From Ari.P.Seitsonen at iki.fi Sun May 2 20:59:15 2004 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Sun, 2 May 2004 20:59:15 +0200 (CEST) Subject: [CPMD-list] ERROR MESSAGE in wavefunction optimization In-Reply-To: <200404300903.08168.a.soon@auckland.ac.nz> References: <200404300903.08168.a.soon@auckland.ac.nz> Message-ID: Dear Aloysius, Since I don't have a pseudo potential for uranium at hand I cannot test your system, but could you either provide me one or at least send the output of your job (how many iterations has CPMD managed to perform before the crash? What is the present convergence at that point?) and the specification of the hardware and software (compiler, libraries, operating system), that might help in finding and hopefully also solving the problem. Some (minor) comments on your input: - You ask for a very, very good convergence on the wave functions, usually 1e-6 is already very good - You want to use the PBE-GGA functional with the Vosko-Wilk-Nusair LDA function, why is that? The former was explicitly designed using the PW92 LDA (which is naturally the default). The difference in the results should not be large, though, I admit - You have a periodic system with a relatively small unit cell but use only the Gamma point for the sampling of the Brillouin zone; in most cases this should lead to converged wave function still (however usually with otherwise bad properties), in some cases the lattice wouldn't even be stable with Gamma only - Just to easen up the creation of the input: "SCALE" in the section '&SYSTEM' allows you to provide the atomic coordinates in scaled units Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland On Fri, 30 Apr 2004, Aloysius Soon Sze Lok wrote: > Dear all, > This was a error msg that I received when I performed a wavefunction > optimization: > > UNIV| THE LEADING MINOR OF ORDER 1 IS NOT POSITIVE DEFINITE, > UNIV| AND THE FACTORIZATION COULD NOT BE COMPLETED. > STOPGM! STACK OF MAIN CALLS: > STOPGM! CALL PCGRAD > STOPGM! CALL RGS > > PROGRAM STOPS IN SUBROUTINE UINV| ILLEGAL RESULTS DPOTRF > > What could the possible reason be? Thanks for your time. > > Attached is the input file. > > > -- > Aloysius Soon SL > Postgraduate Student > Structural & Computational Chemistry > Chemistry Department > The University Of Auckland, New Zealand > Phone: +64 9 373 7599 ext 88291 > Email: a.soon at auckland.ac.nz > From veronique.vanspeybroeck at ugent.be Mon May 3 11:56:38 2004 From: veronique.vanspeybroeck at ugent.be (Veronique Van Speybroeck) Date: Mon, 03 May 2004 11:56:38 +0200 Subject: [CPMD-list] DENSITY.x Message-ID: <40961756.9080102@ugent.be> Hi, does anybody know if the file DENSITY.x is by default written? In my case it is never produced. Do you have to include something special in the input file? Thanks in advance veronique -- ----------------------------------------------------------------------- Dr. ir. Van Speybroeck Veronique Laboratorium voor Theoretische Fysica Universiteit Gent Proeftuinstraat 86 9000 Gent Tel +32-9-264.65.58 GSM : +32/474/259767 Fax +32-9-264.65.60 email : veronique.vanspeybroeck at ugent.be http://inwfaxp2.ugent.be /~web/onderzoek/proj_3.html ----------------------------------------------------------------------- From eunggun.kim at chemistry.gatech.edu Mon May 3 16:40:04 2004 From: eunggun.kim at chemistry.gatech.edu (Eung-Gun Kim) Date: Mon, 3 May 2004 10:40:04 -0400 Subject: [CPMD-list] LSD/KPOINTS and Fermi energy/FEMD Message-ID: <1083595204.409659c4258c5@webmail.mail.gatech.edu> Dear CPMD List Subscribers, While running calculations on an organic crystal and a metal slab with CPMD-3.7.2, I have encountered the following two problems: 1) When I combine LSD with KPOINTS, the program stops with memory-related errors such as "PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (DFNL) [PROC= 0] p0_24396: p4_error: : 999". Reducing the system size doesn't help. 2) How do you obtain the Fermi energy from a FEMD calculation? Thank you very much for reading. Regards, E Kim From Ari.P.Seitsonen at iki.fi Tue May 4 10:45:59 2004 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Tue, 4 May 2004 10:45:59 +0200 (CEST) Subject: [CPMD-list] DENSITY.x In-Reply-To: <40961756.9080102@ugent.be> References: <40961756.9080102@ugent.be> Message-ID: Dear Veronique, The density files are not written by default. They should be written with the keyword 'RHOOUT'. You might also be interested in the option "CUBEFILE DENSITY", however as a &PROPerty calculation. Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland On Mon, 3 May 2004, Veronique Van Speybroeck wrote: > Hi, > > does anybody know if the file DENSITY.x is by default written? In my > case it is never produced. > Do you have to include something special in the input file? > > Thanks in advance > > veronique > > -- > ----------------------------------------------------------------------- > Dr. ir. Van Speybroeck Veronique > Laboratorium voor Theoretische Fysica > Universiteit Gent > Proeftuinstraat 86 > 9000 Gent > Tel +32-9-264.65.58 GSM : +32/474/259767 > Fax +32-9-264.65.60 > email : veronique.vanspeybroeck at ugent.be > http://inwfaxp2.ugent.be /~web/onderzoek/proj_3.html > ----------------------------------------------------------------------- > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From gasser at sciences.univ-metz.fr Wed May 5 00:25:19 2004 From: gasser at sciences.univ-metz.fr (gasser) Date: Wed, 05 May 2004 00:25:19 +0200 Subject: [CPMD-list] Conference LAM12: last circular Message-ID: <4.2.0.58.20040504235606.00ae37c8@bridoux.sciences.univ-metz.fr> (Sorry for crossed posting) Dear Colleagues, With this email we would like to remind you about the: Twelfth International Conference on Liquid and Amorphous Metals (LAM12), which is to be held in Metz 11-16 July 2004 Our main web site: http://lam12.sciences.univ-metz.fr/ contains now all necessary information about the conference and can be considered to be equivalent to the 2nd Circular. Our publication web site: http://www.mines.inpl-nancy.fr/~lam12/ will shortly be updated with instructions for oral and poster presentations as well as for the manuscripts. The papers will be published in Journal of Non Crystalline Solids and will undergo a normal refereering procedure. PLEASE NOTE THAT THE DEADLINE FOR REGISTRATION AND BOOKING OF HOTEL AND STUDENT ROOM ACCOMODATION IS MAY 31, 2004. Please also note that it is still possible to submit an abstract, but for the poster session only. Yours sincerely, With our very best regards. ************************************************ Dr. Monique CALVO-DAHLBORG Pr. Jean-Georges GASSER Chairmen of LAM12 General information and registration mail: lam12 at sciences.univ-metz.fr Abstract and publication mail: lam12 at mines.inpl-nancy.fr or dahlborg at mines.inpl-nancy.fr LAM12-Publication web site http://www.mines.inpl-nancy.fr/~lam12/ LAM12 general information and registration web site http://lam12.sciences.univ-metz.fr/ ************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20040505/a00535f5/attachment.html From FB153746 at atil.cea.fr Mon May 3 11:13:57 2004 From: FB153746 at atil.cea.fr (=?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?=) Date: Mon, 3 May 2004 11:13:57 +0200 Subject: [CPMD-list] Segmentation violation Message-ID: <601BA98F9E8C7645B7A0052ADBFCC714066EB7B2@atil.valrho.cea.fr> Hello Everybody, One of my job is always existing and the computer generates the following lines : _________________________________________________________________ **** 90 Fatal exception PROG=azzero ELN=27(40005ad18) SIGSEGV: Segmentation violation Called from k_odiis ELN=101(40046f9dc) Called from k_forces ELN=321(400477b18) Called from k_updwf ELN=53(40046a0bc) Called from rgmopt ELN=575(40049122c) Called from gmopts ELN=162(4004874a8) Called from cpmd ELN=126(4000018d0) Called from cpmd_stuttgart ELN=3(400000a10) ________________________________________________________________ This is a job running on a NEC, with KPOINTS, and the SCF procedure is sometimes reseting (ODIIS ...). Many thanks to have a look at that and tell me what is wrong. Best regards, Fr?d?ric PS: Could anyone tell me where to find if one functional is spin polarized or not. Many thanks too. From FB153746 at atil.cea.fr Mon May 3 17:04:51 2004 From: FB153746 at atil.cea.fr (=?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?=) Date: Mon, 3 May 2004 17:04:51 +0200 Subject: [CPMD-list] TR : Segmentation violation Message-ID: <601BA98F9E8C7645B7A0052ADBFCC714066EB7B5@atil.valrho.cea.fr> Hello, Even if the line CALL TIHALT(' FNONLOC',ISUB)in fnonloc.F is added (recommended by Juerg Hutter), I have segmentation violation too. Have a look at the followings : ******************* with CPMD recompiled ********************** **** 90 Fatal exception PROG=azzero ELN=27(40005ad18) **** 90 Fatal exception PROG=azzero ELN=27(40005ad18) **** 90 Fatal exception PROG=azzero ELN=26(40005ad00) SIGSEGV: Segmentation violation **** 90 Fatal exception PROG=azzero ELN=27(40005ad18) **** 90 Fatal exception PROG=azzero ELN=27(40005ad18) **** 90 Fatal exception PROG=azzero ELN=26(40005ad00) **** 90 Fatal exception PROG=azzero ELN=27(40005ad18) **** 90 Fatal exception PROG=azzero ELN=27(40005ad10) SIGSEGV: Segmentation violation SIGSEGV: Segmentation violation Called from k_odiis ELN=101(40046fa5c) SIGSEGV: Segmentation violation SIGSEGV: Segmentation violation SIGSEGV: Segmentation violation SIGSEGV: Segmentation violation SIGSEGV: Segmentation violation Called from k_odiis ELN=101(40046fa5c) Called from k_odiis ELN=101(40046fa5c) Called from k_forces ELN=321(400477b98) Called from k_odiis ELN=101(40046fa5c) Called from k_odiis ELN=101(40046fa5c) Called from k_odiis ELN=101(40046fa5c) Called from k_odiis ELN=101(40046fa5c) Called from k_odiis ELN=101(40046fa5c) Called from k_forces ELN=321(400477b98) Called from k_forces ELN=321(400477b98) Called from k_updwf ELN=53(40046a13c) Called from k_forces ELN=321(400477b98) Called from k_forces ELN=321(400477b98) Called from k_forces ELN=321(400477b98) Called from k_forces ELN=321(400477b98) Called from k_forces ELN=321(400477b98) Called from k_updwf ELN=53(40046a13c) Called from k_updwf ELN=53(40046a13c) Called from rgmopt ELN=575(4004912ac) Called from k_updwf ELN=53(40046a13c) Called from k_updwf ELN=53(40046a13c) Called from k_updwf ELN=53(40046a13c) Called from k_updwf ELN=53(40046a13c) Called from k_updwf ELN=53(40046a13c) Called from rgmopt ELN=575(4004912ac) Called from rgmopt ELN=575(4004912ac) Called from gmopts ELN=162(400487528) Called from rgmopt ELN=575(4004912ac) Called from rgmopt ELN=575(4004912ac) Called from rgmopt ELN=575(4004912ac) Called from rgmopt ELN=575(4004912ac) Called from rgmopt ELN=575(4004912ac) Called from gmopts ELN=162(400487528) Called from gmopts ELN=162(400487528) Called from cpmd ELN=126(4000018d0) Called from gmopts ELN=162(400487528) Called from gmopts ELN=162(400487528) Called from gmopts ELN=162(400487528) Called from gmopts ELN=162(400487528) Called from gmopts ELN=162(400487528) Called from cpmd ELN=126(4000018d0) Called from cpmd ELN=126(4000018d0) Called from cpmd_stuttgart ELN=3(400000a10) Called from cpmd ELN=126(4000018d0) Called from cpmd ELN=126(4000018d0) Called from cpmd ELN=126(4000018d0) Called from cpmd ELN=126(4000018d0) Called from cpmd ELN=126(4000018d0) Called from cpmd_stuttgart ELN=3(400000a10) Called from cpmd_stuttgart ELN=3(400000a10) Called from cpmd_stuttgart ELN=3(400000a10) Called from cpmd_stuttgart ELN=3(400000a10) Called from cpmd_stuttgart ELN=3(400000a10) Called from cpmd_stuttgart ELN=3(400000a10) Called from cpmd_stuttgart ELN=3(400000a10) **************************************************** And CPMD is exiting always. Thanks to have a look at that problem. Best regards, Fr?d?ric -----Message d'origine----- De?: BOUYER Fr?d?ric 153746 Envoy??: lundi 3 mai 2004 11:14 ??: cpmd-list at cpmd.org Objet?: Segmentation violation Hello Everybody, One of my job is always exiting and the computer generates the following lines : _________________________________________________________________ **** 90 Fatal exception PROG=azzero ELN=27(40005ad18) SIGSEGV: Segmentation violation Called from k_odiis ELN=101(40046f9dc) Called from k_forces ELN=321(400477b18) Called from k_updwf ELN=53(40046a0bc) Called from rgmopt ELN=575(40049122c) Called from gmopts ELN=162(4004874a8) Called from cpmd ELN=126(4000018d0) Called from cpmd_stuttgart ELN=3(400000a10) ________________________________________________________________ This is a job running on a NEC, with KPOINTS, and the SCF procedure is sometimes reseting (ODIIS ...). Many thanks to have a look at that and tell me what is wrong. Best regards, Fr?d?ric PS: Could anyone tell me where to find if one functional is spin polarized or not. Many thanks too. From jb811713 at hotmail.com Wed May 5 05:44:25 2004 From: jb811713 at hotmail.com (Brian Jerry) Date: Tue, 04 May 2004 23:44:25 -0400 Subject: [CPMD-list] space group of CPMD Message-ID: hi, CPMD guys In the input file, we only need to give SYMMETRY (1 of 14 Bravais lattice types) and POINT GROUP (1 of 32 point groups, or AUTO). We know there are 230 space groups out there. I'm wondering how this program figures out the space group of the crystall I'm dealing with. Jerry _________________________________________________________________ Stop worrying about overloading your inbox - get MSN Hotmail Extra Storage! http://join.msn.com/?pgmarket=en-us&page=hotmail/es2&ST=1/go/onm00200362ave/direct/01/ From magnusukpong1 at yahoo.com Thu May 6 12:24:15 2004 From: magnusukpong1 at yahoo.com (ade tunde) Date: Thu, 6 May 2004 03:24:15 -0700 (PDT) Subject: [CPMD-list] Please Help! Message-ID: <20040506102415.30495.qmail@web13704.mail.yahoo.com> Hello Everyone, I am a new user of the CPMD V3.7.2 code. I have installed the codes on my PC. (Intel Pentium iii). I have problems running the code. Can any one help? I need to diagonalize a large scale Hamiltonian matrix of order > 4096 x 4096. Thanks in anticipation for useful clues. Magnus Mr A. M. Ukpong Department of Physics University of Cape Town Rondebosch 7701 South Africa Tel: + 27 21 650 3345 Fax: +27 21 650 3342 cell: +00927735446651 email: magnusukpong1 at yahoo.com --------------------------------- Do you Yahoo!? Win a $20,000 Career Makeover at Yahoo! HotJobs -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20040506/fab4203b/attachment.html From Ari.P.Seitsonen at iki.fi Thu May 6 13:47:34 2004 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Thu, 6 May 2004 13:47:34 +0200 (CEST) Subject: [CPMD-list] Segmentation violation In-Reply-To: <601BA98F9E8C7645B7A0052ADBFCC714066EB7B2@atil.valrho.cea.fr> References: <601BA98F9E8C7645B7A0052ADBFCC714066EB7B2@atil.valrho.cea.fr> Message-ID: Dear Fr?d?ric, Please change the line 101 in 'k_odiis.F' from CALL AZZERO(NKPNT,GAMMA) to CALL AZZERO(GAMMA,NKPNT) As you see, it's a slight bug in the code... ;) Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland On Mon, 3 May 2004, BOUYER Fr?d?ric 153746 wrote: > Hello Everybody, > > One of my job is always existing and the computer generates the following > lines : > > _________________________________________________________________ > > > **** 90 Fatal exception PROG=azzero ELN=27(40005ad18) > SIGSEGV: Segmentation violation > Called from k_odiis ELN=101(40046f9dc) > Called from k_forces ELN=321(400477b18) > Called from k_updwf ELN=53(40046a0bc) > Called from rgmopt ELN=575(40049122c) > Called from gmopts ELN=162(4004874a8) > Called from cpmd ELN=126(4000018d0) > Called from cpmd_stuttgart ELN=3(400000a10) > > ________________________________________________________________ > > This is a job running on a NEC, with KPOINTS, and the SCF procedure is > sometimes reseting (ODIIS ...). > > Many thanks to have a look at that and tell me what is wrong. > > Best regards, > > Fr?d?ric > > PS: Could anyone tell me where to find if one functional is spin polarized > or not. Many thanks too. > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu May 6 14:55:46 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 6 May 2004 14:55:46 +0200 (CEST) Subject: [CPMD-list] installation of CPMD In-Reply-To: <41706E489B121D448FDE4EF543442C9B0167668B@MBXSRV25.stu.nus.edu.sg> Message-ID: On Mon, 26 Apr 2004, Xu Jing wrote: XJ> Dear all, XJ> XJ> I am a new for CPMD.3.7.2. The workstation is PIII, 2 CPU. I met XJ> problems as follows; [...] XJ> Then make, error is: XJ> XJ> ifc -c -r8 -w90 -w95 -O3 -pc64 -axM -ip -tpp7 ./cpmd.f -o ./cpmd.o XJ> make: ifc: Command not found XJ> make: *** [cpmd.o] Error 127 XJ> XJ> I think the first thing ifc maybe not install successfully. Secondly, XJ> choosing PC-IFC may be not right. dear xu jing, to compile cpmd correctly on any platform you usually need to revise the generated makefile and adapt it to your installation. this is particularly the case for linux machines. in your case, you need to have the intel fortran compiler (IFC) properly installed. if make complains about 'ifc' not found, you should check you installation. for the intel compiler version 8 the executable is named ifort, but ifc still exists as a compatibility wrapper. if your machine really is a pentium-III you also need to change the optimization flags, as your makefile tries to optimize for a pentium-IV cpu. also, most likely you need to adapt the setting for the BLAS/LAPACK libraries. you can find 'cpmd compatible' libraries and some more tips to compile cpmd on linux machines under the URL: you may also want to check out the mailing list archives, since compilation for cpmd on linux machines have occured before and you may already find the answers you need there. good luck, axel kohlmeyer. XJ> XJ> I am looking forward replying. Thanks. XJ> XJ> Regards, XJ> Xu Jing XJ> XJ> XJ> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu May 6 15:05:45 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 6 May 2004 15:05:45 +0200 (CEST) Subject: [CPMD-list] space group of CPMD In-Reply-To: Message-ID: On Tue, 4 May 2004, Brian Jerry wrote: JB> hi, CPMD guys JB> JB> In the input file, we only need to give SYMMETRY (1 of 14 Bravais lattice JB> types) and POINT GROUP (1 of 32 point groups, or AUTO). We know there are JB> 230 space groups out there. I'm wondering how this program figures out the JB> space group of the crystall I'm dealing with. hi jerry, the authoritative answer can be found in the source code. e.g. try the files chksym.F and k290_2.F axel kohlmeyer. JB> JB> Jerry JB> JB> _________________________________________________________________ JB> Stop worrying about overloading your inbox - get MSN Hotmail Extra Storage! JB> http://join.msn.com/?pgmarket=en-us&page=hotmail/es2&ST=1/go/onm00200362ave/direct/01/ JB> JB> _______________________________________________ JB> CPMD-list mailing list JB> CPMD-list at cpmd.org JB> http://www.cpmd.org/mailman/listinfo/cpmd-list JB> JB> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu May 6 15:08:49 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 6 May 2004 15:08:49 +0200 (CEST) Subject: [CPMD-list] Please Help! In-Reply-To: <20040506102415.30495.qmail@web13704.mail.yahoo.com> Message-ID: On Thu, 6 May 2004, ade tunde wrote: MU> MU> Hello Everyone, MU> MU> I am a new user of the CPMD V3.7.2 code. I have installed the codes on MU> my PC. (Intel Pentium iii). I have problems running the code. Can any MU> one help? I need to diagonalize a large scale Hamiltonian matrix of MU> order > 4096 x 4096. Thanks in anticipation for useful clues. MU> MU> Magnus magnus, please be more specific about the kind of problems you are experiencing, e.g. by quoting the error message you see or an example input that fails. axel kohlmeyer. MU> MU> MU> MU> MU> Mr A. M. Ukpong MU> Department of Physics MU> University of Cape Town MU> Rondebosch 7701 MU> South Africa MU> Tel: + 27 21 650 3345 MU> Fax: +27 21 650 3342 MU> cell: +00927735446651 MU> email: magnusukpong1 at yahoo.com MU> MU> --------------------------------- MU> Do you Yahoo!? MU> Win a $20,000 Career Makeover at Yahoo! HotJobs -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= From ZRLSRB at ch.ibm.com Thu May 6 17:07:24 2004 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Thu, 6 May 2004 17:07:24 +0200 Subject: [CPMD-list] Energy variations for calculations with torsional constraints Message-ID: Hi Veronique, there have been a couple of small bug fixes in the constraints code recently, but this problem is quite possibly related to the choice of the geometry optimizer (default GDIIS/BFGS) which can be very efficient but also sometimes gets trapped far from a minimum. You can either restart the optimization from the last point, switch to the L-BFGS whose implementation is very careful in choosing the size of the trust radius and rejecting unsuccessful steps (keyword LBFGS; if you do that, choose also PRINT LSCAL ON to get some diagnostics about the progress of the optimization), or you can choose the conjugate gradient algorithm whose implementation performs a line search to get a good step size. Btw, do you want to do a periodic calculation? If not, ISOLATED MOLECULE alone is not sufficient, SYMMETRY should be set to zero instead of one to decouple the periodic images electrostatically from each other. Best regards, Salomon From veronique.vanspeybroeck at ugent.be Thu May 6 17:13:44 2004 From: veronique.vanspeybroeck at ugent.be (Veronique Van Speybroeck) Date: Thu, 06 May 2004 17:13:44 +0200 Subject: [CPMD-list] Energy variations for calculations with torsional constraints References: Message-ID: <409A5628.3060701@ugent.be> Dear Salomon, thanks for your constructive comments. I will redo some of the calculations and comment later on to this list about the results.. Veronique Salomon Billeter wrote: > > >Hi Veronique, > >there have been a couple of small bug fixes in the constraints code >recently, but this problem is quite possibly related to the choice of the >geometry optimizer (default GDIIS/BFGS) which can be very efficient but >also sometimes gets trapped far from a minimum. You can either restart the >optimization from the last point, switch to the L-BFGS whose implementation >is very careful in choosing the size of the trust radius and rejecting >unsuccessful steps (keyword LBFGS; if you do that, choose also PRINT LSCAL >ON to get some diagnostics about the progress of the optimization), or you >can choose the conjugate gradient algorithm whose implementation performs a >line search to get a good step size. >Btw, do you want to do a periodic calculation? If not, ISOLATED MOLECULE >alone is not sufficient, SYMMETRY should be set to zero instead of one to >decouple the periodic images electrostatically from each other. > >Best regards, >Salomon > > > -- ----------------------------------------------------------------------- Dr. ir. Van Speybroeck Veronique Laboratorium voor Theoretische Fysica Universiteit Gent Proeftuinstraat 86 9000 Gent Tel +32-9-264.65.58 GSM : +32/474/259767 Fax +32-9-264.65.60 email : veronique.vanspeybroeck at ugent.be http://inwfaxp2.ugent.be /~web/onderzoek/proj_3.html ----------------------------------------------------------------------- From knba713 at hotmail.com Thu May 6 17:23:36 2004 From: knba713 at hotmail.com (Ðñ¶« ÌÆ) Date: Thu, 06 May 2004 11:23:36 -0400 Subject: [CPMD-list] geometry optimization Message-ID: hi, I used CPMD to run the Al slab sample in the package, which uses norm-conserving pseudopotential (AL_SGS). I got the same results as sample gives. Compared with their initial position, the inter-layer distance between two most outside layers increases around 0.125(angstrom). Then I try to use Vanderbilt USPP. I modify the input file and do the calculation again. This time I find the results are quit different from the last one. The inter-layer distance between two most outside layers increases around 3.442(angstrom) !!!! I guess there must be something wroing with my input file. Any suggestion? Thanks. Xudong ------------------------------------------------------------------------------------------------------------------------------------------- &CPMD OPTIMIZE GEOMETRY MEMORY BIG CONVERGENCE 1.0e-4 1.0e-4 SPLINE POINTS 1001 STRUCTURE BONDS ANGLES &END &DFT NEWCODE EXCHANGE CORRELATION TABLE NO FUNCTIONAL PBE GC-CUTOFF 5.0e-5 &END &SYSTEM ANGSTROM POINT GROUP AUTO SYMMETRY 8 CELL 2.779 1.0 8.4853 0.0 0.0 0.0 (a=3.93/sqrt(2) A, 8.4853 =12/sqrt(2) ) CUTOFF 50.0 SCALE &END &ATOMS *013-Al-gpw-n-campos.uspp NEWF BINARY LMAX=D 6 0 0 0 1/2 1/2 1/12 0 0 2/12 1/2 1/2 3/12 0 0 4/12 1/2 1/2 5/12 &END ------------------------------------------------------------------------------------------------------------------------------------------- _________________________________________________________________ Is your PC infected? Get a FREE online computer virus scan from McAfee? Security. http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu May 6 18:23:37 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 6 May 2004 18:23:37 +0200 (CEST) Subject: [CPMD-list] geometry optimization In-Reply-To: Message-ID: On Thu, 6 May 2004, ???? ?? wrote: X> hi, X> X> I used CPMD to run the Al slab sample in the package, which uses X> norm-conserving pseudopotential (AL_SGS). I got the same results as sample X> gives. Compared with their initial position, the inter-layer distance X> between two most outside layers increases around 0.125(angstrom). X> X> Then I try to use Vanderbilt USPP. I modify the input file and do the X> calculation again. This time I find the results are quit different from the X> last one. The inter-layer distance between two most outside layers increases X> around 3.442(angstrom) !!!! X> X> I guess there must be something wroing with my input file. Any suggestion? hi, there are two problems: a) you need k-points b) you need the free energy functional you need a) to have a proper k-space sampling or you have to use a much larger (8x8x1=64 times) supercell and you need b) to treat the metal properly. your results therefore must be bogus. IIRC, a) and b) are not supported with vanderbilt pseudopotentials (well, i am sure about a), i have not looked into b) yet), so you're out of luck. axel kohlmeyer. X> X> Thanks. X> X> Xudong X> X> ------------------------------------------------------------------------------------------------------------------------------------------- X> &CPMD X> OPTIMIZE GEOMETRY X> MEMORY BIG X> CONVERGENCE X> 1.0e-4 1.0e-4 X> SPLINE POINTS X> 1001 X> STRUCTURE BONDS ANGLES X> &END X> X> &DFT X> NEWCODE X> EXCHANGE CORRELATION TABLE NO X> FUNCTIONAL PBE X> GC-CUTOFF X> 5.0e-5 X> &END X> X> &SYSTEM X> ANGSTROM X> POINT GROUP X> AUTO X> SYMMETRY X> 8 X> CELL X> 2.779 1.0 8.4853 0.0 0.0 0.0 (a=3.93/sqrt(2) A, 8.4853 X> =12/sqrt(2) ) X> CUTOFF X> 50.0 X> SCALE X> &END X> X> &ATOMS X> *013-Al-gpw-n-campos.uspp NEWF BINARY X> LMAX=D X> 6 X> 0 0 0 X> 1/2 1/2 1/12 X> 0 0 2/12 X> 1/2 1/2 3/12 X> 0 0 4/12 X> 1/2 1/2 5/12 X> &END X> ------------------------------------------------------------------------------------------------------------------------------------------- X> X> _________________________________________________________________ X> Is your PC infected? Get a FREE online computer virus scan from McAfee? X> Security. http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 X> X> _______________________________________________ X> CPMD-list mailing list X> CPMD-list at cpmd.org X> http://www.cpmd.org/mailman/listinfo/cpmd-list X> X> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= From knba713 at hotmail.com Sat May 8 05:14:56 2004 From: knba713 at hotmail.com (Xudong Tang) Date: Fri, 07 May 2004 23:14:56 -0400 Subject: [CPMD-list] geometry optimization problem Message-ID: hi, guys, I have run the sample problem of Al slab in the CPMD package. I find the interlayer distances in the Al slab all get increased. Does that make sense? I think, on the contrary, we should see contraction of the first to second interlayer distance near the surface, right? Any comments... Xudong blow is my input file: &CPMD OPTIMIZE GEOMETRY UNIT HESSIAN BFGS FREE ENERGY FUNCTIONAL LANCZOS DIAGONALISATION LANCZOS PARAMETERS 1 6 10 1.D-18 TROTTER FACTOR 0.001 BOGOLIUBOV CORRECTION OFF GRAM-SCHMIDT ORTHOGONALISATION CONVERGENCE 1.D-4 5.D-4 MAXSTEP 500 BROYDEN MIXING 0.15 200 0.01 0 8 ALEXANDER MIXING 1.1 ELECTRON TEMPERATURE 1000. COMPRESS WRITE32 STRUCTURE BONDS &END &SYSTEM POINT GROUP AUTO SYMMETRY 8 CELL 2.779 1.0 8.4853 0.0 0.0 0.0 (a=3.93/sqrt(2) A, 8.4853 =12/sqrt(2) ) CUTOFF 35.000 ANGSTROMS STATES 20 SCALE TESR 3 KPOINTS MONKHORST-PACK fULL 8 8 1 &END &ATOMS *AL_SGS KLEINMAN-BYLANDER LMAX=D 6 0 0 0 1/2 1/2 1/12 0 0 2/12 1/2 1/2 3/12 0 0 4/12 1/2 1/2 5/12 &END &BASIS PSEUDO AO 2 0 1 &END &DFT NEWCODE &END _________________________________________________________________ Is your PC infected? Get a FREE online computer virus scan from McAfee? Security. http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 From g0306324 at nus.edu.sg Sun May 9 09:47:34 2004 From: g0306324 at nus.edu.sg (Dai Ling) Date: Sun, 9 May 2004 15:47:34 +0800 Subject: [CPMD-list] Error on wavefunction optimization Message-ID: <16995C828ADE054BA57ABEC32E7B3F37E6C957@MBXSRV26.stu.nus.edu.sg> Hi: I am running a program with a copper atom diffusing in some simple polymers. The pseudopotential of copper was generated by fpi98PP. First I need to run a wavefuntion optimization. However, it fails with error information in the output file as shown here. Who can help me to point out what is going wrong? Thanks in advance!! Scott Output file: NFI GEMAX CNORM ETOT DETOT TCPU 1 2.614E-01 5.330E-03 -386.960991 0.000E+00 22.34 2 9.517E-01 5.516E-03 -416.181864 -2.922E+01 21.97 3 1.906E+00 5.704E-03 -426.937920 -1.076E+01 22.34 4 7.482E-01 5.069E-03 -435.833637 -8.896E+00 22.53 5 3.582E-01 4.754E-03 -442.250384 -6.417E+00 22.82 6 3.578E-01 4.217E-03 -447.127227 -4.877E+00 22.65 7 3.283E-01 3.915E-03 -449.857504 -2.730E+00 23.01 ..... ...... 242 5.727E-03 2.154E-05 -462.624369 -1.003E-04 39.88 ODIIS| Insufficient progress; reset! 243 1.227E-03 1.999E-05 -462.624440 -7.136E-05 35.91 244 9.953E-03 2.916E-05 -462.624736 -2.957E-04 35.12 245 1.693E-03 2.044E-05 -462.624993 -2.569E-04 35.18 246 1.211E-03 2.004E-05 -462.625091 -9.767E-05 36.11 247 1.217E-03 1.984E-05 -462.625225 -1.344E-04 35.78 248 1.217E-03 1.978E-05 -462.625448 -2.232E-04 35.46 249 1.212E-03 1.977E-05 -462.625651 -2.031E-04 38.33 250 1.459E-03 2.084E-05 -462.626857 -1.205E-03 38.55 251 1.932E-03 2.313E-05 -462.621708 5.148E-03 39.90 252 1.239E-03 2.059E-05 -462.623149 -1.441E-03 40.31 253 1.236E-03 2.039E-05 -462.623131 1.805E-05 37.82 254 1.797E-03 3.309E-05 -462.615449 7.682E-03 42.32 ODIIS| Insufficient progress; reset! 255 1.255E-03 2.028E-05 -462.624624 -9.175E-03 40.69 256 9.597E-03 3.014E-05 -462.624892 -2.679E-04 39.07 257 1.733E-03 2.006E-05 -462.625188 -2.961E-04 39.48 258 1.229E-03 1.985E-05 -462.625303 -1.148E-04 43.62 SOLVE! INFO= 5 PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 0] SOLVE! INFO= 5 PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 1] ********************************************************************************************** My input file is shown here: &CPMD OPTIMIZE WAVEFUNCTION SPLINE POINTS 3000 TEMPERATURE 300 TEMPCONTROL IONS 300 20 TIMESTEP 4 MAXSTEP 200 &END &SYSTEM ANGSTROM CELL ABSOLUTE DEGREE 10.3651 10.3651 10.3651 90.0000 90.0000 90.0000 SYMMETRY 1 CUTOFF 80 &END &DFT FUNCTIONAL BLYP &END &ATOMS *C_SG_BLYP LMAX=P 64 -7.327815203 -0.400015608 19.38079706 ............. ............ *H_SG_BLYP LMAX=S 36 -8.180763092 -0.941090708 19.70085133 ............... .............. *Cu_MT_GIA_BLYP LMAX=D 1 5.00000 5.00000 5.00000 &END From Ari.P.Seitsonen at iki.fi Sun May 9 10:32:35 2004 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Sun, 9 May 2004 10:32:35 +0200 (CEST) Subject: [CPMD-list] Error on wavefunction optimization In-Reply-To: <16995C828ADE054BA57ABEC32E7B3F37E6C957@MBXSRV26.stu.nus.edu.sg> References: <16995C828ADE054BA57ABEC32E7B3F37E6C957@MBXSRV26.stu.nus.edu.sg> Message-ID: Dear Dai Ling, There are a couple of suspicious options in your input: - Usually one doesn't need to specify the number of spline points explicitly (since a couple of versions); this is not a problem, just a note - The options 'TEMPERATURE' and 'TEMPCONTROL IONS' are degenerate, the latter already defines the starting temperature; again, just a note (Well, in a job for optimising the wave functions the temperature is not yet even used anyway) - Usually it's a good idea to try switching to 'PCG MINIMISE' if the calculation doesn't seem to converge in a reasonable time (~ 100 iterations of DIIS should lead to rather a good convergence already) - Now to the more serious issues: You seem to have an odd number of electrons, however you use restricted scheme; since the multiplicity of the copper is most likely a singlet, the option 'LSD' in section '&CPMD' might help - The most dangerous aspect in your input: You have (implicitly, since not specified) the local component of the copper pseudo potential set to 'd' (= LMAX), however usually it is 's' (or 'p'?). This most likely gives a wrong electronic configuration around the copper atom, and leads to unphysical results Hopefully this helps something. Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland On Sun, 9 May 2004, Dai Ling wrote: > Hi: > > I am running a program with a copper atom diffusing in some simple polymers. The pseudopotential of copper was generated by fpi98PP. First I need to run a wavefuntion optimization. However, it fails with error information in the output file as shown here. Who can help me to point out what is going wrong? > > Thanks in advance!! > > Scott > > Output file: > > NFI GEMAX CNORM ETOT DETOT TCPU > 1 2.614E-01 5.330E-03 -386.960991 0.000E+00 22.34 > 2 9.517E-01 5.516E-03 -416.181864 -2.922E+01 21.97 > 3 1.906E+00 5.704E-03 -426.937920 -1.076E+01 22.34 > 4 7.482E-01 5.069E-03 -435.833637 -8.896E+00 22.53 > 5 3.582E-01 4.754E-03 -442.250384 -6.417E+00 22.82 > 6 3.578E-01 4.217E-03 -447.127227 -4.877E+00 22.65 > 7 3.283E-01 3.915E-03 -449.857504 -2.730E+00 23.01 > ..... > ...... > 242 5.727E-03 2.154E-05 -462.624369 -1.003E-04 39.88 > ODIIS| Insufficient progress; reset! > 243 1.227E-03 1.999E-05 -462.624440 -7.136E-05 35.91 > 244 9.953E-03 2.916E-05 -462.624736 -2.957E-04 35.12 > 245 1.693E-03 2.044E-05 -462.624993 -2.569E-04 35.18 > 246 1.211E-03 2.004E-05 -462.625091 -9.767E-05 36.11 > 247 1.217E-03 1.984E-05 -462.625225 -1.344E-04 35.78 > 248 1.217E-03 1.978E-05 -462.625448 -2.232E-04 35.46 > 249 1.212E-03 1.977E-05 -462.625651 -2.031E-04 38.33 > 250 1.459E-03 2.084E-05 -462.626857 -1.205E-03 38.55 > 251 1.932E-03 2.313E-05 -462.621708 5.148E-03 39.90 > 252 1.239E-03 2.059E-05 -462.623149 -1.441E-03 40.31 > 253 1.236E-03 2.039E-05 -462.623131 1.805E-05 37.82 > 254 1.797E-03 3.309E-05 -462.615449 7.682E-03 42.32 > ODIIS| Insufficient progress; reset! > 255 1.255E-03 2.028E-05 -462.624624 -9.175E-03 40.69 > 256 9.597E-03 3.014E-05 -462.624892 -2.679E-04 39.07 > 257 1.733E-03 2.006E-05 -462.625188 -2.961E-04 39.48 > 258 1.229E-03 1.985E-05 -462.625303 -1.148E-04 43.62 > SOLVE! INFO= 5 > > > PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 0] > SOLVE! INFO= 5 > > > PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 1] > > ********************************************************************************************** > My input file is shown here: > &CPMD > OPTIMIZE WAVEFUNCTION > SPLINE POINTS > 3000 > TEMPERATURE > 300 > TEMPCONTROL IONS > 300 20 > TIMESTEP > 4 > MAXSTEP > 200 > &END > > &SYSTEM > ANGSTROM > CELL ABSOLUTE DEGREE > 10.3651 10.3651 10.3651 90.0000 90.0000 90.0000 > SYMMETRY > 1 > CUTOFF > 80 > &END > > &DFT > FUNCTIONAL BLYP > &END > > &ATOMS > *C_SG_BLYP > LMAX=P > 64 > -7.327815203 -0.400015608 19.38079706 > ............. > ............ > > *H_SG_BLYP > LMAX=S > 36 > -8.180763092 -0.941090708 19.70085133 > ............... > .............. > *Cu_MT_GIA_BLYP > LMAX=D > 1 > 5.00000 5.00000 5.00000 > > &END > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From g0306324 at nus.edu.sg Mon May 10 09:00:24 2004 From: g0306324 at nus.edu.sg (Dai Ling) Date: Mon, 10 May 2004 15:00:24 +0800 Subject: [CPMD-list] compiling cpmd2cube file Message-ID: <16995C828ADE054BA57ABEC32E7B3F37E6C95C@MBXSRV26.stu.nus.edu.sg> I intalled the cpmd2cube file on IBM690/AIX machine and I have checked that the default "-DFFT_xxxx" are the same for the cpmd2cube & cpmd, as mentioned in the README file. When I want to use cpmd2cube to convert WANNIER file to .cube file, it shows "Illegal instruction (core dumped) ". What is going wrong? Thanks & Best Regards! Scott From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Mon May 10 09:36:50 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Mon, 10 May 2004 09:36:50 +0200 (CEST) Subject: [CPMD-list] compiling cpmd2cube file In-Reply-To: <16995C828ADE054BA57ABEC32E7B3F37E6C95C@MBXSRV26.stu.nus.edu.sg> Message-ID: On Mon, 10 May 2004, Dai Ling wrote: DL> I intalled the cpmd2cube file on IBM690/AIX machine and I have checked DL> that the default "-DFFT_xxxx" are the same for the cpmd2cube & cpmd, DL> as mentioned in the README file. DL> When I want to use cpmd2cube to convert WANNIER file to .cube file, DL> it shows "Illegal instruction (core dumped) ". What is going wrong? hi, please make sure that you have the correct -qarch flag (or don't use it at all) and that you link to the proper ESSL library (or use -lessl). optimization does not really matter for cpmd2cube. axel. DL> DL> Thanks & Best Regards! DL> DL> Scott ???? DL> _______________________________________________ DL> CPMD-list mailing list DL> CPMD-list at cpmd.org DL> http://www.cpmd.org/mailman/listinfo/cpmd-list DL> DL> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= From haiderabbasphy at yahoo.co.in Tue May 11 08:01:06 2004 From: haiderabbasphy at yahoo.co.in (=?iso-8859-1?q?haider=20abbas?=) Date: Tue, 11 May 2004 07:01:06 +0100 (BST) Subject: [CPMD-list] request Message-ID: <20040511060106.88195.qmail@web8204.mail.in.yahoo.com> hi Dear all cpmd user i am using cpmd-3.7.2 on installation it on my linux pentium 4 machine when i extract all files of tar package of cpmd there is a folder named cpmd-3.7.2 which contain source codes i also download blas and lapack library and extracted all files in the source directory then i configure the source and used the command Configure PC-IFC>Makefile so compilation starts but after every thousands of lines compilation there is a message "this feature is obsolescent in fortran 95" and after some time compilation stop and there is a message f77blas-ifc -latlas-ifc -Vaxlib ld: cannot find -llapack-ifc make: *** [cpmd.x] Error 1 wasim at swan:~/CPMD-3.7.2/SOURCE> could anybody please help me yours sincerely Haider Abbas ________________________________________________________________________ Yahoo! India Matrimony: Find your partner online. http://yahoo.shaadi.com/india-matrimony/ From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Tue May 11 09:29:45 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Tue, 11 May 2004 09:29:45 +0200 (CEST) Subject: [CPMD-list] request In-Reply-To: <20040511060106.88195.qmail@web8204.mail.in.yahoo.com> Message-ID: On Tue, 11 May 2004, haider abbas wrote: HA> hi Dear all cpmd user HA> HA> i am using cpmd-3.7.2 HA> on installation it on my linux pentium 4 machine HA> when i extract all files of tar package of cpmd there HA> is a folder named cpmd-3.7.2 which contain source HA> codes HA> i also download blas and lapack library and extracted HA> all files in the source directory then i configure the HA> source HA> and used the command Configure PC-IFC>Makefile so HA> compilation starts but after every thousands of lines HA> compilation there is a message "this feature is HA> obsolescent in fortran 95" and after some time this is a 'feature' of the intel compilers and harmless add the flags -w95 -cm to FFLAGS and this will go away. this is documented in the intel compiler users guide. HA> compilation stop and there is a message HA> HA> f77blas-ifc -latlas-ifc -Vaxlib HA> ld: cannot find -llapack-ifc HA> make: *** [cpmd.x] Error 1 HA> wasim at swan:~/CPMD-3.7.2/SOURCE> as i told you in my last mail, you almost always have to adapt the makefile for your installation. especially on linux machines there are few machines installed alike and the cpmd configure script has no way to find out what is needed on you installation. it just has the definitions suitable for the machine of whoever updated this configuration last. so assuming that you downloaded the libatlas_p4.a file from my homepage, your LFLAGS definition should be something like: LFLAGS = -L. -latlas_p4 -Vaxlib -static $(QMMM_LIBS) that should do the trick, axel kohlmeyer. HA> HA> could anybody please help me HA> yours sincerely HA> Haider Abbas HA> HA> ________________________________________________________________________ HA> Yahoo! India Matrimony: Find your partner online. http://yahoo.shaadi.com/india-matrimony/ HA> _______________________________________________ HA> CPMD-list mailing list HA> CPMD-list at cpmd.org HA> http://www.cpmd.org/mailman/listinfo/cpmd-list HA> HA> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= From Ari.P.Seitsonen at iki.fi Tue May 11 22:49:49 2004 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Tue, 11 May 2004 22:49:49 +0200 (CEST) Subject: [CPMD-list] LSD/KPOINTS and Fermi energy/FEMD In-Reply-To: <1083595204.409659c4258c5@webmail.mail.gatech.edu> References: <1083595204.409659c4258c5@webmail.mail.gatech.edu> Message-ID: Dear Eung-Gun Kim, 1) I don't manage to reproduce your problem, could you please send us at least the output with the complete error message, or better, the input and the pseudo potentials. 2) Look for a line like CHEMICAL POTENTIAL = 2.4181249998 EV when the Kohn-Sham eigenvalues are printed out. Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit[e4]t Z[fc]rich (UniZh) Indirizzo: Winterthurerstra[df]e 190, CH-8057 Z[fc]rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland On Mon, 3 May 2004, Eung-Gun Kim wrote: > Dear CPMD List Subscribers, > > While running calculations on an organic crystal and a metal slab with > CPMD-3.7.2, I have encountered the following two problems: > > 1) When I combine LSD with KPOINTS, the program stops with memory-related > errors such as "PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (DFNL) > [PROC= 0] p0_24396: p4_error: : 999". Reducing the system size doesn't help. > > 2) How do you obtain the Fermi energy from a FEMD calculation? > > Thank you very much for reading. > > Regards, > > E Kim > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From kohsj at ihpc.a-star.edu.sg Wed May 12 07:46:44 2004 From: kohsj at ihpc.a-star.edu.sg (kohsj at ihpc.a-star.edu.sg) Date: Wed, 12 May 2004 13:46:44 +0800 Subject: [CPMD-list] CPMD Exercises Message-ID: <9804b9659a.9659a9804b@ihpc.a-star.edu.sg> Dear Prof Hutter, I'm currently trying out the exercises listed on your website. I'm on practice for the h2 molecule. My questions are as follows: 1. What does it mean by the keyword "NEWCODE" under section &DFT? 2. What do the contents under section &ATOMS refer to? They couldn't be found anywhere in the manuals. 3. Also, I realized that there was a section in the Appendix explaining the generation of pseudopotentials for this set of practice. Where and how will these be used? 4. A general question... What are the most basic sections and keywords we need to use in creating an input file? How are the pseudopotentials referred to in the input file? Thank you very much for your kind attention. Rgds, Adrian. -------------- next part -------------- A non-text attachment was scrubbed... Name: kohsj.vcf Type: text/x-vcard Size: 255 bytes Desc: Card for Url : http://cpmd.org/pipermail/cpmd-list/attachments/20040512/1ab54ec3/attachment.bin From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Wed May 12 09:48:30 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Wed, 12 May 2004 09:48:30 +0200 (CEST) Subject: [CPMD-list] CPMD Exercises In-Reply-To: <9804b9659a.9659a9804b@ihpc.a-star.edu.sg> Message-ID: On Wed, 12 May 2004 kohsj at ihpc.a-star.edu.sg wrote: AK> Dear Prof Hutter, dear adrian, although i am not prof. hutter , i hope i can provide the answers you need. AK> I'm currently trying out the exercises listed on your website. I'm on AK> practice for the h2 molecule. My questions are as follows: AK> AK> 1. What does it mean by the keyword "NEWCODE" under section &DFT? there a two implementations of the functionals in CPMD. this activates the newer one (which is also the default and recommended). this is featured in the manual, but at the _end_ of the list of keywords. AK> 2. What do the contents under section &ATOMS refer to? They couldn't AK> be found anywhere in the manuals. the format of the &ATOMS section _is_ explained in the manual. just look under 'Further details of the input'. AK> 3. Also, I realized that there was a section in the Appendix AK> explaining the generation of pseudopotentials for this set of AK> practice. Where and how will these be used? you can take the pseudopotentials you need from the pseudopotential library in the CPMD dowload section. if you want to create pseudopotentials for CPMD yourself (not recommended if you are a beginner) or learn some more about their properties and derivation, then you can for example have a look at the documention provided with paolo gianozzi's pseudopotential code. AK> 4. A general question... What are the most basic sections and AK> keywords we need to use in creating an input file? How are the AK> pseudopotentials referred to in the input file? you need the sections &CPMD, &DFT, &SYSTEM, and &ATOMS. the syntax of pseudopotential specification is discussed in the manual. as for the h2-example. some weeks ago, i started working on a real cpmd-tutorial starting with the material from juerg hutters homepage. since i can only work on it in my (currently very sparse) free time, there is very little there yet (basically only the h2 wavefunction optimization and the and a discussion of the input and output). also it has not been reviewed by anybody, so there are likely to be many errors or omissions. if this doesn't scare you, you can still have a peek at it at: http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-tutor/part2.html also there is a (much more involved) example for studing proton transport in bulk water which, however, assumes, that you have some previous experience in classical MD, at http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-intro.html hope this will help you, axel kohlmeyer. AK> Thank you very much for your kind attention. AK> AK> AK> Rgds, AK> Adrian. AK> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= From kohsj at ihpc.a-star.edu.sg Thu May 13 11:50:27 2004 From: kohsj at ihpc.a-star.edu.sg (kohsj at ihpc.a-star.edu.sg) Date: Thu, 13 May 2004 17:50:27 +0800 Subject: [CPMD-list] CPMD Exercises Message-ID: <81f928442e.8442e81f92@ihpc.a-star.edu.sg> Dear Prof Kohlmeyer, Thanks for your kind response. I've proceeded on to the first exercise and managed to generate the output file. I've used the potentials "H_GIA_BLYP", "H_SG_BLYP" and "H_SG_LDA" (hope you know what these files mean). I noticed that there's this warning message: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! WARNING! XC FUNCTIONALS INCONSISTENT FOR H_GIA_BLYP !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! when the two potentials with subcript "BLYP" were used. What do they mean? Are there any implications for this? Thanks for your attention. Adrian. ----- Original Message ----- From: Axel Kohlmeyer Date: Wednesday, May 12, 2004 3:48 pm Subject: Re: [CPMD-list] CPMD Exercises On Wed, 12 May 2004 kohsj at ihpc.a-star.edu.sg wrote: AK> Dear Prof Hutter, dear adrian, although i am not prof. hutter , i hope i can provide the answers you need. AK> I'm currently trying out the exercises listed on your website. I'm on AK> practice for the h2 molecule. My questions are as follows: AK> AK> 1. What does it mean by the keyword "NEWCODE" under section &DFT? there a two implementations of the functionals in CPMD. this activates the newer one (which is also the default and recommended). this is featured in the manual, but at the _end_ of the list of keywords. AK> 2. What do the contents under section &ATOMS refer to? They couldn'tAK> be found anywhere in the manuals. the format of the &ATOMS section _is_ explained in the manual. just look under 'Further details of the input'. AK> 3. Also, I realized that there was a section in the Appendix AK> explaining the generation of pseudopotentials for this set of AK> practice. Where and how will these be used? you can take the pseudopotentials you need from the pseudopotential library in the CPMD dowload section. if you want to create pseudopotentials for CPMD yourself (not recommended if you are a beginner) or learn some more about their properties and derivation, then you can for example have a look at the documention provided with paolo gianozzi's pseudopotential code. <" target="l">http://www.nest.sns.it/~giannozz/software.html> AK> 4. A general question... What are the most basic sections and AK> keywords we need to use in creating an input file? How are the AK> pseudopotentials referred to in the input file? you need the sections &CPMD, &DFT, &SYSTEM, and &ATOMS. the syntax of pseudopotential specification is discussed in the manual. as for the h2-example. some weeks ago, i started working on a real cpmd-tutorial starting with the material from juerg hutters homepage. since i can only work on it in my (currently very sparse) free time, there is very little there yet (basically only the h2 wavefunction optimization and the and a discussion of the input and output). also it has not been reviewed by anybody, so there are likely to be many errors or omissions. if this doesn't scare you, you can still have a peek at it at: http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd- tutor/part2.html also there is a (much more involved) example for studing proton transport in bulk water which, however, assumes, that you have some previous experience in classical MD, at http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-intro.html hope this will help you, axel kohlmeyer. AK> Thank you very much for your kind attention. AK> AK> AK> Rgds, AK> Adrian. AK> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= _______________________________________________ CPMD-list mailing list CPMD-list at cpmd.org http://www.cpmd.org/mailman/listinfo/cpmd-list -------------- next part -------------- A non-text attachment was scrubbed... Name: kohsj.vcf Type: text/x-vcard Size: 255 bytes Desc: Card for Url : http://cpmd.org/pipermail/cpmd-list/attachments/20040513/7939521e/attachment.bin From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu May 13 12:35:08 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 13 May 2004 12:35:08 +0200 (CEST) Subject: [CPMD-list] CPMD Exercises In-Reply-To: <81f928442e.8442e81f92@ihpc.a-star.edu.sg> Message-ID: On Thu, 13 May 2004 kohsj at ihpc.a-star.edu.sg wrote: AK> Dear Prof Kohlmeyer, AK> AK> Thanks for your kind response. I've proceeded on to the first AK> exercise and managed to generate the output file. I've used the AK> potentials "H_GIA_BLYP", "H_SG_BLYP" and "H_SG_LDA" (hope you know AK> what these files mean). AK> AK> I noticed that there's this warning message: AK> AK> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! AK> WARNING! XC FUNCTIONALS INCONSISTENT FOR H_GIA_BLYP AK> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! AK> AK> when the two potentials with subcript "BLYP" were used. What do they AK> mean? Are there any implications for this? yes. pseudopotentials should be created from an all-electron calculation with the same functional. so in your case, you probably have to change the FUNCTIONAL keyword in the &DFT section to FUNCTIONAL BLYP. axel kohlmeyer. p.s.: for the record. i am not a professor. ;-) AK> AK> Thanks for your attention. AK> AK> AK> Adrian. AK> AK> AK> AK> AK> ----- Original Message ----- AK> From: Axel Kohlmeyer AK> Date: Wednesday, May 12, 2004 3:48 pm AK> Subject: Re: [CPMD-list] CPMD Exercises AK> AK> On Wed, 12 May 2004 kohsj at ihpc.a-star.edu.sg wrote: AK> AK> AK> Dear Prof Hutter, AK> AK> dear adrian, AK> AK> although i am not prof. hutter , i hope i can provide AK> the answers you need. AK> AK> AK> I'm currently trying out the exercises listed on your website. AK> I'm on AK> AK> practice for the h2 molecule. My questions are as follows: AK> AK> AK> AK> 1. What does it mean by the keyword "NEWCODE" under section AK> &DFT? AK> there a two implementations of the functionals in CPMD. this activates AK> the newer one (which is also the default and recommended). this is AK> featured in the manual, but at the _end_ of the list of keywords. AK> AK> AK> AK> 2. What do the contents under section &ATOMS refer to? They AK> couldn'tAK> be found anywhere in the manuals. AK> AK> the format of the &ATOMS section _is_ explained in the manual. just AK> look under 'Further details of the input'. AK> AK> AK> 3. Also, I realized that there was a section in the Appendix AK> AK> explaining the generation of pseudopotentials for this set of AK> AK> practice. Where and how will these be used? AK> AK> you can take the pseudopotentials you need from the pseudopotential AK> library in the CPMD dowload section. if you want to create AK> pseudopotentials for CPMD yourself (not recommended if you are a AK> beginner) or learn some more about their properties and derivation, AK> then you can for example have a look at the documention provided AK> with paolo gianozzi's pseudopotential code. AK> <" target="l">http://www.nest.sns.it/~giannozz/software.html> AK> AK> AK> AK> 4. A general question... What are the most basic sections and AK> AK> keywords we need to use in creating an input file? How are the AK> AK> pseudopotentials referred to in the input file? AK> AK> you need the sections &CPMD, &DFT, &SYSTEM, and &ATOMS. AK> the syntax of pseudopotential specification is discussed AK> in the manual. AK> AK> as for the h2-example. some weeks ago, i started working on a AK> real cpmd-tutorial starting with the material from juerg hutters AK> homepage. since i can only work on it in my (currently very AK> sparse) free time, there is very little there yet (basically only AK> the h2 wavefunction optimization and the and a discussion of the AK> input and output). also it has not been reviewed by anybody, AK> so there are likely to be many errors or omissions. AK> AK> if this doesn't scare you, you can still have a peek at it at: AK> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd- AK> tutor/part2.html AK> also there is a (much more involved) example for studing AK> proton transport in bulk water which, however, assumes, that you AK> have some previous experience in classical MD, at AK> AK> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-intro.html AK> AK> hope this will help you, AK> axel kohlmeyer. AK> AK> AK> Thank you very much for your kind attention. AK> AK> AK> AK> AK> AK> Rgds, AK> AK> Adrian. AK> AK> AK> AK> -- AK> AK> AK> ======================================================================= AK> Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de AK> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 AK> Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 AK> D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ AK> ======================================================================= AK> AK> AK> _______________________________________________ AK> CPMD-list mailing list AK> CPMD-list at cpmd.org AK> http://www.cpmd.org/mailman/listinfo/cpmd-list AK> AK> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= From weiqiao at wag.caltech.edu Thu May 13 23:25:39 2004 From: weiqiao at wag.caltech.edu (Weiqiao Deng) Date: Thu, 13 May 2004 14:25:39 -0700 (PDT) Subject: [CPMD-list] How to fit plane-wave pseudopotentials for customized functional? Message-ID: Dear all, Our group developed a new DFT functional quite similiar to BLYP. I am trying to write it into CPMD code. I have a question whether there is a program to fit the plane-wave pseudopotential for customized functional? I will appreciate it a lot if you can give me some hints. Thanks in advance. Regards, Weiqiao From Ari.P.Seitsonen at iki.fi Fri May 14 00:07:57 2004 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Fri, 14 May 2004 00:07:57 +0200 (CEST) Subject: [CPMD-list] How to fit plane-wave pseudopotentials for customized functional? In-Reply-To: References: Message-ID: Dear Weiqiao, There are a couple of programs for generating pseudo potentials in a form understood by CPMD, you can modify those programs to include your new functional. One such program is 'atomc', available at http://pciwww.unizh.ch/pci/hutter/information/information.html Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland On Thu, 13 May 2004, Weiqiao Deng wrote: > Dear all, > > Our group developed a new DFT functional quite similiar to BLYP. I am > trying to write it into CPMD code. I have a question whether there > is a program to fit the plane-wave pseudopotential for customized > functional? I will appreciate it a lot if you can give me some > hints. Thanks in advance. > > Regards, > Weiqiao > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From eunggun.kim at chemistry.gatech.edu Fri May 14 15:31:42 2004 From: eunggun.kim at chemistry.gatech.edu (Eung-Gun Kim) Date: Fri, 14 May 2004 09:31:42 -0400 Subject: [CPMD-list] LSD/KPOINTS and Fermi energy/FEMD Message-ID: <1084541502.40a4ca3ec6053@webmail.mail.gatech.edu> Dear Dr. Seitsonen, Thanks very much for responding to my message. 1) I must have underestimated the memory requirement of an LSD calculation. It works fine now. The memory error was indeed caused by a failure to allocate memory. 2) The chemical potential becomes equal to the Fermi energy only when T = 0. Does this mean that one needs another FEMD calculation at T = 0 (or by turning off FEMD), possibly with more k points, to get the Fermi energy? Regards, E Kim Quoting Ari P Seitsonen : > > Dear Eung-Gun Kim, > > 1) I don't manage to reproduce your problem, could you please send us at > least the output with the complete error message, or better, the input and > the pseudo potentials. > > 2) Look for a line like > CHEMICAL POTENTIAL = 2.4181249998 EV > when the Kohn-Sham eigenvalues are printed out. > > Greetings, > > apsi > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ > Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 > Anschrift: Physikalisch Chemisches Institut (PCI), Universit[e4]t Z[fc]rich > (UniZh) > Indirizzo: Winterthurerstra[df]e 190, CH-8057 Z[fc]rich > Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland > > On Mon, 3 May 2004, Eung-Gun Kim wrote: > > > Dear CPMD List Subscribers, > > > > While running calculations on an organic crystal and a metal slab with > > CPMD-3.7.2, I have encountered the following two problems: > > > > 1) When I combine LSD with KPOINTS, the program stops with > memory-related > > errors such as "PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED > (DFNL) > > [PROC= 0] p0_24396: p4_error: : 999". Reducing the system size doesn't > help. > > > > 2) How do you obtain the Fermi energy from a FEMD calculation? > > > > Thank you very much for reading. > > > > Regards, > > > > E Kim > > > > > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > From hutter at pci.unizh.ch Fri May 14 17:02:05 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Fri, 14 May 2004 17:02:05 +0200 (MEST) Subject: [CPMD-list] How to fit plane-wave pseudopotentials for customized functional? In-Reply-To: References: Message-ID: Hi the easy way is to modify the file functionals.F (and lsd_func.F) in CPMD. If you only want to change the exchange have a look at BECKE88. Please not that these routines only have to provide the part in addition to the local density part. Exactly the same file (functionals.F) can also be used in the atomic code that you can download from our web page. (mentioned in the mail by Ari). For generating new PP I would use the same parameters that were used for similar XC functionals. You can find the parameters in the info sections of the PP files. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Thu, 13 May 2004, Weiqiao Deng wrote: > Dear all, > > Our group developed a new DFT functional quite similiar to BLYP. I am > trying to write it into CPMD code. I have a question whether there > is a program to fit the plane-wave pseudopotential for customized > functional? I will appreciate it a lot if you can give me some > hints. Thanks in advance. > > Regards, > Weiqiao > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From weiqiao at wag.caltech.edu Fri May 14 23:22:02 2004 From: weiqiao at wag.caltech.edu (Weiqiao Deng) Date: Fri, 14 May 2004 14:22:02 -0700 (PDT) Subject: [CPMD-list] How to fit plane-wave pseudopotentials for customized functional? In-Reply-To: Message-ID: Thank Dr. Hutter and Adri for those useful information. I downloaded the atomc package and will look at it. Thanks again. Regards, Weiqiao On Fri, 14 May 2004, Juerg Hutter wrote: > Hi > > the easy way is to modify the file functionals.F (and lsd_func.F) > in CPMD. If you only want to change the exchange have > a look at BECKE88. Please not that these routines > only have to provide the part in addition to the local > density part. > Exactly the same file (functionals.F) can also be used > in the atomic code that you can download from our web page. > (mentioned in the mail by Ari). > For generating new PP I would use the same parameters that > were used for similar XC functionals. You can find the parameters > in the info sections of the PP files. > > regards > > Juerg > > ---------------------------------------------------------- > Juerg Hutter Phone : ++41 1 635 4491 > Physical Chemistry Institute FAX : ++41 1 635 6838 > University of Zurich E-mail: hutter at pci.unizh.ch > Winterthurerstrasse 190 > CH-8057 Zurich, Switzerland > ---------------------------------------------------------- > > > On Thu, 13 May 2004, Weiqiao Deng wrote: > > > Dear all, > > > > Our group developed a new DFT functional quite similiar to BLYP. I am > > trying to write it into CPMD code. I have a question whether there > > is a program to fit the plane-wave pseudopotential for customized > > functional? I will appreciate it a lot if you can give me some > > hints. Thanks in advance. > > > > Regards, > > Weiqiao > > > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > From g0306324 at nus.edu.sg Sat May 15 15:19:21 2004 From: g0306324 at nus.edu.sg (Dai Ling) Date: Sat, 15 May 2004 21:19:21 +0800 Subject: [CPMD-list] Visualization of CPMD output properties Message-ID: <16995C828ADE054BA57ABEC32E7B3F37E6C970@MBXSRV26.stu.nus.edu.sg> Dear Sirs: I have some question on visualization of CPMD output properties. 1. For the TRAJECTORY file, I have seen there is a perl script in the FAQ to transfer it to other formats. However, I don't know how to use the perl scripts. Or is there any other method to transfer TRAJECTORY file to .cube or .pdb file? 2. For the MOVIE file, which software can visualize it? 3. I tried to get density & band structure of Tantulum. I got DENSITY & ENERGYBANDS files. Which software can visualize the ENERGYBANDS file? 4. For item 3, I have installed cpmd2cube. It works well on transfering WANNIER file. However,when I use it to transfer DENSITY file, it fails with information: **************************************************************** .read input file ... done I think you stored a density (sum^2 = 0.85220979E-02) ERROR in file DENSITY Wannier-functions stored as density, you can not create a cube-file with the wavefunction ****************************************************************** I am confusing because in my input file there is no command for Wannier function. The input file for item 3 & 4 is shown below. The pseudopotential for TA is created by fhi98PP. Any advice will be highly appreciated. Thanks in advance! Scott Input file: &CPMD OPTIMIZE WAVEFUNCTION FREE ENERGY FUNCTIONAL LANCZOS DIAGONALIZATION LANCZOS PARAMETERS N=1 ALL 50 8 0 1.D-8 TROTTER FACTOR 0.001 BOGOLIUBOV CORRECTION CONVERGENCE 5.D-5 5.D-4 ELECTRON TEMPERATURE 300.D0 MAXSTEP 1 ENERGYBANDS &END &SYSTEM SYMMETRY BCC POINT GROUP AUTO SCALE TESR 10 ANGSTROM CELL 3.3062 1.0 1.0 0.0 0.0 0.0 SPHERICAL CUTOFF 63. density cutoff energy 6820 KPOINTS BANDS block=50 51 0 0 0 0 0 1 Gamma to H 51 0 0 1 0 .5 .5 H to N 51 0 .5 .5 .5 .5 .5 N to P 51 .5 .5 .5 0 0 0 P to Gamma 51 0 0 0 .5 .5 0 Gamma to N 51 0 0 1 .5 .5 .5 H to P 0 0 0 0 0 0 0 STATES 9 &END &ATOMS *TA_MT_GIA_BLYP KLEIMAN-BYLANDER REGGIO=1.2 LMAX=D LOC=P 1 0.00D0 0.00D0 0.00D0 &END From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Sat May 15 16:00:15 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Sat, 15 May 2004 16:00:15 +0200 (CEST) Subject: [CPMD-list] Visualization of CPMD output properties In-Reply-To: <16995C828ADE054BA57ABEC32E7B3F37E6C970@MBXSRV26.stu.nus.edu.sg> Message-ID: On Sat, 15 May 2004, Dai Ling wrote: DL> Dear Sirs: DL> hi, DL> I have some question on visualization of CPMD output properties. i have found that VMD is an excellent tool to visualize the results from CPMD simulations, so many of your questions (and some you have not asked yet) may be answered at beginning with version 1.8.2 the VMD program allows you to read in the coordinates from a TRAJECTORY file as format 'cpmd' if you have loaded the matching GEOMETRY.xyz file first. there also is a (perl) program to create an xyz file directly. DL> DL> 1. For the TRAJECTORY file, I have seen there is a perl script in the DL> FAQ to transfer it to other formats. However, I don't know how to use DL> the perl scripts. Or is there any other method to transfer TRAJECTORY to use a perl script you either make them executable (chmod +x xxx.pl) and use them like a regular executable './xxx.pl ...' or you run it with 'perl xxx.pl ...' DL> file to .cube or .pdb file? cube files don't store trajectories and multi-step pdb file support is also not as widespread as .xyz movie support. DL> 2. For the MOVIE file, which software can visualize it? AFAIK, this file is more-or-less obsolete. try using 'TRAJECTORY XYZ' to generated a .xyz file directly. DL> DL> 3. I tried to get density & band structure of Tantulum. I got DENSITY DL> & ENERGYBANDS files. Which software can visualize the ENERGYBANDS DL> file? DL> DL> 4. For item 3, I have installed cpmd2cube. It works well on DL> transfering WANNIER file. However,when I use it to transfer DENSITY DL> file, it fails with information: DL> DL> **************************************************************** DL> DL> .read input file ... done DL> I think you stored a density (sum^2 = 0.85220979E-02) DL> ERROR in file DENSITY DL> Wannier-functions stored as density, you can not DL> create a cube-file with the wavefunction DL> DL> ****************************************************************** DL> DL> I am confusing because in my input file there is no command for Wannier function. the current cpmd2cube sources at cpmd.org have several problems. many of which have already been fixed in the developer version. i assume there will be a new release of cpmd2cube along with the release of cpmd-v3.9. in your specific case you got hit by a little think-o in the commandline argument parsing/guessing. for a density you need to specify the -rho or -dens flag explicitely (the program assumes -psi and the stops if the sanity check fails) and it should work. hope this helps, axel kohlmeyer. DL> DL> The input file for item 3 & 4 is shown below. The pseudopotential for TA is created by fhi98PP. DL> DL> Any advice will be highly appreciated. Thanks in advance! DL> DL> Scott DL> DL> Input file: DL> DL> &CPMD DL> OPTIMIZE WAVEFUNCTION DL> FREE ENERGY FUNCTIONAL DL> LANCZOS DIAGONALIZATION DL> LANCZOS PARAMETERS N=1 ALL DL> 50 8 0 1.D-8 DL> TROTTER FACTOR DL> 0.001 DL> BOGOLIUBOV CORRECTION DL> CONVERGENCE DL> 5.D-5 5.D-4 DL> ELECTRON TEMPERATURE DL> 300.D0 DL> MAXSTEP DL> 1 DL> ENERGYBANDS DL> &END DL> &SYSTEM DL> SYMMETRY DL> BCC DL> POINT GROUP DL> AUTO DL> SCALE DL> DL> TESR DL> 10 DL> ANGSTROM DL> CELL DL> 3.3062 1.0 1.0 0.0 0.0 0.0 DL> SPHERICAL CUTOFF DL> 63. DL> density cutoff energy DL> 6820 DL> KPOINTS BANDS block=50 DL> 51 0 0 0 0 0 1 Gamma to H DL> 51 0 0 1 0 .5 .5 H to N DL> 51 0 .5 .5 .5 .5 .5 N to P DL> 51 .5 .5 .5 0 0 0 P to Gamma DL> 51 0 0 0 .5 .5 0 Gamma to N DL> 51 0 0 1 .5 .5 .5 H to P DL> 0 0 0 0 0 0 0 DL> STATES DL> 9 DL> &END DL> DL> &ATOMS DL> *TA_MT_GIA_BLYP KLEIMAN-BYLANDER REGGIO=1.2 DL> LMAX=D LOC=P DL> 1 DL> 0.00D0 0.00D0 0.00D0 DL> &END DL> DL> DL> DL> DL> DL> DL> DL> _______________________________________________ DL> CPMD-list mailing list DL> CPMD-list at cpmd.org DL> http://www.cpmd.org/mailman/listinfo/cpmd-list DL> DL> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= From a.soon at auckland.ac.nz Tue May 18 06:02:41 2004 From: a.soon at auckland.ac.nz (Aloysius Soon Sze Lok) Date: Tue, 18 May 2004 16:02:41 +1200 Subject: [CPMD-list] "SURFACE" keyword Message-ID: <200405181602.41625.a.soon@auckland.ac.nz> Dear all, According to the manual, the "SURFACE" keyword is used to specify periodic boundary conditions in the x- and y-direction. When I used this keyword, the centre of mass seems to have shifted. Has anyone used this keyword? Is it essential for surface simulations? Cheers! -- Aloysius Soon SL Postgraduate Student Structural & Computational Chemistry Chemistry Department The University Of Auckland, New Zealand Phone: +64 9 373 7599 ext 88291 Email: a.soon at auckland.ac.nz From kohsj at ihpc.a-star.edu.sg Tue May 18 06:45:08 2004 From: kohsj at ihpc.a-star.edu.sg (kohsj at ihpc.a-star.edu.sg) Date: Tue, 18 May 2004 12:45:08 +0800 Subject: [CPMD-list] Examples on H2O and Si Message-ID: <884d586303.86303884d5@ihpc.a-star.edu.sg> Dear Dr. Kohlmeyer, With reference to the a/m examples on Prof. Hutters webpage (the "Monday" ones), I encountered the following error termination found in the output files: PROGRAM CPMD STARTED AT: Mon May 17 21:31:34 2004 CONTROL| ERROR IN READING INPUT FILE THE LAST TWO LINES READ WERE KOHN-SHAM MAXSTEP PROGRAM STOPS IN SUBROUTINE CONTROL| [PROC= 0] This happens when the "Optimize Wavefunction" was replaced with "Kohn-Sham Energies" as was instructed by the tutorial. The one on Si8 and Si64 terminated at the point of basis set generation: GENERATE ATOMIC BASIS SET PROGRAM STOPS IN SUBROUTINE READ_BASIS| SECTION WAVEFUNCTION [PROC= 0] The following is a sample of .inp file for the H2O molecule (with bend bonds): &CPMD KOHN-SHAM ENERGIES MAXSTEP 1000 RHOOUT STRUCTURE BONDS ANGLES &END &DFT NEWCODE FUNCTIONAL BLYP GC-CUTOFF 0.1E-06 &END &SYSTEM SYMMETRY 0 CELL 15.0000 1.0 1.0 0 0 0 CUTOFF 70.0 &END &PROPERTIES DIPOLE MOMENT &END &ATOMS *O_SG_BLYP LMAX=P 1 7.5000 7.3723 7.4919 *H_SG_BLYP LMAX=S 2 8.9608 8.5133 7.5645 6.0392 8.5133 7.5645 &END Here's a sample file for the Si clusters: &CPMD OPTIMIZE WAVEFUNCTION MAXSTEP 1000 &END &DFT NEWCODE FUNCTIONAL BLYP GC-CUTOFF 0.2E-06 &END &SYSTEM SYMMETRY 1 CELL 10.263102 1.0 1.0 0 0 0 CUTOFF 12.0 CHARGE 0.0 &END &ATOMS *Si_SG_BLYP LMAX=P 8 5.130606 10.263102 5.130606 10.263102 5.130606 5.130606 5.130606 5.130606 0.000000 10.263102 10.263102 0.000000 7.696854 2.566248 7.696854 2.566248 2.566248 2.566248 2.566248 7.696854 7.696854 7.696854 7.696854 2.566248 &END &BASIS PSEUDO AO 2 0 1 &END Thanks for your attention :). Adrian. -------------- next part -------------- A non-text attachment was scrubbed... Name: kohsj.vcf Type: text/x-vcard Size: 255 bytes Desc: Card for Url : http://cpmd.org/pipermail/cpmd-list/attachments/20040518/74dfa4c1/attachment.bin From holger.hesske at gmx.de Tue May 18 08:09:39 2004 From: holger.hesske at gmx.de (Holger Hesske) Date: Tue, 18 May 2004 08:09:39 +0200 (MEST) Subject: [CPMD-list] Segmentation fault using Nose-thermostat References: <884d586303.86303884d5@ihpc.a-star.edu.sg> Message-ID: <25302.1084860579@www13.gmx.net> Dear users! After a lot of well running MD?s with TEMPCONTROL IONS, I?ve tried to use the Nose-Hoover-thermostat for producing proton-transfer in an ammonia-water bulk. But in any case (NOSE IONS.... NOSE ELECTRONS or both, even MASSIVE or ULTRA) the program stops with Segmentation fault. Every try leads to this error and I?m very appreciated if anybody could give me a hint. Maybe I?m missing something? Thanks in advance Holger Holger He?ke Institut f?r Anorganische Chemie TU DRESDEN The last lines in the output are --- Atomic coordinates and velocities are read from File Geometry *** PHFAC | the new size of the program is 74924 kBytes *** --- The input are for example: &CPMD FILEPATH /usr/local/CPMD/OUTPUTS/ MOLECULAR DYNAMICS CONVERGENCE 1.0e-5 1.0e-4 RESTART GEOFILE WAVEFUNCTION LATEST SPLINE POINTS 1500 EMASS 600 TEMPERATURE 400 NOSE IONS MASSIVE 400.0 2500.0 NOSE ELECTRONS 0.02 10000.0 MAXSTEP 1000 TRAJECTORY XYZ SAMPLE 10 &END &SYSTEM ANGSTROM CELL ABSOLUTE DEGREE 10.0 10.0 10.0 90.0 90.0 90.0 SYMMETRY 0 POINT GROUP AUTO CHARGE 1 CUTOFF 25 400eV SCALE TESR 1 1 1 &END &DFT NEWCODE FUNCTIONAL BLYP GC-CUTOFF 1.0e-6 &END &ATOMS H_SG_BLYP .... O_SG_BLYP .... N_SG_BLYP .... CONSTRAINTS .. .. END CONSTRAINTS &END -- "Sie haben neue Mails!" - Die GMX Toolbar informiert Sie beim Surfen! Jetzt aktivieren unter http://www.gmx.net/info From ZRLSRB at ch.ibm.com Tue May 18 09:17:31 2004 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Tue, 18 May 2004 09:17:31 +0200 Subject: [CPMD-list] "SURFACE" keyword Message-ID: Hi Aloysius, the default for isolated systems is that the system is centered in the cell (just a parallel shift of all atoms). This is done to ensure that the density at the borders of your cell is as small as possible (the Poisson solvers decoupling the periodic images electrostatically from each other require at least this). This applies also to 2D and 1D periodic systems. If you don't want to have the atoms shifted, you can specify CENTER MOLECULE OFF in the &CPMD section. There are good reasons to use the SURFACE keyword for systems which are periodic in two dimensions only because that way, they don't "see" their periodic images along the Z-direction. There are however a few points to consider: - In the current version, the (default) Poisson solver for 2D and 1D periodic systems is Hockney, which does not work in these cases. Use the Mortensen PS instead (POISSON MORTENSEN in the &SYSTEM section). - For the Mortensen Poisson solver, you need to give more space in the Z-direction than for Hockney to make it decouple the periodic images electrostatically. A good reference for box sizes of isolated systems (in your case just along the Z-direction) is J. Hutter's posting of Aug. 17, 2002 in this list. - The soon-to-be-released version of CPMD sets the default to Mortensen, and a Poisson solver with the box requirements of Hockney is implemented, too. This can save you CPU time and memory considerably. Best regards, Salomon From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Tue May 18 09:56:35 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Tue, 18 May 2004 09:56:35 +0200 (CEST) Subject: [CPMD-list] Re: Examples on H2O and Si In-Reply-To: <884d586303.86303884d5@ihpc.a-star.edu.sg> Message-ID: On Tue, 18 May 2004 kohsj at ihpc.a-star.edu.sg wrote: AK> Dear Dr. Kohlmeyer, dear adrian, AK> AK> With reference to the a/m examples on Prof. Hutters webpage (the AK> "Monday" ones), I encountered the following error termination found in AK> the output files: AK> AK> PROGRAM CPMD STARTED AT: Mon May 17 21:31:34 2004 AK> AK> CONTROL| ERROR IN READING INPUT FILE AK> THE LAST TWO LINES READ WERE AK> KOHN-SHAM AK> MAXSTEP AK> AK> AK> PROGRAM STOPS IN SUBROUTINE CONTROL| [PROC= 0] AK> AK> This happens when the "Optimize Wavefunction" was replaced with AK> "Kohn-Sham Energies" as was instructed by the tutorial. The one on ok, please check the manual. for the kohn-sham energies calculation you need to restart from the previously calculated wavefunction, so you have to add something like 'RESTART COORDINATES WAVEFUNCTION LATEST'. AK> Si8 and Si64 terminated at the point of basis set generation: AK> AK> GENERATE ATOMIC BASIS SET AK> AK> AK> PROGRAM STOPS IN SUBROUTINE READ_BASIS| SECTION WAVEFUNCTION [PROC= 0] you are intructing cpmd to build the initial guess from the (pseudo)wavefunctions in the pseudopotential files. with the SG pseudopotential files these do not exist. you have to either use martins-troullier (or similar) pseudopotentials or delete the &BASIS section (which will have cpmd to use a minimal slater basis to construct the initial guess). hope this helps, axel. AK> AK> The following is a sample of .inp file for the H2O molecule (with bend bonds): AK> AK> &CPMD AK> KOHN-SHAM ENERGIES AK> MAXSTEP AK> 1000 AK> RHOOUT AK> STRUCTURE BONDS ANGLES AK> &END AK> AK> &DFT AK> NEWCODE AK> FUNCTIONAL BLYP AK> GC-CUTOFF AK> 0.1E-06 AK> &END AK> AK> &SYSTEM AK> SYMMETRY AK> 0 AK> CELL AK> 15.0000 1.0 1.0 0 0 0 AK> CUTOFF AK> 70.0 AK> AK> &END AK> AK> &PROPERTIES AK> DIPOLE MOMENT AK> &END AK> AK> &ATOMS AK> *O_SG_BLYP AK> LMAX=P AK> 1 AK> 7.5000 7.3723 7.4919 AK> AK> *H_SG_BLYP AK> LMAX=S AK> 2 AK> 8.9608 8.5133 7.5645 AK> 6.0392 8.5133 7.5645 AK> AK> &END AK> AK> AK> Here's a sample file for the Si clusters: AK> AK> &CPMD AK> OPTIMIZE WAVEFUNCTION AK> MAXSTEP AK> 1000 AK> &END AK> AK> AK> &DFT AK> NEWCODE AK> FUNCTIONAL BLYP AK> GC-CUTOFF AK> 0.2E-06 AK> &END AK> AK> &SYSTEM AK> SYMMETRY AK> 1 AK> CELL AK> 10.263102 1.0 1.0 0 0 0 AK> CUTOFF AK> 12.0 AK> CHARGE AK> 0.0 AK> AK> &END AK> AK> &ATOMS AK> *Si_SG_BLYP AK> LMAX=P AK> 8 AK> 5.130606 10.263102 5.130606 AK> 10.263102 5.130606 5.130606 AK> 5.130606 5.130606 0.000000 AK> 10.263102 10.263102 0.000000 AK> 7.696854 2.566248 7.696854 AK> 2.566248 2.566248 2.566248 AK> 2.566248 7.696854 7.696854 AK> 7.696854 7.696854 2.566248 AK> AK> AK> &END AK> AK> &BASIS AK> PSEUDO AO 2 AK> 0 1 AK> AK> &END AK> AK> AK> Thanks for your attention :). AK> AK> AK> Adrian. AK> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Tue May 18 10:07:22 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Tue, 18 May 2004 10:07:22 +0200 (CEST) Subject: [CPMD-list] Segmentation fault using Nose-thermostat In-Reply-To: <25302.1084860579@www13.gmx.net> Message-ID: On Tue, 18 May 2004, Holger Hesske wrote: HH> Dear users! hi, HH> After a lot of well running MD?s with TEMPCONTROL IONS, I?ve tried to use HH> the Nose-Hoover-thermostat for producing proton-transfer in an ammonia-water HH> bulk. HH> But in any case (NOSE IONS.... NOSE ELECTRONS or both, even MASSIVE or HH> ULTRA) the program stops with Segmentation fault. HH> Every try leads to this error and I?m very appreciated if anybody could give HH> me a hint. Maybe I?m missing something? hmmm, this is difficult to figure out from the information in your mail. you may have tripped over a bug that has already been fixed. would you mind sending me your full input file, so that i can check it against the latest developer version. TIA, axel. p.s.: you are using a very small plane wave cutoff, typical for ultrasoft pseudopotentials. if the pseudopotentials you are using, are really goedecker pseudopotentials (as indicated by the name of the files), you probably need something like 100-120ryd for your system. HH> HH> Thanks in advance HH> Holger HH> HH> HH> Holger He?ke HH> Institut f?r Anorganische Chemie HH> TU DRESDEN HH> HH> The last lines in the output are HH> --- HH> Atomic coordinates and velocities are read from File Geometry HH> HH> *** PHFAC | the new size of the program is 74924 kBytes *** HH> --- HH> The input are for example: HH> HH> &CPMD HH> FILEPATH /usr/local/CPMD/OUTPUTS/ HH> HH> MOLECULAR DYNAMICS HH> CONVERGENCE HH> 1.0e-5 1.0e-4 HH> RESTART GEOFILE WAVEFUNCTION LATEST HH> SPLINE POINTS HH> 1500 HH> EMASS HH> 600 HH> TEMPERATURE HH> 400 HH> NOSE IONS MASSIVE HH> 400.0 2500.0 HH> NOSE ELECTRONS HH> 0.02 10000.0 HH> MAXSTEP HH> 1000 HH> TRAJECTORY XYZ SAMPLE HH> 10 HH> &END HH> &SYSTEM HH> ANGSTROM HH> CELL ABSOLUTE DEGREE HH> 10.0 10.0 10.0 90.0 90.0 90.0 HH> SYMMETRY HH> 0 HH> POINT GROUP HH> AUTO HH> CHARGE HH> 1 HH> CUTOFF HH> 25 HH> 400eV HH> SCALE HH> TESR HH> 1 1 1 HH> &END HH> &DFT HH> NEWCODE HH> FUNCTIONAL BLYP HH> GC-CUTOFF HH> 1.0e-6 HH> &END HH> &ATOMS HH> H_SG_BLYP HH> .... HH> O_SG_BLYP HH> .... HH> N_SG_BLYP HH> .... HH> CONSTRAINTS HH> .. HH> .. HH> END CONSTRAINTS HH> &END HH> HH> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= From ct at chemie.hu-berlin.de Tue May 18 12:45:46 2004 From: ct at chemie.hu-berlin.de (Christian Tuma) Date: Tue, 18 May 2004 12:45:46 +0200 Subject: [CPMD-list] code problem with TISTACK(NTIMX) Message-ID: <20040518104546.GC364815@uranus.chemie.hu-berlin.de> Dear CPMD developers, I run a number of geometry optimisations that always crashed after geometry step 198 or 199. Upon closer investigation I found the reason for that behaviour: In "rlbfgs.F" line 306 CALL DCOPY (NDIM, DXPAR, 1, WLBFGS(IGPNT+NPT_L+1), 1) the variable IGPNT is suddenly changed to an unreasonable high value leading to a crash of DCOPY. The reason for that sudden change of IGPNT is an overflow of the index of the vector TISTACK ! In "time.inc" I found the following declarations: PARAMETER (NTIMX=200) ... CHARACTER*(LENTIM) TISTACK(NTIMX) Later on in "timer.F" lines 44,45 ITSTACK=ITSTACK+1 TISTACK(ITSTACK)=SNAME the variable ITSTACK exceeds the value of NTIMX, i.e. it gets bigger than 200. I tried to set NTIMX to 250 instead of 200, but this only postponed the crash to geometry step 247. From that I conlcude that the number of geometry steps cannot exceed the value of NTIMX. Since that looks like a bug to me I would like to ask the developers of CPMD to have a look at this problem since I have no idea about the concept and realisation of the timing routines etc.. (The platform I used was a Linux-PC, Redhat 9, ifc 7 and ifort 8, CPMD 3.7.2.) Thank you! cheers, Christian. -- Christian Tuma Humboldt-Universitaet Berlin ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer From hutter at pci.unizh.ch Tue May 18 14:26:43 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Tue, 18 May 2004 14:26:43 +0200 (MEST) Subject: [CPMD-list] code problem with TISTACK(NTIMX) In-Reply-To: <20040518104546.GC364815@uranus.chemie.hu-berlin.de> References: <20040518104546.GC364815@uranus.chemie.hu-berlin.de> Message-ID: Hi Christian this type of error is related to unmatched start and stop calls for the timer routine. (TISTART - TIHALT) One known such case has been introduced in version 3.7.2 in fnonloc.F for the case of Vanderbilt and/or Goedecker PP. The easy bug fix is at line 526 of fnonloc.F IF (TIVAN.OR.TISGP) THEN CALL FNONLOC(C2,F,NSTATE,AUXC,DDIA,IKIND,ISPIN) CALL TIHALT(' FNONLOC',ISUB) RETURN ENDIF However, it's possible that you found another such case. Let us know if this doesn't help. regards Juerg Hutter ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Tue, 18 May 2004, Christian Tuma wrote: > Dear CPMD developers, > > I run a number of geometry optimisations that always crashed after > geometry step 198 or 199. Upon closer investigation I found the reason > for that behaviour: > In "rlbfgs.F" line 306 > > CALL DCOPY (NDIM, DXPAR, 1, WLBFGS(IGPNT+NPT_L+1), 1) > > the variable IGPNT is suddenly changed to an unreasonable high value > leading to a crash of DCOPY. > The reason for that sudden change of IGPNT is an overflow of the index > of the vector TISTACK ! In "time.inc" I found the following declarations: > > PARAMETER (NTIMX=200) > ... > CHARACTER*(LENTIM) TISTACK(NTIMX) > > Later on in "timer.F" lines 44,45 > > ITSTACK=ITSTACK+1 > TISTACK(ITSTACK)=SNAME > > the variable ITSTACK exceeds the value of NTIMX, i.e. it gets bigger > than 200. > I tried to set NTIMX to 250 instead of 200, but this only postponed > the crash to geometry step 247. From that I conlcude that the number > of geometry steps cannot exceed the value of NTIMX. Since that looks > like a bug to me I would like to ask the developers of CPMD to have > a look at this problem since I have no idea about the concept and > realisation of the timing routines etc.. > > (The platform I used was a Linux-PC, Redhat 9, ifc 7 and ifort 8, > CPMD 3.7.2.) > > Thank you! > > cheers, > Christian. > > -- > Christian Tuma Humboldt-Universitaet Berlin > ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) > phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY > fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Tue May 18 14:49:01 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Tue, 18 May 2004 14:49:01 +0200 (MEST) Subject: [CPMD-list] Segmentation fault using Nose-thermostat In-Reply-To: <25302.1084860579@www13.gmx.net> References: <884d586303.86303884d5@ihpc.a-star.edu.sg> <25302.1084860579@www13.gmx.net> Message-ID: Hi the integrators have sometimes problems with the Nose thermostats. This is especially true for the thermostats on the electrons. The integration diverges and at some point you get segmentation faults. The way out is to play with the NOSE PARAMETERS. See also the manual (Hints and Tricks section). The other problematic point may be the combination of Constraints with Thermostats. Try to start your job without the Constraints. In principle this should be possible, but may need some adjustments on the NOSE PARAMETERS and/or the way you define your constraints. regards Juerg Hutter ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Tue, 18 May 2004, Holger Hesske wrote: > Dear users! > > After a lot of well running MD?s with TEMPCONTROL IONS, I?ve tried to use > the Nose-Hoover-thermostat for producing proton-transfer in an ammonia-water > bulk. > But in any case (NOSE IONS.... NOSE ELECTRONS or both, even MASSIVE or > ULTRA) the program stops with Segmentation fault. > Every try leads to this error and I?m very appreciated if anybody could give > me a hint. Maybe I?m missing something? > > Thanks in advance > Holger > > > Holger He?ke > Institut f?r Anorganische Chemie > TU DRESDEN > > The last lines in the output are > --- > Atomic coordinates and velocities are read from File Geometry > > *** PHFAC | the new size of the program is 74924 kBytes *** > --- > The input are for example: > > &CPMD > FILEPATH /usr/local/CPMD/OUTPUTS/ > > MOLECULAR DYNAMICS > CONVERGENCE > 1.0e-5 1.0e-4 > RESTART GEOFILE WAVEFUNCTION LATEST > SPLINE POINTS > 1500 > EMASS > 600 > TEMPERATURE > 400 > NOSE IONS MASSIVE > 400.0 2500.0 > NOSE ELECTRONS > 0.02 10000.0 > MAXSTEP > 1000 > TRAJECTORY XYZ SAMPLE > 10 > &END > &SYSTEM > ANGSTROM > CELL ABSOLUTE DEGREE > 10.0 10.0 10.0 90.0 90.0 90.0 > SYMMETRY > 0 > POINT GROUP > AUTO > CHARGE > 1 > CUTOFF > 25 > 400eV > SCALE > TESR > 1 1 1 > &END > &DFT > NEWCODE > FUNCTIONAL BLYP > GC-CUTOFF > 1.0e-6 > &END > &ATOMS > H_SG_BLYP > .... > O_SG_BLYP > .... > N_SG_BLYP > .... > CONSTRAINTS > .. > .. > END CONSTRAINTS > &END > > -- > "Sie haben neue Mails!" - Die GMX Toolbar informiert Sie beim Surfen! > Jetzt aktivieren unter http://www.gmx.net/info > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From ct at chemie.hu-berlin.de Tue May 18 15:04:27 2004 From: ct at chemie.hu-berlin.de (Christian Tuma) Date: Tue, 18 May 2004 15:04:27 +0200 Subject: [CPMD-list] code problem with TISTACK(NTIMX) In-Reply-To: References: <20040518104546.GC364815@uranus.chemie.hu-berlin.de> Message-ID: <20040518130427.GD364815@uranus.chemie.hu-berlin.de> Hello Juerg, Walter and Axel, On Tue, May 18, 2004 at 02:26:43PM +0200, Juerg Hutter wrote: > this type of error is related to unmatched > start and stop calls for the timer routine. > (TISTART - TIHALT) > One known such case has been introduced in version 3.7.2 > in fnonloc.F for the case of Vanderbilt and/or Goedecker PP. > The easy bug fix is at line 526 of fnonloc.F > > IF (TIVAN.OR.TISGP) THEN > CALL FNONLOC(C2,F,NSTATE,AUXC,DDIA,IKIND,ISPIN) > CALL TIHALT(' FNONLOC',ISUB) > RETURN > ENDIF > > However, it's possible that you found another such case. > Let us know if this doesn't help. I just tried this and it didn't help because I'm neither using Vanderbilt nor Goedecker PP. Instead I'm using Troullier-Martins PP, please see this input (it's not meant for producing meaningful results, it's just tuned to make many geometry steps in a short time): ----------------------------------------------------------------------- ! &CPMD OPTIMIZE GEOMETRY CONVERGENCE ORBITALS 1.0E-02 CONVERGENCE GEOMETRY 1.0E-06 HESSIAN UNIT LBFGS &END &SYSTEM CELL 10.86410 0.99867 0.99301 -0.06909 -0.08433 -0.09375 SYMMETRY 14 CUTOFF 10.0 &END &ATOMS *TM/C_TM_PBE_pade_110 KLEINMAN-BYLANDER LMAX=P 1 5.110862 5.055884 8.447798 *TM/H_TM_PBE_pade_070 KLEINMAN-BYLANDER LMAX=S 4 5.985766 6.636814 7.435458 4.636936 3.562167 7.092203 3.387301 5.712451 9.390533 6.440386 4.336236 9.865253 &END &DFT NEWCODE FUNCTIONAL PBE &END ---------------------------------------------------------------------- Maybe a similar call to TIHALT is missing somewhere else, does somebody know where this could be? Thanks and kind regards, Christian. -- Christian Tuma Humboldt-Universitaet Berlin ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer From ZRLSRB at ch.ibm.com Tue May 18 15:49:20 2004 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Tue, 18 May 2004 15:49:20 +0200 Subject: [CPMD-list] code problem with TISTACK(NTIMX) Message-ID: Hi Christian, you can insert the following lines before line 33 of file timer.F (TISET; they are already contained in the newest version): IF(ITSTACK.GT.NTIMX) THEN DO I=1,ITSTACK-1 WRITE(*,'(A,I6,A)') ' NAME STACK ',I,TISTACK(I) ENDDO CALL STOPGM('TISET','ROUTINE STACK OVERFLOW') ENDIF This dumps the stack if there is an overflow, and you'll see where there is a TISET not matched by TIHALT Best regards, Salomon From hutter at pci.unizh.ch Tue May 18 16:58:04 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Tue, 18 May 2004 16:58:04 +0200 (MEST) Subject: [CPMD-list] code problem with TISTACK(NTIMX) In-Reply-To: <20040518130427.GD364815@uranus.chemie.hu-berlin.de> References: <20040518104546.GC364815@uranus.chemie.hu-berlin.de> <20040518130427.GD364815@uranus.chemie.hu-berlin.de> Message-ID: Hi Christian the problem is in cnstfc.F, use the following order of statements at line 19 CNMAX=0.0D0 C No constraints -> return. IF(MCNSTR.EQ.0) RETURN CALL TISET(' CNSTFC',ISUB) This will fix the problem. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Tue, 18 May 2004, Christian Tuma wrote: > Hello Juerg, Walter and Axel, > > On Tue, May 18, 2004 at 02:26:43PM +0200, Juerg Hutter wrote: > > this type of error is related to unmatched > > start and stop calls for the timer routine. > > (TISTART - TIHALT) > > One known such case has been introduced in version 3.7.2 > > in fnonloc.F for the case of Vanderbilt and/or Goedecker PP. > > The easy bug fix is at line 526 of fnonloc.F > > > > IF (TIVAN.OR.TISGP) THEN > > CALL FNONLOC(C2,F,NSTATE,AUXC,DDIA,IKIND,ISPIN) > > CALL TIHALT(' FNONLOC',ISUB) > > RETURN > > ENDIF > > > > However, it's possible that you found another such case. > > Let us know if this doesn't help. > > I just tried this and it didn't help because I'm neither using > Vanderbilt nor Goedecker PP. Instead I'm using Troullier-Martins PP, > please see this input (it's not meant for producing meaningful results, > it's just tuned to make many geometry steps in a short time): > > ----------------------------------------------------------------------- > ! > &CPMD > OPTIMIZE GEOMETRY > CONVERGENCE ORBITALS > 1.0E-02 > CONVERGENCE GEOMETRY > 1.0E-06 > HESSIAN UNIT > LBFGS > &END > &SYSTEM > CELL > 10.86410 0.99867 0.99301 -0.06909 -0.08433 -0.09375 > SYMMETRY > 14 > CUTOFF > 10.0 > &END > &ATOMS > *TM/C_TM_PBE_pade_110 KLEINMAN-BYLANDER > LMAX=P > 1 > 5.110862 5.055884 8.447798 > *TM/H_TM_PBE_pade_070 KLEINMAN-BYLANDER > LMAX=S > 4 > 5.985766 6.636814 7.435458 > 4.636936 3.562167 7.092203 > 3.387301 5.712451 9.390533 > 6.440386 4.336236 9.865253 > &END > &DFT > NEWCODE > FUNCTIONAL PBE > &END > ---------------------------------------------------------------------- > > Maybe a similar call to TIHALT is missing somewhere else, does somebody > know where this could be? > > Thanks and kind regards, > Christian. > > -- > Christian Tuma Humboldt-Universitaet Berlin > ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) > phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY > fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From ct at chemie.hu-berlin.de Tue May 18 17:12:30 2004 From: ct at chemie.hu-berlin.de (Christian Tuma) Date: Tue, 18 May 2004 17:12:30 +0200 Subject: [CPMD-list] code problem with TISTACK(NTIMX) In-Reply-To: References: <20040518104546.GC364815@uranus.chemie.hu-berlin.de> <20040518130427.GD364815@uranus.chemie.hu-berlin.de> Message-ID: <20040518151230.GE364815@uranus.chemie.hu-berlin.de> Hello Juerg and Salomon, On Tue, May 18, 2004 at 04:58:04PM +0200, Juerg Hutter wrote: > the problem is in cnstfc.F, use the following order of > statements at line 19 > > CNMAX=0.0D0 > C No constraints -> return. > IF(MCNSTR.EQ.0) RETURN > CALL TISET(' CNSTFC',ISUB) > > This will fix the problem. > > Juerg Yes, it works fine now. Thank you very much! cheers, Christian. -- Christian Tuma Humboldt-Universitaet Berlin ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer From kohsj at ihpc.a-star.edu.sg Wed May 19 10:02:57 2004 From: kohsj at ihpc.a-star.edu.sg (kohsj at ihpc.a-star.edu.sg) Date: Wed, 19 May 2004 16:02:57 +0800 Subject: [CPMD-list] Ref: Examples on H2O and Si Message-ID: <8ec688739e.8739e8ec68@ihpc.a-star.edu.sg> Dear Dr. Kohlmeyer, I've re-ran the a/m examples by first running the "optimize wavefunction" file and subsequently, running the Kohn-Sham energies file, with the following keywords under the &CPMD section: &CPMD RESTART WAVEFUNCTION COORDINATES LATEST KOHN-SHAM ENERGIES MAXSTEP 1000 RHOOUT STRUCTURE BONDS ANGLES &END The same termination occurred, as follows: PROGRAM CPMD STARTED AT: Wed May 19 15:48:16 2004 CONTROL| ERROR IN READING INPUT FILE THE LAST TWO LINES READ WERE KOHN-SHAM MAXSTEP PROGRAM STOPS IN SUBROUTINE CONTROL| [PROC= 0] I've run the two sets of programs under the same folder. That is, the "optimize wavefunction" file was run first, with the RESTART.1 and LATEST files created, before the "Kohn-Sham Energies" file was run. The manual mentioned that "POTENTIAL" is required for Kohn-Sham energy calculations, is that what I'm missing here? My last two questions: 1. In the event of not completely certain of what keywords to use after RESTART, what are the drawbacks of using the keyword "ALL"? 2. Is it possible to incorporate the "optimize wavefunction" and the "Kohn-Sham Energies" into a single run? Thank you very much for your kind attention. Adrian. ----- Original Message ----- From: Axel Kohlmeyer Date: Tuesday, May 18, 2004 3:56 pm Subject: Re: Examples on H2O and Si On Tue, 18 May 2004 kohsj at ihpc.a-star.edu.sg wrote: AK> Dear Dr. Kohlmeyer, dear adrian, AK> AK> With reference to the a/m examples on Prof. Hutters webpage (the AK> "Monday" ones), I encountered the following error termination found in AK> the output files: AK> AK> PROGRAM CPMD STARTED AT: Mon May 17 21:31:34 2004 AK> AK> CONTROL| ERROR IN READING INPUT FILE AK> THE LAST TWO LINES READ WERE AK> KOHN-SHAM AK> MAXSTEP AK> AK> AK> PROGRAM STOPS IN SUBROUTINE CONTROL| [PROC= 0] AK> AK> This happens when the "Optimize Wavefunction" was replaced with AK> "Kohn-Sham Energies" as was instructed by the tutorial. The one on ok, please check the manual. for the kohn-sham energies calculation you need to restart from the previously calculated wavefunction, so you have to add something like 'RESTART COORDINATES WAVEFUNCTION LATEST'. AK> Si8 and Si64 terminated at the point of basis set generation: AK> AK> GENERATE ATOMIC BASIS SET AK> AK> AK> PROGRAM STOPS IN SUBROUTINE READ_BASIS| SECTION WAVEFUNCTION [PROC= 0] you are intructing cpmd to build the initial guess from the (pseudo)wavefunctions in the pseudopotential files. with the SG pseudopotential files these do not exist. you have to either use martins-troullier (or similar) pseudopotentials or delete the &BASIS section (which will have cpmd to use a minimal slater basis to construct the initial guess). hope this helps, axel. AK> AK> The following is a sample of .inp file for the H2O molecule (with bend bonds): AK> AK> &CPMD AK> KOHN-SHAM ENERGIES AK> MAXSTEP AK> 1000 AK> RHOOUT AK> STRUCTURE BONDS ANGLES AK> &END AK> AK> &DFT AK> NEWCODE AK> FUNCTIONAL BLYP AK> GC-CUTOFF AK> 0.1E-06 AK> &END AK> AK> &SYSTEM AK> SYMMETRY AK> 0 AK> CELL AK> 15.0000 1.0 1.0 0 0 0 AK> CUTOFF AK> 70.0 AK> AK> &END AK> AK> &PROPERTIES AK> DIPOLE MOMENT AK> &END AK> AK> &ATOMS AK> *O_SG_BLYP AK> LMAX=P AK> 1 AK> 7.5000 7.3723 7.4919 AK> AK> *H_SG_BLYP AK> LMAX=S AK> 2 AK> 8.9608 8.5133 7.5645 AK> 6.0392 8.5133 7.5645 AK> AK> &END AK> AK> AK> Here's a sample file for the Si clusters: AK> AK> &CPMD AK> OPTIMIZE WAVEFUNCTION AK> MAXSTEP AK> 1000 AK> &END AK> AK> AK> &DFT AK> NEWCODE AK> FUNCTIONAL BLYP AK> GC-CUTOFF AK> 0.2E-06 AK> &END AK> AK> &SYSTEM AK> SYMMETRY AK> 1 AK> CELL AK> 10.263102 1.0 1.0 0 0 0 AK> CUTOFF AK> 12.0 AK> CHARGE AK> 0.0 AK> AK> &END AK> AK> &ATOMS AK> *Si_SG_BLYP AK> LMAX=P AK> 8 AK> 5.130606 10.263102 5.130606 AK> 10.263102 5.130606 5.130606 AK> 5.130606 5.130606 0.000000 AK> 10.263102 10.263102 0.000000 AK> 7.696854 2.566248 7.696854 AK> 2.566248 2.566248 2.566248 AK> 2.566248 7.696854 7.696854 AK> 7.696854 7.696854 2.566248 AK> AK> AK> &END AK> AK> &BASIS AK> PSEUDO AO 2 AK> 0 1 AK> AK> &END AK> AK> AK> Thanks for your attention :). AK> AK> AK> Adrian. AK> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.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/ ======================================================================= -------------- next part -------------- A non-text attachment was scrubbed... Name: kohsj.vcf Type: text/x-vcard Size: 255 bytes Desc: Card for Url : http://cpmd.org/pipermail/cpmd-list/attachments/20040519/48d43fd5/attachment.bin From hutter at pci.unizh.ch Wed May 19 11:18:23 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Wed, 19 May 2004 11:18:23 +0200 (MEST) Subject: [CPMD-list] Ref: Examples on H2O and Si In-Reply-To: <8ec688739e.8739e8ec68@ihpc.a-star.edu.sg> References: <8ec688739e.8739e8ec68@ihpc.a-star.edu.sg> Message-ID: Hi > &CPMD > RESTART WAVEFUNCTION COORDINATES LATEST > KOHN-SHAM ENERGIES > MAXSTEP > 1000 > RHOOUT > STRUCTURE BONDS ANGLES > &END The "KOHN-SHAM ENERGIES" keyword needs a number of states information on the next line (see manual). The correct input would be KOHN-SHAM ENERGIES 0 for no additional states (only calculate occupied KS states) regards Juerg Hutter From kohsj at ihpc.a-star.edu.sg Fri May 21 10:16:49 2004 From: kohsj at ihpc.a-star.edu.sg (kohsj at ihpc.a-star.edu.sg) Date: Fri, 21 May 2004 16:16:49 +0800 Subject: [CPMD-list] Compilation of cpmd2cube Message-ID: Hi, I'm currently attempting to convert a binary DENSITY file to a readable visual file. I've downloaded cpmd2cube from your website and extracted it. How can I compile and create the cpmd2cube.x file? Thanks! -------------- next part -------------- A non-text attachment was scrubbed... Name: kohsj.vcf Type: text/x-vcard Size: 255 bytes Desc: Card for Url : http://cpmd.org/pipermail/cpmd-list/attachments/20040521/5bf7fd36/attachment.bin From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Fri May 21 12:52:04 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Fri, 21 May 2004 12:52:04 +0200 Subject: [CPMD-list] Compilation of cpmd2cube In-Reply-To: Message-ID: <200405211052.i4LAq4q20333@yello.theochem.ruhr-uni-bochum.de> On Fri, 21 May 2004 16:16:49 +0800 kohsj at ihpc.a-star.edu.sg wrote: > > Hi, > > I'm currently attempting to convert a binary DENSITY file to a readable visual file. I've downloaded cpmd2cube from your website and extracted it. How can I c ompile and create the cpmd2cube.x file? > > Thanks! hi, you need to adapt the makefile, type make and hope for the best. the flags can be largely taken from the cpmd makefile. the version distributed alongside cpmd-v3.9 will have a Configure script similar to the one from cpmd. axel. > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- ======================================================================= 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 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From alex.msilva at uol.com.br Fri May 21 17:57:26 2004 From: alex.msilva at uol.com.br (alex.msilva) Date: Fri, 21 May 2004 12:57:26 -0300 Subject: [CPMD-list] Ag PP Message-ID: