[Pw_forum] error of Gipaw calculation for ethonal
Dear All I am a new user for qe. Since my case study will only take a look at into O elment while it contains other element which don't have a gipaw pseudo in QE. Then I tried to start the calculation for ethonal with by using C.pbe-n-kjpaw_psl.0.1.upf, H.pbe-kjpaw.upf and O.pbe-van_gipaw.upf. However, my gipaw calculation stopped at : negative rho (up, down): 0.369E-01 0.000E+00. Also a error were seen in the log file. Here is my input for gipaw: job = 'nmr' prefix='ethanol' tmp_dir = './scratch/' q_gipaw = 0.01 spline_ps = .true. use_nmr_macroscopic_shape = .true. / Here is the optupt: Program GIPAW v.4.3 starts on 8May2013 at 23: 0:39 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 1 processors Info: using nr1, nr2, nr3 values from input Info: using nr1s, nr2s, nr3s values from input file C.pbe-n-kjpaw_psl.0.1.UPF: wavefunction(s) 2P renormalized WARNING: atomic wfc # 2 for atom type 3 has zero norm WARNING: atomic wfc # 4 for atom type 3 has zero norm WARNING: atomic wfc # 5 for atom type 3 has zero norm Stick Mesh -- nst = 641, nstw = 193, nsts = 641 n.st n.stw n.sts n.g n.gw n.gs min 641 193 641 12053 2103 12053 max 641 193 641 12053 2103 12053 641 193 641 12053 2103 12053 Check: negative/imaginary core charge= -0.000201 0.00 negative rho (up, down): 0.369E-01 0.000E+00 Here is the error in the log file: forrtl: severe (43): file name specification error, unit 14, file "Unknown" Image PC Routine Line Source gipaw.x 008E724A Unknown Unknown Unknown gipaw.x 008E5D46 Unknown Unknown Unknown gipaw.x 00899FA0 Unknown Unknown Unknown gipaw.x 0083588E Unknown Unknown Unknown gipaw.x 00834DCF Unknown Unknown Unknown gipaw.x 00848BBD Unknown Unknown Unknown gipaw.x 0043FDB6 paw_gipaw_mp_read 174 paw_gipaw.f90 gipaw.x 00433CFF gipaw_module_mp_g 410 gipaw_module.f90 gipaw.x 0043FB2C MAIN__ 67 gipaw_main.f90 gipaw.x 0043203C Unknown Unknown Unknown libc.so.6 00364001D994 Unknown Unknown Unknown gipaw.x 00431F39 Unknown Unknown Unknown Here is my input for scf calculation = 'scf' restart_mode = 'from_scratch' prefix = 'ethanol' tstress = .true. tprnfor = .true. pseudo_dir = './' outdir = './scratch/' / ibrav = 1, celldm(1) = 10.D0 nat = 9, ntyp = 3, ecutwfc = 20.0D0 nosym = .true. occupations = 'smearing' degauss = 0.005D0 / conv_thr = 1.D-8 mixing_beta = 0.5D0 / ATOMIC_SPECIES H 1.0 H.pbe-kjpaw.UPF C 12.0 C.pbe-n-kjpaw_psl.0.1.UPF O 16.0 O.pbe-van_gipaw.UPF ATOMIC_POSITIONS angstrom H 3.980599 4.178342 3.295079 H 5.033394 3.43043 4.504759 H 5.71907 4.552257 3.315353 H 3.720235 5.329505 5.509909 H 4.412171 6.433572 4.317001 H 5.911611 5.032284 6.242202 C 4.84694 4.350631 3.941136 C 4.603025 5.518738 4.882532 O 5.746254 5.812705 5.6871 K_POINTS automatic 1 1 1 1 1 1 Thanks -- Ms. Xue Yong(??) Department of Physics and Engineering Physics University of Saskatchewan 116 Science Place Saskatoon, SK S7N 5E2 Canada Tel: +1 306 261 2369 -- Ms. Xue Yong(??) Department of Physics and Engineering Physics University of Saskatchewan 116 Science Place Saskatoon, SK S7N 5E2 Canada Tel: +1 306 261 2369 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130508/b4a7568e/attachment.html
[Pw_forum] PAW
Dear All, Is there any repository of QuantumEspresso where I can get PAW in UPF for Pb, Ti and Ba ? Thanks and regards, Yours sincerely, Suza W R Associate RRI 560080
[Pw_forum] Iron surface Molecular Dynamics
Dear Giuseppe, Thanks for your enail. I've actually optimized several iron surfaces and settings in pw.x but moving on cp.x and ensamble-DFT I had to change many things such as pseudopotential (here i need a GC PP). If this is important I can paste here one of the pw.x relaxation input file. I did also managed to to spinpolarized finding ferromagnetic fundamental state. I agree the other option would be BO MD but I am wondering if that is not gonna take forever...plus i would eventualy scale up fron 50 atoms to a slab as big as 200 Vincenzo Sent from my iPhone On 08/mag/2013, at 17:36, Giuseppe Mattioli wrote: > > Dear Vincenzo > Before discussing your setup, I note that you are using the ensemble-DFT > approach implemented in cp.x. I suspect (but perhaps I may be wrong), that it > cannot be used to propagate ions in a proper (NVT, NPT, ...) molecular > dynamics simulation, but only to optimize structures through damped molecular > dynamics. Have you tried first to optimize your system by using pw.x instead > of cp.x, and some smearing scheme to deal with metallic systems? You could > eventually consider (especially if there are no H atoms involved) a > Born-Oppenheimer MD with pw.x as a good solution... > HTH > Giuseppe > > On Wednesday 08 May 2013 16:00:01 Vincenzo Verdolino wrote: >> Dear all, >> >> I am dealing with Iron surface catalyst and I'm trying to run MD simulation >> with cp.x >> >> Here is My Input file >> >> >>pseudo_dir = '/cluster/home/chab/verdoliv/espresso/pseudo/', >>outdir='/cluster/work/scr1/verdoliv/Initial_wavefunction_min/output' >>prefix='Initial_wavefunction_min', >>title=Initial_wavefunction_min, >>calculation='cp', >>restart_mode = 'from_scratch', >>nstep = 50, >>iprint = 10, >>isave = 100, >>tstress = .FALSE., >>tprnfor = .TRUE., >>dt= 4.0d0, >>etot_conv_thr = 1.d-9, >>ekin_conv_thr = 1.d-4, >>ndr = 50 >>ndw = 51, >> / >> >>ibrav= 8, >>C=38.9305, A=7.02146, B=8.10768, cosAB=0.0, cosAC=0.0, cosBC=0.0, >>nat= 50, >>ntyp= 2, >>ecutwfc = 80.0, ecutrho = 640.0, >>smearing='cs', >>occupations='ensemble', >>nbnd = 550, >>nspin=1, >>nr1b=24, nr2b=24, nr3b=24, >> / >> >> orthogonalization = 'ortho', >> startingwfc = 'random', >> electron_dynamics = 'sd', >> ampre = 0.02, >> tcg = .true., >> passop= 0.3, >> maxiter = 250, >> emass = 300, >> emass_cutoff = 3.00, >> conv_thr=1.d-6 >> n_inner = 2, >> lambda_cold = 0.03, >> niter_cold_restart = 2, >> / >> >> ion_dynamics = 'none', >> ion_temperature = 'not_controlled', >> / >> ATOMIC_SPECIES >> ATOMIC_SPECIES >> Fe 1. Fe.pw91-sp-van_ak.UPF >> N 1. N.pw91-van_ak.UPF >> ATOMIC_POSITIONS angstrom >> Fe 3.517670906 2.029585846 0.473063369 >> Fe 3.517670906 6.078055744 0.473063369 >> Fe 0.010178272 0.0 0.479139716 >> Fe 0.010074125 4.05380 0.476810499 >> Fe 4.689525652 0.0 1.143911287 >> Fe 4.690724988 4.05380 1.146913875 >> Fe 1.178101394 2.026148930 1.147504081 >> Fe 1.178101394 6.081492660 1.147504081 >> ... >> ... >> N2.348065911 4.05380 10.444508962 >> N2.349799703 4.05380 11.564212110 >> >> --- >> - >> >> The output file says >> >> >> PERFORMING CONJUGATE GRADIENT MINIMIZATION OF EL. STATES >> cg_sub: missed minimum, case 3, iteration 2 >> cg_sub: missed minimum, case 3, iteration 3 >> cg_sub: missed minimum, case 1, iteration 5 >> cg_sub: missed minimum, case 1, iteration 8 >> cg_sub: missed minimum, case 1, iteration 10 >> cg_sub: missed minimum, case 1, iteration 11 >> cg_sub: missed minimum, case 1, iteration 13 >> cg_sub: missed minimum, case 1, iteration 14 >> cg_sub: missed minimum, case 1, iteration 16 >> cg_sub: missed minimum, case 1, iteration 18 >> cg_sub: missed minimum, case 1, iteration 20 >> cg_sub: missed minimum, case 1, iteration 22 >> cg_sub: missed minimum, case 1, iteration 23 >> cg_sub: missed minimum, case 1, iteration 25 >> cg_sub: missed minimum, case 1, iteration 27 >> cg_sub: missed minimum, case 1, iteration 28 >> cg_sub: missed minimum, case 1, iteration 30 >> cg_sub: missed minimum, case 1, iteration 32 >> cg_sub: missed minimum, case 1, iteration 34 >> >> >> Could any of you give my hints on this field? >> >> Thanks in advance >> >> Vincenzo > > > > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre
[Pw_forum] Iron surface Molecular Dynamics
Vincenzo, Giuseppe, in principle it was meant to do Born-Oppenheimer MD - i.e. use ensemble-DFT minimization of the electronic-structure (a combination of conjugate-gradient and unitary rotation minimizations), and verlet ionic steps. In practice, I do not think it has ever been tested fully (but it did work e.g. for large Al surfaces). Some of these missed minima refer to the fact that the parabolic interpolation of the energy in the cg step predicts a minimum that turns out not to be lower in energy than the initial point. Maybe we can discuss this offline with Vincenzo, and Paolo Umari? nicola On 08/05/2013 17:36, Giuseppe Mattioli wrote: > > Dear Vincenzo > Before discussing your setup, I note that you are using the ensemble-DFT > approach implemented in cp.x. I suspect (but perhaps I may be wrong), that it > cannot be used to propagate ions in a proper (NVT, NPT, ...) molecular > dynamics simulation, but only to optimize structures through damped molecular > dynamics. Have you tried first to optimize your system by using pw.x instead > of cp.x, and some smearing scheme to deal with metallic systems? You could > eventually consider (especially if there are no H atoms involved) a > Born-Oppenheimer MD with pw.x as a good solution... > HTH > Giuseppe > > On Wednesday 08 May 2013 16:00:01 Vincenzo Verdolino wrote: >> Dear all, >> >> I am dealing with Iron surface catalyst and I'm trying to run MD simulation >> with cp.x >> -- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
[Pw_forum] Performance problems due to files in outdir
On Wed, 2013-05-08 at 17:48 +0200, Henning Glawe wrote: > > Anyway: is your problem solved? if not, please specify > > what you need data file for. > > Basically just for running some code patched into pp.x. if you can run the postprocessing code on the same number of processors that were used in the scf calculation, you should be able to run postprocessing codes without the "wf_collect" option. P. -- Paolo Giannozzi, Dept. Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Performance problems due to files in outdir
On Wed, May 08, 2013 at 04:54:20PM +0200, Paolo Giannozzi wrote: > inside QE there is actually a sort of "wrapper" (PW/src/buffers.f90) > that can read/write to file or to RAM depending upon the value of a > variable. It used to work for a single unit, but now it has been > extended to an arbitrary number of units. Apparently, on modern > parallel machines, the less one writes to disk, the better. This is only part of the truth. Most problems on these modern machines are related to the number of files, not to the size of them. In principle, the FHGFS we use in our cluster could deliver a performance of about 2 gigabyte per second (tested via the usual benchmarking tools). Most problems arise from modifications of directory entries (most prominent creating or deleting a file or subdirectory). AFAIK the reason for this is the caching strategy of the operating system and the hardware (raid controllers). Given the case of shared scratch storage, the 'ideal' strategy would be to use only a few big files, coordinating access via MPIIO. On a higher level, HDF5 could be used. It abstracts the usage of parallel IO while providing an architecture-neutral storage format (binary format, but metadata contains information about data endianness and floating point data formats). My basic idea would be to replace IOTK by a wrapper around HDF5. -- Mit freundlichen Gr??en Henning Glawe Max-Planck-Institut f?r Mikrostrukturphysik Weinberg 2, 06120 Halle (Saale), Germany http://www.mpi-halle.de/~theory Phone: +49-345-5582-613 Fax: +49-345-5511223 Email: glawe at mpi-halle.de
[Pw_forum] Correct patches for Quantum Espresso v5.0.2
On Wed, 2013-05-08 at 17:24 +0200, Thomas Gruber wrote: > from 2013-02-01 this is the date of the release. Unfortunately qe-forge doesn't seem to keep track of the date of the individual files in a release > To patch "missing.diff" after "espresso-5.0.2-5.0.3.diff" is useless it is > and to patch only "missing.diff" will give the correct results? if you have already applied the old patch, "missing.diff" will supply the missing patches P. -- Paolo Giannozzi, Dept. Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Performance problems due to files in outdir
On Wed, May 08, 2013 at 05:00:27PM +0200, Paolo Giannozzi wrote: > On Wed, 2013-05-08 at 15:09 +0200, Henning Glawe wrote: > > As far as I understand the code, all IO to outdir is performed via IOTK; > > actually only "small" xml files and files in "collected" format are > written using iotk (the latter, in binary format). Large temporary > scratch files are written using plain binary fortran I/O. Ok. This complicates the issue a bit. In any case, the performance problems are mainly related to having 'many' files, not 'big' files. > Anyway: is your problem solved? if not, please specify what you need > data file for. Basically just for running some code patched into pp.x. -- Mit freundlichen Gr??en Henning Glawe Max-Planck-Institut f?r Mikrostrukturphysik Weinberg 2, 06120 Halle (Saale), Germany http://www.mpi-halle.de/~theory Phone: +49-345-5582-613 Fax: +49-345-5511223 Email: glawe at mpi-halle.de
[Pw_forum] Iron surface Molecular Dynamics
Dear Vincenzo Before discussing your setup, I note that you are using the ensemble-DFT approach implemented in cp.x. I suspect (but perhaps I may be wrong), that it cannot be used to propagate ions in a proper (NVT, NPT, ...) molecular dynamics simulation, but only to optimize structures through damped molecular dynamics. Have you tried first to optimize your system by using pw.x instead of cp.x, and some smearing scheme to deal with metallic systems? You could eventually consider (especially if there are no H atoms involved) a Born-Oppenheimer MD with pw.x as a good solution... HTH Giuseppe On Wednesday 08 May 2013 16:00:01 Vincenzo Verdolino wrote: > Dear all, > > I am dealing with Iron surface catalyst and I'm trying to run MD simulation > with cp.x > > Here is My Input file > > > pseudo_dir = '/cluster/home/chab/verdoliv/espresso/pseudo/', > outdir='/cluster/work/scr1/verdoliv/Initial_wavefunction_min/output' > prefix='Initial_wavefunction_min', > title=Initial_wavefunction_min, > calculation='cp', > restart_mode = 'from_scratch', > nstep = 50, > iprint = 10, > isave = 100, > tstress = .FALSE., > tprnfor = .TRUE., > dt= 4.0d0, > etot_conv_thr = 1.d-9, > ekin_conv_thr = 1.d-4, > ndr = 50 > ndw = 51, > / > > ibrav= 8, > C=38.9305, A=7.02146, B=8.10768, cosAB=0.0, cosAC=0.0, cosBC=0.0, > nat= 50, > ntyp= 2, > ecutwfc = 80.0, ecutrho = 640.0, > smearing='cs', > occupations='ensemble', > nbnd = 550, > nspin=1, > nr1b=24, nr2b=24, nr3b=24, > / > > orthogonalization = 'ortho', > startingwfc = 'random', > electron_dynamics = 'sd', > ampre = 0.02, > tcg = .true., > passop= 0.3, > maxiter = 250, > emass = 300, > emass_cutoff = 3.00, > conv_thr=1.d-6 > n_inner = 2, > lambda_cold = 0.03, > niter_cold_restart = 2, > / > > ion_dynamics = 'none', > ion_temperature = 'not_controlled', > / > ATOMIC_SPECIES > ATOMIC_SPECIES > Fe 1. Fe.pw91-sp-van_ak.UPF > N 1. N.pw91-van_ak.UPF > ATOMIC_POSITIONS angstrom > Fe 3.517670906 2.029585846 0.473063369 > Fe 3.517670906 6.078055744 0.473063369 > Fe 0.010178272 0.0 0.479139716 > Fe 0.010074125 4.05380 0.476810499 > Fe 4.689525652 0.0 1.143911287 > Fe 4.690724988 4.05380 1.146913875 > Fe 1.178101394 2.026148930 1.147504081 > Fe 1.178101394 6.081492660 1.147504081 > ... > ... > N2.348065911 4.05380 10.444508962 > N2.349799703 4.05380 11.564212110 > > --- > - > > The output file says > > > PERFORMING CONJUGATE GRADIENT MINIMIZATION OF EL. STATES > cg_sub: missed minimum, case 3, iteration 2 > cg_sub: missed minimum, case 3, iteration 3 > cg_sub: missed minimum, case 1, iteration 5 > cg_sub: missed minimum, case 1, iteration 8 > cg_sub: missed minimum, case 1, iteration 10 > cg_sub: missed minimum, case 1, iteration 11 > cg_sub: missed minimum, case 1, iteration 13 > cg_sub: missed minimum, case 1, iteration 14 > cg_sub: missed minimum, case 1, iteration 16 > cg_sub: missed minimum, case 1, iteration 18 > cg_sub: missed minimum, case 1, iteration 20 > cg_sub: missed minimum, case 1, iteration 22 > cg_sub: missed minimum, case 1, iteration 23 > cg_sub: missed minimum, case 1, iteration 25 > cg_sub: missed minimum, case 1, iteration 27 > cg_sub: missed minimum, case 1, iteration 28 > cg_sub: missed minimum, case 1, iteration 30 > cg_sub: missed minimum, case 1, iteration 32 > cg_sub: missed minimum, case 1, iteration 34 > > > Could any of you give my hints on this field? > > Thanks in advance > > Vincenzo - 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: ResearcherID: F-6308-2012
[Pw_forum] Correct patches for Quantum Espresso v5.0.2
Dear all, I am a little bit confused. I compared the "missing.diff" from Paolo G. with the "espresso-5.0.2-5.0.3.diff" from the Home <http://qe-forge.org/> ? Projects <http://qe-forge.org/gf/project/> ? Quantum ESPRESSO <http://qe-forge.org/gf/project/q-e/> ? Files <http://qe-forge.org/gf/project/q-e/frs/?action=index> ? Complete QE distribution <http://qe-forge.org/gf/project/q-e/frs/?action=FrsReleaseBrowse_package_id=18> (5.0.3) from 2013-02-01 (that is still available, but no new patch from May 6). I noticed that "missing.diff" contains only changes that are all in "espresso-5.0.2-5.0.3.diff", but "espresso-5.0.2-5.0.3.diff" contained twice as much changes. To patch "missing.diff" after "espresso-5.0.2-5.0.3.diff" is useless and to patch only "missing.diff" will give the correct results? Thanks. Thomas Gruber On 05/07/2013 12:00 PM, pw_forum-request at pwscf.org wrote: > Date: Tue, 7 May 2013 16:30:12 +0800 From: Wei-Bing Zhang > Subject: Re: [Pw_forum] Correct patches > for Quantum Espresso v5.0.2 To: PWSCF Forum Cc: > Brad Malone , pw_users > Message-ID: > > Content-Type: text/plain; charset="utf-8" Dear all I just give a quick > feedback about the latest patches for QE-5.0.3. A few months ago, I > posted a question about negative frequency of silicene with high > q-points above 6x6x1 ( > http://qe-forge.org/pipermail/pw_forum/2013-January/100945.html ) but > did not get an answer. Today, I have recompiled the code with the > latest patches for QE-5.0.3. The new calculations give reasonable > results with q-point 8x8x1 (i.e. the negative frequencies of silicene > disappear in the high q-points). The results obtained the QE-5.0.2 and > the codes with the latest patches are enclosed. Thanks all for your > effort Wei-Bing Zhang On 06/05/2013, Paolo Giannozzi > wrote: >> > The patch file for v.5.0.2 uploaded to qe-forge was >> > promising in the release notes a number of bug fixes >> > to the phonon code that were not actually present. >> > I have uploaded a new version of the patches under >> > release "5.0.3" to qe-forge. Attached here the missing >> > patches. Sorry for the inconvenience and thanks to the >> > people who noticed it >> > >> > P. >> > -- >> >Paolo Giannozzi, Dept. Chemistry, >> >Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> >Phone +39-0432-558216, fax +39-0432-558222 -- Thomas Gruber Institut f?r Theoretische Physik TU Bergakademie Freiberg Leipziger Str. 23, 09599 Freiberg, Germany Tel: +49 (0)3731 392006 Email: thomas.gruber at physik.tu-freiberg.de -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130508/188dfe1c/attachment.html
[Pw_forum] Performance problems due to files in outdir
On Wed, 2013-05-08 at 15:09 +0200, Henning Glawe wrote: > As far as I understand the code, all IO to outdir is performed via IOTK; actually only "small" xml files and files in "collected" format are written using iotk (the latter, in binary format). Large temporary scratch files are written using plain binary fortran I/O. Anyway: is your problem solved? if not, please specify what you need data file for. P. -- Paolo Giannozzi, Dept. Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Performance problems due to files in outdir
On Wed, 2013-05-08 at 09:48 +0200, Axel Kohlmeyer wrote: > if there are some people here on the list that would be interested in > having such a wrapper and would be volunteering some time testing and > providing feedback, i might be tempted to give it a try and write such > a wrapper. inside QE there is actually a sort of "wrapper" (PW/src/buffers.f90) that can read/write to file or to RAM depending upon the value of a variable. It used to work for a single unit, but now it has been extended to an arbitrary number of units. Apparently, on modern parallel machines, the less one writes to disk, the better. P. -- Paolo Giannozzi, Dept. Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] PAW
Dear Suza, try to search in this web http://theossrv1.epfl.ch/index.php?n=Main.Links Best PhD. Arles V. Gil Rebaza Instituto de F?sica de La Plata Argentina 2013/5/8 Suza W > Dear All, > > Is there any repository of QuantumEspresso where I can get PAW in UPF for > Pb, Ti and Ba ? > > Thanks and regards, > > Yours sincerely, > Suza W > R Associate > RRI 560080 > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- ###-> Arles V. <-### -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130508/09bc142e/attachment.html
[Pw_forum] Iron surface Molecular Dynamics
Dear all, I am dealing with Iron surface catalyst and I'm trying to run MD simulation with cp.x Here is My Input file pseudo_dir = '/cluster/home/chab/verdoliv/espresso/pseudo/', outdir='/cluster/work/scr1/verdoliv/Initial_wavefunction_min/output' prefix='Initial_wavefunction_min', title=Initial_wavefunction_min, calculation='cp', restart_mode = 'from_scratch', nstep = 50, iprint = 10, isave = 100, tstress = .FALSE., tprnfor = .TRUE., dt= 4.0d0, etot_conv_thr = 1.d-9, ekin_conv_thr = 1.d-4, ndr = 50 ndw = 51, / ibrav= 8, C=38.9305, A=7.02146, B=8.10768, cosAB=0.0, cosAC=0.0, cosBC=0.0, nat= 50, ntyp= 2, ecutwfc = 80.0, ecutrho = 640.0, smearing='cs', occupations='ensemble', nbnd = 550, nspin=1, nr1b=24, nr2b=24, nr3b=24, / orthogonalization = 'ortho', startingwfc = 'random', electron_dynamics = 'sd', ampre = 0.02, tcg = .true., passop= 0.3, maxiter = 250, emass = 300, emass_cutoff = 3.00, conv_thr=1.d-6 n_inner = 2, lambda_cold = 0.03, niter_cold_restart = 2, / ion_dynamics = 'none', ion_temperature = 'not_controlled', / ATOMIC_SPECIES ATOMIC_SPECIES Fe 1. Fe.pw91-sp-van_ak.UPF N 1. N.pw91-van_ak.UPF ATOMIC_POSITIONS angstrom Fe 3.517670906 2.029585846 0.473063369 Fe 3.517670906 6.078055744 0.473063369 Fe 0.010178272 0.0 0.479139716 Fe 0.010074125 4.05380 0.476810499 Fe 4.689525652 0.0 1.143911287 Fe 4.690724988 4.05380 1.146913875 Fe 1.178101394 2.026148930 1.147504081 Fe 1.178101394 6.081492660 1.147504081 ... ... N2.348065911 4.05380 10.444508962 N2.349799703 4.05380 11.564212110 The output file says PERFORMING CONJUGATE GRADIENT MINIMIZATION OF EL. STATES cg_sub: missed minimum, case 3, iteration 2 cg_sub: missed minimum, case 3, iteration 3 cg_sub: missed minimum, case 1, iteration 5 cg_sub: missed minimum, case 1, iteration 8 cg_sub: missed minimum, case 1, iteration 10 cg_sub: missed minimum, case 1, iteration 11 cg_sub: missed minimum, case 1, iteration 13 cg_sub: missed minimum, case 1, iteration 14 cg_sub: missed minimum, case 1, iteration 16 cg_sub: missed minimum, case 1, iteration 18 cg_sub: missed minimum, case 1, iteration 20 cg_sub: missed minimum, case 1, iteration 22 cg_sub: missed minimum, case 1, iteration 23 cg_sub: missed minimum, case 1, iteration 25 cg_sub: missed minimum, case 1, iteration 27 cg_sub: missed minimum, case 1, iteration 28 cg_sub: missed minimum, case 1, iteration 30 cg_sub: missed minimum, case 1, iteration 32 cg_sub: missed minimum, case 1, iteration 34 Could any of you give my hints on this field? Thanks in advance Vincenzo -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130508/7e36d3ce/attachment.html
[Pw_forum] graphen with adatoms input
you can use the cell you have created for the pure graphene, or a 2x2, 3x3 version of it and then simply add the adatom in the desired place . the code will recognize the reduced symmetry and will adapt the list of kpoints accordingly. stefano On 05/08/2013 02:23 PM, yelena wrote: > Hello everyone! > I am asking for suggestion. I'm trying to make input for scf > calculation (and then for electron-phonon... ) for graphene with > adatoms. > I've been doing calculation with monolayer graphene and I used > hexagonal lattice to describe it and large c/a with vacuum to simulate > monolayer. I've been using GPU version of code and it works perfectly > (I'll write something more about that on GPU message board) > Now I'd like to add adatoms in the middle of lattice and I'm not sure > how to do that. Is there any way to make input for hexagonal lattice > with adatom or I have to make free lattice ibrav=0 and then use CELL > PARAMETER card? > > Looking forward to your answers, > > Jelena Pesic > PhD Student, > Institute of Physics Belgrade, Serbia > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Performance problems due to files in outdir
On Wed, May 08, 2013 at 09:48:39AM +0200, Axel Kohlmeyer wrote: > have you tried using a ramdisk? if your machine is linux based, then > you can usually access up to half of the physical memory via /dev/shm. Yes, I tried this and it seems to work, in conjunction with tar to transfer data to the postprocessing code. > given the ever increasing amount of RAM that current many-core machine > have, this has become a viable alternative to modifying the source > code to keep data in core. Just keeping the data in the core is also no option, due to the necessity of data exchange with internal and external postprocessing codes. > > Are there any plans to move away from the 'many-small-files' paradigm? Or is > > there any way/switch to make QE use another scheme for the scratch files? > > whatever you do, it will require some programming effort. this can be > done from inside of QE (tedious) or on the outside by using a ramdisk > (as mentioned above) or faking it, e.g. by wrapping the stdio library > to write to huge RAM buffers for all files matching a given pattern. > cray used to provide such a library on their XT series machines to > work around the same kind of problems that you are describing on their > lustre scratch file systems. > > if there are some people here on the list that would be interested in > having such a wrapper and would be volunteering some time testing and > providing feedback, i might be tempted to give it a try and write such > a wrapper. As far as I understand the code, all IO to outdir is performed via IOTK; maybe this could be an attack vector to the io problem... Let's see if I can spare a bit of time to look into this. -- Mit freundlichen Gr??en Henning Glawe Max-Planck-Institut f?r Mikrostrukturphysik Weinberg 2, 06120 Halle (Saale), Germany http://www.mpi-halle.de/~theory Phone: +49-345-5582-613 Fax: +49-345-5511223 Email: glawe at mpi-halle.de
[Pw_forum] Performance problems due to files in outdir
On Wed, May 08, 2013 at 11:39:54AM +0200, Paolo Giannozzi wrote: > On Tue, 2013-05-07 at 22:32 +0200, Henning Glawe wrote: > > > Is this compatible to all postprocessing codes, such as dos.x > > and pp.x and the phonon code ph.x? > > I think it should. It is presently incompatible with option > "wf_collect". Yes, discovered that last night, too... -- Mit freundlichen Gr??en Henning Glawe Max-Planck-Institut f?r Mikrostrukturphysik Weinberg 2, 06120 Halle (Saale), Germany http://www.mpi-halle.de/~theory Phone: +49-345-5582-613 Fax: +49-345-5511223 Email: glawe at mpi-halle.de
[Pw_forum] graphen with adatoms input
Hello everyone! I am asking for suggestion. I'm trying to make input for scf calculation (and then for electron-phonon... ) for graphene with adatoms. I've been doing calculation with monolayer graphene and I used hexagonal lattice to describe it and large c/a with vacuum to simulate monolayer. I've been using GPU version of code and it works perfectly (I'll write something more about that on GPU message board) Now I'd like to add adatoms in the middle of lattice and I'm not sure how to do that. Is there any way to make input for hexagonal lattice with adatom or I have to make free lattice ibrav=0 and then use CELL PARAMETER card? Looking forward to your answers, Jelena Pesic PhD Student, Institute of Physics Belgrade, Serbia
[Pw_forum] Details of partial density of states calculation
(I tried to send this email a few days ago but since it did not appear in the forum, I assume it got lost. Apologies in advance if this is an annoying duplication.) This is a very basic question about the partial density of states calculation using the projwfc.f90 program within the PAW mode. In reading the fortran code, it seems that the weighting factor that is calculated is based on the atom-center projector functions |p^a_i> where a is the atomic site and i represents the radial and spherical harmonic quantum numbers. Is it correct that what is written to the pdos output files is the partial densities with the weight factors |<p^a_i|\psi>|^2, organized by atom number a and l_i? What I wanted to estimate is the charge within the augmentation sphere of each atom for each state, but the sum of all of the |<p^a_i|\psi>|^2 coefficients is not really that. The code is somewhat complicated so perhaps there is some rescaling ?? Or perhaps there is a different code to estimate those charges? Or perhaps there is some experience that the existing code is good good enough for the qualitative analysis of most studies. It slightly worries me that the pdos defined in this way is fairly sensitive to the PAW dataset used.I am having a debate with myself about whether it might be good to append a piece of code I wrote long ago to your code to calculate <p^a_i|\psi> and calculate a better estimate of the charge inside the augmentation sphere. (Assuming it would be possible to figure out the details of that code.) I welcome your advice and commentary. Thanks, Natalie N. A. W. Holzwarth email: natalie at wfu.edu Department of Physics web: http://www.wfu.edu/~natalie Wake Forest University phone: 1-336-758-5510 Winston-Salem, NC 27109 USA office: Rm. 300 Olin Physical Lab -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130508/b953a576/attachment.html
[Pw_forum] Performance problems due to files in outdir
On Tue, 2013-05-07 at 22:32 +0200, Henning Glawe wrote: > Is this compatible to all postprocessing codes, such as dos.x > and pp.x and the phonon code ph.x? I think it should. It is presently incompatible with option "wf_collect". P. -- Paolo Giannozzi, Dept. Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Spin-Unrestricted Calculation for O2 Adsorption
On Tue, 2013-05-07 at 19:28 -0400, Vic Bermudez wrote: > starting_magnetization=0.17 should be starting_magnetization(1)=0.17 and should not be needed if option > occupations='from_input' is present. In general: either you set the occupations or the total magnetization, or you set them free and give a starting magnetization to break the symmetry P/ -- Paolo Giannozzi, Dept. Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Raman cross section for spin-polarized systems?
On Wed, 2013-05-08 at 08:04 +, Ij?s Mari wrote: > the calculation of Raman cross-section is not available for > spin-polarized systems [...] I wonder if there have been advances short answer: no P. -- Paolo Giannozzi, Dept. Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Spin-Unrestricted Calculation for O2 Adsorption
Dear Vic, I think you could just specify the total_magnetization, and if the surface is metallic, or magnetic, use also smearing? nicola On 08/05/2013 01:28, Vic Bermudez wrote: > Hello, > > I want to do a calculation for O2 (in its triplet ground state) > adsorbing > on a surface. The surface, as usual, is modeled using a two-dimensional slab > supercell. For the free O2 molecule I know how to treat the triplet ground > state using > > > . > . > nspin=2, > starting_magnetization=0.17, > nband=8, > occupations='from_input', > . > . > / > > OCCUPATIONS > 1 1 1 1 1 1 1 0 > 1 1 1 1 1 0 0 0 > > > What I don't know is how to extend this type of input to the adsorption > case. It doesn't seem practical to specify "nband" and "occupations" for the > entire supercell + O2. There has to be a better way, but I haven't been able > to find anything in the documentation or at the users' forum. > Any help would be much appreciated. > > 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 > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- -- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
[Pw_forum] Performance problems due to files in outdir
On Tue, May 7, 2013 at 8:57 PM, Henning Glawe wrote: > Moin, > we have recently discovered performance problems on our parallel scratch file > system (fhgfs) in a 400-node-cluster. > Much of the blame went to my quantum espresso jobs (custom-patched 4.3.2). I > am performing calculations on thousands of small crystals, most having no > symmetry, leading to a huge number of irreducable k-points. > At least in this version, QE/iotk creates one directory per k-point, with only > one small file (eigenval.xml) contained in it. > Even if I set '::disk_io="low"', this behaviour seems to have a major > impact on the overall performance of the file system. have you tried using a ramdisk? if your machine is linux based, then you can usually access up to half of the physical memory via /dev/shm. given the ever increasing amount of RAM that current many-core machine have, this has become a viable alternative to modifying the source code to keep data in core. > Are there any plans to move away from the 'many-small-files' paradigm? Or is > there any way/switch to make QE use another scheme for the scratch files? whatever you do, it will require some programming effort. this can be done from inside of QE (tedious) or on the outside by using a ramdisk (as mentioned above) or faking it, e.g. by wrapping the stdio library to write to huge RAM buffers for all files matching a given pattern. cray used to provide such a library on their XT series machines to work around the same kind of problems that you are describing on their lustre scratch file systems. if there are some people here on the list that would be interested in having such a wrapper and would be volunteering some time testing and providing feedback, i might be tempted to give it a try and write such a wrapper. axel. > -- > Mit freundlichen Gr??en > Henning Glawe > > Max-Planck-Institut f?r Mikrostrukturphysik > Weinberg 2, 06120 Halle (Saale), Germany http://www.mpi-halle.de/~theory > Phone: +49-345-5582-613 Fax: +49-345-5511223 Email: glawe at mpi-halle.de > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] Raman cross section for spin-polarized systems?
Dear all, at the present, the calculation of Raman cross-section is not available for spin-polarized systems. In the pwscf forum archives, I was only able to find discussions on the topic dating back to 2010. I wonder if there have been advances since then? Best wishes, Mari Ij?s PhD student Aalto University School of Science, Department of Applied Physics, Helsinki, Finland
