[Pw_forum] error two atoms overlap
Since your system is simple cubic, and your first and second atoms position are (0,0,0) and (-1,0,0), which are both at the vertex position of a cubic, thus the 1st and 2nd atoms at exactly same position (please think about the translation in crystal). Actually, in you input file, atom 1~4 aimed the same position. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-27 06:33:35,"mohamed makhyoun" wrote: | Dear All: By running the given input file for pw.x I get the error: from check_atoms : error # 1 atoms # 1 and # 2 overlap! Although I checked the input by XCRYSDEN visualization program and nothing is wrong. I appreciate any help. Best Regard Mohamed ### &CONTROL calculation = 'scf' , prefix='cu3nbs4' restart_mode = 'from_scratch' , outdir = '$TMP_DIR/' , pseudo_dir = '/home/mohamed/espresso/exec/pseudo' , verbosity = 'default' , / &SYSTEM ibrav=1 celldm(1)= 10.397 , nat = 20, ntyp = 3, ecutwfc = 60. , nbnd=90, / &ELECTRONS conv_thr=1.0D-8 , / ATOMIC_SPECIES Nb 92.9064 Nb.pbe-sR-sc-us.UPF Cu 63.546Cu.pbe-sR-us.UPF S 32.06 S.pbe-van-bm.UPF ATOMIC_POSITIONS crystal Nb 0.0 0.0 0.0 Nb -1.0 0.0 0.0 Nb 0.0 0.0 -1.0 Nb 1.0 0.0 0.0 Cu 0.5 0.0 0.0 Cu 0.0 0.0 -0.5 Cu -0.5 0.0 0.0 Cu 0.0 -0.5 0.0 Cu 0.0 0.5 0.0 Cu 0.0 0.0 0.5 S0.242599953 0.242599953 0.242599953 S0.242599953 -0.242599953 -0.242599953 S -0.242599953 0.242599953 -0.242599953 S -0.242599953 -0.242599953 0.242599953 S -0.757400047 0.242599953 0.242599953 S0.242599953 0.242599953 -0.757400047 S -0.757400047 -0.242599953 -0.242599953 S0.757400047 0.242599953 -0.242599953 S -0.242599953 -0.242599953 -0.757400047 S0.757400047 -0.242599953 0.242599953 K_POINTS gamma | -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120327/e0400c5c/attachment.htm
[Pw_forum] Problems in running check-pw.x.j
Hi Paolo, hello community... your experience could be of great help: I also tried to use check-pw.x.j on QE 4.3.2. First I did not use mpirun: it passed with 1-2 not significant numerical discrepancy. By using "mpirun -n 2" more discrepancies appears (sometimes very different number of iterations, i.e. 86 instead of 57 in lda+U_gamma test). By using "mpirun -n 48" it crash at dipole calculation. Too fast for 48 cores? Up to now I used pw.x "apparently" without problems, but...should I be worried? QE was compiled with gfortran 4.6.1 and acml 5.0.0 (libacml.a and libacml_mv.a) and with amdlibm 3.0.1 Thanks, Carlo Il 26/03/2012 18.42, Paolo Giannozzi ha scritto: > On Mon, 2012-03-26 at 18:18 +0530, Abhinav 122 wrote: > >> I received the following error during check-pw.x.j. >> Please suggest the required steps to remove the following errors. > > most likely, your compiler is buggy. > > P. -- Prof. Carlo Nervi carlo.nervi at unito.it Tel:+39 0116707507/8 Fax: +39 0116707855 - Dipartimento di Chimica, via P. Giuria 7, 10125 Torino, Italy.http://lem.ch.unito.it/
[Pw_forum] Problems in running check-pw.x.j
On Tue, 27 Mar 2012 10:41:46 +0200, Carlo Nervi wrote: > By using "mpirun -n 48" it crash at dipole calculation. Too fast for 48 > cores? Some test are too mall to be run with so many processors. I.e. most tests only have one or a few k-points, so they can only be run with one or a few pools. In particular, the dipole test a FFT grid with only 38 points along the Z axis, hence it cannot parallelized on more then 38 processors per pool (without using bands, taskground or openmp). You can see it at the beginning: sticks: dense smooth PW G-vecs:dense smooth PW Min 7 7 1 728 728 22 Max 8 8 2 816 816 146 Sum 303 303 7529755297553661 Tot 152 152 38 You see that the "tot" value for PW says 38. You can also notice that dimension constraints of the DFFT algorithm make you waste a lot of cpu time (every cpu doubles the size of its FFT grid along z!). Running with 39 cpus you do actually get this error: %% task #38 from n_plane_waves : error # 1 No plane waves found: running on too many processors? %% for some reason this message does not get printed to stdout, but you can get it from the CRASH file. bests -- Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - 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] Problems in running check-pw.x.j
On Tue, 2012-03-27 at 10:41 +0200, Carlo Nervi wrote: > By using "mpirun -n 2" more discrepancies appears (sometimes very > different number of iterations, i.e. 86 instead of 57 in lda+U_gamma test). the lda+U test is especially sensitive to small numerical differences, and the Gamma-only one seems to be the most sensitive of all. I suspect that the origin of such numerical differences between is mainly in mathematical libraries, blas and lapack. If so, there isn't much that can be done P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] problems with band structure calculations for SiC between ibrav 2 and ibrav 0
On Fri, 2012-03-23 at 17:20 -0600, Tram Bui wrote: > However, I did the same calculation process using ibrav=0 to > confirm my band structure, now I used k-point path of simple > cubic BZ including : X,M,R, and gamma points. But my band > structure do not seem to be correct. why? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] Fwd: [xcrysden]:how to get the output structure file as xyz format
The xsf file (standard xcrysden output) contains cartesian coordinates in angstrom. If you substitute by hand Z (numbers) with appropriate atom names you will obtain a xyz file HTH Giuseppe On Monday 26 March 2012 22:01:04 chengyu yang wrote: > Can some one else help please? > Thanks. > > > Chengyu Yang > MMAE, UCF -- - 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:
[Pw_forum] Fwd: [xcrysden]:how to get the output structure file as xyz format
Exatly,
As Giuseppe said, the cartesian coordinates of the atoms are written under the
heading ATOMS in the xsf file in angstrom. Therefore it willbe necessary in
your new QE input to change ATOMIC_POSITIONS{crystal} to
ATOMIC_POSITIONS{angstrom}.? Note also that the followings parameters should be
modified accordingly: nat, celldm(1) or CELL_PARAMETERS.
Bertrand
**
Bertrand SITAMTZE YOUMBI
Laboratory of Material Sciences
University of Yaound? I-Cameroon
De?: Giuseppe Mattioli
??: pw_forum at pwscf.org
Envoy? le : Mardi 27 mars 2012 11h53
Objet?: Re: [Pw_forum] Fwd: [xcrysden]:how to get the output structure file as
xyz format
The xsf file (standard xcrysden output) contains cartesian coordinates in
angstrom. If you substitute
by hand Z (numbers) with appropriate atom names you will obtain a xyz file
HTH
Giuseppe
On Monday 26 March 2012 22:01:04 chengyu yang wrote:
> Can some one else help please?
> Thanks.
>
>
> Chengyu Yang
> MMAE, UCF
--
- 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:
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[Pw_forum] xcrysden
Dear all, I have a file input structure Zinc blenbe relaxed, do I draw this structure with xcrysden? Can you help me out? Thank you. Regards. ** Ramzi Alaya E-mail : ramzialaya at hotmail.fr Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie Unit? de Recherche sur les H?t?ro-Epitaxies et Applications -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120327/d89188f3/attachment-0001.htm
[Pw_forum] Input for lambda.x execution for el-ph coupling
Thanks very much for your response. So if I understood correctly, the points
used for the el-ph calculations (obtained from ph.x) in my case 10 x 10x 1 (14
q points) are the ones to be used in the lambda.in file right? what about the
weight of each point? do we need to give them in the input and how to calculate
them?
Thanks again
Date: Mon, 26 Mar 2012 00:37:24 -0400
From: bahad...@buffalo.edu
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] Input for lambda.x execution for el-ph coupling
if you know the q-grid that you used in elphon calculation, you can
just use kpoint.x and give the information about system as follow:
bravais lattice >> {your bravis lattice no 1...14}
filout [mesh_k] >> {just hit enter}
then it will asks for some info (depends on your lattice), just
enter them
.
.
.
mesh: n1 n2 n3 >> {enter your q-grid in X X X format
"example: 8 8 8"}
mesh: k1 k2 k3 (0 no shift, 1 shifted) >> enter 0 0 0 (no
shift for all direction)
write all k? [f] >> {just hit enter}
then read the file that code creates named mesh_k
hope it works
bahadir
On 03/25/2012 09:10 PM, Elie M wrote:
Dear all,
I want to use the lambda.x executable (within the el-ph
interaction package) to calculate the el-ph coefficient lambda
and also Tc. I have read the input in example07 but have not
quite understood how to produce the points in the input file
(it states using kpoints.x) but still a bit vague for me..Any
clarification regarding this issue would be appreciated.
Thanks
Regards
Elie Moudaes
University of Nottimgham
NG7 2RD
UK
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* Dept. of Chemistry
SUNY Buffalo
NY,USA
* Abant Izzet Baysal University
Dept. of Computer Education
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[Pw_forum] Input for lambda.x execution for el-ph coupling
if you are talking about the q-points in elphon out file(whis are used
for naming elph. files), those are not the q-points that
should be used in lambda.in file. you have to generate q points by the
kpoint.x as i explained in previous reply and obtain mesh_k file as an
output of kpoint.x. it will give you the qpoints and their
weights(should give same number of q points as in elhon output file, if
you say 14q points it should give 14 points in mesh_k file), and yes you
must enter the weights in lambda.in file.
bahadir
On 03/27/2012 01:35 PM, Elie M wrote:
> Thanks very much for your response. So if I understood correctly, the
> points used for the el-ph calculations (obtained from ph.x) in my case
> 10 x 10x 1 (14 q points) are the ones to be used in the lambda.in file
> right? what about the weight of each point? do we need to give them in
> the input and how to calculate them?
>
>
> Thanks again
>
>
> Date: Mon, 26 Mar 2012 00:37:24 -0400
> From: bahadira at buffalo.edu
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Input for lambda.x execution for el-ph coupling
>
>
> if you know the q-grid that you used in elphon calculation, you can
> just use kpoint.x and give the information about system as follow:
>
> bravais lattice >> {your bravis lattice no 1...14}
> filout [mesh_k] >> {just hit enter}
>
> then it will asks for some info (depends on your lattice), just enter them
> .
> .
> .
> mesh: n1 n2 n3 >> {enter your q-grid in X X X format "example: 8 8 8"}
> mesh: k1 k2 k3 (0 no shift, 1 shifted) >> enter 0 0 0 (no shift for
> all direction)
> write all k? [f] >> {just hit enter}
>
> then read the file that code creates named mesh_k
>
> hope it works
>
>
> bahadir
>
>
> On 03/25/2012 09:10 PM, Elie M wrote:
>
> Dear all,
>
> I want to use the lambda.x executable (within the el-ph
> interaction package) to calculate the el-ph coefficient lambda and
> also Tc. I have read the input in example07 but have not quite
> understood how to produce the points in the input file (it states
> using kpoints.x) but still a bit vague for me..Any clarification
> regarding this issue would be appreciated. Thanks
>
>
> Regards
>
> Elie Moudaes
> University of Nottimgham
> NG7 2RD
> UK
>
>
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>
>
>
> --
> Dr.Bahadir Altintas
>
> * Dept. of Chemistry
> SUNY Buffalo
> NY,USA
>
> * Abant Izzet Baysal University
>Dept. of Computer Education
>Bolu,Turkey
>
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>
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Dr.Bahadir Altintas
* Dept. of Chemistry
SUNY Buffalo
NY,USA
* Abant Izzet Baysal University
Dept. of Computer Education
Bolu,Turkey
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[Pw_forum] Input for lambda.x execution for el-ph coupling
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[Pw_forum] Input for lambda.x execution for el-ph coupling
ltintas > > * Dept. of Chemistry > SUNY Buffalo > NY,USA > > * Abant Izzet Baysal University >Dept. of Computer Education >Bolu,Turkey > > ___ 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.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120327/7ab4f954/attachment.htm
