[Pw_forum] Follow up on thread: unitary matrix u
On Feb 9, 2012, at 21:25 , Shela Aboud wrote: > some of my q-points (G-M in graphene) have only a "-1" for each > of the real x,y,z-components of one atom and zero everywhere > else as written under "modes" in the electron-phonon output file. written where exactly? from your description and the mentioned e-mail, these look like the irreps, i.e. the displacement patterns used to perform the calculation. Phonon displacements are calculated at the end and look like phonons. P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] How we can give Temperature to equilibrium system (T=o)
You can obtain thermodynamics properties at finite temperature by calculating phonon (ph.x) and treating phonon through QHA method. If temperature was high, you may need an-harmonic calculation by d3.x -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-09 22:49:27,"bramha pandey" wrote: Dear QE users... i want to know how we can introduce the temperature in our equilibrium system(i.e after running scf with proper setting of lattice parameter, ecut and k point, we get ground state total energy(T=0) in scf run). As i read somewhere that SCF will gives the minimum total energy at T=0, because in DFT there is no term of temperature. May be i am wrong but can we introduce temperature by changing the any parameter in input file of pw.x. Actualy i want to generate the phonon by the thermal excitation in my input file by increasing the temperature of my system or any other means by which i can generate phonon for thermo-dynamical property calculation of the system. Any type of help will be appreciable . -- Thanks and Regards Bramha Prasad Pandey Assistant Professor (Electronics and Communication Engg) GLA Group of Institutions, Mathura. Ph. No. 08954143009 email id pandey.bramha at gmail.com bpglaitm at yahoo.co.in -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/84ba8dc9/attachment.htm
[Pw_forum] optimisation
i have a question about the optimisation 1. for optimising the internal coordinates and lattice parameter i have used 4*4*4 kpoint grid it converged in 10 steps and i get the lattice parameters and internal parameters at equilibrium but when i incresed the kpoint mesh to 8*8*8 then the forces on atoms are large so my equilibrium parametes changes so how can i start whether i should use higher kpoint mesh from start of my calculation? sahu b mumbai -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/c3e965c5/attachment.htm
[Pw_forum] Calculation stopped at the beginning of ph.x process
Dear QE developer and users:
At first, I want to say thanks to Alex Kohlmeyer, who made me realized I still
can run the calculation by normal user access.
I compiled pw.x and ph.x, again, by mpich2 1.4.1p1 which was compiled by PGI
fortran 9.0 (trial version). The pw.x calculation among 12 nodes (24 cores) was
very nice. But when I run the ph.x, the calculation stopped at the initial step.
The terminate displayed as:
mpirun -machinefile nodes -np 24 ${KKK}/ph.x -npool 3 -in ${KKK}/binary.ph.in >
${KKK}/binary.ph.out
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 2
.
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 23
And I checked the output file, binary.ph.out, it did not show the information
about process stopping:
Parallel version (MPI), running on24 processors
K-points division: npool =3
R & G space division: proc/pool =8
Ultrasoft (Vanderbilt) Pseudopotentials
Info: using nr1, nr2, nr3 values from input
Info: using nr1s, nr2s, nr3s values from input
Message from routine read_ions :
PP will be read from ./
Parallelization info
sticks: dense smooth PW G-vecs:dense smooth PW
Min 253 253 72 8611 86111298
Max 254 254 73 8614 86141301
Sum202520255776889168891 10395
Dynamical matrices for ( 3, 3, 3,) uniform grid of q-points
( 4q-points):
N xq(1) xq(2) xq(3)
1 0.0 0.0 0.0
2 0.0 0.0 0.3
3 0.0 0.3 0.3
4 0.3 0.3 0.3
Calculation of q =0.000 0.000 0.000
rank 3 in job 73 node01_35097 caused collective abort of all ranks
exit status of rank 3: killed by signal 9
..
rank 22 in job 73 node01_35097 caused collective abort of all ranks
exit status of rank 22: killed by signal 9
Why did this problem occurred? I ran the same input file in my own computer,
with mpich2 1.4.1p1 and ifort 12. It worked well at least up to the "break
point". Is this problem caused by the fortran compilor PGI 9.0?
Looking forward to any suggestion.
Thanks a lot.
--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
-- next part --
An HTML attachment was scrubbed...
URL:
http://www.democritos.it/pipermail/pw_forum/attachments/20120209/fc8426d2/attachment.htm
[Pw_forum] How we can give Temperature to equilibrium system (T=o)
Dear QE users... i want to know how we can introduce the temperature in our equilibrium system(i.e after running scf with proper setting of lattice parameter, ecut and k point, we get ground state total energy(T=0) in scf run). As i read somewhere that SCF will gives the minimum total energy at T=0, because in DFT there is no term of temperature. May be i am wrong but can we introduce temperature by changing the any parameter in input file of pw.x. Actualy i want to generate the phonon by the thermal excitation in my input file by increasing the temperature of my system or any other means by which i can generate phonon for thermo-dynamical property calculation of the system. Any type of help will be appreciable . -- Thanks and Regards Bramha Prasad Pandey Assistant Professor (Electronics and Communication Engg) GLA Group of Institutions, Mathura. Ph. No. 08954143009 email id pandey.bramha at gmail.com bpglaitm at yahoo.co.in -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/213c50cb/attachment.htm
[Pw_forum] large system parallel execution problem
On Feb 9, 2012, at 19:17 , German Samolyuk wrote: > I have problems with memory for this task. As I understand k-points > parallelisation does not distribute memory [...] Did I understand > it wrong? no, you understood well. It seems to me strange, however, that so much memory is needed. Your job is big but not horribly big. P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] large system parallel execution problem
On Wed, 2012-02-08 at 17:58 -0500, German Samolyuk wrote: > The program runs electronic structure self consistency and calculate forces > but stops at first structure optimization step. Do you know possible reason. since "OOM killer terminated this process", you should discover who OOM killer is (hint: Out Of Memory?) For a better parallelization, you should run with -npool 8 P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] Fwd: Uranium pseudopotenial
Or maybe it has been implemented only recently... indeed, just today I've found some examples of ld1 input files where semicore states have the same L as valence states. Check the ps_library input files (see http://qe-forge.org/projects/pslibrary/)... GS Inizio messaggio inoltrato: > Da: Gabriele Sclauzero > Data: 09 febbraio 2012 10.54.08 GMT+01.00 > A: German Samolyuk > Oggetto: Re: [Pw_forum] Uranium pseudopotenial > > Dear German, > >> How I can add 6s state in the basis of Uranum pseudopotential? >> I could not find any example for two channels with the same L and >> different principal number, > >that's simply because this possibility is not implemented in ld1.x. > Maybe other codes can do this, you could try to search on the forum archives > for some related information, I remember that there were discussions about > that in the past. > > > HTH > > > GS > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA >PH H2 462, Station 3, CH-1015 Lausanne > > > > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -- next part ------ An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/79d3a2e1/attachment.htm
[Pw_forum] Calculation stopped at the beginning of ph.x process
On Thu, 2012-02-09 at 22:15 +0800, GAO Zhe wrote: > I ran the same input file in my own computer, with mpich2 1.4.1p1 > and ifort 12. It worked well at least up to the "break point". > Is this problem caused by the fortran compilor PGI 9.0? likely so. Try to run with debug flags; if it is not a compiler bug you should get some more info P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] Identifying the phonon mode from eigen vector
> > If asked to bet, I would say that modes whose displacements in the unit cell > are "more parallel" would have a more "optic character" Of, course, I meant "acoustic character". Sorry for the misunderstanding. SB
[Pw_forum] LDA+U+non-collinear magnetism
Dear users; Does LDA+U work with non-collinear magnetism? best regards Magdalena Birowska -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/43712426/attachment.htm
[Pw_forum] Uranium pseudopotenial
Dear Gabriele, Thank you. The Fe.pbe-spn-rrkjus.in is what I'm looking for. German On Thu, Feb 9, 2012 at 10:21 AM, Gabriele Sclauzero wrote: > > Or maybe it has been implemented only recently... indeed, just today I've > found some examples of ld1 input files > where semicore states have the same L as valence states. Check > the?ps_library input files (see?http://qe-forge.org/projects/pslibrary/)... > > GS > > Inizio messaggio inoltrato: > > Da: Gabriele Sclauzero > Data: 09 febbraio 2012 10.54.08 GMT+01.00 > A: German Samolyuk > Oggetto: Re: [Pw_forum] Uranium pseudopotenial > > Dear German, > > How I can add 6s state in the basis of Uranum pseudopotential? > I could not find any example for two channels with the same L and > different principal number, > > > ? ?that's simply because this possibility is not implemented in ld1.x. > Maybe other codes can do this, you could try to search on the forum archives > for some related information, I remember that there were discussions about > that in the past. > > > HTH > > > GS > > > ? Gabriele Sclauzero,?EPFL SB ITP CSEA > ?? PH H2 462, Station 3,?CH-1015 Lausanne > > > > > > > > > > ? Gabriele Sclauzero,?EPFL SB ITP CSEA > ?? PH H2 462, Station 3,?CH-1015 Lausanne > > > > > > >
[Pw_forum] large system parallel execution problem
Dear Paolo, Thank you. About -npool 8: I have problems with memory for this task. As I understand k-points parallelisation does not distribute memory but will take processors from r,k-parallelisation, these two distribute memory, and effectively it will increase memory I'll need to run the task. Did I understand it wrong? German On Thu, Feb 9, 2012 at 10:32 AM, Paolo Giannozzi wrote: > On Wed, 2012-02-08 at 17:58 -0500, German Samolyuk wrote: > >> The program runs electronic structure self consistency and calculate forces >> but stops at first structure optimization step. Do you know possible reason. > > since "OOM killer terminated this process", you should discover who OOM > killer is (hint: Out Of Memory?) > > For a better parallelization, you should run with -npool 8 > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > >
[Pw_forum] Your message to Pw_forum awaits moderator approval
Dear Moderator, I sent this post to the forum with the wrong email list and I wanted to let you know that I have registered as a a member. Best, Shela pw_forum-bounces at pwscf.org 12:25 PM (38 minutes ago) to me Your mail to 'Pw_forum' with the subject Follow up on thread: [Pw_forum] unitary matrix u Is being held until the list moderator can review it for approval. The reason it is being held: Post by non-member to a members-only list Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://www.democritos.it/mailman/confirm/pw_forum/55c3cd2dfa905219c7eb97452e37bd4392a0f28f -- Shela Aboud Sr. Research Associate 367 Panama St. GES 077A Stanford University Stanford, CA 94305-2220 shela.aboud at stanford.edu (650) 721-2276
[Pw_forum] Follow up on thread: unitary matrix u
I have searched the Pw_forum but was not able to find a response to a previous post. I am including the portion of the original post that I am curious about below. I have the same question. After running my electron-phonon calculations some of my q-points (G-M in graphene) have only a "-1" for each of the real x,y,z-components of one atom and zero everywhere else as written under "modes" in the electron-phonon output file. I assumed "modes" corresponded to the phonon eigenvectors, but this would imply 6 optical modes at some q values which is not correct (although along different symmetry lines it looks like the correct format for eigenvectors). Thank you, Shela Part of original Post: Date: Thu, 14 May 2009 12:05:53 -0400 Subject: [Pw_forum] unitary matrix u Message-ID: <2C1C44865AA64068BE6465660B5DEA6E at ece.ncsu.edu> ".there is always only one nonzero component. For instance, the first eigenvector is (-1,0,0,0,0,0). Obviously, all six eigenvectors are orthonormal, which is how it's supposed to be. But here is what bothers me. For acoustic phonon modes, the unit cell moves as a whole, i.e. both atoms must move with the same phase. So I expect to see something like (1/sqrt(2),0,0, 1/sqrt(2),0,0), instead of (-1,0,0,0,0,0). For optical branches on the other hand, two atoms have the opposite phase (the center of mass of the unit cell does not move), so I would expect to see something like (1/sqrt(2),0,0, -1/sqrt(2),0,0). My understanding is this: if every eigenvector has only one nonzero component, it means that in each mode, one atom is not moving at all! Maybe, I misunderstood the meaning of components of the matrix u? " -- Shela Aboud CEES Sr. Research Scientist 367 Panama St. GES 077A Stanford University Stanford, CA 94305-2220 shela.aboud at stanford.edu (650) 721-2276
[Pw_forum] The iotk error occurrd in ph.x
Dear Axel, thank you very much. I will try ifort+mpich2 in my own directory, hoping it works and the newest ifort 12 can work in Fedora 7. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-08 22:12:02,"Axel Kohlmeyer" wrote: >2012/2/8 GAO Zhe : >> Dear QE developer and users >> I am using an old cluster for calculation, where mpich2 1.2.1 was compiled >> by gortran 4.1.2 in Fedora 7 x86_64. >> The pw.x calculations were fine, but when I was executing ph.x, the iotk >> error occurred (no matter multi-nodes or single-core, this error occurred as >> soon as the input file read by ph.x) : >> # 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 >> As I known, such a problem is due to the bug of compiler, i.e., gfortran >> 4.1.2. However, since I just have the normal user authority in this cluster, >> I cannot upgrade gfortran or install other fortran compiler. Even mpich2 was >> installed in /usr, so I cannot re-compile it. > >yes, you can compile and install both the GCC compilers >(including gfortran) and the MPI library without superuser >privilege and override the system defaults. it just takes >some effort and requires reading of the corresponding >documentation. i have done both many times on very >different machines without having root access. > >axel. > > >> In such a case, do I have to give up the phonon calculaitons in this cluster >> ? >> >> -- >> GAO Zhe >> CMC Lab, Materials Science & Engineering Department, >> Seoul National University, South Korea >> >> >> >> >> ___ >> 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. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/d413b127/attachment.htm
