[Pw_forum] problems with GPU-accelerated Quantum ESPRESSO
Dear Sirs, May I ask here some questions about GPU Quantum ESPRESSO installation? If I may, here is my problem. I`m installing Quantum GPU-accelerated ESPRESSO on the ?Lomonosov? supercomputer in Russia, You can find us in top500 list on the 38 position, in November 2013 list. So, in the beginning I installed the version without GPU, and I didn`t have any problems. If it is important, I used such configure command: ./install/configure --with-internal-lapack --with-internal-blas CC=icc FC=ifort F77=ifort CCFLAGS=-openmp CPPFLAGS=-openmp --enable-parallel --enable-openmp After that I tried to compile GPU part, just as in the README file I used such configure command: ./configure --enable-parallel --enable-openmp --with-scalapack --enable-cuda --with-cuda-dir=/opt/cuda --disable-magma DFLAGS=-DMPICH_SKIP_MPICXX because I`m using Intel compilers and IntelMPI But, during the compiling process, I had some errors, here they are: /opt/cuda-5.0/bin/nvcc -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_30,code=sm_35 -I../../include -I../include -I/opt/ccoe/espresso-5.0.2/GPU/..//phiGEMM/include -I/opt/cuda-5.0/include -DMPICH_SKIP_MPICXX-c cuda_init.cu cuda_init.cu(361): error: identifier "ngpus_per_process" is undefined cuda_init.cu(363): error: identifier "qe_gpu_bonded" is undefined cuda_init.cu(376): error: identifier "qe_gpu_kernel_launch" is undefined cuda_init.cu(376): error: identifier "update_gpu_kernel_specs" is undefined cuda_init.cu(413): warning: variable "lRankThisNode" was declared but never referenced cuda_init.cu(413): warning: variable "lSizeThisNode" was declared but never referenced 4 errors detected in the compilation of "/tmp/ When I looked into the cuda_init.cu file, I saw such code: #if defined(__CUDA) long ngpus_detected; long ngpus_used; long ngpus_per_process; long procs_per_gpu; #endif and after this using this variables without #if defined #endif So I`m sure that __CUDA flag is not set, but why? Sincerely, Afanasiev Ilya, student of Moscow State University. -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140307/06701952/attachment.html
[Pw_forum] Matlab call pw.x
Do you have mpi installed in machine?
type it in terminal:
locate mpirun
it should give you something like:
/usr/local/openmpi/bin/mpirun
/usr/local/openmpi/share/man/man1/mpirun.1
Regardless your linux provides a mpirun by default, I suggest you to
install it by yourself:
http://www.open-mpi.org/
You'll have more control over the settings.
I.M.H.O.: you should use the matlab to write files you need, then run the
job in terminal.
Best,
On Fri, Mar 7, 2014 at 1:30 PM, Lijuan He wrote:
> Dear everyone,
>
> I am trying to use Matlab to call pw.x but it does not work. My command
> line is
> system('~/espresso/bin/pw.x< ~/debug/H2+H.in >H2+H.out'). I know it
> probably because I need to first run mpi then call pw.x. But I cannot find
> the mpi. Anyone knows how to do this. Thanks very much.
>
> Best,
> Lijuan He
> Ph.D student in Georgia Tech
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
_
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:(11) 3091-6881 (USP)
(11) 97408-2755 (Vivo)
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[Pw_forum] Fwd: Basic Relax Calculation issues
Apologies this is the error message: Error in routine read_namelists (5010): reading namelist cell Thank you for your response. Kind Regards Zarah On Fri, Mar 7, 2014 at 3:56 PM, Paolo Giannozzi wrote: > On Fri, 2014-03-07 at 14:49 +0800, Zarah Baiyee wrote: > > > I am currently having a few issues with VC-Relax input > > files and cannot seem to get them to work, please find > > attached. I consistently get an error: > > > > Error in routine dos (1): > > reading dos namelist > > this happens during the calculation of the density of > states (code dos.x), not during the variable-cell > optimization (code pw.x) > > P. > > -- > Paolo Giannozzi, Dept. 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://pwscf.org/mailman/listinfo/pw_forum > -- next part ------ An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140307/72aaba97/attachment.html
[Pw_forum] QE + EPW
Dear everyone, I'm trying to install EPW. EPW works with version 4.0.3 of QE, so I decided to make separate install QE 4.0.3 for EPW and leave my current 5.0.3 install for other calculations. I'm aware you don't provide support for obsolete versions but I've been having problems with 4.0.3 installation and I was hoping someone could help me. After ./configure everything looks ok (paralel env. detected...) but after make all I get read_upf_v2.f90:437.16-34: ALLOCATE( upf%nn(upf%nwfc), upf%nn(upf%nwfc), & 1 2 Error: Allocate-object at (1) also appears at (2) make[1]: *** [read_upf_v2.o] Error 1 Is there any suggestion how could i fix it? Best regards, J. Pesic PhD Student, Center for Solid State Physics and New Materials, IPB, Serbia
[Pw_forum] Input file for Bulk Gallium
I forgot to attach the reference of the article in my last post. Here I am attaching the link. Dear apsi Thank you very much for your help. I am attaching .jpg file of Alpha-Ga structure and also the article which I am following for this structure. Yes, the number of iterations are large than required. Thanks for pointing this out. Article : O. Z?ger and U. D?rig, Phys. Rev. B 46, 7319 (1992) Thank you Manjusha -- next part -- A non-text attachment was scrubbed... Name: AlphaGa.jpg Type: image/jpeg Size: 20156 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140307/159a8374/attachment.jpg
[Pw_forum] Input file for Bulk Gallium
Dear apsi Thank you very much for your help. I am attaching .jpg file of Alpha-Ga structure and also the article which I am following for this structure. Yes, the number of iterations are large than required. Thanks for pointing this out. Thank you Manjusha -- Manjusha Research Scholar C/O Dr. Madhav Ranganathan Department of Chemistry Indian Institute of Technology,Kanpur U.P., India 208016 Lab-SL302 ph:+91-512-259 6539 -- next part -- A non-text attachment was scrubbed... Name: AlphaGa.jpg Type: image/jpeg Size: 20156 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140307/5dc04c7a/attachment.jpg
[Pw_forum] Fwd: Basic Relax Calculation issues
Thanks Fillipe,
I am currently having a few issues with VC-Relax input files and cannot
seem to get them to work, please find attached. I consistently get an
error:
Error in routine dos (1):
reading dos namelist
Any suggestions would be greatly appreciated.
Thanks
Zarah
On Fri, Mar 7, 2014 at 11:35 AM, Filipe Camargo Dalmatti Alves Lima <
flima at if.usp.br> wrote:
> Dear Zarah,
>
> Have you ever considered that you may want the cell relaxation in this
> case? (vc-relax)
> It will optimize the cell parameter in order to minimize the total energy.
> You'll see that the system might have lots of interactions.
>
> If you want to explore defects in crystals or surfaces, relaxing the
> internal coordinates are essential since you are breaking the symmetry in
> some way: by having impurities; surface interaction; vacancy defects and
> etc. If it is the case you want to explore, you will need to use a
> supercell approach. Remember: crystals are built based on symmetry rules.
>
> If you are really curious, you might try to change the cell symmetry just
> to observe how the internal coordinations behave (just increase z by 0.2).
> It may not converge, but you will see a lot interactions.
>
> Best regards,
>
> Filipe
>
> On Friday, February 28, 2014, Zarah Baiyee wrote:
>
>> Hi All,
>>
>> I am a new user to Quantum Espresso, therefore this may be a bit trivial
>> but I any help would be very welcome.
>>
>> I am attempting a relax calculation using espresso version 5.0.2, for the
>> geometry optimisation of a perovskite structure. For the input below, the
>> calculation runs, however does not compute any forces and convergence
>> without geometry optimisation to the original structure, with 0 bfgs steps.
>> I am able to perform an expected relaxation if alter the initial atomic
>> positions to asymmetric: (i.e.) an oxygen molecule from: O (0.500 0.5
>> 0.0) to O(0.499 0.5 0.0).
>>
>> Please may someone shed some light on to why this is the case, and if
>> there is anything wrong with my input.
>>
>> Thanks
>>
>> Zarah
>> Zbaiyee at gmail.com
>>
>> &CONTROL
>> calculation = "relax",
>> prefix = "CO",
>> pseudo_dir = "/Users/zarahbaiyee/espresso-5.0.2/pseudo",
>> outdir = "/Users/zarahbaiyee/tmp",
>> forc_conv_thr = 1.0D-5
>> /
>> &SYSTEM
>> ibrav = 0,
>> nat = 5,
>> ntyp = 3,
>> ecutwfc = 60,
>> ecutrho = 420,
>> /
>> &ELECTRONS
>> conv_thr= 1.D-7,
>> mixing_beta = 0.7D0,
>> electron_maxstep = 400
>> /
>> &IONS
>> /
>> CELL_PARAMETERS bohr
>> 7.60 0.0 0.0
>> 0.0 7.60 0.0
>> 0.0 0.0 7.60
>> ATOMIC_SPECIES
>> Ba 137.32 Ba.pbe-mt_fhi.UPF
>> Fe 55.84 Fe.pbe-mt_fhi.UPF
>> O 15.99 O.pbe-kjpaw.UPF
>> ATOMIC_POSITIONS {crystal}
>> Ba 0.000 0.0 0.0 0 0 0
>> Fe 0.500 0.5 0.5
>> O 0.000 0.5 0.5
>> O 0.500 0.0 0.5
>> O 0.500 0.5 0.0
>> K_POINTS {automatic}
>> 9 9 9 0 0 0
>>
>>
>
> --
> _
> Filipe Camargo Dalmatti Alves Lima
> PhD Student
> University of S?o Paulo, Physics Institute, Materials Physics Department,
> Nanomol Group, Brazil.
> Phones:(11) 3091-6881 (USP)
> (11) 97408-2755 (Vivo)
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] Problems with interrupted electron-phonon coupling calculation
I am using espresso 5.0.3. Thanks, Sridhar On Fri, Mar 7, 2014 at 1:30 PM, Paolo Giannozzi wrote: > Code version? P. > > On Thu, 2014-03-06 at 23:36 +0530, Sridhar Sadasivam wrote: > > Hello, > > > > > > I am working on an electron-phonon coupling calculation of a large > > system (30 atoms). At each q-point I will have 30 x 3 = 90 irreducible > > representations. This will take a lot of computer time and I expect > > that my calculation will be interrupted (due to max wall time > > limitations in the computing cluster I use). So I will need to restart > > the calculation many times. > > > > > > To test if everything runs fine, I tried to run an electron-phonon > > coupling calculation on a simple 1 atom system. For a particular > > q-point I had 2 irreducible representations and I interrupted my > > calculation after the self-consistent calculation for the 1st > > representation. I then restarted the calculation setting "recover > > = .true.". The calculation starts with the 2nd representation and > > seems to complete, but the electron-phonon linewidths are wrong, i.e., > > the results don't match the results I get when I run without any > > interruption. The phonon frequencies are correct in the interrupted > > calculation but the electron-phonon results are not. For some reason, > > restarting an interrupted ph.x calculation does not give the correct > > results for electron-phonon coupling. > > > > > > Does anyone know how I can resolve this issue? This is crucial as I > > will not be able to run the large system (30 atoms) without having to > > restart many times. > > > > > > I would really appreciate if someone could help me out on this. Please > > let me know if my question isn't clear and I can attach output files > > as well. > > Regards, > > Sridhar > > Purdue University, > > USA > > > > > > > > > > > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > -- > Paolo Giannozzi, Dept. 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://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140307/8f33a25d/attachment.html
[Pw_forum] Problem compiling QE 5.0.2 on IBM iDataPlex
Dear Filippo and Paolo, Thanks for your prompt reply. The HPC people in charge of the cluster were kind enough to help me out with this issue as well. I cleaned out the things that were already compiled as you recommended, then I set some variables as follows: set -x # export ARCH=x86_64 export F90=mpiifort export MPIF90=mpiifort export F77=mpiifort export CC=mpiicc export FFLAGS="-O2 -mcmodel=large" export F90FLAGS="-O2 -mcmodel=large" export CFLAGS="-O2 -mcmodel=large" export LDFLAGS="-mkl=cluster -shared_intel" export LIBDIRS="-mkl=cluster" export BLAS_LIBS="-mkl=cluster" export LAPACK_LIBS="-mkl=cluster" export FFT_LIBS="-mkl=cluster" export SCALAPACK_LIBS=-mkl=cluster # set +x and finally compiled using the make.sys file that is attached with this message. The program compiled fine and I am now running some tests on my system. Thanks for the help! Mario Burbano -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140307/48aff978/attachment.html -- next part -- A non-text attachment was scrubbed... Name: makesys Type: application/octet-stream Size: 4655 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140307/48aff978/attachment.obj
[Pw_forum] Input file for Bulk Gallium
Dear Manjusha, Based from what I see (the lattice constants, the symmetry group, distance between the atoms) I would say that the structure corresponds to the structure in the paper. I do not, however, have the experimental/earlier calculated coordinates of the atoms, so I cannot be fully sure about the atomic coordinates. Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Institut f?r Chemie der Universit?t Z?rich, CH-8057 Z?rich Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 On Fri, 7 Mar 2014, manchugh at iitk.ac.in wrote: > > Dear apsi > > Thank you very much for your help. I am attaching .jpg file of Alpha-Ga > structure and also the article which I am following for this structure. > Yes, the number of iterations are large than required. Thanks for pointing > this out. > > Thank you > Manjusha > > > -- > Manjusha > Research Scholar > C/O Dr. Madhav Ranganathan > Department of Chemistry > Indian Institute of Technology,Kanpur > U.P., India 208016 > Lab-SL302 > ph:+91-512-259 6539 >
[Pw_forum] Fwd: Basic Relax Calculation issues
On Fri, 2014-03-07 at 17:25 +0800, Zarah Baiyee wrote: > Apologies this is the error message: > Error in routine read_namelists (5010): > reading namelist cell there is an error in namelist cell (hint: namelist cell starts with "&cell", ends with "/") P. > Thank you for your response. > > > Kind Regards > > > Zarah > > > On Fri, Mar 7, 2014 at 3:56 PM, Paolo Giannozzi > wrote: > On Fri, 2014-03-07 at 14:49 +0800, Zarah Baiyee wrote: > > > I am currently having a few issues with VC-Relax input > > files and cannot seem to get them to work, please find > > attached. I consistently get an error: > > > > Error in routine dos (1): > > reading dos namelist > > > this happens during the calculation of the density of > states (code dos.x), not during the variable-cell > optimization (code pw.x) > > P. > > -- > Paolo Giannozzi, Dept. 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://pwscf.org/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Matlab call pw.x
Dear everyone,
I am trying to use Matlab to call pw.x but it does not work. My command
line is
system('~/espresso/bin/pw.x< ~/debug/H2+H.in >H2+H.out'). I know it
probably because I need to first run mpi then call pw.x. But I cannot find
the mpi. Anyone knows how to do this. Thanks very much.
Best,
Lijuan He
Ph.D student in Georgia Tech
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[Pw_forum] Input file for Bulk Gallium
Dear QE users
Can anybody help me in creating input file for Bulk Alpha Ga? I am attaching
the file what I have made but I am not sure if it represents alpha Ga or
not.
&CONTROL
calculation = "scf",
title = 'Ga'
verbosity = 'high',
restart_mode = 'from_scratch',
prefix = 'AlphaGa',
pseudo_dir = './',
outdir = './'
/
&SYSTEM
ibrav = 8 ,
celldm(1) = 8.5268 ,
celldm(2) = 1.0013 ,
celldm(3) = 1.6948 ,
nat = 8 ,
ntyp = 1 ,
ecutwfc = 60 ,
ecutrho = 480 ,
occupations = 'smearing',
smearing = 'methfessel-paxton' ,
degauss = 0.05
/
&ELECTRONS
electron_maxstep = 400,
diagonalization='cg',
conv_thr = 1.D-6
/
ATOMIC_SPECIES
Ga 69.723 Ga.pbe-n-van.UPF
ATOMIC_POSITIONS {crystal}
Ga 0.000.07850.1525
Ga 0.500.07850.3475
Ga 0.500.57850.1525
Ga 0.000.57850.3475
Ga 0.00-0.0785-0.1525
Ga 0.50-0.07850.6525
Ga 0.500.4215-0.1525
Ga 0.000.42150.6525
K_POINTS {gamma}
Thanks in advance!
--
Manjusha
Research Scholar
Department of Chemistry
Indian Institute of Technology,Kanpur
U.P., India 208016
[Pw_forum] Input file for Bulk Gallium
Dear Manjusha,
As you have apparently not received any other answer, I quickly give my
comment: I guess that not many people on this mailing list know how the
alpha gallium structure should look like, so it would probably help our
task of "verifying" your input if you would include a .cif file of the
structure, or a reference to an article where the structure has been
enlisted in a clear/simple manner.
The options in the section '&electrons' are a bit worrying to me: Do you
really need up to 400 iterations to reach a self-consistency of "only"
10^-6? How about changing the 'mixing_beta' to a different value? I
usually prefer Davidson as the diagonalisation method and switch to 'cg'
if the former doesn't converge (or I'm just at the limit of the memory,
the latter requiring less of it).
Greetings,
apsi
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
Institut f?r Chemie der Universit?t Z?rich, CH-8057 Z?rich
Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935
On Fri, 7 Mar 2014, manchugh at iitk.ac.in wrote:
> Dear QE users
>
> Can anybody help me in creating input file for Bulk Alpha Ga? I am attaching
> the file what I have made but I am not sure if it represents alpha Ga or
> not.
>
>
>
> &CONTROL
>calculation = "scf",
>title = 'Ga'
>verbosity = 'high',
>restart_mode = 'from_scratch',
>prefix = 'AlphaGa',
>pseudo_dir = './',
>outdir = './'
> /
> &SYSTEM
>ibrav = 8 ,
>celldm(1) = 8.5268 ,
>celldm(2) = 1.0013 ,
>celldm(3) = 1.6948 ,
>nat = 8 ,
>ntyp = 1 ,
>ecutwfc = 60 ,
>ecutrho = 480 ,
>occupations = 'smearing',
>smearing = 'methfessel-paxton' ,
>degauss = 0.05
> /
>
> &ELECTRONS
> electron_maxstep = 400,
> diagonalization='cg',
> conv_thr = 1.D-6
> /
>
> ATOMIC_SPECIES
> Ga 69.723 Ga.pbe-n-van.UPF
>
> ATOMIC_POSITIONS {crystal}
> Ga 0.000.07850.1525
> Ga 0.500.07850.3475
> Ga 0.500.57850.1525
> Ga 0.000.57850.3475
> Ga 0.00-0.0785-0.1525
> Ga 0.50-0.07850.6525
> Ga 0.500.4215-0.1525
> Ga 0.000.42150.6525
>
>
> K_POINTS {gamma}
>
>
> Thanks in advance!
> --
> Manjusha
> Research Scholar
> Department of Chemistry
> Indian Institute of Technology,Kanpur
> U.P., India 208016
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
[Pw_forum] Problems with interrupted electron-phonon coupling calculation
Code version? P. On Thu, 2014-03-06 at 23:36 +0530, Sridhar Sadasivam wrote: > Hello, > > > I am working on an electron-phonon coupling calculation of a large > system (30 atoms). At each q-point I will have 30 x 3 = 90 irreducible > representations. This will take a lot of computer time and I expect > that my calculation will be interrupted (due to max wall time > limitations in the computing cluster I use). So I will need to restart > the calculation many times. > > > To test if everything runs fine, I tried to run an electron-phonon > coupling calculation on a simple 1 atom system. For a particular > q-point I had 2 irreducible representations and I interrupted my > calculation after the self-consistent calculation for the 1st > representation. I then restarted the calculation setting "recover > = .true.". The calculation starts with the 2nd representation and > seems to complete, but the electron-phonon linewidths are wrong, i.e., > the results don't match the results I get when I run without any > interruption. The phonon frequencies are correct in the interrupted > calculation but the electron-phonon results are not. For some reason, > restarting an interrupted ph.x calculation does not give the correct > results for electron-phonon coupling. > > > Does anyone know how I can resolve this issue? This is crucial as I > will not be able to run the large system (30 atoms) without having to > restart many times. > > > I would really appreciate if someone could help me out on this. Please > let me know if my question isn't clear and I can attach output files > as well. > Regards, > Sridhar > Purdue University, > USA > > > > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Fwd: Basic Relax Calculation issues
On Fri, 2014-03-07 at 14:49 +0800, Zarah Baiyee wrote: > I am currently having a few issues with VC-Relax input > files and cannot seem to get them to work, please find > attached. I consistently get an error: > > Error in routine dos (1): > reading dos namelist this happens during the calculation of the density of states (code dos.x), not during the variable-cell optimization (code pw.x) P. -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] phonons
Dear QE users, first of all I apologize if my is a dumb question, and I suspect it's impossible... Anyway, here it is: as chemist I'm looking for a selected vibrational frequency associated to a stretching of a particular bond in a crystal. Since among all vibrations in the crystal I'm interested only in one (the bond stretching, and eventually anything else associated with the motion of a selected atom), is there any way in QE to compute only this mode without the need to compute everything? Second question: what is the most immediate way (program or tool) to assign and find from the output the correct frequency of my vibration? Do I have to perform all the complete DOS phonons? Thank you, Carlo -- 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] Fwd: Basic Relax Calculation issues
Dear Zarah,
Have you ever considered that you may want the cell relaxation in this
case? (vc-relax)
It will optimize the cell parameter in order to minimize the total energy.
You'll see that the system might have lots of interactions.
If you want to explore defects in crystals or surfaces, relaxing the
internal coordinates are essential since you are breaking the symmetry in
some way: by having impurities; surface interaction; vacancy defects and
etc. If it is the case you want to explore, you will need to use a
supercell approach. Remember: crystals are built based on symmetry rules.
If you are really curious, you might try to change the cell symmetry just
to observe how the internal coordinations behave (just increase z by 0.2).
It may not converge, but you will see a lot interactions.
Best regards,
Filipe
On Friday, February 28, 2014, Zarah Baiyee wrote:
> Hi All,
>
> I am a new user to Quantum Espresso, therefore this may be a bit trivial
> but I any help would be very welcome.
>
> I am attempting a relax calculation using espresso version 5.0.2, for the
> geometry optimisation of a perovskite structure. For the input below, the
> calculation runs, however does not compute any forces and convergence
> without geometry optimisation to the original structure, with 0 bfgs steps.
> I am able to perform an expected relaxation if alter the initial atomic
> positions to asymmetric: (i.e.) an oxygen molecule from: O (0.500 0.5
> 0.0) to O(0.499 0.5 0.0).
>
> Please may someone shed some light on to why this is the case, and if
> there is anything wrong with my input.
>
> Thanks
>
> Zarah
> Zbaiyee at gmail.com
>
> &CONTROL
> calculation = "relax",
> prefix = "CO",
> pseudo_dir = "/Users/zarahbaiyee/espresso-5.0.2/pseudo",
> outdir = "/Users/zarahbaiyee/tmp",
> forc_conv_thr = 1.0D-5
> /
> &SYSTEM
> ibrav = 0,
> nat = 5,
> ntyp = 3,
> ecutwfc = 60,
> ecutrho = 420,
> /
> &ELECTRONS
> conv_thr= 1.D-7,
> mixing_beta = 0.7D0,
> electron_maxstep = 400
> /
> &IONS
> /
> CELL_PARAMETERS bohr
> 7.60 0.0 0.0
> 0.0 7.60 0.0
> 0.0 0.0 7.60
> ATOMIC_SPECIES
> Ba 137.32 Ba.pbe-mt_fhi.UPF
> Fe 55.84 Fe.pbe-mt_fhi.UPF
> O 15.99 O.pbe-kjpaw.UPF
> ATOMIC_POSITIONS {crystal}
> Ba 0.000 0.0 0.0 0 0 0
> Fe 0.500 0.5 0.5
> O 0.000 0.5 0.5
> O 0.500 0.0 0.5
> O 0.500 0.5 0.0
> K_POINTS {automatic}
> 9 9 9 0 0 0
>
>
--
_
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:(11) 3091-6881 (USP)
(11) 97408-2755 (Vivo)
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