[Pw_forum] ATOMIC_POSITIONS after 'final coordinates'
Hi, dear espressors, I'm new to espresso (switching from CPMD) and I have a simple question regarding to the output file of a relax calculation. There is an extra "ATOMIC_POSITIONS" section after the "final coordinates". It is neither the final coordinates, nor the starting coordinates, nor cystal coordinates. What's that? See below the output file. I'd appreciate it if someone can tell me where to find the explanation to the output file in the manual. I have searched the maillist and manual online but find no answer. Xijun Wang -- Department of Chemistry and Biochemistry, Concordia University 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 *** output file of the relaxation calculation *** - ... ? ? ?Damped Dynamics: convergence achieved in ?11 steps ? ? ?End of damped dynamics calculation ? ? ?Final energy = ? -3499.4924725209 Ry Begin final coordinates ? ? ?new unit-cell volume = ? 5281.07728 a.u.^3 ( ? 782.57490 Ang^3 ) CELL_PARAMETERS (alat= 19.96079920) ? ?1.0 ? 0.0 ? 0.0 ? ?0.0 ? 0.591661302 ? 0.0 ? -0.254163181 ? 0.0 ? 1.122317102 ATOMIC_POSITIONS (angstrom) Zr ? ? ?-0.000121009 ? 0.0 ? 0.48982 Zr ? ? ? 0.050917464 ? 0.0 ? 6.659231281 ... End final coordinates ? ? ?Entering Dynamics: ? ?iteration = ? ?11 ? ? ? = ? 0.78384260 ATOMIC_POSITIONS (angstrom) Zr ? ? ? 0.33474 ? 0.0 ? 0.000130486 Zr ? ? ? 0.050452867 ? 0.0 ? 6.659368418 ... Writing output data file rx.damp.save ...
[Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '')
Hi Daniel, are you sure you are using pseudopotentials that hold gipaw information? if so, send me the pseudo i'll check what is wrong. thanks emine kucukbenli, phd student, sissa, italy SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/
[Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '')
On Sep 6, 2011, at 18:56 , Daniel Lima wrote: > Thanks in advance and sorry for bad english bad english is not a problem: it is the norm here. The problem is that you haven't specified which version of the code you are talking about. Gipaw, in particular, has undergone serious changes in the last versions P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] wfc files: heavy I/O, handling for restarts
Dear Prof. Paolo, Thanks a lot for your reply. > which QE code and which files are you referring to? < That is phonon code (ph.x) and the files I mentioned before are given below in detail. With the earlier versions up to 4.1.3, phonon code runs fine and I got following files (bold and underlined items are folders) in the tmp directory of a local disk. The nodes which are used by the codes are node186, 036, 139. node186:/tmpscratch/sksct8/tmp$ ls > *pbmno.save* _phpbmno.com1_phpbmno.dwf2 _phpbmno.igk3 > _phpbmno.prd3 > pbmno.wfc1 _phpbmno.com2_phpbmno.dwf3 _phpbmno.mixd1 > _phpbmno.recover > pbmno.wfc2 _phpbmno.com3_phpbmno.ebar1 _phpbmno.mixd2 > _phpbmno.recover2 > pbmno.wfc3 _phpbmno.dvkb31 _phpbmno.ebar2 _phpbmno.mixd3 > _phpbmno.recover3 > _phpbmno.bar1 _phpbmno.dvkb32 _phpbmno.ebar3 *_phpbmno.phsave** * * > _phpbmno.save* > _phpbmno.bar2 _phpbmno.dvkb33 _phpbmno.igk_phpbmno.prd1 > _phpbmno.bar3 _phpbmno.dwf1_phpbmno.igk2 _phpbmno.prd2 > node036:/tmpscratch/sksct8/tmp$ ls pbmno.wfc4 _phpbmno.dwf4 _phpbmno.mixd4 _phpbmno.recover4 pbmno.wfc5 _phpbmno.dwf5 _phpbmno.mixd5 _phpbmno.recover5 _phpbmno.bar4 _phpbmno.igk4 _phpbmno.prd4 _phpbmno.wfc4 _phpbmno.bar5 _phpbmno.igk5 _phpbmno.prd5 _phpbmno.wfc5 node139:/tmpscratch/sksct8/tmp$ ls pbmno.wfc6 _phpbmno.bar8 _phpbmno.igk7 _phpbmno.recover6 _phpbmno.wfc8 pbmno.wfc7 _phpbmno.dwf6 _phpbmno.igk8 _phpbmno.recover7 pbmno.wfc8 _phpbmno.dwf7 _phpbmno.prd6 _phpbmno.recover8 _phpbmno.bar6 _phpbmno.dwf8 _phpbmno.prd7 _phpbmno.wfc6 _phpbmno.bar7 _phpbmno.igk6 _phpbmno.prd8 _phpbmno.wfc7 However, with the new version 4.3.1, for the exactly same input files and job scripts I only get these files and nothing else : node045:/tmpscratch/sksct84/tmp$ ls *pbmno.save* pbmno.wfc1 *_ph0* node111:/tmpscratch/sksct84/tmp$ ls pbmno.wfc2 pbmno.wfc3 node092:/tmpscratch/sksct84/tmp$ ls pbmno.wfc4 pbmno.wfc5 node080:/tmpscratch/sksct84/tmp$ ls pbmno.wfc6 pbmno.wfc7 node072:/tmpscratch/sksct84/tmp$ ls pbmno.wfc8 Note that, the used nodes in this time are node045, node111, node092, node080, node072. So it is clear from the above example that somehow in the new version 4.3.1, _phpbmno.save and _phpbmno.phsave goes inside the directory "_ph0" ; And the same phonon calculation, which was running fine with the earlier version, now stops like this way (a bit abruptly and rudely, with out much informations or error messages) : Electric field: Dielectric constant Born effective charges in two ways Atomic displacements: There are 5 irreducible representations Representation 1 3 modes -T_1u G_15 G_4- To be done Representation 2 3 modes -T_1u G_15 G_4- To be done Representation 3 3 modes -T_1u G_15 G_4- To be done Representation 4 3 modes -T_1u G_15 G_4- To be done Representation 5 3 modes -T_2u G_25 G_5- To be done simply with this error : -- MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD with errorcode 0. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- mpirun has exited due to process rank 2 with PID 8791 on node node111.cvos.cluster exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [node045:11580] 6 more processes have sent help message help-mpi-api.txt / mpi-abort [node045:11580] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages Hope this email explains much better. Thanks and Regards, Saha SK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110906/78efc62c/attachment.htm
[Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '')
you sure you doing the right thing? Did you choose the correct pseudop? your compilation ran perfectly? The system were correctly relaxed? Can you send the pseudos and the input for checks? Eugenio Furtado de Souza Laboratorio de Modelagem Molecular-LABMMOL Universidade Federal do Rio de Janeiro Av. Athos da Silveira Ramos No 149, CT, Bloco A, sala 609 tel: (21) 2562-7132 Cidade Universit?ria, Ilha do Fund?o, Rio de Janeiro-RJ, CEP 21941-90 - Mensagem original - De: "Emine Kucukbenli" Para: "pw forum" Enviadas: Ter?a-feira, 6 de Setembro de 2011 14:11:41 Assunto: Re: [Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '') Hi Daniel, are you sure you are using pseudopotentials that hold gipaw information? if so, send me the pseudo i'll check what is wrong. thanks emine kucukbenli, phd student, sissa, italy SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Eugenio Furtado de Souza Laboratorio de Modelagem Molecular-LABMMOL Universidade Federal do Rio de Janeiro Av. Athos da Silveira Ramos No 149, CT, Bloco A, sala 609 tel: (21) 2562-7132 Cidade Universit?ria, Ilha do Fund?o, Rio de Janeiro-RJ, CEP 21941-90 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110906/76c1483a/attachment.htm
[Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '')
Hi, My name is Daniel Aguiar, and I'm a beginner in Theoretical Calculations. I'm having some troubles with the gipaw.x calculations . The pw.x was sucessed (JOB DONE!!). But in gipaw.x the following mensage appear: At line 174 of file paw_gipaw.f90 (unit = 14, file = '') Fortran runtime error: File '' does not exist I verified in paw_gipaw.f90 and the line is: OPEN ( 14, FILE = filerec_sp ) What's wrong? My nmr input is following below: &inputgipaw job = 'nmr' prefix = 'ADAMANTANE-rev-PBE-vdW-nmr' tmp_dir = '/home/daniel/Softwares/espresso-4.3/tmp/' isolve = 0 iverbosity = 1 q_gipaw = 0.01 spline_ps = .true. use_nmr_macroscopic_shape = .false. / Thanks in advance and sorry for bad english -- Daniel Lima Marques de Aguiar Universidade Federal do Rio de Janeiro / Centro de Tecnologia Instituto de Qu?mica Programa de P?s Gradua??o em Qu?mica Laborat?rio de Resson?ncia Magn?tica Nuclear - Salas 605/608/614 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110906/cf36e007/attachment.htm
[Pw_forum] wfc files: heavy I/O, handling for restarts
On Sep 5, 2011, at 21:05 , S. K. S. wrote: > In the version before QE4.2, the QE codes used to replicate > the same necessary files to the distributed local disks of all > the nodes. which QE code and which files are you referring to? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] heat capacity
Dear Prof. Eyvaz Isaev, I want to calculate heat capacity for the Rhombohedral lattice (ibrav= 5). When I try to use QHA package, I have encountered with this message "Trigonal R: not implemented yet". I have seen similar question in mailing list and your reply. But yet I don't know what should be done? Thanks in advance, Nafise --- Nafise Rezaei Dept of Physics, Isfahan University of Technology Isfahan, Iran -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110906/52b9181f/attachment.htm
