From giannozz at nest.sns.it Tue Jun 3 10:47:23 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 3 Jun 2003 10:47:23 +0200 Subject: [Pw_forum] Phonon DOS In-Reply-To: References: Message-ID: <200306031047.23376.giannozz@nest.sns.it> On Friday 30 May 2003 14:50, Subhradip Ghosh wrote: > Hi, > > I am trying to compute Phonon DOS using the code matdyn.f90. I found that > it worked for an insulator but in my case the system is metallic and while > I ran the code there is some output generated alongwith an error message > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from matdyn : error # -1 > non-analytic term for q=0 missing ! > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > [....] Is it a serious error or should I ignore it? does the code calculate the correct phonon DOS? If yes, you should ignore this error message Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From giannozz at nest.sns.it Tue Jun 3 11:09:14 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 3 Jun 2003 11:09:14 +0200 Subject: [Pw_forum] special points mesh In-Reply-To: <20030530105644.1654.qmail@web9908.mail.yahoo.com> References: <20030530105644.1654.qmail@web9908.mail.yahoo.com> Message-ID: <200306031109.14066.giannozz@nest.sns.it> On Friday 30 May 2003 12:56, ilyes hamdi wrote: > Dear Users > In PWSCF we use six parameters to generate special > points in Monkhorst-Pack method. the 3 last parameters > are defined to be 0 or 1. What's the meaning of these k-point grid offset along the 3 crystal axis (in reciprocal space) > and where can i find their definition in the program. The definition is in PW/kpoint_grid.f90 > Last year i worked on CASTEP, and i have only to > define the grid nk1,nk2,nk3. exemple > structure ZB > 4x4x4 gives 10 points in CASTEP is equivalent to > 4x4x4 001 in PWSCF. equivalent to "4 4 4 0 0 0", I guess. k1 = 0 means no offset in the 1 direction, k1 = 1 means that the k-point grid is translated by one-half of the grid step in the 1 direction : G_1 /(2*nk1). Same on directions 2 and 3. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From mtoso at ts.infn.it Wed Jun 4 11:31:49 2003 From: mtoso at ts.infn.it (Michele Tosolini) Date: Wed, 4 Jun 2003 11:31:49 +0200 (MET DST) Subject: [Pw_forum] info on CINECA SP4 Message-ID: Hello PWSCF and CINECA users. Recently i had some problems running on Cineca SP4. I tried to perform NSC calculations with 16 processors on a tetragonal cell of ~ 340 atoms (320 of silicon) with a cutoff of 12 Ry and with a mesh of 20 K points. I would be immensely pleasing if someone, that it carries out dimensionally similar calculations on SP4, sent me the LoadLeveler flags and eventually the specific make.sys file used for the compilation of the program ? Thanks a lot to all. From pushpa at jncasr.ac.in Thu Jun 5 07:20:32 2003 From: pushpa at jncasr.ac.in (Raghani Pushpa) Date: Thu, 5 Jun 2003 10:50:32 +0530 (IST) Subject: [Pw_forum] 'missing eigenvalue' Message-ID: Dear all, I am doing the calculations on clusters. When I do the calculations at zero temperature (no smearing), I have to restrict the number of bands to the number of filled bands. If I give more number of bands, the program does not converge; I don't understand why is it happening? At degauss=0, the eigenvalues are not same as eigenvalues I get from band structure calculations, I find that in self consistent calculation, the eigenvalue of HOMO is missing and program gives the eigenvalue of LUMO. Could you please tell me why does it happen? regards, Pushpa -- From degironc at sissa.it Thu Jun 5 12:43:04 2003 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 05 Jun 2003 12:43:04 +0200 Subject: [Pw_forum] 'missing eigenvalue' References: Message-ID: <3EDF1EB8.2030605@sissa.it> Are you sure that the HOMO is non degenerate ? If the HOMO orbital is degenerate but the number of electrons in the cluster does not fill it completely this may induce instability in the case you provide more bands than electrons because from one iteration to the next the occupied bands could be different. Another possible problem, related to the fact that the HOMO orbital is missing, could be related to the fact that the code performs iterative diagonalization and if the HOMO has different symmetry from the current approximate wavefunctions the diagonalization will not find it. possible actions: 1) try to start from random wavefunctions instead of atomic ones. This could help if the missing eigenvalue is due to symmetry of the initial guess for the wfcs. 2) try to do calculations with a small smearing using gaussian or Fermi-Dirac broadening (avoid Methfessel-Paxton in this case since the fact that it is not positive definite could lead to spurious effects when using very few k-points). This should clarify what is the level structure for your cluster and should tell you if there are problem of degeneracy at the Fermi level. 3) Usually increasing the number of bands should helps in NOT missing eigenvalues; the fact that you get problems is an hint that there might be problem of degeneracy. Write eigenvalues at every iteration (including more bands than Nelec/2) to see how things evolves and see if there are levels that keep changing. All the best Stefano de Gironcoli Raghani Pushpa wrote: >Dear all, >I am doing the calculations on clusters. When I do the calculations at >zero temperature (no smearing), I have to restrict the number of bands to >the number of filled bands. If I give more number of bands, the program >does not converge; I don't understand why is it happening? > >At degauss=0, the eigenvalues are not same as eigenvalues I get from band >structure calculations, I find that in self consistent calculation, the >eigenvalue of HOMO is missing and program gives the eigenvalue of LUMO. >Could you please tell me why does it happen? > >regards, >Pushpa > > > > From fisicabiomolecular at yahoo.com.br Thu Jun 5 13:06:57 2003 From: fisicabiomolecular at yahoo.com.br (Wyllian) Date: Thu, 5 Jun 2003 08:06:57 -0300 Subject: [Pw_forum] I am with problems to calculate a molecule: adenine (C5H5N5) Message-ID: <004701c32b52$966526f0$47c583c8@pion> Please, I am trying to calculate an adenine molecule (C5H5N5). I do not obtain to get resulted. Input could verify this. Thaks. Wyllian http://www.biophysics.hpg.com.br #/bin/sh #################################################################### # # set the needed environment variables # . ../../../environment_variables # # check whether echo needs the -e option if [ "`echo -e`" = "-e" ]; then echo='echo' else echo='echo -e' fi # $echo ' ' $echo ' running '$0':' $echo ' pw.x to compute the equilibrium' $echo ' geometry of a molecule, C5H5N5 - Adenina. ' $echo ' ' # # check that needed directories and files exist # $echo ' PW_ROOT is defined as '$PW_ROOT' ' $echo ' PSEUDO_DIR is defined as '$PSEUDO_DIR' ' $echo ' TMP_DIR is defined as '$TMP_DIR' ' $echo ' ' $echo ' checking that needed directories and files exist; \c' if [ ! -d $PW_ROOT ]; then $echo;$echo ' STOPPING: directory '$PW_ROOT' does not exist'; exit else if [ ! -f $PW_ROOT/main/pw.x ]; then echo;echo ' STOPPING: executable '$PW_ROOT/main/pw.x' does not exist'; exit fi fi if [ ! -d $PSEUDO_DIR ]; then $echo;$echo ' STOPPING: directory '$PSEUDO_DIR' does not exist'; exit else if [ ! -f $PSEUDO_DIR/H.vbc ]; then $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/H.vbc' does not exist'; exit fi if [ ! -f $PSEUDO_DIR/HUS.RRKJ3 ]; then $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/HUS.RRKJ3' does not exis t'; exit fi if [ ! -f $PSEUDO_DIR/HUSPBE.RRKJ3 ]; then $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/HUSPBE.RRKJ3' does not e xist'; exit fi if [ ! -f $PSEUDO_DIR/C.vbc ]; then $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/C.vbc' does not exist'; exit fi if [ ! -f $PSEUDO_DIR/CUS.RRKJ3 ]; then $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/C.vbc' does not exist'; exit fi if [ ! -f $PSEUDO_DIR/CUSPBE.RRKJ3 ]; then $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/CUSPBE.RRKJ3' does not e xist'; exit fi if [ ! -f $PSEUDO_DIR/NUSPBE.RRKJ3 ]; then $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/NUSPBE.RRKJ3' does not e xist'; exit fi if [ ! -f $PSEUDO_DIR/NUS.RRKJ3 ]; then $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/NUS.RRKJ3' does not exis t'; exit fi fi if [ i! -d $TMP_DIR ]; then $echo;$echo ' STOPPING: directory '$TMP_DIR' does not exist'; exit fi $echo ' done' # # clean TMP_DIR # $echo ' cleaning '$TMP_DIR' ; \c' rm -f $TMP_DIR/* $echo ' done' # # self-consistent calculation # cat > adenina1.in << EOF C5H5N5 molecule + relax C5H5N5 &input ibrav=0, celldm(1)=1.d0, nat=15,ntyp=3, pseudop(1) = 'CUS.RRKJ3', pseudop(2) = 'HUS.RRKJ3', pseudop(3) = 'NUS.RRKJ3', pseudo_dir = '$PSEUDO_DIR/', tmp_dir='$TMP_DIR/', ecut(1)=24.0, dual=6, beta(1)=0.3, upscale=10, tr2 = 1.0d-14, iswitch=1, niter=100, nstep=100, output_pot='c5h5n5pot', &end 14.0 0.0 0.0 0.0 14.0 0.0 0.0 0.0 14.0 cubic -4.279664 -2.380489 0.676900 1 0.015307 -2.366316 0.844708 1 0.010016 0.051590 -0.222799 1 -2.329655 1.250432 -0.851322 1 3.897562 -0.881558 0.346576 1 -6.079629 -3.364659 1.041240 2 3.257511 -4.583532 1.953033 2 5.965679 -8.416466 0.418008 2 -0.491329 4.467314 -2.209657 2 -3.950852 4.517203 -2.374064 2 2.453432 0.933336 -0.511738 3 -2.252932 3.610512 -1.899176 3 2.527699 -2.915659 1.188827 3 -2.199264 -3.629598 1.310904 3 -4.478275 -0.033070 -0.369631 3 'C ' 1 1 1.0 'H ' 1 2 1.0 'N ' 1 3 1.0 0 1 1 1 0 0 0 EOF $echo ' running the geometry relaxation for adenina; \c' $PARA_PREFIX $PW_ROOT/main/pw.x $PARA_POSTFIX < adenina1.in > adenina1.out $echo ' Adenina done' --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.481 / Virus Database: 277 - Release Date: 13/5/2003 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20030605/628a8e1c/attachment.htm From proffess at yandex.ru Fri Jun 6 14:36:22 2003 From: proffess at yandex.ru (Sergei Lisenkov) Date: Fri, 6 Jun 2003 16:36:22 +0400 (MSD) Subject: [Pw_forum] Error: pseudo file is empty or wrong Message-ID: <3EE08AC6.000024.14494@ariel.yandex.ru> Dear All, I compiled the PWscf code on HP PA_RISC machine using option -DCERNFFT. I compiled it without errors. But I got error when I ran example: Program PWSCF 1.2.0 starts ... Today is 6Jun2003 at 16:31: 6 Ultrasoft (Vanderbilt) Pseudopotentials Complex Hamiltonian current dimensions of program pwscf are: ntypx= 6 npsx = 6 lmax = 3 npk =40000 nbrx = 6 lqmax = 7 nqfm = 8 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_ncpp : error # 1 pseudo file is empty or wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... STOP 2 My pseudo file is OK, I use it in another machine. How solve this problem? Thank you for your help, Best wishes, Sergey From giannozz at nest.sns.it Fri Jun 6 15:08:03 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 6 Jun 2003 15:08:03 +0200 Subject: [Pw_forum] Error: pseudo file is empty or wrong In-Reply-To: <3EE08AC6.000024.14494@ariel.yandex.ru> References: <3EE08AC6.000024.14494@ariel.yandex.ru> Message-ID: <200306061508.03835.giannozz@nest.sns.it> Hi > from read_ncpp : error # 1 > pseudo file is empty or wrong read_ncpp reads a norm-conserving pseudopotential: is this what you want ? > [...] My pseudo file is OK, I use it in another machine. verify that pseudo_dir is set to the correct value. The code checks for the existence of the file and issues a different error message in such a case, but you might have an empty file from a preceding failed run. Beware: in the 1.2.0 version, some character variables containing directory and file names are somewhat short. If you still don't see anything wrong: in PW/readin.f90, just before the call to read_ncpp, add a line call system ('cat '//file_pseudo) This will send the content of the pseudo file to the output. If you still don't see anything wrong, you have to go through PW/read_ncpp.f90 and see where the code stops Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From katalin.gaal-nagy at physik.uni-regensburg.de Fri Jun 6 16:14:15 2003 From: katalin.gaal-nagy at physik.uni-regensburg.de (Katalin Gaal-Nagy) Date: Fri, 6 Jun 2003 16:14:15 +0200 (MEST) Subject: [Pw_forum] Error: pseudo file is empty or wrong Message-ID: <200306061414.h56EEGlJ023577@rrzd2.rz.uni-regensburg.de> Dear Sergey! If you have still problems after checking everything Paolo wrote, it might be a bug in the compiler like it happend sometimes before with the pgf90. Greetings, Katalin > Dear All, > > I compiled the PWscf code on HP PA_RISC machine using option -DCERNFFT. I compiled it without errors. But I got error when I ran example: > > Program PWSCF 1.2.0 starts ... > Today is 6Jun2003 at 16:31: 6 > > Ultrasoft (Vanderbilt) Pseudopotentials > Complex Hamiltonian > > current dimensions of program pwscf are: > ntypx= 6 npsx = 6 lmax = 3 npk =40000 > nbrx = 6 lqmax = 7 nqfm = 8 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_ncpp : error # 1 > pseudo file is empty or wrong > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > STOP 2 > > My pseudo file is OK, I use it in another machine. How solve this problem? > > Thank you for your help, > Best wishes, > Sergey > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From breezejd at sbu.ac.uk Fri Jun 6 16:51:38 2003 From: breezejd at sbu.ac.uk (Jonathan Breeze) Date: Fri, 06 Jun 2003 15:51:38 +0100 Subject: [Pw_forum] drho and D3 calculations Message-ID: <3EE0AA7A.5070305@sbu.ac.uk> Dear PWscf users, I have been trying for a long time to calculate the 3rd order anharmonic coefficients at the Gamma point. For a simple system like MgO using the following file for pw.x: Mgo Magnesium Oxide &control calculation='scf' restart_mode='from_scratch', prefix='mgo', pseudo_dir = '/usr/people/breezejd/pwscf/pwscf-parallel/pots/', outdir='/usr/people/breezejd/pwscf/pwscf-parallel/tmp/' / &system ibrav= 2, celldm(1) =7.27303, nat= 2, ntyp= 2, ecutwfc =44.0, occupations ='fixed', / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Mg 24.3050 Mg.pz-vbc.UPF O 15.9994 O.pz-mt.UPF ATOMIC_POSITIONS Mg 0.00 0.00 0.00 O 0.50 0.50 0.50 K_POINTS{automatic} 4,4,4,0,0,0 Everything goes well after the SCF calculation. I then run the phonon code at the Gamma point to produce a drho file. phonons of MgO at Gamma &inputph iverbosity=1, prefix='mgo', amass(1)=24.305, amass(2)=15.9994, tmp_dir='/usr/people/breezejd/pwscf/pwscf-parallel/tmp/', fildrho='mgo.drhoG', fildyn='mgo.dynG', / 0.0 0.0 0.0 Phonon produces the dynamical matrix which seems ok and four drho files: mgo.drho, mgo.drhoG1, mgo.drhoG2, mgo.drhoG3. mgo.drho look like this: which seems a little truncated. 24 24 24 24 24 24 2 2 2 7.27303000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 235.8216583131 4.0000000000 44.0000000000 0 1 Mg 2.00 0.0000000000 0.0000000000 0.0000000000 2 O 6.00 0.5000000000 0.5000000000 0.5000000000 13824*0.E+0 The other three are quite large (about 210K). I have no idea what the numbers in these files mean. Anyway, I have tried to run D3, the input file for this is: third order derivatives of dynamical matrix for MgO at Gamma &inputph iverbosity=1, tmp_dir='/usr/people/breezejd/pwscf/pwscf-parallel/tmp/', filpun='mgo.pun', fildyn='mgo.d3dyn', fildrho='mgo.drhoG', fild0rho='mgo.drhoG', amass(1)=24.3050, amass(2)=15.9994, / 0.0 0.0 0.0 The cards load in OK but then I get an error; Program D3TOTEN1.2.0 starts ... Today is 6Jun2003 at 7:47:46 Parallel version (MPI) Number of processors in use: 1 UltraSoft (Vanderbilt) Pseudopotentials %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from saveall : error # 21 reading file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I'm sorry for this long email, but I have tried posting on the forum a number of times and I have never received a single response. I am running short of time now on the project and may have to abandon using the D3 (2n+1) method in favour of another method such as frozen phonon. Please help!!! Yours pleadingly, Jonathan Breeze From bungaro at physics.rutgers.edu Fri Jun 6 17:51:23 2003 From: bungaro at physics.rutgers.edu (CLAUDIA BUNGARO) Date: Fri, 6 Jun 2003 11:51:23 -0400 (EDT) Subject: [Pw_forum] drho and D3 calculations In-Reply-To: <3EE0AA7A.5070305@sbu.ac.uk> References: <3EE0AA7A.5070305@sbu.ac.uk> Message-ID: Dear Jonathan, one problem could be that the namelist variables controlling input/output file names have been changed in the version 1.2.0 for pw and ph. The variable 'filpun' has been removed and the variable 'prefix' has been introduced. It seems that in the namelist for d3 the 'filpun' variable still exist and the variable 'prefix' does not exist. Maybe the d3 code has not been modified to reflect the changes in pw and ph and it creates problems? This may explain the error you get running d3, which says it cannot read the file that saveall.f90 writes and reads. Claudia __________________________________________________ Dr. Claudia Bungaro Dept. of Physics and Astronomy, Rutgers University 136 Frelinghuysen Road, Piscataway, NJ 08854-8019 tel: +1 732 445 4197 fax: +1 732 445 4343 email: bungaro at physics.rutgers.edu __________________________________________________ On Fri, 6 Jun 2003, Jonathan Breeze wrote: > Dear PWscf users, > > I have been trying for a long time to calculate the 3rd order anharmonic > coefficients at the Gamma point. > For a simple system like MgO using the following file for pw.x: > > Mgo > Magnesium Oxide > &control > calculation='scf' > restart_mode='from_scratch', > prefix='mgo', > pseudo_dir = '/usr/people/breezejd/pwscf/pwscf-parallel/pots/', > outdir='/usr/people/breezejd/pwscf/pwscf-parallel/tmp/' > / > &system > ibrav= 2, celldm(1) =7.27303, nat= 2, ntyp= 2, > ecutwfc =44.0, occupations ='fixed', > / > &electrons > conv_thr = 1.0d-8 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Mg 24.3050 Mg.pz-vbc.UPF > O 15.9994 O.pz-mt.UPF > ATOMIC_POSITIONS > Mg 0.00 0.00 0.00 > O 0.50 0.50 0.50 > K_POINTS{automatic} > 4,4,4,0,0,0 > > Everything goes well after the SCF calculation. I then run the phonon > code at the Gamma point to produce a drho file. > > phonons of MgO at Gamma > &inputph > iverbosity=1, > prefix='mgo', > amass(1)=24.305, > amass(2)=15.9994, > tmp_dir='/usr/people/breezejd/pwscf/pwscf-parallel/tmp/', > fildrho='mgo.drhoG', > fildyn='mgo.dynG', > / > 0.0 0.0 0.0 > > Phonon produces the dynamical matrix which seems ok and four drho files: > mgo.drho, mgo.drhoG1, mgo.drhoG2, mgo.drhoG3. > > mgo.drho look like this: which seems a little truncated. > > 24 24 24 24 24 24 2 2 > 2 7.27303000 0.00000000 0.00000000 0.00000000 0.00000000 > 0.00000000 > 235.8216583131 4.0000000000 44.0000000000 0 > 1 Mg 2.00 0.0000000000 0.0000000000 0.0000000000 > 2 O 6.00 0.5000000000 0.5000000000 0.5000000000 > 13824*0.E+0 > > > The other three are quite large (about 210K). I have no idea what the > numbers in these files mean. > > Anyway, I have tried to run D3, the input file for this is: > > third order derivatives of dynamical matrix for MgO at Gamma > &inputph > iverbosity=1, > tmp_dir='/usr/people/breezejd/pwscf/pwscf-parallel/tmp/', > filpun='mgo.pun', > fildyn='mgo.d3dyn', > fildrho='mgo.drhoG', > fild0rho='mgo.drhoG', > amass(1)=24.3050, > amass(2)=15.9994, > / > 0.0 0.0 0.0 > > The cards load in OK but then I get an error; > > > Program D3TOTEN1.2.0 starts ... > Today is 6Jun2003 at 7:47:46 > > Parallel version (MPI) > Number of processors in use: 1 > > UltraSoft (Vanderbilt) Pseudopotentials > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from saveall : error # 21 > reading file > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > > I'm sorry for this long email, but I have tried posting on the forum a > number of times and I have never received a single response. > I am running short of time now on the project and may have to abandon > using the D3 (2n+1) method in favour of another method such as frozen > phonon. > > Please help!!! > > Yours pleadingly, > > Jonathan Breeze > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From breezejd at sbu.ac.uk Fri Jun 6 18:10:09 2003 From: breezejd at sbu.ac.uk (Jonathan Breeze) Date: Fri, 6 Jun 2003 17:10:09 +0100 Subject: [Pw_forum] drho and D3 calculations Message-ID: <001101c32c46$1a1284e0$95039488@breezy> Thanks for your reply, I checked the D3 code (which came with latest release of PWscf 1.2.0 ). It seems that from the routine d3_readin.f90 takes a filpun card instead of a prefix card. I get a different error if I use prefix like pw.x and ph : error # 4324 reading inputph namelist. From giannozz at nest.sns.it Fri Jun 6 18:24:07 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 6 Jun 2003 18:24:07 +0200 Subject: [Pw_forum] drho and D3 calculations In-Reply-To: <001101c32c46$1a1284e0$95039488@breezy> References: <001101c32c46$1a1284e0$95039488@breezy> Message-ID: <200306061824.07076.giannozz@nest.sns.it> Hi > I checked the D3 code (which came with latest release of PWscf 1.2.0 ). > It seems that from the routine d3_readin.f90 takes a filpun card instead of > a prefix card. > I get a different error if I use prefix like pw.x and ph : error # 4324 > reading inputph namelist. I am afraid that the new version of the 3rd-order code was never really tested. The preceding version (1.1.2) is tested and it works (AFAIK). You can still downoload it from the pwscf web site. There is a test that you can download from: http://www.nest.sns.it/~giannozz/d3_test.tgz Don't ask me more, this is all I know! Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From breezejd at sbu.ac.uk Fri Jun 6 18:25:08 2003 From: breezejd at sbu.ac.uk (Jonathan Breeze) Date: Fri, 6 Jun 2003 17:25:08 +0100 Subject: [Pw_forum] drho and D3 calculations References: <001101c32c46$1a1284e0$95039488@breezy> <200306061824.07076.giannozz@nest.sns.it> Message-ID: <001c01c32c48$33f53040$95039488@breezy> Thanks Paolo, I'll keep at it and won't give up (just yet). > Hi > > > I checked the D3 code (which came with latest release of PWscf 1.2.0 ). > > It seems that from the routine d3_readin.f90 takes a filpun card instead of > > a prefix card. > > I get a different error if I use prefix like pw.x and ph : error # 4324 > > reading inputph namelist. > > I am afraid that the new version of the 3rd-order code was never > really tested. The preceding version (1.1.2) is tested and it works > (AFAIK). You can still downoload it from the pwscf web site. > There is a test that you can download from: > http://www.nest.sns.it/~giannozz/d3_test.tgz > Don't ask me more, this is all I know! > > Paolo > -- > Paolo Giannozzi e-mail: giannozz at nest.sns.it > Scuola Normale Superiore Phone: +39/050509412 > Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 > I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From proffess at yandex.ru Sat Jun 7 10:18:40 2003 From: proffess at yandex.ru (Sergei Lisenkov) Date: Sat, 7 Jun 2003 12:18:40 +0400 (MSD) Subject: [Pw_forum] Error: pseudo file is empty or wrong In-Reply-To: <200306061508.03835.giannozz@nest.sns.it> References: <3EE08AC6.000024.14494@ariel.yandex.ru> <200306061508.03835.giannozz@nest.sns.it> Message-ID: <3EE19FE0.000008.30497@ariel.yandex.ru> Dear Paolo, My input file: &control pseudo_dir = '/nethome/proffess/pseudo/', outdir='./', tprnfor=.true., tstress=.true. / ATOMIC_SPECIES C 12.00 CUS.RRKJ3.UPF ATOMIC_POSITIONS {alat} C 0.062905523 0.3 Sergey From zyli at sina.com Sat Jun 7 15:25:24 2003 From: zyli at sina.com (andrewzyli) Date: Sat, 07 Jun 2003 21:25:24 +0800 Subject: [Pw_forum] USPP for Co Message-ID: <20030607132524.7618.qmail@sina.com> An HTML attachment was scrubbed... URL: /pipermail/attachments/20030607/abd654e4/attachment.htm From zyli at sina.com Sun Jun 8 14:32:05 2003 From: zyli at sina.com (andrewzyli) Date: Sun, 08 Jun 2003 20:32:05 +0800 Subject: [Pw_forum] USPP of Co Message-ID: <20030608123205.18731.qmail@sina.com> Dear PWSCF users I am looking for a ultrasoft pseudopotential of Co, Can any one help me? Thanks. Best Wishes zyli ______________________________________ =================================================================== ???????????????? ????????????????! (http://sms.sina.com.cn/act/fcxhhd.html) From baroni at sissa.it Sun Jun 8 16:32:54 2003 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 08 Jun 2003 16:32:54 +0200 Subject: [Pw_forum] USPP of Co In-Reply-To: <20030608123205.18731.qmail@sina.com> References: <20030608123205.18731.qmail@sina.com> Message-ID: <3EE34916.5030703@sissa.it> Zyli: just in case you do not find the ready-to-use potential you are looking for, this could be the occasion to demonstrate that when others cannot help you, you can always help the others. Build your own pseudo-potential and share it with us! Thank you for being part of our community. Stefano Baroni andrewzyli wrote: > Dear PWSCF users > > I am looking for a ultrasoft pseudopotential of Co, > Can any one help me? Thanks. > > Best Wishes > zyli > ______________________________________ > > =================================================================== > ???????????????? ????????????????! (http://sms.sina.com.cn/act/fcxhhd.html) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From xhongjun at mail.ustc.edu.cn Mon Jun 9 05:01:00 2003 From: xhongjun at mail.ustc.edu.cn (xhongjun) Date: Mon, 09 Jun 2003 11:01:00 +0800 Subject: [Pw_forum] USPP of Co In-Reply-To: <20030608123205.18731.qmail@sina.com> References: <20030608123205.18731.qmail@sina.com> Message-ID: <3EE3F86C.2040405@mail.ustc.edu.cn> Dear andrewzyli: You can find an ultrasoft pseudopotential of Co at: http://www.fysik.dtu.dk/CAMPOS/Documentation/Dacapo/PseudoPotentialOverView/Co/index.html Good luck. andrewzyli wrote: > Dear PWSCF users > > I am looking for a ultrasoft pseudopotential of Co, > Can any one help me? Thanks. > > Best Wishes > zyli > ______________________________________ > > =================================================================== > ???????? ????????! (http://sms.sina.com.cn/act/fcxhhd.html) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From degironc at sissa.it Mon Jun 9 13:52:58 2003 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 09 Jun 2003 13:52:58 +0200 Subject: [Pw_forum] USPP of Co References: <20030608123205.18731.qmail@sina.com> Message-ID: <3EE4751A.4060601@sissa.it> In David Vanderbilt's page there are input files for generation of Fe,Ni, Ru, Rh USPP but not for Co. However using these input files as template and some testing (always a good idea) it should be possible to generate a pseudopotential for Co. Stefano de Gironcoli andrewzyli wrote: >Dear PWSCF users > > I am looking for a ultrasoft pseudopotential of Co, >Can any one help me? Thanks. > >Best Wishes >zyli >______________________________________ > >=================================================================== >???????????????? ????????????????! (http://sms.sina.com.cn/act/fcxhhd.html) >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From katalin.gaal-nagy at physik.uni-regensburg.de Mon Jun 9 14:03:44 2003 From: katalin.gaal-nagy at physik.uni-regensburg.de (Katalin Gaal-Nagy) Date: Mon, 9 Jun 2003 14:03:44 +0200 (MEST) Subject: [Pw_forum] Relaxation for a fixed volume Message-ID: <200306091203.h59C3jlJ011424@rrzd2.rz.uni-regensburg.de> Hello everybody! I'm moreless new in the comunity and I have a question: I want to do a relaxation of a body-centered orthorhombic cell with two atoms in the basis. Is the pwscf able to relax the three lattice constants and one atomic position, keeping the volume and the other atomic position fixed, simultaneously or do I have to relax the lattice constants "by hand" with relaxing the atomic position automatically? The second way I found out already. I'm not sure if I was just overlooking the "switch" for the relaxation mentioned above or if it is simply not implemented yet. Regards, Katalin ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , >>>>>>> Katalin Gaal-Nagy <<<<<<< , , Gemeinerstr. 3 PHY 4.1.30 , , 93053 Regensburg Uni-Regensburg , , 0941/7501574 0941/943-2026 , ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , >>>>>>> katalin.gaal-nagy at physik.uni-regensburg.de <<<<<<< , ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , >>>>>>> Tr"aume nicht Dein Leben, lebe Deinen Traum <<<<<<< , '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' From fisicabiomolecular at yahoo.com.br Mon Jun 9 18:02:04 2003 From: fisicabiomolecular at yahoo.com.br (=?iso-8859-1?q?Wyllian=20Bezerra=20da=20Silva=20-=20WBS?=) Date: Mon, 9 Jun 2003 13:02:04 -0300 (ART) Subject: [Pw_forum] How I must proceed to restart a process from the archives out and in? Message-ID: <20030609160204.46602.qmail@web14609.mail.yahoo.com> Greetings! Please, as I must proceed to restart a process from the archives out and in and of the archives generated in tmp? Thanks. Wyllian Bezerra da Silva _______________________________________________________________________ Yahoo! Mail Mais espa?o, mais seguran?a e gratuito: caixa postal de 6MB, antiv?rus, prote??o contra spam. http://br.mail.yahoo.com/ From fisicabiomolecular at yahoo.com.br Mon Jun 9 20:37:51 2003 From: fisicabiomolecular at yahoo.com.br (=?iso-8859-1?q?Wyllian=20Bezerra=20da=20Silva=20-=20WBS?=) Date: Mon, 9 Jun 2003 15:37:51 -0300 (ART) Subject: [Pw_forum] fron davcio : error # 99 - i/o error in davcio Message-ID: <20030609183751.38098.qmail@web14601.mail.yahoo.com> Please, It was using the PWSCF in a process and appeared the following error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% fron davcio : error # 99 i/o error in davcio %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... It could help me? Thanks! Wyllian _______________________________________________________________________ Yahoo! Mail Mais espa?o, mais seguran?a e gratuito: caixa postal de 6MB, antiv?rus, prote??o contra spam. http://br.mail.yahoo.com/ From eyvaz_isaev at yahoo.com Tue Jun 10 01:36:19 2003 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 9 Jun 2003 16:36:19 -0700 (PDT) Subject: [Pw_forum] fron davcio : error # 99 - i/o error in davcio In-Reply-To: <20030609183751.38098.qmail@web14601.mail.yahoo.com> Message-ID: <20030609233619.59493.qmail@web80513.mail.yahoo.com> Dear Wylliam, If I correctly understood, you tried to do some calculations and for some reasons it was stopped. Then you decided to restart and met a problem from davcio. Did you change something in your input file before restarting? Regards, Eyvaz. --- Wyllian Bezerra da Silva - WBS wrote: > Please, > > It was using the PWSCF in a process and appeared the > following error: > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > fron davcio : error # 99 > i/o error in davcio > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > > > > > It could help me? > > > Thanks! > > > Wyllian > > _______________________________________________________________________ > Yahoo! Mail > Mais espa?o, mais seguran?a e gratuito: caixa postal > de 6MB, antiv?rus, prote??o contra spam. > http://br.mail.yahoo.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum __________________________________ Do you Yahoo!? Yahoo! Calendar - Free online calendar with sync to Outlook(TM). http://calendar.yahoo.com From fisicabiomolecular at yahoo.com.br Tue Jun 10 03:56:24 2003 From: fisicabiomolecular at yahoo.com.br (Wyllian) Date: Mon, 9 Jun 2003 22:56:24 -0300 Subject: [Pw_forum] IOS=80 (from davcio:error # 99, i/o error in davcio) and from mix_potential : error # -1, file not found, restarting) Message-ID: <008901c32ef3$81caad60$47c583c8@pion> BioPhysics Grupo de Pesquisa em Biof?sica Instituto de F?sica Universidade Federal de Uberl?ndia -------------------------------------------------------------------------------- Dear Eyvaz, I tried to make a calculation and the program stopped in the following line: total cpu time spent up to now is 343.15 secs iteration # 4 ecut= 24.00 ryd beta=0.30 Davidson diagonalization with overlap WARNING: e( 15) = -7.58343 is not converged to within 1.7E-07 WARNING: e( 16) = -7.47643 is not converged to within 1.7E-07 WARNING: e( 17) = -7.24087 is not converged to within 1.7E-07 WARNING: e( 18) = -7.16739 is not converged to within 1.7E-07 WARNING: e( 19) = -7.16446 is not converged to within 1.7E-07 WARNING: e( 20) = -7.03029 is not converged to within 1.7E-07 WARNING: e( 21) = -6.95160 is not converged to within 1.7E-07 WARNING: e( 22) = -6.82683 is not converged to within 1.7E-07 WARNING: e( 23) = -6.71619 is not converged to within 1.7E-07 WARNING: e( 24) = -6.61025 is not converged to within 1.7E-07 WARNING: e( 25) = -6.39109 is not converged to within 1.7E-07 WARNING: e( 25) = -6.42661 is not converged to within 1.7E-07 warning : 1 eigenvectors not converged after 2 attemps ethr = 1.72E-07, avg # of iterations = 40.0 IOS = 80 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 99 i/o error in davcio %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... But, before it pointed another problem: total cpu time spent up to now is 740.80 secs iteration # 5 ecut= 20.00 ryd beta=0.70 Davidson diagonalization with overlap ethr = 6.90E-08, avg # of iterations = 8.0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from mix_potential : error # -1 file not found, restarting %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% potential mean squ. error = 9.6E-10 ryd^2 total energy = -194.17379808 ryd Please, click in following links to see the archives generated: timina.in 09-Jun-2003 22:39 1k timina.out 09-Jun-2003 22:39 9k I am using the PWSCF to make calculations in nucleot?deos (DNA: Adenine, Citosina, Guanina, Timina). I am pupil of graduation in physics for the Federal University of Uberl?ndia (Brazil) and am making scientific initiation in biof?sica. It could, for gentility, to help me? Regards, Wyllian. -------------------------------------------------------------------------------- Dear Wylliam, If I correctly understood, you tried to do some calculations and for some reasons it was stopped. Then you decided to restart and met a problem from davcio. Did you change something in your input file before restarting? Regards, Eyvaz. --- Wyllian Bezerra da Silva - WBS wrote: > Please, > > It was using the PWSCF in a process and appeared the > following error: > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > fron davcio : error # 99 > i/o error in davcio > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > > > > > It could help me? > > > Thanks! > > > Wyllian > > -------------------------------------------------------------------------------- W B S Wyllian Bezerra da Silva http://www.biophysics.hpg.com.br/ --- Some files have not been scanned Checked by AVG anti-virus system (http://www.grisoft.com). 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Name: logo_da.gif Type: image/gif Size: 1547 bytes Desc: not available Url : /pipermail/attachments/20030609/73e2270e/attachment-0008.gif From fisicabiomolecular at yahoo.com.br Tue Jun 10 04:18:53 2003 From: fisicabiomolecular at yahoo.com.br (Wyllian) Date: Mon, 9 Jun 2003 23:18:53 -0300 Subject: [Pw_forum] from readin : error # 182, in reading input file Message-ID: <00d701c32ef6$a76a7430$47c583c8@pion> BioPhysics Grupo de Pesquisa em Biof?sica Instituto de F?sica Universidade Federal de Uberl?ndia -------------------------------------------------------------------------------- Greetings! I am with another problem when I am calculating way PWSCF the nucleot?deos Citosina-Guanina. The following error in output appears: Program PWSCF 1.1.2 starts ... Today is 9Jun2003 at 22:57:35 Ultrasoft (Vanderbilt) Pseudopotentials Complex Hamiltonian current dimensions of program pwscf are: ntypx= 6 npsx = 6 lmax = 3 npk =40000 nbrx = 6 lqx = 5 nqfm = 8 Lattice vectors read from STDIN %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from readin : error # 182 in reading input file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... It could help me. Click in following links to see the archives generated: c-g.out 09-Jun-2003 23:05 1k c-g.in 09-Jun-2003 23:05 2k run_c-g 09-Jun-2003 23:04 4k Thanks! Wyllian. -------------------------------------------------------------------------------- W B S Wyllian Bezerra da Silva http://www.biophysics.hpg.com.br/ --- Some files have not been scanned Checked by AVG anti-virus system (http://www.grisoft.com). 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Name: logo_da.gif Type: image/gif Size: 1547 bytes Desc: not available Url : /pipermail/attachments/20030609/35d153de/attachment-0008.gif From fisicabiomolecular at yahoo.com.br Tue Jun 10 03:47:53 2003 From: fisicabiomolecular at yahoo.com.br (Wyllian) Date: Mon, 9 Jun 2003 22:47:53 -0300 Subject: [Pw_forum] IOS=80 (from davcio:error # 99, i/o error in davcio) and from mix_potential : error # -1, file not found, restarting) Message-ID: <004601c32ef2$5195c900$47c583c8@pion> BioPhysics Grupo de Pesquisa em Biof?sica Instituto de F?sica Universidade Federal de Uberl?ndia -------------------------------------------------------------------------------- Dear Eyvaz, I tried to make a calculation and the program stopped in the following line: total cpu time spent up to now is 343.15 secs iteration # 4 ecut= 24.00 ryd beta=0.30 Davidson diagonalization with overlap WARNING: e( 15) = -7.58343 is not converged to within 1.7E-07 WARNING: e( 16) = -7.47643 is not converged to within 1.7E-07 WARNING: e( 17) = -7.24087 is not converged to within 1.7E-07 WARNING: e( 18) = -7.16739 is not converged to within 1.7E-07 WARNING: e( 19) = -7.16446 is not converged to within 1.7E-07 WARNING: e( 20) = -7.03029 is not converged to within 1.7E-07 WARNING: e( 21) = -6.95160 is not converged to within 1.7E-07 WARNING: e( 22) = -6.82683 is not converged to within 1.7E-07 WARNING: e( 23) = -6.71619 is not converged to within 1.7E-07 WARNING: e( 24) = -6.61025 is not converged to within 1.7E-07 WARNING: e( 25) = -6.39109 is not converged to within 1.7E-07 WARNING: e( 25) = -6.42661 is not converged to within 1.7E-07 warning : 1 eigenvectors not converged after 2 attemps ethr = 1.72E-07, avg # of iterations = 40.0 IOS = 80 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 99 i/o error in davcio %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... But, before it pointed another problem: total cpu time spent up to now is 740.80 secs iteration # 5 ecut= 20.00 ryd beta=0.70 Davidson diagonalization with overlap ethr = 6.90E-08, avg # of iterations = 8.0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from mix_potential : error # -1 file not found, restarting %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% potential mean squ. error = 9.6E-10 ryd^2 total energy = -194.17379808 ryd I am sending out and input. I am using the PWSCF to make calculations in nucleot?deos (DNA: Adenine, Citosina, Guanina, Timina). I am pupil of graduation in physics for the Federal University of Uberl?ndia (Brazil) and am making scientific initiation in biof?sica. It could, for gentility, to help me? Regards, Wyllian. -------------------------------------------------------------------------------- Dear Wylliam, If I correctly understood, you tried to do some calculations and for some reasons it was stopped. Then you decided to restart and met a problem from davcio. Did you change something in your input file before restarting? Regards, Eyvaz. --- Wyllian Bezerra da Silva - WBS wrote: > Please, > > It was using the PWSCF in a process and appeared the > following error: > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > fron davcio : error # 99 > i/o error in davcio > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > > > > > It could help me? > > > Thanks! > > > Wyllian > > -------------------------------------------------------------------------------- W B S Wyllian Bezerra da Silva http://www.biophysics.hpg.com.br/ --- Some files have not been scanned Checked by AVG anti-virus system (http://www.grisoft.com). 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Name: timina.out Type: application/octet-stream Size: 8903 bytes Desc: not available Url : /pipermail/attachments/20030609/387cacbd/attachment-0001.obj From eyvaz_isaev at yahoo.com Tue Jun 10 13:20:32 2003 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 10 Jun 2003 04:20:32 -0700 (PDT) Subject: [Pw_forum] from readin : error # 182, in reading input file In-Reply-To: <00d701c32ef6$a76a7430$47c583c8@pion> Message-ID: <20030610112032.58766.qmail@web80510.mail.yahoo.com> Dear Wylliam, For this one you mentioned 30 atoms, but just 29 of them are included. So you lost 1 atom. Are you sure that your system is insulator, i.e. valence and conduction bands are separated by band gap? Otherwise you should include some information about gausssian width and number of gaussians. It looks like degauss=0.02, ngauss=1 restart=.true. option is for interrupted or not converged runs. I am not sure that it is a good idea to include it directly from the start. "upscale" is for ionic dynamics and meaningless for self-consistent calculations. I advice you to carry out self-consistence calculations first and then go to relax you atoms. In this case you should include also iswitch=1 option. niter=100 and nstep=1000 are not a good idea, too. Defaults seem to be good choice (50 and 50). Probably you should also use more "dual" ank k-points, but it depends on computer you are using. Regards, Eyvaz --- Wyllian wrote: > > BioPhysics > > Grupo de Pesquisa em Biof?sica > Instituto de F?sica > Universidade Federal de Uberl?ndia > > > > -------------------------------------------------------------------------------- > > > Greetings! > I am with another problem when I am calculating way > PWSCF the nucleot?deos Citosina-Guanina. The > following error in output appears: > > Program PWSCF 1.1.2 starts ... > Today is 9Jun2003 at 22:57:35 > Ultrasoft (Vanderbilt) Pseudopotentials > Complex Hamiltonian > current dimensions of program pwscf are: > ntypx= 6 npsx = 6 lmax = 3 npk =40000 > nbrx = 6 lqx = 5 nqfm = 8 > Lattice vectors read from STDIN > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from readin : error # 182 > in reading input file > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > > It could help me. Click in following links to see > the archives generated: > c-g.out 09-Jun-2003 23:05 1k > c-g.in 09-Jun-2003 23:05 2k > run_c-g 09-Jun-2003 23:04 4k > > > > Thanks! > > > Wyllian. > > > > -------------------------------------------------------------------------------- > > > > W B S > > Wyllian Bezerra da Silva > > http://www.biophysics.hpg.com.br/ > > > --- > > Some files have not been scanned > > Checked by AVG anti-virus system > (http://www.grisoft.com). > Version: 6.0.481 / Virus Database: 277 - Release > Date: 13/5/2003 > > ATTACHMENT part 1.2 image/gif name=ufu.gif > ATTACHMENT part 1.3 image/gif name=unknown.gif > ATTACHMENT part 1.4 image/gif name=logo_da.gif > ATTACHMENT part 2 image/gif name=ufu.gif > ATTACHMENT part 3 image/gif name=logo_da.gif > ATTACHMENT part 4 image/gif name=ufu.gif > ATTACHMENT part 5 image/gif name=logo_da.gif > ATTACHMENT part 6 image/gif name=ufu.gif > ATTACHMENT part 7 image/gif name=logo_da.gif __________________________________ Do you Yahoo!? Yahoo! Calendar - Free online calendar with sync to Outlook(TM). http://calendar.yahoo.com From pushpa at jncasr.ac.in Wed Jun 11 14:31:39 2003 From: pushpa at jncasr.ac.in (Raghani Pushpa) Date: Wed, 11 Jun 2003 18:01:39 +0530 (IST) Subject: [Pw_forum] (no subject) Message-ID: Dear users, I am trying to calculate the phonon DOS for bulk tin. I am able to calculate it for 6x6x6 q pt mesh but when I calculate it for 12x12x12 mesh, it aborts the execution and 'segmentation fault' error is coming. Could you please tell me why is this happening? Thanks, Pushpa -- From eyvaz_isaev at yahoo.com Wed Jun 11 14:48:38 2003 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 11 Jun 2003 05:48:38 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: Message-ID: <20030611124838.42519.qmail@web80502.mail.yahoo.com> Dear Raghani, Probably you should increase nqx parameter in matdyn.f90 and then recompile it. Regards, Eyvaz. --- Raghani Pushpa wrote: > > Dear users, > I am trying to calculate the phonon DOS for bulk > tin. I am able to > calculate it for 6x6x6 q pt mesh but when I > calculate it for 12x12x12 > mesh, it aborts the execution and 'segmentation > fault' error is coming. > Could you please tell me why is this happening? > > Thanks, > Pushpa > > -- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum __________________________________ Do you Yahoo!? Yahoo! Calendar - Free online calendar with sync to Outlook(TM). http://calendar.yahoo.com From giannozz at nest.sns.it Wed Jun 11 14:54:15 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 11 Jun 2003 14:54:15 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: <200306111454.15264.giannozz@nest.sns.it> On Wednesday 11 June 2003 14:31, Raghani Pushpa wrote: > Dear users, > I am trying to calculate the phonon DOS for bulk tin. I am able to > calculate it for 6x6x6 q pt mesh but when I calculate it for 12x12x12 > mesh, it aborts the execution and 'segmentation fault' error is coming. > Could you please tell me why is this happening? no, we cannot, unless you are more specific :-) which execution is aborted? phonon calculation (ph.x)? phonon DOS calculation (matdyn.x) ? real-space interatomic force constants calculation? other ? Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From fisicabiomolecular at yahoo.com.br Wed Jun 11 15:41:56 2003 From: fisicabiomolecular at yahoo.com.br (=?iso-8859-1?q?Wyllian=20Bezerra=20da=20Silva=20-=20WBS?=) Date: Wed, 11 Jun 2003 10:41:56 -0300 (ART) Subject: [Pw_forum] Necessary to increase the number of interactions: NSTEP and NITER Message-ID: <20030611134156.79170.qmail@web14601.mail.yahoo.com> Greetings! Friends, please necessary to make more of the 100 dynamic and electronic interactions. What I must make to increase the interactions. When I use to niter > 100 and nstep > 100, occurs error: IOS = 80 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 99 i/o error in davcio %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Click in link below to see out of a citosina molecule: INPUT: http://www.biophysics.hpg.com.br/download/simulacoes/PWSCF/DNA/citosina/testes/citosina.in OUTPUT: http://www.biophysics.hpg.com.br/download/simulacoes/PWSCF/DNA/citosina/testes/citosina.out It could help me? Wyllian _______________________________________________________________________ Yahoo! Mail Mais espa?o, mais seguran?a e gratuito: caixa postal de 6MB, antiv?rus, prote??o contra spam. http://br.mail.yahoo.com/ From bungaro at physics.rutgers.edu Wed Jun 11 17:19:53 2003 From: bungaro at physics.rutgers.edu (CLAUDIA BUNGARO) Date: Wed, 11 Jun 2003 11:19:53 -0400 (EDT) Subject: [Pw_forum] Necessary to increase the number of interactions: NSTEP and NITER In-Reply-To: <20030611134156.79170.qmail@web14601.mail.yahoo.com> References: <20030611134156.79170.qmail@web14601.mail.yahoo.com> Message-ID: Dear Wyllian, niter=50 is usually more than enough to reach self consistency, if you cannot reach convergence with 100 scf steps (niter) there might be some problem in the way you describe your system. You should check that all the other input parameters are appropriate to describe your molecule. Things you may want to check, among others: That the electronic occupation scheme you are using is appropriate to describe the electronic structure of your molecule you may need a broadening (DEGAUSS!=0) and more bands (NBND), spin polarized calculation for unpaired electrons (lsda=.true.) A smaller value of mixing parameter beta may help in some cases. __________________________________________________ Dr. Claudia Bungaro Dept. of Physics and Astronomy, Rutgers University 136 Frelinghuysen Road, Piscataway, NJ 08854-8019 tel: +1 732 445 4197 fax: +1 732 445 4343 email: bungaro at physics.rutgers.edu __________________________________________________ On Wed, 11 Jun 2003, [iso-8859-1] Wyllian Bezerra da Silva - WBS wrote: > Greetings! > > > Friends, please necessary to make more of the 100 > dynamic and electronic interactions. What I must make > to increase the interactions. When I use to niter > > 100 and nstep > 100, occurs error: > > IOS = 80 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from davcio : error # 99 > i/o error in davcio > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > > > Click in link below to see out of a citosina molecule: > > > INPUT: > http://www.biophysics.hpg.com.br/download/simulacoes/PWSCF/DNA/citosina/testes/citosina.in > > OUTPUT: > http://www.biophysics.hpg.com.br/download/simulacoes/PWSCF/DNA/citosina/testes/citosina.out > > > > It could help me? > > > Wyllian > > > _______________________________________________________________________ > Yahoo! Mail > Mais espa?o, mais seguran?a e gratuito: caixa postal de 6MB, antiv?rus, prote??o contra spam. > http://br.mail.yahoo.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From hslee at phya.snu.ac.kr Thu Jun 12 09:49:50 2003 From: hslee at phya.snu.ac.kr (=?ks_c_5601-1987?B?wMzIo73E?=) Date: Thu, 12 Jun 2003 16:49:50 +0900 Subject: [Pw_forum] Relationship between pseoudo-charge and wave function Message-ID: Dear pwscf users, I want to figure out wave functions with gamma point. Thus I modified the PP routines for my own purpose. In fact, I changed writting | Psi |^2 routine to writting gamma point wave function(real(Psi)) routine. However, I found that the result was not what I wanted. I guess that it is related with pseoudo-charge. In case the pp.x do writting | Psi |^2 routine, the process which add pseoudo-charge is included. I removed it for my own purpose in writting real(Psi). I want to know how I modify the pseoudo-charge routine to get the wave function. Could give me an advise or a reference for it? Best wishes, Hosik From proffess at yandex.ru Thu Jun 12 14:06:54 2003 From: proffess at yandex.ru (Sergei Lisenkov) Date: Thu, 12 Jun 2003 16:06:54 +0400 (MSD) Subject: [Pw_forum] Error: can"t open a connected unit Message-ID: <3EE86CDE.000001.22552@pantene.yandex.ru> Dear Paolo and Another USers of PWscf, I tried to use the old format of Pseudopotential, and it works!!! But I hot the next error: ........ cryst. coord. k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 2.0000000 G cutoff = 2079.0283 ( 192311 G-vectors) FFT grid: ( 96, 64, 64) G cutoff = 2021.2776 ( 184425 G-vectors) smooth grid: ( 90, 64, 64) nbndx = 1152 nbnd = 288 natomwfc = 480 npwx = 23093 nelec = 480.00 nkb = 120 ngl = 192311 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from seqopn : error # 7 can"t open a connected unit %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... What doest it mean? Thanks, Best wishes, Sergey From giannozz at nest.sns.it Thu Jun 12 15:47:02 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 12 Jun 2003 15:47:02 +0200 Subject: [Pw_forum] Error: can"t open a connected unit In-Reply-To: <3EE86CDE.000001.22552@pantene.yandex.ru> References: <3EE86CDE.000001.22552@pantene.yandex.ru> Message-ID: <200306121547.02106.giannozz@nest.sns.it> > %%%%%%%%%%%%%%%%%%%%%%%%%%%% > from seqopn : error # 7 > can"t open a connected unit > %%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > > What does it mean? it means that unit 7 (used to store indices) cannot be opened because it is already open (see PW/seqopn.f90, presumably called in PW/openfil.f90). It is not an error that is supposed to happen, unless one makes inappropriate changes to the code (such as opening unit 7 ...). So either there is something weird in your executable, or your system does not like that you open unit 7. Once upon the time, it used to be a special unit, maybe the card reader, or the puncher (young people may never have heard of such objects). Try to replace line iunigk = 7 in PW/openfil.f90 with iunigk = 77 for instance. If the code keeps complaining, try to comment out the line in PW/seqopn.f90 if (opnd) call errore ('seqopn', "can't open a connected unit", & abs (unit) ) and see what happens. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From giannozz at nest.sns.it Thu Jun 12 16:01:48 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 12 Jun 2003 16:01:48 +0200 Subject: [Pw_forum] Relationship between pseudo-charge and wave function In-Reply-To: References: Message-ID: <200306121601.48698.giannozz@nest.sns.it> Hi > I want to figure out wave functions with gamma point. > [...] Could give me an advise or a reference for it? I am not sure I understand your problem. Do you want to plot wavefunctions obtained with the Gamma-only code (pwg.x) ? or to plot wavefunctions at Gamma obtained with the "normal" (pw.x) code ? Are there ultrasoft PP in your calculation or not? Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From pushpa at jncasr.ac.in Thu Jun 12 17:23:37 2003 From: pushpa at jncasr.ac.in (Raghani Pushpa) Date: Thu, 12 Jun 2003 20:53:37 +0530 (IST) Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #103 - 2 msgs In-Reply-To: <20030606053503.28085.39499.Mailman@democritos.sissa.it> Message-ID: Dear sir, HOMO is non degenerate, the difference in energy between HOMO and LUMO is around 0.3 ryd. I did the calculation by starting from the random wave functions instead of atomic ones, but it didn't solve the problem of missing eigenvalue. I also wrote the eigenvalues at every iteration and found that there is no band crossing i.e. from the first iteration itself, the HOMO and LUMO are interchanged. Pushpa > > Today's Topics: > > 1. Re: 'missing eigenvalue' (Stefano de Gironcoli) > 2. I am with problems to calculate a molecule: adenine (C5H5N5) (Wyllian) > > --__--__-- > > Message: 1 > Date: Thu, 05 Jun 2003 12:43:04 +0200 > From: Stefano de Gironcoli > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] 'missing eigenvalue' > Reply-To: pw_forum at pwscf.org > > Are you sure that the HOMO is non degenerate ? > If the HOMO orbital is degenerate but the number of electrons > in the cluster does not fill it completely this may induce instability > in the case you provide more bands than electrons because from one > iteration to the next the occupied bands could be different. > Another possible problem, related to the fact that the HOMO orbital is > missing, could be related to the fact that the code performs iterative > diagonalization and if the HOMO has different symmetry from the > current approximate wavefunctions the diagonalization will not find it. > > possible actions: > 1) try to start from random wavefunctions instead of atomic ones. This could > help if the missing eigenvalue is due to symmetry of the initial guess for > the wfcs. > 2) try to do calculations with a small smearing using gaussian or > Fermi-Dirac > broadening (avoid Methfessel-Paxton in this case since the fact that it is > not positive definite could lead to spurious effects when using very few > k-points). > This should clarify what is the level structure for your cluster and should > tell you if there are problem of degeneracy at the Fermi level. > 3) Usually increasing the number of bands should helps in NOT missing > eigenvalues; > the fact that you get problems is an hint that there might be problem of > degeneracy. > Write eigenvalues at every iteration (including more bands than Nelec/2) > to see > how things evolves and see if there are levels that keep changing. > > All the best > > Stefano de Gironcoli > > > Raghani Pushpa wrote: > > >Dear all, > >I am doing the calculations on clusters. When I do the calculations at > >zero temperature (no smearing), I have to restrict the number of bands to > >the number of filled bands. If I give more number of bands, the program > >does not converge; I don't understand why is it happening? > > > >At degauss=0, the eigenvalues are not same as eigenvalues I get from band > >structure calculations, I find that in self consistent calculation, the > >eigenvalue of HOMO is missing and program gives the eigenvalue of LUMO. > >Could you please tell me why does it happen? > > > >regards, > >Pushpa > > > > > > > > > > > > > --__--__-- > > Message: 2 > From: "Wyllian" > To: > Date: Thu, 5 Jun 2003 08:06:57 -0300 > Subject: [Pw_forum] I am with problems to calculate a molecule: adenine (C5H5N5) > Reply-To: pw_forum at pwscf.org > > This is a multi-part message in MIME format. > > ------=_NextPart_000_0044_01C32B39.6F14F300 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > Please, I am trying to calculate an adenine molecule (C5H5N5). I do not = > obtain to get resulted. Input could verify this. Thaks. > > Wyllian > http://www.biophysics.hpg.com.br =20 > > > > #/bin/sh > #################################################################### > # > # set the needed environment variables > # > . ../../../environment_variables > # > # check whether echo needs the -e option > if [ "`echo -e`" =3D "-e" ]; then > echo=3D'echo' > else > echo=3D'echo -e' > fi > # > $echo ' '=20 > $echo ' running '$0':' > $echo ' pw.x to compute the equilibrium' > $echo ' geometry of a molecule, C5H5N5 - Adenina. ' > $echo ' '=20 > # > # check that needed directories and files exist > # > $echo ' PW_ROOT is defined as '$PW_ROOT' ' > $echo ' PSEUDO_DIR is defined as '$PSEUDO_DIR' ' > $echo ' TMP_DIR is defined as '$TMP_DIR' ' > $echo ' ' > $echo ' checking that needed directories and files exist; \c' > if [ ! -d $PW_ROOT ]; then=20 > $echo;$echo ' STOPPING: directory '$PW_ROOT' does not exist'; exit > else > if [ ! -f $PW_ROOT/main/pw.x ]; then=20 > echo;echo ' STOPPING: executable '$PW_ROOT/main/pw.x' does not = > exist'; exit > fi > fi > if [ ! -d $PSEUDO_DIR ]; then=20 > $echo;$echo ' STOPPING: directory '$PSEUDO_DIR' does not exist'; exit > else > if [ ! -f $PSEUDO_DIR/H.vbc ]; then=20 > $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/H.vbc' does not = > exist';=20 > exit > fi > if [ ! -f $PSEUDO_DIR/HUS.RRKJ3 ]; then=20 > $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/HUS.RRKJ3' does = > not exis > t'; exit > fi > if [ ! -f $PSEUDO_DIR/HUSPBE.RRKJ3 ]; then > $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/HUSPBE.RRKJ3' = > does not e > xist'; exit > fi > if [ ! -f $PSEUDO_DIR/C.vbc ]; then > $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/C.vbc' does not = > exist';=20 > exit > fi > if [ ! -f $PSEUDO_DIR/CUS.RRKJ3 ]; then > $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/C.vbc' does not = > exist';=20 > exit > fi > if [ ! -f $PSEUDO_DIR/CUSPBE.RRKJ3 ]; then > $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/CUSPBE.RRKJ3' = > does not e > xist'; exit > fi > if [ ! -f $PSEUDO_DIR/NUSPBE.RRKJ3 ]; then > $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/NUSPBE.RRKJ3' = > does not e > xist'; exit > fi > if [ ! -f $PSEUDO_DIR/NUS.RRKJ3 ]; then > $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/NUS.RRKJ3' does = > not exis > t'; exit > fi > fi > if [ i! -d $TMP_DIR ]; then=20 > $echo;$echo ' STOPPING: directory '$TMP_DIR' does not exist'; exit > fi > > $echo ' done' > # > # clean TMP_DIR > # > $echo ' cleaning '$TMP_DIR' ; \c' > rm -f $TMP_DIR/* > $echo ' done' > # > # self-consistent calculation > # > cat > adenina1.in << EOF > C5H5N5 molecule + relax > C5H5N5 > &input > ibrav=3D0, celldm(1)=3D1.d0, nat=3D15,ntyp=3D3, > pseudop(1) =3D 'CUS.RRKJ3', =20 > pseudop(2) =3D 'HUS.RRKJ3', > pseudop(3) =3D 'NUS.RRKJ3', > pseudo_dir =3D '$PSEUDO_DIR/',=20 > tmp_dir=3D'$TMP_DIR/', > ecut(1)=3D24.0, dual=3D6, > beta(1)=3D0.3, upscale=3D10, > tr2 =3D 1.0d-14, iswitch=3D1, > niter=3D100, nstep=3D100, > output_pot=3D'c5h5n5pot', > &end > 14.0 0.0 0.0 > 0.0 14.0 0.0 > 0.0 0.0 14.0 > cubic > -4.279664 -2.380489 0.676900 1 > 0.015307 -2.366316 0.844708 1 > 0.010016 0.051590 -0.222799 1 > -2.329655 1.250432 -0.851322 1 > 3.897562 -0.881558 0.346576 1 > -6.079629 -3.364659 1.041240 2 > 3.257511 -4.583532 1.953033 2 > 5.965679 -8.416466 0.418008 2 > -0.491329 4.467314 -2.209657 2 > -3.950852 4.517203 -2.374064 2 > 2.453432 0.933336 -0.511738 3 > -2.252932 3.610512 -1.899176 3 > 2.527699 -2.915659 1.188827 3 > -2.199264 -3.629598 1.310904 3 > -4.478275 -0.033070 -0.369631 3 > 'C ' 1 1 1.0 > 'H ' 1 2 1.0 > 'N ' 1 3 1.0 =20 > 0 > 1 1 1 > 0 0 0=20 > EOF > $echo ' running the geometry relaxation for adenina; \c' > $PARA_PREFIX $PW_ROOT/main/pw.x $PARA_POSTFIX < adenina1.in > = > adenina1.out > $echo ' Adenina done' > > > > > --- > Outgoing mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.481 / Virus Database: 277 - Release Date: 13/5/2003 > ------=_NextPart_000_0044_01C32B39.6F14F300 > Content-Type: text/html; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > > > charset=3Diso-8859-1"> > > > > >
>
style=3D"PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; = > PADDING-TOP: 10px"> size=3D4>Please, I am trying to calculate an adenine molecule (C5H5N5). = > I do not=20 > obtain to get resulted. Input could verify this. Thaks.
>
style=3D"PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; = > PADDING-TOP: 10px"> 
>
style=3D"PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; = > PADDING-TOP: 10px"> size=3D4>Wyllian
>
style=3D"PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; = > PADDING-TOP: 10px"> size=3D4> href=3D"http://www.biophysics.hpg.com.br">http://www.biophysics.hpg.com.b= > r=20 >  
>
 
>
 
>
 
>
size=3D2>#/bin/sh
####################################################= > ################
#
#=20 > set the needed environment variables
#
.=20 > ../../../environment_variables
#
# check whether echo needs the -e = > > option
if [ "`echo -e`" =3D "-e" ]; then
  =20 > echo=3D'echo'
else
   echo=3D'echo = > -e'
fi
#
$echo ' '=20 >
$echo ' running '$0':'
$echo ' pw.x to compute the = > equilibrium'
$echo=20 > ' geometry of a molecule, C5H5N5 - Adenina. '
$echo ' '
#
# = > check that=20 > needed directories and files exist
#
$echo ' = > PW_ROOT   =20 > is  defined as '$PW_ROOT' '
$echo ' PSEUDO_DIR is  defined = > as=20 > '$PSEUDO_DIR' '
$echo ' TMP_DIR    is  defined as = > > '$TMP_DIR' '
$echo ' '
$echo ' checking that needed directories = > and files=20 > exist; \c'
if [ ! -d $PW_ROOT ]; then
   $echo;$echo '=20 > STOPPING: directory '$PW_ROOT' does not exist'; exit
else
  = > if [ ! -f=20 > $PW_ROOT/main/pw.x ]; then
     echo;echo ' = > STOPPING:=20 > executable '$PW_ROOT/main/pw.x' does not exist'; exit
  = > fi
fi
if [=20 > ! -d $PSEUDO_DIR ]; then
   $echo;$echo ' STOPPING: = > directory=20 > '$PSEUDO_DIR' does not exist'; exit
else
  if [ ! -f=20 > $PSEUDO_DIR/H.vbc ]; then
      $echo;$echo = > '=20 > STOPPING: pseudop file '$PSEUDO_DIR/H.vbc' does not exist'; = >
exit
 =20 > fi
  if [ ! -f $PSEUDO_DIR/HUS.RRKJ3 ]; then=20 >
      $echo;$echo ' STOPPING: pseudop file=20 > '$PSEUDO_DIR/HUS.RRKJ3' does not exis
t'; exit
  fi
  = > if [ !=20 > -f $PSEUDO_DIR/HUSPBE.RRKJ3 ]; then
     =20 > $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/HUSPBE.RRKJ3' does not = > > e
xist'; exit
  fi
  if [ ! -f $PSEUDO_DIR/C.vbc ];=20 > then
      $echo;$echo ' STOPPING: pseudop = > file=20 > '$PSEUDO_DIR/C.vbc' does not exist';
exit
  fi
  if = > [ ! -f=20 > $PSEUDO_DIR/CUS.RRKJ3 ]; then
      = > $echo;$echo '=20 > STOPPING: pseudop file '$PSEUDO_DIR/C.vbc' does not exist'; = >
exit
 =20 > fi
  if [ ! -f $PSEUDO_DIR/CUSPBE.RRKJ3 ];=20 > then
      $echo;$echo ' STOPPING: pseudop = > file=20 > '$PSEUDO_DIR/CUSPBE.RRKJ3' does not e
xist'; exit
  = > fi
  if [=20 > ! -f $PSEUDO_DIR/NUSPBE.RRKJ3 ]; then
     =20 > $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/NUSPBE.RRKJ3' does not = > > e
xist'; exit
  fi
  if [ ! -f $PSEUDO_DIR/NUS.RRKJ3 = > ];=20 > then
      $echo;$echo ' STOPPING: pseudop = > file=20 > '$PSEUDO_DIR/NUS.RRKJ3' does not exis
t'; exit
  = > fi
fi
if=20 > [   i! -d $TMP_DIR ]; then
   $echo;$echo ' = > STOPPING:=20 > directory '$TMP_DIR' does not exist'; exit
fi
>
 
>
$echo ' done'
#
# = > clean=20 > TMP_DIR
#
 $echo ' cleaning '$TMP_DIR' ; \c'
rm -f=20 > $TMP_DIR/*
$echo ' done'
#
# self-consistent = > calculation
#
cat=20 > > adenina1.in << EOF
C5H5N5 molecule +=20 > relax
C5H5N5
 &input
    ibrav=3D0,=20 > celldm(1)=3D1.d0, nat=3D15,ntyp=3D3,
    pseudop(1) = > =3D=20 > 'CUS.RRKJ3', 
    pseudop(2) =3D=20 > 'HUS.RRKJ3',
    pseudop(3) =3D=20 > 'NUS.RRKJ3',
    pseudo_dir =3D  '$PSEUDO_DIR/',=20 >
    tmp_dir=3D'$TMP_DIR/',
    = > ecut(1)=3D24.0,=20 > dual=3D6,
    beta(1)=3D0.3, = > upscale=3D10,
    tr2=20 > =3D 1.0d-14, iswitch=3D1,
    niter=3D100,=20 > nstep=3D100,
   =20 > output_pot=3D'c5h5n5pot',
 &end
14.0   = > 0.0  =20 > 0.0
 0.0  14.0   0.0
 0.0   = > 0.0 =20 > 14.0
cubic
-4.279664 -2.380489  0.676900 1
 0.015307=20 > -2.366316  0.844708 1
 0.010016  0.051590 -0.222799=20 > 1
-2.329655  1.250432 -0.851322 1
 3.897562 = > -0.881558 =20 > 0.346576 1
-6.079629 -3.364659  1.041240 2
 3.257511=20 > -4.583532  1.953033 2
 5.965679 -8.416466  0.418008=20 > 2
-0.491329  4.467314 -2.209657 2
-3.950852  4.517203 = > -2.374064=20 > 2
 2.453432  0.933336 -0.511738 3
-2.252932  = > 3.610512=20 > -1.899176 3
 2.527699 -2.915659  1.188827 3
-2.199264=20 > -3.629598  1.310904 3
-4.478275 -0.033070 -0.369631 3
'C ' 1 = > 1=20 > 1.0
'H ' 1 2 1.0
'N ' 1 3 1.0 
 0
 1 1 = > 1
 0=20 > 0 0
EOF
$echo ' running the geometry relaxation for adenina;=20 > \c'
$PARA_PREFIX $PW_ROOT/main/pw.x $PARA_POSTFIX < adenina1.in = > >=20 > adenina1.out
$echo ' Adenina done'
>
 
>
 
>

---
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> > ------=_NextPart_000_0044_01C32B39.6F14F300-- > > > > --__--__-- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest > -- From hslee at phya.snu.ac.kr Fri Jun 13 04:02:31 2003 From: hslee at phya.snu.ac.kr (Lee Ho-Sik) Date: Fri, 13 Jun 2003 11:02:31 +0900 (KST) Subject: [Pw_forum] Relationship between pseudo-charge and wave function In-Reply-To: <200306121601.48698.giannozz@nest.sns.it> Message-ID: Dear Paolo, I used "normal" (pw.x) code and ultrasoft PP in my calculation. Because my system contains carbons and hydrogens only, it can be a faster method to do the calculation again with norm-conserving PPs. However, I think it is meaningful to figure out gamma point wavefunction with ultrasoft PPs,too. Could you add the routine in pp.x? I think some people need such a function. Sincerely yours, Hosik On Thu, 12 Jun 2003, Paolo Giannozzi wrote: > Hi > > > I want to figure out wave functions with gamma point. > > [...] Could give me an advise or a reference for it? > > I am not sure I understand your problem. Do you want to plot > wavefunctions obtained with the Gamma-only code (pwg.x) ? > or to plot wavefunctions at Gamma obtained with the "normal" > (pw.x) code ? Are there ultrasoft PP in your calculation or not? > > Paolo > > From giannozz at nest.sns.it Fri Jun 13 10:06:49 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 13 Jun 2003 10:06:49 +0200 Subject: [Pw_forum] Relationship between pseudo-charge and wave function In-Reply-To: References: Message-ID: <200306131006.49026.giannozz@nest.sns.it> Hi > I used "normal" (pw.x) code and ultrasoft PP in my calculation [...] > However, I think it is meaningful to figure out gamma point > wavefunction with ultrasoft PPs,too. - you can plot |psi(r)|^2 for any wavefunction at any k-point, using the appropriate options of program pp.x. It's a little bit clumsy but it is already implemented. I am not sure whether program pp.x can correctly plot wavefunctions produced by codes using only Gamma point (having half of the G components). I am afraid it is not working now but it will sooner or later (any volunteers?) - BUT: what you get is just the soft part of the wavefunction. In the ultrasoft PP method, there is no "complete" wavefunction, just the soft part. A "real", normalized, all-electron wavefunction, can be obtained by applying a non-trivial procedure in the PAW style: see for instance J. Chem. Phys. 115, 5791 (2001). Such procedure is already implemented and it will be added to the distribution ASAFSIW (= As Soon As Francesco Says It Works, Francesco being the guy who wrote the code ... he reads this mailing list ... ). Does this answer your question? Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From hslee at phya.snu.ac.kr Fri Jun 13 12:20:52 2003 From: hslee at phya.snu.ac.kr (???) Date: Fri, 13 Jun 2003 19:20:52 +0900 Subject: [Pw_forum] Relationship between pseudo-charge and wave function In-Reply-To: <200306131006.49026.giannozz@nest.sns.it> Message-ID: Dear Paolo, I plotted |psi(r)|^2 already.However, I want to know the phase information of wavefunctions additionally. That's the reason I asked. Do you mean that the ploting "real" wave functions with ultrasoft PP is not implemented in "pw.x" but in "ASAFSIW" now? If it is, could I get "ASAFSIW" ? Thank you for your answer. Hosik -----Original Message----- From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org]On Behalf Of Paolo Giannozzi Sent: Friday, June 13, 2003 5:07 PM To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Relationship between pseudo-charge and wave function Hi > I used "normal" (pw.x) code and ultrasoft PP in my calculation [...] > However, I think it is meaningful to figure out gamma point > wavefunction with ultrasoft PPs,too. - you can plot |psi(r)|^2 for any wavefunction at any k-point, using the appropriate options of program pp.x. It's a little bit clumsy but it is already implemented. I am not sure whether program pp.x can correctly plot wavefunctions produced by codes using only Gamma point (having half of the G components). I am afraid it is not working now but it will sooner or later (any volunteers?) - BUT: what you get is just the soft part of the wavefunction. In the ultrasoft PP method, there is no "complete" wavefunction, just the soft part. A "real", normalized, all-electron wavefunction, can be obtained by applying a non-trivial procedure in the PAW style: see for instance J. Chem. Phys. 115, 5791 (2001). Such procedure is already implemented and it will be added to the distribution ASAFSIW (= As Soon As Francesco Says It Works, Francesco being the guy who wrote the code ... he reads this mailing list ... ). Does this answer your question? Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at nest.sns.it Fri Jun 13 14:01:20 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 13 Jun 2003 14:01:20 +0200 Subject: [Pw_forum] Relationship between pseudo-charge and wave function In-Reply-To: References: Message-ID: <200306131401.20569.giannozz@nest.sns.it> Hi > I plotted |psi(r)|^2 already.However, I want to know the phase information > of wavefunctions additionally. That's the reason I asked. this is implemented in the version under development: lsign if true and k point is Gamma, save |psi|^2 sign(psi) You can download it using anonymous cvs (see attached instructions) > Do you mean that the ploting "real" wave functions with > ultrasoft PP is not implemented in "pw.x" but in "ASAFSIW" now? > If it is, could I get "ASAFSIW" ? the code for all-electron wavefunction reconstruction is almost, but not yet, ready. When it will be ready (I hope soon), it will be added. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 -------------- next part -------------- The current version is available using anonymous CVS. Define environmental variables: setenv CVS_RSH ssh setenv CVSROOT :pserver:cvsanon at democritos.sissa.it:/home/cvs (tcsh/csh) or export CVS_RSH=ssh export CVSROOT=:pserver:cvsanon at democritos.sissa.it:/home/cvs (sh/bash). Then: cvs login (password: cvsanon). For the first code download: cvs co O-sesame for the entire repository (the code appears in directory O-sesame/). Alternatively, "cvs co pwscf", or "cp", or "fpmd" will download only PWscf, CP, FPMD, respectively, in directories with the same name. For updating the code to the current version: cvs update -d in the directory containing the distribution. PLEASE NOTE: re-run "./configure" if files have been moved/added/removed since the last checkout, otherwise "make" may not work properly due to obsolete or missing dependencies. Do not blindly re-use a "make.sys" file from a preceding version: it may no longer work. PLEASE ALSO NOTE: the development version may not work properly, and sometimes not even compile properly. Use at your own risk. From hslee at phya.snu.ac.kr Sat Jun 14 10:08:34 2003 From: hslee at phya.snu.ac.kr (???) Date: Sat, 14 Jun 2003 17:08:34 +0900 Subject: [Pw_forum] Relationship between pseudo-charge and wave function In-Reply-To: <200306131401.20569.giannozz@nest.sns.it> Message-ID: Dear Paolo, Thank you and SISSA group for your efforts. :) I will try it! By the way, I have one thing to talk about. In PP routines, the contents in projected DOS are hard to read. I mean the "projwave.f90" routines. I think format of previous versions are better to see and work on it. The difference between format of previous versions and that of current version is ordering. However, if one get the all the data(previous version), one can work on it privately. Thus, I think it is good to recover the format of previous version in under development version. It is cheap to work. :) Thank you again for your replies and efforts! Hosik -----Original Message----- From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org]On Behalf Of Paolo Giannozzi Sent: Friday, June 13, 2003 9:01 PM To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Relationship between pseudo-charge and wave function Hi > I plotted |psi(r)|^2 already.However, I want to know the phase information > of wavefunctions additionally. That's the reason I asked. this is implemented in the version under development: lsign if true and k point is Gamma, save |psi|^2 sign(psi) You can download it using anonymous cvs (see attached instructions) > Do you mean that the ploting "real" wave functions with > ultrasoft PP is not implemented in "pw.x" but in "ASAFSIW" now? > If it is, could I get "ASAFSIW" ? the code for all-electron wavefunction reconstruction is almost, but not yet, ready. When it will be ready (I hope soon), it will be added. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From proffess at yandex.ru Sat Jun 14 14:35:38 2003 From: proffess at yandex.ru (Sergei Lisenkov) Date: Sat, 14 Jun 2003 16:35:38 +0400 (MSD) Subject: [Pw_forum] Error: can"t open a connected unit In-Reply-To: <200306121547.02106.giannozz@nest.sns.it> References: <3EE86CDE.000001.22552@pantene.yandex.ru> <200306121547.02106.giannozz@nest.sns.it> Message-ID: <3EEB169A.000002.22784@camay.yandex.ru> Dear PWscf users, How solve this problem? %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cdiaghg : error # 30 info =/= 0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Thanks, Best wishes, Sergey From bungaro at physics.rutgers.edu Sat Jun 14 20:46:34 2003 From: bungaro at physics.rutgers.edu (CLAUDIA BUNGARO) Date: Sat, 14 Jun 2003 14:46:34 -0400 (EDT) Subject: [Pw_forum] Error: can"t open a connected unit In-Reply-To: <3EEB169A.000002.22784@camay.yandex.ru> References: <3EE86CDE.000001.22552@pantene.yandex.ru> <200306121547.02106.giannozz@nest.sns.it> <3EEB169A.000002.22784@camay.yandex.ru> Message-ID: One way to avoid the problem is to use another diagonalization algorithm, for example the Conjugate Gradient Diagonalization: diagonalization='cg' (for 1.2.0 version) isolve=1 (for 1.1.2 version) Claudia __________________________________________________ Dr. Claudia Bungaro Dept. of Physics and Astronomy, Rutgers University 136 Frelinghuysen Road, Piscataway, NJ 08854-8019 tel: +1 732 445 4197 fax: +1 732 445 4343 email: bungaro at physics.rutgers.edu __________________________________________________ On Sat, 14 Jun 2003, Sergei Lisenkov wrote: > Dear PWscf users, > > How solve this problem? > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from cdiaghg : error # 30 > info =/= 0 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Thanks, > Best wishes, > Sergey > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at nest.sns.it Mon Jun 16 10:13:19 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 16 Jun 2003 10:13:19 +0200 Subject: [Pw_forum] Error: can"t open a connected unit In-Reply-To: References: <3EE86CDE.000001.22552@pantene.yandex.ru> <3EEB169A.000002.22784@camay.yandex.ru> Message-ID: <200306161013.19755.giannozz@nest.sns.it> On Saturday 14 June 2003 20:46, CLAUDIA BUNGARO wrote: > One way to avoid the problem is to use another diagonalization > algorithm, for example the Conjugate Gradient Diagonalization: > > diagonalization='cg' (for 1.2.0 version) > > isolve=1 (for 1.1.2 version) > [...] > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from cdiaghg : error # 30 > > info =/= 0 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%% note however that the above error message almost invariably is a sign of something wrong in either the compilation or the data. From the manual: \item {\em pw.x stops in cdiagh or cdiaghg.} Possible reasons: 1) error in data, such as bad atomic positions or bad crystal structure/supercell; 2) a bad PP (for instance, with a ghost); 3) IBM SP3: under some circumstances (typically a large number of k-points) we get an error in cdiaghg that is reproducible but disappears if we change anything in the calculation. We don't know what happens and why. Try to use conjugate-gradient diagonalization ({\tt diagonalization='cg'}). 4) HP-Compaq alphas with {\tt cxml} libraries: try to use compiled Blas/Lapack (or better, Atlas) instead of those contained in {\tt cxml} (just load them before {\tt cxml}). Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From giannozz at nest.sns.it Mon Jun 16 10:17:11 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 16 Jun 2003 10:17:11 +0200 Subject: [Pw_forum] Relationship between pseudo-charge and wave function In-Reply-To: References: Message-ID: <200306161017.11816.giannozz@nest.sns.it> Hi > By the way, I have one thing to talk about. In PP routines, the contents in > projected DOS are hard to read. I mean the "projwave.f90" routines. I think > format of previous versions are better to see and work on it. The > difference between format of previous versions and that of current version > is ordering. However, if one get the all the data(previous version), one > can work on it privately. Thus, I think it is good to recover the format of > previous version in under development version. It is cheap to work. :) in the version under development, two different formats are printed: a "short" format on output and the complete lists of projected DOS in a file. I hope this will satisfy everybody :-) Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From giannozz at nest.sns.it Mon Jun 16 10:53:00 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 16 Jun 2003 10:53:00 +0200 Subject: [Pw_forum] missing eigenvalue In-Reply-To: References: Message-ID: <200306161053.01020.giannozz@nest.sns.it> Hi > HOMO is non degenerate, the difference in energy between HOMO . and LUMO is around 0.3 ryd. eV, not Ry. This is however what you get if you use only Nelec/2 states for scf, which in this particular case leads to the wrong scf charge density. You need to add more states in the scf calculation, AND to add a broadening to the states. If HOMO and LUMO cross during self-consistency, the charge density has discontinuous jumps and the scf procedure may not converge. The broadening (gaussaina or whatever) smoothes the jump and allows self-consistency to proceed smoothly to the good ground state. With the true scf charge density, your system has a 0.1 eV HOMO-LUMO gap. See attached input and output (for the new version of the code) Paolo -------------- next part -------------- &control calculation = 'scf' restart_mode='from_scratch', tprnfor = .true. pseudo_dir = '/home/giannozz/O-sesame/pseudo/', outdir='/home/giannozz/tmp/' / &system ibrav= 1, celldm(1) =24.00, nat= 6, ntyp= 1, ecutwfc=20.0, nbnd = 14, occupations='smearing', smearing='gaussian', degauss=0.05 / &electrons mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Al 26.98 Al.vbc.UPF ATOMIC_POSITIONS {alat} Al 0.149002977 0.010536102 0.000000000 Al -0.149002977 -0.010536102 0.000000000 Al .010536102 0.149002977 0.000000000 Al -.010536102 -0.149002977 0.000000000 Al 0.000000000 0.000000000 0.149002977 Al 0.000000000 0.000000000 -0.149002977 K_POINTS {Gamma} -------------- next part -------------- Program PWSCF 1.2.1 starts ... Today is 16Jun2003 at 10:42:52 Ultrasoft (Vanderbilt) Pseudopotentials, Gamma point Current dimensions of program pwscf are: ntypx = 6 npk =40000 lmax = 3 nchix = 6 ndim = 2000 nbrx = 8 nqfm = 8 bravais-lattice index = 1 lattice parameter (a_0) = 24.0000 a.u. unit-cell volume = 13824.0000 (a.u.)^3 number of atoms/cell = 6 number of atomic types = 1 kinetic-energy cutoff = 20.0000 Ry charge density cutoff = 80.0000 Ry convergence threshold = 1.0E-08 beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PZ NOGX NOGC (1100) iswitch = 0 celldm(1)= 24.00000 celldm(2)= 0.00000 celldm(3)= 0.00000 celldm(4)= 0.00000 celldm(5)= 0.00000 celldm(6)= 0.00000 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.0000 0.0000 0.0000 ) a(2) = ( 0.0000 1.0000 0.0000 ) a(3) = ( 0.0000 0.0000 1.0000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.0000 0.0000 0.0000 ) b(2) = ( 0.0000 1.0000 0.0000 ) b(3) = ( 0.0000 0.0000 1.0000 ) PSEUDO 1 is Al zval = 3.0 lmax= 1 lloc= 0 (in numerical form: 171 grid points, xmin = 0.00, dx = 0.0000) atomic species valence mass pseudopotential Al 3.00 26.98000 Al( 1.00) 8 Sym.Ops. (with inversion) Cartesian axes site n. atom positions (a_0 units) 1 Al tau( 1) = ( 0.1490030 0.0105361 0.0000000 ) 2 Al tau( 2) = ( -0.1490030 -0.0105361 0.0000000 ) 3 Al tau( 3) = ( 0.0105361 0.1490030 0.0000000 ) 4 Al tau( 4) = ( -0.0105361 -0.1490030 0.0000000 ) 5 Al tau( 5) = ( 0.0000000 0.0000000 0.1490030 ) 6 Al tau( 6) = ( 0.0000000 0.0000000 -0.1490030 ) number of k points= 1 gaussian broad. (ryd)= 0.0500 ngauss = 0 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 2.0000000 G cutoff = 1167.2200 ( 83519 G-vectors) FFT grid: ( 72, 72, 72) nbndx = 56 nbnd = 14 natomwfc = 24 npwx = 10408 nelec = 18.00 nkb = 24 ngl = 975 Initial potential from superposition of free atoms starting charge = 17.98766 Starting wfc are atomic total cpu time spent up to now is 7.97 secs iteration # 1 ecut= 20.00 ryd beta=0.70 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 3.0 total energy = -24.07499764 ryd estimated scf accuracy < 0.66195088 ryd total cpu time spent up to now is 22.32 secs iteration # 2 ecut= 20.00 ryd beta=0.70 Davidson diagonalization with overlap ethr = 3.68E-03, avg # of iterations = 3.0 total energy = -23.88371294 ryd estimated scf accuracy < 0.96342749 ryd total cpu time spent up to now is 37.00 secs iteration # 3 ecut= 20.00 ryd beta=0.70 Davidson diagonalization with overlap ethr = 3.68E-03, avg # of iterations = 2.0 total energy = -24.43852687 ryd estimated scf accuracy < 0.00104193 ryd total cpu time spent up to now is 49.96 secs iteration # 4 ecut= 20.00 ryd beta=0.70 Davidson diagonalization with overlap ethr = 5.79E-06, avg # of iterations = 4.0 total energy = -24.44004936 ryd estimated scf accuracy < 0.00014695 ryd total cpu time spent up to now is 67.04 secs iteration # 5 ecut= 20.00 ryd beta=0.70 Davidson diagonalization with overlap ethr = 8.16E-07, avg # of iterations = 2.0 total energy = -24.44008319 ryd estimated scf accuracy < 0.00001476 ryd total cpu time spent up to now is 80.39 secs iteration # 6 ecut= 20.00 ryd beta=0.70 Davidson diagonalization with overlap ethr = 8.20E-08, avg # of iterations = 5.0 total energy = -24.44008813 ryd estimated scf accuracy < 0.00000177 ryd total cpu time spent up to now is 96.25 secs iteration # 7 ecut= 20.00 ryd beta=0.70 Davidson diagonalization with overlap ethr = 9.81E-09, avg # of iterations = 5.0 total energy = -24.44008868 ryd estimated scf accuracy < 0.00000027 ryd total cpu time spent up to now is 111.44 secs iteration # 8 ecut= 20.00 ryd beta=0.70 Davidson diagonalization with overlap ethr = 1.51E-09, avg # of iterations = 4.0 total energy = -24.44008880 ryd estimated scf accuracy < 0.00000001 ryd total cpu time spent up to now is 125.38 secs iteration # 9 ecut= 20.00 ryd beta=0.70 Davidson diagonalization with overlap ethr = 6.13E-11, avg # of iterations = 3.0 k = 0.0000 0.0000 0.0000 (10408 PWs) bands (ev): -11.9006 -8.7303 -8.2956 -7.9044 -5.2864 -5.1763 -4.6844 -4.4611 -4.1198 -4.0166 -2.6876 -2.5753 -2.4730 -1.2740 the Fermi energy is -3.9438 ev ! total energy = -24.44008880 ryd estimated scf accuracy < 0.00000000 ryd band energy sum = -8.87823805 ryd one-electron contribution = -60.53071604 ryd hartree contribution = 31.30455932 ryd xc contribution = -8.41306975 ryd ewald contribution = 13.28117646 ryd correction for metals = -0.08203880 ryd convergence has been achieved Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00707363 -0.01749475 0.00000000 atom 2 type 1 force = -0.00707363 0.01749475 0.00000000 atom 3 type 1 force = -0.01749475 0.00707363 0.00000000 atom 4 type 1 force = 0.01749475 -0.00707363 0.00000000 atom 5 type 1 force = 0.00000000 0.00000000 -0.00257516 atom 6 type 1 force = 0.00000000 0.00000000 0.00257516 Total force = 0.103424 Total SCF correction = 0.000069 Writing file pwscf.pun for program phonon PWSCF : 2m20.74s CPU time init_run : 7.83s CPU electrons : 131.11s CPU forces : 1.63s CPU electrons : 131.11s CPU c_bands : 84.81s CPU ( 9 calls, 9.423 s avg) sum_band : 15.35s CPU ( 9 calls, 1.705 s avg) v_of_rho : 19.41s CPU ( 19 calls, 1.022 s avg) mix_rho : 11.17s CPU ( 9 calls, 1.241 s avg) c_bands : 84.81s CPU ( 9 calls, 9.423 s avg) init_us_2 : 1.30s CPU ( 19 calls, 0.068 s avg) cegterg : 83.17s CPU ( 9 calls, 9.241 s avg) sum_band : 15.35s CPU ( 9 calls, 1.705 s avg) wfcrot : 4.68s CPU cegterg : 83.17s CPU ( 9 calls, 9.241 s avg) h_psi : 77.35s CPU ( 41 calls, 1.887 s avg) g_psi : 0.60s CPU ( 31 calls, 0.019 s avg) overlap : 2.29s CPU ( 31 calls, 0.074 s avg) cdiaghg : 0.33s CPU ( 32 calls, 0.010 s avg) update : 4.39s CPU ( 31 calls, 0.142 s avg) last : 0.88s CPU ( 9 calls, 0.098 s avg) h_psi : 77.35s CPU ( 41 calls, 1.887 s avg) init : 0.49s CPU ( 41 calls, 0.012 s avg) add_vuspsi : 3.95s CPU ( 41 calls, 0.096 s avg) General routines cft3 : 15.46s CPU ( 76 calls, 0.203 s avg) cft3s : 64.82s CPU ( 485 calls, 0.134 s avg) davcio : 0.16s CPU ( 10 calls, 0.016 s avg) From proffess at yandex.ru Mon Jun 16 16:07:36 2003 From: proffess at yandex.ru (Sergei Lisenkov) Date: Mon, 16 Jun 2003 18:07:36 +0400 (MSD) Subject: [Pw_forum] from cdiaghg : error # 30 In-Reply-To: <200306161013.19755.giannozz@nest.sns.it> References: <3EE86CDE.000001.22552@pantene.yandex.ru> <3EEB169A.000002.22784@camay.yandex.ru> <200306161013.19755.giannozz@nest.sns.it> Message-ID: <3EEDCF28.00000A.24189@camay.yandex.ru> Dear Paolo, Thank you very much for your help for my problem with HP machines, it helps me! About my error: from cdiaghg : error # 30 You are right, I am using ALPHA cluster and cxml library. But I recompiled pwscf with lapack and blas, compiled myself but I got againt this error. My example is example3 (Al). I do not know how solve it. HAve you some idea? Best wishes, Sergey From proffess at yandex.ru Mon Jun 16 16:10:27 2003 From: proffess at yandex.ru (Sergei Lisenkov) Date: Mon, 16 Jun 2003 18:10:27 +0400 (MSD) Subject: [Pw_forum] Error: can"t open a connected unit In-Reply-To: <200306161013.19755.giannozz@nest.sns.it> References: <3EE86CDE.000001.22552@pantene.yandex.ru> <3EEB169A.000002.22784@camay.yandex.ru> <200306161013.19755.giannozz@nest.sns.it> Message-ID: <3EEDCFD3.000001.25217@camay.yandex.ru> Dear Paolo, It helps me, but I do not understand, why pw.1.2.0 on HP cannot works with PP in UPF format. It is possible use old format of PP. Why? But PARA version cannot work, I got: error 1: name list &control But I tested it on example3 (Al), it works on serial version. What is problem? Thanks, Best wishes, Sergey From giannozz at nest.sns.it Mon Jun 16 17:51:56 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 16 Jun 2003 17:51:56 +0200 Subject: [Pw_forum] Error: can"t open a connected unit In-Reply-To: <3EEDCFD3.000001.25217@camay.yandex.ru> References: <3EE86CDE.000001.22552@pantene.yandex.ru> <200306161013.19755.giannozz@nest.sns.it> <3EEDCFD3.000001.25217@camay.yandex.ru> Message-ID: <200306161751.56234.giannozz@nest.sns.it> Hi > It helps me, but I do not understand, why pw.1.2.0 on HP cannot > works with PP in UPF format. It is possible use old format of PP. > Why? You tell me why, and not the opposite: I don't have a HP machine ... > But PARA version cannot work, I got: > > error 1: > name list &control the code is not reading anything from standard input. Redirection of input on parallel machines is very machine- dependent. Verify also that nothing is present in input before &control . Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From goranka.bilalbegovic at zg.hinet.hr Mon Jun 16 19:18:03 2003 From: goranka.bilalbegovic at zg.hinet.hr (Goranka Bilalbegovic) Date: Mon, 16 Jun 2003 19:18:03 +0200 Subject: [Pw_forum] Error: can"t open a connected unit References: <3EE86CDE.000001.22552@pantene.yandex.ru> <3EEB169A.000002.22784@camay.yandex.ru> <200306161013.19755.giannozz@nest.sns.it> <3EEDCFD3.000001.25217@camay.yandex.ru> Message-ID: <004501c3342b$75236d80$8a321dc3@gost> > > It helps me, but I do not understand, why pw.1.2.0 on HP cannot works with PP in UPF format. It is possible use old format of PP. Why? > But PARA version cannot work, I got: > > error 1: > name list &control > > But I tested it on example3 (Al), it works on serial version. What is problem? Dear Sergei, Several years ago I had the problem to open files on the HP single processor machine. The same f77 code worked without any problems on many other computers and compilers. I do not now remember details, but I have to go through the code and to change all open statements, and perhaps some other things. I think that you should: (1) look for web or paper manuals of this HP compiler, or man pages on your computer. There you will find specific features of the compiler. (2) search for HP web pages to see whether they have some type of support for compilers, frequently asked questions, user forum... The error "name list &control" I had using the latest version of NAG compiler on linux. Paolo already suggested that you should remove anything before &control. With the nAG compiler I had to use many compiler options, to change some parts of the code, and finally I had run time errors as this name list&control. I found that differences between NAG and other compilers are very big, this is very strict compiler, does not like old and nonstandard things, and has some features of Fortran 2000. I was afraid that even if the program runs, the results on some points are going to be wrong. Also I did not want to make big changes on all future versions of pw, and perhaps cp and fpmd. I am now (both on single linux and linux cluster) very happy user of free Intel compiler ifc, as many other people on this mailing list. I did not try to install it on HP, but system managers on our Linux clusters are not very hard-working and I have to install ifc compiler (both on single and parallel linux) and mpich (on linux cluster) in my own directory. It is not hard. Or you should ask your system manager to install ifc compiler on your HP computer. Some computer managers are happy to help their users. If you do not like this HP compiler, try ifc. I also use a native SGI compiler on O2K, and it is very good for pw. But NaG, and perhaps your HP compilers are different. Best regards, Goranka From francesco.antoniella at aquila.infn.it Wed Jun 18 13:23:35 2003 From: francesco.antoniella at aquila.infn.it (Francesco Antoniella) Date: 18 Jun 2003 13:23:35 +0200 Subject: [Pw_forum] from cdiaghg : error # 30 In-Reply-To: <3EEDCF28.00000A.24189@camay.yandex.ru> References: <3EE86CDE.000001.22552@pantene.yandex.ru> <3EEB169A.000002.22784@camay.yandex.ru> <200306161013.19755.giannozz@nest.sns.it> <3EEDCF28.00000A.24189@camay.yandex.ru> Message-ID: <1055935432.1704.2.camel@altair> Il lun, 2003-06-16 alle 16:07, Sergei Lisenkov ha scritto: > Dear Paolo, > > Thank you very much for your help for my problem with HP machines, it helps me! > > About my error: > from cdiaghg : error # 30 > > You are right, I am using ALPHA cluster and cxml library. But I recompiled pwscf with lapack and blas, compiled myself but I got againt this error. My example is example3 (Al). > > I do not know how solve it. HAve you some idea? Unless you use fftw you need anyway cxml for fft so you must link either cxml and blas-lapack BUT if you invoke the options like -lcxml -lblas -llapack you will obtain the linking of all the cxml routines. Try , if this is the problem issuing -lblas -llapack -lcxml. Regards Francesco - > > Best wishes, > Sergey > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From proffess at yandex.ru Thu Jun 19 11:25:27 2003 From: proffess at yandex.ru (Sergei Lisenkov) Date: Thu, 19 Jun 2003 13:25:27 +0400 (MSD) Subject: [Pw_forum] Alpha platform In-Reply-To: <200306121547.02106.giannozz@nest.sns.it> References: <3EE86CDE.000001.22552@pantene.yandex.ru> <200306121547.02106.giannozz@nest.sns.it> Message-ID: <3EF18187.000001.10871@camay.yandex.ru> Dear Paolo and another users, I installed the new version of compaq fortran on Alpha platform. In linking stage I got: addusstress.o: In function `addusstres': :50: undefined reference to `for_check_mult_overflow64' :50: undefined reference to `for_check_mult_overflow64' :50: undefined reference to `for_check_mult_overflow64' :50: undefined reference to `for_check_mult_overflow64' :50: undefined reference to `for_check_mult_overflow64' addusstress.o::50: more undefined references to `for_check_mult_overflow64' follow collect2: ld returned 1 exit status Is it problem of compiler? Best wishes, Sergey From baknoo at tokyo.rist.or.jp Mon Jun 23 11:35:36 2003 From: baknoo at tokyo.rist.or.jp (NoahPark) Date: Mon, 23 Jun 2003 18:35:36 +0900 Subject: [Pw_forum] Length of tmp_dir References: <3EE86CDE.000001.22552@pantene.yandex.ru> <3EEB169A.000002.22784@camay.yandex.ru> <200306161013.19755.giannozz@nest.sns.it> <3EEDCFD3.000001.25217@camay.yandex.ru> <004501c3342b$75236d80$8a321dc3@gost> Message-ID: <004901c3396a$cce01520$4b00a8c0@computat030u9q> Dear PWscf users; When I initially run the code, I get the following message. >> /S/n006/home006/f0006/tmpX// non existent or non writeable. Now, I comment out the two lines in bottom of input.f90, as the following. >> ! if (ios /= 0 ) call error('reading', & >> ! trim(tmp_dir)//' non existent or non writable',1) By this modification, the code works almost successfully, except the following behaviors. 1. when I gave a somehow short string to 'outdir' in input file, outdir = '/S/n006/home006/f0006/tmpX//' The code works successfully. 2. when I gave a somehow longer string to 'outdir' in input file, outdir = '/S/n006/home006/f0006/tmpX/tmpX.b/tmpX.b.b//' The code iterate with a total energy of a strange value. 3. when I did not include the string of 'outdir' in input file, The code runs successfully, but, 'restart' doesn't work. The code fails in reading wavefunctions written in the previous work. This may be caused by the constraint in the length of the string of 'tmp_dir'. If so, how could I increase its available length. If not, would anybody please guess the reason for the observed phenomena ???? Best regards, Noah From michele.lazzeri at lmcp.jussieu.fr Mon Jun 23 10:49:58 2003 From: michele.lazzeri at lmcp.jussieu.fr (Michele Lazzeri) Date: Mon, 23 Jun 2003 10:49:58 +0200 Subject: [Pw_forum] Length of tmp_dir References: <3EE86CDE.000001.22552@pantene.yandex.ru> <3EEB169A.000002.22784@camay.yandex.ru> <200306161013.19755.giannozz@nest.sns.it> <3EEDCFD3.000001.25217@camay.yandex.ru> <004501c3342b$75236d80$8a321dc3@gost> <004901c3396a$cce01520$4b00a8c0@computat030u9q> Message-ID: <3EF6BF36.2635E3F9@lmcp.jussieu.fr> Dear Noah, You are right, in the code there are constraint in the length of the string 'tmp_dir', if you are just looking for a simple way to skip this problem you can: create a link to a directory with a short name (before running the code ) with the command: ln -sf /scratch/directory/with/a/very/longname// ./scr and use in the input file: tmp_dir='./scr' I guess this should work also for oudir Regards, Michele NoahPark wrote: > Dear PWscf users; > > When I initially run the code, I get the following message. > > >> /S/n006/home006/f0006/tmpX// non existent or non writeable. > > Now, I comment out the two lines in bottom of input.f90, as the following. > > >> ! if (ios /= 0 ) call error('reading', & > >> ! trim(tmp_dir)//' non existent or non writable',1) > > By this modification, the code works almost successfully, except the following behaviors. > > 1. when I gave a somehow short string to 'outdir' in input file, > outdir = '/S/n006/home006/f0006/tmpX//' > The code works successfully. > > 2. when I gave a somehow longer string to 'outdir' in input file, > outdir = '/S/n006/home006/f0006/tmpX/tmpX.b/tmpX.b.b//' > The code iterate with a total energy of a strange value. > > 3. when I did not include the string of 'outdir' in input file, > The code runs successfully, but, 'restart' doesn't work. > The code fails in reading wavefunctions written in the previous work. > > This may be caused by the constraint in the length of the string of 'tmp_dir'. > If so, how could I increase its available length. > If not, would anybody please guess the reason for the observed phenomena ???? From giannozz at nest.sns.it Tue Jun 24 22:03:58 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 24 Jun 2003 22:03:58 +0200 Subject: [Pw_forum] Length of tmp_dir In-Reply-To: <004901c3396a$cce01520$4b00a8c0@computat030u9q> References: <3EE86CDE.000001.22552@pantene.yandex.ru> <004501c3342b$75236d80$8a321dc3@gost> <004901c3396a$cce01520$4b00a8c0@computat030u9q> Message-ID: <200306242203.58377.giannozz@nest.sns.it> Hi > [...] This may be caused by the constraint in the length of the > string of 'tmp_dir'. it is. In the version under development (and soon to be released) the allowed length of tmp_dir has been increased to 80 > If so, how could I increase its available length. you should change the length of tmp_dir in PW/io.f90, but you may need to change other definitions in other routines, plus other intermediate variables, so it is not entirely straightforward. My advice is to use short names and symbolic links, as suggested by Michele, for the time being, and to wait for the new release, where the 1.2.0 mess with character variable lengths has been (hopefully) cleaned up. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From giannozz at nest.sns.it Tue Jun 24 22:49:40 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 24 Jun 2003 22:49:40 +0200 Subject: [Pw_forum] Alpha platform In-Reply-To: <3EF18187.000001.10871@camay.yandex.ru> References: <3EE86CDE.000001.22552@pantene.yandex.ru> <200306121547.02106.giannozz@nest.sns.it> <3EF18187.000001.10871@camay.yandex.ru> Message-ID: <200306242249.40905.giannozz@nest.sns.it> Hi > I installed the new version of compaq fortran on Alpha platform. > In linking stage I got: > > addusstress.o: In function `addusstres': > :50: undefined reference to `for_check_mult_overflow64' > [...] a search of "for_check_mult_overflow64" on www.google.com returns the following page that might answer your question: http://linux.iol.unh.edu/linux/fortran/faq/cfal-X1.0.2.html Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From proffess at yandex.ru Wed Jun 25 11:47:53 2003 From: proffess at yandex.ru (Sergei Lisenkov) Date: Wed, 25 Jun 2003 13:47:53 +0400 (MSD) Subject: [Pw_forum] nmax In-Reply-To: <200306121547.02106.giannozz@nest.sns.it> References: <3EE86CDE.000001.22552@pantene.yandex.ru> <200306121547.02106.giannozz@nest.sns.it> Message-ID: <3EF96FC9.000008.02188@tide.yandex.ru> Dear PW users, Who can know, what is problem: ** C tau(115) = ( -0.1419429 -0.0109929 -0.0484524 ) ** C tau(116) = ( -0.1625076 0.0164245 -0.0654598 ) ** C tau(117) = ( -0.1415671 0.0441615 -0.0484836 ) ** C tau(118) = ( -0.1207771 0.0704580 -0.0648167 ) ** C tau(119) = ( -0.0659324 0.0877122 -0.0541188 ) ** C tau(120) = ( -0.0321743 0.0979790 -0.0819000 ) ** C tau(121) = ( 0.0334254 0.0973001 -0.0819119 ) ** C tau(122) = ( 0.1782192 0.0163140 -0.0620419 ) ** C tau(123) = ( 0.1227185 0.0692080 -0.0989400 ) ** C tau(124) = ( 0.0000000 0.0000000 0.0000000 ) number of k points= 8 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.2500000 k( 2) = ( 0.0000000 0.0000000 -0.2500000), wk = 0.2500000 k( 3) = ( 0.0000000 -0.2500000 -0.2500000), wk = 0.2500000 k( 4) = ( -0.5000000 0.0000000 0.0000000), wk = 0.2500000 k( 5) = ( -0.5000000 0.0000000 -0.2500000), wk = 0.2500000 k( 6) = ( -0.5000000 -0.2500000 -0.2500000), wk = 0.2500000 k( 7) = ( 0.0000000 -0.2500000 0.0000000), wk = 0.2500000 k( 8) = ( 0.5000000 -0.2500000 0.0000000), wk = 0.2500000 cryst. coord. k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.2500000 k( 2) = ( 0.0000000 0.0000000 -0.5000000), wk = 0.2500000 k( 3) = ( 0.0000000 -0.5000000 -0.5000000), wk = 0.2500000 k( 4) = ( -0.5000000 0.0000000 0.0000000), wk = 0.2500000 k( 5) = ( -0.5000000 0.0000000 -0.5000000), wk = 0.2500000 k( 6) = ( -0.5000000 -0.5000000 -0.5000000), wk = 0.2500000 k( 7) = ( 0.0000000 -0.5000000 0.0000000), wk = 0.2500000 k( 8) = ( 0.5000000 -0.5000000 0.0000000), wk = 0.2500000 G cutoff = 5744.3305 (7295015 G-vectors) FFT grid: (160,320,320) G cutoff = 5584.7657 (6992757 G-vectors) smooth grid: (150,300,300) nbndx = 992 nbnd = 248 natomwfc = 496 npwx = 10952 nelec = 496.00 nkb = 992 ngl = 91189 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cft_2 : error # 320 increase nmax %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% BEst wishes, Sergey From eyvaz_isaev at yahoo.com Wed Jun 25 12:02:49 2003 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 25 Jun 2003 03:02:49 -0700 (PDT) Subject: [Pw_forum] nmax In-Reply-To: <3EF96FC9.000008.02188@tide.yandex.ru> Message-ID: <20030625100249.40526.qmail@web80508.mail.yahoo.com> Dear Sergei, It means that you are using a large unit cell and high cutoff energy. You should decrease cutoff or a cell parameter (if it is possible). Number of G-vectros looks fantastic. Regards, Eyvaz. --- Sergei Lisenkov wrote: > Dear PW users, > > Who can know, what is problem: > > > ** C tau(115) = ( -0.1419429 > -0.0109929 -0.0484524 ) > ** C tau(116) = ( -0.1625076 > 0.0164245 -0.0654598 ) > ** C tau(117) = ( -0.1415671 > 0.0441615 -0.0484836 ) > ** C tau(118) = ( -0.1207771 > 0.0704580 -0.0648167 ) > ** C tau(119) = ( -0.0659324 > 0.0877122 -0.0541188 ) > ** C tau(120) = ( -0.0321743 > 0.0979790 -0.0819000 ) > ** C tau(121) = ( 0.0334254 > 0.0973001 -0.0819119 ) > ** C tau(122) = ( 0.1782192 > 0.0163140 -0.0620419 ) > ** C tau(123) = ( 0.1227185 > 0.0692080 -0.0989400 ) > ** C tau(124) = ( 0.0000000 > 0.0000000 0.0000000 ) > > number of k points= 8 > cart. coord. in units 2pi/a_0 > k( 1) = ( 0.0000000 0.0000000 > 0.0000000), wk = 0.2500000 > k( 2) = ( 0.0000000 0.0000000 > -0.2500000), wk = 0.2500000 > k( 3) = ( 0.0000000 -0.2500000 > -0.2500000), wk = 0.2500000 > k( 4) = ( -0.5000000 0.0000000 > 0.0000000), wk = 0.2500000 > k( 5) = ( -0.5000000 0.0000000 > -0.2500000), wk = 0.2500000 > k( 6) = ( -0.5000000 -0.2500000 > -0.2500000), wk = 0.2500000 > k( 7) = ( 0.0000000 -0.2500000 > 0.0000000), wk = 0.2500000 > k( 8) = ( 0.5000000 -0.2500000 > 0.0000000), wk = 0.2500000 > > cryst. coord. > k( 1) = ( 0.0000000 0.0000000 > 0.0000000), wk = 0.2500000 > k( 2) = ( 0.0000000 0.0000000 > -0.5000000), wk = 0.2500000 > k( 3) = ( 0.0000000 -0.5000000 > -0.5000000), wk = 0.2500000 > k( 4) = ( -0.5000000 0.0000000 > 0.0000000), wk = 0.2500000 > k( 5) = ( -0.5000000 0.0000000 > -0.5000000), wk = 0.2500000 > k( 6) = ( -0.5000000 -0.5000000 > -0.5000000), wk = 0.2500000 > k( 7) = ( 0.0000000 -0.5000000 > 0.0000000), wk = 0.2500000 > k( 8) = ( 0.5000000 -0.5000000 > 0.0000000), wk = 0.2500000 > > G cutoff = 5744.3305 (7295015 G-vectors) > FFT grid: (160,320,320) > G cutoff = 5584.7657 (6992757 G-vectors) > smooth grid: (150,300,300) > > nbndx = 992 nbnd = 248 natomwfc = > 496 npwx = 10952 > nelec = 496.00 nkb = 992 ngl = > 91189 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from cft_2 : error # 320 > increase nmax > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > BEst wishes, > Sergey > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum __________________________________ Do you Yahoo!? SBC Yahoo! DSL - Now only $29.95 per month! http://sbc.yahoo.com From nagano at atrc.mhi.co.jp Thu Jun 26 05:31:12 2003 From: nagano at atrc.mhi.co.jp (Ichiro Nagano) Date: Thu, 26 Jun 2003 12:31:12 +0900 Subject: [Pw_forum] WDA and GW approximation method Message-ID: <010901c33b93$68a941a0$0a130190@kibanad.artc.mhi.co.jp> Dear pwscf users, I would like to try calculating band gap of semiconductors. How do you think about capability of Weighted Density Approximation (WDA) and GW approximation method? Thanks for any information, Ichiro Nagano ******************************************************************** Advanced Technology Research Center, Mitsubishi Heavy Industries, Ltd. 8-1, Sachiura, 1-Chome, Kanazawa-ku, Yokohama, 236-8515, Japan Ichiro Nagano E-mail: TEL: + 81 (45) 775-2437 (EXT 9065) FAX: + 81 (45) 771-3879 From katalin.gaal-nagy at physik.uni-regensburg.de Thu Jun 26 10:40:10 2003 From: katalin.gaal-nagy at physik.uni-regensburg.de (Katalin Gaal-Nagy) Date: Thu, 26 Jun 2003 10:40:10 +0200 (MEST) Subject: [Pw_forum] from linmin : error Message-ID: <200306260840.h5Q8eAgV004177@rrzd2.rz.uni-regensburg.de> Dear all! In my calculations I relax one of two atomic positions in z-direction and receive in some cases such an error messages: from linmin : error # 2 unexpected error Sometimes it is also an error # 1 What does this mean exactly and how can I avoid this? Regards, Katalin ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , >>>>>>> Katalin Gaal-Nagy <<<<<<< , , Gemeinerstr. 3 PHY 4.1.30 , , 93053 Regensburg Uni-Regensburg , , 0941/7501574 0941/943-2026 , ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , >>>>>>> katalin.gaal-nagy at physik.uni-regensburg.de <<<<<<< , ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , >>>>>>> Tr"aume nicht Dein Leben, lebe Deinen Traum <<<<<<< , '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' From sprokuda at dnk.ru Thu Jun 26 11:04:49 2003 From: sprokuda at dnk.ru (sprokuda at dnk.ru) Date: Thu, 26 Jun 2003 13:04:49 +0400 Subject: [Pw_forum] (no subject) Message-ID: <6270487123.20030626130449@dnk.ru> Dear PW users, probably anybody had transfered the PW for Windows ? ( in best case to C) ? Or I'm asking to much ? :/ Regards, Sergey Prokudaylo. From marzari at mit.edu Thu Jun 26 11:11:21 2003 From: marzari at mit.edu (Nicola Marzari) Date: Thu, 26 Jun 2003 11:11:21 +0200 Subject: [Pw_forum] WDA and GW approximation method References: <010901c33b93$68a941a0$0a130190@kibanad.artc.mhi.co.jp> Message-ID: <3EFAB8B9.9080904@mit.edu> Dear Ichiro, we had looked at gaps in semiconductors and in oxides with the WDA a few years ago ( J. Phys. Chem. Solids 61 321 (2000), and PRB 62 12724 (2000) ). It makes little difference, albeit in the right direction. For GW there is abundant literature, and it does work well. nicola Ichiro Nagano wrote: > Dear pwscf users, > > I would like to try calculating band gap of semiconductors. > How do you think about capability of Weighted Density Approximation (WDA) > and GW approximation method? > > Thanks for any information, > > Ichiro Nagano > --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 617.2586534 marzari at mit.edu http://nnn.mit.edu From breezejd at sbu.ac.uk Thu Jun 26 15:40:19 2003 From: breezejd at sbu.ac.uk (Jonathan Breeze) Date: Thu, 26 Jun 2003 14:40:19 +0100 Subject: [Pw_forum] ifc and linux Message-ID: <3EFAF7C3.6080606@sbu.ac.uk> Dear PWscf users, I thought I would post a message to you all about my recent experiences with Intel Fortran Compiler and Linux. I noticed a while back that Michal Lemieszewski had a problem with compiling PWscf to run on a Linux PC. I had managed to compile PWscf on a machine running Linux Redhat 8.1 but when I tried to compile on Redhat 9.0, the same errors that Michal reported where found: /opt/intel/compiler70/ia32/lib/libIEPCF90.a(f90file.o)(.text+0x4746): In function `FileOpen': :/ undefined reference to `errno' //opt/intel/compiler70/ia32/lib/libIEPCF90.a(f90fioerr.o)(.text+0x4d3): In function `f_f77ioerr': :/ undefined reference to `__ctype_b' //opt/intel/compiler70/ia32/lib/libIEPCF90.a(f90fioerr.o)(.text+0x6d9): In function `f_fiomess.': :/ undefined reference to `errno' //opt/intel/compiler70/ia32/lib/libIEPCF90.a(f90fioerr.o)(.text+0x76b): In function `f_seterrno': :/ undefined reference to `errno' /make[1]: *** [all] Error 1 make: *** [pw] Error 2 This is due to an incompatability between Intel Fortran Compiler 7.0 and 7.1 with new versions of the GNU libc library. Current versions of ifc are compatible with glibc 2.2.3, 2.2.93 and 2.2.4. Unfortunately, Redhat 9.0 and other recent releases of Linux use glibc 2.3.1 or 2.3.2. The only way I found around this problem was to either to only use Redhat 8.1 or earlier releases or link in a libc-2.2.93.so library during the build process. Once the libc-2.2.93 library is linked in, everything compiles happily. I use the option -L/$(PWDIR)/ -lc-2.2.93 added to the LDFLAGS line, after placing a copy of the library in the PWscf directory. This solution is not very elegant, but works. I was wondering if anyone else has had similar troubles, and if so, have you found a more elegant - less nasty - solution ? Kind regards, Jonathan P.S> Dear Paolo, thankyou for the help with D3. I am getting good results!! From marzari at mit.edu Thu Jun 26 15:52:22 2003 From: marzari at mit.edu (Nicola Marzari) Date: Thu, 26 Jun 2003 15:52:22 +0200 Subject: [Pw_forum] ifc and linux References: <3EFAF7C3.6080606@sbu.ac.uk> Message-ID: <3EFAFA96.5040607@mit.edu> > I was wondering if anyone else has had similar troubles, and if so, have > you found a more elegant - less nasty - solution ? Same solution here. Using RedHat 9.0, ifc 7.1, and MKL 6.0, we link with the libc copied from a PC that had RedHat 8.0 installed. This was suggested in an Intel Fortran compiler forum, for what is worth. Seems to work - although we use it only on a single development PC. nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 617.2586534 marzari at mit.edu http://nnn.mit.edu From breezejd at sbu.ac.uk Thu Jun 26 16:19:12 2003 From: breezejd at sbu.ac.uk (Jonathan Breeze) Date: Thu, 26 Jun 2003 15:19:12 +0100 Subject: [Pw_forum] ifc and linux References: <3EFAF7C3.6080606@sbu.ac.uk> <3EFAFA96.5040607@mit.edu> Message-ID: <3EFB00E0.3060200@sbu.ac.uk> Thanks for that Nicola, I feel better now! I felt a little 'grubby' ... but at least it works. >> I was wondering if anyone else has had similar troubles, and if so, >> have you found a more elegant - less nasty - solution ? > > > > Same solution here. Using RedHat 9.0, ifc 7.1, and MKL 6.0, > we link with the libc copied from a PC that had RedHat 8.0 > installed. This was suggested in an Intel Fortran compiler forum, > for what is worth. Seems to work - although we use it only on > a single development PC. > > > nicola > > > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA > tel 617.4522758 fax 617.2586534 marzari at mit.edu http://nnn.mit.edu > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > . > From baroni at sissa.it Thu Jun 26 16:40:54 2003 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 26 Jun 2003 16:40:54 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <6270487123.20030626130449@dnk.ru> References: <6270487123.20030626130449@dnk.ru> Message-ID: <3EFB05F6.3080802@sissa.it> sprokuda at dnk.ru wrote: > Dear PW users, > > probably anybody had transfered the PW for Windows ? ( in best case > to C) ? > Or I'm asking to much ? :/ I am afraid you are. PWscf is not (yet) a videogame. linux is free and can run on any machine which runs windows. why should anybody care doing scientific computation on windows? Stefano Baroni > > Regards, > Sergey Prokudaylo. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at nest.sns.it Thu Jun 26 17:30:05 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 26 Jun 2003 17:30:05 +0200 Subject: [Pw_forum] from linmin : error In-Reply-To: <200306260840.h5Q8eAgV004177@rrzd2.rz.uni-regensburg.de> References: <200306260840.h5Q8eAgV004177@rrzd2.rz.uni-regensburg.de> Message-ID: <200306261730.05988.giannozz@nest.sns.it> On Thursday 26 June 2003 10:40, Katalin Gaal-Nagy wrote: > Dear all! > > In my calculations I relax one of two atomic positions in z-direction and > receive in some cases such an error messages: > > from linmin : error # 2 > unexpected error > > Sometimes it is also an error # 1 > What does this mean exactly "exactly" ? the line minimization algorithm (linmin) looks for a minimum - using atomic positions and forces at the current and preceding step, and 3rd- or 2nd-degree polynomial interpolation - along a given direction (determined by the BFGS algorithm). If this minimum turns out to be where it shouldn't be (for instance, on the wrong side wrt forces), the code stops with "unexpected error". What does it mean in practise? there is an inconsistency between forces and energies. Usually this is due to imperfect self-consistency: the error on forces is linear, the error on energies is quadratic. When forces are small, the relative error can be sizable (the "Total SCF correction" field gives an idea of how large it is) > and how can I avoid this? it depends. In your case (two atoms, one fixed?), maybe you should simply set larger thresholds for structural optimization convergence See also what is written in the manual: \item {\em Structural optimization goes wild after the first or second step} The algorithm used in structural optimization is not very robust. If you start too far away from minimum, it may lead to badly wrong atomic positions. Restart from a better starting point. \item {\em Structural optimization is slow or does not converge.} Close to convergence the self-consistency error in forces may become large with respect to the value of forces. The resulting mismatch between forces and energies may confuse the line minimization algorithm, which assumes consistency between the two. The code reduces the starting self-consistency threshold {\tt conv\_thr} when approaching the minimum energy configuration, up to a factor defined by {\tt upscale}. Reducing {\tt conv\_thr} (or increasing {\tt upscale}) yields a smoother structural optimization, but if {\tt conv\_thr} becomes too small, electronic self-consistency may not converge. You may also increase variables {\tt etot\_conv\_thr} and {\tt forc\_conv\_thr} that determine the threshold for convergence (the default values are quite strict). Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From breezejd at sbu.ac.uk Thu Jun 26 17:49:48 2003 From: breezejd at sbu.ac.uk (Jonathan Breeze) Date: Thu, 26 Jun 2003 16:49:48 +0100 Subject: [Pw_forum] (no subject) References: <6270487123.20030626130449@dnk.ru> <3EFB05F6.3080802@sissa.it> Message-ID: <000701c33bfa$92d744b0$95039488@breezy> Sergey, Your best bet is to install Linux on your PC. If you have a spare partition big enough, then Linux and Windows could coexist on your machine. When you boot up, you would get a choice between Linux or Windows. I recommend RedHat 8.1, an older version compatible with Intel Fortran Compiler version 7 (which is free). If you don't have a spare partition, you could resize the main Windows partition using NTFS-Linux package on the Knoppix distribution (which boots off a CD) and then install Linux. Another possibility (which I haven't tried) is to use the Cygwin package, a UNIX environment for the PC which runs in Windows. You can compile the FFTW, LAPACK, BLAS and ATLAS libraries using the GNU compilers. Unfortunately, there isn't a Fortran90 compiler available for Cygwin, so you would have to use an old version of the PW source code that uses f77. Unfortunately, Windows and scientific computing are not the greatest of friends, so I can't see anyone going to the great lengths of porting PW over to MS. I recommend you get acquainted with the interesting and free world of Linux. It doesn't hurt! > sprokuda at dnk.ru wrote: > > Dear PW users, > > > > probably anybody had transfered the PW for Windows ? ( in best case > > to C) ? > > Or I'm asking to much ? :/ > > I am afraid you are. PWscf is not (yet) a videogame. linux is free and > can run on any machine which runs windows. why should anybody care doing > scientific computation on windows? > > Stefano Baroni > > > > > Regards, > > Sergey Prokudaylo. > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From ps at ned.sims.nrc.ca Thu Jun 26 18:00:43 2003 From: ps at ned.sims.nrc.ca (Serguei Patchkovskii) Date: Thu, 26 Jun 2003 12:00:43 -0400 (EDT) Subject: [Pw_forum] (no subject) In-Reply-To: <000701c33bfa$92d744b0$95039488@breezy> Message-ID: On Thu, 26 Jun 2003, Jonathan Breeze wrote: > compilers. Unfortunately, there isn't a Fortran90 compiler available for > Cygwin, so you would have to use an old version of the PW source code that > uses f77. Portland group pgf90 works fine with cygwin. I would expect it compile pwscf with no trouble at all (I did use it to compile several other Unix packages, with only minor tweaking). The drawback is that pgf90 is not free - however, neither it is outrageously expensive. See http://www.pgroup.com/ Serguei --- Dr. Serguei Patchkovskii Tel: +1-(613)-990-0945 Fax: +1-(613)-947-2838 E-mail: Serguei.Patchkovskii at nrc.ca Coordinator of Modelling Software Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2011, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada From breezejd at sbu.ac.uk Thu Jun 26 18:08:22 2003 From: breezejd at sbu.ac.uk (Jonathan Breeze) Date: Thu, 26 Jun 2003 17:08:22 +0100 Subject: [Pw_forum] (no subject) References: Message-ID: <001201c33bfd$2a89e270$95039488@breezy> That's nice to know. So, in principle, it should be possible to compile PW on a Windows machine. ----- Original Message ----- From: "Serguei Patchkovskii" To: Sent: Thursday, June 26, 2003 5:00 PM Subject: Re: [Pw_forum] (no subject) > On Thu, 26 Jun 2003, Jonathan Breeze wrote: > > compilers. Unfortunately, there isn't a Fortran90 compiler available for > > Cygwin, so you would have to use an old version of the PW source code that > > uses f77. > > Portland group pgf90 works fine with cygwin. I would expect it compile > pwscf with no trouble at all (I did use it to compile several other > Unix packages, with only minor tweaking). > > The drawback is that pgf90 is not free - however, neither it is > outrageously expensive. See http://www.pgroup.com/ > > Serguei > > --- > Dr. Serguei Patchkovskii > > Tel: +1-(613)-990-0945 > Fax: +1-(613)-947-2838 > E-mail: Serguei.Patchkovskii at nrc.ca > > Coordinator of Modelling Software > Theory and Computation Group > Steacie Institute for Molecular Sciences > National Research Council Canada > Room 2011, 100 Sussex Drive > Ottawa, Ontario > K1A 0R6 Canada > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at nest.sns.it Thu Jun 26 18:49:26 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 26 Jun 2003 18:49:26 +0200 Subject: [Pw_forum] PWscf on WIndows In-Reply-To: <001201c33bfd$2a89e270$95039488@breezy> References: <001201c33bfd$2a89e270$95039488@breezy> Message-ID: <200306261849.26160.giannozz@nest.sns.it> On Thursday 26 June 2003 18:08, Jonathan Breeze wrote: > That's nice to know. So, in principle, it should be possible to > compile PW on a Windows machine. I think that all unix/linux tools needed to compile and run PWscf: the shell, make, C compiler, fortran-90 compiler, mathematical libraries, exist for Windows as well. It is actually much easier to find any software for Windows than it is for Linux (especially commercial software). So I don't see any major hurdle in porting PWscf to Windows, apart from the fact that none of the developers works with Windows, and I guess that nobody has any intention to do so in the future. If however somebody else is willing to try, he is welcome. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From bbouhafs at mail.com Thu Jun 26 22:48:22 2003 From: bbouhafs at mail.com (Bachir Bouhafs) Date: Thu, 26 Jun 2003 21:48:22 +0100 Subject: [Pw_forum] (no subject) Message-ID: <20030626204822.68848.qmail@mail.com> I enjoy your response Pr. Stefano. I want just to ask this windows sicentist, why you want to transfer the PW code for windows. I have done this in the past using the first version of PW, but in that period i haven't linux on my computer, but now it is easy to use the code under linux, wich is more flexible than windows. Also, the memory needed to run pw is more managed under linux than under other system like windows. Bachir Bouhafs ----- Original Message ----- From: Stefano Baroni Date: Thu, 26 Jun 2003 16:40:54 +0200 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] (no subject) > sprokuda at dnk.ru wrote: > > Dear PW users, > > > > probably anybody had transfered the PW for Windows ? ( in best case > > to C) ? > > Or I'm asking to much ? :/ > > I am afraid you are. PWscf is not (yet) a videogame. linux is free and > can run on any machine which runs windows. why should anybody care doing > scientific computation on windows? > > Stefano Baroni > > > > > Regards, > > Sergey Prokudaylo. > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum Dr. Bachir Bouhafs Physics Department University of Sidi Bel Abbes 22000 Sidi Bel Abbes, Algeria Mobil:+213 (0)71 18 21 47 Fax:+213 48 54 11 52 E-mail: bbouhafs at mail.com -- __________________________________________________________ Sign-up for your own FREE Personalized E-mail at Mail.com http://www.mail.com/?sr=signup From fisicabiomolecular at yahoo.com.br Fri Jun 27 01:10:03 2003 From: fisicabiomolecular at yahoo.com.br (fisicabiomolecular at yahoo.com.br) Date: Thu, 26 Jun 2003 20:10:03 -0300 Subject: [Pw_forum] PWSCF - In parallel (PARA_PREFIX= and PARA_POSTFIX=) Message-ID: <00a301c33c38$1751ae50$47c583c8@pion> BioPhysics Grupo de Pesquisa em Biof?sica Instituto de F?sica Universidade Federal de Uberl?ndia -------------------------------------------------------------------------------- Please, What I must insert in: PARA_PREFIX = ??? PARA_POSTFIX = ??? To twirl in parallel? -------------------------------------------------------------------------------- W B S Wyllian Bezerra da Silva http://www.biophysics.hpg.com.br/ --- Some files have not been scanned Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.491 / Virus Database: 290 - Release Date: 18/6/2003 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20030626/8b942f06/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 2230 bytes Desc: not available Url : /pipermail/attachments/20030626/8b942f06/attachment.gif -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 1547 bytes Desc: not available Url : /pipermail/attachments/20030626/8b942f06/attachment-0001.gif -------------- next part -------------- A non-text attachment was scrubbed... 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Name: ufu.gif Type: image/gif Size: 2230 bytes Desc: not available Url : /pipermail/attachments/20030626/8b942f06/attachment-0006.gif -------------- next part -------------- A non-text attachment was scrubbed... Name: logo_da.gif Type: image/gif Size: 1547 bytes Desc: not available Url : /pipermail/attachments/20030626/8b942f06/attachment-0007.gif From giannozz at nest.sns.it Fri Jun 27 09:45:52 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 27 Jun 2003 09:45:52 +0200 Subject: [Pw_forum] PWSCF - In parallel (PARA_PREFIX= and PARA_POSTFIX=) In-Reply-To: <00a301c33c38$1751ae50$47c583c8@pion> References: <00a301c33c38$1751ae50$47c583c8@pion> Message-ID: <200306270945.53198.giannozz@nest.sns.it> On Friday 27 June 2003 01:10, fisicabiomolecular at yahoo.com.br wrote: > What I must insert in: > > PARA_PREFIX = ??? > PARA_POSTFIX = ??? > > To twirl in parallel? to "twirl", I don't know: to run in parallel, you need to add what is appropriate to your parallel environment. From the manual (modified yesterday): ------------------------------------------------- Parallel execution is strongly system- and installation-dependent. Typically one has to specify: \begin{itemize} \item a launcher program, such as {\tt poe}, {\tt mpirun}, {\tt mpiexec}; \item the number of processors, typically as an option to the launcher program, but sometimes {\em after} the program to be executed; \item the program to be executed, with the proper path if needed: for instance, {\tt pw.x}, or {\tt ./pw.x}, or {\tt \$(HOME)/bin/pw.x}, or whatever applies; \item the number of ``pools'' into which processors are to be grouped (see Section ``Parallelization Issues'' below for an explanation of what a pool is). \end{itemize} The last item is optional and is read by the code. The first and second items are machine- and installation-dependent, and may be different for interactive and batch execution. Let us consider the case of execution of {\tt pw.x} on 16 processors divided into 8 pools (2 processors each). Some typical cases: \begin{itemize} \item IBM SP machines, batch: \\ {\tt pw.x -npool 8 < input} \item IBM SP machines, interactive, using {\tt poe}: \\ {\tt poe pw.x -procs 16 -npool 8 < input} \\ \item IBM SP machines, interactive, alternative: \\ {\tt pw.x -npool 8 < input} \\ where environment variable {\tt NPROC} is set to 16, {\tt MP\_HOSTFILE} to the file containing a list of processors. \item SGI Origin, PC clusters using {\tt mpirun}: \\ {\tt mpirun -np 16 pw.x -npool 8 < input} . \item Cray T3E (old): \\ {\tt mpprun -n 16 pw.x -npool 8 < input} . \\item PC clusters using {\tt mpiexec}: \\ {\tt mpiexec -n 16 pw.x -npool 8 < input} . \end{itemize} ------------------------------------------------- Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From proffess at yandex.ru Fri Jun 27 09:54:14 2003 From: proffess at yandex.ru (Sergei Lisenkov) Date: Fri, 27 Jun 2003 11:54:14 +0400 (MSD) Subject: [Pw_forum] Size of temproray files In-Reply-To: <200306270945.53198.giannozz@nest.sns.it> References: <00a301c33c38$1751ae50$47c583c8@pion> <200306270945.53198.giannozz@nest.sns.it> Message-ID: <3EFBF826.000007.08262@pantene.yandex.ru> Dear PWscf authors, I try to calculate sysyem of 124 carbon atoms on 70 CPU Alpha Linux machine. The code are written the 70 *.wfc files and 70 *.igk files. But after 10 minutes the size of *.wfc files=>7Gb. My quota is 7 Gb. Is it possible to reduce the size of these files? Or it ismy problem? Thank you very much, Best wishes, Sergey From katalin.gaal-nagy at physik.uni-regensburg.de Fri Jun 27 10:45:59 2003 From: katalin.gaal-nagy at physik.uni-regensburg.de (Katalin Gaal-Nagy) Date: Fri, 27 Jun 2003 10:45:59 +0200 (MEST) Subject: [Pw_forum] from linmin : error Message-ID: <200306270845.h5R8jx8l031833@rrzd2.rz.uni-regensburg.de> Dear Paolo! Thanks for your answer. I didn't link the linmin-error to a problem of (not) convergence of my structural optimization. Since I decreased all thresholds consistently I thought I avoided an inconsistency between the forces and the energies, but maybe I decreased it to much. Now I'll check if a smaller threshold will give me reliable results. Greetings, Katalin ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , >>>>>>> Katalin Gaal-Nagy <<<<<<< , , Gemeinerstr. 3 PHY 4.1.30 , , 93053 Regensburg Uni-Regensburg , , 0941/7501574 0941/943-2026 , ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , >>>>>>> katalin.gaal-nagy at physik.uni-regensburg.de <<<<<<< , ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , >>>>>>> Tr"aume nicht Dein Leben, lebe Deinen Traum <<<<<<< , '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' From sprokuda at dnk.ru Fri Jun 27 18:20:07 2003 From: sprokuda at dnk.ru (sprokuda at dnk.ru) Date: Fri, 27 Jun 2003 20:20:07 +0400 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: <1324847082.20030627202007@dnk.ru> Dear Dr.Patchkovskii! Thanks a lot for your advise. To be honest I/m far from to be an advanced user of Linux that is why I'm asking. The question is how to install pdf90 to work with it under CYGWIN ? which version should be used for it ( Win of Linux ?). The other problem is how to modify ./configure file to compile PWscf ? (it just reports "The architecture name is not specified" ) Portland group pgf90 works fine with cygwin. I would expect it compile pwscf with no trouble at all (I did use it to compile several other Unix packages, with only minor tweaking). From elwira at fy.chalmers.se Mon Jun 30 16:29:34 2003 From: elwira at fy.chalmers.se (Elwira Wachowicz) Date: Mon, 30 Jun 2003 16:29:34 +0200 Subject: [Pw_forum] phonon DOS error Message-ID: <3F00494E.8020008@fy.chalmers.se> Dear PWSCF user, I try to calculate phonon DOS using tetrahedra method for fcc-lattice with 2 atoms in the unit cell. I calculated phonons in 4x4x4 grid. Now, I'd like to see DOS for, say, 24x24x24 mesh but I cannot do it and the error message is: from tetrahedra : error # 15 cannot locate k point Where could be the reason for such an error? I'd be happy if I could get any help. Best wishes, Elwira Wachowicz From giannozz at nest.sns.it Mon Jun 30 22:33:08 2003 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 30 Jun 2003 22:33:08 +0200 Subject: [Pw_forum] Size of temproray files In-Reply-To: <3EFBF826.000007.08262@pantene.yandex.ru> References: <00a301c33c38$1751ae50$47c583c8@pion> <200306270945.53198.giannozz@nest.sns.it> <3EFBF826.000007.08262@pantene.yandex.ru> Message-ID: <200306302233.08331.giannozz@nest.sns.it> On Friday 27 June 2003 09:54, Sergei Lisenkov wrote: > I try to calculate sysyem of 124 carbon atoms on 70 CPU Alpha Linux > machine. The code are written the 70 *.wfc files and 70 *.igk files. But > after 10 minutes the size of *.wfc files=>7Gb. My quota is 7 Gb. Is it > possible to reduce the size of these files? the size of wavefunction files is proportional to : number of k-points*number of states*number of plane waves. Try to reduce the number of k-points or the kinetic energy cutoff, or the size of the supercell, or to consider only occupied states (this is the default if the number of states is not specified) Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050509412 Piazza dei Cavalieri 7 Fax: +39/050509417, 050563513 I-56126 Pisa, Italy Office: Lab. NEST, Via della Faggiola 19 From patricia at fcq.unc.edu.ar Mon Jun 30 17:51:21 2003 From: patricia at fcq.unc.edu.ar (Patricia Paredes) Date: Mon, 30 Jun 2003 17:51:21 Subject: [Pw_forum] gold surfaces & convergence Message-ID: <3.0.1.32.20030630175121.00d1a318@mail.fcq.unc.edu.ar> Hi, I'am doing calculations on surface systems. I want to calculate some adsorbates on gold 111 surfaces, but i have convergence troubles with the gold slab. I know from the cluster HF calculations that metals, and in particular gold, is a difficult case. I'd already made some PWSCF calculations with cooper, and didn't have any problem. One of my inputs file is the following... tricapa de Au Au &control calculation='scf' restart_mode='from_scratch', prefix='Au1', pseudo_dir = '/home/pwscf/pseudo/', outdir='/home/patricia/mma/oro/temp/' / &system ibrav=0, nat=12, ntyp=1, ecutwfc = 22.0, ecutrho = 180.0 celldm(1)=9.56 degauss=0.03 / &electrons mixing_ndim = 20 mixing_mode = 'local-TF' conv_thr = 1.0d-10 mixing_beta = 0.25 diagonalization = 'diis' / ATOMIC_SPECIES Au 79 Au_pbe-d-van.UPF ATOMIC_POSITIONS {alat} Au 0.0000000 0.0000000 0.0000000 Au 0.5773502 0.0000000 0.0000000 Au 1.1547005 0.0000000 0.0000000 Au 0.2886751 0.1666667 -0.4714045 Au 0.8660254 0.1666667 -0.4714045 Au 0.5773502 -0.3333334 -0.4714045 Au 0.5773502 0.3333334 -0.9428090 Au 0.2886751 -0.1666667 -0.9428090 Au 0.8660254 -0.1666667 -0.9428090 Au 0.0000000 0.0000000 -1.4142135 Au 0.5773502 0.0000000 -1.4142135 Au 1.1547005 0.0000000 -1.4142135 CELL_PARAMETERS {cubic} 0.8660254 0.5 0.0 0.8660254 -0.5 0.0 0.0000000 0.0 4.0 K_POINTS {automatic} 4 4 1 0 0 0 Can someone gime me some hints to converge this kind of calculations? Thank you!! Patricia.