[Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
Thank you very much, Carlo. I delete the line The problem solved. Thank you very much. Regards David Foster Ph.D. Student of Chemistry On Wed, 1/8/14, Carlo Nervi wrote: Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh" To: pw_forum at pwscf.org Date: Wednesday, January 8, 2014, 3:44 AM Hi David, it seems that in the line containing _Symmetry_equiv_pos_as_xyz it does not recognize the three necessary parameters. Have a look of the original .cif file and if there is only spaces after _Symmetry_equiv_pos_as_xyz just delete the line. In any cases, Lorenzo succeed in using the conversion, so maybe it is again a problem related with your version og awk. Preferabily please use gawk (gnu awk). Regards, ??? Carlo Il 08/01/2014 8.56, David Foster ha scritto: > Dear Paolo > > Thank you for reply. I upgrade the file to 5th version. > > I installed gawk 4. Now, I recieve this error: > > > Error in _Symmetry_equiv_pos_as_xyz. Number of fields !=3: [1]= [2]= [3]= > D: > > > > Regards > > David Foster > > Ph.D. Student of Chemistry > > > On Tue, 1/7/14, Paolo Giannozzi wrote: > >???Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh" >???To: pw_forum at pwscf.org >???Date: Tuesday, January 7, 2014, 2:11 PM > >???This is the header of the last >???version. Note the fourth line: >???--- >???#? Version 0.5? Date: 02-Oct-2013 >???#? Version 0.4? Date: 12 Jun 2013 >???#? Version 0.3? Date: 15 Nov 2012 >???# tested with GNU awk v.4 - may not work with earlier >???versions >???--- > >???P. >???On Tue, 2014-01-07 at 07:08 -0800, David Foster wrote: > >???> I will download new version and try. >???> >???> I work on Debian 7.0 which "mwak" has been installed on >???it. Do I need to install "gawk" on it. >???> >???> >???> Regards >???> >???> David Foster >???> >???> Ph.D. Student of Chemistry >???> >???> >???> On Tue, 1/7/14, Lorenzo Paulatto >???wrote: >???> >???>? Subject: Re: [Pw_forum] Error in converting CIF >???to QE by "cif2qe.sh" >???>? To: "PWSCF Forum" >???>? Date: Tuesday, January 7, 2014, 5:45 AM >???> >???>? On 01/07/2014 01:18 PM, David Foster >???>? wrote:> Dear Users, >???>? > I used cif2qe.sh shell in PW/tools directory >???to convert >???>? rutile.cif to >???> >???>? It works for me, I get the following output. >???> >???>? How do you run the code, and which version of >???bash and awk >???>? do you have? Did you change anything in the >???script? >???> >???> >???>? best regards >???> >???>? &CONTROL >???> > >???>? ? ? ???title = 'rutile' >???> > >???>? ???calculation = 'relax' >???> > >???>? restart_mode = 'from_scratch' >???> > >???>? ? ? ? outdir = './1' >???> > >???>? ? pseudo_dir = '../PP/atompaw' >???> > >???>? ? ? ? prefix = 'caz' >???> > >???>? ? ???disk_io = 'none' >???> > >???>? ???verbosity = 'default' >???> >???>? ???etot_conv_thr = 0.1 >???> >???>? ???forc_conv_thr = 0.0001 >???> > >???>? ? ? ???nstep = 680 >???> > >???>? ? ???tstress = .true. >???> > >???>? ? ???tprnfor = .true. >???>???/ >???>???&SYSTEM >???> > >???>? ? ? ???ibrav = 0 >???> > >???>? ? ? ? ???nat = 4 >???> > >???>? ? ? ? ? ntyp = 1 >???> > >???>? ? ???ecutwfc = 60 >???> > >???>? ? ???ecutrho = 600 >???>? ! > >???>? ? ? ? london = .true. >???>???/ >???>???&ELECTRONS >???> >???electron_maxstep = >???>? 200 >???> > >???>? ? ? conv_thr = 1.0D-7 >???> > >???>? diago_thr_init = 1e-4 >???> > >???>? ???startingpot = 'atomic' >???> > >???>? ???startingwfc = 'atomic' >???> > >???>? ???mixing_mode = 'plain' >???> > >???>? ???mixing_beta = 0.5 >???> > >???>? ???mixing_ndim = 8 >???> >???>? ???diagonalization = 'david' >???>???/ >???>? &IONS >???> > >???>? ion_dynamics = 'bfgs' >???>???/ >???> >???> >???>? ATOMIC_SPECIES >???> >? ? ? 0.00 >???>? .pbe-van_ak.UPF >???> >???>? ATOMIC_POSITIONS crystal >???>? ? ? ???0.000 > >???>? ???0.000 >???>? ???0.000 >???>? ? ? ???0.3053000 > >???>? ???0.3053000 >???>? ???0.000 >???>? ? ? ???0.500 > >???>? ???0.500 >???>? ???0.500 >???>? ? ? ???0.8053000 > >???>? ???0.1947000 >???>? ???0.500 >???> >???>? K_POINTS automatic >???>? 5? 5? 8???0 0 0 >???> >???> >???>? CELL_PARAMETERS >???>? ? ? 8.680891628420765 >???>? ???0.000 >???>? ???0.000 >???>? ? ? 0.001 >???>? ???8.680891628420765 >???>? ???0.000 >???>? ? ? 0.000 >???>? ???0.000 >???>? ???5.590036668211679 >???> >???> >???> >???> >???>? -- Dr. Lorenzo Paulatto >???>
[Pw_forum] Query on Double numerical atomic orbitals
Dear QE users, I am new to QE and am trying to do some calculations on GNRs. In the literature i reviewed, it was mentioned that "double numerical atomic orbitals along with polarisation functions" were used as a basis for the tens of atoms in the unitcell. From the little i understood, the double radial functions lead to better accuracy and convergence. I was wondering if it is implemented by default in QE or not. Please let me know. -- Thank You Ajit
[Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
On 01/08/2014 12:44 PM, Carlo Nervi wrote: > In any cases, Lorenzo succeed in using the conversion, so maybe it is > again a problem related with your version og awk. Preferabily please use > gawk (gnu awk). > $ awk --version GNU Awk 4.1.0, API: 1.0 Copyright (C) 1989, 1991-2013 Free Software Foundation. ... -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Universit? Paris 6 +33 (0)1 44 275 084 / skype: paulatz http://www-int.impmc.upmc.fr/~paulatto/ 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -- next part -- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 2956 bytes Desc: S/MIME Cryptographic Signature Url : http://pwscf.org/pipermail/pw_forum/attachments/20140108/72078a1e/attachment.bin
[Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
Hi David, it seems that in the line containing _Symmetry_equiv_pos_as_xyz it does not recognize the three necessary parameters. Have a look of the original .cif file and if there is only spaces after _Symmetry_equiv_pos_as_xyz just delete the line. In any cases, Lorenzo succeed in using the conversion, so maybe it is again a problem related with your version og awk. Preferabily please use gawk (gnu awk). Regards, Carlo Il 08/01/2014 8.56, David Foster ha scritto: > Dear Paolo > > Thank you for reply. I upgrade the file to 5th version. > > I installed gawk 4. Now, I recieve this error: > > > Error in _Symmetry_equiv_pos_as_xyz. Number of fields !=3: [1]= [2]= [3]= > D: > > > > Regards > > David Foster > > Ph.D. Student of Chemistry > > > On Tue, 1/7/14, Paolo Giannozzi wrote: > > Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh" > To: pw_forum at pwscf.org > Date: Tuesday, January 7, 2014, 2:11 PM > > This is the header of the last > version. Note the fourth line: > --- > # Version 0.5 Date: 02-Oct-2013 > # Version 0.4 Date: 12 Jun 2013 > # Version 0.3 Date: 15 Nov 2012 > # tested with GNU awk v.4 - may not work with earlier > versions > --- > > P. > On Tue, 2014-01-07 at 07:08 -0800, David Foster wrote: > > > I will download new version and try. > > > > I work on Debian 7.0 which "mwak" has been installed on > it. Do I need to install "gawk" on it. > > > > > > Regards > > > > David Foster > > > > Ph.D. Student of Chemistry > > > > > > On Tue, 1/7/14, Lorenzo Paulatto > wrote: > > > > Subject: Re: [Pw_forum] Error in converting CIF > to QE by "cif2qe.sh" > > To: "PWSCF Forum" > > Date: Tuesday, January 7, 2014, 5:45 AM > > > > On 01/07/2014 01:18 PM, David Foster > > wrote:> Dear Users, > > > I used cif2qe.sh shell in PW/tools directory > to convert > > rutile.cif to > > > > It works for me, I get the following output. > > > > How do you run the code, and which version of > bash and awk > > do you have? Did you change anything in the > script? > > > > > > best regards > > > > &CONTROL > > > > > title = 'rutile' > > > > > calculation = 'relax' > > > > > restart_mode = 'from_scratch' > > > > >outdir = './1' > > > > >pseudo_dir = '../PP/atompaw' > > > > >prefix = 'caz' > > > > > disk_io = 'none' > > > > > verbosity = 'default' > > > > etot_conv_thr = 0.1 > > > > forc_conv_thr = 0.0001 > > > > > nstep = 680 > > > > > tstress = .true. > > > > > tprnfor = .true. > > / > > &SYSTEM > > > > > ibrav = 0 > > > > > nat = 4 > > > > > ntyp = 1 > > > > > ecutwfc = 60 > > > > > ecutrho = 600 > > ! > > >london = .true. > > / > > &ELECTRONS > > > electron_maxstep = > > 200 > > > > > conv_thr = 1.0D-7 > > > > > diago_thr_init = 1e-4 > > > > > startingpot = 'atomic' > > > > > startingwfc = 'atomic' > > > > > mixing_mode = 'plain' > > > > > mixing_beta = 0.5 > > > > > mixing_ndim = 8 > > > > diagonalization = 'david' > > / > > &IONS > > > > > ion_dynamics = 'bfgs' > > / > > > > > > ATOMIC_SPECIES > > > 0.00 > > .pbe-van_ak.UPF > > > > ATOMIC_POSITIONS crystal > > 0.000 > > > 0.000 > > 0.000 > > 0.3053000 > > > 0.3053000 > > 0.000 > > 0.500 > > > 0.500 > > 0.500 > > 0.8053000 > > > 0.1947000 > > 0.500 > > > > K_POINTS automatic > > 5 5 8 0 0 0 > > > > > > CELL_PARAMETERS > > 8.680891628420765 > > 0.000 > > 0.000 > > 0.001 > > 8.680891628420765 > > 0.000 > > 0.000 > > 0.000 > > 5.590036668211679 > > > > > > > > > > -- Dr. Lorenzo Paulatto > > IdR @ IMPMC -- CNRS & Universit? Paris 6 > > +33 (0)1 44 275 084 / skype: paulatz > > http://www-int.impmc.upmc.fr/~paulatto/ > > 23-24/4?16 Bo?te courrier 115, 4 place Jussieu > 75252 Paris > > C?dex 05 > > > > > > -Inline Attachment Follows- > > > > ___ > > 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&Phys
[Pw_forum] phcg restart problem
Hello, Is there any chance that anyone has an insight on this restart problem in phcg v5.02 which generated some mpi error as mentioned in my earlier thread? ? If not, i will probably have to try the ph or use VASP instead. ?Any suggestions will be very much appreciated. Thanks, wee liat Carnegie Mellon Uni On Saturday, January 4, 2014 12:56 PM, weeliat wrote: Dear All, Thanks for the reply. ?I have since compiled v5.0.2 but got the same error upon restart. The initial output from the phcg run is shown below. ?I stopped it prematurely to test the restart capability: ? ? ?Program PHCG v.5.0.2 (svn rev. 9392) starts on ?3Jan2014 at 13:20:23? ? ? ?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/quote.php ? ? ?Parallel version (MPI), running on ? ?32 processors ? ? ?R & G space division: ?proc/nbgrp/npool/nimage = ? ? ?32 ? ?Info: using nr1, nr2, nr3 values from input ? ?Info: using nr1s, nr2s, nr3s values from input ? ? ?IMPORTANT: XC functional enforced from input : ? ? ?Exchange-correlation ? ? ?= ?SLA ?PZ ? NOGX NOGC ( 1 1 0 0 0) ? ? ?EXX-fraction ? ? ? ? ? ? ?= ? ? ? ?0.00 ? ? ?Any further DFT definition will be discarded ? ? ?Please, verify this is what you really want ? ? ? ? ? ? ? ?file H.pz-vbc.UPF: wavefunction(s) ?1S renormalized ? ? ? ?Parallelization info ? ? ? ? ? ?sticks: ? dense ?smooth ? ? PW ? ? G-vecs: ? ?dense ? smooth ? ? ?PW ? ? ?Min ? ? ? ?1118 ? ?1118 ? ?280 ? ? ? ? ? ? ? 159290 ? 159290 ? 19920 ? ? ?Max ? ? ? ?1120 ? ?1120 ? ?282 ? ? ? ? ? ? ? 159300 ? 159300 ? 19926 ? ? ?Sum ? ? ? 35781 ? 35781 ? 8969 ? ? ? ? ? ? ?5097465 ?5097465 ?637483 ? ? ?Tot ? ? ? 17891 ? 17891 ? 4485 ? ?*** ?Starting Conjugate Gradient minimization ? ? ? ? *** ?*** ?pol. # ? 1 : 138 iterations ?*** ?pol. # ? 2 : 138 iterations ?*** ?pol. # ? 3 : 136 iterations ATOMIC_POSITIONS Se ? ? ? 0.00020 ? 0.55869 ? 0.221532863 Co ? ? ?-0.000378387 ? 0.106617176 ? 0.320298820 Se ? ? ? 0.142919561 ? 0.083743738 ? 0.333072366 P ? ? ? ?0.010001498 ? 0.214824211 ? 0.249814145 .(edited) . . . ?*** ?Starting Conjugate Gradient minimization ? ? ? ? *** ? ? ?d2ion: alpha = ? 0.50 ?*** ?mode # ? 1 : using asr ?*** ?mode # ? 2 : using asr ?*** ?mode # ? 3 : using asr ?*** ?mode # ? 4 : 126 iterations ?*** ?mode # ? 5 : 124 iterations ?*** ?mode # ? 6 : 126 iterations ?*** ?mode # ? 7 : 118 iterations Everything in the initial run seems fine. The restart phcg.x ouput shows this: ? ? ?Program PHCG v.5.0.2 (svn rev. 9392) starts on ?4Jan2014 at 12:29:52? ? ? ?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/quote.php ? ? ?Parallel version (MPI), running on ? ?32 processors ? ? ?R & G space division: ?proc/nbgrp/npool/nimage = ? ? ?32 ? ?Info: using nr1, nr2, nr3 values from input ? ?Info: using nr1s, nr2s, nr3s values from input ? ? ?IMPORTANT: XC functional enforced from input : ? ? ?Exchange-correlation ? ? ?= ?SLA ?PZ ? NOGX NOGC ( 1 1 0 0 0) ? ? ?EXX-fraction ? ? ? ? ? ? ?= ? ? ? ?0.00 ? ? ?Any further DFT definition will be discarded ? ? ?Please, verify this is what you really want ? ? ? ? ? ? ? ?file H.pz-vbc.UPF: wavefunction(s) ?1S renormalized ? ? ? ?Parallelization info ? ? ? ? ? ?sticks: ? dense ?smooth ? ? PW ? ? G-vecs: ? ?dense ? smooth ? ? ?PW ? ? ?Min ? ? ? ?1118 ? ?1118 ? ?280 ? ? ? ? ? ? ? 159290 ? 159290 ? 19920 ? ? ?Max ? ? ? ?1120 ? ?1120 ? ?282 ? ? ? ? ? ? ? 159300 ? 159300 ? 19926 ? ? ?Sum ? ? ? 35781 ? 35781 ? 8969 ? ? ? ? ? ? ?5097465 ?5097465 ?637483 ? ? ?Tot ? ? ? 17891 ? 17891 ? 4485 ? The output stops here with a error msg from the pbs: An error occurred in MPI_Allreduce on communicator MPI COMMUNICATOR 9 SPLIT FROM 7 MPI_ERR_TRUNCATE: message truncated MPI_ERRORS_ARE_FATAL (your MPI job will now abort) I am not sure if this error is due to my compilers or mpi software (seems less probable as the initial run is ok) or is there something with the restart function in phcg? Thanks, wee liat -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140108/82996370/attachment.html
