Re: [QE-users] Phonon - 6.3- problem
Dear Christoph Wolf, Thanks for your support. Yes, I compile it myself using gfortran and openmpi software. 1) Do I have to use other version? Could you please suggest me which version exactly for workstation? I am asking this because you have mentioned "MaX" version could be a problematic one. 2) I did not add full input and out put file due to space. If you want them, to find out where the error is, i can send it to you, sir. And the memory it requires is ( Taken from scf output file): One more thing is we do not have intel compiler in the department workstation. 3) If you don't mind, I would like to ask this. Our computer is workstation. Which one is better one, MPI or OpenMpi? Estimated max dynamical RAM per process > 13.46 MB Estimated total dynamical RAM > 323.13 MB Initial potential from superposition of free atoms starting charge 31.99474, renormalised to 32.0 negative rho (up, down): 1.148E-05 0.000E+00 Starting wfcs are 96 randomized atomic wfcs total cpu time spent up to now is9.7 secs... Thank you Yours Sincerely, A.Suresh, Research Scholar, School of Physics, Madurai Kamaraj University, Madurai. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Gamma_only case not implemented CRASH
Dear Lucas,
please have a look at the input description for the k-points list
and then look at your input for the bands calculation. I guess the
code assumes 0 lines for the bands as the first number in the first
line is a "0".
If you want a path along (G M K G) you should have something like:
K_POINTS crystal_b
4
0.00.00.0 60
0.50.00.0 35
0. 0. 0.0 69
0.00.00.0 1
Cheerio
Thomas
--
Dr. rer. nat. Thomas Brumme
Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
Leipzig University
Phillipp-Rosenthal-Strasse 31
04103 Leipzig
Tel: +49 (0)341 97 36456
email: thomas.bru...@uni-leipzig.de
Zitat von Lucas Dória :
Paolo, thanks for replying.
v.5.4.0.
Regards.
Lucas.
De: users em nome de
Paolo Giannozzi
Enviado: quarta-feira, 10 de outubro de 2018 09:30
Para: Quantum Espresso users Forum
Assunto: Re: [QE-users] Gamma_only case not implemented CRASH
QE version?
On Wed, Oct 10, 2018 at 2:01 PM Lucas Dória
mailto:lucasdoriacarva...@hotmail.com>>
wrote:
Thanks for your reply, Lorenzo.
The first round of calculations is an scf calculation where I use an
automatic grid of k-points:
celldm(1) = 6.04253156,
degauss = 1.0e-02,
ecutrho = 148.,
ecutwfc = 37.,
ibrav = 0,
nat = 7,
nspin = 2,
ntyp = 3,
occupations = 'smearing',
smearing = 'gaussian',
/
conv_thr = 1.0e-10,
electron_maxstep = 200,
mixing_beta = 0.7000,
diagonalization = 'cg',
startingpot = 'atomic',
startingwfc = 'atomic+random',
/
K_POINTS {automatic}
7 7 1 0 0 0
The second one is a band calculation with the k-path calculated with
XCrysDen (Gg M K Gg):
celldm(1) = 6.04253156,
degauss = 1.0e-02,
ecutrho = 148.,
ecutwfc = 37.,
ibrav = 0,
nat = 7,
nspin = 2,
ntyp = 3,
occupations = 'smearing',
smearing = 'gaussian',
/
diagonalization = 'cg',
conv_thr = 1.0e-08,
electron_maxstep = 200,
mixing_beta = 4.0e-01,
startingpot = 'atomic',
startingwfc = 'atomic+random',
/
KPOINTS {tpiba_b}
0.00 0.00 0.00 1 1 1
0.50 0.00 0.00 6 1 1
0.33 0.33 0.00 6 6 1
0.00 0.00 0.00 1 1 1
The third and last one is just an input for bands.x:
filband = 'bands.dat',
lsym= .false.,
prefix = 'bands_F',
outdir = '/tmp/scratch/ldoria/saida',
/
Best regards.
Lucas.
De: users
mailto:users-boun...@lists.quantum-espresso.org>> em nome de Lorenzo Paulatto
mailto:paul...@gmail.com>>
Enviado: quarta-feira, 10 de outubro de 2018 04:39
Para:
users@lists.quantum-espresso.org
Assunto: Re: [QE-users] Gamma_only case not implemented CRASH
Dear Lucas,
please provide you input example (to the list, not to me) because:
1. running bands.x after a calculation at the gamma point only does not
make sense
-or-
2. if you did SCF with gamma only, NSCF with more k-points (which is
questionable but legit) and bands.x afterwards, then this error should
not occur, may be a bug
kind regards
--
Lorenzo Paulatto - Paris
___
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] Gamma_only case not implemented CRASH
Paolo, thanks for replying.
v.5.4.0.
Regards.
Lucas.
De: users em nome de Paolo Giannozzi
Enviado: quarta-feira, 10 de outubro de 2018 09:30
Para: Quantum Espresso users Forum
Assunto: Re: [QE-users] Gamma_only case not implemented CRASH
QE version?
On Wed, Oct 10, 2018 at 2:01 PM Lucas Dória
mailto:lucasdoriacarva...@hotmail.com>> wrote:
Thanks for your reply, Lorenzo.
The first round of calculations is an scf calculation where I use an automatic
grid of k-points:
celldm(1) = 6.04253156,
degauss = 1.0e-02,
ecutrho = 148.,
ecutwfc = 37.,
ibrav = 0,
nat = 7,
nspin = 2,
ntyp = 3,
occupations = 'smearing',
smearing = 'gaussian',
/
conv_thr = 1.0e-10,
electron_maxstep = 200,
mixing_beta = 0.7000,
diagonalization = 'cg',
startingpot = 'atomic',
startingwfc = 'atomic+random',
/
K_POINTS {automatic}
7 7 1 0 0 0
The second one is a band calculation with the k-path calculated with XCrysDen
(Gg M K Gg):
celldm(1) = 6.04253156,
degauss = 1.0e-02,
ecutrho = 148.,
ecutwfc = 37.,
ibrav = 0,
nat = 7,
nspin = 2,
ntyp = 3,
occupations = 'smearing',
smearing = 'gaussian',
/
diagonalization = 'cg',
conv_thr = 1.0e-08,
electron_maxstep = 200,
mixing_beta = 4.0e-01,
startingpot = 'atomic',
startingwfc = 'atomic+random',
/
KPOINTS {tpiba_b}
0.00 0.00 0.00 1 1 1
0.50 0.00 0.00 6 1 1
0.33 0.33 0.00 6 6 1
0.00 0.00 0.00 1 1 1
The third and last one is just an input for bands.x:
filband = 'bands.dat',
lsym= .false.,
prefix = 'bands_F',
outdir = '/tmp/scratch/ldoria/saida',
/
Best regards.
Lucas.
De: users
mailto:users-boun...@lists.quantum-espresso.org>>
em nome de Lorenzo Paulatto mailto:paul...@gmail.com>>
Enviado: quarta-feira, 10 de outubro de 2018 04:39
Para: users@lists.quantum-espresso.org
Assunto: Re: [QE-users] Gamma_only case not implemented CRASH
Dear Lucas,
please provide you input example (to the list, not to me) because:
1. running bands.x after a calculation at the gamma point only does not
make sense
-or-
2. if you did SCF with gamma only, NSCF with more k-points (which is
questionable but legit) and bands.x afterwards, then this error should
not occur, may be a bug
kind regards
--
Lorenzo Paulatto - Paris
___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
users Info Page -
lists.quantum-espresso.org
lists.quantum-espresso.org
This is the mailing list for discussions about the Quantum ESPRESSO
distribution. Only registered users can post. To see the collection of prior
postings to the list, visit the users Archives.. Using users
___
users mailing list
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https://lists.quantum-espresso.org/mailman/listinfo/users
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
___
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Re: [QE-users] Gamma_only case not implemented CRASH
QE version?
On Wed, Oct 10, 2018 at 2:01 PM Lucas Dória
wrote:
> Thanks for your reply, Lorenzo.
>
> The first round of calculations is an scf calculation where I use an
> automatic grid of k-points:
>
>
> celldm(1) = 6.04253156,
> degauss = 1.0e-02,
> ecutrho = 148.,
> ecutwfc = 37.,
> ibrav = 0,
> nat = 7,
> nspin = 2,
> ntyp = 3,
> occupations = 'smearing',
> smearing = 'gaussian',
> /
>
>
>
> conv_thr = 1.0e-10,
> electron_maxstep = 200,
> mixing_beta = 0.7000,
> diagonalization = 'cg',
> startingpot = 'atomic',
> startingwfc = 'atomic+random',
> /
>
> K_POINTS {automatic}
> 7 7 1 0 0 0
>
> The second one is a band calculation with the k-path calculated with
> XCrysDen (Gg M K Gg):
>
>
> celldm(1) = 6.04253156,
> degauss = 1.0e-02,
> ecutrho = 148.,
> ecutwfc = 37.,
> ibrav = 0,
> nat = 7,
> nspin = 2,
> ntyp = 3,
> occupations = 'smearing',
> smearing = 'gaussian',
> /
>
>
> diagonalization = 'cg',
> conv_thr = 1.0e-08,
> electron_maxstep = 200,
> mixing_beta = 4.0e-01,
> startingpot = 'atomic',
> startingwfc = 'atomic+random',
> /
>
> KPOINTS {tpiba_b}
> 0.00 0.00 0.00 1 1 1
> 0.50 0.00 0.00 6 1 1
> 0.33 0.33 0.00 6 6 1
> 0.00 0.00 0.00 1 1 1
>
> The third and last one is just an input for bands.x:
>
>
> filband = 'bands.dat',
> lsym= .false.,
> prefix = 'bands_F',
> outdir = '/tmp/scratch/ldoria/saida',
> /
>
> Best regards.
> Lucas.
>
> --
> *De:* users em nome de Lorenzo
> Paulatto
> *Enviado:* quarta-feira, 10 de outubro de 2018 04:39
> *Para:* users@lists.quantum-espresso.org
> *Assunto:* Re: [QE-users] Gamma_only case not implemented CRASH
>
> Dear Lucas,
> please provide you input example (to the list, not to me) because:
>
> 1. running bands.x after a calculation at the gamma point only does not
> make sense
>
> -or-
>
> 2. if you did SCF with gamma only, NSCF with more k-points (which is
> questionable but legit) and bands.x afterwards, then this error should
> not occur, may be a bug
>
> kind regards
>
>
>
> --
> Lorenzo Paulatto - Paris
> ___
> users mailing list
> users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
> users Info Page - lists.quantum-espresso.org
>
> lists.quantum-espresso.org
> This is the mailing list for discussions about the Quantum ESPRESSO
> distribution. Only registered users can post. To see the collection of
> prior postings to the list, visit the users Archives.. Using users
>
> ___
> users mailing list
> users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
___
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Re: [QE-users] Gamma_only case not implemented CRASH
Thanks for your reply, Lorenzo.
The first round of calculations is an scf calculation where I use an automatic
grid of k-points:
celldm(1) = 6.04253156,
degauss = 1.0e-02,
ecutrho = 148.,
ecutwfc = 37.,
ibrav = 0,
nat = 7,
nspin = 2,
ntyp = 3,
occupations = 'smearing',
smearing = 'gaussian',
/
conv_thr = 1.0e-10,
electron_maxstep = 200,
mixing_beta = 0.7000,
diagonalization = 'cg',
startingpot = 'atomic',
startingwfc = 'atomic+random',
/
K_POINTS {automatic}
7 7 1 0 0 0
The second one is a band calculation with the k-path calculated with XCrysDen
(Gg M K Gg):
celldm(1) = 6.04253156,
degauss = 1.0e-02,
ecutrho = 148.,
ecutwfc = 37.,
ibrav = 0,
nat = 7,
nspin = 2,
ntyp = 3,
occupations = 'smearing',
smearing = 'gaussian',
/
diagonalization = 'cg',
conv_thr = 1.0e-08,
electron_maxstep = 200,
mixing_beta = 4.0e-01,
startingpot = 'atomic',
startingwfc = 'atomic+random',
/
KPOINTS {tpiba_b}
0.00 0.00 0.00 1 1 1
0.50 0.00 0.00 6 1 1
0.33 0.33 0.00 6 6 1
0.00 0.00 0.00 1 1 1
The third and last one is just an input for bands.x:
filband = 'bands.dat',
lsym= .false.,
prefix = 'bands_F',
outdir = '/tmp/scratch/ldoria/saida',
/
Best regards.
Lucas.
De: users em nome de Lorenzo
Paulatto
Enviado: quarta-feira, 10 de outubro de 2018 04:39
Para: users@lists.quantum-espresso.org
Assunto: Re: [QE-users] Gamma_only case not implemented CRASH
Dear Lucas,
please provide you input example (to the list, not to me) because:
1. running bands.x after a calculation at the gamma point only does not
make sense
-or-
2. if you did SCF with gamma only, NSCF with more k-points (which is
questionable but legit) and bands.x afterwards, then this error should
not occur, may be a bug
kind regards
--
Lorenzo Paulatto - Paris
___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
users Info Page -
lists.quantum-espresso.org
lists.quantum-espresso.org
This is the mailing list for discussions about the Quantum ESPRESSO
distribution. Only registered users can post. To see the collection of prior
postings to the list, visit the users Archives.. Using users
___
users mailing list
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https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Phonon - 6.3- problem
I see you are using the MAX version. If I remember correctly I also had a minor problem with that one at some point. Did you compile it yourself? Which compiler and libraries did you use? In my limited experience intels compiler and mkl works with the least hassle. What is the required RAM (scf out file) and the physically available memory? Input files seem OK, except your ecutrho seems high (for norm-conserving pseudos 4*ecutwfc). Best, Chris -- Postdoctoral Researcher Center for Quantum Nanoscience, Institute for Basic Science Ewha Womans University, Seoul, South Korea ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Gamma_only case not implemented CRASH
Dear Lucas, please provide you input example (to the list, not to me) because: 1. running bands.x after a calculation at the gamma point only does not make sense -or- 2. if you did SCF with gamma only, NSCF with more k-points (which is questionable but legit) and bands.x afterwards, then this error should not occur, may be a bug kind regards -- Lorenzo Paulatto - Paris ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Phonon - 6.3- problem
Dear Christoph Wolf, Thanks for your reply. The RAM size in my our department workstation is 32 GB. I will also try to use small jobs. The commands I used are [Dell@centos7 ~]$ /lib64/openmpi/bin/mpirun -np 24 /home/Dell/qe-6.3/bin/ph.x /home/Dell/phonon/relaxed/ph.out^C [Dell@centos7 ~]$ /lib64/openmpi/bin/mpirun -np 24 /home/Dell/qe-6.3/bin/ph.x /home/Dell/phonon/relaxed/ph.out ^Cmpirun: abort is already in progress...hit ctrl-c again to forcibly terminate The following is my input I used for pw.x and ph.in. Below the input file I have added few lines of output of ph.x also. title = 'anat' , calculation = 'scf', restart_mode = 'from_scratch' , wf_collect = .true., prefix = 'anatase', outdir ='/home/Dell/phonon/relaxed/tmp', pseudo_dir = '/home/Dell/phonon/pseudo', tstress = .true. , tprnfor = .true. ,/ ibrav = 7, A = 3.7547, C = 9.1960, nat = 6 , ntyp = 2 , ecutwfc = 90 , ecutrho = 900/ conv_thr = 1.D-16 / ATOMIC_SPECIES Ti 47.86700 Ti.pz-mt_fhi.UPF O 15.99940 O.pz-mt_fhi.UPF ATOMIC_POSITIONS (angstrom) Ti -0.0 0.0 0.0 Ti 0.0 1.877350549 2.299006742 O0.0 0.0 -1.937981509 O -0.0 -0.0 1.937981509 O -0.0 1.877350549 0.361025232 O0.0 1.877350549 4.236988251 K_POINTS automatic 8 8 8 0 0 0 phonons of anatase tr2_ph=1.0d-12, prefix='anatase', ldisp=.true., amass(1)=47.86700, amass(2)=15.99940, outdir ='/home/Dell/phonon/relaxed/tmp', fildyn='ana.dyn', nq1=4, nq2=4, nq3=4 output Program PHONON v.6.3MaX starts on 8Oct2018 at 12:41:19 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); "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017); URL http://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/quote Parallel version (MPI), running on24 processors MPI processes distributed on 1 nodes R & G space division: proc/nbgrp/npool/nimage = 24 Reading data from directory: /home/Dell/phonon/relaxed/tmp/anatase.save/ IMPORTANT: XC functional enforced from input : Exchange-correlation = PW ( 1 4 0 0 0 0) Any further DFT definition will be discarded Please, verify this is what you really want file Ti.pz-mt_fhi.UPF: wavefunction(s) 4f renormalized file O.pz-mt_fhi.UPF: wavefunction(s) 4f renormalized Parallelization info sticks: dense smooth PW G-vecs:dense smooth PW Min 198 79 24 8310 2107 363 Max 199 80 25 8313 2112 366 Sum47531917587 19947950625 8741. And the program stucked at Representation # 9 mode # 9 Self-consistent Calculation iter # 1 total cpu time : 68381.5 secs av.it.: 10.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 2.197E-06 iter # 2 total cpu time : 68609.6 secs av.it.: 18.5 thresh= 1.482E-04 alpha_mix = 0.700 |ddv_scf|^2 = 7.406E-06 iter # 3 total cpu time : 68813.8 secs av.it.: 16.3 thresh= 2.721E-04 alpha_mix = 0.700 |ddv_scf|^2 = 6.015E-08 iter # 4 total cpu time : 69031.9 secs av.it.: 17.6 thresh= 2.452E-05 alpha_mix = 0.700 |ddv_scf|^2 = 1.638E-08 iter # 5 total cpu time : 69241.6 secs av.it.: 16.9 thresh= 1.280E-05 alpha_mix = 0.700 |ddv_scf|^2 = 3.902E-10 iter # 6 total cpu time : 69459.6 secs av.it.: 17.6 thresh= 1.975E-06 alpha_mix = 0.700 |ddv_scf|^2 = 8.914E-11 iter # 7 total cpu time : 69675.9 secs av.it.: 17.4 thresh= 9.441E-07 alpha_mix = 0.700 |ddv_scf|^2 = 5.486E-12 After this "System monitor" showed no processor is running. And the program at terminal was blinking as program is running. Before I get this error, I also find for my earlier run that after ph.x output is created for anatase, q2r.x wasn't run for small number of k point in scf and small number of kpoint in ph.in. I will try to run again for anatase as you suggested for small system. Yours Sincerely, A.Suresh, Research Scholar, School of Physics,
