From adrainzhou at yahoo.com.cn Mon Nov 1 08:22:45 2004 From: adrainzhou at yahoo.com.cn (Adrain Zhou) Date: Mon, 1 Nov 2004 15:22:45 +0800 (CST) Subject: [Pw_forum] How to run pwscf using mpirun in my home directory? Message-ID: <20041101072245.36841.qmail@web15804.mail.cnb.yahoo.com> Dear all, Since LAM-7.0.3 is installed in our cluster, but it doesn't support MPI_REAL8. I have installed LAM7.06 in my home directory. I can compile pwscf and running it at front end successfully. Is there a way to start my calculation from the mpirun(7.06) in my home directory? How to set the lamhost file? Many thanks! Regards, Adrain --------------------------------- Do You Yahoo!? 150??MP3???????????? ??????????????????? 1G??1000??????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041101/0df77d0e/attachment.htm From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Mon Nov 1 10:54:17 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Mon, 1 Nov 2004 10:54:17 +0100 (CET) Subject: [Pw_forum] How to run pwscf using mpirun in my home directory? In-Reply-To: <20041101072245.36841.qmail@web15804.mail.cnb.yahoo.com> Message-ID: On Mon, 1 Nov 2004, Adrain Zhou wrote: AZ> Dear all, AZ> AZ> Since LAM-7.0.3 is installed in our cluster, but it doesn't support AZ> MPI_REAL8. I have installed LAM7.06 in my home directory. I can AZ> compile pwscf and running it at front end successfully. Is there a way AZ> to start my calculation from the mpirun(7.06) in my home directory? AZ> How to set the lamhost file? adrain, to the best of my knowledge there is no difference between lam-7.0.6 and lam-7.0.2 with respect to the MPI_REAL8 data type. both don't have them per se, but if you add -D__LAM to the preprocessor flags when compiling espresso/pwscf it will be worked around. as for starting from your home directory: yes it works, i've been doing it a lot of times. as for how to do this in detail depends very much on the specifics of your cluster, so i can only give a few general hints. please remember: an answer can only be as good as the question. - i assume you want to submit a job from a batch system, so you have to write a small shell script for running the job. - at the beginning of the script you have to reset the PATH, that you lam installation will be before the system installation. - you assemble the list of hosts, that is assigned to your job and put them in a file (e.g. myhosts), one hostname per line. if you have smp nodes then you can list each host name multiple times, if you are supposed to use multiple cpus. - now you run 'lamboot myhosts' you may need to give additional flags or set environment variables. see the lamboot manpage for details. - ... and then run the job, e.g. with: mpirun C $HOME/espresso/bin/pw-mpi.x -npool 2 -in myjob.in > myjob.out - if you don't have a batch system, just put the host names into the hostfile that you are supposed to use. - if you use the PBS batch system, you can just do 'lamboot', as lam-7.x will recognize that it is started under PBS and will query PBS for the assigned hosts and even use the PBS facilities to initialize the lamd processes on the remote machines. regards, axel. AZ> Many thanks! AZ> AZ> Regards, AZ> Adrain AZ> AZ> AZ> AZ> --------------------------------- AZ> Do You Yahoo!? AZ> 150????MP3???????????????????????? AZ> ?????????????????????????????????????? AZ> 1G????1000?????????????????????? -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From adrainzhou at yahoo.com.cn Tue Nov 2 07:25:07 2004 From: adrainzhou at yahoo.com.cn (Adrain Zhou) Date: Tue, 2 Nov 2004 14:25:07 +0800 (CST) Subject: [Pw_forum] Met problem when using LAM-7.1.1 Message-ID: <20041102062507.49866.qmail@web15806.mail.cnb.yahoo.com> Dear all, I have tried pwscf using the latest version LAM-7.1.1. There is no problem for compiling the code. But It seems pwscf is choked at the beginning of running. Pwscf is still running and only output like this Parallel version (MPI) Number of processors in use: 2 R & G space division: nprocp = 2 Ultrasoft (Vanderbilt) Pseudopotentials Current dimensions of program pwscf are: ntypx =10 npk =40000 lmax = 3 nchix = 6 ndim = 2000 nbrx = 8 nqfm = 8 no futher output. Such problems never happen when using LAM7.0.6. Is there anybody else met such problems before? Any comments are highly appreciated. Regards, Adrain --------------------------------- Do You Yahoo!? 150??MP3???????????? ??????????????????? 1G??1000??????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041102/41af00da/attachment.htm From proffess at yandex.ru Tue Nov 2 07:38:39 2004 From: proffess at yandex.ru (Sergey Lisenkov) Date: Tue, 2 Nov 2004 09:38:39 +0300 (MSK) Subject: [Pw_forum] Met problem when using LAM-7.1.1 In-Reply-To: <20041102062507.49866.qmail@web15806.mail.cnb.yahoo.com> References: <20041102062507.49866.qmail@web15806.mail.cnb.yahoo.com> Message-ID: <41872B6F.000023.23420@colgate.yandex.ru> Dear Adrain, It means that code could not read input file. Try to use this combination: mpirun -np .... ./pw.x -input input_file Good luck, Sergey From rjxiao at blem.ac.cn Tue Nov 2 16:55:13 2004 From: rjxiao at blem.ac.cn (rjxiao) Date: Tue, 2 Nov 2004 23:55:13 +0800 Subject: [Pw_forum] a question about LDA+U Message-ID: <20041102235513.9ca6678c@server.blem.ac.cn> Dear Stefano de Gironcoli, Thank you very much. It really does work! By reading your detailed README file,I understand this method further.But I also found a little bug in the espresso-2.1. When plus u is used in the calculation, the projwfc.x can not run successfully.An error "array has already allocated" appears.If plus u is not used,projwfc.x can run without any interruption. I just insert a line "deallocate (swfcatom)" in the projwfc.f90 to slove it.But I think you may have a better way to fix this problem. Thanks a lot. Best regards, Sincerely, Ruijuan Xiao Institute of Physics, Chinese Academy of Sciences From bth20 at cam.ac.uk Wed Nov 3 15:43:13 2004 From: bth20 at cam.ac.uk (B.T. Hope) Date: 03 Nov 2004 14:43:13 +0000 Subject: [Pw_forum] vc-relax Message-ID: Hi there, I am trying to perform a vc-relax calculation but keep getting the error message from read_namelists : error # 1 reading namelist ions Here is my input file: &CONTROL calculation = 'vc-relax' , restart_mode = 'from_scratch' , pseudo_dir = '/scratch/bth/Programs/Espresso/pseudo/' , prefix = 'Co', verbosity = 'high', dt = 100, tstress = .true. tprnfor = .true. / &SYSTEM ibrav = 2, A = 4.738, B = 4.738, C = 7.690, cosAB = -0.5 , cosAC = 0.0 , cosBC = 0.0 , nat = 2, ntyp = 1, ecutwfc = 20 , ecutrho = 80 , starting_magnetization = 1.0, nspin = 2, occupations = 'smearing', degauss = 0.001, / &CELL cell_dynamics = 'damp-pr', / &IONS ion_dynamics = 'damp', tempw = 300.0, / &ELECTRONS diagonalization='$diago' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Co 58.93 Co.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS crystal Co 0.333333333 0.666666667 0.250000000 0 0 0 Co 0.666666667 0.333333333 0.750000000 0 0 0 K_POINTS automatic 2 2 1 1 1 1 Can anyone see what's going wrong? Thanks Ben -- ==================================== Ben Hope C.U.H.&H. Club Captain St. John's College CAMBRIDGE CB2 1TP Tel: - Home: (01223) 578417 - Office: (01223) 760312 - Mobile: 07742 517432 www.cam.ac.uk/societies/cuhh ==================================== From sbraccia at sissa.it Wed Nov 3 15:58:03 2004 From: sbraccia at sissa.it (carlo sbraccia) Date: Wed, 03 Nov 2004 15:58:03 +0100 Subject: [Pw_forum] vc-relax In-Reply-To: References: Message-ID: <1099493882.3060.32.camel@dhpc-5-18.sissa.it> Dear Ben, the order of namelists in the input file is not arbitrary. You must specify namelists in this order (the one given in Doc/INPUT_PW !!!): &CONTROL / &SYSTEM / &ELECTRONS / &IONS <= if needed / &CELL <= if needed / &PHONON <= if needed / &RAMAN <= if needed / carlo On Wed, 2004-11-03 at 15:43, B.T. Hope wrote: > Hi there, > > I am trying to perform a vc-relax calculation but keep getting the error > message > > from read_namelists : error # 1 > reading namelist ions > > > Here is my input file: > > &CONTROL > calculation = 'vc-relax' , > restart_mode = 'from_scratch' , > pseudo_dir = '/scratch/bth/Programs/Espresso/pseudo/' , > prefix = 'Co', > verbosity = 'high', > dt = 100, > tstress = .true. > tprnfor = .true. > > / > &SYSTEM > ibrav = 2, > A = 4.738, > B = 4.738, > C = 7.690, > cosAB = -0.5 , > cosAC = 0.0 , > cosBC = 0.0 , > nat = 2, > ntyp = 1, > ecutwfc = 20 , > ecutrho = 80 , > starting_magnetization = 1.0, > nspin = 2, > occupations = 'smearing', > degauss = 0.001, > / > &CELL > cell_dynamics = 'damp-pr', > / > &IONS > ion_dynamics = 'damp', > tempw = 300.0, > / > &ELECTRONS > diagonalization='$diago' > mixing_mode = 'plain' > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > ATOMIC_SPECIES > Co 58.93 Co.pbe-nd-rrkjus.UPF > ATOMIC_POSITIONS crystal > Co 0.333333333 0.666666667 0.250000000 0 0 0 > Co 0.666666667 0.333333333 0.750000000 0 0 0 > K_POINTS automatic > 2 2 1 1 1 1 > > Can anyone see what's going wrong? > > Thanks > > Ben > From eyvaz_isaev at yahoo.com Wed Nov 3 16:02:31 2004 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 3 Nov 2004 07:02:31 -0800 (PST) Subject: [Pw_forum] vc-relax In-Reply-To: Message-ID: <20041103150231.2172.qmail@web60307.mail.yahoo.com> Hi, What about brackets in ATOMIC_POSITIONS and K_POINTS sections? I.e. they should look like: ATOMIC_POSITIONS {crystal} K_POINTS {automatic} Besides, are you sure about k-points shift? Best regards, Eyvaz. --- "B.T. Hope" wrote: > Hi there, > > I am trying to perform a vc-relax calculation but > keep getting the error > message > > from read_namelists : error # 1 > reading namelist ions > > > Here is my input file: > > &CONTROL > calculation = 'vc-relax' , > restart_mode = 'from_scratch' , > pseudo_dir = > '/scratch/bth/Programs/Espresso/pseudo/' , > prefix = 'Co', > verbosity = 'high', > dt = 100, > tstress = .true. > tprnfor = .true. > > / > &SYSTEM > ibrav = 2, > A = 4.738, > B = 4.738, > C = 7.690, > cosAB = -0.5 , > cosAC = 0.0 , > cosBC = 0.0 , > nat = 2, > ntyp = 1, > ecutwfc = 20 , > ecutrho = 80 , > starting_magnetization = 1.0, > nspin = 2, > occupations = 'smearing', > degauss = 0.001, > / > &CELL > cell_dynamics = 'damp-pr', > / > &IONS > ion_dynamics = 'damp', > tempw = 300.0, > / > &ELECTRONS > diagonalization='$diago' > mixing_mode = 'plain' > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > ATOMIC_SPECIES > Co 58.93 Co.pbe-nd-rrkjus.UPF > ATOMIC_POSITIONS crystal > Co 0.333333333 0.666666667 0.250000000 > 0 0 0 > Co 0.666666667 0.333333333 0.750000000 > 0 0 0 > K_POINTS automatic > 2 2 1 1 1 1 > > Can anyone see what's going wrong? > > Thanks > > Ben > > > -- > ==================================== > Ben Hope > C.U.H.&H. Club Captain > St. John's College > CAMBRIDGE > CB2 1TP > > Tel: - Home: (01223) 578417 > - Office: (01223) 760312 > - Mobile: 07742 517432 > > www.cam.ac.uk/societies/cuhh > ==================================== > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > __________________________________ Do you Yahoo!? Check out the new Yahoo! Front Page. www.yahoo.com From giannozz at nest.sns.it Wed Nov 3 17:34:31 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 3 Nov 2004 17:34:31 +0100 Subject: [Pw_forum] vc-relax In-Reply-To: <20041103150231.2172.qmail@web60307.mail.yahoo.com> References: <20041103150231.2172.qmail@web60307.mail.yahoo.com> Message-ID: <200411031734.31008.giannozz@nest.sns.it> On Wednesday 03 November 2004 16:02, Eyvaz Isaev wrote: > What about brackets in ATOMIC_POSITIONS > and K_POINTS sections? they shouldn't matter, actually Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From yi.kong at gmail.com Thu Nov 4 02:26:20 2004 From: yi.kong at gmail.com (Yi Kong) Date: Thu, 4 Nov 2004 09:26:20 +0800 Subject: [Pw_forum] a question about example06 Message-ID: <8c9dc66c041103172662be6c7a@mail.gmail.com> Dear all, I have followed the example06 to calculate the phonon spectra of B2 FeAl alloy. The pwscf program run and ended normally, but the two files named matdyn.out and phdos.out only have the following messages: %%%%%%%%%%%%%%%%%%%%%%%%%%% from matdyn : error # -1 non-analytic term for q=0 missing ! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% can anyone give me some advice? thanks for your attention! sincerely Y. Kong From degironc at sissa.it Thu Nov 4 10:58:12 2004 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 04 Nov 2004 10:58:12 +0100 Subject: [Pw_forum] a question about LDA+U References: <20041102235513.9ca6678c@server.blem.ac.cn> Message-ID: <4189FD34.7090206@sissa.it> Thank you for spotting the problem, it should be solved now in the CVS version. Best regards, Stefano de Gironcoli rjxiao wrote: >Dear Stefano de Gironcoli, > >Thank you very much. It really does work! By reading your detailed README file,I understand this method further.But I also found a little bug in the espresso-2.1. When plus u is used in the calculation, the projwfc.x can not run successfully.An error "array has already allocated" appears.If plus u is not used,projwfc.x can run without any interruption. I just insert a line "deallocate (swfcatom)" in the projwfc.f90 to slove it.But I think you may have a better way to fix this problem. >Thanks a lot. > > >Best regards, > >Sincerely, >Ruijuan Xiao >Institute of Physics, >Chinese Academy of Sciences > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > > From eyvaz_isaev at yahoo.com Thu Nov 4 13:36:05 2004 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 4 Nov 2004 04:36:05 -0800 (PST) Subject: [Pw_forum] a question about example06 In-Reply-To: <8c9dc66c041103172662be6c7a@mail.gmail.com> Message-ID: <20041104123606.81081.qmail@web60307.mail.yahoo.com> Hi, This is usually connected to splitting of optical phonon modes at the \Gamma-point for polar semiconductors and insulators. I have already done phonon calculations for FeAl and there was no problem (please find attached file). More likely, you consider FeAl as a semiconductor, if you follow the example 6. Try removing epsil=.true., and then adding keywords for the metallic case (occupations,smearing, degauss) in scf.in and nscf.in files. Best regards, Eyvaz. --- Yi Kong wrote: > Dear all, > I have followed the example06 to calculate the > phonon spectra of B2 > FeAl alloy. The pwscf program run and ended > normally, but the two > files named matdyn.out and phdos.out only have the > following messages: > %%%%%%%%%%%%%%%%%%%%%%%%%%% > from matdyn : error # -1 > non-analytic term for q=0 missing ! > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > can anyone give me some advice? > > thanks for your attention! > > sincerely > > Y. Kong > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > __________________________________ Do you Yahoo!? Check out the new Yahoo! Front Page. www.yahoo.com -------------- next part -------------- A non-text attachment was scrubbed... Name: FeAl_phonon_THz_exp.ps Type: application/postscript Size: 20139 bytes Desc: FeAl_phonon_THz_exp.ps Url : /pipermail/attachments/20041104/f1cc69f6/attachment.ps From giannozz at nest.sns.it Thu Nov 4 14:30:34 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 4 Nov 2004 14:30:34 +0100 Subject: [Pw_forum] a question about example06 In-Reply-To: <8c9dc66c041103172662be6c7a@mail.gmail.com> References: <8c9dc66c041103172662be6c7a@mail.gmail.com> Message-ID: <200411041430.34505.giannozz@nest.sns.it> On Thursday 04 November 2004 02:26, Yi Kong wrote: > I have followed the example06 to calculate the phonon spectra of B2 > FeAl alloy. The pwscf program run and ended normally, but the two > files named matdyn.out and phdos.out only have the following messages: > %%%%%%%%%%%%%%%%%%%%%%%%%%% > from matdyn : error # -1 > non-analytic term for q=0 missing ! > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% the meaning and reasons of the message is explained here: http://www.democritos.it/pipermail/pw_forum/2003-May/000320.html http://www.democritos.it/pipermail/pw_forum/2004-August/001249.html http://www.democritos.it/pipermail/pw_forum/2004-August/001250.html Anyway the code does not stop, it goes on. The desired output files should be produced with no LO-TO splitting at q=0 (if any). Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From yi.kong at gmail.com Thu Nov 4 15:44:28 2004 From: yi.kong at gmail.com (Yi Kong) Date: Thu, 4 Nov 2004 22:44:28 +0800 Subject: [Pw_forum] Re: a question about example06 Message-ID: <8c9dc66c041104064416280fb2@mail.gmail.com> Dear Isaevl and others, Thanks for your helpful suggesion. The following is my input file, please help me to find the problem. Thanks a lot for your attention! sincelely Yi Kong ps: # self-consistent calculation cat > AlFe.scf.in << EOF &control calculation='scf' restart_mode='from_scratch', tstress = .true. tprnfor = .true. prefix='AlFe', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav= 1, celldm(1) =5.480, NAT= 2, ntyp= 2, ecutwfc =40.0 ecutrho =400 occupations= 'smearing' degauss=0.02 smearing='mazari-vanderbilt' / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 mixing_mode='local-TF' diagonalization='cg' / ATOMIC_SPECIES Al 26.98 Al.pbe-n-van.UPF Fe 55.845 Fe.pbe-sp-van_mit.UPF ATOMIC_POSITIONS Al 0.00 0.00 0.00 Fe 0.50 0.50 0.50 K_POINTS AUTOMATIC 4 4 4 0 0 0 EOF $ECHO " running the scf calculation...\c" $PW_COMMAND < AlFe.scf.in > AlFe.scf.out $ECHO " done" # phonons cat > AlFe.phG.in << EOF phonons of AlFe at Gamma &inputph tr2_ph=1.0d-12, prefix='AlFe', amass(1)=26.98, amass(2)=55.845, outdir='$TMP_DIR/', fildyn='AlFe.dynG', / 0.0 0.0 0.0 EOF $ECHO " running the phonon calculation at Gamma...\c" $PH_COMMAND < AlFe.phG.in > AlFe.phG.out $ECHO " done" # These are k-points of a (444) uniform grid in the irreducible # Brillouin Zone of the bcc lattice (Gamma is treated separately) /bin/rm AlFe.nscf.out AlFe.ph.out qpoints="0.00,0.00,0.25\ 0.00,0.00,-0.50\ 0.00,0.25,0.25\ 0.00,0.25,-0.50\ 0.00,-0.50,-0.50\ 0.25,0.25,0.25\ 0.25,0.25,-0.50\ 0.25,-0.50,-0.50\ -0.50,-0.50,-0.50" for qpoint in $qpoints ; do # non self-consistent calculation qx=`$ECHO $qpoint | cut -d, -f1` qy=`$ECHO $qpoint | cut -d, -f2` qz=`$ECHO $qpoint | cut -d, -f3` cat > AlFe.nscf.in << EOF &control calculation='phonon' restart_mode='from_scratch', prefix='AlFe', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav= 1, celldm(1) =5.480,nat=2, ntyp= 2, ecutwfc =40.0 ecutrho =400 occupations='smearing' degauss=0.02 smearing='marzari-vanderbilt' / &electrons conv_thr = 1.0d-8 mixing_mode='local-TF' diagonalization='cg' / &phonon xqq(1) = $qx, xqq(2) = $qy, xqq(3) = $qz / ATOMIC_SPECIES Al 26.98 Al.pbe-n-van.UPF Fe 55.845 Fe.pbe-sp-van_mit.UPF ATOMIC_POSITIONS Al 0.00 0.00 0.00 Fe 0.50 0.50 0.50 #K_POINTS AUTOMATIC # 4 4 4 0 0 0 K_POINTS 2 0.00 0.00 0.25 1.00 0.00 0.25 0.25 2.00 EOF $ECHO " running the nscf calculation at q=$qpoint...\c" $PW_COMMAND < AlFe.nscf.in >> AlFe.nscf.out $ECHO " done" # the following line prevents the appearence of a bug with PGI compiler if test -f $TMP_DIR/AlFe.bar ; then /bin/rm $TMP_DIR/AlFe.bar ; fi # phonon calculation cat > AlFe.ph.in << EOF phonons of AlFe at $qpoint &inputph tr2_ph=1.0d-12, prefix='AlFe', amass(1)=26.98, amass(2)=55.845, outdir='$TMP_DIR/', fildyn='dyn.$qpoint' / $qpoint EOF $ECHO " running the phonon calculation at q=$qpoint...\c" $PH_COMMAND < AlFe.ph.in >> AlFe.ph.out $ECHO " done" done cat >q2r.in <C(R)...\c" $Q2R_COMMAND < q2r.in > q2r.out $ECHO "done" cat > matdyn.in << EOF &input asr=.true., amass(1)=26.98, amass(2)=55.845, flfrc='AlFe444.fc', flfrq='AlFe.freq' / 9 0.000 0.0 0.0 0.0 0.125 0.0 0.0 0.0 0.250 0.0 0.0 0.0 0.375 0.0 0.0 0.0 0.500 0.0 0.0 0.0 0.625 0.0 0.0 0.0 0.750 0.0 0.0 0.0 0.875 0.0 0.0 0.0 1.000 0.0 0.0 0.0 EOF $ECHO "recalculating omega(q) from C(R)...\c" $MATDYN_COMMAND < matdyn.in > matdyn.out $ECHO "done" cat >phdos.in < phdos.out $ECHO " done " $ECHO $ECHO "$EXAMPLE_DIR: done" -- ============================= Yi Kong Department of MSE Tsinghua University PR China, 100084 ============================= From adrainzhou at yahoo.com.cn Fri Nov 5 08:14:04 2004 From: adrainzhou at yahoo.com.cn (Adrain Zhou) Date: Fri, 5 Nov 2004 15:14:04 +0800 (CST) Subject: [Pw_forum] How to reduce the size of temporary wavfunction file? Message-ID: <20041105071404.28265.qmail@web15810.mail.cnb.yahoo.com> Dear all, I am running neb calculation, which needs a lot of disk space to store the temporary wavfunction file. Could anybody tell me some tricks on reduce the size of these files? Many thanks! Regards, Adrain --------------------------------- Do You Yahoo!? 150??MP3???????????? ??????????????????? 1G??1000??????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041105/63b35b92/attachment.htm From bth20 at cam.ac.uk Fri Nov 5 09:28:04 2004 From: bth20 at cam.ac.uk (B.T. Hope) Date: 05 Nov 2004 08:28:04 +0000 Subject: [Pw_forum] vc-relax Message-ID: When I run a vc-relax calculation, the output only seems to give atomic force information and not the relaxed positions which is what I am after. Why is this? Ben Hope From giannozz at nest.sns.it Fri Nov 5 09:55:12 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 5 Nov 2004 09:55:12 +0100 Subject: [Pw_forum] vc-relax In-Reply-To: References: Message-ID: <200411050955.13193.giannozz@nest.sns.it> On Friday 05 November 2004 09:28, B.T. Hope wrote: > When I run a vc-relax calculation, the output only seems to give atomic > force information and not the relaxed positions which is what I am after. please try the following patch and report if it works: http://web1.sns.it/~giannozz/pw/pw-2-1-1.patch.gz Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From giannozz at nest.sns.it Fri Nov 5 10:27:56 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 5 Nov 2004 10:27:56 +0100 Subject: [Pw_forum] How to reduce the size of temporary wavfunction file? In-Reply-To: <20041105071404.28265.qmail@web15810.mail.cnb.yahoo.com> References: <20041105071404.28265.qmail@web15810.mail.cnb.yahoo.com> Message-ID: <200411051027.56397.giannozz@nest.sns.it> On Friday 05 November 2004 08:14, Adrain Zhou wrote: > I am running neb calculation, which needs a lot of disk space to store > the temporary wavefunction file. Could anybody tell me some tricks on > reduce the size of these files? Many thanks! the manual contains some information on disk space requirements in the last two sections. If you want to reduce the size of each wavefunction file, you have either to reduce the number of states, or the number of plane waves, or both Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From bth20 at cam.ac.uk Fri Nov 5 12:10:28 2004 From: bth20 at cam.ac.uk (B.T. Hope) Date: 05 Nov 2004 11:10:28 +0000 Subject: [Pw_forum] vc-relax In-Reply-To: <200411050955.13193.giannozz@nest.sns.it> References: <200411050955.13193.giannozz@nest.sns.it> Message-ID: > please try the following patch and report if it works: > http://web1.sns.it/~giannozz/pw/pw-2-1-1.patch.gz It still does not print out atomic position information - just forces. Ben -- ==================================== Ben Hope C.U.H.&H. Club Captain St. John's College CAMBRIDGE CB2 1TP Tel: - Home: (01223) 578417 - Office: (01223) 760312 - Mobile: 07742 517432 www.cam.ac.uk/societies/cuhh ==================================== From giannozz at nest.sns.it Fri Nov 5 12:30:39 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 5 Nov 2004 12:30:39 +0100 Subject: [Pw_forum] vc-relax In-Reply-To: References: <200411050955.13193.giannozz@nest.sns.it> Message-ID: <200411051230.39429.giannozz@nest.sns.it> On Friday 05 November 2004 12:10, B.T. Hope wrote: > > please try the following patch and report if it works: > > http://web1.sns.it/~giannozz/pw/pw-2-1-1.patch.gz > > It still does not print out atomic position information - just forces. please provide a test job and output Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From swblelia at sw.ehu.es Fri Nov 5 16:45:22 2004 From: swblelia at sw.ehu.es (Aritz Leonardo) Date: Fri, 05 Nov 2004 16:45:22 +0100 Subject: [Pw_forum] output writting error Message-ID: <418BA012.3050603@sw.ehu.es> hi! whenever I run a nscf calculation with a dense grid, and if the number of k-points is bigger than 9999, I get the following output: k(9997) = ( -0.2500000 -0.4330127 0.2396111), wk = 0.0003858 k(9998) = ( -0.2500000 -0.3688627 0.2909563), wk = 0.0000000 k(9999) = ( -0.2500000 0.4330127 -0.2396111), wk = 0.0003858 k(****) = ( -0.2500000 0.4971627 -0.1882659), wk = 0.0000000 k(****) = ( 0.2500000 -0.4330127 -0.2396111), wk = 0.0003858 k(****) = ( 0.2500000 -0.3688627 -0.1882659), wk = 0.0000000 k(****) = ( 0.5000000 0.0000000 0.2396111), wk = 0.0003858 Does anybody know WHICH SUBRUTINE CREATES THIS OUTPUT so I can change to a bigger k-integer? Thank you very much From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Fri Nov 5 16:54:09 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Fri, 5 Nov 2004 16:54:09 +0100 (CET) Subject: [Pw_forum] output writting error In-Reply-To: <418BA012.3050603@sw.ehu.es> Message-ID: On Fri, 5 Nov 2004, Aritz Leonardo wrote: hi! did you try using grep? e.g. like this: [40|16:51]~/compile/pwscf-cvs> grep 'wk =' */*.f90 CPV/restart.f90: wk = 1.0d0 CPV/restart.f90: wk = 1.0d0 D3/d3_summary.f90: WRITE( stdout, '(8x,"k(",i5,") = (",3f12.7,"), wk =",f12.7)') ik, & D3/d3_summary.f90: WRITE( stdout, '(8x,"k(",i5,") = (",3f12.7,"), wk =",f12.7)') & FPMD/restart.f90: wk = kp%weight(i) PH/phq_summary.f90: WRITE( stdout, '(8x,"k(",i5,") = (",3f12.7,"), wk =",f12.7)') ik, & PH/phq_summary.f90: WRITE( stdout, '(8x,"k(",i5,") = (",3f12.7,"), wk =",f12.7)') & PP/pw2wan.f90: igwk = 0 PW/summary.f90: WRITE( stdout, '(8x,"k(",i4,") = (",3f12.7,"), wk =",f12.7)') ik, & PW/summary.f90: WRITE( stdout, '(8x,"k(",i4,") = (",3f12.7,"), wk =",f12.7)') & axel. AL> hi! AL> AL> whenever I run a nscf calculation with a dense grid, and if the number AL> of k-points is bigger than 9999, I get the following output: AL> AL> k(9997) = ( -0.2500000 -0.4330127 0.2396111), wk = 0.0003858 AL> k(9998) = ( -0.2500000 -0.3688627 0.2909563), wk = 0.0000000 AL> k(9999) = ( -0.2500000 0.4330127 -0.2396111), wk = 0.0003858 AL> k(****) = ( -0.2500000 0.4971627 -0.1882659), wk = 0.0000000 AL> k(****) = ( 0.2500000 -0.4330127 -0.2396111), wk = 0.0003858 AL> k(****) = ( 0.2500000 -0.3688627 -0.1882659), wk = 0.0000000 AL> k(****) = ( 0.5000000 0.0000000 0.2396111), wk = 0.0003858 AL> AL> Does anybody know WHICH SUBRUTINE CREATES THIS OUTPUT so I can change to AL> a bigger k-integer? AL> AL> Thank you very much AL> AL> _______________________________________________ AL> Pw_forum mailing list AL> Pw_forum at pwscf.org AL> http://www.democritos.it/mailman/listinfo/pw_forum AL> AL> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From swblelia at sw.ehu.es Fri Nov 5 17:09:29 2004 From: swblelia at sw.ehu.es (Aritz Leonardo) Date: Fri, 05 Nov 2004 17:09:29 +0100 Subject: [Pw_forum] output writting error In-Reply-To: References: Message-ID: <418BA5B9.1050901@sw.ehu.es> Thanks a lot! I am going to compile again to see if works Axel Kohlmeyer escribi?: >On Fri, 5 Nov 2004, Aritz Leonardo wrote: > >hi! > >did you try using grep? e.g. like this: > >[40|16:51]~/compile/pwscf-cvs> grep 'wk =' */*.f90 >CPV/restart.f90: wk = 1.0d0 >CPV/restart.f90: wk = 1.0d0 >D3/d3_summary.f90: WRITE( stdout, '(8x,"k(",i5,") = (",3f12.7,"), wk =",f12.7)') ik, & >D3/d3_summary.f90: WRITE( stdout, '(8x,"k(",i5,") = (",3f12.7,"), wk =",f12.7)') & >FPMD/restart.f90: wk = kp%weight(i) >PH/phq_summary.f90: WRITE( stdout, '(8x,"k(",i5,") = (",3f12.7,"), wk =",f12.7)') ik, & >PH/phq_summary.f90: WRITE( stdout, '(8x,"k(",i5,") = (",3f12.7,"), wk =",f12.7)') & >PP/pw2wan.f90: igwk = 0 >PW/summary.f90: WRITE( stdout, '(8x,"k(",i4,") = (",3f12.7,"), wk =",f12.7)') ik, & >PW/summary.f90: WRITE( stdout, '(8x,"k(",i4,") = (",3f12.7,"), wk =",f12.7)') & > > >axel. > > >AL> hi! >AL> >AL> whenever I run a nscf calculation with a dense grid, and if the number >AL> of k-points is bigger than 9999, I get the following output: >AL> >AL> k(9997) = ( -0.2500000 -0.4330127 0.2396111), wk = 0.0003858 >AL> k(9998) = ( -0.2500000 -0.3688627 0.2909563), wk = 0.0000000 >AL> k(9999) = ( -0.2500000 0.4330127 -0.2396111), wk = 0.0003858 >AL> k(****) = ( -0.2500000 0.4971627 -0.1882659), wk = 0.0000000 >AL> k(****) = ( 0.2500000 -0.4330127 -0.2396111), wk = 0.0003858 >AL> k(****) = ( 0.2500000 -0.3688627 -0.1882659), wk = 0.0000000 >AL> k(****) = ( 0.5000000 0.0000000 0.2396111), wk = 0.0003858 >AL> >AL> Does anybody know WHICH SUBRUTINE CREATES THIS OUTPUT so I can change to >AL> a bigger k-integer? >AL> >AL> Thank you very much >AL> >AL> _______________________________________________ >AL> Pw_forum mailing list >AL> Pw_forum at pwscf.org >AL> http://www.democritos.it/mailman/listinfo/pw_forum >AL> >AL> > > > From swblelia at sw.ehu.es Mon Nov 8 11:17:11 2004 From: swblelia at sw.ehu.es (Aritz Leonardo) Date: Mon, 08 Nov 2004 11:17:11 +0100 Subject: [Pw_forum] nscf error Message-ID: <418F47A7.40501@sw.ehu.es> Hello: I am runing an electron-phonon calculation in an ALPHA machine with UNIX 5.1 The thing is that when the second nscf calculation is done with a DENSE automatic grid (24 24 18) The execution stops (without aborting) and produces the following error file: stty: tcgetattr: Not a typewriter forrtl: error (72): floating overflow 0: __FINI_00_remove_gp_range [0x3ff81a6de38] 1: __FINI_00_remove_gp_range [0x3ff81a76a20] 2: __FINI_00_remove_gp_range [0x3ff800d5b90] 3: WFCINIT_K forrtl: error (78): process killed (SIGTERM) 0: __FINI_00_remove_gp_range [0x3ff81a6de38] 1: __FINI_00_remove_gp_range [0x3ff81a772c0] 2: __FINI_00_remove_gp_range [0x3ff800d5b90] 3: __FINI_00_remove_gp_range [0x3ff81ac9bcc] 4: __FINI_00_remove_gp_range [0x3ff81aaf3c0] 5: __FINI_00_remove_gp_range [0x3ff81a6de38] 6: __FINI_00_remove_gp_range [0x3ff81a76a20] 7: __FINI_00_remove_gp_range [0x3ff800d5b90] 8: WFCINIT_K The output file (mg.nscf2.out) where the process stops is: k(10798) = ( -0.3333333 0.7698004 -0.0855754), wk = 0.0000000 k(10799) = ( -0.3333333 0.5773503 -0.2738413), wk = 0.0003858 k(10800) = ( -0.3333333 0.7698004 -0.1198056), wk = 0.0000000 G cutoff = 79.9791 ( 4187 G-vectors) FFT grid: ( 18, 18, 30) nbndx = 24 nbnd = 6 natomwfc = 8 npwx = 549 nelec = 4.00 nkb = 2 ngl = 256 The initial potential is read from file mg.pot Starting wfc are atomic And the subrutine where I think that crasses is the last part of--> wfcinit_k.f90, because I obtain good results for gamma point. I think it has to be something with DEALLOCATE From jcconesa at icp.csic.es Mon Nov 8 14:08:39 2004 From: jcconesa at icp.csic.es (Jose C. Conesa) Date: Mon, 8 Nov 2004 14:08:39 +0100 Subject: [Pw_forum] Further problems with vc-relax Message-ID: <418F7DE7.30761.39159293@localhost> Dear all, After installing espresso 2.1 I found problems with vc-relax: at the difference with the behavior unit cell is not changed, and the stress pressure remains high and unchanged. Indeed, after the first occurrence of "entering subroutine stress" no reference to "Damped Cell-Dynamics Minimization" appeared , which did appear with the similar input file when running pwscf v 2.0! Then I observed the message by Paolo Giannozzi on Nov. 5 stating that vc-relax in espresso does not work, and indicating a patch. I applied the patch and after make all (which seemed to go well), running the same input file the "Damped Cell-Dynamics Minimization" does appear, but now after the second scf cycle is finished and the second cycle of dynamics begins, the following lines ending in error appear: Entering Dynamics; it = 2 time = 0.00484 pico-seconds new lattice vectors (alat unit) : -0.499764095 0.000000478 0.499763968 -0.000000310 0.499764404 0.499764219 -0.499764360 0.499764418 0.000000301 new unit-cell volume = 308.4070 (a.u.)^3 new positions in cryst coord Ga 0.000000000 0.000000000 0.000000000 P 0.250000000 0.250000000 0.250000000 new positions in cart coord (alat unit) Ga -0.000000000 0.000000000 0.000000000 P -0.249882191 0.249882325 0.249882122 Ekin = 0.00012185 Ryd T = 4.3 K Etot = -17.79484077 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from checkallsym : error # 2 not orthogonal operation %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... p0_22507: p4_error: : 0 I attach the input file. Someone can help? Best regards, Jose C. Conesa Instituto de Catalisis y Petroleoquimica, CSIC Campus de Cantoblanco 28049 Madrid - Spain Phone Nr. 34-91-5854766 Fax Nr. 34-91-5854760 -------------- next part -------------- &CONTROL title = 'GaP_opti_PZ Norm-conserving' ,calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = '/home/jcconesa/esprdir/semicond/gap/temp//' , pseudo_dir = '/usr/local/softext/espresso-2.1/pseudoext//' , prefix = 'gapop' , tstress = .true. , tprnfor = .true. ,dt = 100.0 / &SYSTEM ibrav = 2, celldm(1) = 10.73,nat = 2, ntyp = 2, ecutwfc = 16.0 / &ELECTRONS conv_thr = 1.0d-8 ,mixing_beta = 0.7 / &IONS ion_dynamics = 'damp' / &CELL cell_dynamics = 'damp-w' / ATOMIC_SPECIES Ga 69.72000 Ga.pz-bhs.UPF P 30.97000 P.pz-bhs.UPF ATOMIC_POSITIONS crystal Ga 0.00 0.00 0.00 P 0.25 0.25 0.25 K_POINTS automatic 6 6 6 0 0 0 From giannozz at nest.sns.it Mon Nov 8 14:22:39 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 8 Nov 2004 14:22:39 +0100 Subject: [Pw_forum] nscf error In-Reply-To: <418F47A7.40501@sw.ehu.es> References: <418F47A7.40501@sw.ehu.es> Message-ID: <200411081422.39441.giannozz@nest.sns.it> On Monday 08 November 2004 11:17, Aritz Leonardo wrote: > forrtl: error (72): floating overflow > [...] > I think it has to be something with DEALLOCATE ?!? Seriously: try the same job on a different machine; try to understand if the problem is machine-specific or not, and if it is related to the number of k-points (i.e. it appears only when the number of k-points exceeds some limit). In the latter case, compile with boundary check on and verify if something is going out of bounds. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From swblelia at sw.ehu.es Mon Nov 8 14:55:56 2004 From: swblelia at sw.ehu.es (Aritz Leonardo) Date: Mon, 08 Nov 2004 14:55:56 +0100 Subject: [Pw_forum] nscf error In-Reply-To: <200411081422.39441.giannozz@nest.sns.it> References: <418F47A7.40501@sw.ehu.es> <200411081422.39441.giannozz@nest.sns.it> Message-ID: <418F7AEC.9090402@sw.ehu.es> The problem is machine-specific, because I run the same script in a parallel cluster of Linux PC-s and every thing goes OK. I am almost sure that the problems appear whenever the number ok k-points is bigger than 9999. Paolo Giannozzi escribi?: >On Monday 08 November 2004 11:17, Aritz Leonardo wrote: > > > >>forrtl: error (72): floating overflow >>[...] >>I think it has to be something with DEALLOCATE >> >> > >?!? > >Seriously: try the same job on a different machine; >try to understand if the problem is machine-specific >or not, and if it is related to the number of k-points >(i.e. it appears only when the number of k-points >exceeds some limit). In the latter case, compile with >boundary check on and verify if something is going >out of bounds. > >Paolo > > > From giannozz at nest.sns.it Mon Nov 8 17:08:10 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 8 Nov 2004 17:08:10 +0100 Subject: [Pw_forum] nscf error In-Reply-To: <418F7AEC.9090402@sw.ehu.es> References: <418F47A7.40501@sw.ehu.es> <200411081422.39441.giannozz@nest.sns.it> <418F7AEC.9090402@sw.ehu.es> Message-ID: <200411081708.10291.giannozz@nest.sns.it> On Monday 08 November 2004 14:55, Aritz Leonardo wrote: > The problem is machine-specific, because I run the same script > in a parallel cluster of Linux PC-s and every thing goes OK. the former statement does not derive from the latter, unfortunately, but it is anyway an interesting piece of information. Is the error arising in serial or parallel or both cases ? > I am almost sure that the problems appear whenever the number > ok k-points is bigger than 9999. compile with debug and bound check on; run once with 9999 k-points, and then with > 9999. Presently there is a limit of 40000 to the number of k-points, and there are checks that this limit is never reached, but who knows. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From swblelia at sw.ehu.es Mon Nov 8 19:26:51 2004 From: swblelia at sw.ehu.es (Aritz Leonardo) Date: Mon, 08 Nov 2004 19:26:51 +0100 Subject: [Pw_forum] nscf error In-Reply-To: <200411081708.10291.giannozz@nest.sns.it> References: <418F47A7.40501@sw.ehu.es> <200411081422.39441.giannozz@nest.sns.it> <418F7AEC.9090402@sw.ehu.es> <200411081708.10291.giannozz@nest.sns.it> Message-ID: <418FBA6B.1040102@sw.ehu.es> The error arises ONLY in the serial cluster (alpha machines). To compile the program I used: ./configure -enable-shared -disable-parallel The parallel version running on Linux-PC-s works correctly. They both run the same script with the same parameters. I will do what you say Aritz Paolo Giannozzi escribi?: >On Monday 08 November 2004 14:55, Aritz Leonardo wrote: > > > >>The problem is machine-specific, because I run the same script >>in a parallel cluster of Linux PC-s and every thing goes OK. >> >> > >the former statement does not derive from the latter, unfortunately, >but it is anyway an interesting piece of information. Is the error >arising in serial or parallel or both cases ? > > > >>I am almost sure that the problems appear whenever the number >>ok k-points is bigger than 9999. >> >> > >compile with debug and bound check on; run once with 9999 k-points, >and then with > 9999. Presently there is a limit of 40000 to the number >of k-points, and there are checks that this limit is never reached, but >who knows. > >Paolo > > From giannozz at nest.sns.it Tue Nov 9 11:12:02 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 9 Nov 2004 11:12:02 +0100 Subject: [Pw_forum] Further problems with vc-relax In-Reply-To: <418F7DE7.30761.39159293@localhost> References: <418F7DE7.30761.39159293@localhost> Message-ID: <200411091112.02441.giannozz@nest.sns.it> On Monday 08 November 2004 14:08, Jose C. Conesa wrote: > [...] after the second scf cycle is finished and the second cycle > of dynamics begins, the following lines ending in error appear: > [...] > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from checkallsym : error # 2 > not orthogonal operation > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% this error disappears if the cutoff is raised or if the time step is reduced. So maybe it is just the check that is too paranoid. BTW: using variable-cell for crystalline GaP is a waste of time Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From swblelia at sw.ehu.es Tue Nov 9 15:13:20 2004 From: swblelia at sw.ehu.es (Aritz Leonardo) Date: Tue, 09 Nov 2004 15:13:20 +0100 Subject: [Pw_forum] nscf error Message-ID: <4190D080.4050300@sw.ehu.es> hi! Does anybody recognise this error? It happens whenever the nscf calculation needs more than 9999 k-points. The program is compiled in an ALPHA machine with UNIX 5.1 in the following way ./configure -enable-shared -disable-parallel OUTPUT: k(13198) = ( -0.3333333 0.6415003 -0.2007133), wk = 0.0000000 k(13199) = ( -0.3333333 0.5773503 -0.2800650), wk = 0.0003157 k(13200) = ( -0.3333333 0.6415003 -0.2287198), wk = 0.0000000 G cutoff = 79.9791 ( 4187 G-vectors) FFT grid: ( 18, 18, 30) nbndx = 24 nbnd = 6 natomwfc = 8 npwx = 549 nelec = 4.00 nkb = 2 ngl = 256 The initial potential is read from file mg.pot Starting wfc are atomic IOS = 38 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 i/o error in davcio %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... DBX message: enter object file name (default is `a.out'): pw_deb.x dbx version 5.1 Type 'help' for help. pwscf: Source not available (dbx) run pw_deb.x < nscf.in > nscf.out 2 forrtl: severe (28): CLOSE error, unit 10, file "Unknown" 0: __FINI_00_remove_gp_range [0x3ff81a21488] 1: __FINI_00_remove_gp_range [0x3ff81a23140] 2: __FINI_00_remove_gp_range [0x3ff81a62990] 3: errore_ [error.f90: 108, 0x1202726c0] 4: davcio_ [davcio.f90: 47, 0x12007f420] 5: WFCINIT_K [wfcinit.f90: 474, 0x1201d7e70] 6: wfcinit_ [wfcinit.f90: 53, 0x1201d8150] 7: init_run_ [init_run.f90: 43, 0x1200fead8] 8: pwscf_ [pwscf.f90: 78, 0x120031fa4] 9: main [for_main.c: 203, 0x1202724bc] 10: __start [0x120031b98] Program terminated normally From konstantin_kudin at yahoo.com Tue Nov 9 17:08:55 2004 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Tue, 9 Nov 2004 08:08:55 -0800 (PST) Subject: [Pw_forum] Espresso 2.1 - lots of missing 'shmem_include.o' In-Reply-To: <4190D080.4050300@sw.ehu.es> Message-ID: <20041109160855.88831.qmail@web52002.mail.yahoo.com> Hi, This is probably a known issue, but anyway. When I fully compile the 2.1 official package on IBM AIX 4.3, it appears that shmem_include.o is missing in a whole bunch of Makefiles. Here is where it is present: ~/Sesame/2.1>grep shmem */Makefile Modules/Makefile:shmem_include.o \ PW/Makefile:../Modules/shmem_include.o \ pwtools/Makefile:../Modules/shmem_include.o \ All the other ones like PP, PH, Gamma, etc. also seem to need this file to link properly, however, it is not in those Makefiles. Perhaps, the object files from Modules/* could be packed into a library? Then each time things are updated the Makefiles would not need to be edited. Kostya __________________________________ Do you Yahoo!? Check out the new Yahoo! Front Page. www.yahoo.com From giannozz at nest.sns.it Tue Nov 9 17:21:35 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 9 Nov 2004 17:21:35 +0100 Subject: [Pw_forum] nscf error In-Reply-To: <4190D080.4050300@sw.ehu.es> References: <4190D080.4050300@sw.ehu.es> Message-ID: <200411091721.35999.giannozz@nest.sns.it> On Tuesday 09 November 2004 15:13, Aritz Leonardo wrote: > Does anybody recognise this error? It happens whenever the nscf > calculation needs more than 9999 k-points. not enough disk space? > The program is compiled in an ALPHA machine with UNIX 5.1 there is no such thing as "UNIX 5.1" Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From giannozz at nest.sns.it Tue Nov 9 17:28:30 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 9 Nov 2004 17:28:30 +0100 Subject: [Pw_forum] Espresso 2.1 - lots of missing 'shmem_include.o' In-Reply-To: <20041109160855.88831.qmail@web52002.mail.yahoo.com> References: <20041109160855.88831.qmail@web52002.mail.yahoo.com> Message-ID: <200411091728.30592.giannozz@nest.sns.it> On Tuesday 09 November 2004 17:08, Konstantin Kudin wrote: > This is probably a known issue it is > When I fully compile the 2.1 official package on IBM AIX 4.3, > it appears that shmem_include.o is missing in a whole bunch > of Makefiles. please try the following patch and report if it works now: http://web1.sns.it/~giannozz/pw/pw-2-1-1.patch.gz > Perhaps, the object files from Modules/* could be packed into a > library? perhaps, but it has to be tested on many architectures Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From konstantin_kudin at yahoo.com Tue Nov 9 21:35:02 2004 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Tue, 9 Nov 2004 12:35:02 -0800 (PST) Subject: [Pw_forum] Espresso 2.1 - lots of missing 'shmem_include.o' In-Reply-To: <200411091728.30592.giannozz@nest.sns.it> Message-ID: <20041109203502.3465.qmail@web52002.mail.yahoo.com> --- Paolo Giannozzi wrote: > please try the following patch and report if it works now: > http://web1.sns.it/~giannozz/pw/pw-2-1-1.patch.gz The patch works for the most part, but some other object files are missing. Specifically, "../Modules/path_formats.o" is missing from "PWNC " and "pwtools". In addition, "../Modules/parallel_include.o" is missing from "upftools". > > Perhaps, the object files from Modules/* could be packed into a > > library? > > perhaps, but it has to be tested on many architectures On IBM, things seem to proceed almost smoothly if modules are packed into a library file. There are some inconsistencies found with such an approach. Specifically, the Makefile in "Modules" has "path_formats.f90" instead of "path_formats.o". In addition, it also seems to want to have "basic_algebra_routines.o", otherwise, the library linking fails. The addition to Modules/Makefile for creating a library is: all : modules.a modules.a : $(MODULES) $(AR) $(ARFLAGS) $@ $? $(RANLIB) $@ Then this "modules.a" needs to be added to make.sys as in: LIBOBJS = ../Modules/modules.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a Renaming MODULES to MODULES1 in other Makefiles reveals that in a couple of cases (Gamma,atomic) $(MODULES) include some files from the PW directory. Moving those *.o's to other variables fixes the issue such that all the *.x files link properly. Moreover, exactly the same thing can be done to PWOBJS files. These object files are used in many places, so making a library out of them would clean up the Makefiles. That will improve maintainability. Kostya __________________________________ Do you Yahoo!? Check out the new Yahoo! Front Page. www.yahoo.com From jcconesa at icp.csic.es Tue Nov 9 13:03:29 2004 From: jcconesa at icp.csic.es (Jose C.Conesa) Date: Tue, 09 Nov 2004 13:03:29 +0100 Subject: [Pw_forum] Further problems with vc-relax Message-ID: <20041109120329.2A2709A01CE@ciruelo2.csic.es> An embedded and charset-unspecified text was scrubbed... Name: not available Url: /pipermail/attachments/20041109/61268dcf/attachment.txt From adrainzhou at yahoo.com.cn Thu Nov 11 05:43:34 2004 From: adrainzhou at yahoo.com.cn (Adrain Zhou) Date: Thu, 11 Nov 2004 12:43:34 +0800 (CST) Subject: [Pw_forum] temporary file size diffrence on different machine Message-ID: <20041111044334.8896.qmail@web15807.mail.cnb.yahoo.com> Dear all, I run PWSCF on HP-COMPAQ alpha and LINUX cluster respectively. For the same input, the size of the temporary wavefucntion file in linux cluster is four times bigger than that in HP-COMPAQ alpha machine. Could anybody please tell me why the diffrence is so big? Many thanks, Cheers, Adrain --------------------------------- Do You Yahoo!? 150??MP3???????????? ??????????????????? 1G??1000??????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041111/58c71829/attachment.htm From kai_braun at gmx.de Thu Nov 11 23:32:36 2004 From: kai_braun at gmx.de (Kai-Felix Braun) Date: Thu, 11 Nov 2004 23:32:36 +0100 (MET) Subject: [Pw_forum] (no subject) Message-ID: <23402.1100212356@www7.gmx.net> Dear all, I am trying to install pwscf on 1. an intel p4 cluster and 2. pc/xeon. 1. Configuration and compilation just works fine, but by executing I get: running the scf calculation for Si..../run_example: /home/ohu0235/espresso/bin/pw.x: /usr/lib/libc.so.1: bad ELF interpreter: No such file or directory I tried to configure with -enable/disable-shared and also -disable-parallel because of following warnings: /usr/local/intel-8.0-20040716/lib/libifcoremt.a(for_open_proc.o)(.text+0x3c4f): In function `for__compute_filename': : Using 'getpwnam' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking /usr/local/intel-8.0-20040716/lib/libifcoremt.a(for_open_proc.o)(.text+0x3d32): In function `for__compute_filename': : Using 'getpwuid' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking /usr/local/mpich-1.2.6-ib/lib/libmpich.a(pmgr_client_mpirun_rsh.o)(.text+0x22e): In function `pmgr_exchange_addresses': : Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking The mpif90 is working with ifc and worked with other parallel programs. 2. Using the ifc7.1 under red hat 9 on a pc/xeon works except of FPMD/print_out.f90 where it stops with an internal compiler error. I tried as well with ifc 8.1 but the configuration stops at: checking for Fortran 77 compiler default output file name Any comments or suggestions would be kindly appreciated Kai Braun Ohio University -- Geschenkt: 3 Monate GMX ProMail + 3 Top-Spielfilme auf DVD ++ Jetzt kostenlos testen http://www.gmx.net/de/go/mail ++ From giannozz at nest.sns.it Fri Nov 12 22:12:08 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 12 Nov 2004 22:12:08 +0100 Subject: [Pw_forum] temporary file size diffrence on different machine In-Reply-To: <20041111044334.8896.qmail@web15807.mail.cnb.yahoo.com> References: <20041111044334.8896.qmail@web15807.mail.cnb.yahoo.com> Message-ID: <200411122212.08490.giannozz@nest.sns.it> On Thursday 11 November 2004 05:43, Adrain Zhou wrote: > For the same input, the size of the temporary wavefunction file in linux > cluster is four times bigger than that in HP-COMPAQ alpha machine. Intel compiler v.8 or later? the geniuses at Intel keep changing the behavior of their compiler all the time. They used bytes as units for direct access record lenght, now they use 32-bit words, tomorrow maybe quarters of bits. You need the compiler option (which should be automatically added by configure) "-assume byterecl" Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From giannozz at nest.sns.it Sun Nov 14 19:10:53 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sun, 14 Nov 2004 19:10:53 +0100 Subject: [Pw_forum] (no subject) In-Reply-To: <23402.1100212356@www7.gmx.net> References: <23402.1100212356@www7.gmx.net> Message-ID: <200411141910.53498.giannozz@nest.sns.it> On Thursday 11 November 2004 23:32, Kai-Felix Braun wrote: > /home/ohu0235/espresso/bin/pw.x: /usr/lib/libc.so.1: bad ELF interpreter: > No such file or directory libc.so.1 ??? the current version is libc.so.6 . Anyway: "ldd" lists the shared libraries required by an executable. These have to be present (and to be the same, or at least, to be compatible versions) on all processors for parallel execution. > 2. Using the ifc7.1 under red hat 9 on a pc/xeon works except of > FPMD/print_out.f90 where it stops with an internal compiler error. from the manual: Some releases of Intel compiler v. 7 and 8 yield ``Compiler Internal Error''. Update to the last version (presently 7.1.41, 8.0.046 or 8.1.018, respectively), available via Intel Premier support (registration free of charge for Linux): http://developer.intel.com/software/products/support/#premier > I tried as well with ifc 8.1 but the configuration stops at: > checking for Fortran 77 compiler default output file name this means that the compiler is either not working, or not working as expected Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From yanming_ma at hotmail.com Mon Nov 15 03:13:58 2004 From: yanming_ma at hotmail.com (ma Yanming) Date: Mon, 15 Nov 2004 10:13:58 +0800 Subject: [Pw_forum] spin-orbital coupling Message-ID: Dear Pwscf Users, Does anyone know how to calculate the phonons in pwscf with including the spin-orbital coupling for heavy elements? I will highly appreciate your help. Yanming Ma _________________________________________________________________ ?????????????? MSN Messenger: http://messenger.msn.com/cn From xywu at imr.ac.cn Mon Nov 15 10:12:22 2004 From: xywu at imr.ac.cn (xywu) Date: Mon, 15 Nov 2004 10:12:22 Subject: [Pw_forum] help about install pWscf on Redhat9 with ifc 8.0 Message-ID: <20041115030752.0DFD111273A@democritos.sissa.it> Dear all PWscf users, I download the new version (2.1) of the PWscf package. The OS is redhat 9 with ifort 8.0.046 on Intel P4. When ./configure, the following occurs: Checking the system.......i686-pc-linux-gnu Checking architecture......linux32 Check for ifort....ifort checking for Fortran 77 compile default output....a.out Checking whether the fortran77 compiler works.....configure: error:cannot run Fortran 77 compiled programs. If you want to cross compile,use '--host' See 'config.log' for more details. -------------------- In 'config.log', the follows are related to the error: ................. configure:1579: checking for Fortran77 compile default output configure:1582: ifort conftest.f >&5 configure:1585: $? = 0 configure:1631: result: a.out configure:1636: whether the fortran77 compiler works configure:1642: ./a.out ./a.out: error while loading shared libraries:libcxa.so.5:cannot open shared object file :No such file or directory configure:1645: $? =127 configure:1654: error:cannot run Fortran 77 compiled programs. If you want to cross compile,use '--host' See 'config.log' for more details. ............................... --------------------------- I cannot find the file conftest.f in the directory, maybe it's a temp file during configure. Please help me to resolve it, thank you in advance! X.Y.Wu In IMR,CAS From xywu at imr.ac.cn Mon Nov 15 05:30:30 2004 From: xywu at imr.ac.cn (xywu) Date: Mon, 15 Nov 2004 12:30:30 +0800 Subject: [Pw_forum] help about install pWscf on Redhat9 with ifc 8.0 Message-ID: <000801c4cacb$d6cc94c0$338248d2@www> For the encode is GB2312 before, i send the email again. Dear all PWscf users, I download the new version (2.1) of the PWscf package. The OS is redhat 9 with ifort 8.0.046 on Intel P4. When ./configure, the following occurs: Checking the system.......i686-pc-linux-gnu Checking architecture......linux32 Check for ifort....ifort checking for Fortran 77 compile default output....a.out Checking whether the fortran77 compiler works.....configure: error:cannot run Fortran 77 compiled programs. If you want to cross compile,use '--host' See 'config.log' for more details. -------------------- In 'config.log', the follows are related to the error: ................. configure:1579: checking for Fortran77 compile default output configure:1582: ifort conftest.f >&5 configure:1585: $? = 0 configure:1631: result: a.out configure:1636: whether the fortran77 compiler works configure:1642: ./a.out ./a.out: error while loading shared libraries:libcxa.so.5:cannot open shared object file :No such file or directory configure:1645: $? =127 configure:1654: error:cannot run Fortran 77 compiled programs. If you want to cross compile,use '--host' See 'config.log' for more details. ............................... --------------------------- I cannot find the file conftest.f in the directory, maybe it's a temp file during configure. Please help me to resolve it, thank you in advance! X.Y.Wu In IMR,CAS -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041115/acef3e19/attachment.htm From giovanni.cangiani at epfl.ch Mon Nov 15 07:40:57 2004 From: giovanni.cangiani at epfl.ch (Giovanni Cangiani) Date: Mon, 15 Nov 2004 07:40:57 +0100 Subject: [Pw_forum] help about install pWscf on Redhat9 with ifc 8.0 In-Reply-To: <20041115030752.0DFD111273A@democritos.sissa.it> References: <20041115030752.0DFD111273A@democritos.sissa.it> Message-ID: <4E480B62-36D1-11D9-8BB7-000393849986@epfl.ch> The configure scripts finds the compiler but cannot execute the test program because your LD_LIBRARY_PATH is not correctly defined. This variable is defined inside initialization scripts distributed together with the intel compiler. You should execute these scripts at each login (i.e. by sourcing them from a file in the /etc/profile.d directory). Try to . PATH_TO_YOUT_INTEL_INSTALL_DIR/bin/ifortvars.sh ./configure may be it helps. BTW what happens if you write a simple fortran program (hello world) and compile it with ifort ? can you execute it ? giovanni On Nov 15, 2004, at 11:12 AM, xywu wrote: > Dear all PWscf users, > > I download the new version (2.1) of the PWscf package. The OS is > redhat 9 with ifort 8.0.046 on Intel P4. > When ./configure, the following occurs: > Checking the system.......i686-pc-linux-gnu > Checking architecture......linux32 > Check for ifort....ifort > checking for Fortran 77 compile default output....a.out > Checking whether the fortran77 compiler works.....configure: > error:cannot run Fortran 77 compiled programs. > If you want to cross compile,use '--host' > See 'config.log' for more details. > -------------------- > In 'config.log', the follows are related to the error: > ................. > configure:1579: checking for Fortran77 compile default output > configure:1582: ifort conftest.f >&5 > configure:1585: $? = 0 > configure:1631: result: a.out > configure:1636: whether the fortran77 compiler works > configure:1642: ./a.out > ./a.out: error while loading shared libraries:libcxa.so.5:cannot open > shared object file :No such file or directory > configure:1645: $? =127 > configure:1654: error:cannot run Fortran 77 compiled programs. > If you want to cross compile,use '--host' > See 'config.log' for more details. > ............................... > --------------------------- > I cannot find the file conftest.f in the directory, maybe it's a temp > file during configure. > > Please help me to resolve it, thank you in advance! > > > X.Y.Wu > > In IMR,CAS From cazzato at democritos.it Mon Nov 15 09:37:42 2004 From: cazzato at democritos.it (cazzato at democritos.it) Date: Mon, 15 Nov 2004 09:37:42 +0100 Subject: [Pw_forum] Further problems with vc-relax Message-ID: <1100507862.41986ad66f5dd@mail.democritos.it> Scrive "Jose C.Conesa" : > My initial vc-relax run attempt used dt= 4.8 fs and ecutwfc = 16 Ry. The > error kept arising even using dt =0.5 fs and/or ecutwfc = 35 Ry (well, in > the first case it went a few steps further, but crashed anyway before > arriving to time = 4.5 fs). I would say that it is unreasonable that the > program crashes due to these parameter values for a GaP system and using > a standard LDA norm-conserving pseudopotential. Should the program be > changed? Or is the reason for the crash elsewhere? Dear Jos?, running the job you provide, it also occurs to me that pw early stops using the initial guess of dt and ecutwfc. Nevertheless, a slight adjustment of the parameter values, like Paolo Giannozzi suggested, seems to work well. Please check if the input file in attachment runs fine for you Paolo Cazzato ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ -------------- next part -------------- A non-text attachment was scrubbed... Name: GaP.vc-rx.damp-w.in Type: application/octet-stream Size: 664 bytes Desc: not available Url : /pipermail/attachments/20041115/6bea394d/attachment.obj From cjtan at OptimaNumerics.com Mon Nov 15 10:08:56 2004 From: cjtan at OptimaNumerics.com (C J Kenneth Tan -- OptimaNumerics) Date: Mon, 15 Nov 2004 09:08:56 +0000 (UTC) Subject: [Pw_forum] PWscf performance Message-ID: Paolo, Do you know if anyone has compared the performance of PWscf using NETLIB LAPACK vs. MKL on an IA32 or IA64 machine? Thanks a lot! Best wishes, Kenneth Tan ----------------------------------------------------------------------- C. J. Kenneth Tan, Ph.D. OptimaNumerics Ltd. E-mail: cjtan at OptimaNumerics.com Telephone: +44 798 941 7838 Web: http://www.OptimaNumerics.com Facsimile: +44 289 066 3015 ----------------------------------------------------------------------- This e-mail (and any attachments) is confidential and privileged. It is intended only for the addressee(s) stated above. If you are not an addressee, please accept my apologies and please do not use, disseminate, disclose, copy, publish or distribute information in this e-mail nor take any action through knowledge of its contents: to do so is strictly prohibited and may be unlawful. Please inform me that this e-mail has gone astray, and delete this e-mail from your system. Thank you for your co-operation. ----------------------------------------------------------------------- From xywu at imr.ac.cn Tue Nov 16 08:39:45 2004 From: xywu at imr.ac.cn (xywu) Date: Tue, 16 Nov 2004 15:39:45 +0800 Subject: [Pw_forum] Re:help about install pWscf on Redhat9 with ifc 8.0 Message-ID: <000801c4cbaf$71ecb4b0$338248d2@www> Thank you for giovanni. I've edit the .bashrc for ifort. But the following occurs. I've selected BLAS and LAPACK package during RH9 setup, and the FFTW lib is also installed. [root at localhost espresso]# ./configure checking build system type... i686-pc-linux-gnu checking architecture... linux32 checking for mpif90... no checking for ifort... ifort checking for Fortran 77 compiler default output... a.out checking whether the Fortran 77 compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... no checking whether ifort accepts -g... yes checking version of ifort... ifort 8.0 checking for ifort... ifort checking whether we are using the GNU Fortran 77 compiler... no checking whether ifort accepts -g... yes checking for icc... no checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking version of gcc... gcc 3.2.2 setting FFLAGS... -Vaxlib -O2 -tpp6 -assume byterecl setting F90FLAGS... $(FFLAGS) -nomodule setting CFLAGS... -O3 -fomit-frame-pointer checking how to run the C preprocessor... gcc -E setting CPP... cpp setting CPPFLAGS... -P -traditional setting LD... ifort setting LDFLAGS... -Vaxlib -static setting AR... ar setting ARFLAGS... ruv checking whether Fortran files must be preprocessed... no checking for library containing zggev... no in /usr/local/lib: checking for library containing zggev... no in /opt/intel/mkl70/lib/32: checking for library containing zggev... no in /opt/intel/mkl/mkl61/lib/32: checking for library containing zggev... no in /opt/intel/mkl/lib/32: checking for library containing zggev... no in /opt/intel/mkl61/lib/32: checking for library containing zggev... no in /cineca/lib: checking for library containing zggev... no in /cineca/prod/intel/lib: checking for library containing zggev... no in /opt/intel_fc_80/lib: checking for library containing zggev... no checking for library containing fftwnd... -lfftw checking for library containing dgemm... no in /usr/local/lib: checking for library containing dgemm... no in /opt/intel/mkl70/lib/32: checking for library containing dgemm... no in /opt/intel/mkl/mkl61/lib/32: checking for library containing dgemm... no in /opt/intel/mkl/lib/32: checking for library containing dgemm... no in /opt/intel/mkl61/lib/32: checking for library containing dgemm... no in /cineca/lib: checking for library containing dgemm... no in /cineca/prod/intel/lib: checking for library containing dgemm... no in /opt/intel_fc_80/lib: checking for library containing dgemm... no checking for library containing dgemm... no in /usr/local/lib: checking for library containing dgemm... no in /opt/intel/mkl70/lib/32: checking for library containing dgemm... no in /opt/intel/mkl/mkl61/lib/32: checking for library containing dgemm... no in /opt/intel/mkl/lib/32: checking for library containing dgemm... no in /opt/intel/mkl61/lib/32: checking for library containing dgemm... no in /cineca/lib: checking for library containing dgemm... no in /cineca/prod/intel/lib: checking for library containing dgemm... no in /opt/intel_fc_80/lib: checking for library containing dgemm... no checking for library containing zggev... no in /usr/local/lib: checking for library containing zggev... no in /opt/intel/mkl70/lib/32: checking for library containing zggev... no in /opt/intel/mkl/mkl61/lib/32: checking for library containing zggev... no in /opt/intel/mkl/lib/32: checking for library containing zggev... no in /opt/intel/mkl61/lib/32: checking for library containing zggev... no in /cineca/lib: checking for library containing zggev... no in /cineca/prod/intel/lib: checking for library containing zggev... no in /opt/intel_fc_80/lib: checking for library containing zggev... no checking for library containing mpi_init... no setting LIBS... -lfftw checking for library containing mpi_init... (cached) no checking for library containing zggev... (cached) no checking for library containing fftwnd... (cached) -lfftw checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking fftw.h usability... yes checking fftw.h presence... yes checking for fftw.h... yes setting DFLAGS... -D__LINUX -D__INTEL -D__FFTW setting FDFLAGS... $(DFLAGS) setting RANLIB... echo setting MYLIB... blas_and_lapack checking module dependencies... done configure: creating ./config.status config.status: creating make.sys config.status: creating make.rules ----------------------------------------------------------------- PWscf can take advantage of several optimized numerical libraries (essl, fftw, mkl...). This configure script attempts to find them, but may fail if they have been installed in non-standard locations. The following libraries have been found: LIBS= -lfftw If any libraries are missing, you may specify a list of directories to search and retry, as follows: ./configure LIBDIRS="list of directories, separated by spaces" For more information, read the README.INSTALL file or the PWscf manuals. ----------------------------------------------------------------- ---------------------------------------------- WARNING: parallel environment not detected this program will run in single-processor mode ---------------------------------------------- [root at localhost espresso]# make all test -d bin || mkdir bin ( cd Modules; make all ) make[1]: Entering directory `/root/software/pwscf/espresso/Modules' ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c io_global.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c kind.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c parameters.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c atom.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c parallel_include.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c mp.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c shmem_include.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c mp_global.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c recvec.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c stick_base.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c berry_phase.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c basic_algebra_routines.f 90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c constants.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c io_files.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c parser.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c bfgs_module.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c cell_base.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c check_stop.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c clocks.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c control_flags.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c cp_emass.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c fft_types.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c mp_buffers.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c fft_base.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c griddim.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c smallbox.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c uspp.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c cp_fpmd.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c parallel_types.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c descriptors.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c electrons_base.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c energies.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c fft_scalar.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c functionals.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c input_parameters.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c mp_wave.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c io_base.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c ions_base.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c path_formats.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c path_variables.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c supercell.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c path_io_routines.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c path_opt_routines.f90 ifort -Vaxlib -O2 -tpp6 -assume byterecl -I. -I../include -I../Modules -I../PW - I../PH -nomodule -fpp -D__LINUX -D__INTEL -D__FFTW -c path_base.f90 0_9458 fortcom: Severe: **Internal compiler error: internal abort** Please report this error along with the circumstances in which it occurred in a Software Problem Re port. Note: File and line given may not be explicit cause of this error. in file (null), line 0, column 0 compilation aborted for path_base.f90 (code 3) make[1]: *** [path_base.o] Error 3 make[1]: Leaving directory `/root/software/pwscf/espresso/Modules' make: *** [mods] Error 2 [root at localhost espresso]# -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041116/8ed2949e/attachment.htm From giannozz at nest.sns.it Tue Nov 16 09:11:03 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 16 Nov 2004 09:11:03 +0100 Subject: [Pw_forum] Re:help about install pWscf on Redhat9 with ifc 8.0 In-Reply-To: <000801c4cbaf$71ecb4b0$338248d2@www> References: <000801c4cbaf$71ecb4b0$338248d2@www> Message-ID: <200411160911.03745.giannozz@nest.sns.it> On Tuesday 16 November 2004 08:39, xywu wrote: > fortcom: Severe: **Internal compiler error: internal abort** Please report > this error along with the circumstances in which it occurred in a Software > Problem Re port. Note: File and line given may not be explicit cause of > this error. in file (null), line 0, column 0 http://www.democritos.it/pipermail/pw_forum/2004-November/001548.html -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From jcconesa at icp.csic.es Tue Nov 16 13:46:23 2004 From: jcconesa at icp.csic.es (Jose C. Conesa) Date: Tue, 16 Nov 2004 13:46:23 +0100 Subject: [Pw_forum] error in phonon calculation Message-ID: <419A04AF.10492.6236AD96@localhost> Dear all, I tried to run a phonon calculation. When launching the ph.x program (after successfully completing the previous steps) I obtain the following output: .............(start of output) ......... Program PHONON v.2.0 starts ... Today is 16Nov2004 at 11:24:56 Parallel version (MPI) Number of processors in use: 4 R & G space division: nprocp = 4 Ultrasoft (Vanderbilt) Pseudopotentials Planes per process (thick) : nr3 = 30 npp = 8 ncplane = 900 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 8 166 3224 8 166 3224 48 502 2 8 167 3225 8 167 3225 48 502 3 7 166 3222 7 166 3222 48 502 4 7 166 3222 7 166 3222 49 501 0 30 665 12893 30 665 12893 193 2007 nbndx = 38 nbnd = 30 natomwfc = 38 npwx = 409 nelec = 41.00 nkb = 71 ngl = 178 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from phq_setup : error # -1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% occupation numbers probably wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from phq_setup : error # -1 occupation numbers probably wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from phq_setup : error # -1 occupation numbers probably wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from phq_setup : error # -1 occupation numbers probably wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% (TITLE from input file) crystal is bravais-lattice index = 12 lattice parameter (a_0) = 10.2030 a.u. ... ..................(ouput continues further)............... The subsequent operation seems to go ahead without errors. Can someone tell me if these warning messages on occupation numbers imply that the calculation will not give good phonon results? Thanks, Jose C. Conesa Instituto de Catalisis y Petroleoquimica, CSIC Campus de Cantoblanco 28049 Madrid - Spain Phone Nr. 34-91-5854766 Fax Nr. 34-91-5854760 From eyvaz_isaev at yahoo.com Tue Nov 16 14:05:56 2004 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 16 Nov 2004 05:05:56 -0800 (PST) Subject: [Pw_forum] error in phonon calculation In-Reply-To: <419A04AF.10492.6236AD96@localhost> Message-ID: <20041116130556.5112.qmail@web60307.mail.yahoo.com> Hi, More likely, in self-consistent calculations you used occupations='tetrahedra' option. If so, you have to change to occupations='smearing' keyword. In this case, definitely, you should also add smearing='m-p' (or other) and degauss=XX keywords. Hope it helps. Best regrds, Eyvaz. --- "Jose C. Conesa" wrote: > Dear all, > I tried to run a phonon calculation. When launching > the ph.x program (after successfully > completing the previous steps) I obtain the > following output: > > .............(start of output) ......... > > Program PHONON v.2.0 starts ... > Today is 16Nov2004 at 11:24:56 > > Parallel version (MPI) > Number of processors in use: 4 > R & G space division: nprocp = 4 > > > Ultrasoft (Vanderbilt) Pseudopotentials > > Planes per process (thick) : nr3 = 30 npp = 8 > ncplane = 900 > > Proc/ planes cols G planes cols G > columns G > Pool (dense grid) (smooth grid) > (wavefct grid) > 1 8 166 3224 8 166 3224 48 > 502 > 2 8 167 3225 8 167 3225 48 > 502 > 3 7 166 3222 7 166 3222 48 > 502 > 4 7 166 3222 7 166 3222 49 > 501 > 0 30 665 12893 30 665 12893 193 > 2007 > > > nbndx = 38 nbnd = 30 natomwfc = > 38 npwx = 409 > nelec = 41.00 nkb = 71 ngl = > 178 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from phq_setup : error # -1 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > occupation numbers probably wrong > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from phq_setup : error # -1 > occupation numbers probably wrong > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from phq_setup : error # -1 > occupation numbers probably wrong > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from phq_setup : error # -1 > occupation numbers probably wrong > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > (TITLE from input file) > > crystal is > > bravais-lattice index = 12 > lattice parameter (a_0) = 10.2030 a.u. > ... > ..................(ouput continues > further)............... > > The subsequent operation seems to go ahead without > errors. Can someone tell me if these > warning messages on occupation numbers imply that > the calculation will not give good phonon > results? > Thanks, > Jose C. Conesa > Instituto de Catalisis y Petroleoquimica, CSIC > Campus de Cantoblanco > 28049 Madrid - Spain > Phone Nr. 34-91-5854766 > Fax Nr. 34-91-5854760 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > __________________________________ Do you Yahoo!? The all-new My Yahoo! - Get yours free! http://my.yahoo.com From degironc at sissa.it Tue Nov 16 14:02:55 2004 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 16 Nov 2004 14:02:55 +0100 Subject: [Pw_forum] error in phonon calculation References: <419A04AF.10492.6236AD96@localhost> Message-ID: <4199FA7F.9020109@sissa.it> The message you mention should come out when performing a calculation with lsda flag on and fixed occupation . is this your situation ? Since in lsda one should allow spin up and down state to find their selfconsistent value this choice is probably wrong. However if you know that what you are doing is right, go ahead. stefano Jose C. Conesa wrote: >Dear all, >I tried to run a phonon calculation. When launching the ph.x program (after successfully >completing the previous steps) I obtain the following output: > > >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from phq_setup : error # -1 > > >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > From eyvaz_isaev at yahoo.com Tue Nov 16 14:22:25 2004 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 16 Nov 2004 05:22:25 -0800 (PST) Subject: [Pw_forum] error in phonon calculation In-Reply-To: <419A04AF.10492.6236AD96@localhost> Message-ID: <20041116132225.50308.qmail@web60305.mail.yahoo.com> I am sorry. Stefano's reply seems more appropriate. Bests, Eyvaz. --- "Jose C. Conesa" wrote: > Dear all, > I tried to run a phonon calculation. When launching > the ph.x program (after successfully > completing the previous steps) I obtain the > following output: > > .............(start of output) ......... > > Program PHONON v.2.0 starts ... > Today is 16Nov2004 at 11:24:56 > > Parallel version (MPI) > Number of processors in use: 4 > R & G space division: nprocp = 4 > > > Ultrasoft (Vanderbilt) Pseudopotentials > > Planes per process (thick) : nr3 = 30 npp = 8 > ncplane = 900 > > Proc/ planes cols G planes cols G > columns G > Pool (dense grid) (smooth grid) > (wavefct grid) > 1 8 166 3224 8 166 3224 48 > 502 > 2 8 167 3225 8 167 3225 48 > 502 > 3 7 166 3222 7 166 3222 48 > 502 > 4 7 166 3222 7 166 3222 49 > 501 > 0 30 665 12893 30 665 12893 193 > 2007 > > > nbndx = 38 nbnd = 30 natomwfc = > 38 npwx = 409 > nelec = 41.00 nkb = 71 ngl = > 178 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from phq_setup : error # -1 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > occupation numbers probably wrong > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from phq_setup : error # -1 > occupation numbers probably wrong > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from phq_setup : error # -1 > occupation numbers probably wrong > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from phq_setup : error # -1 > occupation numbers probably wrong > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > (TITLE from input file) > > crystal is > > bravais-lattice index = 12 > lattice parameter (a_0) = 10.2030 a.u. > ... > ..................(ouput continues > further)............... > > The subsequent operation seems to go ahead without > errors. Can someone tell me if these > warning messages on occupation numbers imply that > the calculation will not give good phonon > results? > Thanks, > Jose C. Conesa > Instituto de Catalisis y Petroleoquimica, CSIC > Campus de Cantoblanco > 28049 Madrid - Spain > Phone Nr. 34-91-5854766 > Fax Nr. 34-91-5854760 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > __________________________________ Do you Yahoo!? The all-new My Yahoo! - Get yours free! http://my.yahoo.com From giannozz at nest.sns.it Tue Nov 16 14:42:19 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 16 Nov 2004 14:42:19 +0100 Subject: [Pw_forum] error in phonon calculation In-Reply-To: <4199FA7F.9020109@sissa.it> References: <419A04AF.10492.6236AD96@localhost> <4199FA7F.9020109@sissa.it> Message-ID: <200411161442.19981.giannozz@nest.sns.it> On Tuesday 16 November 2004 14:02, Stefano de Gironcoli wrote: > The message you mention should come out when performing a > calculation with lsda flag on and fixed occupation actually this message shows up also in a spin-polarized calculation with free occupations but no smearing or tetrahedron technique. This case used to be forbidden in the self-consistent calculation, but I think it is allowed now, so the message might be obsolete Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From tim_teatro at rogers.com Tue Nov 16 23:06:10 2004 From: tim_teatro at rogers.com (Timothy A.V. Teatro) Date: Tue, 16 Nov 2004 17:06:10 -0500 Subject: [Pw_forum] Driving me nuts! In-Reply-To: <20041111063656.8635.28075.Mailman@democritos.sissa.it> Message-ID: <000101c4cc28$7bbcdeb0$1d02a8c0@oncampus.local> Hi. I'm really sorry to ask a question like this. I wrote this input file a while ago. I have been fiddling with it for a while now, and I can't figure out why I can't get two simple little silicon atoms to move! I am accustomed to using PWscf, but I am not trying to switch to FPMD for more accurate dynamics. But I cannot get any dynamics out of this thing! Even when I try putting the Si atoms very close to each other, where the forces should be enormous I can't get them to move. Thanks a lot for looking at this. I'm sure I did something very silly, which is going to embarrass me later. Here is a verbatim listing of the input script: #!/bin/sh PW_ROOT=$HOME/cpmd/FPMD PSEUDO=$HOME/cpmd/pseudo TMP_DIR=$HOME/cpmd/tmp0 if [ ! -d results ]; then mkdir results fi cd results rm -rf $TMP_DIR/* cat > sih.cp1.in << EOF &CONTROL title = ' Silicon ', calculation = 'cp', restart_mode = 'from_scratch', pseudo_dir = '$PSEUDO/', outdir='$TMP_DIR/', ndr = 51, ndw = 51, nstep = 50, iprint = 10, isave = 100, tstress = .TRUE., tprnfor = .TRUE., dt = 5.0d0, etot_conv_thr = 1.d-9, ekin_conv_thr = 1.d-4, prefix = 'si' / &SYSTEM ibrav = 1, celldm = 10.61, nat = 2, ntyp = 1, nbnd = 4, nelec = 8, ecutwfc = 8.0, xc_type = 'BLYP' / &ELECTRONS emass = 400.d0, emass_cutoff = 2.5d0, orthogonalization = 'ortho', ortho_eps = 5.d-8, ortho_max = 15, electron_dynamics = 'sd', ! electron_damping = 0.3, electron_velocities = 'zero', electron_temperature = 'not_controlled', / &IONS ion_dynamics = 'verlet', ion_damping = 0.2, ion_radius(1) = 0.8d0, ion_radius(2) = 0.8d0, ion_velocities = 'zero', ion_temperature = 'nose', tempw = 1000, fnosep = 1.2, tolp=100, ion_nstepe = 10 / &CELL cell_dynamics = 'pr', cell_velocities = 'zero', press = 0.0d0, / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF 4 ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.00 0.00 0.10 K_POINTS 1 0.0 0.0 0.0 1.0 EOF $PW_ROOT/par2.x < sih.cp1.in > Si.md64H.out From aaron at nemo.physics.ncsu.edu Wed Nov 17 12:05:23 2004 From: aaron at nemo.physics.ncsu.edu (aaron at nemo.physics.ncsu.edu) Date: Wed, 17 Nov 2004 06:05:23 -0500 (EST) Subject: [Pw_forum] Driving me nuts! In-Reply-To: <000101c4cc28$7bbcdeb0$1d02a8c0@oncampus.local> Message-ID: Hi Timothy, Just some thoughts on your job... Have you tried a more physical distance between the two Si atoms? It can be very difficult to optimize the electronic wavefunction when they are almost right on top of each other. Also from what I understand, the procedure can be to fix the atoms, optimize the electronic wavefunction (e-kinetic energy goes to approximately zero) and then begin with moving the ions (in fact this becomes more than one input file). Finally if you can show your output we can more correctly diagnose your problem(s). I hope this helps, Aaron On Tue, 16 Nov 2004, Timothy A.V. Teatro wrote: > Hi. I'm really sorry to ask a question like this. I wrote this input > file a while ago. I have been fiddling with it for a while now, and I > can't figure out why I can't get two simple little silicon atoms to > move! I am accustomed to using PWscf, but I am not trying to switch to > FPMD for more accurate dynamics. But I cannot get any dynamics out of > this thing! Even when I try putting the Si atoms very close to each > other, where the forces should be enormous I can't get them to move. > > Thanks a lot for looking at this. I'm sure I did something very silly, > which is going to embarrass me later. > > Here is a verbatim listing of the input script: > > #!/bin/sh > > PW_ROOT=$HOME/cpmd/FPMD > PSEUDO=$HOME/cpmd/pseudo > TMP_DIR=$HOME/cpmd/tmp0 > > if [ ! -d results ]; then > mkdir results > fi > cd results > > rm -rf $TMP_DIR/* > > cat > sih.cp1.in << EOF > > &CONTROL > title = ' Silicon ', > calculation = 'cp', > restart_mode = 'from_scratch', > pseudo_dir = '$PSEUDO/', > outdir='$TMP_DIR/', > ndr = 51, > ndw = 51, > nstep = 50, > iprint = 10, > isave = 100, > tstress = .TRUE., > tprnfor = .TRUE., > dt = 5.0d0, > etot_conv_thr = 1.d-9, > ekin_conv_thr = 1.d-4, > prefix = 'si' > / > > &SYSTEM > ibrav = 1, > celldm = 10.61, > nat = 2, > ntyp = 1, > nbnd = 4, > nelec = 8, > ecutwfc = 8.0, > xc_type = 'BLYP' > / > > &ELECTRONS > emass = 400.d0, > emass_cutoff = 2.5d0, > orthogonalization = 'ortho', > ortho_eps = 5.d-8, > ortho_max = 15, > electron_dynamics = 'sd', > ! electron_damping = 0.3, > electron_velocities = 'zero', > electron_temperature = 'not_controlled', > / > > &IONS > ion_dynamics = 'verlet', > ion_damping = 0.2, > ion_radius(1) = 0.8d0, > ion_radius(2) = 0.8d0, > ion_velocities = 'zero', > ion_temperature = 'nose', > tempw = 1000, > fnosep = 1.2, > tolp=100, > ion_nstepe = 10 > / > > &CELL > cell_dynamics = 'pr', > cell_velocities = 'zero', > press = 0.0d0, > / > > ATOMIC_SPECIES > Si 28.086 Si.vbc.UPF 4 > > ATOMIC_POSITIONS > Si 0.00 0.00 0.00 > Si 0.00 0.00 0.10 > > K_POINTS > 1 > 0.0 0.0 0.0 1.0 > EOF > > $PW_ROOT/par2.x < sih.cp1.in > Si.md64H.out > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at nest.sns.it Wed Nov 17 18:24:36 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 17 Nov 2004 18:24:36 +0100 Subject: [Pw_forum] error in phonon calculation In-Reply-To: <419B5382.4237.675293EE@localhost> References: <419B5382.4237.675293EE@localhost> Message-ID: <200411171824.36444.giannozz@nest.sns.it> On Wednesday 17 November 2004 13:34, Jose C. Conesa wrote: > Concerning the answers by Stefano, Paolo and Eyvaz to my question: > > From Stefano: > > The message you mention should come out when performing a calculation > > with lsda flag on and fixed occupation . is this your situation ? > > No. The system is indeed spin-polarized (nspin = 2, > starting_magnetization(1) = 1) and uses lda, but I have > "occupations = 'tetrahedra' " are you sure? Phonon calculation in metals with the tetrahedron method is not implemented: the code stops immediately if you try. Only smearing is implemented. > From Paolo: > >actually this message shows up also in a spin-polarized calculation > > with free occupations but no smearing or tetrahedron technique. > > This case used to be forbidden in the self-consistent calculation, > > but I think it is allowed now, so the message might be obsolete. > > Well, then: should I disregard the message, and rely on the calculation > (from this point of view) after all? I am not sure, but it seems to me that in a spin-polarized system the number of occupied bands might be incorrectly computed by the phonon code in that particular case Please do not post to pw_forum-admin at pwscf.org Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From alessandra.satta at dsf.unica.it Thu Nov 18 13:36:36 2004 From: alessandra.satta at dsf.unica.it (Alessandra Satta) Date: Thu, 18 Nov 2004 13:36:36 +0100 Subject: [Pw_forum] efermi? In-Reply-To: <1099493882.3060.32.camel@dhpc-5-18.sissa.it> References: <1099493882.3060.32.camel@dhpc-5-18.sissa.it> Message-ID: <419C9754.7070505@dsf.unica.it> To whom has already got this trouble and found out the solution: To compute the Fermi energy in a relaxed doped silicon (i.e. odd number of elects.) I perform a "scf" calculation whith both "gaussian smearing" and "tetrahedra" methods. It happens that when the run accidentally stops before the convergence is reached (because the simulation cell is big and the computing time per run is limited) the next run in the "restart" mode stops in the second case (tetrahedra) with the message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from efermit : error # 1 unexpected error %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I figured out that in the restart mode the eigenvalues "et (nbnd, nks)" calculated in the previous run do NOT arrive to this routine, since they result to be 0.000000000000000E+000 and the sumkt is, as a consequence, also zero. The check-point-"if"-condition is then satisfied calling the error. All this, is also verified in the first case, using the gaussian smearing. It does not stop only because the first guess of Eup and Elw is calculated adding/subtracting 2*degauss. Degauss is 'known' and the calculation goes on. In conclusion: If the scf calculation is performed in one-shot the fermi energy is correct. On the contrary, I'm not sure. In a quick&dirty solution I can comment the "if-line" but this is not the right way.... Hope to have made myself clear..... Did someone of you run into such a problem? thanks a lot.... alessandra P.S.: I refer to the ESPRESSO package. -- Alessandra Satta Dipartimento di Fisica dell'Universit? di Cagliari Cittadella Universitaria - SP Monserrato-Sestu Km. 0,700 09042 - Monserrato (Ca) Tel.: +39 070 675 4847 Fax : +39 070 510171 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041118/2b00efbe/attachment.htm From fabris at democritos.it Thu Nov 18 13:43:44 2004 From: fabris at democritos.it (Stefano Fabris) Date: Thu, 18 Nov 2004 13:43:44 +0100 Subject: [Pw_forum] efermi? In-Reply-To: <419C9754.7070505@dsf.unica.it> References: <1099493882.3060.32.camel@dhpc-5-18.sissa.it> <419C9754.7070505@dsf.unica.it> Message-ID: <419C9900.6000803@democritos.it> > It happens that when the run accidentally stops before > the convergence is reached (because the simulation cell is big and > the computing time per run is limited) A possible solution to your problem could be to add the instruction "max_seconds = n" in the input file. This force the program to exit after n seconds, writing all the files it needs for restarting (provided that n is shorter than the time limit for you run ...). Stefano. -- ----------------------------------------------------------------- Stefano Fabris fabris at democritos.it INFM DEMOCRITOS - SISSA tel: +39 040 3787405 via Beirut 2-4, I-34014 Trieste, Italy fax: +39 040 3787528 ------------------------------------------------------------------ From alessandra.satta at dsf.unica.it Thu Nov 18 16:22:48 2004 From: alessandra.satta at dsf.unica.it (Alessandra Satta) Date: Thu, 18 Nov 2004 16:22:48 +0100 Subject: [Pw_forum] efermi? In-Reply-To: <419C9900.6000803@democritos.it> References: <1099493882.3060.32.camel@dhpc-5-18.sissa.it> <419C9754.7070505@dsf.unica.it> <419C9900.6000803@democritos.it> Message-ID: <419CBE48.9010503@dsf.unica.it> Thank you, Stefano, for your answer,. Unfortunately, it does not work. It is a matter of missing variables in the restart files ( .rho?). I should find out how to let the code write them down. alessandra Stefano Fabris wrote: > >> It happens that when the run accidentally stops before >> the convergence is reached (because the simulation cell is big and >> the computing time per run is limited) > > > A possible solution to your problem could be to add the instruction > "max_seconds = n" in the input file. This force the program to exit > after n seconds, writing all the files it needs for restarting > (provided that n is shorter than the time limit for you run ...). > > Stefano. > > -- Alessandra Satta Dipartimento di Fisica dell'Universit? di Cagliari Cittadella Universitaria - SP Monserrato-Sestu Km. 0,700 09042 - Monserrato (Ca) Tel.: +39 070 675 4847 Fax : +39 070 510171 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041118/2bd9b808/attachment.htm From nakhmans at physics.rutgers.edu Thu Nov 18 22:29:41 2004 From: nakhmans at physics.rutgers.edu (Serge Nakhmanson) Date: Thu, 18 Nov 2004 16:29:41 -0500 Subject: [Pw_forum] Problem with bfgs relaxation Message-ID: <419D1445.9070104@physics.rutgers.edu> Dear All, I am trying to relax a small (BaTiO_3)_1/(CaTiO_3)_1 superlattice with new bfgs routine (PWscf in ESPRESSO 2.1). However, the routine seems to completely ignore the force convergence threshold (forc_conv_thr) in my input file and claims that it has converged even when forces in the system are large. Here is my input file: ********************************** &CONTROL title = '(BaTiO_3)_1/(CaTiO_3)_1 superlattice' , calculation = 'relax' , restart_mode = 'from_scratch' , outdir = './', pseudo_dir = '/home/nakhmans/Codes/PWSCF/PSP/Ultrasoft/USPP_UPF/' , prefix = 'B1C1.c_fit' , verbosity = 'high', tstress = .true., nstep = 100, etot_conv_thr = 5.e-5, forc_conv_thr = 4.e-5, / &SYSTEM ibrav = 6, celldm(1) = 7.29064, celldm(3) = 2.00, nat = 10, ntyp = 4, ecutwfc = 25, ecutrho = 225, / &ELECTRONS conv_thr = 1.e-8 , startingpot = 'atomic' , startingwfc = 'atomic' , mixing_mode = 'plain' , mixing_beta = 0.7 , / &IONS ion_dynamics = 'bfgs', / ATOMIC_SPECIES Ba 137.32700 056-Ba-ca-sp-vgrp.uspp.UPF Ca 40.07800 020-Ca-ca-sp-vgrp.uspp.UPF Ti 47.86700 022-Ti-ca-sp-vgrp.uspp.UPF O 16.00000 008-O-ca--vgrp.uspp.UPF ATOMIC_POSITIONS alat Ba 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.500000000 O 0.000000000 0.500000000 0.500000000 O 0.500000000 0.000000000 0.500000000 O 0.500000000 0.500000000 0.000000000 Ca 0.000000000 0.000000000 1.005000000 Ti 0.500000000 0.500000000 1.500000000 O 0.000000000 0.500000000 1.500000000 O 0.500000000 0.000000000 1.500000000 O 0.500000000 0.500000000 1.000000000 K_POINTS automatic 6 6 3 0 0 0 ********************************* A small change in the Ca atom position along Z is to enforce P4mm symmetry during relaxation. Here's what I get in the output: *********************************** ! total energy = -552.10767780 ryd estimated scf accuracy < 7.8E-10 ryd band energy sum = -26.93676693 ryd one-electron contribution = -158.68930900 ryd hartree contribution = 123.78105246 ryd xc contribution = -88.35663862 ryd ewald contribution = -428.84278264 ryd convergence has been achieved Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000000 0.00000000 0.00111050 atom 2 type 3 force = 0.00000000 0.00000000 0.00011367 atom 3 type 4 force = 0.00000000 0.00000000 -0.00017387 atom 4 type 4 force = 0.00000000 0.00000000 -0.00017387 atom 5 type 4 force = 0.00000000 0.00000000 -0.00064692 atom 6 type 2 force = 0.00000000 0.00000000 0.00067175 atom 7 type 3 force = 0.00000000 0.00000000 -0.00046149 atom 8 type 4 force = 0.00000000 0.00000000 0.00008750 atom 9 type 4 force = 0.00000000 0.00000000 0.00008750 atom 10 type 4 force = 0.00000000 0.00000000 -0.00061476 Total force = 0.001668 Total SCF correction = 0.000063 entering subroutine stress ... total stress (ryd/bohr**3) (kbar) P= -26.63 -0.00016828 0.00000000 0.00000000 -24.75 0.00 0.00 0.00000000 -0.00016828 0.00000000 0.00 -24.75 0.00 0.00000000 0.00000000 -0.00020644 0.00 0.00 -30.37 [ ... cut ... ] number of scf cycles = 38 number of bfgs steps = 23 energy old = -552.1076788015 ryd energy new = -552.1076778004 ryd CASE: energy_new > energy_old new trust radius = 0.0000000818 bohr bfgs converged in 38 scf cycles and 23 bfgs steps End of BFGS geometry calculation Final energy = -552.1076788015 ryd Saving the approximate inverse hessian [ ... cut ... ] ************************** How could this thing be converged if total force is 0.001668 and I asked for < 0.00004? Here's grep on "Total force" in my output file: ************************** Total force = 0.058112 Total SCF correction = 0.000056 Total force = 0.124018 Total SCF correction = 0.000195 Total force = 0.156460 Total SCF correction = 0.000459 Total force = 0.016897 Total SCF correction = 0.000249 Total force = 0.007370 Total SCF correction = 0.000379 Total force = 0.000659 Total SCF correction = 0.000384 Total force = 0.000629 Total SCF correction = 0.000263 Total force = 0.000587 Total SCF correction = 0.000093 Total force = 0.000705 Total SCF correction = 0.000024 Total force = 0.001393 Total SCF correction = 0.000055 Total force = 0.001880 Total SCF correction = 0.000052 Total force = 0.001596 Total SCF correction = 0.000088 Total force = 0.002010 Total SCF correction = 0.000037 Total force = 0.001721 Total SCF correction = 0.000059 Total force = 0.002024 Total SCF correction = 0.000051 Total force = 0.001842 Total SCF correction = 0.000032 Total force = 0.001772 Total SCF correction = 0.000145 Total force = 0.001728 Total SCF correction = 0.000180 Total force = 0.001743 Total SCF correction = 0.000130 Total force = 0.001733 Total SCF correction = 0.000094 Total force = 0.001745 Total SCF correction = 0.000154 Total force = 0.001726 Total SCF correction = 0.000095 Total force = 0.001744 Total SCF correction = 0.000144 Total force = 0.001718 Total SCF correction = 0.000101 Total force = 0.001677 Total SCF correction = 0.000142 Total force = 0.001705 Total SCF correction = 0.000066 Total force = 0.001675 Total SCF correction = 0.000196 Total force = 0.001706 Total SCF correction = 0.000082 Total force = 0.001674 Total SCF correction = 0.000058 Total force = 0.001674 Total SCF correction = 0.000056 Total force = 0.001661 Total SCF correction = 0.000164 Total force = 0.001673 Total SCF correction = 0.000032 Total force = 0.001668 Total SCF correction = 0.000100 Total force = 0.001653 Total SCF correction = 0.000168 Total force = 0.001662 Total SCF correction = 0.000085 Total force = 0.001666 Total SCF correction = 0.000043 Total force = 0.001657 Total SCF correction = 0.000069 Total force = 0.001668 Total SCF correction = 0.000063 ************************** The force does not go down and something is definitely wrong here! I run a few similar calculations with a slightly different c (celldm(3) = 2.05 and 2.10), which converge much better, to total force of 0.000018 and 0.000064 respectively. In the latter case it is still not what I asked for. Would appreciate any ideas on how to fix this and get forces below the treshold that I want. If this treshold is ridiculous or I need to switch to a different relaxation routine, PLZ let me know as well. Thanks, Serge -- ****************************************************************************** Serge M. Nakhmanson phone: +1 (732) 445-4603 Postdoctoral RA fax: +1 (732) 445-4400 Department of Physics & Astronomy Rutgers, The State University of New Jersey 136 Frelinghuysen Road nakhmans at physics.rutgers.edu Piscataway, NJ 08854-8019 ****************************************************************************** From sbraccia at sissa.it Sat Nov 20 13:37:08 2004 From: sbraccia at sissa.it (Carlo Sbraccia) Date: Sat, 20 Nov 2004 13:37:08 +0100 Subject: [Pw_forum] Problem with bfgs relaxation References: <419D1445.9070104@physics.rutgers.edu> Message-ID: <419F3A74.4050009@sissa.it> Dear Serge, First a comment on forc_conv_thr: the threshold on the forces means that the convergence is achieved when all the components of the force vector are smaller than forc_conv_thr. Mathematicians would say that you ask the L-infinity-norm of the vector F to be smaller than forc_conv_thr. Instead Total force is the L-2-norm of the force vector and is generally used to check that the threshold on the self-consistency is adeguate for the forces (this is roughly true when Total force >> Total SCF correction). Nevertheless BFGS claims that it's converged because the trust radius is smaller that the minimum value, even if the minimum has not been found. This means that something wrong is appening during the relaxation. If you post the complete output file I'll try to trace where is the error. best, carlo Serge Nakhmanson wrote: > Dear All, > > I am trying to relax a small (BaTiO_3)_1/(CaTiO_3)_1 superlattice with > new > bfgs routine (PWscf in ESPRESSO 2.1). However, the routine seems to > completely > ignore the force convergence threshold (forc_conv_thr) in my input > file and > claims that it has converged even when forces in the system are large. > > Here is my input file: > > ********************************** > > &CONTROL > title = '(BaTiO_3)_1/(CaTiO_3)_1 superlattice' , > calculation = 'relax' , > restart_mode = 'from_scratch' , > outdir = './', > pseudo_dir = > '/home/nakhmans/Codes/PWSCF/PSP/Ultrasoft/USPP_UPF/' , > prefix = 'B1C1.c_fit' , > verbosity = 'high', > tstress = .true., > nstep = 100, > etot_conv_thr = 5.e-5, > forc_conv_thr = 4.e-5, > / > &SYSTEM > ibrav = 6, > celldm(1) = 7.29064, > celldm(3) = 2.00, > nat = 10, > ntyp = 4, > ecutwfc = 25, > ecutrho = 225, > / > &ELECTRONS > conv_thr = 1.e-8 , > startingpot = 'atomic' , > startingwfc = 'atomic' , > mixing_mode = 'plain' , > mixing_beta = 0.7 , > / > > &IONS > ion_dynamics = 'bfgs', > / > ATOMIC_SPECIES > Ba 137.32700 056-Ba-ca-sp-vgrp.uspp.UPF > Ca 40.07800 020-Ca-ca-sp-vgrp.uspp.UPF > Ti 47.86700 022-Ti-ca-sp-vgrp.uspp.UPF > O 16.00000 008-O-ca--vgrp.uspp.UPF > ATOMIC_POSITIONS alat > Ba 0.000000000 0.000000000 0.000000000 > Ti 0.500000000 0.500000000 0.500000000 > O 0.000000000 0.500000000 0.500000000 > O 0.500000000 0.000000000 0.500000000 > O 0.500000000 0.500000000 0.000000000 > Ca 0.000000000 0.000000000 1.005000000 > Ti 0.500000000 0.500000000 1.500000000 > O 0.000000000 0.500000000 1.500000000 > O 0.500000000 0.000000000 1.500000000 > O 0.500000000 0.500000000 1.000000000 > K_POINTS automatic > 6 6 3 0 0 0 > > ********************************* > > A small change in the Ca atom position along Z is to enforce P4mm > symmetry > during relaxation. > > Here's what I get in the output: > > *********************************** > > ! total energy = -552.10767780 ryd > estimated scf accuracy < 7.8E-10 ryd > > > band energy sum = -26.93676693 ryd > one-electron contribution = -158.68930900 ryd > hartree contribution = 123.78105246 ryd > xc contribution = -88.35663862 ryd > ewald contribution = -428.84278264 ryd > > > convergence has been achieved > > > Forces acting on atoms (Ry/au): > > > atom 1 type 1 force = 0.00000000 0.00000000 > 0.00111050 > atom 2 type 3 force = 0.00000000 0.00000000 > 0.00011367 > atom 3 type 4 force = 0.00000000 0.00000000 > -0.00017387 > atom 4 type 4 force = 0.00000000 0.00000000 > -0.00017387 > atom 5 type 4 force = 0.00000000 0.00000000 > -0.00064692 > atom 6 type 2 force = 0.00000000 0.00000000 > 0.00067175 > atom 7 type 3 force = 0.00000000 0.00000000 > -0.00046149 > atom 8 type 4 force = 0.00000000 0.00000000 > 0.00008750 > atom 9 type 4 force = 0.00000000 0.00000000 > 0.00008750 > atom 10 type 4 force = 0.00000000 0.00000000 > -0.00061476 > > > Total force = 0.001668 Total SCF correction = 0.000063 > > > entering subroutine stress ... > > > total stress (ryd/bohr**3) (kbar) > P= -26.63 > -0.00016828 0.00000000 0.00000000 -24.75 0.00 0.00 > 0.00000000 -0.00016828 0.00000000 0.00 -24.75 0.00 > 0.00000000 0.00000000 -0.00020644 0.00 0.00 -30.37 > > > > > [ ... cut ... ] > > > number of scf cycles = 38 > number of bfgs steps = 23 > > energy old = -552.1076788015 ryd > energy new = -552.1076778004 ryd > > > CASE: energy_new > energy_old > > > new trust radius = 0.0000000818 bohr > > > > > bfgs converged in 38 scf cycles and 23 bfgs steps > > > End of BFGS geometry calculation > > > Final energy = -552.1076788015 ryd > > > Saving the approximate inverse hessian > > > [ ... cut ... ] > > > ************************** > > How could this thing be converged if total force is 0.001668 and I > asked for < 0.00004? > > Here's grep on "Total force" in my output file: > > ************************** > > Total force = 0.058112 Total SCF correction = 0.000056 > Total force = 0.124018 Total SCF correction = 0.000195 > Total force = 0.156460 Total SCF correction = 0.000459 > Total force = 0.016897 Total SCF correction = 0.000249 > Total force = 0.007370 Total SCF correction = 0.000379 > Total force = 0.000659 Total SCF correction = 0.000384 > Total force = 0.000629 Total SCF correction = 0.000263 > Total force = 0.000587 Total SCF correction = 0.000093 > Total force = 0.000705 Total SCF correction = 0.000024 > Total force = 0.001393 Total SCF correction = 0.000055 > Total force = 0.001880 Total SCF correction = 0.000052 > Total force = 0.001596 Total SCF correction = 0.000088 > Total force = 0.002010 Total SCF correction = 0.000037 > Total force = 0.001721 Total SCF correction = 0.000059 > Total force = 0.002024 Total SCF correction = 0.000051 > Total force = 0.001842 Total SCF correction = 0.000032 > Total force = 0.001772 Total SCF correction = 0.000145 > Total force = 0.001728 Total SCF correction = 0.000180 > Total force = 0.001743 Total SCF correction = 0.000130 > Total force = 0.001733 Total SCF correction = 0.000094 > Total force = 0.001745 Total SCF correction = 0.000154 > Total force = 0.001726 Total SCF correction = 0.000095 > Total force = 0.001744 Total SCF correction = 0.000144 > Total force = 0.001718 Total SCF correction = 0.000101 > Total force = 0.001677 Total SCF correction = 0.000142 > Total force = 0.001705 Total SCF correction = 0.000066 > Total force = 0.001675 Total SCF correction = 0.000196 > Total force = 0.001706 Total SCF correction = 0.000082 > Total force = 0.001674 Total SCF correction = 0.000058 > Total force = 0.001674 Total SCF correction = 0.000056 > Total force = 0.001661 Total SCF correction = 0.000164 > Total force = 0.001673 Total SCF correction = 0.000032 > Total force = 0.001668 Total SCF correction = 0.000100 > Total force = 0.001653 Total SCF correction = 0.000168 > Total force = 0.001662 Total SCF correction = 0.000085 > Total force = 0.001666 Total SCF correction = 0.000043 > Total force = 0.001657 Total SCF correction = 0.000069 > Total force = 0.001668 Total SCF correction = 0.000063 > > ************************** > > The force does not go down and something is definitely wrong here! > I run a few similar calculations with a slightly different c > (celldm(3) = 2.05 and 2.10), which converge much better, to total > force of 0.000018 and 0.000064 respectively. In the latter case it > is still not what I asked for. > > Would appreciate any ideas on how to fix this and get forces below > the treshold that I want. If this treshold is ridiculous or I need > to switch to a different relaxation routine, PLZ let me know as well. > > Thanks, > > Serge > From timtro at rogers.com Thu Nov 18 18:13:21 2004 From: timtro at rogers.com (Timothy A.V. Teatro) Date: Thu, 18 Nov 2004 12:13:21 -0500 Subject: [Pw_forum] RE: Pw_forum digest, Vol 1 #456 - 2 msgs In-Reply-To: <20041118063653.24873.15570.Mailman@democritos.sissa.it> Message-ID: <000401c4cd91$e843b580$1d02a8c0@oncampus.local> Hi Aaron. Thank you very much for responding. Yes, I have tried a more physically phesable distance. I initially had it set at <0.25, 0.25, 0.25>, which I am assuming should also lead to zero force, since the PBC's would create a 0k lattice right? So I'm thinking great, now let's move it in slightly to perturb the system and create some vibration. But no matter where I moved the second Si atom, it didn't help. I want to thank you again very much. I have attached the output file you requested. From cbarreteau at cea.fr Fri Nov 19 11:20:19 2004 From: cbarreteau at cea.fr (Cyrille Barreteau) Date: Fri, 19 Nov 2004 11:20:19 +0100 (CET) Subject: [Pw_forum] fully relativistic US-PP for Fe Message-ID: <45787.132.166.21.1.1100859619.squirrel@132.166.21.1> Dear pwscf... I would like to perform a pwscf calculation of Iron including spin-orbit. I would therefore need a fully relativistic US-PP For Fe. It would be very nice if some of you could either provide me such US-PP or tell me how I can generate such pseudos.. thanks cyrille -- ================================================ Cyrille Barreteau | phone:+33 (0)1 69 08 29 51 CEA Saclay | fax : +33 (0)1 69 08 84 46 DSM/DRECAM/SPCSI | email: cbarreteau at cea.fr Batiment 462 | 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ web : http://www-drecam.cea.fr/spcsi/index.php groupe theorie ================================================ From pmdung at gmail.com Fri Nov 19 13:49:31 2004 From: pmdung at gmail.com (Pham Minh Dung) Date: Fri, 19 Nov 2004 19:49:31 +0700 Subject: [Pw_forum] Configure and compile pwscf 2.1 on Mandrake Linux 10.0 Message-ID: <1e51b2b804111904496e7a5c49@mail.gmail.com> Hi, I'm studying about PWscf and I downloaded the last version (2.1) from your site (http://www.pwscf.org/downloads/PWcodes/codes/2.1/pw_src-2.1.tar.gz). When I download and run pwgui for linux and an another version for windows, these program work fine. Unfortunely, I can't configure and compile your program on my machine (PC Pentium 4 3.0GHz with MandrakeLinux 10.0, pakage gcc-g77-3.3.2 installed by default). When I run "./configure", I got message 1 (file attached). I tried by insert this line before line 1585 in file configure: F77="g77" Then run "./configure" again and see message 2. I think that it could be configure OK and I call "make all". I got message 3 with some error. I tried to seach some solution on the internet and in your forum but I found nothing. Then I have to ask your help! Thank you very much -- PHAM Minh Dung -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: message1.txt Url: /pipermail/attachments/20041119/6e9fd8dd/attachment.txt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: message2.txt Url: /pipermail/attachments/20041119/6e9fd8dd/attachment-0001.txt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: message3.txt Url: /pipermail/attachments/20041119/6e9fd8dd/attachment-0002.txt From eyvaz_isaev at yahoo.com Fri Nov 19 14:20:02 2004 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 19 Nov 2004 05:20:02 -0800 (PST) Subject: [Pw_forum] Configure and compile pwscf 2.1 on Mandrake Linux 10.0 In-Reply-To: <1e51b2b804111904496e7a5c49@mail.gmail.com> Message-ID: <20041119132002.57463.qmail@web60310.mail.yahoo.com> Hi, >g77: avrec.F90: linker input >file unused because linking not >done The message, more likely, means that there is no compiled avrec.F90, i.e. there is no avrec.o file. As far as I know, g77 is not able to compile the code. And according your message you have no Fortran90 compiler, even g95. I this case you can download Intel Fortran Compiler from http://www.intel.com/software/products/compilers/flin/index.htm Download also the MKL libraries from the same website. The comination IFC+MKL should work well on Intel based computers. Good lucks, Eyvaz. --- Pham Minh Dung wrote: > Hi, > I'm studying about PWscf and I downloaded the last > version (2.1) from > your site > (http://www.pwscf.org/downloads/PWcodes/codes/2.1/pw_src-2.1.tar.gz). > When I download and run pwgui for linux and an > another version for > windows, these program work fine. > Unfortunely, I can't configure and compile your > program on my machine > (PC Pentium 4 3.0GHz with MandrakeLinux 10.0, pakage > gcc-g77-3.3.2 > installed by default). > When I run "./configure", I got message 1 (file > attached). > I tried by insert this line before line 1585 in file > configure: F77="g77" > Then run "./configure" again and see message 2. > I think that it could be configure OK and I call > "make all". I got > message 3 with some error. > I tried to seach some solution on the internet and > in your forum but I > found nothing. > Then I have to ask your help! > Thank you very much > > -- > PHAM Minh Dung > > checking build system type... i686-pc-linux-gnu > checking architecture... linux32 > checking for mpif90... no > checking for ifort... no > checking for ifc... no > checking for pgf90... no > checking for g95... no > checking for f90... no > checking for Fortran 77 compiler default output file > name... configure: error: Fortran 77 compiler cannot > create executables > See `config.log' for more details.> checking build system type... i686-pc-linux-gnu > checking architecture... linux32 > checking for mpif90... no > checking for ifort... no > checking for ifc... no > checking for pgf90... no > checking for g95... no > checking for f90... no > checking for Fortran 77 compiler default output file > name... a.out > checking whether the Fortran 77 compiler works... > yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU Fortran 77 > compiler... yes > checking whether g77 accepts -g... yes > checking version of g77... g95 3.3.2 > checking for g77... g77 > checking whether we are using the GNU Fortran 77 > compiler... yes > checking whether g77 accepts -g... yes > checking for gcc... gcc > checking whether we are using the GNU C compiler... > yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ANSI C... none > needed > checking version of gcc... gcc 3.3.2 > setting FFLAGS... -O3 > setting F90FLAGS... $(FFLAGS) > setting CFLAGS... -O3 -fomit-frame-pointer > checking how to run the C preprocessor... gcc -E > setting CPP... cpp > setting CPPFLAGS... -P -traditional > setting LD... g77 > setting LDFLAGS... > setting AR... ar > setting ARFLAGS... ruv > checking whether Fortran files must be > preprocessed... yes > checking for library containing zggev... no > checking for library containing fftwnd... no > checking for library containing dgemm... no > checking for library containing dgemm... no > checking for library containing zggev... no > checking for library containing mpi_init... no > setting LIBS... > checking for library containing mpi_init... (cached) > no > checking for library containing zggev... (cached) no > checking for library containing fftwnd... (cached) > no > setting DFLAGS... -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW > setting FDFLAGS... $(DFLAGS) > setting RANLIB... echo > setting MYLIB... blas_and_lapack > checking module dependencies... done > configure: creating ./config.status > config.status: creating make.sys > config.status: creating make.rules > ----------------------------------------------------------------- > PWscf can take advantage of several optimized > numerical libraries > (essl, fftw, mkl...). This configure script attempts > to find them, > but may fail if they have been installed in > non-standard locations. > > The following libraries have been found: > LIBS= > > If any libraries are missing, you may specify a list > of directories > to search and retry, as follows: > ./configure LIBDIRS="list of directories, > separated by spaces" > > For more information, read the README.INSTALL file > or the PWscf manuals. > ----------------------------------------------------------------- > ---------------------------------------------- > WARNING: parallel environment not detected > this program will run in single-processor mode > ----------------------------------------------> test -d bin || mkdir bin > ( cd Modules; make all ) > make[1]: Entering directory `/root/pwscf/Modules' > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH io_global.f90 io_global.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c io_global.F90 -o > io_global.o > g77: io_global.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH kind.f90 kind.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c kind.F90 -o kind.o > g77: kind.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH parameters.f90 parameters.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c parameters.F90 -o > parameters.o > g77: parameters.F90: linker input file unused > because linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH atom.f90 atom.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c atom.F90 -o atom.o > g77: atom.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH parallel_include.f90 > parallel_include.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c parallel_include.F90 -o > parallel_include.o > g77: parallel_include.F90: linker input file unused > because linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH mp.f90 mp.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c mp.F90 -o mp.o > g77: mp.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH shmem_include.f90 shmem_include.F90 > > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c shmem_include.F90 -o > shmem_include.o > g77: shmem_include.F90: linker input file unused > because linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH mp_global.f90 mp_global.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c mp_global.F90 -o > mp_global.o > g77: mp_global.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH recvec.f90 recvec.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c recvec.F90 -o recvec.o > g77: recvec.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH stick_base.f90 stick_base.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c stick_base.F90 -o > stick_base.o > g77: stick_base.F90: linker input file unused > because linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH berry_phase.f90 berry_phase.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c berry_phase.F90 -o > berry_phase.o > g77: berry_phase.F90: linker input file unused > because linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH basic_algebra_routines.f90 > basic_algebra_routines.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c basic_algebra_routines.F90 > -o basic_algebra_routines.o > g77: basic_algebra_routines.F90: linker input file > unused because linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH constants.f90 constants.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c constants.F90 -o > constants.o > g77: constants.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH io_files.f90 io_files.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c io_files.F90 -o io_files.o > g77: io_files.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH parser.f90 parser.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c parser.F90 -o parser.o > g77: parser.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH bfgs_module.f90 bfgs_module.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c bfgs_module.F90 -o > bfgs_module.o > g77: bfgs_module.F90: linker input file unused > because linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH cell_base.f90 cell_base.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c cell_base.F90 -o > cell_base.o > g77: cell_base.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH check_stop.f90 check_stop.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c check_stop.F90 -o > check_stop.o > g77: check_stop.F90: linker input file unused > because linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH clocks.f90 clocks.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c clocks.F90 -o clocks.o > g77: clocks.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH control_flags.f90 control_flags.F90 > > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c control_flags.F90 -o > control_flags.o > g77: control_flags.F90: linker input file unused > because linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH cp_emass.f90 cp_emass.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c cp_emass.F90 -o cp_emass.o > g77: cp_emass.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH fft_types.f90 fft_types.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -c fft_types.F90 -o > fft_types.o > g77: fft_types.F90: linker input file unused because > linking not done > cpp -P -traditional -D__LINUX -D__G95 -D__FFTW > -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules > -I../PW -I../PH mp_buffers.f90 mp_buffers.F90 > g77 -O3 -I. -I../include -I../Modules -I../PW > -I../PH === message truncated === __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From pmdung at gmail.com Fri Nov 19 15:33:13 2004 From: pmdung at gmail.com (Pham Minh Dung) Date: Fri, 19 Nov 2004 21:33:13 +0700 Subject: [Pw_forum] Configure and compile pwscf 2.1 on Mandrake Linux 10.0 In-Reply-To: <20041119132002.57463.qmail@web60310.mail.yahoo.com> References: <1e51b2b804111904496e7a5c49@mail.gmail.com> <20041119132002.57463.qmail@web60310.mail.yahoo.com> Message-ID: <1e51b2b8041119063335163ee7@mail.gmail.com> Thanks you very much, I'll try it! -- PHAM Minh Dung On Fri, 19 Nov 2004 05:20:02 -0800 (PST), Eyvaz Isaev wrote: > Hi, > > >g77: avrec.F90: linker input >file unused because > linking not >done > > The message, more likely, means that there is no > compiled avrec.F90, i.e. there is no avrec.o file. > > As far as I know, g77 is not able to compile the code. > And according your message you have no Fortran90 > compiler, even g95. > I this case you can download Intel Fortran Compiler > from > http://www.intel.com/software/products/compilers/flin/index.htm > Download also the MKL libraries from the same website. > The comination IFC+MKL should work well on Intel based > computers. > > Good lucks, > Eyvaz. From pmdung at gmail.com Sat Nov 20 06:41:17 2004 From: pmdung at gmail.com (Pham Minh Dung) Date: Sat, 20 Nov 2004 12:41:17 +0700 Subject: [Pw_forum] Configure and compile pwscf 2.1 on Mandrake Linux 10.0 In-Reply-To: <1e51b2b8041119063335163ee7@mail.gmail.com> References: <1e51b2b804111904496e7a5c49@mail.gmail.com> <20041119132002.57463.qmail@web60310.mail.yahoo.com> <1e51b2b8041119063335163ee7@mail.gmail.com> Message-ID: <1e51b2b8041119214138cdf0c5@mail.gmail.com> Hi, I installed Intel Fortran Compiler and I think that I run "./configure" fine. Now I "make all" then there is an another problem (message 4 attached). My LD_LIBRARY_PATH already has content: /opt/intel_fc_80/lib/;/opt/intel/mkl701/lib/32/. I don't know what library is absent? On Fri, 19 Nov 2004 21:33:13 +0700, Pham Minh Dung wrote: > Thanks you very much, I'll try it! > -- > PHAM Minh Dung > > > > On Fri, 19 Nov 2004 05:20:02 -0800 (PST), Eyvaz Isaev > wrote: > > Hi, > > > > >g77: avrec.F90: linker input >file unused because > > linking not >done > > > > The message, more likely, means that there is no > > compiled avrec.F90, i.e. there is no avrec.o file. > > > > As far as I know, g77 is not able to compile the code. > > And according your message you have no Fortran90 > > compiler, even g95. > > I this case you can download Intel Fortran Compiler > > from > > http://www.intel.com/software/products/compilers/flin/index.htm > > Download also the MKL libraries from the same website. > > The comination IFC+MKL should work well on Intel based > > computers. > > > > Good lucks, > > Eyvaz. > -- PHAM Minh Dung -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: message4.txt Url: /pipermail/attachments/20041120/494c2ef3/attachment.txt From eyvaz_isaev at yahoo.com Sat Nov 20 14:06:20 2004 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 20 Nov 2004 05:06:20 -0800 (PST) Subject: [Pw_forum] Configure and compile pwscf 2.1 on Mandrake Linux 10.0 In-Reply-To: <1e51b2b8041119214138cdf0c5@mail.gmail.com> Message-ID: <20041120130620.14806.qmail@web60303.mail.yahoo.com> Hi, The message means that the loader could not find a math library. On Linux systems libm.so.6 should be displayed in the /lib directory. You can try "locate libm.so.6" from command line and then include the path you found to your LD_LIBRARY_PATH. Hope it helps. Eyvaz. --- Pham Minh Dung wrote: > Hi, > I installed Intel Fortran Compiler and I think that > I run > "./configure" fine. Now I "make all" then there is > an another problem > (message 4 attached). My LD_LIBRARY_PATH already has > content: > /opt/intel_fc_80/lib/;/opt/intel/mkl701/lib/32/. I > don't know what > library is absent? > > On Fri, 19 Nov 2004 21:33:13 +0700, Pham Minh Dung > wrote: > > Thanks you very much, I'll try it! > > -- > > PHAM Minh Dung > > > > > > > > On Fri, 19 Nov 2004 05:20:02 -0800 (PST), Eyvaz > Isaev > > wrote: > > > Hi, > > > > > > >g77: avrec.F90: linker input >file unused > because > > > linking not >done > > > > > > The message, more likely, means that there is no > > > compiled avrec.F90, i.e. there is no avrec.o > file. > > > > > > As far as I know, g77 is not able to compile the > code. > > > And according your message you have no Fortran90 > > > compiler, even g95. > > > I this case you can download Intel Fortran > Compiler > > > from > > > > http://www.intel.com/software/products/compilers/flin/index.htm > > > Download also the MKL libraries from the same > website. > > > The comination IFC+MKL should work well on Intel > based > > > computers. > > > > > > Good lucks, > > > Eyvaz. > > > > > -- > PHAM Minh Dung > > make[1]: Entering directory `/root/pwscf/PW' > ifort -o memory.x memory.o add_efield.o add_vuspsi.o > addusdens.o addusforce.o addusstress.o > allocate_fft.o allocate_locpot.o allocate_nlpot.o > allocate_wfc.o atomic_rho.o atomic_wfc.o bachel.o > becmod.o bfgs.o bp_bess.o bp_c_phase.o bp_calc_btq.o > bp_dbess.o bp_qvan3.o bp_radin.o bp_strings.o > bp_ylm_q.o c_bands.o c_gemm.o ccalbec.o ccgdiagg.o > cdiagh.o cdiaghg.o cegterg.o cft3.o cft3s.o cft_3.o > cft_sgi.o cft_sp.o cft_sun.o cft_t3e.o cfts_3.o > cgramg1.o checkallsym.o checksym.o cinitcgg.o > clean_pw.o close_files.o compute_dip.o compute_scf.o > constraints_module.o coset.o cryst_to_car.o > cubicsym.o d_matrix.o data_structure.o davcio.o > delta_e.o deriv_drhoc.o diis_base.o > real_diis_module.o complex_diis_module.o diropn.o > divide.o divide_et_impera.o dndepsilon.o dndtau.o > dprojdepsilon.o dprojdtau.o dqvan2.o drhoc.o > dvloc_of_g.o dynamics.o efermig.o efermit.o > electrons.o eqvect.o error_handler.o estimate.o > ewald.o ewald_dipole.o fftw.o force_cc.o > force_corr.o force_ew.o force_hub.o force_lc.o > force_us.o forces.o functionals.o g_psi.o > g_psi_mod.o gen_at_dj.o gen_at_dy.o gen_us_dj.o > gen_us_dy.o ggen.o gk_sort.o gradcorr.o gweights.o > h_1psi.o h_psi.o hexsym.o hinit0.o hinit1.o > init_ns.o init_paw_1.o init_paw_2.o init_pool.o > init_run.o init_us_1.o init_us_2.o init_at_1.o > init_vloc.o input.o interpolate.o io_pot.o ions.o > irrek.o iweights.o kpoint_grid.o lchk_tauxk.o > linmin.o lsda_functionals.o make_pointlists.o > mix_pot.o mix_rho.o mode_group.o move_ions.o > multable.o n_plane_waves.o new_ns.o ns_adj.o newd.o > noncol.o openfil.o ortho.o orthoatwfc.o output_tau.o > para.o paw.o potinit.o print_clock_pw.o psymrho.o > punch.o pw_gemm.o pwcom.o qvan2.o rdiaghg.o > read_conf_from_file.o read_file.o read_ncpp.o > read_pseudo.o readin.o readnewvan.o readvan.o > regterg.o remove_atomic_rho.o reset_k_points.o > restart.o restart_from_file.o restart_in_electrons.o > restart_in_ions.o rgen.o rho2zeta.o rotate_wfc.o > rotate_wfc_gamma.o ruotaijk.o s_1psi.o > s_axis_to_ca.o s_gemm.o s_psi.o save_in_cbands.o > save_in_electrons.o save_in_ions.o scala_cdiag.o > scala_cdiaghg.o scala_utils.o scale_h.o scopy_t3e.o > seqopn.o set_fft_dim.o set_hubbard_l.o set_kplusb.o > set_kplusq.o set_kup_and_kdw.o set_rhoc.o set_vrs.o > setlocal.o setqf.o setup.o setupkpt.o sgam_at.o > sgam_at_mag.o sgam_ph.o sgama.o show_memory.o > smallg_q.o spinor.o sph_ind.o startup.o stop_pw.o > stres_cc.o stres_ewa.o stres_gradcorr.o stres_har.o > stres_hub.o stres_knl.o stres_loc.o stres_us.o > stress.o struct_fact.o sum_band.o sumkg.o sumkt.o > summary.o swap.o symrho.o symtns.o symvect.o symz.o > tabd.o trntns.o trnvecc.o trnvect.o tweights.o > update_pot.o updathes.o upf_to_internal.o usnldiag.o > v_of_rho.o vcsmd.o vcsubs.o vhpsi.o vloc_of_g.o > vloc_psi.o vpack.o w0gauss.o w1gauss.o wfcinit.o > wgauss.o write_config_to_file.o write_ns.o > wsweight.o ../Modules/atom.o > ../Modules/basic_algebra_routines.o > ../Modules/berry_phase.o ../Modules/bfgs_module.o > ../Modules/cell_base.o ../Modules/check_stop.o > ../Modules/clocks.o ../Modules/constants.o > ../Modules/control_flags.o ../Modules/fft_base.o > ../Modules/fft_scalar.o ../Modules/fft_types.o > ../Modules/functionals.o > ../Modules/input_parameters.o ../Modules/io_base.o > ../Modules/io_files.o ../Modules/io_global.o > ../Modules/ions_base.o ../Modules/kind.o > ../Modules/mp_buffers.o ../Modules/mp_global.o > ../Modules/mp_wave.o ../Modules/mp.o > ../Modules/path_base.o ../Modules/path_formats.o > ../Modules/path_variables.o > ../Modules/path_opt_routines.o > ../Modules/path_io_routines.o > ../Modules/parallel_include.o > ../Modules/parameters.o ../Modules/parser.o > ../Modules/pseudo_types.o ../Modules/read_cards.o > ../Modules/read_namelists.o ../Modules/readpseudo.o > ../Modules/recvec.o ../Modules/stick_base.o > ../Modules/shmem_include.o ../Modules/supercell.o > ../Modules/uspp.o ../Modules/version.o > ../Modules/wavefunctions.o -Vaxlib -static > ../flib/ptools.a ../flib/flib.a ../clib/clib.a > ld: cannot find -lm > make[1]: *** [memory.x] Erreur 1 > make[1]: Leaving directory `/root/pwscf/PW' > make: *** [pw] Erreur 2 > __________________________________ Do you Yahoo!? The all-new My Yahoo! - Get yours free! http://my.yahoo.com From mpayami at aeoi.org.ir Sun Nov 21 10:45:51 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Sun, 21 Nov 2004 13:15:51 +0330 Subject: [Pw_forum] convergence NOT achieved, stopping Message-ID: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> Dear PW users, I have checked example03 which deals with CO dimer and changed the input file appropriate for O2 case which gives a bond legth of 2.322 bohrs. Further, I prepared the input for O3 case but I encounter with the message (after 1000 iterations): convergence NOT achieved, stopping I tried again with a mixing factor of beta=0.1 but nothing new happened. For information, the initial positions of O atoms are (-3,0,0), (3,0,0) and (0,3,0). I would be grateful if somebody comments how to manage it. Best regards, Mahmoud Payami -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041121/c1dc4777/attachment.htm From mpayami at aeoi.org.ir Sun Nov 21 11:47:51 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Sun, 21 Nov 2004 14:17:51 +0330 Subject: [Pw_forum] convergence NOT achieved, stopping(additional information) References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> Message-ID: <001a01c4cfb7$8c40fa90$a06510ac@aeoi.org.ir> The cubic cell dimension is assummed to be 20.0 a.u. M. Payami Dear PW users, I have checked example03 which deals with CO dimer and changed the input file appropriate for O2 case which gives a bond legth of 2.322 bohrs. Further, I prepared the input for O3 case but I encounter with the message (after 1000 iterations): convergence NOT achieved, stopping I tried again with a mixing factor of beta=0.1 but nothing new happened. For information, the initial positions of O atoms are (-3,0,0), (3,0,0) and (0,3,0). I would be grateful if somebody comments how to manage it. Best regards, Mahmoud Payami -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041121/a0eb1c47/attachment.htm From rjxiao at blem.ac.cn Mon Nov 22 05:05:49 2004 From: rjxiao at blem.ac.cn (rjxiao) Date: Mon, 22 Nov 2004 12:05:49 +0800 Subject: [Pw_forum] Re:Configure and compile pwscf 2.1 on Mandrake Linux 10.0 Message-ID: <20041122120549.548a1844@server.blem.ac.cn> Dear PHAM Minh Dung, Don't worry about it.In fact,I have met the same problem before.You can try the following method to slove it.As what Eyvaz said,it can't find the math library. First, you can look into the file 'configure'. In the '# search for libraries (unless LIBS has been set from the environment)' part, you can find that the default path for MKL7 is '/opt/intel/mkl70/lib/32', you may change it to your MKL path '/opt/intel/mkl701/lib/32/'. Second,use the command './configure --enable-shared' instead of './configure'.The reason for this has been mentioned by Paolo on 'http://www.democritos.it/pipermail/pw_forum/2004-September/001355.html '. By using this method, I have installed the nearest version on my Mandrake 9.2. Hope it helpful. Best regards, Sincerely, Ruijuan Xiao Institute of Physics, Chinese Academy of Sciences From yi.kong at gmail.com Mon Nov 22 08:20:51 2004 From: yi.kong at gmail.com (Yi Kong) Date: Mon, 22 Nov 2004 15:20:51 +0800 Subject: [Pw_forum] error with SGI irix6.5 Message-ID: <8c9dc66c04112123201162acde@mail.gmail.com> Dear all, I met a problem when I compiled the PWSCF at a SGI irix6.5 workstation. The configure can find the needed libraries as following: LIBS=-lmpi -L/disk/usr/kongy/fftw/lib -lfftw -lcomplib.sgimath But when I compile, the PWSCF stopped with the following error messages: ********************** error messages******************************** test -d bin || mkdir bin ( cd Modules; make all ) f90 -mips4 -64 -O2 -r10000 -r8 -I. -I../include -I../Modules -I../PW -I../PH -I/disk/usr/kongy/fftw/include -cpp -D__SGI -D__SGI64 -D__ORIGIN -D__MPI -D__PARA -D__FFTW -c path_base.f90 MODULE path_base ^ f90-855 mfef90: ERROR PATH_BASE, File = path_base.f90, Line = 11, Column = 8 The compiler has detected errors in module "PATH_BASE". No module information file will be created for this module. FORALL( mode = 1 : num_of_modes ) ^ f90-113 mfef90: ERROR INITIALIZE_PATH, File = path_base.f90, Line = 153, Column = 10 IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "FORALL". ^ f90-508 mfef90: ERROR INITIALIZE_PATH, File = path_base.f90, Line = 153, Column = 10 The parent-string of a substring reference must be of type character. END FORALL ^ f90-186 mfef90: ERROR INITIALIZE_PATH, File = path_base.f90, Line = 157, Column = 14 Unexpected syntax: Expecting "IF" to follow the END keyword, but found "FORALL". FORALL( i = 1: ( input_images - 1 ) ) ^ f90-508 mfef90: ERROR INITIALIZE_PATH, File = path_base.f90, Line = 234, Column = 10 The parent-string of a substring reference must be of type character. END FORALL ^ f90-186 mfef90: ERROR INITIALIZE_PATH, File = path_base.f90, Line = 238, Column = 14 Unexpected syntax: Expecting "IF" to follow the END keyword, but found "FORALL". f90: MIPSpro Fortran 90 Version 7.2.1 (f39) Tue Nov 16, 2004 04:40:29 f90: 1643 source lines f90: 6 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s) *** Error code 2 (bu21) *** Error code 1 (bu21) ********************* end ************************** I don't know how to solve this problem, any suggestion is welcome! best regards Yi Kong -- ============================= Yi Kong Department of MSE Tsinghua University PR China, 100084 ============================= From giannozz at nest.sns.it Mon Nov 22 09:25:49 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 22 Nov 2004 09:25:49 +0100 Subject: [Pw_forum] error with SGI irix6.5 In-Reply-To: <8c9dc66c04112123201162acde@mail.gmail.com> References: <8c9dc66c04112123201162acde@mail.gmail.com> Message-ID: <200411220925.49727.giannozz@nest.sns.it> On Monday 22 November 2004 08:20, Yi Kong wrote: > FORALL( mode = 1 : num_of_modes ) > ^ > f90-113 mfef90: ERROR INITIALIZE_PATH, File = path_base.f90, Line = > 153, Column = 10 > IMPLICIT NONE is specified in the local scope, therefore an explicit > type must be specified for data object "FORALL". > ^ try to put a space between "FORALL" and "(" . Please report if it works. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From yi.kong at gmail.com Mon Nov 22 09:56:42 2004 From: yi.kong at gmail.com (Yi Kong) Date: Mon, 22 Nov 2004 16:56:42 +0800 Subject: [Pw_forum] error with SGI irix6.5 Message-ID: <8c9dc66c04112200562a0bed64@mail.gmail.com> Dear Mr. Giannozzi, I have tried your suggestion, but the error messages still appeared. **************** error messages **************************** f90 -mips4 -64 -O2 -r10000 -r8 -I. -I../include -I../Modules -I../PW -I../PH -I/disk/usr/kongy/fftw/include -cpp -D__SGI -D__SGI64 -D__ORIGIN -D__MPI -D__PARA -D__FFTW -c path_base.f90 MODULE path_base ^ f90-855 mfef90: ERROR PATH_BASE, File = path_base.f90, Line = 11, Column = 8 The compiler has detected errors in module "PATH_BASE". No module information file will be created for this module. FORALL ( mode = 1 : num_of_modes ) ^ f90-113 mfef90: ERROR INITIALIZE_PATH, File = path_base.f90, Line = 153, Column = 10 IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "FORALL". ^ f90-508 mfef90: ERROR INITIALIZE_PATH, File = path_base.f90, Line = 153, Column = 10 The parent-string of a substring reference must be of type character. END FORALL ^ f90-186 mfef90: ERROR INITIALIZE_PATH, File = path_base.f90, Line = 157, Column = 14 Unexpected syntax: Expecting "IF" to follow the END keyword, but found "FORALL". FORALL ( i = 1: ( input_images - 1 ) ) ^ f90-508 mfef90: ERROR INITIALIZE_PATH, File = path_base.f90, Line = 234, Column = 10 The parent-string of a substring reference must be of type character. END FORALL ^ f90-186 mfef90: ERROR INITIALIZE_PATH, File = path_base.f90, Line = 238, Column = 14 Unexpected syntax: Expecting "IF" to follow the END keyword, but found "FORALL". f90: MIPSpro Fortran 90 Version 7.2.1 (f39) Tue Nov 23, 2004 05:13:48 f90: 1643 source lines f90: 6 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s) *** Error code 2 (bu21) *** Error code 1 (bu21) *************************** end ************************* best regards! Yi Kong -- ============================= Yi Kong Department of MSE Tsinghua University PR China, 100084 ============================= From giannozz at nest.sns.it Mon Nov 22 10:26:23 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 22 Nov 2004 10:26:23 +0100 Subject: [Pw_forum] error with SGI irix6.5 In-Reply-To: <8c9dc66c04112200562a0bed64@mail.gmail.com> References: <8c9dc66c04112200562a0bed64@mail.gmail.com> Message-ID: <200411221026.23494.giannozz@nest.sns.it> On Monday 22 November 2004 09:56, Yi Kong wrote: > I have tried your suggestion, but the error messages still appeared. then you are out of luck: your compiler does not support the FORALL construct. FORALL is standard in fortran-95 but not in fortran-90. Most so-called "fortran-90" compilers are actually "fortran-95" compilers, but apparently yours is not. You have either to change all occurrences of FORALL with DO...END DO, or to upgrade your compiler (if possible), or to move to a machine with more recent software Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From yi.kong at gmail.com Mon Nov 22 11:08:09 2004 From: yi.kong at gmail.com (Yi Kong) Date: Mon, 22 Nov 2004 18:08:09 +0800 Subject: [Pw_forum] error with SGI irix6.5 Message-ID: <8c9dc66c0411220208644366c6@mail.gmail.com> Dear Mr. Giannozzi, Thanks for your helpful reply, I will try to change the FORALL to the DO...END DO since there are just a little FORALL appearing. best regards! Yi Kong -- ============================= Yi Kong Department of MSE Tsinghua University PR China, 100084 ============================= From yi.kong at gmail.com Tue Nov 23 04:03:43 2004 From: yi.kong at gmail.com (Yi Kong) Date: Tue, 23 Nov 2004 11:03:43 +0800 Subject: [Pw_forum] error with SGI irix6.5 (another problem) Message-ID: <8c9dc66c041122190354d8dadc@mail.gmail.com> Dear Mir. Giannozzi and other pwscf users, I have changed all of the FORALL term into DO...ENDDO in the PWSCF program but there are still errors in my compiling on the SGI irix6.5. Are these errors still caused by the obsolete compiler? ******** error messages ********************************* ld64: WARNING 85: definition of dlaswp_ in ../flib/flib.a(lapack.o) preempts that definition in /usr/lib64/mips4/libcomplib.sgimath.so. ld64: WARNING 85: definition of zlassq_ in ../flib/flib.a(lapack.o) preempts that definition in /usr/lib64/mips4/libcomplib.sgimath.so. ld64: WARNING 85: definition of dlasrt_ in ../flib/flib.a(lapack.o) preempts that definition in /usr/lib64/mips4/libcomplib.sgimath.so. ld64: WARNING 85: definition of dlassq_ in ../flib/flib.a(lapack.o) preempts that definition in /usr/lib64/mips4/libcomplib.sgimath.so. ld64: Giving up after printing 50 warnings. Use -wall to print all warnings. ld64: ERROR 33: Unresolved text symbol "cpu_time_" -- 1st referenced by ../flib/flib.a(scnds.o). Use linker option -v to see when and which objects, archives and dsos are loaded. ld64: INFO 152: Output file removed because of error. *** Error code 2 (bu21) *** Error code 1 (bu21) *************** end *************************************** best regards Yi Kong -- ============================= Yi Kong Department of MSE Tsinghua University PR China, 100084 ============================= From giannozz at nest.sns.it Tue Nov 23 11:09:24 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 23 Nov 2004 11:09:24 +0100 Subject: [Pw_forum] error with SGI irix6.5 (another problem) In-Reply-To: <8c9dc66c041122190354d8dadc@mail.gmail.com> References: <8c9dc66c041122190354d8dadc@mail.gmail.com> Message-ID: <200411231109.24543.giannozz@nest.sns.it> On Tuesday 23 November 2004 04:03, Yi Kong wrote: > ******** error messages ********************************* > ld64: WARNING 85: definition of dlaswp_ in ../flib/flib.a(lapack.o) > preempts that definition in /usr/lib64/mips4/libcomplib.sgimath.so. > [...] these are warning, not error messages > warnings. ld64: ERROR 33: Unresolved text symbol "cpu_time_" -- 1st > referenced by ../flib/flib.a(scnds.o). cpu_time is standard fortran (90 or 95 I don't know), but apparently some compilers don't get it. Edit flib/scnds.f90 to remove or replace the call to cpu_time. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From cazzato at democritos.it Tue Nov 23 14:31:15 2004 From: cazzato at democritos.it (cazzato at democritos.it) Date: Tue, 23 Nov 2004 14:31:15 +0100 Subject: [Pw_forum] Driving me nuts! In-Reply-To: <000101c4cc28$7bbcdeb0$1d02a8c0@oncampus.local> References: <000101c4cc28$7bbcdeb0$1d02a8c0@oncampus.local> Message-ID: <1101216675.41a33ba3e3ea9@mail.democritos.it> Dear Timothy, are you sure that you are following the manual in your fpmd calculation: The first run, when starting from scratch, is always an electronic minimization, with fixed ions and cell, to bring the electronic system on the ground state (GS) relative to the starting atomic configuration. I'm using the current version of espresso and, running your job after the electronic minimization, atoms move at least. Paolo Cazzato Scrive "Timothy A.V. Teatro" : > Hi. I'm really sorry to ask a question like this. I wrote this input > file a while ago. I have been fiddling with it for a while now, and I > can't figure out why I can't get two simple little silicon atoms to > move! I am accustomed to using PWscf, but I am not trying to switch to > FPMD for more accurate dynamics. But I cannot get any dynamics out of > this thing! Even when I try putting the Si atoms very close to each > other, where the forces should be enormous I can't get them to move. > > Thanks a lot for looking at this. I'm sure I did something very silly, > which is going to embarrass me later. > > Here is a verbatim listing of the input script: > > #!/bin/sh > > PW_ROOT=$HOME/cpmd/FPMD > PSEUDO=$HOME/cpmd/pseudo > TMP_DIR=$HOME/cpmd/tmp0 > > if [ ! -d results ]; then > mkdir results > fi > cd results > > rm -rf $TMP_DIR/* > > cat > sih.cp1.in << EOF > > &CONTROL > title = ' Silicon ', > calculation = 'cp', > restart_mode = 'from_scratch', > pseudo_dir = '$PSEUDO/', > outdir='$TMP_DIR/', > ndr = 51, > ndw = 51, > nstep = 50, > iprint = 10, > isave = 100, > tstress = .TRUE., > tprnfor = .TRUE., > dt = 5.0d0, > etot_conv_thr = 1.d-9, > ekin_conv_thr = 1.d-4, > prefix = 'si' > / > > &SYSTEM > ibrav = 1, > celldm = 10.61, > nat = 2, > ntyp = 1, > nbnd = 4, > nelec = 8, > ecutwfc = 8.0, > xc_type = 'BLYP' > / > > &ELECTRONS > emass = 400.d0, > emass_cutoff = 2.5d0, > orthogonalization = 'ortho', > ortho_eps = 5.d-8, > ortho_max = 15, > electron_dynamics = 'sd', > ! electron_damping = 0.3, > electron_velocities = 'zero', > electron_temperature = 'not_controlled', > / > > &IONS > ion_dynamics = 'verlet', > ion_damping = 0.2, > ion_radius(1) = 0.8d0, > ion_radius(2) = 0.8d0, > ion_velocities = 'zero', > ion_temperature = 'nose', > tempw = 1000, > fnosep = 1.2, > tolp=100, > ion_nstepe = 10 > / > > &CELL > cell_dynamics = 'pr', > cell_velocities = 'zero', > press = 0.0d0, > / > > ATOMIC_SPECIES > Si 28.086 Si.vbc.UPF 4 > > ATOMIC_POSITIONS > Si 0.00 0.00 0.00 > Si 0.00 0.00 0.10 > > K_POINTS > 1 > 0.0 0.0 0.0 1.0 > EOF > > $PW_ROOT/par2.x < sih.cp1.in > Si.md64H.out > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From giannozz at nest.sns.it Tue Nov 23 18:58:56 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 23 Nov 2004 18:58:56 +0100 Subject: [Pw_forum] convergence NOT achieved, stopping(additional information) In-Reply-To: <001a01c4cfb7$8c40fa90$a06510ac@aeoi.org.ir> References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> <001a01c4cfb7$8c40fa90$a06510ac@aeoi.org.ir> Message-ID: <200411231858.56005.giannozz@nest.sns.it> On Sunday 21 November 2004 11:47, Mahmoud Payami wrote: > I prepared the input for O3 case but I encounter with the message [...] > convergence NOT achieved, stopping use a small gaussian broadening -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From mpayami at aeoi.org.ir Wed Nov 24 09:41:03 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 24 Nov 2004 12:11:03 +0330 Subject: [Pw_forum] convergence NOT achieved, stopping(additional information) References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> <001a01c4cfb7$8c40fa90$a06510ac@aeoi.org.ir> <200411231858.56005.giannozz@nest.sns.it> Message-ID: <000601c4d201$5509c380$a06510ac@aeoi.org.ir> Dear Paolo, Thank you very much for your reply. But I am not doing a metal slab claculation ( for example Al001). As I understood, degauss is used for metals' Brillouin Z integrations and it is available in the input file for the slab example. But in the CO input file, there is no entry for degauss and the default is taken to be 0.d0. My input file is as follows: ----------------- &CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/home/nis/mahmoud/tmp/' , pseudo_dir = '/home/nis/SHARED_FOLDER/pw2.1/pseudo/' , prefix = 'O3' , / &SYSTEM ibrav = 0, nat = 3, ntyp = 1, ecutwfc = 24.0 , ecutrho = 144.0 , / &ELECTRONS electron_maxstep = 1000, conv_thr = 1.0d-6 , mixing_beta = 0.7 , / &IONS upscale = 10 , / CELL_PARAMETERS cubic 20.000000000 0.000000000 0.000000000 0.000000000 20.000000000 0.000000000 0.000000000 0.000000000 20.000000000 ATOMIC_SPECIES O 16.00000 O.LDA.US.RRKJ3.UPF ATOMIC_POSITIONS bohr O 1.356000000 0.000000000 0.000000000 1 1 1 O -1.356000000 0.000000000 0.000000000 1 1 1 O 0.000000000 1.356000000 0.000000000 1 1 1 K_POINTS gamma ----------------------------- Should I change/add any parameters to achieve the convergency? Best regards, Mahmoud Payami > On Sunday 21 November 2004 11:47, Mahmoud Payami wrote: > >> I prepared the input for O3 case but I encounter with the message [...] >> convergence NOT achieved, stopping > > use a small gaussian broadening > > -- > Paolo Giannozzi e-mail: giannozz at nest.sns.it > Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 > Piazza dei Cavalieri 7 I-56126 Pisa, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at nest.sns.it Wed Nov 24 09:53:12 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 24 Nov 2004 09:53:12 +0100 Subject: [Pw_forum] convergence NOT achieved, stopping(additional information) In-Reply-To: <000601c4d201$5509c380$a06510ac@aeoi.org.ir> References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> <200411231858.56005.giannozz@nest.sns.it> <000601c4d201$5509c380$a06510ac@aeoi.org.ir> Message-ID: <200411240953.12943.giannozz@nest.sns.it> On Wednesday 24 November 2004 09:41, Mahmoud Payami wrote: > [...] I am not doing a metal slab calculation ( for example Al001). from the manual: -- Self-consistency is slow or does not converge. [...] If the highest occupied and lowest unoccupied state(s) keep exchanging place during self-consistency, forget about reaching convergence. A typical sign of such behavior is that the self-consistency error goes down, down, down, than all of a sudden up again, and so on. Usually one can solve the problem by adding a few empty bands and a broadening. -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From mpayami at aeoi.org.ir Wed Nov 24 10:34:17 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 24 Nov 2004 13:04:17 +0330 Subject: [Pw_forum] convergence NOT achieved, stopping(additional information) References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> <200411231858.56005.giannozz@nest.sns.it> <000601c4d201$5509c380$a06510ac@aeoi.org.ir> <200411240953.12943.giannozz@nest.sns.it> Message-ID: <001101c4d208$c4e9bb40$a06510ac@aeoi.org.ir> Dear Paolo, Thank you very much for your advice and I appologize that I did not notice this point in the manual. My case is exactly the same as you mentioned. I should learn how to add empty bands. Thank you again. Best regards, Mahmoud > On Wednesday 24 November 2004 09:41, Mahmoud Payami wrote: > >> [...] I am not doing a metal slab calculation ( for example Al001). > > from the manual: > -- > Self-consistency is slow or does not converge. > > [...] If the highest occupied and lowest unoccupied state(s) keep > exchanging place during self-consistency, forget about reaching > convergence. A typical sign of such behavior is that the self-consistency > error goes down, down, down, than all of a sudden up again, and so on. > Usually one can solve the problem by adding a few empty bands and a > broadening. > -- > Paolo Giannozzi e-mail: giannozz at nest.sns.it > Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 > Piazza dei Cavalieri 7 I-56126 Pisa, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From gn203 at hermes.cam.ac.uk Thu Nov 25 10:49:47 2004 From: gn203 at hermes.cam.ac.uk (Gana Natarajan) Date: Thu, 25 Nov 2004 09:49:47 +0000 (GMT) Subject: [Pw_forum] Ionic temperature control Message-ID: Dear Authors, Could you please clarify whether the Nose thermostat and velocity rescaling features in PWSCF 2.1 are working or let me know if it will be possible to get them to work. I need these to create a glass using the melt and quench MD method, but I don't wish to use the Car-Parrinello dynamics found in CP or FPMD. Thanks, Gana ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Gana Natarajan Ph. D Student Amorphous Materials Group Department of Chemistry Lensfield Road Cambridge CB2 1EW United Kingdom Tel: +44 -(01223) 336 532 Fax: +44- (01223) 336 362 From sbraccia at sissa.it Fri Nov 26 11:54:31 2004 From: sbraccia at sissa.it (sbraccia carlo) Date: Fri, 26 Nov 2004 11:54:31 +0100 Subject: [Pw_forum] Ionic temperature control In-Reply-To: References: Message-ID: <41A70B67.4040204@sissa.it> Dear Gana, Nose thermostat is not implemented in the pwscf code whereas it is in both the CP codes of the espresso package. PWscf implements a simple velocity rescaling (it is coded in the routine PW/dynamics.f90, where you can find also some instructions on how to use it) whose control variables are described in the Doc/INPUT_PW file. If you absolutely need the nose-hoover thermostat and if you have a routine that implements it (as those typically used in classical MD codes), I'll try to include it in the pwscf. Best, carlo Gana Natarajan wrote: > Dear Authors, > > Could you please clarify whether the Nose thermostat and velocity > rescaling features in PWSCF 2.1 are working or let me know if it will be > possible to get them to work. > I need these to create a glass using the melt and quench MD method, but I > don't wish to use the Car-Parrinello dynamics found in CP or FPMD. > > Thanks, > > Gana > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > Gana Natarajan > Ph. D Student > Amorphous Materials Group Department of Chemistry > Lensfield Road > Cambridge CB2 1EW > United Kingdom > Tel: +44 -(01223) 336 532 > Fax: +44- (01223) 336 362 > > > > > > > > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From ggarcia at fis.puc.cl Fri Nov 26 23:22:02 2004 From: ggarcia at fis.puc.cl (Griselda Garcia) Date: Fri, 26 Nov 2004 19:22:02 -0300 Subject: [Pw_forum] about the option "ocupations = 'from_input'" Message-ID: <200411262234.iAQMYfc1017783@fis.puc.cl> Dear PW's users, We are new users of PWscf program and we are having troubles to set up calculations on small Pd clusters. We want to use the occupation given in the input instead of occupation='smearing' option but we do not know how to write the corresponding lines in the right way; we just obtain the message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from setup: error # strange occupations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... In some of the examples given with the code, we found some references to this options but we could really do not understand them. In the input file we should put the lines OCCUPATIONS AA BB CC DD (and in the spin-polarized case we should put two lines, one for each spin type.) Which is the meaning of AA, BB, CC, DD?? ... is the total s-charge, p-charge, d-charge and f-charge? or are the occupation of each bands (related to nbns)? We had trying putting, for Pd for instance ([Kr]4d10), OCCUPATIONS 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.0 but the message was the showed above. We tried to find some comment about this topic in the mailing list but we did not find nothing. In the attach file we send onde of the input that we use. Thanks a lot!! ... your help will be very welcome. Regards, Jose and Griselda. -------------- next part -------------- &CONTROL title = 'Un dimero de Paladio PBE' , calculation = 'relax' , restart_mode = 'from_scratch' , outdir = './' , pseudo_dir = '/home/jrogan/ab-initio/PWscf/pseudo/' , prefix = 'Pd' , verbosity = 'high' , / &SYSTEM ibrav = 0, celldm(1) = 0, nat = 2, ntyp = 1, ecutwfc = 90 , ecutrho = 360 , nosym = .true. , occupations = 'from_input', nbnd = 8 , nspin = 2, starting_magnetization(1) = 0.5d0, / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / &IONS upscale = 10 , / CELL_PARAMETERS cubic 32.000000000 0.000000000 0.000000000 0.000000000 32.000000000 0.000000000 0.000000000 0.000000000 32.000000000 ATOMIC_SPECIES Pd 106.42 Pd.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS angstrom Pd 9.20000000 8.00000000 8.00000000 1 1 1 Pd 6.80000000 8.00000000 8.00000000 1 1 1 K_POINTS AUTOMATIC 1 1 1 0 0 0 OCCUPATIONS 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.0 From mpayami at aeoi.org.ir Sun Nov 28 10:54:49 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Sun, 28 Nov 2004 13:24:49 +0330 Subject: [Pw_forum] convergence NOT achieved, stopping(additional information) References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> <200411231858.56005.giannozz@nest.sns.it> <000601c4d201$5509c380$a06510ac@aeoi.org.ir> <200411240953.12943.giannozz@nest.sns.it> Message-ID: <000901c4d530$4cb6c750$a06510ac@aeoi.org.ir> Dear Paolo, Thank you very much for your advice. It works well by broadening. With kind regards, Mahmoud > from the manual: > -- > Self-consistency is slow or does not converge. > > [...] If the highest occupied and lowest unoccupied state(s) keep > exchanging place during self-consistency, forget about reaching > convergence. A typical sign of such behavior is that the self-consistency > error goes down, down, down, than all of a sudden up again, and so on. > Usually one can solve the problem by adding a few empty bands and a > broadening. > -- > Paolo Giannozzi e-mail: giannozz at nest.sns.it > Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 > Piazza dei Cavalieri 7 I-56126 Pisa, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mpayami at aeoi.org.ir Sun Nov 28 10:56:45 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Sun, 28 Nov 2004 13:26:45 +0330 Subject: [Pw_forum] Whirlgif References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> <200411231858.56005.giannozz@nest.sns.it> <000601c4d201$5509c380$a06510ac@aeoi.org.ir> <200411240953.12943.giannozz@nest.sns.it> Message-ID: <000c01c4d530$92294060$a06510ac@aeoi.org.ir> Dear Tone, Where can I find "whirlgif" executable file? Best regards, Mahmoud From proffess at yandex.ru Sun Nov 28 18:55:07 2004 From: proffess at yandex.ru (Sergey Lisenkov) Date: Sun, 28 Nov 2004 20:55:07 +0300 (MSK) Subject: [Pw_forum] Ge ultrasoft pseudopotential Message-ID: <41AA10FB.000043.16124@tide.yandex.ru> Dear PWscf users and authors, Does anybody have a pseudopotential (ultrasoft) for Germanium? There is no this PP in Vanderbilt official library, but there is PP in CAMPOS format (binary). Thanks for your help, Best wishes, Sergey From xywu at imr.ac.cn Mon Nov 29 09:30:24 2004 From: xywu at imr.ac.cn (xywu) Date: Mon, 29 Nov 2004 16:30:24 +0800 Subject: [Pw_forum] how to investigate the electric field effect by pwscf Message-ID: <000d01c4d5ed$aca81ac0$0200a8c0@wang> Dear all PWscf users, I want to investigate the electric field effect by pwscf . How to use pwscf by density-functional perturbation theory or self-consistent finite electric field. I did not find those from the manual. Thank you in advance! -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041129/c6036159/attachment.htm From xywu at imr.ac.cn Mon Nov 29 09:36:05 2004 From: xywu at imr.ac.cn (xywu) Date: Mon, 29 Nov 2004 16:36:05 +0800 Subject: [Pw_forum] : how to investigate the electric field effect by pwscf Message-ID: <000801c4d5ee$77d66ad0$0200a8c0@wang> Dear all PWscf users, I want to investigate the electric field effect by pwscf . How to use pwscf by density-functional perturbation theory or self-consistent finite electric field. I did not find those from the manual. Thank you in advance! From sunsr at ihep.ac.cn Mon Nov 29 10:06:22 2004 From: sunsr at ihep.ac.cn (Shaorui Sun) Date: Mon, 29 Nov 2004 17:6:22 +0800 Subject: [Pw_forum] question about the core charge Message-ID: <200411290845.iAT8jHi3017676@mail.ihep.ac.cn> Dear all: when I use the pwscf to calculate the HgS crystal,there is a warning occurring before the 1st iteration as follows: warning: negative or imaginary core charge -0.000077 0.000000 who can tell me what is the matter, and how can I solve it? Best Regards! S. R. Sun --------------------------------------------- Beijing Synchrotron Radiation Facility Institute of High Energy Physics Chinese Academy of Sciences P. O. Box 918, 100049 Beijing P. R. China Tel: 0086+10 88236710 email:sunsr at ihep.ac.cn From proffess at yandex.ru Mon Nov 29 10:23:50 2004 From: proffess at yandex.ru (Sergey Lisenkov) Date: Mon, 29 Nov 2004 12:23:50 +0300 (MSK) Subject: [Pw_forum] question about the core charge In-Reply-To: <200411290845.iAT8jHi3017676@mail.ihep.ac.cn> References: <200411290845.iAT8jHi3017676@mail.ihep.ac.cn> Message-ID: <41AAEAA6.000001.10517@soapbox.yandex.ru> Dear S.R. Sun, Please read carefully the manual, it is fully explained there. Sergey From giannozz at nest.sns.it Mon Nov 29 10:32:36 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 29 Nov 2004 10:32:36 +0100 Subject: [Pw_forum] question about the core charge In-Reply-To: <200411290845.iAT8jHi3017676@mail.ihep.ac.cn> References: <200411290845.iAT8jHi3017676@mail.ihep.ac.cn> Message-ID: <200411291032.36344.giannozz@nest.sns.it> On Monday 29 November 2004 10:06, Shaorui Sun wrote: > when I use the pwscf to calculate the HgS crystal,there is a warning > occurring before the 1st iteration as follows: warning: negative or > imaginary core charge -0.000077 0.000000 who can tell me what > is the matter, and how can I solve it? see http://www.democritos.it/pipermail/pw_forum/2004-July/001127.html (you can ignore the warning, anyway) To everybody: in the home page www.pwscf.org, under "Users' forum", there is a link "Search Archive". Use it before posting: your questions might have been already answered (I followed this link and typed "pw_forum negative charge" to find the above message) Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From sbraccia at sissa.it Mon Nov 29 10:32:13 2004 From: sbraccia at sissa.it (sbraccia carlo) Date: Mon, 29 Nov 2004 10:32:13 +0100 Subject: [Pw_forum] question about the core charge In-Reply-To: <200411290845.iAT8jHi3017676@mail.ihep.ac.cn> References: <200411290845.iAT8jHi3017676@mail.ihep.ac.cn> Message-ID: <41AAEC9D.3030801@sissa.it> Dear Shaorui Sun, consider that on the web-page of pwscf (www.pwscf.org) there is the possibility of doing searches on previous questions and answers appeared in the mailing list (the column on the right). If you type "core charge" you will get a lot of messages that will answer your doubts. Best, carlo From baroni at sissa.it Mon Nov 29 10:35:03 2004 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 29 Nov 2004 10:35:03 +0100 Subject: [Pw_forum] question about the core charge In-Reply-To: <200411290845.iAT8jHi3017676@mail.ihep.ac.cn> References: <200411290845.iAT8jHi3017676@mail.ihep.ac.cn> Message-ID: Hi Sun: here attached I join a copy of one of the many answers already given to your question which has been asked many times already. We know that the manual is (still ;-) far from being perfect, but I recommend that, before, you post questions like this, you make a search in the archive of the pw users' mailing list (righ-bottom button in the Pwscf.org home page). The Message attached was found in less than 10 secs! Thank you for your interest and support. Yours - SB On Nov 29, 2004, at 10:06 AM, Shaorui Sun wrote: > Dear all: > when I use the pwscf to calculate the HgS crystal,there is a > warning occurring before the 1st iteration as follows: > warning: negative or imaginary core charge -0.000077 0.000000 > who can tell me what is the matter, and how can I solve it? > > Best Regards! > S. R. Sun > --------------------------------------------- > Beijing Synchrotron Radiation Facility > Institute of High Energy Physics > Chinese Academy of Sciences > P. O. Box 918, 100049 Beijing > P. R. China > Tel: 0086+10 88236710 > email:sunsr at ihep.ac.cn > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > [Pw_forum] Warning message - negative or imaginary core charge Paolo Giannozzi pw_forum at pwscf.org Thu, 1 Jul 2004 16:27:53 +0200 ? Previous message: [Pw_forum] Warning message - negative or imaginary core charge ? Next message: [Pw_forum] Setting the scale in plotrho ? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] On Thursday 01 July 2004 05:37, Aloysius Soon Sze Lok wrote: > warning: negative or imaginary core charge -0.000003 0.000000 > [...] Is this a serious warning? no > Or is the value of -0.000003 small enough to ignore? definitely > May I know the implications, please? in this particular case, none. In general: if you transform a positive function in real space to Fourier space and truncate at some finite cutoff, your positive function is no longer guaranteed to be positive when you transform back to real space. This happens only with core corrections and with ultrasoft pseudopotentials. It can be a a source of trouble, but it is usually solved by increasing the cutoff for the charge density Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy ? Previous message: [Pw_forum] Warning message - negative or imaginary core charge ? Next message: [Pw_forum] Setting the scale in plotrho ? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] --- Stefano Baroni --- SISSA & DEMOCRITOS National Simulation Center via Beirut 2-4 34014 Trieste Grignano / [+39] 040 3787 406 (tel) -528 (fax) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 4708 bytes Desc: not available Url : /pipermail/attachments/20041129/18ed7379/attachment.bin From xywu at imr.ac.cn Mon Nov 29 11:30:24 2004 From: xywu at imr.ac.cn (xywu) Date: Mon, 29 Nov 2004 18:30:24 +0800 Subject: [Pw_forum] how to investigate the electric field effect by pwscf Message-ID: <000501c4d5fe$6fcc3580$338248d2@www> For the encode is unshown, i send it again. Dear all PWscf users, I want to investigate the electric field effect by pwscf . How to use pwscf by density-functional perturbation theory or self-consistent finite electric field. I did not find those from the manual. Thank you in advance! From dalcorso at sissa.it Mon Nov 29 11:35:02 2004 From: dalcorso at sissa.it (Andrea Dal Corso) Date: 29 Nov 2004 11:35:02 +0100 Subject: [Pw_forum] how to investigate the electric field effect by pwscf In-Reply-To: <000501c4d5fe$6fcc3580$338248d2@www> References: <000501c4d5fe$6fcc3580$338248d2@www> Message-ID: <1101724502.1449.19.camel@localhost.localdomain> From giannozz at nest.sns.it Mon Nov 29 11:54:16 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 29 Nov 2004 11:54:16 +0100 Subject: [Pw_forum] how to investigate the electric field effect by pwscf In-Reply-To: <000d01c4d5ed$aca81ac0$0200a8c0@wang> References: <000d01c4d5ed$aca81ac0$0200a8c0@wang> Message-ID: <200411291154.16735.giannozz@nest.sns.it> On Monday 29 November 2004 09:30, xywu wrote: > How to use pwscf by density-functional perturbation theory see documentaion for code "phonon" > or self-consistent finite electric field "true" finite field is not presently implemented. Somebody promised an implementation months ago: I am still waiting. What is implemented is the addition of a sawlike potential that simulates the effect of the electric field in a supercell (see the preceding message by Andrea) Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From Tone.Kokalj at ijs.si Mon Nov 29 11:53:12 2004 From: Tone.Kokalj at ijs.si (Tone Kokalj) Date: Mon, 29 Nov 2004 11:53:12 +0100 Subject: [Pw_forum] Whirlgif In-Reply-To: <000c01c4d530$92294060$a06510ac@aeoi.org.ir> References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> <200411231858.56005.giannozz@nest.sns.it> <000601c4d201$5509c380$a06510ac@aeoi.org.ir> <200411240953.12943.giannozz@nest.sns.it> <000c01c4d530$92294060$a06510ac@aeoi.org.ir> Message-ID: <20041129105311.GB21723@crysden.ijs.si> On Sun, Nov 28, 2004 at 01:26:45PM +0330, Mahmoud Payami wrote: > Dear Tone, > > Where can I find "whirlgif" executable file? Well, the source is available from: http://www.danbbs.dk/~dino/whirlgif/ For Debain based Linux systems, you can simply do: apt-get install whirlgif You can also get the package in RPM form: http://rpmfind.net/linux/RPM/contrib/libc6/i386/whirlgif-2.01-8.i386.html Regards, Tone -- +------------------------------------------------------------------------+ | Anton Kokalj Email: Tone.Kokalj at ijs.si | | Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 | | Jozef Stefan Institute Fax: x 386 1 477 3811 | | Jamova 39, SI-1000 Ljubljana | | SLOVENIA | +------------------------------------------------------------------------+ !!! *** please, do not send me attachments in any Microsoft format *** !!! From mpayami at aeoi.org.ir Mon Nov 29 13:09:30 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Mon, 29 Nov 2004 15:39:30 +0330 Subject: [Pw_forum] Whirlgif References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> <200411231858.56005.giannozz@nest.sns.it> <000601c4d201$5509c380$a06510ac@aeoi.org.ir> <200411240953.12943.giannozz@nest.sns.it> <000c01c4d530$92294060$a06510ac@aeoi.org.ir> <20041129105311.GB21723@crysden.ijs.si> Message-ID: <000601c4d60c$4822d350$a06510ac@aeoi.org.ir> Dear Tone, Thank you very much for your reply. Last night I downloaded the second choice (rpm) and installed. But I could not make an animated gif from the output of running pw.x with 'relax' (i.e. example 03). Does it need any elaboration or just clicking the buttons should work? Best regards, Mahmoud > > Well, the source is available from: > > http://www.danbbs.dk/~dino/whirlgif/ > > For Debain based Linux systems, you can simply do: > > apt-get install whirlgif > > > You can also get the package in RPM form: > > http://rpmfind.net/linux/RPM/contrib/libc6/i386/whirlgif-2.01-8.i386.html > > Regards, Tone > > -- > +------------------------------------------------------------------------+ > | Anton Kokalj Email: Tone.Kokalj at ijs.si | > | Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 | > | Jozef Stefan Institute Fax: x 386 1 477 3811 | > | Jamova 39, SI-1000 Ljubljana | > | SLOVENIA | > +------------------------------------------------------------------------+ > !!! *** please, do not send me attachments in any Microsoft format *** !!! > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From gn203 at cam.ac.uk Wed Nov 24 12:25:34 2004 From: gn203 at cam.ac.uk (Gana Natarajan) Date: Wed, 24 Nov 2004 11:25:34 +0000 Subject: [Pw_forum] Nose thermostat Message-ID: <41A46FAE.7020907@cam.ac.uk> Dear all, I wish to use the Nose thermostat for MD creation of a glass using pwscf 2.1. The input option 'nose' for the ion_temperature keyword is not recognised but there seem to be routines in pwscf for the Nose thermostat. Please clarify this and let me know if it is possible to use the Nose thermostat. Thanks, Gana From asen at iitk.ac.in Mon Nov 29 13:50:12 2004 From: asen at iitk.ac.in (A Sen) Date: Mon, 29 Nov 2004 18:20:12 +0530 (IST) Subject: [Pw_forum] compilation error Message-ID: <2459.172.28.37.41.1101732612.squirrel@nwebmail.iitk.ac.in> Dear Friends, While trying to compile the ESPRESSO package I came across the following errors: MODULE complex_diis_module ^ f90-855 f90: ERROR COMPLEX_DIIS_MODULE, File = complex_diis_module.f90, Line = 24, Column = 8 The compiler has detected errors in module "COMPLEX_DIIS_MODULE". No module information file will be created for this module. FORALL( ib = 1: nbnd, ( .NOT. conv(ib) ) ) ^ f90-197 f90: ERROR INIT_STEPS, File = complex_diis_module.f90, Line = 339, Column = 35 Unexpected syntax: "index-name or mask expression" was expected but found "(". END FORALL ^ f90-289 f90: ERROR INIT_STEPS, File = complex_diis_module.f90, Line = 343, Column = 13 This END FORALL statement has no matching FORALL statement. FORALL( ib = 1: nbnd_diis, ( .NOT. conv(ib) ) ) ^ f90-197 f90: ERROR DIIS_WITH_ORTHO, File = complex_diis_module.f90, Line = 673, Column = 37 Unexpected syntax: "index-name or mask expression" was expected but found "(". END FORALL ^ f90-289 f90: ERROR DIIS_WITH_ORTHO, File = complex_diis_module.f90, Line = 677, Column = 10 This END FORALL statement has no matching FORALL statement. f90: MIPSpro Fortran 90 Version 7.3 (f52) Mon Nov 29, 2004 17:31:27 f90: 1189 source lines f90: 5 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s) cf90: "explain cf90-message number" gives more information about each message *** Error code 2 (bu21) *** Error code 1 (bu21) I would greatly appreciate if you kindly help me detect as to where I was specifically wrong in the compilation of the ESPRESSO package. With regards, A. Sen ================================================================ Arijit Sen, PhD | Tel: +91-5122597092 Research Associate | Fax: +91-5122590914 480,Faculty Building | Mobile: +91-9935388842 Department of Physics | Email: asen at iitk.ac.in Indian Institute of Technology | dr_asen at yahoo.co.in Kanpur 208016, INDIA | Dr.Arijit.Sen at gmail.com ================================================================ From Tone.Kokalj at ijs.si Mon Nov 29 15:03:41 2004 From: Tone.Kokalj at ijs.si (Tone Kokalj) Date: Mon, 29 Nov 2004 15:03:41 +0100 Subject: [Pw_forum] Whirlgif In-Reply-To: <000601c4d60c$4822d350$a06510ac@aeoi.org.ir> References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> <200411231858.56005.giannozz@nest.sns.it> <000601c4d201$5509c380$a06510ac@aeoi.org.ir> <200411240953.12943.giannozz@nest.sns.it> <000c01c4d530$92294060$a06510ac@aeoi.org.ir> <20041129105311.GB21723@crysden.ijs.si> <000601c4d60c$4822d350$a06510ac@aeoi.org.ir> Message-ID: <20041129140341.GA21832@crysden.ijs.si> On Mon, Nov 29, 2004 at 03:39:30PM +0330, Mahmoud Payami wrote: > Dear Tone, > > Thank you very much for your reply. Last night I downloaded the second > choice (rpm) and installed. But I could not make an animated gif from the > output of running pw.x with 'relax' (i.e. example 03). I would need more description of problem in order to help you. > Does it need any elaboration or just clicking the buttons should work? You should edit the $HOME/.xcrysden/custom-definitions file and defined the whirlgif as follows: # ------------------------------------------------------------------------ # With "whirlgif" program XCRYSDEN can create an Animated-GIF image # ------------------------------------------------------------------------ set xcMisc(whirlgif) /usr/bin/whirlgif On my computer whirlgif is in /usr/bin, you should replace /usr/bin with your path of whirlgif. Regards, Tone -- +------------------------------------------------------------------------+ | Anton Kokalj Email: Tone.Kokalj at ijs.si | | Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 | | Jozef Stefan Institute Fax: x 386 1 477 3811 | | Jamova 39, SI-1000 Ljubljana | | SLOVENIA | +------------------------------------------------------------------------+ !!! *** please, do not send me attachments in any Microsoft format *** !!! From sbraccia at sissa.it Mon Nov 29 15:12:05 2004 From: sbraccia at sissa.it (sbraccia carlo) Date: Mon, 29 Nov 2004 15:12:05 +0100 Subject: [Pw_forum] compilation error In-Reply-To: <2459.172.28.37.41.1101732612.squirrel@nwebmail.iitk.ac.in> References: <2459.172.28.37.41.1101732612.squirrel@nwebmail.iitk.ac.in> Message-ID: <41AB2E35.3050001@sissa.it> Dear A Sen, try to search in the mailing list (in the home page www.pwscf.org, under "Users' forum",there is a link "Search Archive") for "compilation error sgi". You will see that a similar question has already been answered in september. Bset, carlo A Sen wrote: > Dear Friends, > While trying to compile the ESPRESSO package I came across the > following errors: > > MODULE complex_diis_module > ^ > f90-855 f90: ERROR COMPLEX_DIIS_MODULE, File = complex_diis_module.f90, > Line = 24, Column = 8 > The compiler has detected errors in module "COMPLEX_DIIS_MODULE". No > module information file will be created for this module. > > FORALL( ib = 1: nbnd, ( .NOT. conv(ib) ) ) > ^ > f90-197 f90: ERROR INIT_STEPS, File = complex_diis_module.f90, Line = 339, > Column = 35 > Unexpected syntax: "index-name or mask expression" was expected but > found "(". > END FORALL > ^ > f90-289 f90: ERROR INIT_STEPS, File = complex_diis_module.f90, Line = 343, > Column = 13 > This END FORALL statement has no matching FORALL statement. > > FORALL( ib = 1: nbnd_diis, ( .NOT. conv(ib) ) ) > ^ > f90-197 f90: ERROR DIIS_WITH_ORTHO, File = complex_diis_module.f90, Line = > 673, > Column = 37 > Unexpected syntax: "index-name or mask expression" was expected but > found "(". > END FORALL > ^ > f90-289 f90: ERROR DIIS_WITH_ORTHO, File = complex_diis_module.f90, Line = > 677, > Column = 10 > This END FORALL statement has no matching FORALL statement. > > f90: MIPSpro Fortran 90 Version 7.3 (f52) Mon Nov 29, 2004 17:31:27 > f90: 1189 source lines > f90: 5 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s) > cf90: "explain cf90-message number" gives more information about each message > *** Error code 2 (bu21) > *** Error code 1 (bu21) > > I would greatly appreciate if you kindly help me detect as to where I was > specifically wrong in the compilation of the ESPRESSO package. > > With regards, > A. Sen > > ================================================================ > Arijit Sen, PhD | Tel: +91-5122597092 > Research Associate | Fax: +91-5122590914 > 480,Faculty Building | Mobile: +91-9935388842 > Department of Physics | Email: asen at iitk.ac.in > Indian Institute of Technology | dr_asen at yahoo.co.in > Kanpur 208016, INDIA | Dr.Arijit.Sen at gmail.com > ================================================================ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mpayami at aeoi.org.ir Mon Nov 29 15:50:09 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Mon, 29 Nov 2004 18:20:09 +0330 Subject: [Pw_forum] Whirlgif References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> <200411231858.56005.giannozz@nest.sns.it> <000601c4d201$5509c380$a06510ac@aeoi.org.ir> <200411240953.12943.giannozz@nest.sns.it> <000c01c4d530$92294060$a06510ac@aeoi.org.ir> <20041129105311.GB21723@crysden.ijs.si> <000601c4d60c$4822d350$a06510ac@aeoi.org.ir> <20041129140341.GA21832@crysden.ijs.si> Message-ID: <001201c4d622$b8e11f50$a06510ac@aeoi.org.ir> my "whirlgif" is also in /usr/bin so i did not change the custom-defs. I obtain a lot (say some 10) of gif files named anim-x.gif (x=0,1,2,3,..) using the arrow key pointing to the right and clicking repeatedly until it shows "slide 21/21". Then by stopping, i enter a name which creates a large file (about 8 MB) with name we enter in the process of saving. However, I do not know how to run animation. Best regards, Mahmoud > > I would need more description of problem in order to help you. > > >> Does it need any elaboration or just clicking the buttons should work? > > You should edit the $HOME/.xcrysden/custom-definitions file and > defined the whirlgif as follows: > > # ------------------------------------------------------------------------ > # With "whirlgif" program XCRYSDEN can create an Animated-GIF image > # ------------------------------------------------------------------------ > > set xcMisc(whirlgif) /usr/bin/whirlgif > > On my computer whirlgif is in /usr/bin, you should replace /usr/bin > with your path of whirlgif. > > Regards, Tone > > -- > +------------------------------------------------------------------------+ > | Anton Kokalj Email: Tone.Kokalj at ijs.si | > | Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 | > | Jozef Stefan Institute Fax: x 386 1 477 3811 | > | Jamova 39, SI-1000 Ljubljana | > | SLOVENIA | > +------------------------------------------------------------------------+ > !!! *** please, do not send me attachments in any Microsoft format *** !!! > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From Tone.Kokalj at ijs.si Mon Nov 29 16:16:23 2004 From: Tone.Kokalj at ijs.si (Tone Kokalj) Date: Mon, 29 Nov 2004 16:16:23 +0100 Subject: [Pw_forum] Whirlgif In-Reply-To: <001201c4d622$b8e11f50$a06510ac@aeoi.org.ir> References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> <200411231858.56005.giannozz@nest.sns.it> <000601c4d201$5509c380$a06510ac@aeoi.org.ir> <200411240953.12943.giannozz@nest.sns.it> <000c01c4d530$92294060$a06510ac@aeoi.org.ir> <20041129105311.GB21723@crysden.ijs.si> <000601c4d60c$4822d350$a06510ac@aeoi.org.ir> <20041129140341.GA21832@crysden.ijs.si> <001201c4d622$b8e11f50$a06510ac@aeoi.org.ir> Message-ID: <20041129151623.GA22123@crysden.ijs.si> On Mon, Nov 29, 2004 at 06:20:09PM +0330, Mahmoud Payami wrote: > my "whirlgif" is also in /usr/bin so i did not change the custom-defs. > I obtain a lot (say some 10) of gif files named anim-x.gif (x=0,1,2,3,..) > using the arrow key pointing to the right and clicking repeatedly until it > shows "slide 21/21". Then by stopping, i enter a name which creates a large > file (about 8 MB) with name we enter in the process of saving. > However, I do not know how to run animation. OK, this large file is the animated GIF. You can use some animated GIF viewer to view it. Here are some possibilities: + xanim + WEB browsers (mozilla, netscape, ...) + OpenOffice impress (for presentations) + ... Regards, Tone -- +------------------------------------------------------------------------+ | Anton Kokalj Email: Tone.Kokalj at ijs.si | | Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 | | Jozef Stefan Institute Fax: x 386 1 477 3811 | | Jamova 39, SI-1000 Ljubljana | | SLOVENIA | +------------------------------------------------------------------------+ !!! *** please, do not send me attachments in any Microsoft format *** !!! From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Mon Nov 29 16:41:38 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Mon, 29 Nov 2004 16:41:38 +0100 (CET) Subject: [Pw_forum] Whirlgif In-Reply-To: <20041129151623.GA22123@crysden.ijs.si> Message-ID: On Mon, 29 Nov 2004, Tone Kokalj wrote: hi folks, sorry to butt in on this, but you should also consider looking into gifsicle (http://www.lcdf.org/gifsicle/) which is in many ways superior to whirlgif and has a simple viewer for (animated) gifs (=gifview) included. regards, axel. TK> On Mon, Nov 29, 2004 at 06:20:09PM +0330, Mahmoud Payami wrote: TK> > my "whirlgif" is also in /usr/bin so i did not change the custom-defs. TK> > I obtain a lot (say some 10) of gif files named anim-x.gif (x=0,1,2,3,..) TK> > using the arrow key pointing to the right and clicking repeatedly until it TK> > shows "slide 21/21". Then by stopping, i enter a name which creates a large TK> > file (about 8 MB) with name we enter in the process of saving. TK> > However, I do not know how to run animation. TK> TK> OK, this large file is the animated GIF. You can use some animated GIF TK> viewer to view it. Here are some possibilities: TK> TK> + xanim TK> + WEB browsers (mozilla, netscape, ...) TK> + OpenOffice impress (for presentations) TK> + ... TK> TK> Regards, Tone TK> TK> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From mpayami at aeoi.org.ir Mon Nov 29 16:45:32 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Mon, 29 Nov 2004 19:15:32 +0330 Subject: [Pw_forum] Whirlgif References: <000b01c4cfae$e327ec00$a06510ac@aeoi.org.ir> <200411231858.56005.giannozz@nest.sns.it> <000601c4d201$5509c380$a06510ac@aeoi.org.ir> <200411240953.12943.giannozz@nest.sns.it> <000c01c4d530$92294060$a06510ac@aeoi.org.ir> <20041129105311.GB21723@crysden.ijs.si> <000601c4d60c$4822d350$a06510ac@aeoi.org.ir> <20041129140341.GA21832@crysden.ijs.si> <001201c4d622$b8e11f50$a06510ac@aeoi.org.ir> <20041129151623.GA22123@crysden.ijs.si> Message-ID: <001b01c4d62a$75aeb190$a06510ac@aeoi.org.ir> Dear Tone, Thanks a lot! I used Mozzilla. Best regards, Mahmoud > OK, this large file is the animated GIF. You can use some animated GIF > viewer to view it. Here are some possibilities: > > + xanim > + WEB browsers (mozilla, netscape, ...) > + OpenOffice impress (for presentations) > + ... > > Regards, Tone > > -- > +------------------------------------------------------------------------+ > | Anton Kokalj Email: Tone.Kokalj at ijs.si | > | Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 | > | Jozef Stefan Institute Fax: x 386 1 477 3811 | > | Jamova 39, SI-1000 Ljubljana | > | SLOVENIA | > +------------------------------------------------------------------------+ > !!! *** please, do not send me attachments in any Microsoft format *** !!! > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sunsr at ihep.ac.cn Tue Nov 30 04:42:54 2004 From: sunsr at ihep.ac.cn (Shaorui Sun) Date: Tue, 30 Nov 2004 11:42:54 +0800 Subject: [Pw_forum] question about the Hg pseudopotentiel Message-ID: <200411300321.iAU3Lli3020235@mail.ihep.ac.cn> Dear all: when I produce the pseudopotential for the Hg atom, I set the input file for all-electron as follows: ----------------------------------------------- Mercury all-electron &input atom='Hg',file_wavefunctions='hgae1.wfc' config='[Xe] 4f14 5d10 6s2 6p0' rd=3.0, emin=-1.5, emax=0.5, dft='pw91',file_logder='hgae1' &end -------------------------------------------------------------- and the pseudopotential input file as dollows: ------------------------------------------------- Pseudo-Mercury &input atom='Hg',file_wavefunctions='hgps1.wfc' file_pseudo='hgae1.mt', config='5d10 6s2 6p0' rd=3.0, emin=-1.5, emax=0.5,dft='pw91', file_logder='hgae1' &end ------------------------------------------------- but in the pseudopotential output file, there is a warining as follows: ------------------------------------------------ from ld1 : error # -1 warning: convergence not achieved !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Hg MT 6S2.00 Rc=2.77 6P0.00 Rc=2.77 5D**** Rc=2.77 DFT level: SLA-PW -PW91-PW91 Logarithmic grid: 331 points, r(last)= 61.43461 xmin=-8.00 dx=.05000 Convergence (1.0E-14) NOT reached (3.0E-11) in 50 iterations, beta=0.50 ------------------------------------------------------------------ What is the matter, is it a fatal warning, and how can I solve it? Best Regards! S. R. Sun --------------------------------------------- Beijing Synchrotron Radiation Facility Institute of High Energy Physics Chinese Academy of Sciences P. O. Box 918, 100049 Beijing P. R. China Tel: 0086+10 88236710 email:sunsr at ihep.ac.cn From zhupwscf at yahoo.com.cn Tue Nov 30 05:08:14 2004 From: zhupwscf at yahoo.com.cn (=?gb2312?q?=C1=D9=20=D7=A1?=) Date: Tue, 30 Nov 2004 12:08:14 +0800 (CST) Subject: [Pw_forum] electron-band question? Message-ID: <20041130040814.55192.qmail@web15509.mail.cnb.yahoo.com> Dear Dr;: I'm a new user of pwscf.After runing, where can I draw the density of states(DOS) and electronic band graphs? When I calculate the magnetic moment, where can I find the magnetic moment of each atoms and the total magnetic moment of the unit cell? --------------------------------- Do You Yahoo!? ??????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041130/c03a2ff1/attachment.htm -------------- next part -------------- An embedded message was scrubbed... From: =?gb2312?q?=C1=D9=20=D7=A1?= Subject: electron-band question? Date: Tue, 30 Nov 2004 11:56:03 +0800 (CST) Size: 1556 Url: /pipermail/attachments/20041130/c03a2ff1/attachment.eml From mpayami at aeoi.org.ir Tue Nov 30 06:03:36 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Tue, 30 Nov 2004 08:33:36 +0330 Subject: [Pw_forum] Whirlgif References: Message-ID: <000f01c4d699$faab30c0$a06510ac@aeoi.org.ir> Hi Axel, Thank you very much for gifsicle, I downloaded it. Cheers, Mahmoud > hi folks, > > sorry to butt in on this, but you should also consider > looking into gifsicle (http://www.lcdf.org/gifsicle/) > which is in many ways superior to whirlgif and has > a simple viewer for (animated) gifs (=gifview) included. > > regards, > axel. > From giannozz at nest.sns.it Mon Nov 29 01:53:09 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 29 Nov 2004 00:53:09 +0000 Subject: [Pw_forum] about the option "ocupations = 'from_input'" In-Reply-To: <200411262234.iAQMYfc1017783@fis.puc.cl> References: <200411262234.iAQMYfc1017783@fis.puc.cl> Message-ID: <200411290053.09705.giannozz@nest.sns.it> On Friday 26 November 2004 22:22, Griselda Garcia wrote: > Which is the meaning of AA, BB, CC, DD?? ... is the total s-charge, > p-charge, d-charge and f-charge? or are the occupation of each > bands (related to nbns)? the latter > We had trying putting, for Pd for instance ([Kr]4d10), > OCCUPATIONS > 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.0 > 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.0 you cannot do this, in a Kohn-Sham framework: occupied states must have lower energy than empty states > but the message was the showed above. 5 electrons up + 5 electrons down = 10 e ; Pd2 = 20 e => "strange occupations" Paolo From ggarcia at fis.puc.cl Tue Nov 30 13:04:09 2004 From: ggarcia at fis.puc.cl (Griselda Garcia) Date: Tue, 30 Nov 2004 09:04:09 -0300 Subject: [Pw_forum] about the option "ocupations = 'from_input'" In-Reply-To: <200411290053.09705.giannozz@nest.sns.it> References: <200411262234.iAQMYfc1017783@fis.puc.cl> <200411290053.09705.giannozz@nest.sns.it> Message-ID: <200411301217.iAUCHhc1028999@fis.puc.cl> Hello! Thank you! Paolo ... we were wrong considering that the occupation is por type of atoms (ntyp=1). Regards, Griselda. From FB153746 at ATIL.CEA.FR Tue Nov 30 17:08:45 2004 From: FB153746 at ATIL.CEA.FR (=?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?=) Date: Tue, 30 Nov 2004 17:08:45 +0100 Subject: [Pw_forum] mpeg_encode Message-ID: <884193C06D478A4B97B5212C8120A501DC4E71@atil.intra.cea.fr> Dear All, Similarly to the whirlgif program, where can I find mpeg_encode ? Many thanks in advance. Fr?d?ric -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20041130/cdedebac/attachment.htm From sunsr at ihep.ac.cn Sat Nov 13 02:11:37 2004 From: sunsr at ihep.ac.cn (Shaorui Sun) Date: Sat, 13 Nov 2004 9:11:37 +0800 Subject: [Pw_forum] question about special points of Brillouin zone Message-ID: <200503130050.j2D0o7t7017298@mail.ihep.ac.cn> Dear all: I want calculate the phonon of hexagonal structure, and who could tell me the coordinates in reciprocal space of the special points on Brillouin zone boundary, such as M, K, A, H, and L. Best Regards! S. R. Sun --------------------------------------------- Beijing Synchrotron Radiation Facility Institute of High Energy Physics Chinese Academy of Sciences P. O. Box 918, 100049 Beijing P. R. China Tel: 0086+10 88236710 email:sunsr at ihep.ac.cn