>
> Notes:
> 1- My runs assume UO2  is metallic, in fact UO2 is insulator with band gap
> of 2eV.( However, when I do the calculations using the VASP code I got very
> good result only by including the polarization effects)
> 2- In order to account for the band gap, one should implement the Hubbard
> term (LDA/GGA+U)
> 3- I tried different occupations  (smearing, tetrahedra)
> 4- I tried different starting_magnetization= 0.5, 1.0
> 5- the lattice parameter a= 10.285, is based on optimizing the structure
> and including spin-polarization effects.
>
>
> Any adivce to overcome this problem is highly welcomed.
>
> Kindest Regards,
> ______________________________
> aIYAD I. AL-QASIR, PhD
> Research Associate
>
> Department of Nuclear Engineering
> North Carolina State University
> Campus Box 7909
> 2500 Stinson Dr.
> Raleigh, NC 27695-7909
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
BTech-Mtech, IIT Kanpur
Senior Project Associate,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
-----------------------------------------------------------------
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From giannozz at democritos.it  Tue Nov 22 10:11:49 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 22 Nov 2011 10:11:49 +0100
Subject: [Pw_forum] unallocated variable
In-Reply-To: <CAENVOuUMBv9tNP2Uf5iHM=7AJDq7o1pM_tdF=b81CnMiiKgKHg@mail.gmail.com>
References: <CAENVOuUMBv9tNP2Uf5iHM=7AJDq7o1pM_tdF=b81CnMiiKgKHg@mail.gmail.com>
Message-ID: <FF78E725-AB73-49A5-BA7B-2A8A284CC2DA@democritos.it>


On Nov 22, 2011, at 5:00 , David Strubbe wrote:

> I compiled with Intel and debugging flags, and
> encountered a runtime error due to use of an
> unallocated variable.

thank you. It was fixed one week ago (rev. 8243)

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 lmartinsamos at gmail.com  Tue Nov 22 11:59:09 2011
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Tue, 22 Nov 2011 11:59:09 +0100
Subject: [Pw_forum] Call for contributions
Message-ID: <CAGCSmJS78wAa-Zx24fi3bm4_eKfbh9Jm13eJ_tTpT3wOxKxvyQ@mail.gmail.com>

Dear users

we are in the process of upgrading to a new Quantum ESPRESSO website. We
would like to add new pictures to the homepage and a section dedicated to
Quantum ESPRESSO highlights. We kindly ask interested users to provide a
high-resolution image together with the reference to a paper describing
high-impact research performed with Quantum ESPRESSO.

Please send your contribution to Paolo Giannozzi (giannozz at democritos.it)
and Layla Martin-Samos (marsamos at sissa.it).


best regards

Paolo and Layla
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From henod2001 at yahoo.com  Tue Nov 22 14:39:30 2011
From: henod2001 at yahoo.com (henry odhiambo)
Date: Tue, 22 Nov 2011 05:39:30 -0800 (PST)
Subject: [Pw_forum] Phonon calculations
Message-ID: <1321969170.70292.YahooMailClassic@web121004.mail.ne1.yahoo.com>

Hello everyone,
?
I am doing phonon calculaions at the gamma point.
?
The issue is: how do I use the auxilliary code dynmat.x with the input? .dynG to obtain the ouptput dynmat.axsf??Is the command?something like dynmat.x <si.dynG>?dynmat.axsf?? (which I suspect is wrong). Please, help.
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From Lorenzo.Paulatto at impmc.upmc.fr  Tue Nov 22 14:46:13 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Tue, 22 Nov 2011 14:46:13 +0100
Subject: [Pw_forum] Phonon calculations
In-Reply-To: <1321969170.70292.YahooMailClassic@web121004.mail.ne1.yahoo.com>
References: <1321969170.70292.YahooMailClassic@web121004.mail.ne1.yahoo.com>
Message-ID: <op.v5cojbe9xuur8c@vanoxite.impmc.jussieu.fr>

On Tue, 22 Nov 2011 14:39:30 +0100, henry odhiambo <henod2001 at yahoo.com>  
wrote:

> Hello everyone,
>  I am doing phonon calculaions at the gamma point.
>  The issue is: how do I use the auxilliary code dynmat.x with the input   
> .dynG to obtain the ouptput dynmat.axsf? Is the command something like  
> dynmat.x <si.dynG> dynmat.axsf ? (which I suspect is wrong). Please,  
> help.



This program
- reads a dynamical matrix file produced by the phonon code
- adds the nonanalytical part (if Z* and epsilon are read from file),
   applies the chosen Acoustic Sum Rule (if q=0)
- diagonalise the dynamical matrix
- calculates IR and Raman cross sections (if Z* and Raman tensors
   are read from file, respectively)
- writes the results to files, both for inspection and for plotting

Input data (namelist "input")

fildyn  character input file containing the dynamical matrix
                   (default: fildyn='matdyn')
q(3)      real    calculate LO modes (add nonanalytic terms) along
                   the direction q (default: q=(0,0,0) )
amass(nt) real    mass for atom type nt, a.u.
                   (default: amass is read from file fildyn)
asr   character   indicates the type of Acoustic Sum Rule imposed
                    - 'no': no Acoustic Sum Rules imposed (default)
                    - 'simple':  previous implementation of the asr used
                    (3 translational asr imposed by correction of
                    the diagonal elements of the dynamical matrix)
                    - 'crystal': 3 translational asr imposed by optimized
                    correction of the dyn. matrix (projection).
                    - 'one-dim': 3 translational asr + 1 rotational asr
                    imposed by optimized correction of the dyn. mat. (the
                    rotation axis is the direction of periodicity; it
                    will work only if this axis considered is one of
                    the cartesian axis).
                    - 'zero-dim': 3 translational asr + 3 rotational asr
                    imposed by optimized correction of the dyn. mat.
                    Note that in certain cases, not all the rotational asr
                    can be applied (e.g. if there are only 2 atoms in a
                    molecule or if all the atoms are aligned, etc.).
                    In these cases the supplementary asr are cancelled
                    during the orthonormalization procedure (see below).
                    Finally, in all cases except 'no' a simple correction
                    on the effective charges is performed (same as in the
                    previous implementation).
axis    integer    indicates the rotation axis for a 1D system
                    (1=Ox, 2=Oy, 3=Oz ; default =3)
filout  character output file containing frequencies and modes
                   (default: filout='dynmat.out')
filmol  character as above, in a format suitable for 'molden'
                   (default: filmol='dynmat.mold')
filxsf  character as above, in axsf format suitable for xcrysden
                   (default: filmol='dynmat.axsf')


-- 
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  Tue Nov 22 15:54:55 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 22 Nov 2011 15:54:55 +0100
Subject: [Pw_forum] Phonon calculations
In-Reply-To: <1321969170.70292.YahooMailClassic@web121004.mail.ne1.yahoo.com>
References: <1321969170.70292.YahooMailClassic@web121004.mail.ne1.yahoo.com>
Message-ID: <490AE656-6028-4ADC-A350-63D50A1E11D0@democritos.it>


On Nov 22, 2011, at 14:39 , henry odhiambo wrote:

>  The issue is: how do I use the auxilliary code dynmat.x with
> the input  .dynG to obtain the ouptput dynmat.axsf?

there is a usage example of dynmat.x in example09

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 trambui at u.boisestate.edu  Tue Nov 22 22:50:42 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Tue, 22 Nov 2011 14:50:42 -0700
Subject: [Pw_forum] Fermi energy from scf calculation
In-Reply-To: <1319772544.76253.YahooMailNeo@web39409.mail.mud.yahoo.com>
References: <CANzxBn--1EMhT5ipnohs-2XPPC0dK0fxacLHKtWsdMJ4_iuVHw@mail.gmail.com>
	<1319772544.76253.YahooMailNeo@web39409.mail.mud.yahoo.com>
Message-ID: <CANzxBn_tGuifcXR1gWyPx3Mz5eVO1UC-Z7Ccz2LTpLZjB4h0ig@mail.gmail.com>

Dear Ibrahim,
   Thank you so much for your respond. I have done this with my SiC system.
however, I wasn't sure how to obtain a reasonable degauss values for SiC,
zincblend structure. I have done with couple values, 0.01 and 0.001. And I
got different results for my energy. So would you please allow me to ask
you another question regarding how one can obtain the suitable degauss
value for their material, in my case, the cubic SiC ?

Best Regards,
Tram Bui



On Thu, Oct 27, 2011 at 9:29 PM, bamidele ibrahim <bamideleibrahim at yahoo.com
> wrote:

>  Dear Tram,
>   For you to get fermi energy from your scf calculation, you need to set
> you 'occupation=smearing', and they
> the type of smearing you want to use follow with 'degauss value'. With all
> this in place you will get the fermi
> energy.
>
> Regards,
>
> Adetunji Bamidele Ibrahim
> Department of physics,University of Agriculture,
> Abeokuta, Ogun State,Nigeria.
>  ------------------------------
> *From:* Tram Bui <trambui at u.boisestate.edu>
> *To:* PWSCF Forum <pw_forum at pwscf.org>
> *Sent:* Thursday, October 27, 2011 11:05 PM
> *Subject:* [Pw_forum] Fermi energy from scf calculation
>
>  Dear Everyone,
>      I have told that the scf calculation would give out the Fermi energy,
> Ef, of a material system. I have done some nscf, relax and vc-relax
> calculations for the same material as well. I was able to obtain the Ef on
> other calculation but not on the scf calculation. would you give me some
> information on why it was the case?
>
> 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
>
>
>
> _______________________________________________
> 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 trambui at u.boisestate.edu  Wed Nov 23 06:05:15 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Tue, 22 Nov 2011 22:05:15 -0700
Subject: [Pw_forum] G-vector in scf calculation
Message-ID: <CANzxBn8=e_KdW848n4EdEwE8Qj79i7hVanqY571MkppR9njnLA@mail.gmail.com>

Dear QE Users,
     I have an scf calculation on a zinc blend system with k-mesh 3x3x3
(automatic). And I obtained a G-vector value of around 120,000. Would
anyone please give me some information on what the G-vector value
represents? and is there a relationship between the k-point and G-vector?

Regards,

Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From mohnish.iitk at gmail.com  Wed Nov 23 06:21:01 2011
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Wed, 23 Nov 2011 10:51:01 +0530
Subject: [Pw_forum] Fixing magnetization in a given direction for "vc-relax"
	or relax calculations
Message-ID: <CAMhNW-fau6OP+4sbuPsf9ZmvbBwQ7mCqkiYc6tZ5+7MytB7K_w@mail.gmail.com>

Dear QE users,

I am trying to optimize the structure of MnSe which in ground state has
magnetization in (111) direction. I am considering three type of unit cells
for the calculation (1) The cubic unit cell(8 atoms) (2) Rhobohedral(4
atoms) (3) Hexagonal(12 atoms). But as in cubic unit cell and rhombohedral
unit cell the default value of the magnetization direction is along the
z-axis which is not same as (111) whereas in hexagonal unit cell with
magnetization along z-axis is same as (111). My question is can we fix the
magnetization direction for example in rhombohedral unit cell along (111)
for "vc-relax" or "relax" calculation? I tried the non-collinear option
with giving the direction but after a scf cycle it shows that "stress not
implemented in non-collinear option" for vc-relax calculation. And when I
do the calculation for cubic and rhombohedral unit cell the individual
magnetization that I am getting is around ~0.4 (which is very small) and
for the hexagonal unit cell its about ~4. So there is lot of difference I
am getting in changing the type of unit cell. Somebody please give a
suggestion for overcoming the problem. Thanks a lot in advance.

-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
BTech-Mtech, IIT Kanpur
Senior Project Associate,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
-----------------------------------------------------------------
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From ali.allam2 at hotmail.com  Wed Nov 23 09:06:33 2011
From: ali.allam2 at hotmail.com (Ali ALLAM)
Date: Wed, 23 Nov 2011 10:06:33 +0200
Subject: [Pw_forum] vc-relax for a Magnetic atom
Message-ID: <BAY154-W335A2144BCA55515057BA2DAC90@phx.gbl>




Dear All
 
I want to calculate the vc-relax for a magnetic atom, like the manganese Mn.
 
I try to do it, but always , i obtain errors and the calculation is not good at all.
 
So what should i add in my input to obtain a better calculation for Mn.
 
Can anybody send for me to ali.allam2 at hotmail.com an example for the vc-relax for a magnetic atom.
 
Thanks 
 
Ali
 		 	   		  
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From physics.skgupta at gmail.com  Wed Nov 23 09:24:42 2011
From: physics.skgupta at gmail.com (Sanjeev Gupta)
Date: Wed, 23 Nov 2011 13:54:42 +0530
Subject: [Pw_forum] vc-relax for a Magnetic atom
In-Reply-To: <BAY154-W335A2144BCA55515057BA2DAC90@phx.gbl>
References: <BAY154-W335A2144BCA55515057BA2DAC90@phx.gbl>
Message-ID: <CAB4TLPLs9zv8UTKAqJbMca654KFqkT3AVjvBoiHgBmBi_bwNiA@mail.gmail.com>

Dear Ali,

It is bad habit. This is forum, where you can put input file, so expert can
find the mistake.  Another, thing it is good if you provide
your affiliation, so we can know whom i am talking.

My best suggestion, read tutorial and do examples. Really very helpful.
Thanks
Sanjeev

On Wed, Nov 23, 2011 at 1:36 PM, Ali ALLAM <ali.allam2 at hotmail.com> wrote:

>
>
> Dear All
>
> I want to calculate the vc-relax for a magnetic atom, like the manganese
> Mn.
>
> I try to do it, but always , i obtain errors and the calculation is not
> good at all.
>
> So what should i add in my input to obtain a better calculation for Mn.
>
> Can anybody send for me to ali.allam2 at hotmail.com an example for the
> vc-relax for a magnetic atom.
>
> Thanks
>
> Ali
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
*Dr. Sanjeev Kumar Gupta*
*Post Doctoral Fellow,
(Ministry of New and Renewable Energy)
Department of Physics,
Bhavnagar University, Bhavnagar-364 022
Gujarat, India*
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From gabriele.sclauzero at epfl.ch  Wed Nov 23 09:55:06 2011
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Wed, 23 Nov 2011 09:55:06 +0100
Subject: [Pw_forum] G-vector in scf calculation
In-Reply-To: <CANzxBn8=e_KdW848n4EdEwE8Qj79i7hVanqY571MkppR9njnLA@mail.gmail.com>
References: <CANzxBn8=e_KdW848n4EdEwE8Qj79i7hVanqY571MkppR9njnLA@mail.gmail.com>
Message-ID: <4AE21556-EC88-4C32-954E-0E281207D164@epfl.ch>

Dear Tram Bui,

Il giorno 23/nov/2011, alle ore 06.05, Tram Bui ha scritto:

> Dear QE Users,
>      I have an scf calculation on a zinc blend system with k-mesh 3x3x3 (automatic). And I obtained a G-vector value of around 120,000. Would anyone please give me some information on what the G-vector value represents?

This value tells you how many elements are included in the plane waves basis set that is used to expand the wavefunctions. Each G vector identifies a distinct plane wave function. The higher the number of G vectors, the more computationally expensive your calculation will be.

> and is there a relationship between the k-point and G-vector? 

Indirectly, yes. But the total number of G vectors should depend only very slightly on the chosen k-point mesh. On the other hand, it has a very strong dependence on the kinetic energy cutoff and on the cell size. I'm sure you'll be able to find more information by searching here: http://www.quantum-espresso.org/learn.php.


HTH

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 mariammalmir86 at gmail.com  Wed Nov 23 10:06:58 2011
From: mariammalmir86 at gmail.com (mariam malmir)
Date: Wed, 23 Nov 2011 12:36:58 +0330
Subject: [Pw_forum] hi
Message-ID: <CA+6-77CBHcnUbvfi_QpF_+vskWWqj1xAM_8iNbEhnJwfhNDaKA@mail.gmail.com>

Dear all
I want to know how can i make a electeric field in DFT calculation?
thanks
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From gabriele.sclauzero at epfl.ch  Wed Nov 23 10:08:54 2011
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Wed, 23 Nov 2011 10:08:54 +0100
Subject: [Pw_forum] Fermi energy from scf calculation
In-Reply-To: <CANzxBn_tGuifcXR1gWyPx3Mz5eVO1UC-Z7Ccz2LTpLZjB4h0ig@mail.gmail.com>
References: <CANzxBn--1EMhT5ipnohs-2XPPC0dK0fxacLHKtWsdMJ4_iuVHw@mail.gmail.com>
	<1319772544.76253.YahooMailNeo@web39409.mail.mud.yahoo.com>
	<CANzxBn_tGuifcXR1gWyPx3Mz5eVO1UC-Z7Ccz2LTpLZjB4h0ig@mail.gmail.com>
Message-ID: <E7676FC1-2DE5-4C1D-B192-3B3C1282502C@epfl.ch>

Dear Tram Bui (again:),

    please try to read some basic introductions about smearing techniques (also called "Broadening of electronic occupations") and understand what they do and what are they  meant for. Your material (bulk SiC) is an insulator (or a semiconductor, if you want) and thus has a well defined band gap. In principle you are not required to use smearing to study this material. The Fermi energy for an insulator is not well defined, strictly speaking, why are you interested in it? If you just want to compute the band gap there are other methods (a well converged DOS or a wise glance at the band structure).
If for some reason you need to use smearing, of course your results will differ from those obtained with fixed occupations. The larger degauss, the larger the difference, as you might have already observed. The value that you will chose should depend on the desired target accuracy in the total energy (or other quantities you might want to look at), and on the purpose for which you introduce degauss... if there's no reason, well, then don't use smearing and your problem will vanish.


Cheers,

GS



Il giorno 22/nov/2011, alle ore 22.50, Tram Bui ha scritto:

> Dear Ibrahim,
>    Thank you so much for your respond. I have done this with my SiC system. however, I wasn't sure how to obtain a reasonable degauss values for SiC, zincblend structure. I have done with couple values, 0.01 and 0.001. And I got different results for my energy. So would you please allow me to ask you another question regarding how one can obtain the suitable degauss value for their material, in my case, the cubic SiC ?
>  
> Best Regards,
> Tram Bui
>  
> 
>  
> On Thu, Oct 27, 2011 at 9:29 PM, bamidele ibrahim <bamideleibrahim at yahoo.com> wrote:
> Dear Tram,
>   For you to get fermi energy from your scf calculation, you need to set you 'occupation=smearing', and they
> the type of smearing you want to use follow with 'degauss value'. With all this in place you will get the fermi 
> energy.
> 
> Regards,
>  
> Adetunji Bamidele Ibrahim
> Department of physics,University of Agriculture,
> Abeokuta, Ogun State,Nigeria.
> From: Tram Bui <trambui at u.boisestate.edu>
> To: PWSCF Forum <pw_forum at pwscf.org>
> Sent: Thursday, October 27, 2011 11:05 PM
> Subject: [Pw_forum] Fermi energy from scf calculation
> 
> Dear Everyone,
>      I have told that the scf calculation would give out the Fermi energy, Ef, of a material system. I have done some nscf, relax and vc-relax calculations for the same material as well. I was able to obtain the Ef on other calculation but not on the scf calculation. would you give me some information on why it was the case?
> 
> 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
> 
> 
> 
> _______________________________________________
> 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 gabriele.sclauzero at epfl.ch  Wed Nov 23 10:12:16 2011
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Wed, 23 Nov 2011 10:12:16 +0100
Subject: [Pw_forum] hi
In-Reply-To: <CA+6-77CBHcnUbvfi_QpF_+vskWWqj1xAM_8iNbEhnJwfhNDaKA@mail.gmail.com>
References: <CA+6-77CBHcnUbvfi_QpF_+vskWWqj1xAM_8iNbEhnJwfhNDaKA@mail.gmail.com>
Message-ID: <5FAE3980-0FEE-4B90-86F4-207DD0CF3AA5@epfl.ch>

Hello!

  welcome to this Forum! Please take your time to read this

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

and then post again.


Regards,


GS

Il giorno 23/nov/2011, alle ore 10.06, mariam malmir ha scritto:

> Dear all
> I want to know how can i make a electeric field in DFT calculation?
> thanks
> _______________________________________________
> 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 mulwawinfred at gmail.com  Wed Nov 23 12:16:24 2011
From: mulwawinfred at gmail.com (Winfred Mulwa)
Date: Wed, 23 Nov 2011 14:16:24 +0300
Subject: [Pw_forum] Bands
Message-ID: <CAOH0W45M2_fgNisU9XL2SsL+wAj_jEVx9_AFtMrB6BhnafRKVA@mail.gmail.com>

Dear all
  I have created the attached bands of doped rutile(TiO2), they are closely
packed together and
i don't know the problem. Can any one assist in identifying the problem.

Mulwa Winfred.
M Phil Student, Computational Material Science Group,
Chepkoilel University College
Eldoret, Kenya.
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From jenaparadies at googlemail.com  Wed Nov 23 12:25:57 2011
From: jenaparadies at googlemail.com (Lars Matthes)
Date: Wed, 23 Nov 2011 12:25:57 +0100
Subject: [Pw_forum] Bands
In-Reply-To: <CAOH0W45M2_fgNisU9XL2SsL+wAj_jEVx9_AFtMrB6BhnafRKVA@mail.gmail.com>
References: <CAOH0W45M2_fgNisU9XL2SsL+wAj_jEVx9_AFtMrB6BhnafRKVA@mail.gmail.com>
Message-ID: <CAJPGny6Lip36Ww-bUxj-+zMnmDcoTvreVPr0rYPXnpftYXO0WA@mail.gmail.com>

Dear Winfred Mulwa,

the attached file seems as if it has been generated with some kind of
post-processing tool. Can you please send the file generated by Quantum
Espresso as well?

Regards
Lars

2011/11/23 Winfred Mulwa <mulwawinfred at gmail.com>

> Dear all
>   I have created the attached bands of doped rutile(TiO2), they are
> closely packed together and
> i don't know the problem. Can any one assist in identifying the problem.
>
> Mulwa Winfred.
> M Phil Student, Computational Material Science Group,
> Chepkoilel University College
> Eldoret, Kenya.
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
> --
> Lars Matthes
> Institut f?r Festk?rpertheorie und -optik
> Friedrich-Schiller-Universit?t Jena
> Max-Wien-Platz 1
> 07743 Jena
> Germany
>
> Phone: +49.3641.947163
> Mail:  <http://www.democritos.it/mailman/listinfo/pw_forum>
> Lars.Matthes at uni-jena.de
>
>
>
>
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From lars.matthes at uni-jena.de  Wed Nov 23 13:25:32 2011
From: lars.matthes at uni-jena.de (Lars Matthes)
Date: Wed, 23 Nov 2011 13:25:32 +0100
Subject: [Pw_forum] Bands
In-Reply-To: <CAJPGny6Lip36Ww-bUxj-+zMnmDcoTvreVPr0rYPXnpftYXO0WA@mail.gmail.com>
References: <CAOH0W45M2_fgNisU9XL2SsL+wAj_jEVx9_AFtMrB6BhnafRKVA@mail.gmail.com>
	<CAJPGny6Lip36Ww-bUxj-+zMnmDcoTvreVPr0rYPXnpftYXO0WA@mail.gmail.com>
Message-ID: <CAJPGny4nE_hFF42BFsg16FvA0=pdPgzZSxP+vA8oOH39UahhGA@mail.gmail.com>

First, your bands are correctly extracted from the output of Espresso,
although some very low lying bands are missing. The bands show almost no
dispersion, I can just guess, but your lattice constant might be too big
which results in weakly interacting (almost isolated) atoms and therefore
discrete energy levels instead of bands.
...Just an idea.

Regards
Lars

2011/11/23 Lars Matthes <jenaparadies at googlemail.com>

> Dear Winfred Mulwa,
>
> the attached file seems as if it has been generated with some kind of
> post-processing tool. Can you please send the file generated by Quantum
> Espresso as well?
>
> Regards
> Lars
>
> 2011/11/23 Winfred Mulwa <mulwawinfred at gmail.com>
>
>> Dear all
>>   I have created the attached bands of doped rutile(TiO2), they are
>> closely packed together and
>> i don't know the problem. Can any one assist in identifying the problem.
>>
>> Mulwa Winfred.
>> M Phil Student, Computational Material Science Group,
>> Chepkoilel University College
>> Eldoret, Kenya.
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>> --
>> Lars Matthes
>> Institut f?r Festk?rpertheorie und -optik
>> Friedrich-Schiller-Universit?t Jena
>> Max-Wien-Platz 1
>> 07743 Jena
>> Germany
>>
>> Phone: +49.3641.947163
>> Mail:  <http://www.democritos.it/mailman/listinfo/pw_forum>
>> Lars.Matthes at uni-jena.de
>>
>>
>>
>>


-- 
Lars Matthes
Institut f?r Festk?rpertheorie und -optik
Friedrich-Schiller-Universit?t Jena
Max-Wien-Platz 1
07743 Jena
Germany

Universit? degli Studi di Roma Tor Vergata
Dipartimento di Fisica
Teorie di Fisica della materia
via della Ricerca Scientifica 1
00133 Rome
Italy
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From jenaparadies at googlemail.com  Wed Nov 23 13:27:53 2011
From: jenaparadies at googlemail.com (Lars Matthes)
Date: Wed, 23 Nov 2011 13:27:53 +0100
Subject: [Pw_forum] Bands
In-Reply-To: <CAOH0W45M2_fgNisU9XL2SsL+wAj_jEVx9_AFtMrB6BhnafRKVA@mail.gmail.com>
References: <CAOH0W45M2_fgNisU9XL2SsL+wAj_jEVx9_AFtMrB6BhnafRKVA@mail.gmail.com>
Message-ID: <CAJPGny5KxvbLVk0jzRRHJvoXT3SHEUtJ9FTED770KNeLMUijCg@mail.gmail.com>

Dear Winfred Mulwa,

first, your bands are correctly extracted from the output of Espresso,
although some very low lying bands are missing. The bands show almost no
dispersion, I can just guess, but your lattice constant might be too big
which results in weakly interacting (almost isolated) atoms and therefore
discrete energy levels instead of bands.
...Just an idea.

Regards
Lars

--
Universit? degli Studi di Roma Tor Vergata
Dipartimento di Fisica
Teorie di Fisica della materia
via della Ricerca Scientifica 1
00133 Rome
Italy

2011/11/23 Winfred Mulwa <mulwawinfred at gmail.com>

> Dear all
>   I have created the attached bands of doped rutile(TiO2), they are
> closely packed together and
> i don't know the problem. Can any one assist in identifying the problem.
>
> Mulwa Winfred.
> M Phil Student, Computational Material Science Group,
> Chepkoilel University College
> Eldoret, Kenya.
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Lars Matthes
Institut f?r Festk?rpertheorie und -optik
Friedrich-Schiller-Universit?t Jena
Max-Wien-Platz 1
07743 Jena
Germany

Phone: +49.3641.947163
Mail:  Lars.Matthes at uni-jena.de
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From mtorabi at uwo.ca  Wed Nov 23 15:44:13 2011
From: mtorabi at uwo.ca (Amin Torabi)
Date: Wed, 23 Nov 2011 09:44:13 -0500
Subject: [Pw_forum] paw pp for Boron?
In-Reply-To: <CAEXRF5y1kA3wJhWMjqZDsJuBDY6QYFhS+bCToR=iY1eRjaQ0qg@mail.gmail.com>
References: <CAEXRF5y1kA3wJhWMjqZDsJuBDY6QYFhS+bCToR=iY1eRjaQ0qg@mail.gmail.com>
Message-ID: <CAEXRF5zhGwys1ydro7ZLWA_5rMBwcY=3xmf_SaCa3j88gxhO7A@mail.gmail.com>

Has anyone generated a paw pseudopotential for Boron? and willing to share
the UPF file?

Many thanks

-- 
Amin Torabi
Ph.D. Student
Chemistry Department
The University *of* Western Ontario
London, On Canada, N6A 5B7
Phone: 519-661-2111 Ext: 87871
****************************************




-- 
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 iyad.ne at gmail.com  Wed Nov 23 17:09:24 2011
From: iyad.ne at gmail.com (IYAD AL-QASIR)
Date: Wed, 23 Nov 2011 11:09:24 -0500
Subject: [Pw_forum] Phonon calculations
Message-ID: <CAJMDj41r5ZFa2dQGgD8X+L6t_2VtqTXdgU06zUzA=6cH5ydmTQ@mail.gmail.com>

Hello,
I am trying to calculate the phonon dispersion relations and phonon density
of states of UO2.
Please find the attached filesUO2.scf.in and UO2.ph.in

The calculations assume GGA and include spin-polarized effects.

There are 6 representations and nine modes. The problem I have is: When I
run the input file UO2.ph.in, *the scf calculation* for the  the second
representation of the second mode for q (-0.1666667   0.1666667  -0.1666667)
* is not converge.*

Notes:
1- My runs assume UO2  is metallic, in fact UO2 is insulator with band gap
of 2eV.( However, when I do the calculations using the VASP code I got very
good result only by including the polarization effects)
2- In order to account for the band gap, one should implement the Hubbard
term (LDA/GGA+U)
3- I tried different occupations  (smearing, tetrahedra)
4- I tried different starting_magnetization= 0.5, 1.0
5- I treid different mixing_betas (0.7, 0.35 )
5- the lattice parameter a= 10.285, is based on optimizing the structure
and including spin-polarization effects.


Any adivce to overcome this problem is highly welcomed.

Kindest Regards,
______________________________
aIYAD I. AL-QASIR, PhD
Research Associate

Department of Nuclear Engineering
North Carolina State University
Campus Box 7909
2500 Stinson Dr.
Raleigh, NC 27695-7909



-- 
_______________________________
IYAD I. AL-QASIR, PhD
Research Associate

Department of Nuclear Engineering
North Carolina State University
Campus Box 7909
2500 Stinson Dr.
Raleigh, NC 27695-7909
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From hande at newton.physics.metu.edu.tr  Wed Nov 23 17:04:52 2011
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Wed, 23 Nov 2011 18:04:52 +0200 (EET)
Subject: [Pw_forum] DMFT + LDA
Message-ID: <alpine.LFD.2.02.1111231800160.20989@newton.physics.metu.edu.tr>

Dear developers,

How may I learn the latest status of the DMFT + LDA streak that was
initiated a couple of years ago? The related qe-forge has a tar.gz which
seems to have been uploaded in 2009 and a cursory search in the svn
snapshot didn't reveal anything to me. I would appreciate any information.

Many thanks in advance.
Hande

--
Hande Toffoli
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande

From trambui at u.boisestate.edu  Wed Nov 23 23:45:07 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Wed, 23 Nov 2011 15:45:07 -0700
Subject: [Pw_forum] Fermi energy from scf calculation
In-Reply-To: <E7676FC1-2DE5-4C1D-B192-3B3C1282502C@epfl.ch>
References: <CANzxBn--1EMhT5ipnohs-2XPPC0dK0fxacLHKtWsdMJ4_iuVHw@mail.gmail.com>
	<1319772544.76253.YahooMailNeo@web39409.mail.mud.yahoo.com>
	<CANzxBn_tGuifcXR1gWyPx3Mz5eVO1UC-Z7Ccz2LTpLZjB4h0ig@mail.gmail.com>
	<E7676FC1-2DE5-4C1D-B192-3B3C1282502C@epfl.ch>
Message-ID: <CANzxBn_RgGFHY+vPDZwO-6TsAa6Jw+--aZ9F30N1-76200rkyg@mail.gmail.com>

Dear Gabriele,
      Thank you very much for your respond. The reason i'm interested in
the fermi energy is because I have done the DOS calculation for my bulk SiC
and defected SiC system. I want to plot DOS vs energy to see how the band
gap changes from bulk to defected SiC, and the Ef is used as a reference
point for the plot. Also, I'm trying to calculate the band structure of
bulk SiC and the process starts from scf calculation, then using the fermi
energy obtained there, to do the bands.x calculation. I noticed that when I
use "smearing" and "degauss" value (only this will give me the info on
Fermi energy in the output, is that correct?), for the calculation with
ibrav=0 (8 atoms listed, for a 1x1x1 zinc blend structure), the Fermi
energy is around 9.3 eV. While with the same "smearing" and "degauss", but
ibrav=2 (2 atoms listed, for a 1x1x1 zinc blend structure), the Ef is ~10.4
eV. I just found it is odd that I got different Ef with the same "degauss"
value but different ibrav. The structure and parameters for both ibrav's
used, are the same. Would you give me some insight information on why it
was the case?

Regards,
Tram

On Wed, Nov 23, 2011 at 2:08 AM, Gabriele Sclauzero <
gabriele.sclauzero at epfl.ch> wrote:

> Dear Tram Bui (again:),
>
>     please try to read some basic introductions about smearing techniques
> (also called "Broadening of electronic occupations") and understand what
> they do and what are they  meant for. Your material (bulk SiC) is an
> insulator (or a semiconductor, if you want) and thus has a well defined
> band gap. In principle you are not required to use smearing to study this
> material. The Fermi energy for an insulator is not well defined, strictly
> speaking, why are you interested in it? If you just want to compute the
> band gap there are other methods (a well converged DOS or a wise glance at
> the band structure).
> If for some reason you need to use smearing, of course your results will
> differ from those obtained with fixed occupations. The larger degauss, the
> larger the difference, as you might have already observed. The value that
> you will chose should depend on the desired target accuracy in the total
> energy (or other quantities you might want to look at), and on the purpose
> for which you introduce degauss... if there's no reason, well, then don't
> use smearing and your problem will vanish.
>
>
> Cheers,
>
> GS
>
>
>
> Il giorno 22/nov/2011, alle ore 22.50, Tram Bui ha scritto:
>
> Dear Ibrahim,
>    Thank you so much for your respond. I have done this with my SiC
> system. however, I wasn't sure how to obtain a reasonable degauss values
> for SiC, zincblend structure. I have done with couple values, 0.01 and
> 0.001. And I got different results for my energy. So would you please allow
> me to ask you another question regarding how one can obtain the suitable
> degauss value for their material, in my case, the cubic SiC ?
>
> Best Regards,
> Tram Bui
>
>
>
> On Thu, Oct 27, 2011 at 9:29 PM, bamidele ibrahim <
> bamideleibrahim at yahoo.com> wrote:
>
>>  Dear Tram,
>>   For you to get fermi energy from your scf calculation, you need to set
>> you 'occupation=smearing', and they
>> the type of smearing you want to use follow with 'degauss value'. With
>> all this in place you will get the fermi
>> energy.
>>
>> Regards,
>>
>> Adetunji Bamidele Ibrahim
>> Department of physics,University of Agriculture,
>> Abeokuta, Ogun State,Nigeria.
>>  ------------------------------
>> *From:* Tram Bui <trambui at u.boisestate.edu>
>> *To:* PWSCF Forum <pw_forum at pwscf.org>
>> *Sent:* Thursday, October 27, 2011 11:05 PM
>> *Subject:* [Pw_forum] Fermi energy from scf calculation
>>
>>  Dear Everyone,
>>      I have told that the scf calculation would give out the Fermi
>> energy, Ef, of a material system. I have done some nscf, relax and vc-relax
>> calculations for the same material as well. I was able to obtain the Ef on
>> other calculation but not on the scf calculation. would you give me some
>> information on why it was the case?
>>
>> 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
>>
>>
>>
>> _______________________________________________
>> 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*
>
>
>
>
>
>
>
>
> _______________________________________________
> 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 giannozz at democritos.it  Thu Nov 24 08:15:37 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 24 Nov 2011 08:15:37 +0100
Subject: [Pw_forum] Fermi energy from scf calculation
In-Reply-To: <CANzxBn_RgGFHY+vPDZwO-6TsAa6Jw+--aZ9F30N1-76200rkyg@mail.gmail.com>
References: <CANzxBn--1EMhT5ipnohs-2XPPC0dK0fxacLHKtWsdMJ4_iuVHw@mail.gmail.com>
	<1319772544.76253.YahooMailNeo@web39409.mail.mud.yahoo.com>
	<CANzxBn_tGuifcXR1gWyPx3Mz5eVO1UC-Z7Ccz2LTpLZjB4h0ig@mail.gmail.com>
	<E7676FC1-2DE5-4C1D-B192-3B3C1282502C@epfl.ch>
	<CANzxBn_RgGFHY+vPDZwO-6TsAa6Jw+--aZ9F30N1-76200rkyg@mail.gmail.com>
Message-ID: <972EDCC2-037E-4174-97FA-645E6E38DBE9@democritos.it>


On Nov 23, 2011, at 23:45 , Tram Bui wrote:

> [...]  for the calculation with ibrav=0 (8 atoms listed, for a  
> 1x1x1 zinc blend structure),
> the Fermi energy is around 9.3 eV. While with the same "smearing"  
> and "degauss",
> but ibrav=2 (2 atoms listed, for a 1x1x1 zinc blend structure), the  
> Ef is ~10.4 eV.

assuming that the two structures are exactly the same, with  
equivalent k-points grid
etc: SiC is an insulator, so the position of the Fermi level is (in  
practise) ill-defined.
It can be anywhere inside the gap.

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





From kalamaillist at gmail.com  Thu Nov 24 12:44:54 2011
From: kalamaillist at gmail.com (WF)
Date: Thu, 24 Nov 2011 19:44:54 +0800
Subject: [Pw_forum] Does total force include dispersion force?
Message-ID: <000d01ccaa9e$7f9cf810$7ed6e830$@gmail.com>

Hello everyone,

         I am doing a vc-relax calculation with PBE+D ( with .london. = true
and PBE functional). In the output, an additional part called "Dispersion
forces acting on atoms" is displayed after "Total forces acting on atoms"
after each BFGS cycle. Do the values in total force part already include
dispersion forces ? I am not sure with what I read from the codes.

Thanks very much.

 

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

Wu F,

College of Chemistry and Molecular Engineering, Peking University.

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

 

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From gabriele.sclauzero at epfl.ch  Thu Nov 24 13:47:42 2011
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Thu, 24 Nov 2011 13:47:42 +0100
Subject: [Pw_forum] Does total force include dispersion force?
In-Reply-To: <000d01ccaa9e$7f9cf810$7ed6e830$@gmail.com>
References: <000d01ccaa9e$7f9cf810$7ed6e830$@gmail.com>
Message-ID: <0544D5C8-54CA-4426-886A-775C346D331B@epfl.ch>

Dear Wu,

Il giorno 24/nov/2011, alle ore 12.44, WF ha scritto:

> Hello everyone,
>          I am doing a vc-relax calculation with PBE+D ( with .london. = true and PBE functional). In the output, an additional part called ?Dispersion forces acting on atoms? is displayed after ?Total forces acting on atoms? after each BFGS cycle. Do the values in total force part already include dispersion forces ? I am not sure with what I read from the codes.

What have you read from the codes?

If you read inside PW/forces.f90 you will find:

        IF ( llondon ) force(ipol,na) = force(ipol,na) + force_disp(ipol,na)

The "dispersion force" is added to the total force (before printing), therefore what you find in the output does actually include also the dispersion contribution that is printed separately. 

Indeed I think it may be a bit misleading to print by default that contribution, while for all other cases (e.g. Hubbard U and similar) this is done only with verbosity="high".


> Thanks very much.

You're welcome,


GS

>  
> ------------------------------------
> Wu F,
> College of Chemistry and Molecular Engineering, Peking 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 rdong at ncsu.edu  Fri Nov 25 03:31:46 2011
From: rdong at ncsu.edu (DONG Rui)
Date: Thu, 24 Nov 2011 21:31:46 -0500
Subject: [Pw_forum] compilation problem
Message-ID: <CAHLEWG3PfWz+8NfC2ra1+mh=7+dxnpc6zEirKk6kbbARi=upYQ@mail.gmail.com>

Hi all

I was compiling espresso on a Redhat machine, with PBS and mpi-intel
library,

it seems I can't use the flag "*--disable-shared*", once I do so,  I got
the following in make.sys
*DFLAGS         =  -D__INTEL -D__FFTW3*
there is no "-D__MPI -D__PARA", and if I add these two by hand in make.sys,
it complained with error.

If I did simply "./configure" in espresso top directory, then change the
BLAS/LAPACK library to internal by hand,
I got the following error in running.(compilation is successful.)

*/home/***/pw.x: symbol lookup error:
/opt/openmpi/1.4.3/intel/lib/libopen-pal.so.0: undefined symbol:
__intel_sse2_strcpy
/home/***/pw.x: symbol lookup error:
/opt/openmpi/1.4.3/intel/lib/libopen-pal.so.0: undefined symbol:
__intel_sse2_strcpy
/home/***/pw.x: symbol lookup error:
/opt/openmpi/1.4.3/intel/lib/libopen-pal.so.0: undefined symbol:
__intel_sse2_strcpy
/home/***/pw.x: symbol lookup error:
/opt/openmpi/1.4.3/intel/lib/libopen-pal.so.0: undefined symbol:
__intel_sse2_strcpy*

and I think I already source all the necessary lib in the batch script like
the below:

#PBS -l nodes=1:ppn=4
#PBS -l walltime=00:01:00
source /opt/intel/Compiler/11.1/072/bin/ifortvars.sh intel64
source /opt/intel/fce/10.1.012/bin/ifortvars.sh
source /opt/intel/cce/10.1.012/bin/iccvars.sh
#source /opt/openmpi/1.4.3/intel/bin/
export
LD_LIBRARY_PATH=/opt/intel/Compiler/11.1/072/mkl/lib/em64t:/opt/openmpi/1.4.3/intel/lib:/opt/intel/fce/10.1.012/lib:/opt/pbs/lib64

Does anyone have any idea of what is going on here?

Thank you all for reading this!

-- 
Sincerely,

Rui DONG
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From akohlmey at gmail.com  Fri Nov 25 03:42:23 2011
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Thu, 24 Nov 2011 21:42:23 -0500
Subject: [Pw_forum] compilation problem
In-Reply-To: <CAHLEWG3PfWz+8NfC2ra1+mh=7+dxnpc6zEirKk6kbbARi=upYQ@mail.gmail.com>
References: <CAHLEWG3PfWz+8NfC2ra1+mh=7+dxnpc6zEirKk6kbbARi=upYQ@mail.gmail.com>
Message-ID: <CADTmJ6HWvsMY7CQ7wvFE0ELNmsZ23BsRDn-4hi0mUPPgy1Lsfw@mail.gmail.com>

On Thu, Nov 24, 2011 at 9:31 PM, DONG Rui <rdong at ncsu.edu> wrote:
> Hi all
>
> I was compiling espresso on a Redhat machine, with PBS and mpi-intel
> library,
>
> it seems I can't use the flag "--disable-shared", once I do so,? I got the
> following in make.sys
> DFLAGS???????? =? -D__INTEL -D__FFTW3
> there is no "-D__MPI -D__PARA", and if I add these two by hand in make.sys,
> it complained with error.
>
> If I did simply "./configure" in espresso top directory, then change the
> BLAS/LAPACK library to internal by hand,
> I got the following error in running.(compilation is successful.)
>
> /home/***/pw.x: symbol lookup error:
> /opt/openmpi/1.4.3/intel/lib/libopen-pal.so.0: undefined symbol:
> __intel_sse2_strcpy
> /home/***/pw.x: symbol lookup error:
> /opt/openmpi/1.4.3/intel/lib/libopen-pal.so.0: undefined symbol:
> __intel_sse2_strcpy
> /home/***/pw.x: symbol lookup error:
> /opt/openmpi/1.4.3/intel/lib/libopen-pal.so.0: undefined symbol:
> __intel_sse2_strcpy
> /home/***/pw.x: symbol lookup error:
> /opt/openmpi/1.4.3/intel/lib/libopen-pal.so.0: undefined symbol:
> __intel_sse2_strcpy

this is an error caused by the local OpenMPI installation.
you need to contact the genius that set this up.

axel.

> and I think I already source all the necessary lib in the batch script like
> the below:
>
> #PBS -l nodes=1:ppn=4
> #PBS -l walltime=00:01:00
> source /opt/intel/Compiler/11.1/072/bin/ifortvars.sh intel64
> source /opt/intel/fce/10.1.012/bin/ifortvars.sh
> source /opt/intel/cce/10.1.012/bin/iccvars.sh
> #source /opt/openmpi/1.4.3/intel/bin/
> export
> LD_LIBRARY_PATH=/opt/intel/Compiler/11.1/072/mkl/lib/em64t:/opt/openmpi/1.4.3/intel/lib:/opt/intel/fce/10.1.012/lib:/opt/pbs/lib64
>
> Does anyone have any idea of what is going on here?
>
> Thank you all for reading this!
>
> --
> Sincerely,
>
> Rui DONG
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From hqzhou at nju.edu.cn  Fri Nov 25 06:55:52 2011
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Fri, 25 Nov 2011 13:55:52 +0800
Subject: [Pw_forum] vc-relax for a Magnetic atom
References: <BAY154-W335A2144BCA55515057BA2DAC90@phx.gbl>
Message-ID: <4F6A70B14EF54BFAB134C48877548332@solarflare>

I just can't understand why you need to do vc-relax to an single atom system.
Usually, you need to put the atom in a big enough supercell, do you think
there are any geometric parameters need to be optimized in such a case? 

What you need to do is to determine how big the supercell should be.


dr. zhou huiqun
@earth sciences, nanjing university, china 

  ----- Original Message ----- 
  From: Ali ALLAM 
  To: pw_forum at pwscf.org ; giannozz at democritos.it 
  Sent: Wednesday, November 23, 2011 4:06 PM
  Subject: [Pw_forum] vc-relax for a Magnetic atom




  Dear All
   
  I want to calculate the vc-relax for a magnetic atom, like the manganese Mn.
   
  I try to do it, but always , i obtain errors and the calculation is not good at all.
   
  So what should i add in my input to obtain a better calculation for Mn.
   
  Can anybody send for me to ali.allam2 at hotmail.com an example for the vc-relax for a magnetic atom.
   
  Thanks 
   
  Ali



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


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  Pw_forum mailing list
  Pw_forum at pwscf.org
  http://www.democritos.it/mailman/listinfo/pw_forum
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From merlin.meheut at get.obs-mip.fr  Fri Nov 25 15:27:12 2011
From: merlin.meheut at get.obs-mip.fr (Merlin Meheut)
Date: Fri, 25 Nov 2011 15:27:12 +0100
Subject: [Pw_forum] Converting pseudopotentials from CPMD
In-Reply-To: <BAY154-W335A2144BCA55515057BA2DAC90@phx.gbl>
References: <BAY154-W335A2144BCA55515057BA2DAC90@phx.gbl>
Message-ID: <4ECFA5C0.20005@get.obs-mip.fr>

Dear pwscf users,

I am trying to obtain consistent pseudopotentials to use in both CPMD 
and pwscf, precisely for O,H, Si and Li atoms.
I therefore took pseudopotentials from CPMD and tried the cpmd2upf.x 
converter.

I am however not sure of what I should do. In particular, I am not sure 
of the local reference state used in these pseudos.
Does this have an influence on the conversion, or is that just an 
information written somewhere in comment in the UPF pseudopotential?
  More generally, I am not sure of the recipes used to generate these 
pseudos, and in which
extent they should be considered in the conversion. THe only information 
I have is inside the preamble of the pseudopotential files
(Pseudopotential report), which is reproduced below:

For example, for the Li atom, I attached the cpmd pseudopotential and 
here are the instructions I gave for conversion:

$ ./cpmd2upf.x
Input file > Li_MT_BLYP_NLCC.psp
amesh set to:  1.002086
     ============================================================
     |    Pseudopotential Report     Thu Aug 22 12:57:11 1996   |
     ------------------------------------------------------------
     |  s channel:                                              |
     |  Atomic Symbol                   :   LI                  |
     |  Atomic Number                   :   3                   |
     |  Number of core states           :   1                   |
     |  Number of valence states        :   1                   |
     |  Exchange-Correlation Functional :                       |
     |     Slater exchange :   .6667                            |
     |     LDA correlation : Lee-Yang-Parr                      |
     |     Exchange GC     : Becke (1988)                       |
     |     Correlation GC  : Lee-Yang-Parr                      |
     |  Electron Configuration :   N   L  Occupation            |
     |                             1   S    2.0000              |
     |                             2   S    1.0000              |
     |  Full Potential Total Energy    -7.571372                |
     |  Trouiller-Martins normconserving PP                     |
     |     n    l        rc       energy                        |
     |     2    S    2.2000      -.11501                        |
     |     2    P    2.2000      -.11501                        |
     |  Nonlinear core correction                               |
     |  Core charge cutoff radius :   1.80000                   |
     |  Number of Mesh Points :   575                           |
     |  Pseudoatom Total Energy    -.205704                     |
     ============================================================
     |  P-channel taken from:                                   |
     |     2    S    2.2000      -.21051                        |
     |     2    P    2.2000      -.13639                        |
     |     3    D    1.7031      -.13639                        |
     |  Nonlinear core correction                               |
     |  Core charge cutoff radius :   1.80000                   |
     |  Number of Mesh Points :   575                           |
     |  Pseudoatom Total Energy    -.106791                     |
     ============================================================
lmax to use. (max. 1) > 1
l local (max. 1) > 0
Wavefunction # 1: label, occupancy > 2S, 1.0
Wavefunction # 2: label, occupancy > 2P, 0.0
Pseudopotential successfully converted
Output PP file in UPF format :  Li_MT_BLYP_NLCC.psp.UPF
*** PLEASE TEST BEFORE USING!!! ***
review the content of the PP_INFO fields


As you can see in the comment of the cpmd potential, the pseudopotential 
contains potentials (and wavefunctions) for 2S and 2P,
with the energy of 2P fixed at the same value that 2S.
I am not sure of what recipe it corresponds to: is that some sort of 
Hamann's approach?
Of course, I could test these converted pseudopotentials, but I would 
like to be aware of potential problems before.

I would be very thankfull for any help,

Best regards,

Merlin M?heut

-- 
Merlin M?heut
adresse labo:
G?osciences Environnement Toulouse
OMP   - Universit? Paul Sabatier
14 avenue Edouard Belin
31400 Toulouse
FRANCE
tel: (+33) 5 61 33 26 21
adresse personelle:
3 rue du Puits Vert
31000 Toulouse
port: (+33) 6 34 67 57 02
pseudo skype: quantification

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From akohlmey at gmail.com  Fri Nov 25 16:03:36 2011
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Fri, 25 Nov 2011 10:03:36 -0500
Subject: [Pw_forum] Converting pseudopotentials from CPMD
In-Reply-To: <4ECFA5C0.20005@get.obs-mip.fr>
References: <BAY154-W335A2144BCA55515057BA2DAC90@phx.gbl>
	<4ECFA5C0.20005@get.obs-mip.fr>
Message-ID: <CADTmJ6EcBuYiiF9_tpxPkwSfhn8CsFh0PtfBVhqbVpn4H04KUQ@mail.gmail.com>

On Fri, Nov 25, 2011 at 9:27 AM, Merlin Meheut
<merlin.meheut at get.obs-mip.fr> wrote:
> Dear pwscf users,
>
> I am trying to obtain consistent pseudopotentials to use in both CPMD and
> pwscf, precisely for O,H, Si and Li atoms.
> I therefore took pseudopotentials from CPMD and tried the cpmd2upf.x
> converter.
>
> I am however not sure of what I should do. In particular, I am not sure of
> the local reference state used in these pseudos.
> Does this have an influence on the conversion, or is that just an
> information written somewhere in comment in the UPF pseudopotential?
> ?More generally, I am not sure of the recipes used to generate these
> pseudos, and in which
> extent they should be considered in the conversion. THe only information I
> have is inside the preamble of the pseudopotential files
> (Pseudopotential report), which is reproduced below:
>
> For example, for the Li atom, I attached the cpmd pseudopotential and here
> are the instructions I gave for conversion:
>
> $ ./cpmd2upf.x
> Input file > Li_MT_BLYP_NLCC.psp

i don't think that anybody every got the NLCC conversion
from CPMD to UPF working correctly. i remember i tried
several iterations back and forth with paolo many years
ago and then finally went the other route and regenerated
pseudopotentials with from the same settings with paulo's
atomic code and then converted the output to cpmd format
and UPF alike.


> amesh set to: ?1.002086
> ? ?============================================================
> ? ?| ? ?Pseudopotential Report ? ? Thu Aug 22 12:57:11 1996 ? |
> ? ?------------------------------------------------------------
> ? ?| ?s channel: ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?|
> ? ?| ?Atomic Symbol ? ? ? ? ? ? ? ? ? : ? LI ? ? ? ? ? ? ? ? ?|
> ? ?| ?Atomic Number ? ? ? ? ? ? ? ? ? : ? 3 ? ? ? ? ? ? ? ? ? |
> ? ?| ?Number of core states ? ? ? ? ? : ? 1 ? ? ? ? ? ? ? ? ? |
> ? ?| ?Number of valence states ? ? ? ?: ? 1 ? ? ? ? ? ? ? ? ? |
> ? ?| ?Exchange-Correlation Functional : ? ? ? ? ? ? ? ? ? ? ? |
> ? ?| ? ? Slater exchange : ? .6667 ? ? ? ? ? ? ? ? ? ? ? ? ? ?|
> ? ?| ? ? LDA correlation : Lee-Yang-Parr ? ? ? ? ? ? ? ? ? ? ?|
> ? ?| ? ? Exchange GC ? ? : Becke (1988) ? ? ? ? ? ? ? ? ? ? ? |
> ? ?| ? ? Correlation GC ?: Lee-Yang-Parr ? ? ? ? ? ? ? ? ? ? ?|
> ? ?| ?Electron Configuration : ? N ? L ?Occupation ? ? ? ? ? ?|
> ? ?| ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 ? S ? ?2.0000 ? ? ? ? ? ? ?|
> ? ?| ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 ? S ? ?1.0000 ? ? ? ? ? ? ?|
> ? ?| ?Full Potential Total Energy ? ?-7.571372 ? ? ? ? ? ? ? ?|
> ? ?| ?Trouiller-Martins normconserving PP ? ? ? ? ? ? ? ? ? ? |
> ? ?| ? ? n ? ?l ? ? ? ?rc ? ? ? energy ? ? ? ? ? ? ? ? ? ? ? ?|
> ? ?| ? ? 2 ? ?S ? ?2.2000 ? ? ?-.11501 ? ? ? ? ? ? ? ? ? ? ? ?|
> ? ?| ? ? 2 ? ?P ? ?2.2000 ? ? ?-.11501 ? ? ? ? ? ? ? ? ? ? ? ?|
> ? ?| ?Nonlinear core correction ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? |
> ? ?| ?Core charge cutoff radius : ? 1.80000 ? ? ? ? ? ? ? ? ? |
> ? ?| ?Number of Mesh Points : ? 575 ? ? ? ? ? ? ? ? ? ? ? ? ? |
> ? ?| ?Pseudoatom Total Energy ? ?-.205704 ? ? ? ? ? ? ? ? ? ? |
> ? ?============================================================
> ? ?| ?P-channel taken from: ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? |
> ? ?| ? ? 2 ? ?S ? ?2.2000 ? ? ?-.21051 ? ? ? ? ? ? ? ? ? ? ? ?|
> ? ?| ? ? 2 ? ?P ? ?2.2000 ? ? ?-.13639 ? ? ? ? ? ? ? ? ? ? ? ?|
> ? ?| ? ? 3 ? ?D ? ?1.7031 ? ? ?-.13639 ? ? ? ? ? ? ? ? ? ? ? ?|
> ? ?| ?Nonlinear core correction ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? |
> ? ?| ?Core charge cutoff radius : ? 1.80000 ? ? ? ? ? ? ? ? ? |
> ? ?| ?Number of Mesh Points : ? 575 ? ? ? ? ? ? ? ? ? ? ? ? ? |
> ? ?| ?Pseudoatom Total Energy ? ?-.106791 ? ? ? ? ? ? ? ? ? ? |
> ? ?============================================================
> lmax to use. (max. 1) > 1
> l local (max. 1) > 0
> Wavefunction # 1: label, occupancy > 2S, 1.0
> Wavefunction # 2: label, occupancy > 2P, 0.0
> Pseudopotential successfully converted
> Output PP file in UPF format : ?Li_MT_BLYP_NLCC.psp.UPF
> *** PLEASE TEST BEFORE USING!!! ***
> review the content of the PP_INFO fields
>
>
> As you can see in the comment of the cpmd potential, the pseudopotential
> contains potentials (and wavefunctions) for 2S and 2P,
> with the energy of 2P fixed at the same value that 2S.

never trust those comments in CPMD pseudopotentials.
the atomic code creates bogus entries in there (and
nobody seemed to care to fix that issue) and some
people "fix" them afterwards, others don't and some
actually "fix" those tables incorrectly. several potentials
also mix results from different calculations and then
the comments can be completely bogus.

> I am not sure of what recipe it corresponds to: is that some sort of
> Hamann's approach?

the atomic code shipped with CPMD is based on
hamann's code, but heavily hacked.

> Of course, I could test these converted pseudopotentials, but I would like
> to be aware of potential problems before.

i would be very, *very* careful. particularly
on pseudopotentials with NLCC. i suspect,
but never found proof, that there are some
cases where a bug in the atomic code related
to NLCC is compensated by a corresponding
bug in the CPMD code.

axel.

> I would be very thankfull for any help,
>
> Best regards,
>
> Merlin M?heut
>
> --
> Merlin M?heut
> adresse labo:
> G?osciences Environnement Toulouse
> OMP ? - Universit? Paul Sabatier
> 14 avenue Edouard Belin
> 31400 Toulouse
> FRANCE
> tel: (+33) 5 61 33 26 21
> adresse personelle:
> 3 rue du Puits Vert
> 31000 Toulouse
> port: (+33) 6 34 67 57 02
> pseudo skype: quantification
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From merlin.meheut at get.obs-mip.fr  Fri Nov 25 17:02:27 2011
From: merlin.meheut at get.obs-mip.fr (Merlin Meheut)
Date: Fri, 25 Nov 2011 17:02:27 +0100
Subject: [Pw_forum] Converting pseudopotentials from CPMD
In-Reply-To: <CADTmJ6EcBuYiiF9_tpxPkwSfhn8CsFh0PtfBVhqbVpn4H04KUQ@mail.gmail.com>
References: <BAY154-W335A2144BCA55515057BA2DAC90@phx.gbl>	<4ECFA5C0.20005@get.obs-mip.fr>
	<CADTmJ6EcBuYiiF9_tpxPkwSfhn8CsFh0PtfBVhqbVpn4H04KUQ@mail.gmail.com>
Message-ID: <4ECFBC13.8080301@get.obs-mip.fr>


Hi Axel,

Thanks for your help,

To have some understanding on the problem, I compared the original and 
converted pseudopotential files: if they are not exactly the same,
the spatial grid (<PP_R> in the UPF file, first column of all fields for 
CPMD format), the wavefunction values (for 2S and 2P: <PP_PSWFC>
in the UPF file, &WAVEFUNCTION in CPMD) , and the NLCC fields
(<PP_NLCC> in the UPF file, &NLCC in CPMD) are exactly the same in both 
files. I was not too much worried about the nlcc correction, for this 
reason...

However, for the rest of the file, the CPMD file has only a &POTENTIAL 
field wit 2S and 2P potentials, whereas the UPF file have <PP_RAB> ,
<PP_LOCAL>, and <PP_NONLOCAL> fields, and I do not see any agreement 
between the two. What should be the connection?

The cpmd file seems quite simple, with two wavefunctions, two potentials 
and one nlcc field. Where is the difficulty of the conversion?
How are the two formats differing for the potentials? Since I have the 
same values for the wavefunctions, spatial grid and nlcc,
shouldn't I have the same also for  potentials? Maybe this is related to 
a wrong choice for the local part?

By the way, I began by the most difficult case: the O, H and Si 
pseudopotentials I have do not contain nlcc corrections:
do you think that I can trust the conversion, even if I do not give the 
correct local l?

My problem for re-generating a pseudo is that I am not quite confident 
in which recipe to use... Especially for Li....

Since you say cpmd comments can't be trusted, do you think rc are all 
bogus?

Best regards,

Merlin M?heut



On 25/11/2011 16:03, Axel Kohlmeyer wrote:
> On Fri, Nov 25, 2011 at 9:27 AM, Merlin Meheut
> <merlin.meheut at get.obs-mip.fr>  wrote:
>> Dear pwscf users,
>>
>> I am trying to obtain consistent pseudopotentials to use in both CPMD and
>> pwscf, precisely for O,H, Si and Li atoms.
>> I therefore took pseudopotentials from CPMD and tried the cpmd2upf.x
>> converter.
>>
>> I am however not sure of what I should do. In particular, I am not sure of
>> the local reference state used in these pseudos.
>> Does this have an influence on the conversion, or is that just an
>> information written somewhere in comment in the UPF pseudopotential?
>>   More generally, I am not sure of the recipes used to generate these
>> pseudos, and in which
>> extent they should be considered in the conversion. THe only information I
>> have is inside the preamble of the pseudopotential files
>> (Pseudopotential report), which is reproduced below:
>>
>> For example, for the Li atom, I attached the cpmd pseudopotential and here
>> are the instructions I gave for conversion:
>>
>> $ ./cpmd2upf.x
>> Input file>  Li_MT_BLYP_NLCC.psp
> i don't think that anybody every got the NLCC conversion
> from CPMD to UPF working correctly. i remember i tried
> several iterations back and forth with paolo many years
> ago and then finally went the other route and regenerated
> pseudopotentials with from the same settings with paulo's
> atomic code and then converted the output to cpmd format
> and UPF alike.
>
>
>> amesh set to:  1.002086
>>     ============================================================
>>     |    Pseudopotential Report     Thu Aug 22 12:57:11 1996   |
>>     ------------------------------------------------------------
>>     |  s channel:                                              |
>>     |  Atomic Symbol                   :   LI                  |
>>     |  Atomic Number                   :   3                   |
>>     |  Number of core states           :   1                   |
>>     |  Number of valence states        :   1                   |
>>     |  Exchange-Correlation Functional :                       |
>>     |     Slater exchange :   .6667                            |
>>     |     LDA correlation : Lee-Yang-Parr                      |
>>     |     Exchange GC     : Becke (1988)                       |
>>     |     Correlation GC  : Lee-Yang-Parr                      |
>>     |  Electron Configuration :   N   L  Occupation            |
>>     |                             1   S    2.0000              |
>>     |                             2   S    1.0000              |
>>     |  Full Potential Total Energy    -7.571372                |
>>     |  Trouiller-Martins normconserving PP                     |
>>     |     n    l        rc       energy                        |
>>     |     2    S    2.2000      -.11501                        |
>>     |     2    P    2.2000      -.11501                        |
>>     |  Nonlinear core correction                               |
>>     |  Core charge cutoff radius :   1.80000                   |
>>     |  Number of Mesh Points :   575                           |
>>     |  Pseudoatom Total Energy    -.205704                     |
>>     ============================================================
>>     |  P-channel taken from:                                   |
>>     |     2    S    2.2000      -.21051                        |
>>     |     2    P    2.2000      -.13639                        |
>>     |     3    D    1.7031      -.13639                        |
>>     |  Nonlinear core correction                               |
>>     |  Core charge cutoff radius :   1.80000                   |
>>     |  Number of Mesh Points :   575                           |
>>     |  Pseudoatom Total Energy    -.106791                     |
>>     ============================================================
>> lmax to use. (max. 1)>  1
>> l local (max. 1)>  0
>> Wavefunction # 1: label, occupancy>  2S, 1.0
>> Wavefunction # 2: label, occupancy>  2P, 0.0
>> Pseudopotential successfully converted
>> Output PP file in UPF format :  Li_MT_BLYP_NLCC.psp.UPF
>> *** PLEASE TEST BEFORE USING!!! ***
>> review the content of the PP_INFO fields
>>
>>
>> As you can see in the comment of the cpmd potential, the pseudopotential
>> contains potentials (and wavefunctions) for 2S and 2P,
>> with the energy of 2P fixed at the same value that 2S.
> never trust those comments in CPMD pseudopotentials.
> the atomic code creates bogus entries in there (and
> nobody seemed to care to fix that issue) and some
> people "fix" them afterwards, others don't and some
> actually "fix" those tables incorrectly. several potentials
> also mix results from different calculations and then
> the comments can be completely bogus.
>
>> I am not sure of what recipe it corresponds to: is that some sort of
>> Hamann's approach?
> the atomic code shipped with CPMD is based on
> hamann's code, but heavily hacked.
>
>> Of course, I could test these converted pseudopotentials, but I would like
>> to be aware of potential problems before.
> i would be very, *very* careful. particularly
> on pseudopotentials with NLCC. i suspect,
> but never found proof, that there are some
> cases where a bug in the atomic code related
> to NLCC is compensated by a corresponding
> bug in the CPMD code.
>
> axel.
>
>> I would be very thankfull for any help,
>>
>> Best regards,
>>
>> Merlin M?heut
>>
>> --
>> Merlin M?heut
>> adresse labo:
>> G?osciences Environnement Toulouse
>> OMP   - Universit? Paul Sabatier
>> 14 avenue Edouard Belin
>> 31400 Toulouse
>> FRANCE
>> tel: (+33) 5 61 33 26 21
>> adresse personelle:
>> 3 rue du Puits Vert
>> 31000 Toulouse
>> port: (+33) 6 34 67 57 02
>> pseudo skype: quantification
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>


-- 
Merlin M?heut
adresse labo:
G?osciences Environnement Toulouse
OMP   - Universit? Paul Sabatier
14 avenue Edouard Belin
31400 Toulouse
FRANCE
tel: (+33) 5 61 33 26 21
adresse personelle:
3 rue du Puits Vert
31000 Toulouse
port: (+33) 6 34 67 57 02
pseudo skype: quantification


From dmitry at korotin.name  Fri Nov 25 17:21:12 2011
From: dmitry at korotin.name (Dmitry Korotin)
Date: Fri, 25 Nov 2011 22:21:12 +0600
Subject: [Pw_forum] DMFT + LDA
In-Reply-To: <alpine.LFD.2.02.1111231800160.20989@newton.physics.metu.edu.tr>
References: <alpine.LFD.2.02.1111231800160.20989@newton.physics.metu.edu.tr>
Message-ID: <CADfewa6WPwoH3DNNifme1feVQ__W9HMfUxLmocrJ-4dvPj2kBA@mail.gmail.com>

Dear Hande,
your first impression is the right one. The was only one release of
the DMFT code and after that point of my reseach changed a little bit.


2011/11/23 Hande Ustunel <hande at newton.physics.metu.edu.tr>:
> Dear developers,
>
> How may I learn the latest status of the DMFT + LDA streak that was
> initiated a couple of years ago? The related qe-forge has a tar.gz which
> seems to have been uploaded in 2009 and a cursory search in the svn
> snapshot didn't reveal anything to me. I would appreciate any information.
>
> Many thanks in advance.
> Hande
>
> --
> Hande Toffoli
> Department of Physics
> Office 439
> Middle East Technical University
> Ankara 06531, Turkey
> Tel : +90 312 210 3264
> http://www.physics.metu.edu.tr/~hande
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Best regards,
Dmitry Korotin

Institute of Metal Physics
S. Kovalevskaya, 18
620990 Ekaterinburg GSP-170
Russia

From akohlmey at gmail.com  Fri Nov 25 17:24:20 2011
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Fri, 25 Nov 2011 11:24:20 -0500
Subject: [Pw_forum] Converting pseudopotentials from CPMD
In-Reply-To: <4ECFBC13.8080301@get.obs-mip.fr>
References: <BAY154-W335A2144BCA55515057BA2DAC90@phx.gbl>
	<4ECFA5C0.20005@get.obs-mip.fr>
	<CADTmJ6EcBuYiiF9_tpxPkwSfhn8CsFh0PtfBVhqbVpn4H04KUQ@mail.gmail.com>
	<4ECFBC13.8080301@get.obs-mip.fr>
Message-ID: <CADTmJ6EXHtE+1_+Nwy9khDtAsPdVJ24__PuMofn-T_hhbB0zPg@mail.gmail.com>

On Fri, Nov 25, 2011 at 11:02 AM, Merlin Meheut
<merlin.meheut at get.obs-mip.fr> wrote:
>
> Hi Axel,
>
> Thanks for your help,
>
> To have some understanding on the problem, I compared the original and
> converted pseudopotential files: if they are not exactly the same,
> the spatial grid (<PP_R> in the UPF file, first column of all fields for
> CPMD format), the wavefunction values (for 2S and 2P: <PP_PSWFC>
> in the UPF file, &WAVEFUNCTION in CPMD) , and the NLCC fields
> (<PP_NLCC> in the UPF file, &NLCC in CPMD) are exactly the same in both
> files. I was not too much worried about the nlcc correction, for this
> reason...
>
> However, for the rest of the file, the CPMD file has only a &POTENTIAL
> field wit 2S and 2P potentials, whereas the UPF file have <PP_RAB> ,
> <PP_LOCAL>, and <PP_NONLOCAL> fields, and I do not see any agreement
> between the two. What should be the connection?

with CPMD potentials you have to indicate the local potential
in the CPMD input file and then the kleinman-bylander procedure
is done internally in CPMD, whereas in UPF this is already
encoded in the pseudopotential. CPMD also offers to use
gauss-hermite integration instead of kleinman-bylander
(more expensive, but may be needed to avoid ghost
states, e.g. for transition metals).

> The cpmd file seems quite simple, with two wavefunctions, two potentials
> and one nlcc field. Where is the difficulty of the conversion?
> How are the two formats differing for the potentials? Since I have the
> same values for the wavefunctions, spatial grid and nlcc,
> shouldn't I have the same also for ?potentials? Maybe this is related to
> a wrong choice for the local part?

the problems are related to having to anticipate correctly
the transformations, regridding, and re-normalizations that
CPMD is doing. add to that that the occasional factor 2
since CPMD uses hartree atomic units while Q-E uses
rydberg atomic units.

> By the way, I began by the most difficult case: the O, H and Si
> pseudopotentials I have do not contain nlcc corrections:
> do you think that I can trust the conversion, even if I do not give the
> correct local l?

it is always better to start with the easiest case and
make sure that it works. i am not saying that it is
impossible what you want to do, but one has to make
fairly detailed tests and know how the potentials were
created to fill in the blanks. for exactly that reason,
i found it simpler to start from a consistent atomic
code that can produce both, CPMD format and UPF
output, and then feed those potentials to both codes
to see, if they can work well.

> My problem for re-generating a pseudo is that I am not quite confident
> in which recipe to use... Especially for Li....

Li is a quite difficult case. i think the NLCC version
only works well for metallic Li and you may be better
off to do a "semi-core" style potential for ionic Li.

> Since you say cpmd comments can't be trusted, do you think rc are all
> bogus?

cannot trusted means, that you don't know. some are correct,
some are bogus. it all depends on who created the potential
and what this person assumed about how and by whom the
potential will be used. most are more-or-less accurate.
 often you can tell bogus entries if  the energy eigenvalue is
identical to the previous state. but i also have seen potentials,
where the comment section was that of a completely different potential...

that is what i mean by unreliable... you can't really know from the file.

axel.

> Best regards,
>
> Merlin M?heut
>
>
>
> On 25/11/2011 16:03, Axel Kohlmeyer wrote:
>> On Fri, Nov 25, 2011 at 9:27 AM, Merlin Meheut
>> <merlin.meheut at get.obs-mip.fr> ?wrote:
>>> Dear pwscf users,
>>>
>>> I am trying to obtain consistent pseudopotentials to use in both CPMD and
>>> pwscf, precisely for O,H, Si and Li atoms.
>>> I therefore took pseudopotentials from CPMD and tried the cpmd2upf.x
>>> converter.
>>>
>>> I am however not sure of what I should do. In particular, I am not sure of
>>> the local reference state used in these pseudos.
>>> Does this have an influence on the conversion, or is that just an
>>> information written somewhere in comment in the UPF pseudopotential?
>>> ? More generally, I am not sure of the recipes used to generate these
>>> pseudos, and in which
>>> extent they should be considered in the conversion. THe only information I
>>> have is inside the preamble of the pseudopotential files
>>> (Pseudopotential report), which is reproduced below:
>>>
>>> For example, for the Li atom, I attached the cpmd pseudopotential and here
>>> are the instructions I gave for conversion:
>>>
>>> $ ./cpmd2upf.x
>>> Input file> ?Li_MT_BLYP_NLCC.psp
>> i don't think that anybody every got the NLCC conversion
>> from CPMD to UPF working correctly. i remember i tried
>> several iterations back and forth with paolo many years
>> ago and then finally went the other route and regenerated
>> pseudopotentials with from the same settings with paulo's
>> atomic code and then converted the output to cpmd format
>> and UPF alike.
>>
>>
>>> amesh set to: ?1.002086
>>> ? ? ============================================================
>>> ? ? | ? ?Pseudopotential Report ? ? Thu Aug 22 12:57:11 1996 ? |
>>> ? ? ------------------------------------------------------------
>>> ? ? | ?s channel: ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?|
>>> ? ? | ?Atomic Symbol ? ? ? ? ? ? ? ? ? : ? LI ? ? ? ? ? ? ? ? ?|
>>> ? ? | ?Atomic Number ? ? ? ? ? ? ? ? ? : ? 3 ? ? ? ? ? ? ? ? ? |
>>> ? ? | ?Number of core states ? ? ? ? ? : ? 1 ? ? ? ? ? ? ? ? ? |
>>> ? ? | ?Number of valence states ? ? ? ?: ? 1 ? ? ? ? ? ? ? ? ? |
>>> ? ? | ?Exchange-Correlation Functional : ? ? ? ? ? ? ? ? ? ? ? |
>>> ? ? | ? ? Slater exchange : ? .6667 ? ? ? ? ? ? ? ? ? ? ? ? ? ?|
>>> ? ? | ? ? LDA correlation : Lee-Yang-Parr ? ? ? ? ? ? ? ? ? ? ?|
>>> ? ? | ? ? Exchange GC ? ? : Becke (1988) ? ? ? ? ? ? ? ? ? ? ? |
>>> ? ? | ? ? Correlation GC ?: Lee-Yang-Parr ? ? ? ? ? ? ? ? ? ? ?|
>>> ? ? | ?Electron Configuration : ? N ? L ?Occupation ? ? ? ? ? ?|
>>> ? ? | ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 ? S ? ?2.0000 ? ? ? ? ? ? ?|
>>> ? ? | ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 ? S ? ?1.0000 ? ? ? ? ? ? ?|
>>> ? ? | ?Full Potential Total Energy ? ?-7.571372 ? ? ? ? ? ? ? ?|
>>> ? ? | ?Trouiller-Martins normconserving PP ? ? ? ? ? ? ? ? ? ? |
>>> ? ? | ? ? n ? ?l ? ? ? ?rc ? ? ? energy ? ? ? ? ? ? ? ? ? ? ? ?|
>>> ? ? | ? ? 2 ? ?S ? ?2.2000 ? ? ?-.11501 ? ? ? ? ? ? ? ? ? ? ? ?|
>>> ? ? | ? ? 2 ? ?P ? ?2.2000 ? ? ?-.11501 ? ? ? ? ? ? ? ? ? ? ? ?|
>>> ? ? | ?Nonlinear core correction ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? |
>>> ? ? | ?Core charge cutoff radius : ? 1.80000 ? ? ? ? ? ? ? ? ? |
>>> ? ? | ?Number of Mesh Points : ? 575 ? ? ? ? ? ? ? ? ? ? ? ? ? |
>>> ? ? | ?Pseudoatom Total Energy ? ?-.205704 ? ? ? ? ? ? ? ? ? ? |
>>> ? ? ============================================================
>>> ? ? | ?P-channel taken from: ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? |
>>> ? ? | ? ? 2 ? ?S ? ?2.2000 ? ? ?-.21051 ? ? ? ? ? ? ? ? ? ? ? ?|
>>> ? ? | ? ? 2 ? ?P ? ?2.2000 ? ? ?-.13639 ? ? ? ? ? ? ? ? ? ? ? ?|
>>> ? ? | ? ? 3 ? ?D ? ?1.7031 ? ? ?-.13639 ? ? ? ? ? ? ? ? ? ? ? ?|
>>> ? ? | ?Nonlinear core correction ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? |
>>> ? ? | ?Core charge cutoff radius : ? 1.80000 ? ? ? ? ? ? ? ? ? |
>>> ? ? | ?Number of Mesh Points : ? 575 ? ? ? ? ? ? ? ? ? ? ? ? ? |
>>> ? ? | ?Pseudoatom Total Energy ? ?-.106791 ? ? ? ? ? ? ? ? ? ? |
>>> ? ? ============================================================
>>> lmax to use. (max. 1)> ?1
>>> l local (max. 1)> ?0
>>> Wavefunction # 1: label, occupancy> ?2S, 1.0
>>> Wavefunction # 2: label, occupancy> ?2P, 0.0
>>> Pseudopotential successfully converted
>>> Output PP file in UPF format : ?Li_MT_BLYP_NLCC.psp.UPF
>>> *** PLEASE TEST BEFORE USING!!! ***
>>> review the content of the PP_INFO fields
>>>
>>>
>>> As you can see in the comment of the cpmd potential, the pseudopotential
>>> contains potentials (and wavefunctions) for 2S and 2P,
>>> with the energy of 2P fixed at the same value that 2S.
>> never trust those comments in CPMD pseudopotentials.
>> the atomic code creates bogus entries in there (and
>> nobody seemed to care to fix that issue) and some
>> people "fix" them afterwards, others don't and some
>> actually "fix" those tables incorrectly. several potentials
>> also mix results from different calculations and then
>> the comments can be completely bogus.
>>
>>> I am not sure of what recipe it corresponds to: is that some sort of
>>> Hamann's approach?
>> the atomic code shipped with CPMD is based on
>> hamann's code, but heavily hacked.
>>
>>> Of course, I could test these converted pseudopotentials, but I would like
>>> to be aware of potential problems before.
>> i would be very, *very* careful. particularly
>> on pseudopotentials with NLCC. i suspect,
>> but never found proof, that there are some
>> cases where a bug in the atomic code related
>> to NLCC is compensated by a corresponding
>> bug in the CPMD code.
>>
>> axel.
>>
>>> I would be very thankfull for any help,
>>>
>>> Best regards,
>>>
>>> Merlin M?heut
>>>
>>> --
>>> Merlin M?heut
>>> adresse labo:
>>> G?osciences Environnement Toulouse
>>> OMP ? - Universit? Paul Sabatier
>>> 14 avenue Edouard Belin
>>> 31400 Toulouse
>>> FRANCE
>>> tel: (+33) 5 61 33 26 21
>>> adresse personelle:
>>> 3 rue du Puits Vert
>>> 31000 Toulouse
>>> port: (+33) 6 34 67 57 02
>>> pseudo skype: quantification
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>
>>
>
>
> --
> Merlin M?heut
> adresse labo:
> G?osciences Environnement Toulouse
> OMP ? - Universit? Paul Sabatier
> 14 avenue Edouard Belin
> 31400 Toulouse
> FRANCE
> tel: (+33) 5 61 33 26 21
> adresse personelle:
> 3 rue du Puits Vert
> 31000 Toulouse
> port: (+33) 6 34 67 57 02
> pseudo skype: quantification
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From merlin.meheut at get.obs-mip.fr  Fri Nov 25 18:08:19 2011
From: merlin.meheut at get.obs-mip.fr (Merlin Meheut)
Date: Fri, 25 Nov 2011 18:08:19 +0100
Subject: [Pw_forum] Converting pseudopotentials from CPMD
In-Reply-To: <CADTmJ6EXHtE+1_+Nwy9khDtAsPdVJ24__PuMofn-T_hhbB0zPg@mail.gmail.com>
References: <BAY154-W335A2144BCA55515057BA2DAC90@phx.gbl>	<4ECFA5C0.20005@get.obs-mip.fr>	<CADTmJ6EcBuYiiF9_tpxPkwSfhn8CsFh0PtfBVhqbVpn4H04KUQ@mail.gmail.com>	<4ECFBC13.8080301@get.obs-mip.fr>
	<CADTmJ6EXHtE+1_+Nwy9khDtAsPdVJ24__PuMofn-T_hhbB0zPg@mail.gmail.com>
Message-ID: <4ECFCB83.6010307@get.obs-mip.fr>


Dear Axel,

So you say you used ld1.x to generate both UPF and cpmd 
pseudopotentials, or did you use another software?
In INPUT_LD1.txt they say this is still an "experimental feature"...

Which software would you recommend to generate both pseudopotentials 
consistently?
I must admit I am not very confident with using ld1, but if it does the 
job I should be able to handle it
(with a little bit of help probably...) .

Another question: I have a very simple case, the O pseudopotential 
(attached), which seems quite straightforward to convert
(with a 2s2 2p4 configuration, and no other l in the potential):
do you think that with these commands the result should be correct? Even 
if I do not give the local projector originally used?

$ ./cpmd2upf.x
Input file > O_MT_GIA_BLYP
Oxygen  2s2 2p4  BLYP  rc= 1.05 1.05
lmax to use. (max. 1) > 1
l local (max. 1) > 1
Wavefunction # 1: label, occupancy > 2S, 2.0
Wavefunction # 2: label, occupancy > 2P, 4.0
Pseudopotential successfully converted
Output PP file in UPF format :  O_MT_GIA_BLYP.UPF

Thanks in advance,

Merlin M?heut



On 25/11/2011 17:24, Axel Kohlmeyer wrote:
> On Fri, Nov 25, 2011 at 11:02 AM, Merlin Meheut
> <merlin.meheut at get.obs-mip.fr>  wrote:
>> Hi Axel,
>>
>> Thanks for your help,
>>
>> To have some understanding on the problem, I compared the original and
>> converted pseudopotential files: if they are not exactly the same,
>> the spatial grid (<PP_R>  in the UPF file, first column of all fields for
>> CPMD format), the wavefunction values (for 2S and 2P:<PP_PSWFC>
>> in the UPF file,&WAVEFUNCTION in CPMD) , and the NLCC fields
>> (<PP_NLCC>  in the UPF file,&NLCC in CPMD) are exactly the same in both
>> files. I was not too much worried about the nlcc correction, for this
>> reason...
>>
>> However, for the rest of the file, the CPMD file has only a&POTENTIAL
>> field wit 2S and 2P potentials, whereas the UPF file have<PP_RAB>  ,
>> <PP_LOCAL>, and<PP_NONLOCAL>  fields, and I do not see any agreement
>> between the two. What should be the connection?
> with CPMD potentials you have to indicate the local potential
> in the CPMD input file and then the kleinman-bylander procedure
> is done internally in CPMD, whereas in UPF this is already
> encoded in the pseudopotential. CPMD also offers to use
> gauss-hermite integration instead of kleinman-bylander
> (more expensive, but may be needed to avoid ghost
> states, e.g. for transition metals).
>
>> The cpmd file seems quite simple, with two wavefunctions, two potentials
>> and one nlcc field. Where is the difficulty of the conversion?
>> How are the two formats differing for the potentials? Since I have the
>> same values for the wavefunctions, spatial grid and nlcc,
>> shouldn't I have the same also for  potentials? Maybe this is related to
>> a wrong choice for the local part?
> the problems are related to having to anticipate correctly
> the transformations, regridding, and re-normalizations that
> CPMD is doing. add to that that the occasional factor 2
> since CPMD uses hartree atomic units while Q-E uses
> rydberg atomic units.
>
>> By the way, I began by the most difficult case: the O, H and Si
>> pseudopotentials I have do not contain nlcc corrections:
>> do you think that I can trust the conversion, even if I do not give the
>> correct local l?
> it is always better to start with the easiest case and
> make sure that it works. i am not saying that it is
> impossible what you want to do, but one has to make
> fairly detailed tests and know how the potentials were
> created to fill in the blanks. for exactly that reason,
> i found it simpler to start from a consistent atomic
> code that can produce both, CPMD format and UPF
> output, and then feed those potentials to both codes
> to see, if they can work well.
>
>> My problem for re-generating a pseudo is that I am not quite confident
>> in which recipe to use... Especially for Li....
> Li is a quite difficult case. i think the NLCC version
> only works well for metallic Li and you may be better
> off to do a "semi-core" style potential for ionic Li.
>
>> Since you say cpmd comments can't be trusted, do you think rc are all
>> bogus?
> cannot trusted means, that you don't know. some are correct,
> some are bogus. it all depends on who created the potential
> and what this person assumed about how and by whom the
> potential will be used. most are more-or-less accurate.
>   often you can tell bogus entries if  the energy eigenvalue is
> identical to the previous state. but i also have seen potentials,
> where the comment section was that of a completely different potential...
>
> that is what i mean by unreliable... you can't really know from the file.
>
> axel.
>
>> Best regards,
>>
>> Merlin M?heut
>>
>>
>>
>> On 25/11/2011 16:03, Axel Kohlmeyer wrote:
>>> On Fri, Nov 25, 2011 at 9:27 AM, Merlin Meheut
>>> <merlin.meheut at get.obs-mip.fr>    wrote:
>>>> Dear pwscf users,
>>>>
>>>> I am trying to obtain consistent pseudopotentials to use in both CPMD and
>>>> pwscf, precisely for O,H, Si and Li atoms.
>>>> I therefore took pseudopotentials from CPMD and tried the cpmd2upf.x
>>>> converter.
>>>>
>>>> I am however not sure of what I should do. In particular, I am not sure of
>>>> the local reference state used in these pseudos.
>>>> Does this have an influence on the conversion, or is that just an
>>>> information written somewhere in comment in the UPF pseudopotential?
>>>>    More generally, I am not sure of the recipes used to generate these
>>>> pseudos, and in which
>>>> extent they should be considered in the conversion. THe only information I
>>>> have is inside the preamble of the pseudopotential files
>>>> (Pseudopotential report), which is reproduced below:
>>>>
>>>> For example, for the Li atom, I attached the cpmd pseudopotential and here
>>>> are the instructions I gave for conversion:
>>>>
>>>> $ ./cpmd2upf.x
>>>> Input file>    Li_MT_BLYP_NLCC.psp
>>> i don't think that anybody every got the NLCC conversion
>>> from CPMD to UPF working correctly. i remember i tried
>>> several iterations back and forth with paolo many years
>>> ago and then finally went the other route and regenerated
>>> pseudopotentials with from the same settings with paulo's
>>> atomic code and then converted the output to cpmd format
>>> and UPF alike.
>>>
>>>
>>>> amesh set to:  1.002086
>>>>      ============================================================
>>>>      |    Pseudopotential Report     Thu Aug 22 12:57:11 1996   |
>>>>      ------------------------------------------------------------
>>>>      |  s channel:                                              |
>>>>      |  Atomic Symbol                   :   LI                  |
>>>>      |  Atomic Number                   :   3                   |
>>>>      |  Number of core states           :   1                   |
>>>>      |  Number of valence states        :   1                   |
>>>>      |  Exchange-Correlation Functional :                       |
>>>>      |     Slater exchange :   .6667                            |
>>>>      |     LDA correlation : Lee-Yang-Parr                      |
>>>>      |     Exchange GC     : Becke (1988)                       |
>>>>      |     Correlation GC  : Lee-Yang-Parr                      |
>>>>      |  Electron Configuration :   N   L  Occupation            |
>>>>      |                             1   S    2.0000              |
>>>>      |                             2   S    1.0000              |
>>>>      |  Full Potential Total Energy    -7.571372                |
>>>>      |  Trouiller-Martins normconserving PP                     |
>>>>      |     n    l        rc       energy                        |
>>>>      |     2    S    2.2000      -.11501                        |
>>>>      |     2    P    2.2000      -.11501                        |
>>>>      |  Nonlinear core correction                               |
>>>>      |  Core charge cutoff radius :   1.80000                   |
>>>>      |  Number of Mesh Points :   575                           |
>>>>      |  Pseudoatom Total Energy    -.205704                     |
>>>>      ============================================================
>>>>      |  P-channel taken from:                                   |
>>>>      |     2    S    2.2000      -.21051                        |
>>>>      |     2    P    2.2000      -.13639                        |
>>>>      |     3    D    1.7031      -.13639                        |
>>>>      |  Nonlinear core correction                               |
>>>>      |  Core charge cutoff radius :   1.80000                   |
>>>>      |  Number of Mesh Points :   575                           |
>>>>      |  Pseudoatom Total Energy    -.106791                     |
>>>>      ============================================================
>>>> lmax to use. (max. 1)>    1
>>>> l local (max. 1)>    0
>>>> Wavefunction # 1: label, occupancy>    2S, 1.0
>>>> Wavefunction # 2: label, occupancy>    2P, 0.0
>>>> Pseudopotential successfully converted
>>>> Output PP file in UPF format :  Li_MT_BLYP_NLCC.psp.UPF
>>>> *** PLEASE TEST BEFORE USING!!! ***
>>>> review the content of the PP_INFO fields
>>>>
>>>>
>>>> As you can see in the comment of the cpmd potential, the pseudopotential
>>>> contains potentials (and wavefunctions) for 2S and 2P,
>>>> with the energy of 2P fixed at the same value that 2S.
>>> never trust those comments in CPMD pseudopotentials.
>>> the atomic code creates bogus entries in there (and
>>> nobody seemed to care to fix that issue) and some
>>> people "fix" them afterwards, others don't and some
>>> actually "fix" those tables incorrectly. several potentials
>>> also mix results from different calculations and then
>>> the comments can be completely bogus.
>>>
>>>> I am not sure of what recipe it corresponds to: is that some sort of
>>>> Hamann's approach?
>>> the atomic code shipped with CPMD is based on
>>> hamann's code, but heavily hacked.
>>>
>>>> Of course, I could test these converted pseudopotentials, but I would like
>>>> to be aware of potential problems before.
>>> i would be very, *very* careful. particularly
>>> on pseudopotentials with NLCC. i suspect,
>>> but never found proof, that there are some
>>> cases where a bug in the atomic code related
>>> to NLCC is compensated by a corresponding
>>> bug in the CPMD code.
>>>
>>> axel.
>>>
>>>> I would be very thankfull for any help,
>>>>
>>>> Best regards,
>>>>
>>>> Merlin M?heut
>>>>
>>>> --
>>>> Merlin M?heut
>>>> adresse labo:
>>>> G?osciences Environnement Toulouse
>>>> OMP   - Universit? Paul Sabatier
>>>> 14 avenue Edouard Belin
>>>> 31400 Toulouse
>>>> FRANCE
>>>> tel: (+33) 5 61 33 26 21
>>>> adresse personelle:
>>>> 3 rue du Puits Vert
>>>> 31000 Toulouse
>>>> port: (+33) 6 34 67 57 02
>>>> pseudo skype: quantification
>>>>
>>>>
>>>> _______________________________________________
>>>> Pw_forum mailing list
>>>> Pw_forum at pwscf.org
>>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>>
>>>>
>>>
>>
>> --
>> Merlin M?heut
>> adresse labo:
>> G?osciences Environnement Toulouse
>> OMP   - Universit? Paul Sabatier
>> 14 avenue Edouard Belin
>> 31400 Toulouse
>> FRANCE
>> tel: (+33) 5 61 33 26 21
>> adresse personelle:
>> 3 rue du Puits Vert
>> 31000 Toulouse
>> port: (+33) 6 34 67 57 02
>> pseudo skype: quantification
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>


-- 
Merlin M?heut
adresse labo:
G?osciences Environnement Toulouse
OMP   - Universit? Paul Sabatier
14 avenue Edouard Belin
31400 Toulouse
FRANCE
tel: (+33) 5 61 33 26 21
adresse personelle:
3 rue du Puits Vert
31000 Toulouse
port: (+33) 6 34 67 57 02
pseudo skype: quantification

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From hande at newton.physics.metu.edu.tr  Fri Nov 25 18:27:58 2011
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Fri, 25 Nov 2011 19:27:58 +0200 (EET)
Subject: [Pw_forum] DMFT + LDA
In-Reply-To: <CADfewa6WPwoH3DNNifme1feVQ__W9HMfUxLmocrJ-4dvPj2kBA@mail.gmail.com>
References: <alpine.LFD.2.02.1111231800160.20989@newton.physics.metu.edu.tr>
	<CADfewa6WPwoH3DNNifme1feVQ__W9HMfUxLmocrJ-4dvPj2kBA@mail.gmail.com>
Message-ID: <alpine.LFD.2.02.1111251927270.11340@newton.physics.metu.edu.tr>

Dear Dmitry,

Many thanks for the update.

Best wishes,
Hande

On Fri, 25 Nov 2011, Dmitry Korotin wrote:

> Dear Hande,
> your first impression is the right one. The was only one release of
> the DMFT code and after that point of my reseach changed a little bit.
>
>
> 2011/11/23 Hande Ustunel <hande at newton.physics.metu.edu.tr>:
>> Dear developers,
>>
>> How may I learn the latest status of the DMFT + LDA streak that was
>> initiated a couple of years ago? The related qe-forge has a tar.gz which
>> seems to have been uploaded in 2009 and a cursory search in the svn
>> snapshot didn't reveal anything to me. I would appreciate any information.
>>
>> Many thanks in advance.
>> Hande
>>
>> --
>> Hande Toffoli
>> Department of Physics
>> Office 439
>> Middle East Technical University
>> Ankara 06531, Turkey
>> Tel : +90 312 210 3264
>> http://www.physics.metu.edu.tr/~hande
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
> -- 
> Best regards,
> Dmitry Korotin
>
> Institute of Metal Physics
> S. Kovalevskaya, 18
> 620990 Ekaterinburg GSP-170
> Russia
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

--
Hande Toffoli
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande

From akohlmey at gmail.com  Fri Nov 25 18:34:36 2011
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Fri, 25 Nov 2011 12:34:36 -0500
Subject: [Pw_forum] Converting pseudopotentials from CPMD
In-Reply-To: <4ECFCB83.6010307@get.obs-mip.fr>
References: <BAY154-W335A2144BCA55515057BA2DAC90@phx.gbl>
	<4ECFA5C0.20005@get.obs-mip.fr>
	<CADTmJ6EcBuYiiF9_tpxPkwSfhn8CsFh0PtfBVhqbVpn4H04KUQ@mail.gmail.com>
	<4ECFBC13.8080301@get.obs-mip.fr>
	<CADTmJ6EXHtE+1_+Nwy9khDtAsPdVJ24__PuMofn-T_hhbB0zPg@mail.gmail.com>
	<4ECFCB83.6010307@get.obs-mip.fr>
Message-ID: <CADTmJ6GT=ZUXTxkLq+gKLz0Xy3ev=OmJJRNuzrbd7FS-OZWWfQ@mail.gmail.com>

On Fri, Nov 25, 2011 at 12:08 PM, Merlin Meheut
<merlin.meheut at get.obs-mip.fr> wrote:
>
> Dear Axel,
>
> So you say you used ld1.x to generate both UPF and cpmd pseudopotentials, or
> did you use another software?

i used a different software and that was many years ago.

> In INPUT_LD1.txt they say this is still an "experimental feature"...
>
> Which software would you recommend to generate both pseudopotentials
> consistently?

i have no recommendation. i have not created
any pseudopotentials since then and thus have
no idea what shape the various programs are in.

> I must admit I am not very confident with using ld1, but if it does the job
> I should be able to handle it
> (with a little bit of help probably...) .
>
> Another question: I have a very simple case, the O pseudopotential
> (attached), which seems quite straightforward to convert
> (with a 2s2 2p4 configuration, and no other l in the potential):
> do you think that with these commands the result should be correct? Even if
> I do not give the local projector originally used?

the only way to know if the conversion is correct is
to run some test calculations. i don't know what you
mean by " I do not give the local projector originally used?"

axel.


>
> $ ./cpmd2upf.x
> Input file > O_MT_GIA_BLYP
> Oxygen ?2s2 2p4 ?BLYP ?rc= 1.05 1.05
> lmax to use. (max. 1) > 1
> l local (max. 1) > 1
> Wavefunction # 1: label, occupancy > 2S, 2.0
> Wavefunction # 2: label, occupancy > 2P, 4.0
> Pseudopotential successfully converted
> Output PP file in UPF format : ?O_MT_GIA_BLYP.UPF
>
> Thanks in advance,
>
> Merlin M?heut
>
>
>
> On 25/11/2011 17:24, Axel Kohlmeyer wrote:
>>
>> On Fri, Nov 25, 2011 at 11:02 AM, Merlin Meheut
>> <merlin.meheut at get.obs-mip.fr> ?wrote:
>>>
>>> Hi Axel,
>>>
>>> Thanks for your help,
>>>
>>> To have some understanding on the problem, I compared the original and
>>> converted pseudopotential files: if they are not exactly the same,
>>> the spatial grid (<PP_R> ?in the UPF file, first column of all fields for
>>> CPMD format), the wavefunction values (for 2S and 2P:<PP_PSWFC>
>>> in the UPF file,&WAVEFUNCTION in CPMD) , and the NLCC fields
>>> (<PP_NLCC> ?in the UPF file,&NLCC in CPMD) are exactly the same in both
>>> files. I was not too much worried about the nlcc correction, for this
>>> reason...
>>>
>>> However, for the rest of the file, the CPMD file has only a&POTENTIAL
>>> field wit 2S and 2P potentials, whereas the UPF file have<PP_RAB> ?,
>>> <PP_LOCAL>, and<PP_NONLOCAL> ?fields, and I do not see any agreement
>>> between the two. What should be the connection?
>>
>> with CPMD potentials you have to indicate the local potential
>> in the CPMD input file and then the kleinman-bylander procedure
>> is done internally in CPMD, whereas in UPF this is already
>> encoded in the pseudopotential. CPMD also offers to use
>> gauss-hermite integration instead of kleinman-bylander
>> (more expensive, but may be needed to avoid ghost
>> states, e.g. for transition metals).
>>
>>> The cpmd file seems quite simple, with two wavefunctions, two potentials
>>> and one nlcc field. Where is the difficulty of the conversion?
>>> How are the two formats differing for the potentials? Since I have the
>>> same values for the wavefunctions, spatial grid and nlcc,
>>> shouldn't I have the same also for ?potentials? Maybe this is related to
>>> a wrong choice for the local part?
>>
>> the problems are related to having to anticipate correctly
>> the transformations, regridding, and re-normalizations that
>> CPMD is doing. add to that that the occasional factor 2
>> since CPMD uses hartree atomic units while Q-E uses
>> rydberg atomic units.
>>
>>> By the way, I began by the most difficult case: the O, H and Si
>>> pseudopotentials I have do not contain nlcc corrections:
>>> do you think that I can trust the conversion, even if I do not give the
>>> correct local l?
>>
>> it is always better to start with the easiest case and
>> make sure that it works. i am not saying that it is
>> impossible what you want to do, but one has to make
>> fairly detailed tests and know how the potentials were
>> created to fill in the blanks. for exactly that reason,
>> i found it simpler to start from a consistent atomic
>> code that can produce both, CPMD format and UPF
>> output, and then feed those potentials to both codes
>> to see, if they can work well.
>>
>>> My problem for re-generating a pseudo is that I am not quite confident
>>> in which recipe to use... Especially for Li....
>>
>> Li is a quite difficult case. i think the NLCC version
>> only works well for metallic Li and you may be better
>> off to do a "semi-core" style potential for ionic Li.
>>
>>> Since you say cpmd comments can't be trusted, do you think rc are all
>>> bogus?
>>
>> cannot trusted means, that you don't know. some are correct,
>> some are bogus. it all depends on who created the potential
>> and what this person assumed about how and by whom the
>> potential will be used. most are more-or-less accurate.
>> ?often you can tell bogus entries if ?the energy eigenvalue is
>> identical to the previous state. but i also have seen potentials,
>> where the comment section was that of a completely different potential...
>>
>> that is what i mean by unreliable... you can't really know from the file.
>>
>> axel.
>>
>>> Best regards,
>>>
>>> Merlin M?heut
>>>
>>>
>>>
>>> On 25/11/2011 16:03, Axel Kohlmeyer wrote:
>>>>
>>>> On Fri, Nov 25, 2011 at 9:27 AM, Merlin Meheut
>>>> <merlin.meheut at get.obs-mip.fr> ? ?wrote:
>>>>>
>>>>> Dear pwscf users,
>>>>>
>>>>> I am trying to obtain consistent pseudopotentials to use in both CPMD
>>>>> and
>>>>> pwscf, precisely for O,H, Si and Li atoms.
>>>>> I therefore took pseudopotentials from CPMD and tried the cpmd2upf.x
>>>>> converter.
>>>>>
>>>>> I am however not sure of what I should do. In particular, I am not sure
>>>>> of
>>>>> the local reference state used in these pseudos.
>>>>> Does this have an influence on the conversion, or is that just an
>>>>> information written somewhere in comment in the UPF pseudopotential?
>>>>> ? More generally, I am not sure of the recipes used to generate these
>>>>> pseudos, and in which
>>>>> extent they should be considered in the conversion. THe only
>>>>> information I
>>>>> have is inside the preamble of the pseudopotential files
>>>>> (Pseudopotential report), which is reproduced below:
>>>>>
>>>>> For example, for the Li atom, I attached the cpmd pseudopotential and
>>>>> here
>>>>> are the instructions I gave for conversion:
>>>>>
>>>>> $ ./cpmd2upf.x
>>>>> Input file> ? ?Li_MT_BLYP_NLCC.psp
>>>>
>>>> i don't think that anybody every got the NLCC conversion
>>>> from CPMD to UPF working correctly. i remember i tried
>>>> several iterations back and forth with paolo many years
>>>> ago and then finally went the other route and regenerated
>>>> pseudopotentials with from the same settings with paulo's
>>>> atomic code and then converted the output to cpmd format
>>>> and UPF alike.
>>>>
>>>>
>>>>> amesh set to: ?1.002086
>>>>> ? ? ============================================================
>>>>> ? ? | ? ?Pseudopotential Report ? ? Thu Aug 22 12:57:11 1996 ? |
>>>>> ? ? ------------------------------------------------------------
>>>>> ? ? | ?s channel: ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?|
>>>>> ? ? | ?Atomic Symbol ? ? ? ? ? ? ? ? ? : ? LI ? ? ? ? ? ? ? ? ?|
>>>>> ? ? | ?Atomic Number ? ? ? ? ? ? ? ? ? : ? 3 ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ?Number of core states ? ? ? ? ? : ? 1 ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ?Number of valence states ? ? ? ?: ? 1 ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ?Exchange-Correlation Functional : ? ? ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ? ? Slater exchange : ? .6667 ? ? ? ? ? ? ? ? ? ? ? ? ? ?|
>>>>> ? ? | ? ? LDA correlation : Lee-Yang-Parr ? ? ? ? ? ? ? ? ? ? ?|
>>>>> ? ? | ? ? Exchange GC ? ? : Becke (1988) ? ? ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ? ? Correlation GC ?: Lee-Yang-Parr ? ? ? ? ? ? ? ? ? ? ?|
>>>>> ? ? | ?Electron Configuration : ? N ? L ?Occupation ? ? ? ? ? ?|
>>>>> ? ? | ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 ? S ? ?2.0000 ? ? ? ? ? ? ?|
>>>>> ? ? | ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 ? S ? ?1.0000 ? ? ? ? ? ? ?|
>>>>> ? ? | ?Full Potential Total Energy ? ?-7.571372 ? ? ? ? ? ? ? ?|
>>>>> ? ? | ?Trouiller-Martins normconserving PP ? ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ? ? n ? ?l ? ? ? ?rc ? ? ? energy ? ? ? ? ? ? ? ? ? ? ? ?|
>>>>> ? ? | ? ? 2 ? ?S ? ?2.2000 ? ? ?-.11501 ? ? ? ? ? ? ? ? ? ? ? ?|
>>>>> ? ? | ? ? 2 ? ?P ? ?2.2000 ? ? ?-.11501 ? ? ? ? ? ? ? ? ? ? ? ?|
>>>>> ? ? | ?Nonlinear core correction ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ?Core charge cutoff radius : ? 1.80000 ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ?Number of Mesh Points : ? 575 ? ? ? ? ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ?Pseudoatom Total Energy ? ?-.205704 ? ? ? ? ? ? ? ? ? ? |
>>>>> ? ? ============================================================
>>>>> ? ? | ?P-channel taken from: ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ? ? 2 ? ?S ? ?2.2000 ? ? ?-.21051 ? ? ? ? ? ? ? ? ? ? ? ?|
>>>>> ? ? | ? ? 2 ? ?P ? ?2.2000 ? ? ?-.13639 ? ? ? ? ? ? ? ? ? ? ? ?|
>>>>> ? ? | ? ? 3 ? ?D ? ?1.7031 ? ? ?-.13639 ? ? ? ? ? ? ? ? ? ? ? ?|
>>>>> ? ? | ?Nonlinear core correction ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ?Core charge cutoff radius : ? 1.80000 ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ?Number of Mesh Points : ? 575 ? ? ? ? ? ? ? ? ? ? ? ? ? |
>>>>> ? ? | ?Pseudoatom Total Energy ? ?-.106791 ? ? ? ? ? ? ? ? ? ? |
>>>>> ? ? ============================================================
>>>>> lmax to use. (max. 1)> ? ?1
>>>>> l local (max. 1)> ? ?0
>>>>> Wavefunction # 1: label, occupancy> ? ?2S, 1.0
>>>>> Wavefunction # 2: label, occupancy> ? ?2P, 0.0
>>>>> Pseudopotential successfully converted
>>>>> Output PP file in UPF format : ?Li_MT_BLYP_NLCC.psp.UPF
>>>>> *** PLEASE TEST BEFORE USING!!! ***
>>>>> review the content of the PP_INFO fields
>>>>>
>>>>>
>>>>> As you can see in the comment of the cpmd potential, the
>>>>> pseudopotential
>>>>> contains potentials (and wavefunctions) for 2S and 2P,
>>>>> with the energy of 2P fixed at the same value that 2S.
>>>>
>>>> never trust those comments in CPMD pseudopotentials.
>>>> the atomic code creates bogus entries in there (and
>>>> nobody seemed to care to fix that issue) and some
>>>> people "fix" them afterwards, others don't and some
>>>> actually "fix" those tables incorrectly. several potentials
>>>> also mix results from different calculations and then
>>>> the comments can be completely bogus.
>>>>
>>>>> I am not sure of what recipe it corresponds to: is that some sort of
>>>>> Hamann's approach?
>>>>
>>>> the atomic code shipped with CPMD is based on
>>>> hamann's code, but heavily hacked.
>>>>
>>>>> Of course, I could test these converted pseudopotentials, but I would
>>>>> like
>>>>> to be aware of potential problems before.
>>>>
>>>> i would be very, *very* careful. particularly
>>>> on pseudopotentials with NLCC. i suspect,
>>>> but never found proof, that there are some
>>>> cases where a bug in the atomic code related
>>>> to NLCC is compensated by a corresponding
>>>> bug in the CPMD code.
>>>>
>>>> axel.
>>>>
>>>>> I would be very thankfull for any help,
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Merlin M?heut
>>>>>
>>>>> --
>>>>> Merlin M?heut
>>>>> adresse labo:
>>>>> G?osciences Environnement Toulouse
>>>>> OMP ? - Universit? Paul Sabatier
>>>>> 14 avenue Edouard Belin
>>>>> 31400 Toulouse
>>>>> FRANCE
>>>>> tel: (+33) 5 61 33 26 21
>>>>> adresse personelle:
>>>>> 3 rue du Puits Vert
>>>>> 31000 Toulouse
>>>>> port: (+33) 6 34 67 57 02
>>>>> pseudo skype: quantification
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Pw_forum mailing list
>>>>> Pw_forum at pwscf.org
>>>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>>>
>>>>>
>>>>
>>>
>>> --
>>> Merlin M?heut
>>> adresse labo:
>>> G?osciences Environnement Toulouse
>>> OMP ? - Universit? Paul Sabatier
>>> 14 avenue Edouard Belin
>>> 31400 Toulouse
>>> FRANCE
>>> tel: (+33) 5 61 33 26 21
>>> adresse personelle:
>>> 3 rue du Puits Vert
>>> 31000 Toulouse
>>> port: (+33) 6 34 67 57 02
>>> pseudo skype: quantification
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>
>>
>
>
> --
> Merlin M?heut
> adresse labo:
> G?osciences Environnement Toulouse
> OMP ? - Universit? Paul Sabatier
> 14 avenue Edouard Belin
> 31400 Toulouse
> FRANCE
> tel: (+33) 5 61 33 26 21
> adresse personelle:
> 3 rue du Puits Vert
> 31000 Toulouse
> port: (+33) 6 34 67 57 02
> pseudo skype: quantification
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From giannozz at democritos.it  Fri Nov 25 18:46:34 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 25 Nov 2011 18:46:34 +0100
Subject: [Pw_forum] Converting pseudopotentials from CPMD
In-Reply-To: <4ECFBC13.8080301@get.obs-mip.fr>
References: <BAY154-W335A2144BCA55515057BA2DAC90@phx.gbl>	<4ECFA5C0.20005@get.obs-mip.fr>
	<CADTmJ6EcBuYiiF9_tpxPkwSfhn8CsFh0PtfBVhqbVpn4H04KUQ@mail.gmail.com>
	<4ECFBC13.8080301@get.obs-mip.fr>
Message-ID: <130864D5-53AB-4CF1-8FEE-D16868649453@democritos.it>

On Nov 25, 2011, at 17:02 , Merlin Meheut wrote:

> However, for the rest of the file, the CPMD file has only a &POTENTIAL
> field with 2S and 2P potentials, whereas the UPF file have <PP_RAB> ,
> <PP_LOCAL>, and <PP_NONLOCAL> fields, and I do not see any agreement
> between the two. What should be the connection?

the contents of the UPF file is documented (sort of) (but more than  
most other
file formats) here:
    http://www.quantum-espresso.org/wiki/index.php/ 
Unified_pseudopotential_format
UPF always assumes a fully nonlocal form. Most other file formats  
assume the
semilocal form. Transforming the latter into the former requires  
atomic (pseudo-)
orbitals and a choice for the local reference term (Kleinman-Bylander  
transformation).
Unless you use the Gauss-Hermite technique, you also need to choose a
local potential in CPMD (for light elements, l=1 is the typical  
choice). Of course,
the choice of the local potential affects the results, sometimes in  
catastrophic
ways.

> The cpmd file seems quite simple, with two wavefunctions, two  
> potentials
> and one nlcc field. Where is the difficulty of the conversion?

oh, nothing: trivial stuff. You just have to spend a few days chasing  
errors
before realizing that there is a missing 2 or r^2 or 1/r factor  
somewhere.
And don't count on documentation: reverse engineering is the only thing
that (sometimes) works.

I have recently used and extended the cpmd2upf converter. All  
improvements
are in the 4.3.2 version: more checks, more CPMD formats are recognized.
I am not aware of any major problem, but I haven't tried anything with
core corrections.

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 iyad.ne at gmail.com  Fri Nov 25 18:50:48 2011
From: iyad.ne at gmail.com (IYAD AL-QASIR)
Date: Fri, 25 Nov 2011 12:50:48 -0500
Subject: [Pw_forum] PH_DFT+U_Occupation Matrix
Message-ID: <CAJMDj41rkLfSYdeb15poArFb_KF9SfREb2gvteP60Mfmaj10ow@mail.gmail.com>

Hello,
I have two questions regarding phonon calculations of UO2:
1- Does QE support phonon calculations with DFT+U? When I try to apply this
functional, I got a message " DFT+U " is not implemented yet for phonon
calculations, Please confirm, or advice if there is an alternative way.

2- How can I monitor the occupation matrix of the correlated electrons. In
case of DFT+U, there are many metastable states, so it is difficult to
reach the true ground state.  In literature (Phys. Rev B 79, 235125) they
try to monitor this matrix and imposed an initial particular
diagonalization, How can I control this in QE?

Note:occupation matrix represents the way of filling the electrons, for
example for 5f levels, we have two* f *electrons (in case of UO2) so the
matrix has 7x7 ( where *mi* and *mj* goes form -3 to +3), and there are 21
possibility of filling this matrix.


Kindest Regards,
_______________________________
IYAD I. AL-QASIR, PhD
Research Associate

Department of Nuclear Engineering
North Carolina State University
Campus Box 7909
2500 Stinson Dr.
Raleigh, NC 27695-7909
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From giannozz at democritos.it  Fri Nov 25 22:13:22 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 25 Nov 2011 22:13:22 +0100
Subject: [Pw_forum] PH_DFT+U_Occupation Matrix
In-Reply-To: <CAJMDj41rkLfSYdeb15poArFb_KF9SfREb2gvteP60Mfmaj10ow@mail.gmail.com>
References: <CAJMDj41rkLfSYdeb15poArFb_KF9SfREb2gvteP60Mfmaj10ow@mail.gmail.com>
Message-ID: <D0564B0F-528A-4A97-B7D4-1FB2B849A42A@democritos.it>


On Nov 25, 2011, at 18:50 , IYAD AL-QASIR wrote:

> 1- Does QE support phonon calculations with DFT+U?

http://www.democritos.it/pipermail/pw_forum/2011-April/019992.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 iyad.ne at gmail.com  Sat Nov 26 00:09:52 2011
From: iyad.ne at gmail.com (IYAD AL-QASIR)
Date: Fri, 25 Nov 2011 18:09:52 -0500
Subject: [Pw_forum] PH_DFT+U_Occupation Matrix
In-Reply-To: <D0564B0F-528A-4A97-B7D4-1FB2B849A42A@democritos.it>
References: <CAJMDj41rkLfSYdeb15poArFb_KF9SfREb2gvteP60Mfmaj10ow@mail.gmail.com>
	<D0564B0F-528A-4A97-B7D4-1FB2B849A42A@democritos.it>
Message-ID: <CAJMDj4242vkQ-JkqUeJu=6bpK+Gh7iwqGvHg3gp+uJkjKr8iNg@mail.gmail.com>

Thanks Paolo,
Does that mean only the latest versions of (QE) Phonon code support DFT+U.
I am using QE version 4.0.3 because this is the only version compatible
with EPW code (Electron-Phonon with Wannier 90).

Thanks again.


On Fri, Nov 25, 2011 at 4:13 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Nov 25, 2011, at 18:50 , IYAD AL-QASIR wrote:
>
> > 1- Does QE support phonon calculations with DFT+U?
>
> http://www.democritos.it/pipermail/pw_forum/2011-April/019992.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
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
_______________________________
IYAD I. AL-QASIR, PhD
Research Associate

Department of Nuclear Engineering
North Carolina State University
Campus Box 7909
2500 Stinson Dr.
Raleigh, NC 27695-7909
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From iyad.ne at gmail.com  Sat Nov 26 00:31:08 2011
From: iyad.ne at gmail.com (IYAD AL-QASIR)
Date: Fri, 25 Nov 2011 18:31:08 -0500
Subject: [Pw_forum] PH_DFT+U_Occupation Matrix
In-Reply-To: <CAJMDj4242vkQ-JkqUeJu=6bpK+Gh7iwqGvHg3gp+uJkjKr8iNg@mail.gmail.com>
References: <CAJMDj41rkLfSYdeb15poArFb_KF9SfREb2gvteP60Mfmaj10ow@mail.gmail.com>
	<D0564B0F-528A-4A97-B7D4-1FB2B849A42A@democritos.it>
	<CAJMDj4242vkQ-JkqUeJu=6bpK+Gh7iwqGvHg3gp+uJkjKr8iNg@mail.gmail.com>
Message-ID: <CAJMDj40hVKLQm-35V19ynV8SD11zU=S-MreqDvFumJaJKD2HtQ@mail.gmail.com>

Hello Paolo,

One more thing, I was looking at phonon.f90 ( QE version 4.3.) There is a
comment says
! Not implemented in ph.x:
  ! [6] [5] + constraints on the magnetization
  ! [7] [6] + Hubbard U
  ! [8] [7] + Hybrid functionals
  ! [9] ? + External Electric field

Could you explain?
Thanks


On Fri, Nov 25, 2011 at 6:09 PM, IYAD AL-QASIR <iyad.ne at gmail.com> wrote:

> Thanks Paolo,
> Does that mean only the latest versions of (QE) Phonon code support DFT+U.
> I am using QE version 4.0.3 because this is the only version compatible
> with EPW code (Electron-Phonon with Wannier 90).
>
> Thanks again.
>
>
>
> On Fri, Nov 25, 2011 at 4:13 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:
>
>>
>> On Nov 25, 2011, at 18:50 , IYAD AL-QASIR wrote:
>>
>> > 1- Does QE support phonon calculations with DFT+U?
>>
>> http://www.democritos.it/pipermail/pw_forum/2011-April/019992.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
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
> --
> _______________________________
> IYAD I. AL-QASIR, PhD
> Research Associate
>
> Department of Nuclear Engineering
> North Carolina State University
> Campus Box 7909
> 2500 Stinson Dr.
> Raleigh, NC 27695-7909
>



-- 
_______________________________
IYAD I. AL-QASIR, PhD
Research Associate

Department of Nuclear Engineering
North Carolina State University
Campus Box 7909
2500 Stinson Dr.
Raleigh, NC 27695-7909
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From giannozz at democritos.it  Sat Nov 26 09:03:28 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 26 Nov 2011 09:03:28 +0100
Subject: [Pw_forum] PH_DFT+U_Occupation Matrix
In-Reply-To: <CAJMDj4242vkQ-JkqUeJu=6bpK+Gh7iwqGvHg3gp+uJkjKr8iNg@mail.gmail.com>
References: <CAJMDj41rkLfSYdeb15poArFb_KF9SfREb2gvteP60Mfmaj10ow@mail.gmail.com>
	<D0564B0F-528A-4A97-B7D4-1FB2B849A42A@democritos.it>
	<CAJMDj4242vkQ-JkqUeJu=6bpK+Gh7iwqGvHg3gp+uJkjKr8iNg@mail.gmail.com>
Message-ID: <2ADF171C-74BA-4F52-896E-CCEB67985C39@democritos.it>


On Nov 26, 2011, at 24:09 , IYAD AL-QASIR wrote:

> Does that mean only the latest versions of (QE) Phonon code support  
> DFT+U.

no, it means that wotk is under way, but there is (yet ) no public  
version of QE
supporting phonons in DFT+U

---
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 tribhuwan.physics at gmail.com  Sun Nov 27 06:07:35 2011
From: tribhuwan.physics at gmail.com (Tribhuwan Pandey)
Date: Sun, 27 Nov 2011 10:37:35 +0530
Subject: [Pw_forum] phonon life time calculation
Message-ID: <CACKvTSM+HkhmP_ua13=oAR3ex=fmvhVRtq0sEP372xSWH_u40Q@mail.gmail.com>

Hi all
       I am doing phonon life time calculation for Silicon on a 2*2*2
supercell using Quantum Espresso.In phonon calculation at gamma point my
Calculation is showing some error.

My Scf calculation input file is
&control
    calculation='scf'
    restart_mode='from_scratch',
    !pseudo_dir='directory where ps
    !outdir='directory where large files are written/'
    pseudo_dir='./',
    outdir='./',
    prefix='PH',
    !ldisp=.true.
/
 &system
    ibrav=0,
    celldm(1)=20.40,
    nat=64, ntyp=1,
    ecutwfc =24.0
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
/
 CELL_PARAMETERS
      1.00  0.00  0.00
l
    calculation='scf'
    restart_mode='from_scratch',
    !pseudo_dir='directory where ps
    !outdir='directory where large files are written/'
    pseudo_dir='./',
    outdir='./',
    prefix='PH',
    !ldisp=.true.
/
 &system
    ibrav=0,
    celldm(1)=20.40,
    nat=64, ntyp=1,
    ecutwfc =24.0
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
/
 CELL_PARAMETERS
"si.scf.in" [converted] 94L, 1711C                            1,1
Top

      0.00  1.00  0.00
      0.00  0.00  1.00
ATOMIC_SPECIES
 Si  28.0855  Si.vbc.UPF
ATOMIC_POSITIONS
Si      0.25    0       0.25
Si      0.75    0       0.25
Si      0.25    0.5     0.25
Si      0.75    0.5     0.25
Si      0.25    0       0.75
Si      0.75    0       0.75
Si      0.25    0.5     0.75
Si      0.75    0.5     0.75
Si      0       0.25    0.25
Si      0.5     0.25    0.25
Si      0       0.75    0.25
Si      0.5     0.75    0.25
Si      0       0.25    0.75
Si      0.5     0.25    0.75
Si      0       0.75    0.75
Si      0.5     0.75    0.75
Si      0.125   0.125   0.125
Si      0.625   0.125   0.125
Si      0.125   0.625   0.125
Si      0.625   0.625   0.125
Si      0.125   0.125   0.625
Si      0.625   0.125   0.625
Si      0.125   0.625   0.625
Si      0.625   0.625   0.625
Si      0.125   0.375   0.375
Si      0.625   0.375   0.375
Si      0.125   0.875   0.375
Si      0.625   0.875   0.375
Si      0.125   0.375   0.875
Si      0.625   0.375   0.875
Si      0.125   0.875   0.875
Si      0.625   0.875   0.875
Si      0.375   0.375   0.125
Si      0.875   0.375   0.125
Si      0.375   0.875   0.125
Si      0.875   0.875   0.125
Si      0.375   0.375   0.625
Si      0.875   0.375   0.625
Si      0.375   0.875   0.625
Si      0.875   0.875   0.625
Si      0.375   0.125   0.375
Si      0.875   0.125   0.375
Si      0.375   0.625   0.375
Si      0.875   0.625   0.375
Si      0.375   0.125   0.875
Si      0.875   0.125   0.875
Si      0.375   0.625   0.875
Si      0.875   0.625   0.875
Si      0       0       0
Si      0.5     0       0
Si      0       0.5     0
Si      0.5     0.5     0
Si      0       0       0.5
Si      0.5     0       0.5
Si      0       0.5     0.5
Si      0.5     0.5     0.5
Si      0.25    0.25    0
Si      0.75    0.25    0
Si      0.25    0.75    0
Si      0.75    0.75    0
Si      0.25    0.25    0.5
Si      0.75    0.25    0.5
Si      0.25    0.75    0.5
Si      0.75    0.75    0.5
K_POINTS {automatic}
2 2 2 0 0 0





My si.phG.in File is
phonons of Si at Gamma
 &inputph
  tr2_ph=1.0d-12,
  prefix='PH',
  epsil=.false.,
  trans=.true.,
  zue=.false.,
amass(1)=28.0855
amass(2)=28.0855
amass(3)=28.0855
amass(4)=28.0855
amass(5)=28.0855
amass(6)=28.0855
amass(7)=28.0855
amass(8)=28.0855
amass(9)=28.0855
amass(10)=28.0855
amass(11)=28.0855
amass(12)=28.0855
amass(13)=28.0855
amass(14)=28.0855
amass(15)=28.0855
amass(16)=28.0855
amass(17)=28.0855
amass(18)=28.0855
amass(19)=28.0855
amass(20)=28.0855
amass(21)=28.0855
amass(22)=28.0855
amass(23)=28.0855
amass(24)=28.0855
amass(25)=28.0855
amass(26)=28.0855
amass(27)=28.0855
amass(28)=28.0855
amass(29)=28.0855
amass(30)=28.0855
amass(31)=28.0855
amass(32)=28.0855
amass(33)=28.0855
amass(34)=28.0855
amass(35)=28.0855
amass(36)=28.0855
amass(37)=28.0855
amass(38)=28.0855
amass(39)=28.0855
amass(40)=28.0855
amass(41)=28.0855
amass(42)=28.0855
amass(43)=28.0855
amass(44)=28.0855
amass(45)=28.0855
amass(46)=28.0855
amass(47)=28.0855
amass(48)=28.0855
amass(49)=28.0855
amass(50)=28.0855
amass(51)=28.0855
amass(52)=28.0855
amass(53)=28.0855
amass(54)=28.0855
amass(55)=28.0855
amass(56)=28.0855
amass(57)=28.0855
amass(58)=28.0855
amass(59)=28.0855
amass(60)=28.0855
amass(61)=28.0855
amass(62)=28.0855
amass(63)=28.0855
amass(64)=28.0855
  outdir='./',
  fildyn='si.dyn_G',
 fildrho='si.drho_G',
 /
0.0 0.0 0.0


And the error is
reading inputph namelist
     from phq_readin : error #        19
     reading inputph namelist
     from phq_readin : error #        19


I am a new user to quatum espresso .
*Can anyone help me in this matter?

Thanks a lot

*with regards
Tribhuwan
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From jun.physics at gmail.com  Sun Nov 27 07:37:31 2011
From: jun.physics at gmail.com (Jun Liu)
Date: Sun, 27 Nov 2011 00:37:31 -0600
Subject: [Pw_forum] hybrid xc implemented in QE?
Message-ID: <CA+1PuT_JCyvO=YDr6nsetb=UXiCJQe+QwpNwvsSThji4bkM_xw@mail.gmail.com>

Dear All,

I downloaded the latest QE and found that "exact exchange (HF) and hybrid
functionals (PBE0, B3LYP, HSE)" can be done. But in the code "setup.f90"
there are several lines of code saying:

#if ! defined (EXX)
  IF ( dft_is_hybrid() ) CALL errore( 'setup ', &
                         'HYBRID XC not implemented in PWscf', 1 )
#else
  IF ( dft_is_hybrid() ) THEN
     IF (.NOT. lscf) CALL errore( 'setup ', &
                         'HYBRID XC not allowed in non-scf calculations', 1
)
     IF ( okvan .OR. okpaw ) CALL errore( 'setup ', &
                         'HYBRID XC not implemented for USPP or PAW', 1 )
  END IF
#endif

I then am confused. It seems that if exx_fraction is set nonzero, then
setup will complain "HYBRID XC not implemented in PWscf"

Thanks for clarification.

-- 
Sincerely,
Jun
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From zdw2000 at gmail.com  Sun Nov 27 12:02:59 2011
From: zdw2000 at gmail.com (Wei Zhou)
Date: Sun, 27 Nov 2011 19:02:59 +0800
Subject: [Pw_forum] does anyone has a TM PBE pseudopotential of Se that can
	work at 300GPa?
Message-ID: <CALT5NLe+kUJZySpAMBoQS=kOfFO7Mt+r9si63LnZkqjwg2UoAA@mail.gmail.com>

I need it to some calculations, thank you in advance.
there are only ultrasoft pseudo potential in the pwscf pseudo potential
libary.

-- 
ZhouDawei
JiLin Universiyt ,ChangChun ,China
zdw2000 at gmail.com
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From giuseppe.mattioli at mlib.ism.cnr.it  Sun Nov 27 12:12:49 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it)
Date: Sun, 27 Nov 2011 12:12:49 +0100
Subject: [Pw_forum] hybrid xc implemented in QE?
In-Reply-To: <CA+1PuT_JCyvO=YDr6nsetb=UXiCJQe+QwpNwvsSThji4bkM_xw@mail.gmail.com>
References: <CA+1PuT_JCyvO=YDr6nsetb=UXiCJQe+QwpNwvsSThji4bkM_xw@mail.gmail.com>
Message-ID: <20111127121249.1xw1ue468gwk48sw@webmail.sic.rm.cnr.it>


Dear Jun Liu
Please read the
$ yourQE/examples/EXX_example/README file

Giuseppe


Giuseppe Mattioli
ISM-CNR
Italy

Quoting Jun Liu <jun.physics at gmail.com>:

> Dear All,
>
> I downloaded the latest QE and found that "exact exchange (HF) and hybrid
> functionals (PBE0, B3LYP, HSE)" can be done. But in the code "setup.f90"
> there are several lines of code saying:
>
> #if ! defined (EXX)
>   IF ( dft_is_hybrid() ) CALL errore( 'setup ', &
>                          'HYBRID XC not implemented in PWscf', 1 )
> #else
>   IF ( dft_is_hybrid() ) THEN
>      IF (.NOT. lscf) CALL errore( 'setup ', &
>                          'HYBRID XC not allowed in non-scf calculations', 1
> )
>      IF ( okvan .OR. okpaw ) CALL errore( 'setup ', &
>                          'HYBRID XC not implemented for USPP or PAW', 1 )
>   END IF
> #endif
>
> I then am confused. It seems that if exx_fraction is set nonzero, then
> setup will complain "HYBRID XC not implemented in PWscf"
>
> Thanks for clarification.
>
> --
> Sincerely,
> Jun
>





From akohlmey at gmail.com  Sun Nov 27 20:40:04 2011
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Sun, 27 Nov 2011 14:40:04 -0500
Subject: [Pw_forum] hybrid xc implemented in QE?
In-Reply-To: <CA+1PuT_JCyvO=YDr6nsetb=UXiCJQe+QwpNwvsSThji4bkM_xw@mail.gmail.com>
References: <CA+1PuT_JCyvO=YDr6nsetb=UXiCJQe+QwpNwvsSThji4bkM_xw@mail.gmail.com>
Message-ID: <CADTmJ6Hnz-HSrSR2VGJPXT4umNjLOp8hZxWxxWNGjvoQQ7ifdg@mail.gmail.com>

On Sun, Nov 27, 2011 at 1:37 AM, Jun Liu <jun.physics at gmail.com> wrote:
> Dear All,
>
> I downloaded the latest QE and found that "exact exchange (HF) and hybrid
> functionals (PBE0, B3LYP, HSE)" can be done. But in the code "setup.f90"
> there are several lines of code saying:
>
> #if ! defined (EXX)
> ? IF ( dft_is_hybrid() ) CALL errore( 'setup ', &
> ???????????????????????? 'HYBRID XC not implemented in PWscf', 1 )
> #else
> ? IF ( dft_is_hybrid() ) THEN
> ???? IF (.NOT. lscf) CALL errore( 'setup ', &
> ???????????????????????? 'HYBRID XC not allowed in non-scf calculations', 1
> )
> ???? IF ( okvan .OR. okpaw ) CALL errore( 'setup ', &
> ???????????????????????? 'HYBRID XC not implemented for USPP or PAW', 1 )
> ? END IF
> #endif
>
> I then am confused. It seems that if exx_fraction is set nonzero, then setup
> will complain "HYBRID XC not implemented in PWscf"

please note the #if !defined(EXX) clause.

this is a preprocessor directive, requiring you to compile the entire source
with -DEXX to include support for exact exchange. thus regular default
executables (which do not have this set) will give you the error, but properly
compiled ones won't.

cheers,
    axel.

> Thanks for clarification.
>
> --
> Sincerely,
> Jun
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From payam.norouzzadeh at gmail.com  Sun Nov 27 20:59:09 2011
From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh)
Date: Sun, 27 Nov 2011 23:29:09 +0330
Subject: [Pw_forum] Symmetry rotational matrix
Message-ID: <CAND4gJHOGfUc7=35P29OYDiWnLH_FTa9KoerY+emYOoR5vtojg@mail.gmail.com>

Hello Q.E users
A quick question: Does pwscf calculate symmetry rotation matrices?
Best regards,Payam Norouzzadeh
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From giannozz at democritos.it  Sun Nov 27 20:59:29 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 27 Nov 2011 20:59:29 +0100
Subject: [Pw_forum] phonon life time calculation
In-Reply-To: <CACKvTSM+HkhmP_ua13=oAR3ex=fmvhVRtq0sEP372xSWH_u40Q@mail.gmail.com>
References: <CACKvTSM+HkhmP_ua13=oAR3ex=fmvhVRtq0sEP372xSWH_u40Q@mail.gmail.com>
Message-ID: <3DD9B860-0294-4A73-A6DE-46B0014C086B@democritos.it>


On Nov 27, 2011, at 6:07 , Tribhuwan Pandey wrote:

> amass(1)=28.0855
> [...]
> amass(64)=28.0855

amass should specified for each type of atoms. There is
just one type of atoms, not 64, in your input

> I am a new user to quastum espresso .

new users need to read the documentation more than old users

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 avallabh at purdue.edu  Mon Nov 28 01:19:00 2011
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Sun, 27 Nov 2011 19:19:00 -0500 (EST)
Subject: [Pw_forum] Query on "e-ph interaction coefficients
In-Reply-To: <245719357.155288.1322438721451.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <701665415.155337.1322439540928.JavaMail.root@mailhub016.itcs.purdue.edu>

Dear users,

                 I had recently started working on Quantum espresso. I was doing the tutorials on e-ph interaction coeff's tutorial on aluminium. I ran the simulation at point X. The following is a part of the output in which i want to know what few things represent. 

- what does the two irreducible representations mean ? It shows that it is related to atomic displacements, but i could not see what does the terms "Representation  1 1 modes -A_2u X_4' M_4' To be done " means and what does the term 1 modes  and 2 modes stand for ?


Thanks
Ajit  
 



************************************************************************************
     Atomic displacements:
     There are   2 irreducible representations

     Representation     1      1 modes -A_2u X_4' M_4' To be done

     Representation     2      2 modes -E_u  X_5' M_5' To be done


     Representation #  1 mode #   1

     Self-consistent Calculation

      iter #   1 total cpu time :    27.1 secs   av.it.:   3.9
      thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.735E-04

      iter #   2 total cpu time :    28.0 secs   av.it.:   5.4
      thresh= 0.857E-03 alpha_mix =  0.700 |ddv_scf|^2 =  0.311E-04

      iter #   3 total cpu time :    29.0 secs   av.it.:   5.1
      thresh= 0.558E-03 alpha_mix =  0.700 |ddv_scf|^2 =  0.526E-08

      iter #   4 total cpu time :    29.9 secs   av.it.:   5.4
      thresh= 0.725E-05 alpha_mix =  0.700 |ddv_scf|^2 =  0.289E-10

      iter #   5 total cpu time :    30.8 secs   av.it.:   5.1
      thresh= 0.537E-06 alpha_mix =  0.700 |ddv_scf|^2 =  0.779E-14

     End of self-consistent calculation

     Convergence has been achieved 


     Representation #  2 modes #   2  3

     Self-consistent Calculation

      iter #   1 total cpu time :    33.4 secs   av.it.:   3.5
      thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.298E-06

      iter #   2 total cpu time :    35.4 secs   av.it.:   6.2
      thresh= 0.546E-04 alpha_mix =  0.700 |ddv_scf|^2 =  0.406E-08

      iter #   3 total cpu time :    37.3 secs   av.it.:   5.7
      thresh= 0.637E-05 alpha_mix =  0.700 |ddv_scf|^2 =  0.401E-09

      iter #   4 total cpu time :    39.2 secs   av.it.:   5.5
      thresh= 0.200E-05 alpha_mix =  0.700 |ddv_scf|^2 =  0.119E-13

      iter #   5 total cpu time :    41.3 secs   av.it.:   6.4
      thresh= 0.109E-07 alpha_mix =  0.700 |ddv_scf|^2 =  0.471E-15

     End of self-consistent calculation

     Convergence has been achieved 
 
     Number of q in the star =    3
     List of q in the star:
          1   0.000000000   0.000000000   1.000000000
          2   0.000000000   1.000000000   0.000000000
          3   1.000000000   0.000000000   0.000000000

     Diagonalizing the dynamical matrix

     q = (    0.000000000   0.000000000   1.000000000 ) 

 **************************************************************************
     omega( 1) =       6.001070 [THz] =     200.174161 [cm-1]
     omega( 2) =       6.001070 [THz] =     200.174161 [cm-1]
     omega( 3) =       9.595361 [THz] =     320.066785 [cm-1]
 **************************************************************************

     Mode symmetry, D_4h(4/mmm) point group:

     omega(  1 -  2) =        200.2  [cm-1]   --> E_u  X_5' M_5'     
     omega(  3 -  3) =        320.1  [cm-1]   --> A_2u X_4' M_4'     

 **************************************************************************

From mtorabi at uwo.ca  Mon Nov 28 06:12:31 2011
From: mtorabi at uwo.ca (Amin Torabi)
Date: Mon, 28 Nov 2011 00:12:31 -0500
Subject: [Pw_forum] input structure for ibrav=9
Message-ID: <CAEXRF5yntH6kDQ80OstjM8rsEkBZEc0b9ckP+0BirrkxTKBbXQ@mail.gmail.com>

Dear QE users,

I have some problem in introducing a base-centered orthorhombic
structure (ibrav=9) to QE.

I have entered the cell parameters in A, B, C, cosAB, cosBC, cosAC, and
atomic positions in fractional coordinate (crystal) in my input file;
however, Xcrysden does not show me what I expected to see. for example, not
all the angles are 90 degrees.

Lets say I have a crystal with space group Cmcm (#63) and a=2.406, b=4.615,
c=2.749 (A), and one atom at (0, 0.0703, 0.25)
Now, what do you put for A,B,C and the atomic positions?

Thanks for your time!

P.S: The numbers are taken from the table 2 of the supplemental material
of: Phys. Rev. B 84, 104118 (2011)

-- 
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 germaneau at gucas.ac.cn  Mon Nov 28 19:28:20 2011
From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=)
Date: Mon, 28 Nov 2011 13:28:20 -0500
Subject: [Pw_forum] input structure for ibrav=9
In-Reply-To: <522455035.01473@gscas.net.cn>
References: <522455035.01473@gscas.net.cn>
Message-ID: <4ED3D2C4.4090205@gucas.ac.cn>

Hey Amin,

it seems to ma that when you set ibrav you have to set celldm variables 
as well.
In you case, try to not use A,B,C, ... but rather to set celldm(1) to 
the value of A (in Bohr!!), celldm(2) and celldm(3) to b/a and c/a 
respectively.
Hope it helps,

              ?ric.

On 11/28/2011 12:12 AM, Amin Torabi wrote:
> Dear QE users,
>
> I have some problem in introducing a base-centered orthorhombic 
> structure (ibrav=9) to QE.
>
> I have entered the cell parameters in A, B, C, cosAB, cosBC, cosAC, 
> and atomic positions in fractional coordinate (crystal) in my input 
> file; however, Xcrysden does not show me what I expected to see. for 
> example, not all the angles are 90 degrees.
>
> Lets say I have a crystal with space group Cmcm (#63) and a=2.406, 
> b=4.615, c=2.749 (A), and one atom at (0, 0.0703, 0.25)
> Now, what do you put for A,B,C and the atomic positions?
>
> Thanks for your time!
>
> P.S: The numbers are taken from the table 2 of the supplemental 
> material of: Phys. Rev. B 84, 104118 (2011)
>
> -- 
> 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 
<http://www.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>

Graduate University of Chinese Academy of Sciences
College of Physical 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 giannozz at democritos.it  Mon Nov 28 08:10:09 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 28 Nov 2011 08:10:09 +0100
Subject: [Pw_forum] input structure for ibrav=9
In-Reply-To: <4ED3D2C4.4090205@gucas.ac.cn>
References: <522455035.01473@gscas.net.cn> <4ED3D2C4.4090205@gucas.ac.cn>
Message-ID: <BC29EB12-38CD-4DA8-87EC-2B02140BAA66@democritos.it>


On Nov 28, 2011, at 19:28 , ?ric Germaneau wrote:

> it seems to ma that when you set ibrav you have to set celldm  
> variables as well.

not necessarily so

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  Mon Nov 28 09:38:51 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 28 Nov 2011 09:38:51 +0100
Subject: [Pw_forum] input structure for ibrav=9
In-Reply-To: <CAEXRF5yntH6kDQ80OstjM8rsEkBZEc0b9ckP+0BirrkxTKBbXQ@mail.gmail.com>
References: <CAEXRF5yntH6kDQ80OstjM8rsEkBZEc0b9ckP+0BirrkxTKBbXQ@mail.gmail.com>
Message-ID: <01E3A5D7-F401-4284-9D23-EED8A57AD4C7@democritos.it>


On Nov 28, 2011, at 6:12 , Amin Torabi wrote:

> I have some problem in introducing a base-centered orthorhombic  
> structure (ibrav=9) to QE.
>
> I have entered the cell parameters in A, B, C, cosAB, cosBC, cosAC

you need only A, B, C (in Angstrom); cosAB, cosBC, cosAB are ignored.
Or: celldm(1)=a (in Bohr), celldm(2)=b/a, celldm(3)=c/a (celldm(4:6)  
ignored).

This is what you will get for the three unit translations v1, v2, v3
                 9          Orthorhombic base-centered(bco) celldm(2) 
=b/a
                                                            celldm(3) 
=c/a
                     v1 = (a/2, b/2,0),  v2 = (-a/2,b/2,0),  v3 =  
(0,0,c)

In the development version of QE, also ibrav=-9 is present:
                -9          as 9, alternate description
                     v1 = (a/2,-b/2,0),  v2 = (a/2,-b/2,0),  v3 =  
(0,0,c)

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 mulwawinfred at gmail.com  Mon Nov 28 14:33:20 2011
From: mulwawinfred at gmail.com (Winfred Mulwa)
Date: Mon, 28 Nov 2011 16:33:20 +0300
Subject: [Pw_forum] Bands of Doped rutile(TiO2)
Message-ID: <CAOH0W45844K4NFSUhqiE7hgcRvFS+WzYwec7Y-SAQA=JiEKzJg@mail.gmail.com>

Dear all,
  I am creating bands of doped rutile, i want to show a different color for
the dopant band.
Please some body assist me on how to do it.
                    Regards.

Mulwa Winfred.
M Phil Student, Computational Material Science Group,
Chepkoilel University College
Eldoret, Kenya.
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From mtorabi at uwo.ca  Mon Nov 28 15:19:33 2011
From: mtorabi at uwo.ca (Amin Torabi)
Date: Mon, 28 Nov 2011 09:19:33 -0500
Subject: [Pw_forum] input structure for ibrav=9
In-Reply-To: <01E3A5D7-F401-4284-9D23-EED8A57AD4C7@democritos.it>
References: <CAEXRF5yntH6kDQ80OstjM8rsEkBZEc0b9ckP+0BirrkxTKBbXQ@mail.gmail.com>
	<01E3A5D7-F401-4284-9D23-EED8A57AD4C7@democritos.it>
Message-ID: <CAEXRF5y+SxTghQ4r5MEALquWQL17CqaeTr=so0savda5-vKuAA@mail.gmail.com>

Dear Paolo,
I did exactly the same thing, but I expect to see all the angles to be 90,
while Xcrysden does not exhibit this.
How come V1 and V2 are not orthogonal?
And do I have to express the fractional atomic position in terms of A,B,C
or V1, V2 and V3?
Amin

On Mon, Nov 28, 2011 at 3:38 AM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Nov 28, 2011, at 6:12 , Amin Torabi wrote:
>
> > I have some problem in introducing a base-centered orthorhombic
> > structure (ibrav=9) to QE.
> >
> > I have entered the cell parameters in A, B, C, cosAB, cosBC, cosAC
>
> you need only A, B, C (in Angstrom); cosAB, cosBC, cosAB are ignored.
> Or: celldm(1)=a (in Bohr), celldm(2)=b/a, celldm(3)=c/a (celldm(4:6)
> ignored).
>
> This is what you will get for the three unit translations v1, v2, v3
>                 9          Orthorhombic base-centered(bco) celldm(2)
> =b/a
>                                                            celldm(3)
> =c/a
>                     v1 = (a/2, b/2,0),  v2 = (-a/2,b/2,0),  v3 =
> (0,0,c)
>
> In the development version of QE, also ibrav=-9 is present:
>                -9          as 9, alternate description
>                     v1 = (a/2,-b/2,0),  v2 = (a/2,-b/2,0),  v3 =
> (0,0,c)
>
> 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
>



-- 
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 giannozz at democritos.it  Mon Nov 28 17:06:16 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 28 Nov 2011 17:06:16 +0100
Subject: [Pw_forum] input structure for ibrav=9
In-Reply-To: <CAEXRF5y+SxTghQ4r5MEALquWQL17CqaeTr=so0savda5-vKuAA@mail.gmail.com>
References: <CAEXRF5yntH6kDQ80OstjM8rsEkBZEc0b9ckP+0BirrkxTKBbXQ@mail.gmail.com>
	<01E3A5D7-F401-4284-9D23-EED8A57AD4C7@democritos.it>
	<CAEXRF5y+SxTghQ4r5MEALquWQL17CqaeTr=so0savda5-vKuAA@mail.gmail.com>
Message-ID: <0B170A6B-A0ED-4210-BA84-7B94B52E92CE@democritos.it>


On Nov 28, 2011, at 15:19 , Amin Torabi wrote:

> How come V1 and V2 are not orthogonal?

why should they be orthogonal? The three basis vectors are orthogonal
only for simple orthorhombic.

> And do I have to express the fractional atomic position in terms of  
> A,B,C
> or V1, V2 and V3?

this is something that you have to know. Atomic positions are sometimes
given as cartesian coordinates, sometimes as fractional coordinates
xV_1 + yV_2 + yV_3. Of course the values of x,y,z may depend upon
the choice of V_1, V_2, V_3

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  Mon Nov 28 17:19:38 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 28 Nov 2011 17:19:38 +0100
Subject: [Pw_forum] Query on "e-ph interaction coefficients
In-Reply-To: <701665415.155337.1322439540928.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <701665415.155337.1322439540928.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <DA180D42-B071-4454-B425-28E48ACADDB1@democritos.it>

On Nov 28, 2011, at 1:19 , Ajit Vallabhaneni wrote:

> what does the term 1 modes  and 2 modes stand for ?

one-dimensional, two dimensional irreducible representations.
Do you know group theory?

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  Mon Nov 28 17:20:20 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 28 Nov 2011 17:20:20 +0100
Subject: [Pw_forum] Symmetry rotational matrix
In-Reply-To: <CAND4gJHOGfUc7=35P29OYDiWnLH_FTa9KoerY+emYOoR5vtojg@mail.gmail.com>
References: <CAND4gJHOGfUc7=35P29OYDiWnLH_FTa9KoerY+emYOoR5vtojg@mail.gmail.com>
Message-ID: <805E884C-D466-429F-98E0-8464ADCE3103@democritos.it>


On Nov 27, 2011, at 20:59 , Payam Norouzzadeh wrote:

> A quick question: Does pwscf calculate symmetry rotation matrices?

and prints them if you specify " verbosity='high' "

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 avallabh at purdue.edu  Mon Nov 28 17:34:17 2011
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Mon, 28 Nov 2011 11:34:17 -0500 (EST)
Subject: [Pw_forum] Query on "e-ph interaction coefficients
In-Reply-To: <DA180D42-B071-4454-B425-28E48ACADDB1@democritos.it>
Message-ID: <215934586.157481.1322498057432.JavaMail.root@mailhub016.itcs.purdue.edu>

Dear Paolo,

            I studied little bit of group theory in the context of algebra a while back. Can you please suggest any reference in the present context if possible? 

Thanks
Ajit

From baroni at sissa.it  Mon Nov 28 18:24:01 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 28 Nov 2011 18:24:01 +0100
Subject: [Pw_forum] Symmetry rotational matrix
In-Reply-To: <CAND4gJHOGfUc7=35P29OYDiWnLH_FTa9KoerY+emYOoR5vtojg@mail.gmail.com>
References: <CAND4gJHOGfUc7=35P29OYDiWnLH_FTa9KoerY+emYOoR5vtojg@mail.gmail.com>
Message-ID: <8FB87EF1-DE8B-41BF-8624-B5D06B5FEDA8@sissa.it>

An even quicker answer: yes. SB

On Nov 27, 2011, at 8:59 PM, Payam Norouzzadeh wrote:

> Hello Q.E users
> A quick question: Does pwscf calculate symmetry rotation matrices?
> Best regards,Payam Norouzzadeh
> _______________________________________________
> 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

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From baroni at sissa.it  Mon Nov 28 18:31:47 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 28 Nov 2011 18:31:47 +0100
Subject: [Pw_forum] Query on "e-ph interaction coefficients
In-Reply-To: <215934586.157481.1322498057432.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <215934586.157481.1322498057432.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <76B54BEF-537D-484A-96B4-133D5E443D1F@sissa.it>


On Nov 28, 2011, at 5:34 PM, Ajit Vallabhaneni wrote:

> Dear Paolo,
> 
>            I studied little bit of group theory in the context of algebra a while back.

this is probably not quite enough for your purposes

> Can you please suggest any reference in the present context if possible? 

Group theory used to be a standard component of any graduate course in solid-state theory, when I was a student (i.e. quite some time ago). Plenty of references on this topic. You may want to start from:

Symmetry in the Solid State, by Knox & Gold
Symmetry principles in solid state and molecular physics, by Lax
Group theory in quantum mechanics, by Heine

or many other titles that you will easily discover by "googling"

HTH - SB

> 
> Thanks
> Ajit
> _______________________________________________
> 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

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From payam.norouzzadeh at gmail.com  Mon Nov 28 18:44:30 2011
From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh)
Date: Mon, 28 Nov 2011 11:44:30 -0600
Subject: [Pw_forum] Symmetry rotational matrix
Message-ID: <CAND4gJFJA8P1fcAtthtxcnVdRHKPbEQ+aQN1Fw6g=LdUkmNHzA@mail.gmail.com>

Thank you Prof.Giannozzi for your answer.
Best regards,Payam Norouzzadeh
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From tanyciquantum at gmail.com  Tue Nov 29 01:59:53 2011
From: tanyciquantum at gmail.com (Tian yongchao)
Date: Tue, 29 Nov 2011 08:59:53 +0800
Subject: [Pw_forum] how to make a input file for the vdW_kernel_table
Message-ID: <CAKQZyJoEZaDtQDzb3f4E0JHnWPSX77LYhE+gsYc1N+f__o2O8g@mail.gmail.com>

*Dear all

   i'm facing a problem about how to make a input file for the**
vdW_**kernel_table
. i have read the " generate_vdw_kernel_table.f90 " . there are still some
questions about it . in this file , i found this :

"
 CHANGE THESE VALUES AT YOUR OWN RISK

  integer, parameter :: Nqs = 20

  real(dp), dimension(Nqs):: q_mesh = (/  1.00D-5, 0.0449420825586261D0,
0.0975593700991365D0, &
       0.159162633466142D0, 0.231286496836006D0, 0.315727667369529D0,
0.414589693721418D0, &
       0.530335368404141D0, 0.665848079422965D0, 0.824503639537924D0,
1.010254382520950D0, &
       1.227727621364570D0, 1.482340921174910D0, 1.780437058359530D0,
2.129442028133640D0, &
       2.538050036534580D0, 3.016440085356680D0, 3.576529545442460D0,
4.232271035198720D0, &
       5.0D0 /)
"

i do not know what " q_mesh " means , whether it is diffierent if i
calcualte differenet systems .

**thanks in advance



tanyci

nankai university , tinajin

China *
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From w2agz at w2agz.com  Tue Nov 29 07:58:39 2011
From: w2agz at w2agz.com (W2AGZ)
Date: Mon, 28 Nov 2011 22:58:39 -0800
Subject: [Pw_forum] PlotPhon Questions...Again
Message-ID: <2cea01ccae64$54384c00$fca8e400$@w2agz.com>

A few weeks ago I posted a request for information on the pw.x, ph.x and
q2r.x input files used to create the Al444.fc file employed in the relevant
PlotPhon example.  I did receive some feedback on "how to use" PlotPhon, but
that was not what I was after.  In addition, I am particularly interested in
the protocol used to create the various templates in the its (PlotPhon)
Include directory.   For example, the opening comments to the Fortran source
file, K_for_bands.f90,  in the PlotPhon package, contains the statement, in
effect, that "the basis vectors for the reciprocal lattice are taken from
scf.out."  It seems clear this was not the case for Al444.at least not that
I could discern from other QE examples addressing Al.e.g., Example07.
Moreover,  the text file for "Al444 fcc Include" seems not to follow the
usual Bouchardt-Smoluchosky-Wigner (sorry for the spelling.I've been out of
graduate school a long time) notation and respective high symmetry k-vector
lengths for the fcc lattice.at least as set out in the Setyawan-Curtarolo
review  (ComMatSci 49 (2010) 299-312).  And I was unable to reproduce the
contents of "ph.grid" using the k-path tool of XCrySDen applied to fcc Al.
Is there today a generally agreed-upon standard formulation for space
groups, especially for those symmetries less than cubic, hexagonal,
tetragonal, and orthorhombic?  Say on the Bilbao website, or those for DFT
resources other than QE (VASP, Crystal, CASTEP.)?  And conversion tools to
switch back and forth between POSCAR, CIF, "pw.x input," and whatever?

 

Sorry for the above polemic and my likely ignorance in overlooking possibly
important resources.

 

Paul Michael Grant, PhD

Physicist and Science Writer

Senior Life Fellow, American Physical Society

Fellow, Institute of Physics, United Kingdom

Staff Associate, Jet Propulsion Laboratory, NASA (2011)

Visiting Scholar, Applied Physics, Stanford (2005-2008)

EPRI Science Fellow (Retired)

IBM Research Staff Member Emeritus

Principal, W2AGZ Technologies

 <mailto:w2agz at w2agz.com> w2agz at w2agz.com

 <http://www.w2agz.com/> http://www.w2agz.com

 

 

 

 

 

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From giannozz at democritos.it  Tue Nov 29 09:36:25 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 29 Nov 2011 09:36:25 +0100
Subject: [Pw_forum] does anyone has a TM PBE pseudopotential of Se that
	can work at 300GPa?
In-Reply-To: <CALT5NLe+kUJZySpAMBoQS=kOfFO7Mt+r9si63LnZkqjwg2UoAA@mail.gmail.com>
References: <CALT5NLe+kUJZySpAMBoQS=kOfFO7Mt+r9si63LnZkqjwg2UoAA@mail.gmail.com>
Message-ID: <3FDA9F34-FB83-4FBE-9968-5ADBA1A36538@democritos.it>

The development version of QE can translate GTH
(Goedecker-Teter-Hutter) pseudopotentials from CPMD
to UPF format. GTH PPs are quite hard so they should
work well at high pressures. See here:
http://www.fisica.uniud.it/~giannozz/public/Se-q6.txt.UPF
May or may not work. Note that you may need to
manually add the pseudo-orbitals to the PP_PSWFC section

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 zdw2000 at gmail.com  Tue Nov 29 10:57:41 2011
From: zdw2000 at gmail.com (Wei Zhou)
Date: Tue, 29 Nov 2011 17:57:41 +0800
Subject: [Pw_forum] does anyone has a TM PBE pseudopotential of Se that
 can work at 300GPa?
In-Reply-To: <3FDA9F34-FB83-4FBE-9968-5ADBA1A36538@democritos.it>
References: <CALT5NLe+kUJZySpAMBoQS=kOfFO7Mt+r9si63LnZkqjwg2UoAA@mail.gmail.com>
	<3FDA9F34-FB83-4FBE-9968-5ADBA1A36538@democritos.it>
Message-ID: <CALT5NLcuw50=nU=p2-f_LOhuux83JFdCT+aAVNLqvgLMJYOKMA@mail.gmail.com>

thanks for Paolo's replies in details,
I will try .
BestRegards

2011/11/29 Paolo Giannozzi <giannozz at democritos.it>

> The development version of QE can translate GTH
> (Goedecker-Teter-Hutter) pseudopotentials from CPMD
> to UPF format. GTH PPs are quite hard so they should
> work well at high pressures. See here:
> http://www.fisica.uniud.it/~giannozz/public/Se-q6.txt.UPF
> May or may not work. Note that you may need to
> manually add the pseudo-orbitals to the PP_PSWFC section
>
> 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
>



-- 
ZhouDawei
JiLin Universiyt ,ChangChun ,China
zdw2000 at gmail.com
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From deepak.p.thakur at gmail.com  Tue Nov 29 17:35:00 2011
From: deepak.p.thakur at gmail.com (Dipak Thakur)
Date: Tue, 29 Nov 2011 22:05:00 +0530
Subject: [Pw_forum] change in Fermi Energy with ecutoff, Vacuum and degauss
Message-ID: <CAHvg=eK6=u=4HCRdOn1Y9YGT1gmOek8mf7D=1ZRVs+J_Tcr2Jg@mail.gmail.com>

Hello every one.

I am perplexed by change in Fermi energy with change in ecutoff, Vacuum and
degauss.

I have done some calculations using a set of ecutoff, Vacuum and degauss
and then repeated the same for other set of ecutoff, Vacuum and degauss.

I have obtained a value of -0.756 eV for Fermi energy in case where the
ecutoff was 60 Ry., Vacuum was 20 A and degauss was 0.02, whereas for the
second set with ecutoff of 20 Ry., Vacuum of 10 A and degauss of 0.002 the
Fermi energy was 3.0097 eV.

Can anyone help me which value of Fermi energy is correct and why?

Please help me in understanding the what wrong am I doing?

The calculations are related to graphene with Aluminium dopant (one atom of
Al and 31 carbon atoms).

Thanks and regards
Deepak Thakur
Research student
Swami Ramanand Teerth Marathwada University, Nanded.
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From giannozz at democritos.it  Tue Nov 29 21:31:40 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 29 Nov 2011 21:31:40 +0100
Subject: [Pw_forum] change in Fermi Energy with ecutoff,
	Vacuum and degauss
In-Reply-To: <CAHvg=eK6=u=4HCRdOn1Y9YGT1gmOek8mf7D=1ZRVs+J_Tcr2Jg@mail.gmail.com>
References: <CAHvg=eK6=u=4HCRdOn1Y9YGT1gmOek8mf7D=1ZRVs+J_Tcr2Jg@mail.gmail.com>
Message-ID: <70DAA912-9C42-4868-AD01-C9C68EAF4F50@democritos.it>


On Nov 29, 2011, at 17:35 , Dipak Thakur wrote:

> I am perplexed by change in Fermi energy with change in ecutoff,  
> Vacuum and degauss.

http://www.quantum-espresso.org/user_guide/ 
node64.html#SECTION000137090000000000000
>


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 eariel99 at gmail.com  Wed Nov 30 12:34:47 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Wed, 30 Nov 2011 12:34:47 +0100
Subject: [Pw_forum] change in Fermi Energy with ecutoff,
	Vacuum and degauss
Message-ID: <CAM5Vcw8csLmyW94biPqJFMKJFutv6VVYYC-tvzZ-XBENb6WfYQ@mail.gmail.com>

Deepak,
Periodic calculations have several components of the electrostatic energy
that are separately infinite, but added they cancel. Instead of dealing
with infinites, they are usually eliminated in plane wave codes setting to
0 the G=0 components of the Fourier transforms. I guess that Quantum
ESPRESSO  satisfies this rule. A component V(G=0)  is just the spatial
average of V(r), meaning in practice that  the electrostatic potential (the
Hartree part) is adjusted to zero. The amount of vacuum volume in the
supercell represents a weight for the spatial averages. If you change from
10 to 20 angstroms of vacumm width, you are doubling the weight of the
vacuum part in the average.

If the average were not adjusted to zero,  then I would expect that the
average tends softly to cero for infinite vacuum volume, and the Fermi
level converge to a constant value. As the average potential is
artificially shifted to zero, the Fermi level experiments the opposite
shift. For more interesting details, take a look at PRB 77, 115139 (2008).

Best regards


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

---------- Mensaje reenviado ----------
From: Dipak Thakur <deepak.p.thakur at gmail.com>
To: pw_forum at pwscf.org
Date: Tue, 29 Nov 2011 22:05:00 +0530
Subject: [Pw_forum] change in Fermi Energy with ecutoff, Vacuum and degauss
Hello every one.

I am perplexed by change in Fermi energy with change in ecutoff, Vacuum and
degauss.

I have done some calculations using a set of ecutoff, Vacuum and degauss
and then repeated the same for other set of ecutoff, Vacuum and degauss.

I have obtained a value of -0.756 eV for Fermi energy in case where the
ecutoff was 60 Ry., Vacuum was 20 A and degauss was 0.02, whereas for the
second set with ecutoff of 20 Ry., Vacuum of 10 A and degauss of 0.002 the
Fermi energy was 3.0097 eV.

Can anyone help me which value of Fermi energy is correct and why?

Please help me in understanding the what wrong am I doing?

The calculations are related to graphene with Aluminium dopant (one atom of
Al and 31 carbon atoms).

Thanks and regards
Deepak Thakur
Research student
Swami Ramanand Teerth Marathwada University, Nanded.
--
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From nicvok at freenet.de  Wed Nov 30 17:16:53 2011
From: nicvok at freenet.de (Nicki Frank Hinsche)
Date: Wed, 30 Nov 2011 17:16:53 +0100
Subject: [Pw_forum] site-projected bandstructre
References: <C03C7B7C-B875-490C-96A9-9C2817565D0E@physik.uni-halle.de>
Message-ID: <393A9F3B-B0E8-4091-A228-768B4E3A9E8F@freenet.de>

Dear all,

is there a possibility to gain a "site-projected" bandstructure in QE?  
Assuming I have an ordered compound ABC.
Is it possible to project the contribution of A,B,C to the  
wavefunction coefficients at a certain k-vector and energy?
I want to gain informations like: the bands in this area of the  
Brillouin zone at this energy are mainly formed by
atom sort A (B,C). I want to go definitely beyond site-projected  
density of states.

I am thankful for every idea,

bests Nicki

-------------------------------------------------------------
Nicki Frank Hinsche, Dipl. Phys.
Institute of physics - Theoretical physics,
Martin-Luther-University Halle-Wittenberg,
Von-Seckendorff-Platz 1, Room 1.18/1.07
D-06120 Halle/Saale, Germany
Tel.: ++49 345 5525450
Tel.: ++49 345 5525462
-------------------------------------------------------------
Fellow of the International Max Planck Re-
search School-MPI for Microstructure Physics
-------------------------------------------------------------



From s.m.rezaeisani at gmail.com  Wed Nov 30 19:49:30 2011
From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani)
Date: Wed, 30 Nov 2011 22:19:30 +0330
Subject: [Pw_forum] Phonon calculations
In-Reply-To: <CAJMDj41r5ZFa2dQGgD8X+L6t_2VtqTXdgU06zUzA=6cH5ydmTQ@mail.gmail.com>
References: <CAJMDj41r5ZFa2dQGgD8X+L6t_2VtqTXdgU06zUzA=6cH5ydmTQ@mail.gmail.com>
Message-ID: <CAADUHk=XwuTZP2q_PGsC3gFWr5PG9JdxqFniwF1Zc+UkMnP2hQ@mail.gmail.com>

Dear IYAD I. AL-QASIR

1. Reduce the alpha_mix(1) by default 0.7, e.g. to 0.4.
2. If it doesn't work, open PH/phcom.f90 and change
  INTEGER, PARAMETER :: maxter = 100
to something larger. ***Then recompile the
code***.

On Wed, Nov 23, 2011 at 7:39 PM, IYAD AL-QASIR <iyad.ne at gmail.com> wrote:

> Hello,
> I am trying to calculate the phonon dispersion relations and phonon
> density of states of UO2.
> Please find the attached filesUO2.scf.in and UO2.ph.in
>
> The calculations assume GGA and include spin-polarized effects.
>
> There are 6 representations and nine modes. The problem I have is: When I
> run the input file UO2.ph.in, *the scf calculation* for the  the second
> representation of the second mode for q (-0.1666667   0.1666667  -0.1666667)
> * is not converge.*
>
> Notes:
> 1- My runs assume UO2  is metallic, in fact UO2 is insulator with band gap
> of 2eV.( However, when I do the calculations using the VASP code I got very
> good result only by including the polarization effects)
> 2- In order to account for the band gap, one should implement the Hubbard
> term (LDA/GGA+U)
> 3- I tried different occupations  (smearing, tetrahedra)
> 4- I tried different starting_magnetization= 0.5, 1.0
> 5- I treid different mixing_betas (0.7, 0.35 )
> 5- the lattice parameter a= 10.285, is based on optimizing the structure
> and including spin-polarization effects.
>
>
> Any adivce to overcome this problem is highly welcomed.
>
> Kindest Regards,
> ______________________________
> aIYAD I. AL-QASIR, PhD
> Research Associate
>
> Department of Nuclear Engineering
> North Carolina State University
> Campus Box 7909
> 2500 Stinson Dr.
> Raleigh, NC 27695-7909
>
>
>
> --
> _______________________________
> IYAD I. AL-QASIR, PhD
> Research Associate
>
> Department of Nuclear Engineering
> North Carolina State University
> Campus Box 7909
> 2500 Stinson Dr.
> Raleigh, NC 27695-7909
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
==========================================
Seyed Mojtaba Rezaei Sani
Computational Materials Science 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 kacper.druzbicki at uj.edu.pl  Wed Nov 30 19:46:36 2011
From: kacper.druzbicki at uj.edu.pl (=?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?=)
Date: Wed, 30 Nov 2011 19:46:36 +0100
Subject: [Pw_forum] dynmat.x - segmentation fault error
In-Reply-To: <70DAA912-9C42-4868-AD01-C9C68EAF4F50@democritos.it>
References: <CAHvg=eK6=u=4HCRdOn1Y9YGT1gmOek8mf7D=1ZRVs+J_Tcr2Jg@mail.gmail.com>
	<70DAA912-9C42-4868-AD01-C9C68EAF4F50@democritos.it>
Message-ID: <fb47124a56a2.4ed6881c@uj.edu.pl>

Dear QE users,

I get the following error while trying to diagonalize the dynamic matrix for the 186 atomic system.

"
     Reading Dynamical Matrix from file matdyn
     ...Force constants read
     ...epsilon and Z* read
Segmentation fault
"

Below you can find the dynmat file and the input for dynmat.x.

http://www.sendspace.com/file/pd9w9u

Any ideas? I would appreciate if one could check the file on his machine.

Thank you in advance,
Casper

Kacper Dru?bicki,
Faculty of Chemistry,
Department of Chemical Physics,
Jagiellonian University,
Ingardena Street 3, 30-060 Krak?w, Poland
phone: +48 12 6632265


From suza.rri at gmail.com  Wed Nov 30 22:32:15 2011
From: suza.rri at gmail.com (Suza W)
Date: Wed, 30 Nov 2011 22:32:15 +0100
Subject: [Pw_forum] DC & BEC
Message-ID: <CALN9FpQvushRa6mtNbzPeDPc7JLp_td+=ab8AqLt5O-g_xgPXg@mail.gmail.com>

Dear All,

Being an epitome of ferroelectric, BaTiO3 has extensively been
studied using PWSCF. However,  unfortunately, with several
standard available USPP, I encounter  following unphysical  results :


     Dielectric constant in cartesian axis

          (-8142842.391767483       0.000000000       0.000000000 )
          (       0.000000000-8142842.391767481       0.000000000 )
          (       0.000000000       0.000000000-8142842.391767476 )

          Effective charges (d Force / dE) in cartesian axis

           atom      1   Ba
      Ex  (    -1136.43937        0.00000        0.00000 )
      Ey  (        0.00000    -1136.43937        0.00000 )
      Ez  (        0.00000        0.00000    -1136.43937 )
           atom      2   Ti
      Ex  (    -1874.03151        0.00000        0.00000 )
      Ey  (        0.00000    -1874.03151        0.00000 )
      Ez  (        0.00000        0.00000    -1874.03151 )
           atom      3   O
      Ex  (      931.42284        0.00000        0.00000 )
      Ey  (        0.00000     1067.39482        0.00000 )
      Ez  (        0.00000        0.00000     1067.39482 )
           atom      4   O
      Ex  (     1067.39482        0.00000        0.00000 )
      Ey  (        0.00000      931.42284        0.00000 )
      Ez  (        0.00000        0.00000     1067.39482 )
           atom      5   O
      Ex  (     1067.39482        0.00000        0.00000 )
      Ey  (        0.00000     1067.39482        0.00000 )
      Ez  (        0.00000        0.00000      931.42284 )

Any suggestion for correcting these errors will be highly appreciated.
Here goes the input file which renders such a blunder.
 &system
    ibrav =  1,
    celldm(1) = 7.5589,
    nat = 5,
    ntyp=3,
    ecutwfc = 30.0,
        ecutrho = 240.0,
 /
 &electrons
    diagonalization = 'david'
    conv_thr =  1.0d-9
    mixing_beta = 0.7
 /
 &ions
 /
 &cell
 /
ATOMIC_SPECIES
 Ba  137.327       Ba.pbe-nsp-van.UPF
 Ti   47.867       Ti.pbe-sp-van_ak.UPF
 O    15.9994      O.pbe-van_ak.UPF
ATOMIC_POSITIONS (alat)
Ba  0.0  0.0  0.0
Ti  0.5  0.5  0.5
O  0.0  0.5  0.5
O  0.5  0.0  0.5
O  0.5  0.5  0.0
K_POINTS {automatic}
 8 8 8  1 1 1

Thanking you,
Yours sincerely,
Suza W
PhD Student
Department of Materials Science
Bangalore
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From w2agz at w2agz.com  Wed Nov 30 22:49:43 2011
From: w2agz at w2agz.com (W2AGZ)
Date: Wed, 30 Nov 2011 13:49:43 -0800
Subject: [Pw_forum] PWgui Locate Error
Message-ID: <518201ccafa9$f9414580$ebc3d080$@w2agz.com>

Using a freshly installed PWgui-4.3, either "standalone" or "source," trying
to open any pw.x input file, either from the example folder or elsewhere
gives the following error message.  All other input types (ph.x, pp.x, etc.)
load just fine.  BTW, this error was reported on an ubuntu forum here
http://old.nabble.com/PWgui-td32021638.html several months ago.

 

As far as I can tell, all my tcl/tk libs are current.

*************************************************

 

ERROR: failed to locate object from identifier path_inter_nimages

 

ERROR: failed to locate object from identifier path_inter_nimages

 

    while executing

"error $::tclu::error(errMsg) $::tclu::error(info) $::tclu::error(code)"

    ("uplevel" body line 2)

    invoked from within

"uplevel 1 {

               error $::tclu::error(errMsg) $::tclu::error(info)
$::tclu::error(code)

    }"

    (procedure "::tclu::ERROR" line 20)

    invoked from within

"::tclu::ERROR "failed to locate object from identifier $varIdent""

    (object "::guib::PWmoduleObj12" method
"::guib::moduleObj::valueToTextvalue" body line 11)

    invoked from within

"valueToTextvalue $ident $value"

    (object "::guib::PWmoduleObj12" method "::guib::moduleObj::varset" body
line 4)

    invoked from within

"$moduleObj varset path_inter_nimages -value $ni"

    (procedure "::pwscf::pwReadFilter" line 59)

    invoked from within

"$readFilter $this $fileChannel"

    (object "::guib::PWmoduleObj12" method "::guib::moduleObj::readFile"
body line 8)

    invoked from within

"::guib::PWmoduleObj12 readFile file11"

    (in namespace eval "::guib" script line 1)

    invoked from within

"namespace eval ::guib [list $obj readFile $fileChannel]"

    (object "::gUI0" method "::guib::GUI::_openInput" body line 27)

    invoked from within

"::gUI0 _openInput pw PW.X
/home/pmpgrant/Downloads/pwgui-4.3/espresso-4.3/PWgui-4.3/modules/pw/pw.tcl"

    (in namespace inscope "::guib::GUI" script line 1)

    invoked from within

"namespace inscope ::guib::GUI {::gUI0 _openInput pw PW.X
/home/pmpgrant/Downloads/pwgui-4.3/espresso-4.3/PWgui-4.3/modules/pw/pw.tcl}
"

    invoked from within

".gui0.shellchildsite.menubar.menubar.file.menu.openinp invoke active"

    ("uplevel" body line 1)

    invoked from within

"uplevel #0 [list $w invoke active]"

    (procedure "tk::MenuInvoke" line 50)

    invoked from within

"tk::MenuInvoke .gui0.shellchildsite.menubar.menubar.file.menu.openinp 1"

    (command bound to event)

 

Paul Grant

W2AGZ Technologies

JPL/Cal Tech

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From Ari.P.Seitsonen at iki.fi  Wed Nov 30 23:07:49 2011
From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen)
Date: Wed, 30 Nov 2011 23:07:49 +0100 (CET)
Subject: [Pw_forum] site-projected bandstructre
In-Reply-To: <393A9F3B-B0E8-4091-A228-768B4E3A9E8F@freenet.de>
References: <C03C7B7C-B875-490C-96A9-9C2817565D0E@physik.uni-halle.de>
	<393A9F3B-B0E8-4091-A228-768B4E3A9E8F@freenet.de>
Message-ID: <alpine.LNX.2.00.1111302305490.20273@pcihpc19.uzh.ch>


Dear Nicki,

   Please check 'projwfc.x', option

         var kresolveddos -type LOGICAL {
             default { .false. }
             info {
                 if .true. the k-resolved DOS is computed: not summed over
                 all k-points but written as a function of the k-point index.
                 In this case all k-point weights are set to unity
             }
         }

   Hopefully this helps.

     Greetings from Nov? Hrady / Czech Republic,

        apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
   Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
   Physikalisch-Chemisches Institut der Universitaet Zuerich
   Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935


On Wed, 30 Nov 2011, Nicki Frank Hinsche wrote:

> Dear all,
>
> is there a possibility to gain a "site-projected" bandstructure in QE?
> Assuming I have an ordered compound ABC.
> Is it possible to project the contribution of A,B,C to the
> wavefunction coefficients at a certain k-vector and energy?
> I want to gain informations like: the bands in this area of the
> Brillouin zone at this energy are mainly formed by
> atom sort A (B,C). I want to go definitely beyond site-projected
> density of states.
>
> I am thankful for every idea,
>
> bests Nicki
>
> -------------------------------------------------------------
> Nicki Frank Hinsche, Dipl. Phys.
> Institute of physics - Theoretical physics,
> Martin-Luther-University Halle-Wittenberg,
> Von-Seckendorff-Platz 1, Room 1.18/1.07
> D-06120 Halle/Saale, Germany
> Tel.: ++49 345 5525450
> Tel.: ++49 345 5525462
> -------------------------------------------------------------
> Fellow of the International Max Planck Re-
> search School-MPI for Microstructure Physics
> -------------------------------------------------------------
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>