From natasa.mateljevic at yale.edu Tue Sep 3 22:28:08 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Tue, 3 Sep 2002 16:28:08 -0400 (EDT) Subject: [CPMD-list] cant compile Message-ID: Hi, I ran into the following problem when I tryed to compile the .3 version curie1% make pgf77 -c -fast -Mr8 -pc64 -Msignextend -Msecond_underscore ./cpmd.f -o ./cpmd.o pgf77-linux86: LICENSE MANAGER PROBLEM: Cannot connect to license server (-15,12:111 "Connection refused") make: *** [cpmd.o] Error 1 curie1% /usr/local/pgi/linux86/bin/lmgrd /usr/local/pgi/linux86/bin/lmgrd: Command not found. I had no problem compiling the .2 version, so I am not sure whats the problem here, and I need to get this working in order to use the Vanderbilt PPs. Thanks, Natasa From Ari.P.Seitsonen at iki.fi Tue Sep 3 23:54:35 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Tue, 3 Sep 2002 23:54:35 +0200 Subject: [CPMD-list] cant compile In-Reply-To: (message from Natasa Mateljevic on Tue, 3 Sep 2002 16:28:08 -0400 (EDT)) References: Message-ID: <200209032154.g83LsZe25973@magadino.cscs.ch> Dear Natasa, > I ran into the following problem when I tryed to compile the .3 version > curie1% make > pgf77 -c -fast -Mr8 -pc64 -Msignextend -Msecond_underscore ./cpmd.f -o > ./cpmd.o > pgf77-linux86: LICENSE MANAGER PROBLEM: Cannot connect to license server > (-15,12:111 "Connection refused") > make: *** [cpmd.o] Error 1 > curie1% /usr/local/pgi/linux86/bin/lmgrd > /usr/local/pgi/linux86/bin/lmgrd: Command not found. > I had no problem compiling the .2 version, so I am not sure whats the > problem here, and I need to get this working in order to use the > Vanderbilt PPs. This is certainly a problem of your local computer system and has nothing to do with the CPMD code. Please try later again, or contact your system administrator, maybe there's a temporary problem in your license manager. 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 From cur Wed Sep 4 08:39:50 2002 From: cur (Alessandro Curioni) Date: Wed, 4 Sep 2002 08:39:50 +0200 (MDT) Subject: [CPMD-list] Re: compilation problem on a IBM SP In-Reply-To: <3D74DAD5.2C44DF36@puc.cl> from "Ricardo Ramirez" at Sep 03, 2002 11:52:53 AM Message-ID: <200209040639.IAA14298@cpmd.org> Dear Ricardo, You have simply to locate where the lapack library is installed on your system, then modify the -L/usr/local/lib and the -llapack_pwr3 flags. In most systems you will find this under -L/usr/local/lib and -llapack. Note that the lapack library is not installed as a standard component under AIX. Regards, A. Curioni > > I am trying to compile the cpmd code on an IBM SP Blue Horizon Power3 > machine. I have used > the option Configure IBM-SP3-SMP, but I am having trouble with the > lapack libraries. I got the > following messages: > > ld: 0706-006 Cannot find or open library file: -l lapack_pwr3 > ld:open(): A file or directory in the path name does not exist. > ld: 0706-006 Cannot find or open library file: -l lapack_pwr3 > ld:open(): A file or directory in the path name does not exist. > make: 1254-004 The error code from the last command is 255. > > I wonder if somebody else has encountered such problem before. > > Thank tou for your help. > > > Ricardo Ramirez > > > > From natasa.mateljevic at yale.edu Wed Sep 4 23:51:03 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Wed, 4 Sep 2002 17:51:03 -0400 (EDT) Subject: [CPMD-list] cant run Vanderbilt PPs In-Reply-To: <200209032154.g83LsZe25973@magadino.cscs.ch> Message-ID: Hi, I have compiled the new version od CPMD, so that I can use the Vanderbilt PPs, and this is what part of my input file looks like (graphite + oxygen ), so I am adding what you suggested: &CPMD OPTIMIZE GEOMETRY LSD <---- STRUCTURE BONDS ANGLES DIHEDRALS &END &SYSTEM CELL VECTORS 18.57084 0.0 0.0, 9.28542 16.08282 0.0, 0.0 0.0 20.00000 CUTOFF 25.<----- TESR 4 &END &DFT FUNCTIONAL PBE <----- GC-CUTOFF 1.0D-7 &END &ATOMS *006-C-gpbe--bm.uspp NEWF BINARY <----- 0 0 0 <----- LMAX=P 32 2.32136 0.00000 0.00000 0.00000 1.34023 0.00000 5.98294 2.68046 0.00000 2.32136 5.36094 0.00000 6.96406 8.04141 0.00000 I am using the same input for oxygen but this is not working I get the following error when I do: cpmd.x surface2o ~/Vanderbilt/uspp-734/Pot > surface2o.out EXCHANGE CORRELATION FUNCTIONALS LDA EXCHANGE: NONE LDA XC THROUGH PADE APPROXIMATION S.GOEDECKER, J.HUTTER, M.TETER PRB 54 1703 (1996) GRADIENT CORRECTED FUNCTIONAL DENSITY THRESHOLD: 1.00000E-07 EXCHANGE ENERGY [PBE: J.P. PERDEW ET AL. PRL 77, 3865 (1996)] CORRELATION ENERGY [PBE: J.P. PERDEW ET AL. PRL 77, 3865 (1996)] RATOM: ERROR WHILE READING ON UNIT 5 PROGRAM STOPS IN SUBROUTINE DETSP| I am not sure what is wrong wiht this and how I can fix it. Thanks for your advice. Natasa From Ari.P.Seitsonen at iki.fi Thu Sep 5 09:37:15 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Thu, 5 Sep 2002 09:37:15 +0200 Subject: [CPMD-list] cant run Vanderbilt PPs In-Reply-To: (message from Natasa Mateljevic on Wed, 4 Sep 2002 17:51:03 -0400 (EDT)) References: Message-ID: <200209050737.g857bF308372@magadino.cscs.ch> Dear Natasa, > I have compiled the new version od CPMD, so that I can use the Vanderbilt > PPs, and this is what part of my input file looks like (graphite + oxygen > ), so I am adding what you suggested: > &CPMD > OPTIMIZE GEOMETRY > LSD <---- > STRUCTURE BONDS ANGLES DIHEDRALS > &END > &SYSTEM > CELL VECTORS > 18.57084 0.0 0.0, 9.28542 16.08282 0.0, 0.0 0.0 > 20.00000 > CUTOFF > 25.<----- > TESR > 4 > &END > &DFT > FUNCTIONAL PBE <----- > GC-CUTOFF > 1.0D-7 > &END > &ATOMS > *006-C-gpbe--bm.uspp NEWF BINARY <----- > 0 0 0 <----- > LMAX=P > 32 > 2.32136 0.00000 0.00000 > 0.00000 1.34023 0.00000 > 5.98294 2.68046 0.00000 > 2.32136 5.36094 0.00000 > 6.96406 8.04141 0.00000 > I am using the same input for oxygen but this is not working I get the > following error when I do: cpmd.x surface2o ~/Vanderbilt/uspp-734/Pot > > surface2o.out > EXCHANGE CORRELATION FUNCTIONALS > LDA EXCHANGE: NONE > LDA XC THROUGH PADE APPROXIMATION > S.GOEDECKER, J.HUTTER, M.TETER PRB 54 1703 (1996) > GRADIENT CORRECTED FUNCTIONAL > DENSITY THRESHOLD: 1.00000E-07 > EXCHANGE ENERGY > [PBE: J.P. PERDEW ET AL. PRL 77, 3865 (1996)] > CORRELATION ENERGY > [PBE: J.P. PERDEW ET AL. PRL 77, 3865 (1996)] > > RATOM: ERROR WHILE READING ON UNIT 5 > > PROGRAM STOPS IN SUBROUTINE DETSP| > > I am not sure what is wrong wiht this and how I can fix it. What is this line with the '0 0 0' for? It looks like too much for me, as you also specify 'LMAX=P' for the pseudo potential. Does it still stop if you remove that line? 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 From natasa.mateljevic at yale.edu Thu Sep 5 20:41:51 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Thu, 5 Sep 2002 14:41:51 -0400 (EDT) Subject: [CPMD-list] cant run Vanderbilt PPs In-Reply-To: <200209050737.g857bF308372@magadino.cscs.ch> Message-ID: Hi, I still cant get thsi to work I get the following error: curie1% cpmd.x surface2o ~/Vanderbilt/uspp-734/Pot > surface2o.out PGFIO-F-219/unformatted read/unit=22/attempt to read/write past end of record. File name = /home/natasa/Vanderbilt/uspp-734/Pot/006-C-gpbe--bm.uspp unformatted, sequential access record = 7 In source file ./readvan.f, at line number 417 Natasa From natasa.mateljevic at yale.edu Thu Sep 5 21:14:19 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Thu, 5 Sep 2002 15:14:19 -0400 (EDT) Subject: [CPMD-list] cant run Vanderbilt PPs In-Reply-To: <200209050737.g857bF308372@magadino.cscs.ch> Message-ID: Hi, I forgot to include what my input looks like, and its not working when I take out the zeros either, Jureg told me to include the following lines: &ATOMS *006-C-gpbe--bm.uspp NEWF BINARY 32 0 0 0 2.32136 0.00000 0.00000 0.00000 1.34023 0.00000 5.98294 2.68046 0.00000 2.32136 5.36094 0.00000 Natasa From ricardo at irsamc.ups-tlse.fr Thu Sep 5 23:10:49 2002 From: ricardo at irsamc.ups-tlse.fr (JOSE LUIS RICARDO-CHAVEZ) Date: Thu, 05 Sep 2002 23:10:49 +0200 Subject: [CPMD-list] cant run Vanderbilt PPs References: Message-ID: <3D77C859.8000106@irsamc.ups-tlse.fr> Natasa Mateljevic wrote: >Hi, >I still cant get thsi to work I get the following error: >curie1% cpmd.x surface2o ~/Vanderbilt/uspp-734/Pot > surface2o.out >PGFIO-F-219/unformatted read/unit=22/attempt to read/write past end of >record. > File name = /home/natasa/Vanderbilt/uspp-734/Pot/006-C-gpbe--bm.uspp >unformatted, sequential access record = 7 > In source file ./readvan.f, at line number 417 >Natasa > >_______________________________________________ >CPMD-list mailing list >CPMD-list at cpmd.org >http://www.cpmd.org/mailman/listinfo/cpmd-list > > > Dear Natasa the error message means that either the file /home/natasa/Vanderbilt/uspp-734/Pot/006-C-gpbe--bm.uspp does not exist or it is not the correct one. Unless you changed the name and the location of the pseudopotential files they should be /home/natasa/Vanderbilt/uspp-734/Pot/006-C-gpbe--bm/c_ps.uspp and /home/natasa/Vanderbilt/uspp-734/Pot/008-O/008-O-gpbe--bm/o_ps.uspp Regards, - Jose Luis -- Jose Luis RICARDO-CHAVEZ Tel. +33-5-61-55-68-33 Laboratoire de Physique Quantique Fax +33-5-61-55-60-65 Universite Paul Sabatier 118 route de Narbonne F-31062 Toulouse, France e-mail: ricardo at irsamc1.ups-tlse.fr From fparnold at chem.northwestern.edu Thu Sep 5 23:57:36 2002 From: fparnold at chem.northwestern.edu (Fred P. Arnold) Date: Thu, 5 Sep 2002 16:57:36 -0500 (CDT) Subject: [CPMD-list] Extra channels in Vanderbilt PP Message-ID: Hello, In small molecule calculations, it is common to use basis sets that are at least 'double zeta', i.e. two functions per l channel, and often augmented by a polarization function (higher l value). So, when generating PPs, do you follow the same policy as you would with gaussian or slater type orbitals, or do you only put in channels for the occupied space, and then increase the plane-wave cutoff? I've been having problems with convergence properties of the USPPs within cpmd3.5.3, and was therefore curious if a smaller potential would help. -Fred Frederick P. Arnold, Jr. NUIT, Northwestern U. f-arnold at northwestern.edu From cakmak at gazi.edu.tr Fri Sep 6 09:38:12 2002 From: cakmak at gazi.edu.tr (Mehmet Cakmak) Date: Fri, 06 Sep 2002 09:38:12 EEST Subject: [CPMD-list] Ag lat_par Message-ID: Dear All, I am having a problem to calculate the lattice parameter of Ag. Has anybody succesfully calculated the Ag lattice parameter using uspp? Second question is about the k points problem which is I am not able to put kpoints in the input file when I want to use the Vanderblit uspp. Any idea about it? thanks -mehmet From eyvaz_isaev at yahoo.com Fri Sep 6 11:32:32 2002 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 6 Sep 2002 02:32:32 -0700 (PDT) Subject: [CPMD-list] Ag lat_par In-Reply-To: Message-ID: <20020906093232.66106.qmail@web40007.mail.yahoo.com> Dear Mehmet, According to recent Ari's mail Vanderbilt+k-points combination is not (yet?) allowed. Please try increase cutoff energy in order to have converged results. Regards, Eyvaz Theoretical Physics Department Moscow Steel and Alloys Institute --- Mehmet Cakmak wrote: > > Dear All, > > I am having a problem to calculate > the lattice parameter of Ag. > Has anybody succesfully calculated the Ag > lattice parameter using uspp? > > Second question is about the k points problem which > is I am not able to put kpoints in the input file > when I want to use the Vanderblit uspp. Any idea > about it? > > thanks > -mehmet > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list __________________________________________________ Do You Yahoo!? Yahoo! Finance - Get real-time stock quotes http://finance.yahoo.com From Ari.P.Seitsonen at iki.fi Fri Sep 6 11:51:49 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Fri, 6 Sep 2002 11:51:49 +0200 Subject: [CPMD-list] Ag lat_par In-Reply-To: (message from Mehmet Cakmak on Fri, 06 Sep 2002 09:38:12 EEST) References: Message-ID: <200209060951.g869pnW24630@magadino.cscs.ch> Dear Mehmet, > I am having a problem to calculate > the lattice parameter of Ag. > Has anybody succesfully calculated the Ag > lattice parameter using uspp? What is your problem, the convergence? > Second question is about the k points problem which > is I am not able to put kpoints in the input file > when I want to use the Vanderblit uspp. Any idea about it? The Vanderbilt part does not work with k points, i.e. it is not fully implemented. 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 From cakmak at gazi.edu.tr Fri Sep 6 12:41:17 2002 From: cakmak at gazi.edu.tr (Mehmet Cakmak) Date: Fri, 06 Sep 2002 12:41:17 EEST Subject: [CPMD-list] Ag lat_par Message-ID: The energies (using the difference lattice parameter for Ag) are fluctuating. I mean I cannot see the parabolic behaviour of energy versus lat par. Do you have any input file using uspp for Ag to calculate the lattice parameter? thank you -mehmet On 06 Sep 2002 12:56 EEST you wrote: > > Dear Mehmet, > > > I am having a problem to calculate > > the lattice parameter of Ag. > > Has anybody succesfully calculated the Ag > > lattice parameter using uspp? > > What is your problem, the convergence? > > > Second question is about the k points problem which > > is I am not able to put kpoints in the input file > > when I want to use the Vanderblit uspp. Any idea about it? > > The Vanderbilt part does not work with k points, i.e. it is not fully > implemented. > > 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 From Ari.P.Seitsonen at iki.fi Sun Sep 8 12:12:46 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Sun, 8 Sep 2002 12:12:46 +0200 Subject: [CPMD-list] Ag lat_par In-Reply-To: (message from Mehmet Cakmak on Fri, 06 Sep 2002 12:41:17 EEST) References: Message-ID: <200209081012.g88ACk028044@magadino.cscs.ch> Dear Mehmet, > The energies (using the difference lattice parameter for Ag) > are fluctuating. I mean I cannot see the parabolic behaviour > of energy versus lat par. Do you at least see a minimum close to the experimental lattice constant? How many atoms do you have in your unit cell (if you can only use Gamma point, you need plenty of atoms, which, unfortunately, causes problems in the convergence, one has to switch to the free energy functional, if it works with the Vdb pseudos, ...) Greetings, apsi > > On 06 Sep 2002 12:56 EEST you wrote: > > > > > Dear Mehmet, > > > > > I am having a problem to calculate > > > the lattice parameter of Ag. > > > Has anybody succesfully calculated the Ag > > > lattice parameter using uspp? > > > > What is your problem, the convergence? > > > > > Second question is about the k points problem which > > > is I am not able to put kpoints in the input file > > > when I want to use the Vanderblit uspp. Any idea about it? > > > > The Vanderbilt part does not work with k points, i.e. it is not fully > > implemented. > > > > 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 > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- 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 From cakmak at gazi.edu.tr Sun Sep 8 13:05:33 2002 From: cakmak at gazi.edu.tr (Mehmet Cakmak) Date: Sun, 08 Sep 2002 13:05:33 EEST Subject: [CPMD-list] Ag lat_par Message-ID: Thank you for your explanations. Yes, exactly I can see the minimum near to the experimental lattice constant when I make bulk calculation for Ag. Can I use cpmd uspp for the *Ag surface* within only gamma point? I mean the accuracy could be trustable for such metal surfaces? > > Dear Mehmet, > > > The energies (using the difference lattice parameter for Ag) > > are fluctuating. I mean I cannot see the parabolic behaviour > > of energy versus lat par. > > Do you at least see a minimum close to the experimental lattice > constant? How many atoms do you have in your unit cell (if you > can only use Gamma point, you need plenty of atoms, which, > unfortunately, causes problems in the convergence, one has to switch > to the free energy functional, if it works with the Vdb pseudos, ...) > > Greetings, > > apsi > > > > > On 06 Sep 2002 12:56 EEST you wrote: > > > > > > > > Dear Mehmet, > > > > > > > I am having a problem to calculate > > > > the lattice parameter of Ag. > > > > Has anybody succesfully calculated the Ag > > > > lattice parameter using uspp? > > > > > > What is your problem, the convergence? > > > > > > > Second question is about the k points problem which > > > > is I am not able to put kpoints in the input file > > > > when I want to use the Vanderblit uspp. Any idea about it? > > > > > > The Vanderbilt part does not work with k points, i.e. it is not fully > > > implemented. > > > > > > 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 > > > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > > -- > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > 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 From psy at postech.ac.kr Tue Sep 10 05:01:58 2002 From: psy at postech.ac.kr (Jung Mee Park) Date: Tue, 10 Sep 2002 12:01:58 +0900 Subject: [CPMD-list] Ultrasoft Vanderbilt PP for Ag Message-ID: <3D7D60A6.28F0496B@postech.ac.kr> Dear all, I am looking for USPP for Ag atom with PBE functional. In the library of Vanderbilts PP's website, there is no available PP for Ag. I have found that one of cpmd-list members is using USPP for Ag. Is there anybody who generated/collected that PP? Where can I find that? Thanks, Jung Mee, ------------------------------------------------ Jung Mee Park, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea Tel: +82-54-279-2785 Fax: +82-54-279-8137 E-mail: psy at postech.ac.kr From hutter at pci.unizh.ch Tue Sep 10 10:08:34 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Tue, 10 Sep 2002 10:08:34 +0200 (MEST) Subject: [CPMD-list] Re: Problems with Vanderbilt PPs for Fe, Cu, Y etc In-Reply-To: Message-ID: On Mon, 9 Sep 2002, Fernando Alvarez Ramirez wrote: > > Hi Juerg > > I am trying to run the CPMD code using Vanderbilt pseudopotentials for Cu. > I have down loaded the home page Vanderbilt pseudopotential generator > uspp-734-2.tgz from his webpage > > http://www.physics.rutgers.edu/~dhv/uspp/ > > Some pseudopotentials work without problems like Si, C, O, etc, but I > have problems when I use other pseudopotential like Fe, Cu etc. > > I have put the typical input line > > *fe_ps.uspp NEWF BINARY TPSEU > LMAX=D > > but the program gives me the next outlines > > !!! ERROR !!! AP(ILP,IL,IK) = 28.03090******* 1 6 9 > > PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 0] > > Do you know how to solve this problem? > > > thaks in advance > > > Fernando Alvarez Ramirez > Hi This most likely related to one of the restrictions of the implementation of USPP's in CPMD. 1) maximum L is d, no f functions possible 2) all L channels need the same number of projectors 3) the channels are given by the PP program, they can not be changed in the CPMD input, i.e. LMAX=D doesn't have any effect. Last possibility: your USPP has only s,p,d channels and 2 channels each, then this might be a new bug in CPMD. Please reply to the mailing list thank you Juerg From Veronique.VanSpeybroeck at rug.ac.be Tue Sep 10 11:41:06 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Tue, 10 Sep 2002 11:41:06 +0200 (MEST) Subject: [CPMD-list] Re: Problems with Vanderbilt PPs for Fe, Cu, Y etc In-Reply-To: Message-ID: On Tue, 10 Sep 2002, Juerg Hutter wrote: > > On Mon, 9 Sep 2002, Fernando Alvarez Ramirez wrote: > > > > > Hi Juerg > > > > I am trying to run the CPMD code using Vanderbilt pseudopotentials for Cu. > > I have down loaded the home page Vanderbilt pseudopotential generator > > uspp-734-2.tgz from his webpage > > > > http://www.physics.rutgers.edu/~dhv/uspp/ > > > > Some pseudopotentials work without problems like Si, C, O, etc, but I > > have problems when I use other pseudopotential like Fe, Cu etc. > > > > I have put the typical input line > > > > *fe_ps.uspp NEWF BINARY TPSEU > > LMAX=D > > > > but the program gives me the next outlines > > > > !!! ERROR !!! AP(ILP,IL,IK) = 28.03090******* 1 6 9 > > > > PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 0] > > > > Do you know how to solve this problem? > > > > > > thaks in advance > > > > > > Fernando Alvarez Ramirez > > > Hi > > This most likely related to one of the restrictions of the > implementation of USPP's in CPMD. > > 1) maximum L is d, no f functions possible > 2) all L channels need the same number of projectors > 3) the channels are given by the PP program, they can not > be changed in the CPMD input, i.e. LMAX=D doesn't have > any effect. > > Last possibility: your USPP has only s,p,d channels and 2 channels > each, then this might be a new bug in CPMD. > > Please reply to the mailing list > > thank you > > Juerg Hi, I experience a similar problem with a Rh pseudopotential. I have a typical input line of the form : &ATOMS *../../Rh_VDB_U BINARY NEWF LMAX=D 1 2.32027 -0.02273 0.00629 &END as the output I get : !!! ERROR !!! AP(ILP,IL,IK) = 6.27358-7.03724 1 4 9 PROGRAM STOPS IN SUBROUTINE AAINIT| The Rh pseudopotential was generated with LMAX=D. Can I solve this problem, or is it not possible to treat atoms with D functions in the current version of the CPMD code? 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 rug.ac.be http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html ----------------------------------------------------------------------- > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From Magali.BENOIT at LDV.univ-montp2.fr Tue Sep 10 11:59:04 2002 From: Magali.BENOIT at LDV.univ-montp2.fr (Magali BENOIT) Date: Tue, 10 Sep 2002 11:59:04 +0200 Subject: [CPMD-list] Compilation on IBM-SP4 Message-ID: <200209100959.LAA03155@ares.ldv.univ-montp2.fr> Dear all, I am having problems with the compilation of CPMD on the IBM-SP4 platform. I tried all the configurations proposed on the cpmd-list but it still doesn't work. Here is the makefile: ------------------------------------------------------------------------------- - SRC = . DEST = . BIN = . #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = -O3 -qmaxmem=32768 -qarch=pwr4 -qtune=pwr4 -q64 LFLAGS = -lessl \ -bbinder:/usr/lib/bind -bmaxdata:0x40000000 -qarch=pwr4 $(QMMM_LIBS) CFLAGS = -O3 -qarch=pwr4 -qtune=pwr4 -q64 CPP = /usr/ccs/lib/cpp -P CPPFLAGS = -D__IBM -DESSL -DPOINTER8 -DPARALLEL -DMP_LIBRARY=__MPI -DFFT_ESSL CC = cc FC = mpxlf_r -c LD = mpxlf_r AR = /usr/bin/ar NODE = $(SCALAPACK_I4S4D8) ------------------------------------------------------------------------------- - And here are the warnings I get when I run the compilation: "system.h", line 77.6: 1520-035 (I) The common block size will increase in 64-bit mode because it contains at least one integer pointer. "system.h", line 184.6: 1520-035 (I) The common block size will increase in 64-bit mode because it contains at least one integer pointer. .... "shop.inc", line 5.6: 1520-035 (I) The common block size will increase in 64-bit mode because it contains at least one integer pointer. "./control.f", 1514-008 (W) Variable ip_zxmat is misaligned. This may affect the efficiency of the code. "./control.f", 1514-008 (W) Variable ip_catom is misaligned. This may affect the efficiency of the code. "./control.f", 1514-008 (W) Variable ip_pxpar is misaligned. This may affect the efficiency of the code. ... and so on for all the pointers. Does anyone know how I can solve this problem ? Thanks in advance, Magali -- ___________________________________________________________________ Dr. Magali BENOIT magali.benoit at ldv.univ-montp2.fr Laboratoire des Verres, cc69 Universite Montpellier II **NEW** Tel :+33 (0)4 67 14 34 53 34095 Montpellier Cedex 05 Fax :+33 (0)4 67 14 34 98 FRANCE ___________________________________________________________________ From cur at zurich.ibm.com Tue Sep 10 12:21:56 2002 From: cur at zurich.ibm.com (Alessandro Curioni) Date: Tue, 10 Sep 2002 12:21:56 +0200 Subject: [CPMD-list] Compilation on IBM-SP4 Message-ID: Magali, your Makefile looks strange. -1) you need the LAPACK ; you don't solve the fact of having missing lapack with the -DESSL flag . One solution is to have -DLAPACK -DFFT_ESSL , and link thelapack in the following way - lessl -llapack -lessl. Or better, retrieve the cci libraries from the ACTC ibm site (www. research.ibm.com/actc) and link in the following way -lcci -llapack -lessl -2): if you want to poduce a 64bit code you have to link a 64bit lapack - 3): the only reason to produce 64bit executables is to be able to run exe files that require more than 4GB of memory allocation (the 64bit it is indeed slower than the 32bit): so if you need that you should increase bmaxdata: -bmaxdata:0x80000000 As I wrote in a previous e-mail, full support for the PWR4 will be included in the next version of CPMD, with around 40% increased performance. Alessandro CURIONI, PhD Research Staff Member Computational Biochemistry and Material Science group IBM Research Division - Zurich Research Laboratory Saumerstrasse 4 8003 Rueschlikon - Switzerland e-mail: cur at zurich.ibm.com www: www.zurich.ibm.com Tel: +41-1-7248633 Fax: +41-1-7248958 Magali BENOIT cc: Sent by: cpmd-list- Subject: [CPMD-list] Compilation on IBM-SP4 admin at cpmd.org 09/10/2002 11:59 AM Dear all, I am having problems with the compilation of CPMD on the IBM-SP4 platform. I tried all the configurations proposed on the cpmd-list but it still doesn't work. Here is the makefile: ------------------------------------------------------------------------------- - SRC = . DEST = . BIN = . #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = -O3 -qmaxmem=32768 -qarch=pwr4 -qtune=pwr4 -q64 LFLAGS = -lessl \ -bbinder:/usr/lib/bind -bmaxdata:0x40000000 -qarch=pwr4 $(QMMM_LIBS) CFLAGS = -O3 -qarch=pwr4 -qtune=pwr4 -q64 CPP = /usr/ccs/lib/cpp -P CPPFLAGS = -D__IBM -DESSL -DPOINTER8 -DPARALLEL -DMP_LIBRARY=__MPI - DFFT_ESSL CC = cc FC = mpxlf_r -c LD = mpxlf_r AR = /usr/bin/ar NODE = $(SCALAPACK_I4S4D8) ------------------------------------------------------------------------------- - And here are the warnings I get when I run the compilation: "system.h", line 77.6: 1520-035 (I) The common block size will increase in 64-bit mode because it contains at least one integer pointer. "system.h", line 184.6: 1520-035 (I) The common block size will increase in 64-bit mode because it contains at least one integer pointer. .... "shop.inc", line 5.6: 1520-035 (I) The common block size will increase in 64-bit mode because it contains at least one integer pointer. "./control.f", 1514-008 (W) Variable ip_zxmat is misaligned. This may affect the efficiency of the code. "./control.f", 1514-008 (W) Variable ip_catom is misaligned. This may affect the efficiency of the code. "./control.f", 1514-008 (W) Variable ip_pxpar is misaligned. This may affect the efficiency of the code. ... and so on for all the pointers. Does anyone know how I can solve this problem ? Thanks in advance, Magali -- ___________________________________________________________________ Dr. Magali BENOIT magali.benoit at ldv.univ-montp2.fr Laboratoire des Verres, cc69 Universite Montpellier II **NEW** Tel :+33 (0)4 67 14 34 53 34095 Montpellier Cedex 05 Fax :+33 (0)4 67 14 34 98 FRANCE ___________________________________________________________________ _______________________________________________ CPMD-list mailing list CPMD-list at cpmd.org http://www.cpmd.org/mailman/listinfo/cpmd-list -------------- next part -------------- An HTML attachment was scrubbed... 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Name: pic03264.gif Type: image/gif Size: 1255 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20020910/559f9f04/attachment-0002.gif From hutter at pci.unizh.ch Tue Sep 10 13:22:45 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Tue, 10 Sep 2002 13:22:45 +0200 (MEST) Subject: [CPMD-list] Re: Problems with Vanderbilt PPs for Fe, Cu, Y etc In-Reply-To: Message-ID: Hi this is the PP report printed in CPMD for an iron USPP that works on my computer. Any noticable differences to your USPP's? ------------------------------------------------------------ | iron PBE - GGA exchange-corr | | z = 26.00 zv = 16.00 exfact = 5.00000 | | etot =-252.61135 | | index orbital occupation energy | | 1 300 2.00 -7.01 | | 2 310 6.00 -4.52 | | 3 320 6.50 -.69 | | 4 400 1.00 -.59 | | 5 410 .00 -.28 | | keyps = 3 ifpcor = 0 | | rinner = 1.50 for L= 1 | | rinner = 1.50 for L= 2 | | rinner = 1.50 for L= 3 | | rinner = 1.50 for L= 4 | | rinner = 1.50 for L= 5 | | new generation scheme: | | nbeta = 6 kkbeta = 599 rcloc = 2.0000 | | ibeta l epsilon rcut iptype | | 1 0 -7.01 2.00 2 | | 2 0 -.59 2.00 2 | | 3 1 -4.52 2.00 2 | | 4 1 -.28 2.00 2 | | 5 2 -.69 2.00 2 | | 6 2 .60 2.00 2 | | npf = 8 ptryc = 10.000 | | lloc = 3 eloc = .000 | | ifqopt = 3 nqf = 8 qtryc = 10.000 | | all electron calculation used koelling-harmon equation | | ************logarithmic mesh************ | ============================================================ 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 ---------------------------------------------------------- From Veronique.VanSpeybroeck at rug.ac.be Tue Sep 10 13:44:40 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Tue, 10 Sep 2002 13:44:40 +0200 (MEST) Subject: [CPMD-list] Re: Problems with Vanderbilt PPs for Fe, Cu, Y etc In-Reply-To: Message-ID: Hi my pseudopotential report looks like this (there are differences) ============================================================ | pseudopotential report: version 3.0.0 date 0- 0- 0 | ------------------------------------------------------------ | rhodium ceperley-alder exchange-corr | | z = 45.00 zv = 17.00 exfact = 0.00000 | | etot =-221.70208 | | index orbital occupation energy | | 1 400 2.00 -5.65 | | 2 410 6.00 -3.61 | | 3 420 8.00 -0.48 | | 4 500 1.00 -0.31 | | keyps = 3 ifpcor = 0 rinner = 1.3000 | | new generation scheme: | | nbeta = 6 kkbeta = 475 rcloc = 1.9000 | | ibeta l epsilon rcut iptype | | 1 0 -5.65 2.00 * | | 2 0 -0.31 2.00 * | | 3 1 -3.61 2.00 * | | 4 1 -5.65 2.00 * | | 5 2 -0.48 2.00 * | | 6 2 -5.65 2.00 * | | lloc =-1 eloc = 0.000 | | ifqopt = 0 nqf = 3 qtryc = 10.000 | | all electron calculation used schroedinger equation | | ************logarithmic mesh************ | ===================================================== regards 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 rug.ac.be http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html ----------------------------------------------------------------------- On Tue, 10 Sep 2002, Juerg Hutter wrote: > Hi > > this is the PP report printed in CPMD for an iron USPP > that works on my computer. Any noticable differences to > your USPP's? > > ------------------------------------------------------------ > | iron PBE - GGA exchange-corr | > | z = 26.00 zv = 16.00 exfact = 5.00000 | > | etot =-252.61135 | > | index orbital occupation energy | > | 1 300 2.00 -7.01 | > | 2 310 6.00 -4.52 | > | 3 320 6.50 -.69 | > | 4 400 1.00 -.59 | > | 5 410 .00 -.28 | > | keyps = 3 ifpcor = 0 | > | rinner = 1.50 for L= 1 | > | rinner = 1.50 for L= 2 | > | rinner = 1.50 for L= 3 | > | rinner = 1.50 for L= 4 | > | rinner = 1.50 for L= 5 | > | new generation scheme: | > | nbeta = 6 kkbeta = 599 rcloc = 2.0000 | > | ibeta l epsilon rcut iptype | > | 1 0 -7.01 2.00 2 | > | 2 0 -.59 2.00 2 | > | 3 1 -4.52 2.00 2 | > | 4 1 -.28 2.00 2 | > | 5 2 -.69 2.00 2 | > | 6 2 .60 2.00 2 | > | npf = 8 ptryc = 10.000 | > | lloc = 3 eloc = .000 | > | ifqopt = 3 nqf = 8 qtryc = 10.000 | > | all electron calculation used koelling-harmon equation | > | ************logarithmic mesh************ | > ============================================================ > > 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 > ---------------------------------------------------------- > > > > From hutter at pci.unizh.ch Tue Sep 10 13:54:47 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Tue, 10 Sep 2002 13:54:47 +0200 (MEST) Subject: [CPMD-list] Re: Problems with Vanderbilt PPs for Fe, Cu, Y etc In-Reply-To: Message-ID: Hi The current version of the USPP atomic code is 7.3.4 . Your PP was produced with > ============================================================ > | pseudopotential report: version 3.0.0 date 0- 0- 0 | > ------------------------------------------------------------ I don't think this will work. The current version of CPMD was only tested with USPP produced by the atomic code with versions higher than 7.3.2 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, 10 Sep 2002, Veronique Van Speybroeck wrote: > > Hi my pseudopotential report looks like this (there are differences) > > ============================================================ > | pseudopotential report: version 3.0.0 date 0- 0- 0 | > ------------------------------------------------------------ > | rhodium ceperley-alder exchange-corr | > | z = 45.00 zv = 17.00 exfact = 0.00000 | > | etot =-221.70208 | > | index orbital occupation energy | > | 1 400 2.00 -5.65 | > | 2 410 6.00 -3.61 | > | 3 420 8.00 -0.48 | > | 4 500 1.00 -0.31 | > | keyps = 3 ifpcor = 0 rinner = 1.3000 | > | new generation scheme: | > | nbeta = 6 kkbeta = 475 rcloc = 1.9000 | > | ibeta l epsilon rcut iptype | > | 1 0 -5.65 2.00 * | > | 2 0 -0.31 2.00 * | > | 3 1 -3.61 2.00 * | > | 4 1 -5.65 2.00 * | > | 5 2 -0.48 2.00 * | > | 6 2 -5.65 2.00 * | > | lloc =-1 eloc = 0.000 | > | ifqopt = 0 nqf = 3 qtryc = 10.000 | > | all electron calculation used schroedinger equation | > | ************logarithmic mesh************ | > ===================================================== > > regards > > 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 rug.ac.be > http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html > ----------------------------------------------------------------------- > > On Tue, 10 Sep 2002, Juerg Hutter wrote: > > > Hi > > > > this is the PP report printed in CPMD for an iron USPP > > that works on my computer. Any noticable differences to > > your USPP's? > > > > ------------------------------------------------------------ > > | iron PBE - GGA exchange-corr | > > | z = 26.00 zv = 16.00 exfact = 5.00000 | > > | etot =-252.61135 | > > | index orbital occupation energy | > > | 1 300 2.00 -7.01 | > > | 2 310 6.00 -4.52 | > > | 3 320 6.50 -.69 | > > | 4 400 1.00 -.59 | > > | 5 410 .00 -.28 | > > | keyps = 3 ifpcor = 0 | > > | rinner = 1.50 for L= 1 | > > | rinner = 1.50 for L= 2 | > > | rinner = 1.50 for L= 3 | > > | rinner = 1.50 for L= 4 | > > | rinner = 1.50 for L= 5 | > > | new generation scheme: | > > | nbeta = 6 kkbeta = 599 rcloc = 2.0000 | > > | ibeta l epsilon rcut iptype | > > | 1 0 -7.01 2.00 2 | > > | 2 0 -.59 2.00 2 | > > | 3 1 -4.52 2.00 2 | > > | 4 1 -.28 2.00 2 | > > | 5 2 -.69 2.00 2 | > > | 6 2 .60 2.00 2 | > > | npf = 8 ptryc = 10.000 | > > | lloc = 3 eloc = .000 | > > | ifqopt = 3 nqf = 8 qtryc = 10.000 | > > | all electron calculation used koelling-harmon equation | > > | ************logarithmic mesh************ | > > ============================================================ > > > > 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 > > ---------------------------------------------------------- > > > > > > > > > > From Veronique.VanSpeybroeck at rug.ac.be Tue Sep 10 13:59:48 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Tue, 10 Sep 2002 13:59:48 +0200 (MEST) Subject: [CPMD-list] Re: Problems with Vanderbilt PPs for Fe, Cu, Y etc In-Reply-To: Message-ID: Hi again, All the other USPP I use are generated with this early version, and they seem to work (f.e. N,O,C,..), the only problem occurs with Rh. Do you think it is save to user the USPP for the atoms for which it works or should I regenerate the PP's with the newer version. Regards veronique On Tue, 10 Sep 2002, Juerg Hutter wrote: > Hi > > The current version of the USPP atomic code is 7.3.4 . > Your PP was produced with > > ============================================================ > > | pseudopotential report: version 3.0.0 date 0- 0- 0 | > > ------------------------------------------------------------ > > I don't think this will work. The current version of CPMD > was only tested with USPP produced by the atomic code > with versions higher than 7.3.2 > > 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, 10 Sep 2002, Veronique Van Speybroeck wrote: > > > > > Hi my pseudopotential report looks like this (there are differences) > > > > ============================================================ > > | pseudopotential report: version 3.0.0 date 0- 0- 0 | > > ------------------------------------------------------------ > > | rhodium ceperley-alder exchange-corr | > > | z = 45.00 zv = 17.00 exfact = 0.00000 | > > | etot =-221.70208 | > > | index orbital occupation energy | > > | 1 400 2.00 -5.65 | > > | 2 410 6.00 -3.61 | > > | 3 420 8.00 -0.48 | > > | 4 500 1.00 -0.31 | > > | keyps = 3 ifpcor = 0 rinner = 1.3000 | > > | new generation scheme: | > > | nbeta = 6 kkbeta = 475 rcloc = 1.9000 | > > | ibeta l epsilon rcut iptype | > > | 1 0 -5.65 2.00 * | > > | 2 0 -0.31 2.00 * | > > | 3 1 -3.61 2.00 * | > > | 4 1 -5.65 2.00 * | > > | 5 2 -0.48 2.00 * | > > | 6 2 -5.65 2.00 * | > > | lloc =-1 eloc = 0.000 | > > | ifqopt = 0 nqf = 3 qtryc = 10.000 | > > | all electron calculation used schroedinger equation | > > | ************logarithmic mesh************ | > > ===================================================== > > > > regards > > > > 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 rug.ac.be > > http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html > > ----------------------------------------------------------------------- > > > > On Tue, 10 Sep 2002, Juerg Hutter wrote: > > > > > Hi > > > > > > this is the PP report printed in CPMD for an iron USPP > > > that works on my computer. Any noticable differences to > > > your USPP's? > > > > > > ------------------------------------------------------------ > > > | iron PBE - GGA exchange-corr | > > > | z = 26.00 zv = 16.00 exfact = 5.00000 | > > > | etot =-252.61135 | > > > | index orbital occupation energy | > > > | 1 300 2.00 -7.01 | > > > | 2 310 6.00 -4.52 | > > > | 3 320 6.50 -.69 | > > > | 4 400 1.00 -.59 | > > > | 5 410 .00 -.28 | > > > | keyps = 3 ifpcor = 0 | > > > | rinner = 1.50 for L= 1 | > > > | rinner = 1.50 for L= 2 | > > > | rinner = 1.50 for L= 3 | > > > | rinner = 1.50 for L= 4 | > > > | rinner = 1.50 for L= 5 | > > > | new generation scheme: | > > > | nbeta = 6 kkbeta = 599 rcloc = 2.0000 | > > > | ibeta l epsilon rcut iptype | > > > | 1 0 -7.01 2.00 2 | > > > | 2 0 -.59 2.00 2 | > > > | 3 1 -4.52 2.00 2 | > > > | 4 1 -.28 2.00 2 | > > > | 5 2 -.69 2.00 2 | > > > | 6 2 .60 2.00 2 | > > > | npf = 8 ptryc = 10.000 | > > > | lloc = 3 eloc = .000 | > > > | ifqopt = 3 nqf = 8 qtryc = 10.000 | > > > | all electron calculation used koelling-harmon equation | > > > | ************logarithmic mesh************ | > > > ============================================================ > > > > > > 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 > > > ---------------------------------------------------------- > > > > > > > > > > > > > > > > > > From hutter at pci.unizh.ch Tue Sep 10 14:10:57 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Tue, 10 Sep 2002 14:10:57 +0200 (MEST) Subject: [CPMD-list] Re: Problems with Vanderbilt PPs for Fe, Cu, Y etc In-Reply-To: Message-ID: Hi I would suggest to use the PP generated with the new version of the atomic code. In addition I would use the parameters from the USPP library provided with the code. These PP are tested and comparison to others is easier. 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, 10 Sep 2002, Veronique Van Speybroeck wrote: > > Hi again, > > All the other USPP I use are generated with this early version, and they > seem to work (f.e. N,O,C,..), the only problem occurs with Rh. > Do you think it is save to user the USPP for the atoms for which it works > or should I regenerate the PP's with the newer version. > > Regards > > veronique > > > On Tue, 10 Sep 2002, Juerg Hutter wrote: > > > Hi > > > > The current version of the USPP atomic code is 7.3.4 . > > Your PP was produced with > > > ============================================================ > > > | pseudopotential report: version 3.0.0 date 0- 0- 0 | > > > ------------------------------------------------------------ > > > > I don't think this will work. The current version of CPMD > > was only tested with USPP produced by the atomic code > > with versions higher than 7.3.2 > > > > 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, 10 Sep 2002, Veronique Van Speybroeck wrote: > > > > > > > > Hi my pseudopotential report looks like this (there are differences) > > > > > > ============================================================ > > > | pseudopotential report: version 3.0.0 date 0- 0- 0 | > > > ------------------------------------------------------------ > > > | rhodium ceperley-alder exchange-corr | > > > | z = 45.00 zv = 17.00 exfact = 0.00000 | > > > | etot =-221.70208 | > > > | index orbital occupation energy | > > > | 1 400 2.00 -5.65 | > > > | 2 410 6.00 -3.61 | > > > | 3 420 8.00 -0.48 | > > > | 4 500 1.00 -0.31 | > > > | keyps = 3 ifpcor = 0 rinner = 1.3000 | > > > | new generation scheme: | > > > | nbeta = 6 kkbeta = 475 rcloc = 1.9000 | > > > | ibeta l epsilon rcut iptype | > > > | 1 0 -5.65 2.00 * | > > > | 2 0 -0.31 2.00 * | > > > | 3 1 -3.61 2.00 * | > > > | 4 1 -5.65 2.00 * | > > > | 5 2 -0.48 2.00 * | > > > | 6 2 -5.65 2.00 * | > > > | lloc =-1 eloc = 0.000 | > > > | ifqopt = 0 nqf = 3 qtryc = 10.000 | > > > | all electron calculation used schroedinger equation | > > > | ************logarithmic mesh************ | > > > ===================================================== > > > > > > regards > > > > > > 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 rug.ac.be > > > http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html > > > ----------------------------------------------------------------------- > > > > > > On Tue, 10 Sep 2002, Juerg Hutter wrote: > > > > > > > Hi > > > > > > > > this is the PP report printed in CPMD for an iron USPP > > > > that works on my computer. Any noticable differences to > > > > your USPP's? > > > > > > > > ------------------------------------------------------------ > > > > | iron PBE - GGA exchange-corr | > > > > | z = 26.00 zv = 16.00 exfact = 5.00000 | > > > > | etot =-252.61135 | > > > > | index orbital occupation energy | > > > > | 1 300 2.00 -7.01 | > > > > | 2 310 6.00 -4.52 | > > > > | 3 320 6.50 -.69 | > > > > | 4 400 1.00 -.59 | > > > > | 5 410 .00 -.28 | > > > > | keyps = 3 ifpcor = 0 | > > > > | rinner = 1.50 for L= 1 | > > > > | rinner = 1.50 for L= 2 | > > > > | rinner = 1.50 for L= 3 | > > > > | rinner = 1.50 for L= 4 | > > > > | rinner = 1.50 for L= 5 | > > > > | new generation scheme: | > > > > | nbeta = 6 kkbeta = 599 rcloc = 2.0000 | > > > > | ibeta l epsilon rcut iptype | > > > > | 1 0 -7.01 2.00 2 | > > > > | 2 0 -.59 2.00 2 | > > > > | 3 1 -4.52 2.00 2 | > > > > | 4 1 -.28 2.00 2 | > > > > | 5 2 -.69 2.00 2 | > > > > | 6 2 .60 2.00 2 | > > > > | npf = 8 ptryc = 10.000 | > > > > | lloc = 3 eloc = .000 | > > > > | ifqopt = 3 nqf = 8 qtryc = 10.000 | > > > > | all electron calculation used koelling-harmon equation | > > > > | ************logarithmic mesh************ | > > > > ============================================================ > > > > > > > > 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 > > > > ---------------------------------------------------------- > > > > > > > > > > > > > > > > > > > > > > > > > > > > From arnaud.travert at ismra.fr Tue Sep 10 16:43:04 2002 From: arnaud.travert at ismra.fr (Arnaud Travert) Date: Tue, 10 Sep 2002 16:43:04 +0200 Subject: [CPMD-list] Re: Problems with Vanderbilt PPs for Fe, Cu, Y etc In-Reply-To: Message-ID: <000001c258d8$5ee7b960$c9655dc0@cat01> Hi, I had the same kind of errors with Vanderbilt PPs for alcali and alcali earth metals. It seems (at least in "my" case) that the error occurs when I include sp semi-core states. For example, the following PP for Ca (for which 3s,3p are semi-core states) produces the same kind of errors as reported in the previous messages. ============================================================ | pseudopotential report: version 7.3.4 date 9- 9-2002 | ------------------------------------------------------------ | calcium ceperley-alder exchange-corr | | z = 20.00 zv = 10.00 exfact = 0.00000 | | etot = -72.93096 | | index orbital occupation energy | | 1 300 2.00 -3.95 | | 2 310 6.00 -2.57 | | 3 400 1.00 -0.67 | | keyps = 3 ifpcor = 0 | | rinner = 1.20 for L= 1 | | rinner = 1.20 for L= 2 | | rinner = 1.20 for L= 3 | | rinner = 1.20 for L= 4 | | rinner = 1.20 for L= 5 | | new generation scheme: | | nbeta = 4 kkbeta = 589 rcloc = 1.4000 | | ibeta l epsilon rcut iptype | | 1 0 -3.95 1.80 0 | | 2 0 -0.67 1.80 0 | | 3 1 -2.57 1.40 2 | | 4 2 -0.30 1.80 2 | | npf = 6 ptryc = 10.000 | | lloc =-1 eloc = 0.000 | | ifqopt = 2 nqf = 6 qtryc = 10.000 | | all electron calculation used koelling-harmon equation | | ************logarithmic mesh************ | ============================================================ with the following error : !!! ERROR !!! AP(ILP,IL,IK) = 0.00000******** 13 7 7 PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 1] !!! ERROR !!! AP(ILP,IL,IK) = 9.27067-1.21777 1 8 9 PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 0] !!! ERROR !!! AP(ILP,IL,IK) = 0.00000******** 13 7 7 PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 2] !!! ERROR !!! AP(ILP,IL,IK) = 0.00000******** 13 7 7 PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 3]. On the other hand, the Following PP (no semi-core state) works fine (at least with no error !!!) : ============================================================ | pseudopotential report: version 7.3.4 date 7-30-2002 | ------------------------------------------------------------ | Calcium ceperley-alder exchange-corr | | z = 20.00 zv = 2.00 exfact = 0.00000 | | etot = -1.32226 | | index orbital occupation energy | | 1 400 2.00 -0.28 | | keyps = 3 ifpcor = 0 | | rinner = 0.60 for L= 1 | | new generation scheme: | | nbeta = 1 kkbeta = 691 rcloc = 1.8000 | | ibeta l epsilon rcut iptype | | 1 0 -0.28 1.80 2 | | npf = 8 ptryc = 10.000 | | lloc =-1 eloc = 0.000 | | ifqopt = 2 nqf = 8 qtryc = 10.000 | | all electron calculation used koelling-harmon equation | | ************logarithmic mesh************ | ============================================================ Hence, my question is : does CPMD handle semi-core states with Vanderbilt PPs ? or am I completely wrong ? (I am new in using CPMD) regards, Arnaud. From hutter at pci.unizh.ch Tue Sep 10 17:46:32 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Tue, 10 Sep 2002 17:46:32 +0200 (MEST) Subject: [CPMD-list] Re: Problems with Vanderbilt PPs for Fe, Cu, Y etc In-Reply-To: <000001c258d8$5ee7b960$c9655dc0@cat01> Message-ID: Hi your semi-core PP has 2 s, 1p and 1d channel, this is not allowed in CPMD. 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, 10 Sep 2002, Arnaud Travert wrote: > > Hi, > > I had the same kind of errors with Vanderbilt PPs for alcali and alcali > earth metals. > It seems (at least in "my" case) that the error occurs when I include sp > semi-core states. For example, the following PP for Ca (for which 3s,3p are > semi-core states) produces the same kind of errors as reported in the > previous messages. > > ============================================================ > | pseudopotential report: version 7.3.4 date 9- 9-2002 | > ------------------------------------------------------------ > | calcium ceperley-alder exchange-corr | > | z = 20.00 zv = 10.00 exfact = 0.00000 | > | etot = -72.93096 | > | index orbital occupation energy | > | 1 300 2.00 -3.95 | > | 2 310 6.00 -2.57 | > | 3 400 1.00 -0.67 | > | keyps = 3 ifpcor = 0 | > | rinner = 1.20 for L= 1 | > | rinner = 1.20 for L= 2 | > | rinner = 1.20 for L= 3 | > | rinner = 1.20 for L= 4 | > | rinner = 1.20 for L= 5 | > | new generation scheme: | > | nbeta = 4 kkbeta = 589 rcloc = 1.4000 | > | ibeta l epsilon rcut iptype | > | 1 0 -3.95 1.80 0 | > | 2 0 -0.67 1.80 0 | > | 3 1 -2.57 1.40 2 | > | 4 2 -0.30 1.80 2 | > | npf = 6 ptryc = 10.000 | > | lloc =-1 eloc = 0.000 | > | ifqopt = 2 nqf = 6 qtryc = 10.000 | > | all electron calculation used koelling-harmon equation | > | ************logarithmic mesh************ | > ============================================================ > > with the following error : > > > !!! ERROR !!! AP(ILP,IL,IK) = 0.00000******** 13 7 7 > > PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 1] > !!! ERROR !!! AP(ILP,IL,IK) = 9.27067-1.21777 1 8 9 > > PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 0] > !!! ERROR !!! AP(ILP,IL,IK) = 0.00000******** 13 7 7 > > PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 2] > !!! ERROR !!! AP(ILP,IL,IK) = 0.00000******** 13 7 7 > > PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 3]. > > > On the other hand, the Following PP (no semi-core state) works fine (at > least with no error !!!) : > > ============================================================ > | pseudopotential report: version 7.3.4 date 7-30-2002 | > ------------------------------------------------------------ > | Calcium ceperley-alder exchange-corr | > | z = 20.00 zv = 2.00 exfact = 0.00000 | > | etot = -1.32226 | > | index orbital occupation energy | > | 1 400 2.00 -0.28 | > | keyps = 3 ifpcor = 0 | > | rinner = 0.60 for L= 1 | > | new generation scheme: | > | nbeta = 1 kkbeta = 691 rcloc = 1.8000 | > | ibeta l epsilon rcut iptype | > | 1 0 -0.28 1.80 2 | > | npf = 8 ptryc = 10.000 | > | lloc =-1 eloc = 0.000 | > | ifqopt = 2 nqf = 8 qtryc = 10.000 | > | all electron calculation used koelling-harmon equation | > | ************logarithmic mesh************ | > ============================================================ > > Hence, my question is : does CPMD handle semi-core states with Vanderbilt > PPs ? or am I completely wrong ? (I am new in using CPMD) > > regards, > > Arnaud. > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From Veronique.VanSpeybroeck at rug.ac.be Wed Sep 11 12:09:43 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Wed, 11 Sep 2002 12:09:43 +0200 (MEST) Subject: [CPMD-list] MEMORY ALLOCATION Message-ID: Hi, I have a problem running a job that requires a large amount of memory. I get something like this : *** MEMORY| THE NEW SIZE OF THE PROGRAM IS 1876066 kBYTES *** ================================================================ BIG MEMORY ALLOCATIONS PME 100521120 C2 20104216 C0 20104216 YLMB 15729183 YF 14378114 XF 14378114 TWNL 8740960 RHOPS 8738435 VPS 8738435 QRAD 6650100 ---------------------------------------------------------------- [PEAK NUMBER 88] PEAK MEMORY 230758164 = 1846.1 MBytes ================================================================ PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (GDE) Although my machine has 4GB RAM memory. How can I solve this problem? Thanks 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 rug.ac.be http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html ----------------------------------------------------------------------- From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Wed Sep 11 12:29:01 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Wed, 11 Sep 2002 12:29:01 +0200 Subject: [CPMD-list] MEMORY ALLOCATION In-Reply-To: Your message of "Wed, 11 Sep 2002 12:09:43 +0200." Message-ID: <200209111029.g8BAT1J25378@yello.theochem.ruhr-uni-bochum.de> >>> "VVS" == Veronique Van Speybroeck writes: VVS> Hi, VVS> I have a problem running a job that requires a large amount of memory. VVS> I get something like this : VVS> *** MEMORY| THE NEW SIZE OF THE PROGRAM IS 1876066 kBYTES *** VVS> ================================================================ VVS> BIG MEMORY ALLOCATIONS VVS> PME 100521120 C2 20104216 VVS> C0 20104216 YLMB 15729183 VVS> YF 14378114 XF 14378114 VVS> TWNL 8740960 RHOPS 8738435 VVS> VPS 8738435 QRAD 6650100 VVS> ---------------------------------------------------------------- VVS> [PEAK NUMBER 88] PEAK MEMORY 230758164 = 1846.1 MBytes VVS> ================================================================ VVS> PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (GDE) VVS> Although my machine has 4GB RAM memory. How can I solve this problem? hello veronique, it would help a lot if you would tell us, _what_ type of machine you have (i.e cpu type, operating system, etc). cheers, axel. VVS> Thanks VVS> Veronique VVS> ----------------------------------------------------------------------- VVS> Dr. ir. Van Speybroeck Veronique VVS> Laboratorium voor Theoretische Fysica VVS> Universiteit Gent VVS> Proeftuinstraat 86 VVS> 9000 Gent VVS> Tel +32-9-264.65.58 GSM : +32/474/259767 VVS> Fax +32-9-264.65.60 VVS> email : veronique.vanspeybroeck at rug.ac.be VVS> http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html VVS> ----------------------------------------------------------------------- VVS> _______________________________________________ VVS> CPMD-list mailing list VVS> CPMD-list at cpmd.org VVS> 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 ZRLSRB at ch.ibm.com Wed Sep 11 18:42:55 2002 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Wed, 11 Sep 2002 12:42:55 -0400 Subject: [CPMD-list] MEMORY ALLOCATION Message-ID: Hi, this problem has more than one solution, depending on your system architecture. Although 4GB is the maximum amount of memory 32bit (unsigned) pointers can address, the space addressable within one segment is often limited to 2GB, the maximum of a signed 32bit pointer. These are possible solutions: 1) You tell the linker to limit the data segment to more than 2GB if your system supports this with 32bit pointers. The manpage of your 'ld' program should tell you how. 2) You compile CPMD for 64bit pointers if your system supports this. This will slow down your program somewhat. 3) You compile CPMD to run parallel using MPI and let two processes run on the same node. If you have one processor, this will slow down your program, but if you have more than one processor in your machine, it could even result in faster execution because much more parts of CPMD will run in parallel compared to the SMP parallelism. Best regards, Salomon -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020911/dda4caf6/attachment.html From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Wed Sep 11 13:00:16 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Wed, 11 Sep 2002 13:00:16 +0200 Subject: [CPMD-list] MEMORY ALLOCATION In-Reply-To: Your message of "Wed, 11 Sep 2002 12:40:34 +0200." Message-ID: <200209111100.g8BB0GV27075@yello.theochem.ruhr-uni-bochum.de> >>> "VVS" == Veronique Van Speybroeck writes: VVS> On Wed, 11 Sep 2002, Axel Kohlmeyer wrote: >> >> >>> "VVS" == Veronique Van Speybroeck writes: >> VVS> Hi, >> VVS> I have a problem running a job that requires a large amount of memory. VVS> I get something like this : VVS> *** MEMORY| THE NEW SIZE OF THE PROGRAM IS 1876066 kBYTES *** >> VVS> ================================================================ VVS> BIG MEMORY ALLOCATIONS VVS> PME 100521120 C2 20104216 VVS> C0 20104216 YLMB 15729183 VVS> YF 14378114 XF 14378114 VVS> TWNL 8740960 RHOPS 8738435 VVS> VPS 8738435 QRAD 6650100 VVS> ---------------------------------------------------------------- VVS> [PEAK NUMBER 88] PEAK MEMORY 230758164 = 1846.1 MBytes VVS> ================================================================ >> >> VVS> PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (GDE) >> VVS> Although my machine has 4GB RAM memory. How can I solve this problem? >> >> hello veronique, >> >> it would help a lot if you would tell us, _what_ type of machine you >> have (i.e cpu type, operating system, etc). >> >> cheers, >> axel. >> VVS> Thanks VVS> Veronique >> VVS> VVS> ----------------------------------------------------------------------- VVS> Dr. ir. Van Speybroeck Veronique VVS> Laboratorium voor Theoretische Fysica VVS> Universiteit Gent VVS> Proeftuinstraat 86 VVS> 9000 Gent VVS> Tel +32-9-264.65.58 GSM : +32/474/259767 VVS> Fax +32-9-264.65.60 VVS> email : veronique.vanspeybroeck at rug.ac.be VVS> http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html VVS> ----------------------------------------------------------------------- >> VVS> _______________________________________________ VVS> CPMD-list mailing list VVS> CPMD-list at cpmd.org VVS> http://www.cpmd.org/mailman/listinfo/cpmd-list >> VVS> I have tried the calculation on an Origin 2000 SGI machine with 4 VVS> processors and 4 GB RAM memory. Operating system IRIX 6.5 VVS> I also tried the calculation on a PC with linux redhat 7.2, with 2 GB RAM VVS> memory and two processors. ok, VVS> *** MEMORY| THE NEW SIZE OF THE PROGRAM IS 1876066 kBYTES *** this means you already have successfully allocated nearly 2 gigabyte of memory and the _next_ allocation is failing. on a pc, since it is a 32-bit cpu and due to limitations of its memory management unit, you cannot (easily) have more than 2GB of (virtual) memory per process (although you may have more memory+swap in total that are used). on the SGI you have to be careful to compile cpmd in 64-bit mode. otherwise the same concerns as with the pc apply. furthermore you need an appropriate amount of swap to back up all physical memory. if you do not have enough physical swap you may get away with configuring 'virtual swap'. to explain: in it's default configuration the irix 6.x operating system _requires_ to have enough swap available to cover _all_ allocated physical memory, even for shared memory mappings so that you might under some circumstances need much more than twice the amount of physical memory as swap to simply use all the physical memory. with virtual swap you are basically 'faking' this swap, which is perfectly ok in most cases. hope this helps, axel. VVS> Regards VVS> veronique >> >> >> -- >> >> ======================================================================= >> 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. >> -- ======================================================================= 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 Ari.P.Seitsonen at iki.fi Wed Sep 11 13:23:20 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Wed, 11 Sep 2002 13:23:20 +0200 Subject: [CPMD-list] MEMORY ALLOCATION In-Reply-To: (message from Veronique Van Speybroeck on Wed, 11 Sep 2002 12:09:43 +0200 (MEST)) References: Message-ID: <200209111123.g8BBNKe21172@magadino.cscs.ch> Hi Veronique, > I have a problem running a job that requires a large amount of memory. > I get something like this : > *** MEMORY| THE NEW SIZE OF THE PROGRAM IS 1876066 kBYTES *** > > ================================================================ > BIG MEMORY ALLOCATIONS > PME 100521120 C2 20104216 > C0 20104216 YLMB 15729183 > YF 14378114 XF 14378114 > TWNL 8740960 RHOPS 8738435 > VPS 8738435 QRAD 6650100 > ---------------------------------------------------------------- > [PEAK NUMBER 88] PEAK MEMORY 230758164 = 1846.1 MBytes > ================================================================ > > > PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (GDE) > > Although my machine has 4GB RAM memory. How can I solve this problem? Which machine is it? Have you got a 64-bit compiler and operating system? Are some of the personal settings too small (e.g. 'ulimit -a')? 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 From Veronique.VanSpeybroeck at rug.ac.be Wed Sep 11 14:04:27 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Wed, 11 Sep 2002 14:04:27 +0200 (MEST) Subject: [CPMD-list] MEMORY ALLOCATION In-Reply-To: <200209111123.g8BBNKe21172@magadino.cscs.ch> Message-ID: Hi I now recompiled the program with the 64 bit compiler. The program gets somewhat further but still crashes. The last lines I get are : *** RINFORCE| THE NEW SIZE OF THE PROGRAM IS 520503 kBYTES *** *** FFTPRP| THE NEW SIZE OF THE PROGRAM IS 750567 kBYTES *** GENERATE ATOMIC BASIS SET P SLATER ORBITALS 3S ALPHA= 1.8806 OCCUPATION= 2.00 3P ALPHA= 1.6288 OCCUPATION= 3.00 N SLATER ORBITALS 2S ALPHA= 1.9237 OCCUPATION= 2.00 2P ALPHA= 1.9170 OCCUPATION= 3.00 O SLATER ORBITALS 2S ALPHA= 2.2458 OCCUPATION= 2.00 2P ALPHA= 2.2266 OCCUPATION= 4.00 C SLATER ORBITALS 2S ALPHA= 1.6083 OCCUPATION= 2.00 2P ALPHA= 1.5679 OCCUPATION= 2.00 H SLATER ORBITALS 1S ALPHA= 1.0000 OCCUPATION= 1.00 Bus error (core dumped) Thanks for all your help 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 rug.ac.be http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html ----------------------------------------------------------------------- On Wed, 11 Sep 2002 Ari.P.Seitsonen at iki.fi wrote: > > Hi Veronique, > > > I have a problem running a job that requires a large amount of memory. > > I get something like this : > > *** MEMORY| THE NEW SIZE OF THE PROGRAM IS 1876066 kBYTES *** > > > > ================================================================ > > BIG MEMORY ALLOCATIONS > > PME 100521120 C2 20104216 > > C0 20104216 YLMB 15729183 > > YF 14378114 XF 14378114 > > TWNL 8740960 RHOPS 8738435 > > VPS 8738435 QRAD 6650100 > > ---------------------------------------------------------------- > > [PEAK NUMBER 88] PEAK MEMORY 230758164 = 1846.1 MBytes > > ================================================================ > > > > > > PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (GDE) > > > > Although my machine has 4GB RAM memory. How can I solve this problem? > > Which machine is it? Have you got a 64-bit compiler and operating > system? Are some of the personal settings too small (e.g. 'ulimit -a')? > > 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 > From ZRLSRB at ch.ibm.com Wed Sep 11 20:17:35 2002 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Wed, 11 Sep 2002 14:17:35 -0400 Subject: [CPMD-list] MEMORY ALLOCATION Message-ID: Hi, > Bus error (core dumped) did you define POINTER8 for the preprocessor in the 64bit case? Also, the value of IRAT is very important, but most likely correct already. Best regards, Salomon -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020911/0c8facf0/attachment.html From Ari.P.Seitsonen at iki.fi Wed Sep 11 14:52:31 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Wed, 11 Sep 2002 14:52:31 +0200 Subject: [CPMD-list] MEMORY ALLOCATION In-Reply-To: (message from Veronique Van Speybroeck on Wed, 11 Sep 2002 14:04:27 +0200 (MEST)) References: Message-ID: <200209111252.g8BCqVJ22220@magadino.cscs.ch> Hi, > Hi I now recompiled the program with the 64 bit compiler. The program > gets somewhat further but still crashes. The last lines I get are : Did you use the option '-DPOINTER8' for the preprocessor or not? And what system/compiler do you use (SGI, IBM p690, ...?)? 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 From Veronique.VanSpeybroeck at rug.ac.be Wed Sep 11 15:03:29 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Wed, 11 Sep 2002 15:03:29 +0200 (MEST) Subject: [CPMD-list] MEMORY ALLOCATION In-Reply-To: <200209111252.g8BCqVJ22220@magadino.cscs.ch> Message-ID: I used the flag -DPOINTER8 Here you see the resume of my makefile #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = -O3 -nocpp -r8 LFLAGS = -lcomplib.sgimath -lblas $(QMMM_LIBS) CFLAGS = -D__SGI -mips4 -64 CPP = /usr/lib/acpp -E -P CPPFLAGS = -D__SGI -DPOINTER8 -D__DERF -DFFT_DEFAULT -DLAPACK CC = cc -O3 -c FC = f90 -mips4 -64 -c LD = f90 -mips4 -64 AR = veronique On Wed, 11 Sep 2002 Ari.P.Seitsonen at iki.fi wrote: > > Hi, > > > Hi I now recompiled the program with the 64 bit compiler. The program > > gets somewhat further but still crashes. The last lines I get are : > > Did you use the option '-DPOINTER8' for the preprocessor or not? And > what system/compiler do you use (SGI, IBM p690, ...?)? > > 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 > From natasa.mateljevic at yale.edu Wed Sep 11 19:53:37 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Wed, 11 Sep 2002 13:53:37 -0400 (EDT) Subject: [CPMD-list] Vanderbilt PPs Message-ID: Hi, I am trying to get CPMD to run using Vanderbilt PPs, and I cant get it to work no matter what I do. Here is the error I keep getting: PGFIO-F-219/unformatted read/unit=22/attempt to read/write past end of record. File name = /home/natasa/temp/uspp-734/Pot/006-C-gpbe--bm.uspp unformatted, sequential access record = 7 In source file ./readvan.f, at line number 417 I tryed formatting the file by uning the directions in README in the Utils directory of PPs but that didnt work either, so I am not sure what to do about this. Thanks for any advice, Natasa From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Wed Sep 11 21:18:34 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Wed, 11 Sep 2002 21:18:34 +0200 Subject: [CPMD-list] Vanderbilt PPs In-Reply-To: Message-ID: <200209111918.g8BJIYD16543@yello.theochem.ruhr-uni-bochum.de> On Wed, 11 Sep 2002 13:53:37 -0400 (EDT) Natasa Mateljevic wrote: > Hi, > I am trying to get CPMD to run using Vanderbilt PPs, and I cant get it to > work no matter what I do. > Here is the error I keep getting: > PGFIO-F-219/unformatted read/unit=22/attempt to read/write past end of > record. > File name = /home/natasa/temp/uspp-734/Pot/006-C-gpbe--bm.uspp > unformatted, sequential access record = 7 natasa, you either have to compile your cpmd binary with -Mbyteswapio (because you are reading big-endian pseudopotential files on a little-endian platform) or get/generate little endian pseudopentential files. i think, this has been discussed several times before. please check the mailing list archives if you need a more detailed description. cheers, axel. > In source file ./readvan.f, at line number 417 > I tryed formatting the file by uning the directions in README in the Utils > directory of PPs but that didnt work either, so I am not sure what to do > about this. > Thanks for any advice, > Natasa > > _______________________________________________ > 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 Ari.P.Seitsonen at iki.fi Wed Sep 11 22:17:08 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Wed, 11 Sep 2002 22:17:08 +0200 Subject: [CPMD-list] Vanderbilt PPs In-Reply-To: <200209111918.g8BJIYD16543@yello.theochem.ruhr-uni-bochum.de> (axel.kohlmeyer@theochem.ruhr-uni-bochum.de) References: <200209111918.g8BJIYD16543@yello.theochem.ruhr-uni-bochum.de> Message-ID: <200209112017.g8BKH8l25813@magadino.cscs.ch> Hi to all, > you either have to compile your cpmd binary with -Mbyteswapio (because you > are reading big-endian pseudopotential files on a little-endian > platform) or get/generate little endian pseudopentential files. > > i think, this has been discussed several times before. please check the > mailing list archives if you need a more detailed description. I think that this smells like a FAQ to me!! > > > In source file ./readvan.f, at line number 417 > > I tryed formatting the file by uning the directions in README in the Utils > > directory of PPs but that didnt work either, so I am not sure what to do > > about this. > > Thanks for any advice, > > Natasa > > > > _______________________________________________ > > 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. > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- 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 From natasa.mateljevic at yale.edu Wed Sep 11 22:23:05 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Wed, 11 Sep 2002 16:23:05 -0400 (EDT) Subject: [CPMD-list] Vanderbilt PPs In-Reply-To: <200209112017.g8BKH8l25813@magadino.cscs.ch> Message-ID: Hi, I am not sure if I am understanding you, do you mean that I have to recompile the new version and then where do I put this FLAG in the Makefile?So this problem has nothing to do with the Vanderbilt PPs, because I thought that the problem was that I had to format those, since they are unformatted. thanks, Natasa From hutter at pci.unizh.ch Thu Sep 12 08:58:30 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 12 Sep 2002 08:58:30 +0200 (MEST) Subject: [CPMD-list] Thanks In-Reply-To: <200209120556.HAA07608@internet-fence.zurich.ihost.com> Message-ID: Hi Xiong in my last post on the Lahey compiler I mentioned that csize.F can not be compiled correctly. I did send you a patched version. Did you use that new code? I only compiled the code for serial use, maybe the problem in my_para.F only appears with the PARALLLEL option on. What is the error message when you compile it? 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 2002 xxx 2012, ?????? wrote: > Dear apsi,Eyvaz,Juerg > Thanks for your help. I compiled the CPMD3.5.2 and CPMD3.5.3 using Lahey Fortran 95 successfully. In fact, I had not linked the proper librarys to the options. When I added lapack blas and parallel Library to my Makefile, I compiled it successfully. But now, I find a new problem, when I compile the source, I can not get the csize.o and my_para.o files, while I can find the item of the ruler to generate the two files in Makefile. I dont know what's wrong with it. In fact, when I copy the two files to my source, I can pass the compiler. > Thanks > yours > xiong > _______________________________________________ > 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 Sep 12 12:54:58 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 12 Sep 2002 12:54:58 +0200 Subject: [CPMD-list] Vanderbilt PPs In-Reply-To: Your message of "Wed, 11 Sep 2002 16:23:05 EDT." Message-ID: <200209121054.g8CAsw814739@yello.theochem.ruhr-uni-bochum.de> >>> "NM" == Natasa Mateljevic writes: NM> Hi, NM> I am not sure if I am understanding you, do you mean that I have to NM> recompile the new version and then where do I put this FLAG in the NM> Makefile?So this problem has nothing to do with the Vanderbilt PPs, NM> because I thought that the problem was that I had to format those, since NM> they are unformatted. NM> thanks, NM> Natasa hello natasa, your problem is in fact two problems: 1.) you have misunderstood the concept of unformatted fortran i/o. 2.) you probably picked a set of pseudopotential files that does not match your computer architecture. since this seems to become a FAQ, i will try to explain this in a more general way so it can be copied into the q&a section of the cpmd-webpage. 1.) Q: what is formatted i/o? A: 'formatted' fortran i/o means that you produce human readable ascii-files. this is the normal output format. 'UNformatted' fortran i/o basically means that you write the contents of your variables to a file by directly copying the memory contents into the file (plus some information about the amount of data copied to the file). as a result you get a file that is not directly readable, but your data is stored in a very compact way. this is NO WAY related to say formatting floppies or harddrives. the downside of unformatted fortran i/o is that unformatted files are not generally readable on all platforms since they depend on the size of the integers (32-bit or 64-bit) and the order in which the variables' contents are stored in memory, the byte-order. luckily most of the current (workstation) computers use 32-bit integers and either little endian (x86, alpha) or big endian (ibm, hp, sun, sgi) byte ordering. so you generally have to deal only with the byte ordering. see 2.) 2.) Q: I am trying to get CPMD to run using Vanderbilt PPs, and I cant get it to work no matter what I do. Here is the error I keep getting: PGFIO-F-219/unformatted read/unit=22/attempt to read/write past end of record? A: vanderbilt pseudopotentials are stored in an unformatted (binary) fortran file. since unformatted fortran files are generally not exchangeable between platforms (see 1.)) you have to either: - pick the set of pseudopotential files suitable for your platform - recreate the pseudopotential files for your platform - recompile or modify your cpmd executable, so that reads (and writes) unformatted fortran files in the 'wrong' byte order. this is usually only a good idea if you have to run or distribute your jobs on machines with different byte ordering. for the pgi fortran compilers you can add the flag '-Mbyteswapio' to the definition of the FC variable in the makefile to achieve this effect. i hope this helps. cheers, axel. -- ======================================================================= 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 hutter at pci.unizh.ch Thu Sep 12 13:34:12 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 12 Sep 2002 13:34:12 +0200 (MEST) Subject: [CPMD-list] Re: compile In-Reply-To: <200209121114.g8CBE2nR007683@zimail1.unizh.ch> Message-ID: Hi problem 1: variable I at line 82 in file util.f is not declared. easy fix: add a line INTEGER I in that subroutine problem 2: did you use the csize.F I sent you? I have fixed this problem there. problem 3: If you want to use the parallel code with MPI you have to tell the compiler where to find the MPI include file (mpif.h) easy fix: copy it to the SOURCE directory or add the appropriate compiler directive 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 2002 xxx 2013, ?????? wrote: > Dear Juerg > Thanks for your help. I think you must hear from my last mail about the csize.F and my_para.F. Here I send you the compiler information when I compiled the cpmd-3.5.3, I think it should have some question on the util.F and util.f files. As I copy the two files from cpmd-3.5.2, the util.o can be generated, and the same information happened, just the compiler told me it can not find csize.o. hehe, as I told you the question in my last mail, when I copy the two .o files, and the question has been settled. I think you should right to patch the csize.F and use parallel lib to my_para.f. Would you please help me to settle it. Thanks. > > the information as followed > Script started on Thu Sep 12 18:54:32 2002 > ]0;yuming at localhost:~/cpmd3.5.3/SOURCE[yuming at localhost SOURCE]$ make > lf95 -c ./util.f -o ./util.o > 2018-S: "./util.f", line 82: When IMPLICIT NONE is specified, I must be declared in a type declaration statement. > Encountered 1 error, 0 warnings in file ./util.f. > lf95 -c ./csize.f -o ./csize.o > f95: Compilation abnormally ended due to SIGSEGV. > > Internal compiler error. > Please forward the code to: > Lahey Technical Support. > 865 Tahoe Blvd. > P. O. Box 6091 > Incline Village NV 89451 > Email: support at lahey.com > lf95 -c ./my_para.f -o ./my_para.o > 1431-S: "./my_para.f", line 18: Filename specified in INCLUDE line not available. > 1431-S: "./my_para.f", line 41: Filename specified in INCLUDE line not available. > 1431-S: "./my_para.f", line 115: Filename specified in INCLUDE line not available. > 2018-S: "./my_para.f", line 119: When IMPLICIT NONE is specified, MPI_COMM_WORLD must be declared in a type declaration statement. > 1431-S: "./my_para.f", line 137: Filename specified in INCLUDE line not available. > 2018-S: "./my_para.f", line 140: When IMPLICIT NONE is specified, MPI_COMM_WORLD must be declared in a type declaration statement. > 1431-S: "./my_para.f", line 174: Filename specified in INCLUDE line not available. > 2018-S: "./my_para.f", line 178: When IMPLICIT NONE is specified, MPI_COMM_WORLD must be declared in a type declaration statement. > 1431-S: "./my_para.f", line 192: Filename specified in INCLUDE line not available. > 2018-S: "./my_para.f", line 194: When IMPLICIT NONE is specified, MPI_COMM_WORLD must be declared in a type declaration statement. > 1431-S: "./my_para.f", line 209: Filename specified in INCLUDE line not available. > 2018-S: "./my_para.f", line 217: When IMPLICIT NONE is specified, MPI_BYTE must be declared in a type declaration statement. > 1431-S: "./my_para.f", line 270: Filename specified in INCLUDE line not available. > 2018-S: "./my_para.f", line 278: When IMPLICIT NONE is specified, MPI_COMM_WORLD must be declared in a type declaration statement. > 2018-S: "./my_para.f", line 278: When IMPLICIT NONE is specified, MPI_BYTE must be declared in a type declaration statement. > 1431-S: "./my_para.f", line 297: Filename specified in INCLUDE line not available. > 2018-S: "./my_para.f", line 299: When IMPLICIT NONE is specified, MPI_STATUS_SIZE must be declared in a type declaration statement. > 2038-S: "./my_para.f", line 299: MPI_STATUS_SIZE cannot be specified in a specification expression. > 2018-S: "./my_para.f", line 305: When IMPLICIT NONE is specified, MPI_COMM_WORLD must be declared in a type declaration statement. > 2018-S: "./my_para.f", line 305: When IMPLICIT NONE is specified, MPI_BYTE must be declared in a type declaration statement. > 1431-S: "./my_para.f", line 323: Filename specified in INCLUDE line not available. > 2018-S: "./my_para.f", line 327: When IMPLICIT NONE is specified, MPI_BYTE must be declared in a type declaration statement. > 1431-S: "./my_para.f", line 347: Filename specified in INCLUDE line not available. > 2018-S: "./my_para.f", line 371: When IMPLICIT NONE is specified, MPI_BYTE must be declared in a type declaration statement. > 1431-S: "./my_para.f", line 396: Filename specified in INCLUDE line not available. > 2018-S: "./my_para.f", line 413: When IMPLICIT NONE is specified, MPI_SUM must be declared in a type declaration statement. > 2018-S: "./my_para.f", line 413: When IMPLICIT NONE is specified, MPI_DOUBLE_PRECISION must be declared in a type declaration statement. > 2018-S: "./my_para.f", line 418: When IMPLICIT NONE is specified, MPI_INTEGER must be declared in a type declaration statement. > 2018-S: "./my_para.f", line 423: When IMPLICIT NONE is specified, MPI_MAX must be declared in a type declaration statement. > 2018-S: "./my_para.f", line 429: When IMPLICIT NONE is specified, MPI_MIN must be declared in a type declaration statement. > 2018-S: "./my_para.f", line 435: When IMPLICIT NONE is specified, MPI_PROD must be declared in a type declaration statement. > 1431-S: "./my_para.f", line 463: Filename specified in INCLUDE line not available. > 2018-S: "./my_para.f", line 465: When IMPLICIT NONE is specified, MPI_STATUS_SIZE must be declared in a type declaration statement. > 2038-S: "./my_para.f", line 465: MPI_STATUS_SIZE cannot be specified in a specification expression. > 2018-S: "./my_para.f", line 478: When IMPLICIT NONE is specified, MPI_BYTE must be declared in a type declaration statement. > Encountered 35 errors, 0 warnings in file ./my_para.f. > rm -f timetag.f > /lib/cpp -P -C -traditional -D__Linux -D__NOINT8 -D__PGI -DLAPACK -DFFT_DEFAULT -DPARALLEL -DMP_LIBRARY=__MPI -DMYRINET ./timetag.F ./timetag.f > lf95 -c ./timetag.f > Encountered 0 errors, 0 warnings in file ./timetag.f. > rm -f cpmd.x > if [ "." != "." ]; then ln -s ./cpmd.x cpmd.x; fi > lf95 -o ./cpmd.x timetag.o cpmd.o softex.o envir.o setcnst.o control.o control_def.o control_pri.o control_bcast.o control_test.o header.o inscan.o memory.o freem.o readsr.o timer.o ttimp.o timec.o stopgm.o util.o dftin.o sysin.o ratom.o recpnew.o ghermit.o detsp.o coninp.o prmem.o setsys.o genxc.o setsc.o numpw.o cry.o latgen.o recips.o functionals.o lsd_func.o rinit.o rinforce.o fftprp.o rggen.o formf.o rnlset.o ylmr.o glopar.o rnlin.o sort.o radin.o bessm.o ylmr2.o pbc.o ortho.o finalp.o forcep.o rhopri.o phfac.o wrener.o rrane.o ranp.o rinitwf.o mltfft.o wrgeo.o rnlsm1.o rnlsm2.o fft.o ffts.o fftsg.o forces.o lowdin.o rgs.o rgsvan.o atomwf.o atrho.o xcener.o graden.o gcener.o hesele.o noforce.o rhoofr.o vpsi.o nlforce.o rotate.o hnlmat.o ovlap.o dotp.o fnonloc.o gsize.o csize.o rscpot.o csmat.o ksmat.o vofrho.o vofrhoa.o vofrhob.o vofrhoh.o vofrhot.o initclust.o jacobi.o rnlrh.o rnlfor.o potfor.o ppener.o reigs.o geofile.o rpiiint.o eicalc.o testex.o densto.o proja.o atoms.o fitpack.o wv30.o rv30.o wr30wfn.o setbasis.o gfft.o fftchk.o nfunc.o gcxctbl.o rhoofr_c.o jacobi_c.o velocitinp.o setirec.o compress.o interp3d.o ptheory.o clinbcg.o elstpo.o exterp.o mulliken.o espchg.o atomc.o eextern.o interpt.o egointer.o fileopen.o scratch.o forcedr.o initrun.o ldos.o fnlalloc.o dqgalloc.o anneal.o ylmr3.o rnlsm.o vofrhos.o get_addr.o teststore.o loadse.o rnlsmd.o wfnio.o density_functionals.o wfopts.o rwfopt.o updwf.o odiis.o pcgrad.o gmopts.o rgmopt.o fstart.o struc.o empfor.o puttau.o constr.o rrfo.o rbfgs.o rgdiis.o sdion.o hessin.o hessout.o hessup.o dum2.o detdof.o cnstfc.o fixcom.o cnstpr.o moverho.o elf.o lsd_elf.o mdpt.o mdmain.o dynit.o shake.o rattle.o resetac.o dispp.o nosalloc.o noseinit.o nospinit.o noseng.o nosepa.o noseup.o enosmove.o pnosmove.o ekinpp.o freqs.o printave.o printp.o rekine.o rinvel.o rscvp.o rscve.o deort.o quenbo.o velupa.o velupi.o posupa.o posupi.o rortog.o rortv.o crotwf.o noscinit.o prpcnosmove.o prpcmove.o prpnosmove.o prcnosmove.o ddipo.o opeigr.o sample.o sd_wannier.o wannier n.o mdshop.o davidson.o ksdiag.o vgsortho.o hpsi.o spsi.o gsortho.o rhov1.o secdpt.o secder.o sdlinres.o sd_ii.o sd_loc2.o sd_nl2.o rnlsm_2d.o nl_res.o sd_loc.o sd_nl.o rho1ofr.o v1ofrho1.o lr_force.o opt_lr.o lr_upd.o dd_xc.o eind_ii.o eind_loc.o eind_nl.o lr_in.o lr_xcpot.o lr_ortho.o lr_pcg.o canon.o proppt.o prowfn.o dipo.o lodipo.o exdipo.o cmaos.o difrho.o conduct.o polarise.o calc_pij.o localize.o jrotation.o orbhard.o ohfd.o ohlr.o specpt.o td_dav.o td_nhdav.o lr_diag.o vhk.o gettrans.o rho1pri.o rw_linres.o td_force.o tdnlfor.o td_pcg.o orbrot.o vtd2.o stcop.o readvan.o aainit.o vdbinit.o rhov.o qvan1.o qvan2.o newd.o rnlfl.o augchg.o readvdb.o nlccset.o copot.o corec.o cofor.o nlccstr.o startpa.o loadpa.o sumfnl.o glosum.o summat.o my_para.o glomax.o glomin.o groups.o hipin.o hip.o mtin.o stress.o vlocst.o htrstr.o xcstr.o drhov.o nlsl.o nlsm1_s.o dqvan2.o dylmr.o ffsum.o qrada_s.o totstr.o putbet.o ranc.o newcell.o sdcell.o prpt.o prcpmd.o npt_md.o symmetry.o chksym.o symtrz.o multtb.o molsym.o lsfbtr.o friesner.o friesner_c.o ehpsi.o rrandd.o updrho.o anderson.o adjmu.o forces_diag.o mddiag.o extrap.o bogol.o calc_alm.o vbeta.o rhodiis.o rwswap.o frsblk.o frsblk_c.o mixing_r.o mixing_g.o broyden.o enbandpri.o rkpnt.o k290.o k290_2.o kpclean.o pi_cntl.o pi_init.o pi_mdpt.o pi_wf.o pi_md.o pi_diag.o rreadf.o repgen.o fharm.o global.o stagetrans.o pinmtrans.o getfu.o getfnm.o getgyr.o getcor.o prtgyr.o evirial.o wr_temps.o cl_init.o mdclas.o readff.o clas_force.o h0psi1_p.o v1ofrho_p.o fnonloc_p.o do_gga_p.o mddiag-interaction_p.o gndstate_p.o legendre_p.o interaction_p.o rotate_my_wannier_p.o BYLM_p.o hess_eta_p.o inr_dr.o lanc_phon_p.o dmudn_p.o hesele_p.o do_perturbation_p.o pcgrad_p.o rnlsm_p.o vpsi_p.o perturbation_p.o eigensystem_p.o phonons_p.o rwfopt_p.o d_mat_p.o updwf_p.o forces_p.o rhoofr_p.o raman_p.o opeigr_p.o nmr_p.o nmr_util_p.o nmr_chi_p.o nmr_shift_p.o nmr_current_p.o nmr_para_p.o hardness_p.o respin_p.o response_p.o kdp_diag.o kdp_prep.o kdp_rho.o kdp_stre _init.o mm_dim.o mm_qmmm_forcedr.o mm_mdmain.o mm_coninp.o mm_cpmd_add_MM_forces_f77.o mm_cpmd_esp_charges_f77.o mm_cpmd_ext_pot_f77.o sysdepend.o shmemory.o -L/usr/local/lf9560/lib -llapackmt -lblasmt -lfst --parallel -L. -lmm > ERROR -- Could not find specified object file util.o. > make: *** [cpmd.x] Error 4 > ]0;yuming at localhost:~/cpmd3.5.3/SOURCE[yuming at localhost SOURCE]$ emacst       xit > > Script done on Thu Sep 12 18:54:39 2002 > > From jarek at elrond.chem.uni.wroc.pl Sat Sep 14 01:01:32 2002 From: jarek at elrond.chem.uni.wroc.pl (jarek at elrond.chem.uni.wroc.pl) Date: Sat, 14 Sep 2002 01:01:32 +0200 (CEST) Subject: [CPMD-list] a "quality" criterion in plane-wave calculations Message-ID: Dear CPMD Users, what is your opinion on the choice of quality crierion in the plane wave computations? The cutoff energy comes to mind first, but I have seen other proposals in the literature. People have tried to keep constant the number of plane waves per electronic state or the "density", i.e. number of plane waves per unit volume. Do these parameters help when comparing e.g. systems with different numbers of electrons, or can they help with variable cell problems? I would be grateful to read your opinions. With regards, Jaroslaw Panek, PhD University of Wroclaw, Faculty of Chemistry ul. F. Joliot-Curie 14, 50-383 Wroclaw, Poland From Ari.P.Seitsonen at iki.fi Sun Sep 15 21:27:12 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Sun, 15 Sep 2002 21:27:12 +0200 Subject: [CPMD-list] Extra channels in Vanderbilt PP In-Reply-To: (fparnold@chem.northwestern.edu) References: Message-ID: <200209151927.g8FJRCo00701@magadino.cscs.ch> Dear Fred, In case that you haven't got any reply to your answer yet... (Everyone would answer to the list, wouldn't one?!?!) > In small molecule calculations, it is common to use basis sets that are at > least 'double zeta', i.e. two functions per l channel, and often augmented > by a polarization function (higher l value). > > So, when generating PPs, do you follow the same policy as you would with > gaussian or slater type orbitals, or do you only put in channels for the > occupied space, and then increase the plane-wave cutoff? There's a small misunderstanding here: The double zeta etc is related to the _basis_ set, whereas the projectors in the Vandertbilt pseudo potentials are for describing the valence-core interaction, and has thus directly nothing to do with the basis set. Thus the number projectors per l channel is in principle not related to the size of the basis set, unless some of the projectors require a higher cutoff. The advantage of more projectors is to increase the transferability, or the accuracy, of the pseudo potential, i.e. the valence electrons feel a potential which is close to the true one caused by the nuclear charge and the core electrons if they'd be included. > I've been having problems with convergence properties of the USPPs within > cpmd3.5.3, and was therefore curious if a smaller potential would help. Well, you can always try e.g. Troullier-Martins pseudo potentials, however there's no guarantee that the system would converge even then. Do you have a metallic system, degenerate/radical one, ...? 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 From Ari.P.Seitsonen at iki.fi Sun Sep 15 23:11:45 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Sun, 15 Sep 2002 23:11:45 +0200 Subject: [CPMD-list] a "quality" criterion in plane-wave calculations In-Reply-To: (jarek@elrond.chem.uni.wroc.pl) References: Message-ID: <200209152111.g8FLBjQ02365@magadino.cscs.ch> Dear Jaroslaw, > what is your opinion on the choice of quality crierion in the plane wave > computations? The cutoff energy comes to mind first, but I have seen other > proposals in the literature. People have tried to keep constant the number > of plane waves per electronic state or the "density", i.e. number of plane > waves per unit volume. Do these parameters help when comparing e.g. > systems with different numbers of electrons, or can they help with > variable cell problems? I would be grateful to read your opinions. The constant number of plane waves is only used/useful when the size and/or shape of the cell is changed, like you write. This doesn't make a difference when the number of electrons is altered. Now, the discussion on the constant number versus constant cutoff has been discussed a couple of times in the literature, and there are for example the papers by Payne et al and Gonze et al - mentioned earlier on this mailing list - which are related to the topic. 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 From natasa.mateljevic at yale.edu Mon Sep 16 18:14:18 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Mon, 16 Sep 2002 12:14:18 -0400 (EDT) Subject: [CPMD-list] getting PPs to work Message-ID: Hi, thanks for your explanation. Its more clear to me now. But I am not sure what I am actually suppose to modify. Should I do this: g77 -o-Mbyteswapio cpmd.f cpmd.o or am I suppose to: (look in the make file for the compiling statement for cpmd, and put " -Mbyteswapio" in it), and then run the above. Where do I add this statement? I am sure if somehow there is two types of CMPD a "big endian" and a "little endian", and you have piece of each type (in which case I don't know how this would fix it. The "reform" sound more likely. So should I do the reform thing: reform.x C_345_XX.uspp > C_345_XX.dat where C_345_XX is the name of the pseudo potential file you want to convert, and i am not sure what the appropriate extensions are. I tryed the above but still cnat get this to work. Thanks for your help, Natasa From natasa.mateljevic at yale.edu Mon Sep 16 18:46:06 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Mon, 16 Sep 2002 12:46:06 -0400 (EDT) Subject: [CPMD-list] problems compiling Message-ID: Hi, to explain what I have done: I added this in the Makefile #--------------- Default Configuration for PC-PGI --------------- SRC = . DEST = . BIN = . #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = -Mr8 -pc64 -Msignextend -Msecond_underscore -Mbyteswapio LFLAGS = -llapack -lf77blas -latlas $(QMMM_LIBS) CFLAGS = CPP = /lib/cpp -P -C -traditional CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT CC = gcc -O2 -Wall FC = pgf77 -c -fast LD = pgf77 -fast AR = #---------------------------------------------------------------------------- I ran this command: g77 -o-Mbyteswapio cpmd.f cpmd.o and I got this error: INTEGER MAPGP(*) 1 cpmd.f:185: (continued): END 2 Invalid declaration of or reference to symbol `mapgp' at (2) [initially seen at (1)] system.h:193: INTEGER NATPE,NORBPE,IATPT,IPEPT,IATPE 1 cpmd.f:185: (continued): END 2 Invalid declaration of or reference to symbol `iatpt' at (2) [initially seen at (1)] system.h:193: INTEGER NATPE,NORBPE,IATPT,IPEPT,IATPE 1 cpmd.f:185: (continued): END 2 Invalid declaration of or reference to symbol `iatpe' at (2) [initially seen at Thanks for looking into this, Natasa From Ari.P.Seitsonen at iki.fi Mon Sep 16 19:17:33 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Mon, 16 Sep 2002 19:17:33 +0200 Subject: [CPMD-list] problems compiling In-Reply-To: (message from Natasa Mateljevic on Mon, 16 Sep 2002 12:46:06 -0400 (EDT)) References: Message-ID: <200209161717.g8GHHX630545@magadino.cscs.ch> > #--------------- Default Configuration for PC-PGI --------------- > ... > FC = pgf77 -c -fast > ... > #---------------------------------------------------------------------------- versus > I ran this command: > g77 -o-Mbyteswapio cpmd.f cpmd.o You CANNOT use GNU F77 compiler (g77), you have to use e.g. the pgf77 compiler like specified in the Makefile; did you try to compile with 'make'? Yours, 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 From natasa.mateljevic at yale.edu Mon Sep 16 19:29:04 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Mon, 16 Sep 2002 13:29:04 -0400 (EDT) Subject: [CPMD-list] problems compiling In-Reply-To: <200209161717.g8GHHX630545@magadino.cscs.ch> Message-ID: Hi I tryed compiling wiht make, and it sorked but I still get teh same error: *** DETSP| THE NEW SIZE OF THE PROGRAM IS 1132 kBYTES *** PGFIO-F-219/unformatted read/unit=22/attempt to read/write past end of record. File name = /home/natasa/temp/uspp-734/Pot/006-C-gpbe--bm.uspp unformatted, sequential access record = 7 In source file ./readvan.f, at line number 417 even when I add this flag FFLAGS =-Mbyteswapio -Mr8 -pc64 -Msignextend -Msecond_underscore So I am not sure waht I can try next, maybe I can go into Utils and to reform.x C_345_XX.uspp > C_345_XX.dat to format the PPs files. Thanks for your help, Natasa From natasa.mateljevic at yale.edu Mon Sep 16 19:31:15 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Mon, 16 Sep 2002 13:31:15 -0400 (EDT) Subject: [CPMD-list] problems compiling In-Reply-To: <200209161717.g8GHHX630545@magadino.cscs.ch> Message-ID: Hi, actually I get this when I run make: points.o rhoofr_kdp.o mm_detsp.o mm_init.o mm_dim.o mm_qmmm_forcedr.o mm_mdmain.o mm_coninp.o mm_cpmd_add_MM_forces_f77.o mm_cpmd_esp_charges_f77.o mm_cpmd_ext_pot_f77.o sysdepend.o shmemory.o -llapack -lblas cpmd.o: In function `cpmd_': cpmd.o(.text+0x184): undefined reference to `build_cleanup_' cpmd.o(.text+0x1ac): undefined reference to `mm_detsp_' cpmd.o(.text+0x1b1): undefined reference to `mm_init_' cpmd.o(.text+0x1d9): undefined reference to `respin_p_' cpmd.o(.text+0x1f8): undefined reference to `pi_cntl_' cpmd.o(.text+0x1fd): undefined reference to `pi_init_' cpmd.o(.text+0x20c): undefined reference to `nmr_para_p_' cpmd.o(.text+0x358): undefined reference to `pi_mdpt_' cpmd.o(.text+0x369): undefined reference to `pi_wf_' cpmd.o(.text+0x41a): undefined reference to `response_p_' cpmd.o(.text+0x42d): undefined reference to `end_swap_' make: *** [cpmd.x] Error 1 I am not sure if this is Ok. Natasa From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Mon Sep 16 20:32:26 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Mon, 16 Sep 2002 20:32:26 +0200 Subject: [CPMD-list] problems compiling In-Reply-To: Message-ID: <200209161832.g8GIWQc26109@yello.theochem.ruhr-uni-bochum.de> On Mon, 16 Sep 2002 13:31:15 -0400 (EDT) Natasa Mateljevic wrote: > Hi, > actually I get this when I run make: > points.o rhoofr_kdp.o mm_detsp.o mm_init.o mm_dim.o mm_qmmm_forcedr.o > mm_mdmain.o mm_coninp.o mm_cpmd_add_MM_forces_f77.o > mm_cpmd_esp_charges_f77.o mm_cpmd_ext_pot_f77.o sysdepend.o shmemory.o > -llapack -lblas > cpmd.o: In function `cpmd_': > cpmd.o(.text+0x184): undefined reference to `build_cleanup_' > cpmd.o(.text+0x1ac): undefined reference to `mm_detsp_' > cpmd.o(.text+0x1b1): undefined reference to `mm_init_' > cpmd.o(.text+0x1d9): undefined reference to `respin_p_' > cpmd.o(.text+0x1f8): undefined reference to `pi_cntl_' > cpmd.o(.text+0x1fd): undefined reference to `pi_init_' > cpmd.o(.text+0x20c): undefined reference to `nmr_para_p_' > cpmd.o(.text+0x358): undefined reference to `pi_mdpt_' > cpmd.o(.text+0x369): undefined reference to `pi_wf_' > cpmd.o(.text+0x41a): undefined reference to `response_p_' > cpmd.o(.text+0x42d): undefined reference to `end_swap_' > make: *** [cpmd.x] Error 1 > I am not sure if this is Ok. > Natasa no, of course it is not. if you change options in the makefile you usually have to compile _everything_ with the same set of options. in order to do that please type: make clean to delete all objects and then make to recompile. cheers, 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 erichu_linux at yahoo.com Mon Sep 16 21:07:55 2002 From: erichu_linux at yahoo.com (eric hu) Date: Mon, 16 Sep 2002 12:07:55 -0700 (PDT) Subject: [CPMD-list] analysis tools In-Reply-To: <200209161832.g8GIWQc26109@yello.theochem.ruhr-uni-bochum.de> Message-ID: <20020916190755.17251.qmail@web13402.mail.yahoo.com> I am a new user to this field and wonder if someone can provide the analysis tools for wannier center and md calculations results. By the way, are there any tutorials about cpmd? Thanks! Eric __________________________________________________ Do you Yahoo!? Yahoo! News - Today's headlines http://news.yahoo.com From natasa.mateljevic at yale.edu Mon Sep 16 21:39:13 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Mon, 16 Sep 2002 15:39:13 -0400 (EDT) Subject: [CPMD-list] problems compiling In-Reply-To: <200209161717.g8GHHX630545@magadino.cscs.ch> Message-ID: Hi, I am still having the same problem, i did make clean and make, which worked but I still cant link to the PPs PGFIO-F-219/unformatted read/unit=22/attempt to read/write past end of record. File name = /home/natasa/temp/uspp-734/Pot/006-C-gpbe--bm.uspp unformatted, sequential access record = 7 In source file ./readvan.f, at line number 417 I am not sure what else to try? Thanks, Natasa From dft_cpmd at yahoo.com Mon Sep 16 23:01:14 2002 From: dft_cpmd at yahoo.com (R Jkhurdakar) Date: Mon, 16 Sep 2002 14:01:14 -0700 (PDT) Subject: [CPMD-list] Problem with dimer optimization Message-ID: <20020916210114.90428.qmail@web13206.mail.yahoo.com> __________________________________________________ Do you Yahoo!? Yahoo! News - Today's headlines http://news.yahoo.com -------------- next part -------------- A non-text attachment was scrubbed... Name: q1 Type: application/x-unknown Size: 15121 bytes Desc: q1 Url : http://cpmd.org/pipermail/cpmd-list/attachments/20020916/87b13e54/attachment.bin From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Mon Sep 16 23:26:18 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Mon, 16 Sep 2002 23:26:18 +0200 Subject: [CPMD-list] problems compiling In-Reply-To: Message-ID: <200209162126.g8GLQIY02910@yello.theochem.ruhr-uni-bochum.de> On Mon, 16 Sep 2002 15:39:13 -0400 (EDT) Natasa Mateljevic wrote: > Hi, I am still having the same problem, i did make clean and make, which > worked but I still cant link to the PPs > PGFIO-F-219/unformatted read/unit=22/attempt to read/write past end of > record. > File name = /home/natasa/temp/uspp-734/Pot/006-C-gpbe--bm.uspp > unformatted, sequential access record = 7 > In source file ./readvan.f, at line number 417 > I am not sure what else to try? did you compile with -Mbyteswapio (or without)? remove (or add) that flag and recompile again. axel. > Thanks, > Natasa > > _______________________________________________ > 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 cakmak at gazi.edu.tr Tue Sep 17 14:38:36 2002 From: cakmak at gazi.edu.tr (Mehmet Cakmak) Date: Tue, 17 Sep 2002 14:38:36 EEST Subject: [CPMD-list] k-points for uspp Message-ID: Dear Ari > >The Vanderbilt part does not work with k points, i.e. it > >is not fully implemented. some weeks ago, you wrote above sentence. Any idea when do they implemente? I mean Is there any progress about it? thanks -mehmet From Ari.P.Seitsonen at iki.fi Tue Sep 17 15:36:06 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Tue, 17 Sep 2002 15:36:06 +0200 Subject: [CPMD-list] k-points for uspp In-Reply-To: (message from Mehmet Cakmak on Tue, 17 Sep 2002 14:38:36 EEST) References: Message-ID: <200209171336.g8HDa6q30420@magadino.cscs.ch> Dear Mehmet, > > >The Vanderbilt part does not work with k points, i.e. it > > >is not fully implemented. > > some weeks ago, you wrote above sentence. > Any idea when do they implemente? I mean Is there any > progress about it? I don't know if _anyone_ is working on the k point implementation for the Vanderbilt part, does anyone know? 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 From dft_cpmd at yahoo.com Tue Sep 17 16:24:46 2002 From: dft_cpmd at yahoo.com (R Jkhurdakar) Date: Tue, 17 Sep 2002 07:24:46 -0700 (PDT) Subject: [CPMD-list] Problem in dimer optimization Message-ID: <20020917142446.25481.qmail@web13208.mail.yahoo.com> Hello Everybody! I'm a novice user of CPMD interested in using it for studying finite size molecules or clusters. I ran into some problems while testing the ultrasoft pseudopotentials (uspp) for Ti and Au. I obtained these potentials from Prof. Vanderbilt's home page. I understand that these potentials are intended for bulk. Before generating any new uspp , I wanted to test the applicability of these exisiting uspp for finite size systems. For this purpose I performed geometry optimization for a dimer of these elements where I always ran into a problem irrespective of the choice for geometry optimization. I'm including an output of one of my runs at the end of this mail. I would appreciate any help on this problem. I also want to note that with the choice of preconditioned conjuagte gradient the total energy started going down very slowly but did not converge until 1300 steps/intration in the first step of geometry optimization. Thanks, Jkhurdkar ---------------------------------------------------------------------------------- Sample input file for RUNS: &CPMD OPTIMIZE GEOMETRY &END &SYSTEM SYMMETRY 0 CELL 22.000 1.0 1.0 0 0 0 CUTOFF 30.0 &END &ATOMS *ti_ps.uspp BINARY NEWF xSKIP 2 0.0 0.0 0.0 0.0 0.0 5.5 &END &DFT NEWCODE FUNCTIONAL LDA &ENDOutputs:/ OPTIMIZATION OF IONIC POSITIONS PATH TO THE RESTART FILES: ./ GRAM-SCHMIDT ORTHOGONALIZATION MAXIMUM NUMBER OF STEPS: 10000 STEPS PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS STORE INTERMEDIATE RESULTS EVERY 10001 STEPS STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS NUMBER OF DISTINCT RESTART FILES: 1 TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR FICTITIOUS ELECTRON MASS: 400.0000 TIME STEP: 5.0000 CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-05 WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS THRESHOLD FOR THE WF-HESSIAN IS 0.5000 MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 10 FULL ELECTRONIC GRADIENT IS USED CONVERGENCE CRITERIA FOR GEOMETRY OPTIMIZATION: 5.000000E-04 GEOMETRY OPTIMIZATION BY GDIIS/BFGS SIZE OF GDIIS MATRIX: 5 EMPIRICAL INITIAL HESSIAN (DISCO PARAMETRISATION) SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS NUMBER OF SPLINE POINTS: 501 EXCHANGE CORRELATION FUNCTIONALS LDA EXCHANGE: NONE LDA XC THROUGH PADE APPROXIMATION S.GOEDECKER, J.HUTTER, M.TETER PRB 54 1703 (1996) *** DETSP| THE NEW SIZE OF THE PROGRAM IS 1156 kBYTES *** >>>>>>>> CENTER OF MASS HAS BEEN MOVED TO CENTER OF BOX <<<<<<<< ***************************** ATOMS **************************** NR TYPE X(bohr) Y(bohr) Z(bohr) MBL 1 Ti 11.000000 11.000000 8.250000 3 2 Ti 11.000000 11.000000 13.750000 3 **************************************************************** NUMBER OF STATES: 12 NUMBER OF ELECTRONS: 24.00000 CHARGE: 0.00000 ELECTRON TEMPERATURE(KELVIN): 0.00000 OCCUPATION 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 ============================================================ | pseudopotential report: version 7.3.4 date 13- 9- 2 | ------------------------------------------------------------ | titanium ceperley-alder exchange-corr | | z = 22.00 zv = 12.00 exfact = 0.00000 | | etot =-115.30032 | | index orbital occupation energy | | 1 300 2.00 -5.53 | | 2 310 6.00 -3.79 | | 3 400 2.00 -0.89 | | 4 320 1.00 -1.19 | | keyps = 3 ifpcor = 0 | | rinner = 1.00 for L= 1 | | rinner = 1.00 for L= 2 | | rinner = 1.00 for L= 3 | | rinner = 1.00 for L= 4 | | rinner = 1.00 for L= 5 | | new generation scheme: | | nbeta = 6 kkbeta = 585 rcloc = 1.8000 | | ibeta l epsilon rcut iptype | | 1 0 -5.53 1.80 2 | | 2 0 -0.89 1.80 2 | | 3 1 -3.79 1.80 2 | | 4 1 1.00 1.80 2 | | 5 2 -1.19 1.80 2 | | 6 2 0.30 1.80 2 | | npf = 5 ptryc = 10.000 | | lloc = 3 eloc = 0.000 | | ifqopt = 2 nqf = 5 qtryc = 10.000 | | all electron calculation used koelling-harmon equation | | ************logarithmic mesh************ | ============================================================ **************************************************************** * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * * Ti 47.9000 1.2000 NO VANDERBILT * **************************************************************** *** RGGEN| THE NEW SIZE OF THE PROGRAM IS 9840 kBYTES *** ************************** SUPERCELL *************************** THIS IS AN ISOLATED SYSTEM CALCULATION POISSON EQUATION SOLVER : HOCKNEY COULOMB SMOOTHING RADIUS : 1.571 SYMMETRY: SIMPLE CUBIC LATTICE CONSTANT(a.u.): 22.00000 CELL DIMENSION: 22.0000 1.0000 1.0000 0.0000 0.0000 0.0000 VOLUME(OMEGA IN BOHR^3): 10648.00000 LATTICE VECTOR A1(BOHR): 22.0000 0.0000 0.0000 LATTICE VECTOR A2(BOHR): 0.0000 22.0000 0.0000 LATTICE VECTOR A3(BOHR): 0.0000 0.0000 22.0000 RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0455 0.0000 0.0000 RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0455 0.0000 RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0455 REAL SPACE MESH: 80 80 80 WAVEFUNCTION CUTOFF(RYDBERG): 30.00000 DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 120.00000 NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 14712 NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 118301 **************************************************************** *** RINFORCE| THE NEW SIZE OF THE PROGRAM IS 39096 kBYTES *** *** FFTPRP| THE NEW SIZE OF THE PROGRAM IS 54024 kBYTES *** *** CLUSTER| THE NEW SIZE OF THE PROGRAM IS 59180 kBYTES *** GENERATE ATOMIC BASIS SET Ti SLATER ORBITALS 3S ALPHA= 3.5833 OCCUPATION= 2.00 3P ALPHA= 3.5833 OCCUPATION= 6.00 3D ALPHA= 3.8833 OCCUPATION= 2.00 4S ALPHA= 0.8514 OCCUPATION= 2.00 INITIALIZATION TIME: 23.90 SECONDS *** GMOPTS| THE NEW SIZE OF THE PROGRAM IS 59412 kBYTES *** *** ATOMWF| THE NEW SIZE OF THE PROGRAM IS 59588 kBYTES *** *** PHFAC| THE NEW SIZE OF THE PROGRAM IS 59612 kBYTES *** ATRHO| CHARGE(R-SPACE): 24.000000 (G-SPACE): 24.000000 **************************************************************** **************************************************************** * ATOMIC COORDINATES * **************************************************************** 1 Ti 11.000000 11.000000 8.250000 2 Ti 11.000000 11.000000 13.750000 **************************************************************** DEGREES OF FREEDOM FOR SYSTEM: 3 INITIALIZE EMPIRICAL HESSIAN <<<<< ASSUMED BONDS >>>>> 2 <--> 1 TOTAL NUMBER OF MOLECULAR STRUCTURES: 1 **************************************************************** * ATOMIC COORDINATES * **************************************************************** 1 Ti 11.000000 11.000000 8.250000 2 Ti 11.000000 11.000000 13.750000 **************************************************************** CPU TIME FOR INITIALIZATION 40.04 SECONDS ================================================================ = GEOMETRY OPTIMIZATION = ================================================================ NFI GEMAX CNORM ETOT DETOT TCPU EWALD SUM IN REAL SPACE OVER 1* 1* 1 CELLS 1 1.383E-01 3.871E-02 -102.649800 -1.026E+02 57.85 2 4.319E-01 5.649E-02 -101.431469 1.218E+00 56.98 3 2.545E-01 3.123E-02 -110.980031 -9.549E+00 57.62 4 1.262E-01 1.016E-02 -115.283772 -4.304E+00 57.72 5 9.540E-02 1.387E-02 -115.475092 -1.913E-01 57.85 6 6.693E-02 9.970E-03 -115.729152 -2.541E-01 58.04 7 7.031E-02 5.987E-03 -115.884149 -1.550E-01 58.26 8 3.390E-02 4.790E-03 -115.903652 -1.950E-02 58.47 9 8.401E-01 2.766E-02 -83.899840 3.200E+01 57.57 10 7.394E-01 4.069E-02 -74.838023 9.062E+00 57.75 11 6.328E-01 3.718E-02 -76.922449 -2.084E+00 57.89 12 5.898E-01 3.209E-02 ODIIS| Insufficient progress; reset! 13 7.014E-01 3.132E-02 -77.582411 1.584E+01 56.86 14 1.062E+00 2.310E-02 -94.920054 -1.734E+01 56.98 15 3.744E-01 2.253E-02 -102.742401 -7.822E+00 57.81 16 3.876E-01 1.614E-02 -108.050155 -5.308E+00 57.91 17 3.909E-01 1.117E-02 -110.946571 -2.896E+00 58.17 18 7.449E-02 1.045E-02 -113.130150 -2.184E+00 58.39 19 8.380E-02 6.735E-03 -114.467696 -1.338E+00 58.61 20 6.672E-02 5.500E-03 -115.316048 -8.484E-01 58.69 21 8.476E-02 4.607E-03 -115.657620 -3.416E-01 58.79 22 3.413E-02 2.599E-03 -115.814860 -1.572E-01 58.93 23 2.287E-02 1.842E-03 -115.864258 -4.940E-02 58.94 24 2.831E-02 1.471E-03 -115.897318 -3.306E-02 58.92 25 1.187E-02 8.199E-04 -115.923817 -2.650E-02 58.91 26 1.064E-02 7.063E-04 -115.947009 -2.319E-02 58.87 27 1.196E-02 7.409E-04 -115.969203 -2.219E-02 58.86 28 9.580E-03 8.091E-04 -115.982930 -1.373E-02 58.85 29 1.199E-02 4.196E-04 -115.991820 -8.890E-03 58.84 30 1.027E-02 4.728E-04 -115.997720 -5.900E-03 58.87 31 6.081E-03 2.612E-04 -116.001983 -4.264E-03 58.89 32 4.791E-03 3.857E-04 -116.004741 -2.757E-03 58.88 33 5.708E-03 3.446E-04 -116.006003 -1.262E-03 58.89 34 2.842E-03 2.021E-04 -116.007685 -1.682E-03 58.90 35 2.807E-03 2.190E-04 -116.008958 -1.273E-03 58.91 36 2.252E-03 1.856E-04 -116.009775 -8.172E-04 58.91 37 1.414E-03 1.254E-04 -116.010585 -8.101E-04 58.90 38 1.372E-03 1.371E-04 -116.011344 -7.589E-04 58.91 39 1.180E-03 1.222E-04 -116.012041 -6.963E-04 58.93 40 1.370E-03 1.033E-04 -116.012597 -5.561E-04 58.92 41 1.093E-03 1.014E-04 -116.013089 -4.918E-04 58.92 42 1.733E-03 8.998E-05 -116.013365 -2.770E-04 58.93 43 1.103E-03 9.103E-05 -116.013860 -4.948E-04 58.90 44 1.304E-03 7.759E-05 -116.014127 -2.671E-04 58.93 45 8.793E-04 6.359E-05 -116.014328 -2.008E-04 58.95 46 1.056E-03 6.582E-05 -116.014674 -3.459E-04 58.93 47 6.942E-04 6.570E-05 -116.014944 -2.697E-04 58.92 48 7.266E-04 5.574E-05 -116.015167 -2.229E-04 58.95 49 6.572E-04 5.893E-05 -116.015442 -2.752E-04 58.95 50 4.630E-04 5.536E-05 -116.015659 -2.168E-04 58.95 51 3.863E-04 5.448E-05 -116.015883 -2.247E-04 58.92 52 3.652E-04 5.008E-05 -116.016093 -2.092E-04 58.95 53 3.634E-04 5.152E-05 -116.016212 -1.198E-04 58.96 54 3.612E-04 5.004E-05 -116.016412 -1.993E-04 58.96 55 3.591E-04 4.804E-05 -116.016602 -1.903E-04 58.94 56 3.588E-04 4.663E-05 -116.016648 -4.556E-05 58.96 57 3.594E-04 4.636E-05 -116.016772 -1.242E-04 58.97 58 3.601E-04 4.614E-05 -116.016879 -1.070E-04 58.96 59 3.608E-04 4.574E-05 -116.016940 -6.124E-05 58.96 60 3.602E-04 4.569E-05 -116.017036 -9.644E-05 58.94 61 3.597E-04 4.574E-05 -116.017083 -4.640E-05 58.96 62 3.610E-04 4.553E-05 -116.017128 -4.561E-05 58.96 63 3.618E-04 4.542E-05 -116.017166 -3.739E-05 58.96 ODIIS| Insufficient progress; reset! and this repeats ..... __________________________________________________ Do you Yahoo!? Yahoo! News - Today's headlines http://news.yahoo.com From natasa.mateljevic at yale.edu Tue Sep 17 19:53:36 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Tue, 17 Sep 2002 13:53:36 -0400 (EDT) Subject: [CPMD-list] Fortran In-Reply-To: <200209171336.g8HDa6q30420@magadino.cscs.ch> Message-ID: Dear Axel, Thank you for your advice, maybe you can suggest a good book on Fortran? And by the way can you explain to me what does my question have to do with Fortran? I didnt ask a question about Fortran I asked you a question about how to interface Vanderbilt PPs to CPMD, after I got the files formatted. Also, I might be ignorant, but I never heard of small and big endian and I am also not sure what this has to do with my programming skills.I just did what was the most logical thing to do when I got the error that the files are unformatted, and now I have a problem because I cant get the code to work, with the formatted files. If you answered my questions straight I wouldnt be bugging you, but you are giving me answers that I dont understand and I still cant get this to work. Natasa From jsst2 at hermes.cam.ac.uk Tue Sep 17 20:30:09 2002 From: jsst2 at hermes.cam.ac.uk (Justin Toh) Date: Tue, 17 Sep 2002 19:30:09 +0100 (BST) Subject: [CPMD-list] Memory problems on 2GB P4- unable to allocate >1GB memory Message-ID: Hello, I run cpmd on a P4 machine with 2GB of RAM. The OS is redhat 4.2.19. I'm having a problem running jobs larger than 960 MB in size. Above this limit, the following sorts of error messages appear: ------------------------------------------------------------------- GENERATE ATOMIC BASIS SET Pt PSEUDO ATOMIC ORBITALS L VALUE=S OCCUPATION= 1.00 [....] PROCESSOR 0 ALLOCATION OF 21901544 WORDS OF MEMORY FAILED **************************************************************** *** MEMORY| THE NEW SIZE OF THE PROGRAM IS 163608 kBYTES *** ================================================================ BIG MEMORY ALLOCATIONS C0 109507688 CM 21901544 TWNL 11407050 SCR 7097615 XF 1929098 DQG 1929098 YF 1929098 HGKP 1013945 HGKM 1013945 VPS 608367 ---------------------------------------------------------------- [PEAK NUMBER 56] PEAK MEMORY 153768836 = 1230.2 MBytes ================================================================ PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (C2) --------------------------------------------------------------------~ limit settings are: cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 3072 openfiles 1024 The flags and options are: FFLAGS = -w90 -w95 LFLAGS = -L${MKL_LIB} -lmkl_lapack -lmkl_p4 -lpthread -lguide -Vaxlib $(QMMM_LIBS) CFLAGS = CPP = /lib/cpp -P -C -traditional CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DLINUX_IFC CC = gcc -O2 -Wall FC = ifc -c -O3 -tp p6 -axiM LD = ifc -O3 -tp p6 -axiM AR = Actually, this is problem is common to Fortran programs on the system- a simple fortran matrix-matrix mutiplication routine crashes at the 960 MB mark, whereas a c-program can allocate 1.5 GB easily. We've played around with the kernel (although the fact that allocation works in c makes me think that this isn't the problem). Has anyone else encountered this problem? Any suggestions would be greatly appreciated. Cheers, Justin Justin Toh Mob: 07970 657027 Lab: +44 (01223) 336350 Trinity College Department of Chemistry Cambridge UK Lensfield Road CB2 1TQ From ricardo at irsamc.ups-tlse.fr Tue Sep 17 20:55:05 2002 From: ricardo at irsamc.ups-tlse.fr (JOSE LUIS RICARDO-CHAVEZ) Date: Tue, 17 Sep 2002 20:55:05 +0200 Subject: [Fwd: [CPMD-list] Problem in dimer optimization] Message-ID: <3D877A89.9060302@irsamc.ups-tlse.fr> Hi, in order to improve convergence I suggest you to increase the cutoff values for both the wavefunction and the density (DUAL option). With a cutoff of 30 Rydbergs expect a convergence to a few hundredths of eV. Also it would be helpful to increase the value of the GC-CUTOFF parameter in the &DFT section of the input file. If you don't know if the dimer is magnetic or not I suggest you to perform a LSD calculation with different spin multiplicities. Hope that it helps, - Jos? Luis -------- Original Message -------- Subject: [CPMD-list] Problem in dimer optimization Date: Tue, 17 Sep 2002 07:24:46 -0700 (PDT) From: R Jkhurdakar To: cpmd-list at cpmd.org Hello Everybody! I'm a novice user of CPMD interested in using it for studying finite size molecules or clusters. I ran into some problems while testing the ultrasoft pseudopotentials (uspp) for Ti and Au. I obtained these potentials from Prof. Vanderbilt's home page. I understand that these potentials are intended for bulk. Before generating any new uspp , I wanted to test the applicability of these exisiting uspp for finite size systems. For this purpose I performed geometry optimization for a dimer of these elements where I always ran into a problem irrespective of the choice for geometry optimization. I'm including an output of one of my runs at the end of this mail. I would appreciate any help on this problem. I also want to note that with the choice of preconditioned conjuagte gradient the total energy started going down very slowly but did not converge until 1300 steps/intration in the first step of geometry optimization. Thanks, Jkhurdkar ---------------------------------------------------------------------------------- Sample input file for RUNS: &CPMD OPTIMIZE GEOMETRY &END &SYSTEM SYMMETRY 0 CELL 22.000 1.0 1.0 0 0 0 CUTOFF 30.0 &END &ATOMS *ti_ps.uspp BINARY NEWF xSKIP 2 0.0 0.0 0.0 0.0 0.0 5.5 &END &DFT NEWCODE FUNCTIONAL LDA &ENDOutputs:/ OPTIMIZATION OF IONIC POSITIONS PATH TO THE RESTART FILES: ./ GRAM-SCHMIDT ORTHOGONALIZATION MAXIMUM NUMBER OF STEPS: 10000 STEPS PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS STORE INTERMEDIATE RESULTS EVERY 10001 STEPS STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS NUMBER OF DISTINCT RESTART FILES: 1 TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR FICTITIOUS ELECTRON MASS: 400.0000 TIME STEP: 5.0000 CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-05 WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS THRESHOLD FOR THE WF-HESSIAN IS 0.5000 MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 10 FULL ELECTRONIC GRADIENT IS USED CONVERGENCE CRITERIA FOR GEOMETRY OPTIMIZATION: 5.000000E-04 GEOMETRY OPTIMIZATION BY GDIIS/BFGS SIZE OF GDIIS MATRIX: 5 EMPIRICAL INITIAL HESSIAN (DISCO PARAMETRISATION) SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS NUMBER OF SPLINE POINTS: 501 EXCHANGE CORRELATION FUNCTIONALS LDA EXCHANGE: NONE LDA XC THROUGH PADE APPROXIMATION S.GOEDECKER, J.HUTTER, M.TETER PRB 54 1703 (1996) *** DETSP| THE NEW SIZE OF THE PROGRAM IS 1156 kBYTES *** >>>>>>>> CENTER OF MASS HAS BEEN MOVED TO CENTER OF BOX <<<<<<<< ***************************** ATOMS **************************** NR TYPE X(bohr) Y(bohr) Z(bohr) MBL 1 Ti 11.000000 11.000000 8.250000 3 2 Ti 11.000000 11.000000 13.750000 3 **************************************************************** NUMBER OF STATES: 12 NUMBER OF ELECTRONS: 24.00000 CHARGE: 0.00000 ELECTRON TEMPERATURE(KELVIN): 0.00000 OCCUPATION 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 ============================================================ | pseudopotential report: version 7.3.4 date 13- 9- 2 | ------------------------------------------------------------ | titanium ceperley-alder exchange-corr | | z = 22.00 zv = 12.00 exfact = 0.00000 | | etot =-115.30032 | | index orbital occupation energy | | 1 300 2.00 -5.53 | | 2 310 6.00 -3.79 | | 3 400 2.00 -0.89 | | 4 320 1.00 -1.19 | | keyps = 3 ifpcor = 0 | | rinner = 1.00 for L= 1 | | rinner = 1.00 for L= 2 | | rinner = 1.00 for L= 3 | | rinner = 1.00 for L= 4 | | rinner = 1.00 for L= 5 | | new generation scheme: | | nbeta = 6 kkbeta = 585 rcloc = 1.8000 | | ibeta l epsilon rcut iptype | | 1 0 -5.53 1.80 2 | | 2 0 -0.89 1.80 2 | | 3 1 -3.79 1.80 2 | | 4 1 1.00 1.80 2 | | 5 2 -1.19 1.80 2 | | 6 2 0.30 1.80 2 | | npf = 5 ptryc = 10.000 | | lloc = 3 eloc = 0.000 | | ifqopt = 2 nqf = 5 qtryc = 10.000 | | all electron calculation used koelling-harmon equation | | ************logarithmic mesh************ | ============================================================ **************************************************************** * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * * Ti 47.9000 1.2000 NO VANDERBILT * **************************************************************** *** RGGEN| THE NEW SIZE OF THE PROGRAM IS 9840 kBYTES *** ************************** SUPERCELL *************************** THIS IS AN ISOLATED SYSTEM CALCULATION POISSON EQUATION SOLVER : HOCKNEY COULOMB SMOOTHING RADIUS : 1.571 SYMMETRY: SIMPLE CUBIC LATTICE CONSTANT(a.u.): 22.00000 CELL DIMENSION: 22.0000 1.0000 1.0000 0.0000 0.0000 0.0000 VOLUME(OMEGA IN BOHR^3): 10648.00000 LATTICE VECTOR A1(BOHR): 22.0000 0.0000 0.0000 LATTICE VECTOR A2(BOHR): 0.0000 22.0000 0.0000 LATTICE VECTOR A3(BOHR): 0.0000 0.0000 22.0000 RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0455 0.0000 0.0000 RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0455 0.0000 RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0455 REAL SPACE MESH: 80 80 80 WAVEFUNCTION CUTOFF(RYDBERG): 30.00000 DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 120.00000 NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 14712 NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 118301 **************************************************************** *** RINFORCE| THE NEW SIZE OF THE PROGRAM IS 39096 kBYTES *** *** FFTPRP| THE NEW SIZE OF THE PROGRAM IS 54024 kBYTES *** *** CLUSTER| THE NEW SIZE OF THE PROGRAM IS 59180 kBYTES *** GENERATE ATOMIC BASIS SET Ti SLATER ORBITALS 3S ALPHA= 3.5833 OCCUPATION= 2.00 3P ALPHA= 3.5833 OCCUPATION= 6.00 3D ALPHA= 3.8833 OCCUPATION= 2.00 4S ALPHA= 0.8514 OCCUPATION= 2.00 INITIALIZATION TIME: 23.90 SECONDS *** GMOPTS| THE NEW SIZE OF THE PROGRAM IS 59412 kBYTES *** *** ATOMWF| THE NEW SIZE OF THE PROGRAM IS 59588 kBYTES *** *** PHFAC| THE NEW SIZE OF THE PROGRAM IS 59612 kBYTES *** ATRHO| CHARGE(R-SPACE): 24.000000 (G-SPACE): 24.000000 **************************************************************** **************************************************************** * ATOMIC COORDINATES * **************************************************************** 1 Ti 11.000000 11.000000 8.250000 2 Ti 11.000000 11.000000 13.750000 **************************************************************** DEGREES OF FREEDOM FOR SYSTEM: 3 INITIALIZE EMPIRICAL HESSIAN <<<<< ASSUMED BONDS >>>>> 2 <--> 1 TOTAL NUMBER OF MOLECULAR STRUCTURES: 1 **************************************************************** * ATOMIC COORDINATES * **************************************************************** 1 Ti 11.000000 11.000000 8.250000 2 Ti 11.000000 11.000000 13.750000 **************************************************************** CPU TIME FOR INITIALIZATION 40.04 SECONDS ================================================================ = GEOMETRY OPTIMIZATION = ================================================================ NFI GEMAX CNORM ETOT DETOT TCPU EWALD SUM IN REAL SPACE OVER 1* 1* 1 CELLS 1 1.383E-01 3.871E-02 -102.649800 -1.026E+02 57.85 2 4.319E-01 5.649E-02 -101.431469 1.218E+00 56.98 3 2.545E-01 3.123E-02 -110.980031 -9.549E+00 57.62 4 1.262E-01 1.016E-02 -115.283772 -4.304E+00 57.72 5 9.540E-02 1.387E-02 -115.475092 -1.913E-01 57.85 6 6.693E-02 9.970E-03 -115.729152 -2.541E-01 58.04 7 7.031E-02 5.987E-03 -115.884149 -1.550E-01 58.26 8 3.390E-02 4.790E-03 -115.903652 -1.950E-02 58.47 9 8.401E-01 2.766E-02 -83.899840 3.200E+01 57.57 10 7.394E-01 4.069E-02 -74.838023 9.062E+00 57.75 11 6.328E-01 3.718E-02 -76.922449 -2.084E+00 57.89 12 5.898E-01 3.209E-02 ODIIS| Insufficient progress; reset! 13 7.014E-01 3.132E-02 -77.582411 1.584E+01 56.86 14 1.062E+00 2.310E-02 -94.920054 -1.734E+01 56.98 15 3.744E-01 2.253E-02 -102.742401 -7.822E+00 57.81 16 3.876E-01 1.614E-02 -108.050155 -5.308E+00 57.91 17 3.909E-01 1.117E-02 -110.946571 -2.896E+00 58.17 18 7.449E-02 1.045E-02 -113.130150 -2.184E+00 58.39 19 8.380E-02 6.735E-03 -114.467696 -1.338E+00 58.61 20 6.672E-02 5.500E-03 -115.316048 -8.484E-01 58.69 21 8.476E-02 4.607E-03 -115.657620 -3.416E-01 58.79 22 3.413E-02 2.599E-03 -115.814860 -1.572E-01 58.93 23 2.287E-02 1.842E-03 -115.864258 -4.940E-02 58.94 24 2.831E-02 1.471E-03 -115.897318 -3.306E-02 58.92 25 1.187E-02 8.199E-04 -115.923817 -2.650E-02 58.91 26 1.064E-02 7.063E-04 -115.947009 -2.319E-02 58.87 27 1.196E-02 7.409E-04 -115.969203 -2.219E-02 58.86 28 9.580E-03 8.091E-04 -115.982930 -1.373E-02 58.85 29 1.199E-02 4.196E-04 -115.991820 -8.890E-03 58.84 30 1.027E-02 4.728E-04 -115.997720 -5.900E-03 58.87 31 6.081E-03 2.612E-04 -116.001983 -4.264E-03 58.89 32 4.791E-03 3.857E-04 -116.004741 -2.757E-03 58.88 33 5.708E-03 3.446E-04 -116.006003 -1.262E-03 58.89 34 2.842E-03 2.021E-04 -116.007685 -1.682E-03 58.90 35 2.807E-03 2.190E-04 -116.008958 -1.273E-03 58.91 36 2.252E-03 1.856E-04 -116.009775 -8.172E-04 58.91 37 1.414E-03 1.254E-04 -116.010585 -8.101E-04 58.90 38 1.372E-03 1.371E-04 -116.011344 -7.589E-04 58.91 39 1.180E-03 1.222E-04 -116.012041 -6.963E-04 58.93 40 1.370E-03 1.033E-04 -116.012597 -5.561E-04 58.92 41 1.093E-03 1.014E-04 -116.013089 -4.918E-04 58.92 42 1.733E-03 8.998E-05 -116.013365 -2.770E-04 58.93 43 1.103E-03 9.103E-05 -116.013860 -4.948E-04 58.90 44 1.304E-03 7.759E-05 -116.014127 -2.671E-04 58.93 45 8.793E-04 6.359E-05 -116.014328 -2.008E-04 58.95 46 1.056E-03 6.582E-05 -116.014674 -3.459E-04 58.93 47 6.942E-04 6.570E-05 -116.014944 -2.697E-04 58.92 48 7.266E-04 5.574E-05 -116.015167 -2.229E-04 58.95 49 6.572E-04 5.893E-05 -116.015442 -2.752E-04 58.95 50 4.630E-04 5.536E-05 -116.015659 -2.168E-04 58.95 51 3.863E-04 5.448E-05 -116.015883 -2.247E-04 58.92 52 3.652E-04 5.008E-05 -116.016093 -2.092E-04 58.95 53 3.634E-04 5.152E-05 -116.016212 -1.198E-04 58.96 54 3.612E-04 5.004E-05 -116.016412 -1.993E-04 58.96 55 3.591E-04 4.804E-05 -116.016602 -1.903E-04 58.94 56 3.588E-04 4.663E-05 -116.016648 -4.556E-05 58.96 57 3.594E-04 4.636E-05 -116.016772 -1.242E-04 58.97 58 3.601E-04 4.614E-05 -116.016879 -1.070E-04 58.96 59 3.608E-04 4.574E-05 -116.016940 -6.124E-05 58.96 60 3.602E-04 4.569E-05 -116.017036 -9.644E-05 58.94 61 3.597E-04 4.574E-05 -116.017083 -4.640E-05 58.96 62 3.610E-04 4.553E-05 -116.017128 -4.561E-05 58.96 63 3.618E-04 4.542E-05 -116.017166 -3.739E-05 58.96 ODIIS| Insufficient progress; reset! and this repeats ..... __________________________________________________ Do you Yahoo!? Yahoo! News - Today's headlines http://news.yahoo.com _______________________________________________ CPMD-list mailing list CPMD-list at cpmd.org http://www.cpmd.org/mailman/listinfo/cpmd-list -- Jose Luis RICARDO-CHAVEZ Tel. +33-5-61-55-68-33 Laboratoire de Physique Quantique Fax +33-5-61-55-60-65 Universite Paul Sabatier 118 route de Narbonne F-31062 Toulouse, France e-mail: ricardo at irsamc1.ups-tlse.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020917/a0ee6225/attachment.html From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Tue Sep 17 23:34:11 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Tue, 17 Sep 2002 23:34:11 +0200 Subject: [CPMD-list] Fortran In-Reply-To: Message-ID: <200209172134.g8HLYBh11438@yello.theochem.ruhr-uni-bochum.de> On Tue, 17 Sep 2002 13:53:36 -0400 (EDT) Natasa Mateljevic wrote: natatsa, > Dear Axel, > Thank you for your advice, maybe you can suggest a good book > on Fortran? And by the way can you explain to me what does my question probably any book, that explains fortran binary i/o. > have to do with Fortran? I didnt ask a question about Fortran I asked you everything. because you get the kind of error message you initially got only if you supply either a text file or a file from a different platform, when a fortran-binary file was expected. to understand this error, you have to understand the destinction between 'formatted' and 'unformatted' files in fortran. after all cpmd _is_ a fortran program. > a question about how to interface Vanderbilt PPs to CPMD, after I got the > files formatted. Also, I might be ignorant, but I never heard of small and > big endian and I am also not sure what this has to do with my programming i wrote about this IN DETAIL in an earlier mail. it means that a big endian machine stores the bytes in a different way in its memory (i.e. big end first) that a little endian machine. since fortran unformatted files can be seen as a direct dump from memory to the file, this ordering matters. > skills.I just did what was the most logical thing to do when I got the > error that the files are unformatted, and now I have a problem because I > cant get the code to work, with the formatted files. If you answered my > questions straight I wouldnt be bugging you, but you are giving me answers > that I dont understand and I still cant get this to work. Natasa ^^^^^^^^^^^^^^ doesn't this tell you anything? if you still can't figure out, what to do, then you should ask someone else. i cannot tell you anything more, than i have already said. just reread the old emails. bye, axel. p.s.: don't you think it to be kindof rude to send a reply to a personal email on a mailing list? > > _______________________________________________ > 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 fer at ariel.iimatercu.unam.mx Tue Sep 10 19:24:22 2002 From: fer at ariel.iimatercu.unam.mx (Fernando Alvarez Ramirez) Date: Tue, 10 Sep 2002 12:24:22 -0500 Subject: [CPMD-list] Re: Problems with Vanderbilt PPs for Fe, Cu, Y etc (fwd) Message-ID: ---------- Forwarded message ---------- Date: Tue, 10 Sep 2002 10:08:34 +0200 (MEST) From: Juerg Hutter To: cpmd-list at cpmd.org Cc: Fernando Alvarez Ramirez Subject: Re: Problems with Vanderbilt PPs for Fe, Cu, Y etc On Mon, 9 Sep 2002, Fernando Alvarez Ramirez wrote: > > Hi Juerg > > I am trying to run the CPMD code using Vanderbilt pseudopotentials for Cu. > I have down loaded the home page Vanderbilt pseudopotential generator > uspp-734-2.tgz from his webpage > > http://www.physics.rutgers.edu/~dhv/uspp/ > > Some pseudopotentials work without problems like Si, C, O, etc, but I > have problems when I use other pseudopotential like Fe, Cu etc. > > I have put the typical input line > > *fe_ps.uspp NEWF BINARY TPSEU > LMAX=D > > but the program gives me the next outlines > > !!! ERROR !!! AP(ILP,IL,IK) = 28.03090******* 1 6 9 > > PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 0] > > Do you know how to solve this problem? > > > thaks in advance > > > Fernando Alvarez Ramirez > Hi This most likely related to one of the restrictions of the implementation of USPP's in CPMD. 1) maximum L is d, no f functions possible 2) all L channels need the same number of projectors 3) the channels are given by the PP program, they can not be changed in the CPMD input, i.e. LMAX=D doesn't have any effect. Last possibility: your USPP has only s,p,d channels and 2 channels each, then this might be a new bug in CPMD. Please reply to the mailing list thank you Juerg From hjg212 at yahoo.com Thu Sep 12 18:22:30 2002 From: hjg212 at yahoo.com (J G Han) Date: Thu, 12 Sep 2002 09:22:30 -0700 (PDT) Subject: [CPMD-list] input of isolate cluster Message-ID: <20020912162230.2651.qmail@web10605.mail.yahoo.com> Dear Sir I have downloaded the CPMD V3.5, I write a input of CPMD for isolate water and Cr cluster (Cr.2H2O), however, I can give a correct input, would you please give me a help and send me an example of input. Sincerely yours J G Han --------------------------------- Do you Yahoo!? Yahoo! News - Today's headlines -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020912/a05f4797/attachment.html From baki at chemres.hu Wed Sep 18 10:24:06 2002 From: baki at chemres.hu (baki at chemres.hu) Date: Wed, 18 Sep 2002 10:24:06 +0200 Subject: [CPMD-list] Question about Pd usp pseudopotential Message-ID: <3.0.6.32.20020918102406.00937440@mailgw.chemres.hu> Dear Everybody Have somebody some suggestion how can I generated USP pseudopotential for Pd. I have already tried to use the new version of USp-7-3.4 but I can not make all electron calculation for this element (For O,Cu and any other works well) Best Imre Bak? Imre MTA K?miai Kutat?k?zpont, K?miai Int?zet 1525 Budapest Pf. 17 Telefon From eyvaz_isaev at yahoo.com Wed Sep 18 11:58:58 2002 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 18 Sep 2002 02:58:58 -0700 (PDT) Subject: [CPMD-list] Question about Pd usp pseudopotential In-Reply-To: <3.0.6.32.20020918102406.00937440@mailgw.chemres.hu> Message-ID: <20020918095858.64249.qmail@web80303.mail.yahoo.com> Dear Imre, Probably, you should decrease (or increase) "damp" (mixing parameter) in your AE input file. Regards, Eyvaz Senior Scientific Researcher, PhD Theoretical Physics Department Moscow Steel and Alloys Institute --- baki at chemres.hu wrote: > Dear Everybody > Have somebody some suggestion how can I generated > USP pseudopotential for > Pd. I have already tried to use the new version of > USp-7-3.4 but I can not > make all electron calculation for this element > (For O,Cu and any other > works well) > Best > Imre > Bak? Imre > MTA K?miai Kutat?k?zpont, K?miai Int?zet > 1525 Budapest Pf. 17 > Telefon > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list __________________________________________________ Do you Yahoo!? Yahoo! News - Today's headlines http://news.yahoo.com From natasa.mateljevic at yale.edu Wed Sep 18 17:37:43 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Wed, 18 Sep 2002 11:37:43 -0400 (EDT) Subject: [CPMD-list] (no subject) Message-ID: Dear Axel, I think you gave new meaning to the word rude, sorry I have been asking you questions and your email doesnt tell me how to fix the program I didnt write. Thanks for all your help. Natasa From crsu at cams.tsinghua.edu.cn Thu Sep 19 09:27:24 2002 From: crsu at cams.tsinghua.edu.cn (Changrong SU) Date: Thu, 19 Sep 2002 00:27:24 -0700 Subject: [CPMD-list] BUS error Message-ID: Hello, everyone, When I compiled the cpmd v3.53 on SGI Oringin2000, everything is OK and the executive file is achieved. However, there are BUS error when it is executed after "GENERATE ATOMIC BASIS SET". Does anyone has experence to overcome this question? Yours, SU Changrong Center for Atomic and Molecular NanoScience Department of Tsinghua University,Beijing 100084 P.R.CHINA From Veronique.VanSpeybroeck at rug.ac.be Thu Sep 19 08:18:17 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Thu, 19 Sep 2002 08:18:17 +0200 (MEST) Subject: [CPMD-list] BUS error In-Reply-To: Message-ID: Hello, I do not know how to solve this problem, but I experience the same. If I compile in 32 bit precision I do not have this. So then you have the flags -n32 If I compile in 64 bit precision as standard done in the makefile, I also have this problem. For large problems you need however the 64 bit version to allocate the memory. I do not know how to solve Best regards 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 rug.ac.be http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html ----------------------------------------------------------------------- On Thu, 19 Sep 2002, Changrong SU wrote: > Hello, everyone, > > When I compiled the cpmd v3.53 on SGI Oringin2000, > everything is OK and the executive file is achieved. > However, there are BUS error when it is executed after > "GENERATE ATOMIC BASIS SET". Does anyone has experence > to overcome this question? > > > Yours, > > SU Changrong > > Center for Atomic and Molecular NanoScience > Department of Tsinghua University,Beijing 100084 > P.R.CHINA > > > > > > > > > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From Veronique.VanSpeybroeck at rug.ac.be Thu Sep 19 10:17:09 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Thu, 19 Sep 2002 10:17:09 +0200 (MEST) Subject: [CPMD-list] MOVIE file Message-ID: Hi, I have a problem generating a MOVIE file. I use the following input &CPMD RESTART LATEST WAVEFUNCTION MOLECULAR DYNAMICS QUENCH IONS ELECTRONS TIMESTEP 5 MAXSTEP 5000 NOSE IONS 300 2000 PRINT 10 ISOLATED MOLECULE STRUCTURE BONDS ANGLES MOVIE &END With the previous version of the CPMD code, such inputfile generated a MOVIE file. Now I only get the coordinates of the first step : -0.0539 -0.0971 -0.0339 7 0 0.1197 -0.0722 0.9662 1 0 0.8501 0.0077 -0.4856 1 0 -0.5846 0.7402 -0.2543 1 0 What is wrong Thanks 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 rug.ac.be http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html ----------------------------------------------------------------------- From Christel.Nonnenberg at cup.uni-muenchen.de Thu Sep 19 10:30:16 2002 From: Christel.Nonnenberg at cup.uni-muenchen.de (Christel Nonnenberg) Date: Thu, 19 Sep 2002 10:30:16 +0200 Subject: [CPMD-list] MOVIE file In-Reply-To: References: Message-ID: <200209190830.g8J8UH405037@blue.cup.uni-muenchen.de> Hi Veronique, you have to use the keyword "MOVIE SAMPLE" and a number in the next line, which determines the steps after which the next structure is written to the MOVIE-file, e.g. 10, so every 10th step you will write a structure -- Christel Nonnenberg Ludwig-Maximilians-Universit?t M?nchen Department Chemie Butenandtstr. 5-13, Haus E D-81377 M?nchen Tel.: (089) 2180-7572 e-mail: Christel.Nonnenberg at cup.uni-muenchen.de From Veronique.VanSpeybroeck at rug.ac.be Thu Sep 19 13:48:46 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Thu, 19 Sep 2002 13:48:46 +0200 (MEST) Subject: [CPMD-list] MOVIE file In-Reply-To: <200209190830.g8J8UH405037@blue.cup.uni-muenchen.de> Message-ID: Thanks these changes work. 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 rug.ac.be http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html ----------------------------------------------------------------------- On Thu, 19 Sep 2002, Christel Nonnenberg wrote: > Hi Veronique, > > you have to use the keyword "MOVIE SAMPLE" and a number in the next line, > which determines the steps after which the next structure is written to the > MOVIE-file, e.g. 10, so every 10th step you will write a structure > > > > -- > Christel Nonnenberg > Ludwig-Maximilians-Universit?t M?nchen > Department Chemie > Butenandtstr. 5-13, Haus E > D-81377 M?nchen > Tel.: (089) 2180-7572 > e-mail: Christel.Nonnenberg at cup.uni-muenchen.de > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From ymxiong at icpm.syb.ac.cn Fri Sep 20 11:22:28 2002 From: ymxiong at icpm.syb.ac.cn (ÐÜÓñÃ÷) Date: Fri, 20 Sep 2002 11:22:28 Subject: [CPMD-list] lf95 Message-ID: <200209200323.FAA07694@internet-fence.zurich.ihost.com> Dear All and Juerg Thanks for your help. I compiled cpmd using your csiez.F again, oh, I found the csize.o could be generated no problem. But I found the line of "INTEGEN I" exsited in the file util.F,so i could not generate the util.o file. But I found when I compile the util.F using lf95 independently, although there were still some references could not be known, the util.o could be found in source. then I make it again, I could pass compile and generate cpmd.x file. when I ran the file, it is good. yours xiong From Veronique.VanSpeybroeck at rug.ac.be Fri Sep 20 16:16:06 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Fri, 20 Sep 2002 16:16:06 +0200 (MEST) Subject: [CPMD-list] Problems Rh uspp potentials Message-ID: Hi, a few weeks ago I experienced problems using uspp potentials of Rhodium. These potentials were generated with the old version of the uspp program. I now regenerated the Rh uspp with the new version, but my problems running the CPMD code remain. All other atoms like C,N,O run fine. I get an output as follows : ============================================================ | pseudopotential report: version 7.3.3 date 9-20-2002 | ------------------------------------------------------------ | rhodium ceperley-alder exchange-corr | | z = 45.00 zv = 17.00 exfact = 0.00000 | | etot =-221.70348 | | index orbital occupation energy | | 1 400 2.00 -5.65 | | 2 410 6.00 -3.61 | | 3 420 8.00 -0.48 | | 4 500 1.00 -0.31 | | keyps = 3 ifpcor = 0 | | rinner = 1.30 for L= 1 | | rinner = 1.30 for L= 2 | | rinner = 1.30 for L= 3 | | rinner = 1.30 for L= 4 | | rinner = 1.30 for L= 5 | | new generation scheme: | | nbeta = 6 kkbeta = 475 rcloc = 1.9000 | | ibeta l epsilon rcut iptype | | 1 0 -5.65 2.00 0 | | 2 0 -0.31 2.00 0 | | 3 1 -3.61 2.00 0 | | 4 1 -5.65 2.00 0 | | 5 2 -0.48 2.00 0 | | 6 2 -5.65 2.00 0 | | lloc =-1 eloc = 0.000 | | ifqopt = 0 nqf = 8 qtryc = 10.000 | | all electron calculation used schroedinger equation | | ************logarithmic mesh************ | ============================================================ **************************************************************** * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * * Rh 102.9050 1.2000 NO VANDERBILT * **************************************************************** *** RGGEN| THE NEW SIZE OF THE PROGRAM IS 122486 kBYTES *** ************************** SUPERCELL *************************** SYMMETRY: SIMPLE CUBIC LATTICE CONSTANT(a.u.): 66.14041 CELL DIMENSION: 66.1404 1.0000 1.0000 0.0000 0.0000 0.0000 VOLUME(OMEGA IN BOHR^3): 289334.77897 LATTICE VECTOR A1(BOHR): 66.1404 0.0000 0.0000 LATTICE VECTOR A2(BOHR): 0.0000 66.1404 0.0000 LATTICE VECTOR A3(BOHR): 0.0000 0.0000 66.1404 RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0151 0.0000 0.0000 RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0151 0.0000 RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0151 REAL SPACE MESH: 192 192 192 WAVEFUNCTION CUTOFF(RYDBERG): 20.00000 DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 80.00000 NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 218524 NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 1747687 **************************************************************** !!! ERROR !!! AP(ILP,IL,IK) = -6.27356 7.03722 1 4 9 PROGRAM STOPS IN SUBROUTINE AAINIT| Can anybody help me with this problem? Thanks to everybode for the help with previous problems 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 rug.ac.be http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html ----------------------------------------------------------------------- From gary.martin at ucl.ac.uk Sat Sep 21 21:03:39 2002 From: gary.martin at ucl.ac.uk (Gary Martin) Date: Sat, 21 Sep 2002 20:03:39 +0100 Subject: [CPMD-list] Energies Message-ID: <3D8CC28B.7020909@ucl.ac.uk> A simple question here I hope! I just wanted to check, for my peace of mind, what the energy unit "A.U." refers to in the output of CPMD. I don't think that I have missed anything completely obvious that states this unequivocally but sorry if I missed something! Cheers Gary Ps. Apologies if the above message appears twice on this list. From Ari.P.Seitsonen at iki.fi Sat Sep 21 21:43:11 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Sat, 21 Sep 2002 21:43:11 +0200 Subject: [CPMD-list] Energies In-Reply-To: <3D8CC28B.7020909@ucl.ac.uk> (message from Gary Martin on Sat, 21 Sep 2002 20:03:39 +0100) References: <3D8CC28B.7020909@ucl.ac.uk> Message-ID: <200209211943.g8LJhB429659@magadino.cscs.ch> Dear Gary, > A simple question here I hope! I hope that the answer is simple as well! :) > I just wanted to check, for my peace of mind, what the energy unit > "A.U." refers to in the output of CPMD. I don't think that I have missed > anything completely obvious that states this unequivocally but sorry if > I missed something! A.U. in the energies refers to "Hartree atomic units" (to make sure the difference with "Rydberg atomic units"), and 1 Hartree = 1 Ha ~= 27.2116 eV. 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 From ymxiong at icpm.syb.ac.cn Mon Sep 23 13:00:56 2002 From: ymxiong at icpm.syb.ac.cn (ÐÜÓñÃ÷) Date: Mon, 23 Sep 2002 13:00:56 Subject: [CPMD-list] lf95 Message-ID: <200209230501.HAA05954@internet-fence.zurich.ihost.com> >Dear All and Juerg > Thanks for your help. I compiled cpmd using your csiez.F again, oh, I found >the csize.o could be generated no problem. But I found the line of "INTEGEN I" exsited >in the file util.F,so i could not generate the util.o file. But I found when I compile >the util.F using lf95 independently, although there were still some references could not >be known, the util.o could be found in source. then I make it again, I could pass >compile and generate cpmd.x file. when I ran the file, it is good. > >yours xiong From cakmak at gazi.edu.tr Mon Sep 23 10:03:07 2002 From: cakmak at gazi.edu.tr (Mehmet Cakmak) Date: Mon, 23 Sep 2002 10:03:07 EEST Subject: [CPMD-list] k-points for uspp Message-ID: > Dear Mehmet, > > > > >The Vanderbilt part does not work with k points, i.e. it > > > >is not fully implemented. > > > > some weeks ago, you wrote above sentence. > > Any idea when do they implemente? I mean Is there any > > progress about it? > > I don't know if _anyone_ is working on the k point implementation for > the Vanderbilt part, does anyone know? > > Greetings, > > apsi Dear Ari, Thank you very much for your reply I havent seen any comments on this subject until today. Should I understand that nobody is working on this issue! thanks -mehmet From M.A.Zwijnenburg at tnw.tudelft.nl Mon Sep 23 13:55:03 2002 From: M.A.Zwijnenburg at tnw.tudelft.nl (Martijn Zwijnenburg) Date: Mon, 23 Sep 2002 13:55:03 +0200 Subject: [CPMD-list] k-points & SIGSEGV Message-ID: <3D8F1D29.28669.43AE22B9@localhost> Hi, We are having a problem with CPMD v3.5.1 (we haven't come round to installing the latest release yet). When we do the simple wavefunction optimization of a eight silicon periodic system (example 1 on page 49 of the manual) everything proceeds perfectly. However, when we include k-points by means of adding the following lines: POINT GROUP AUTO K-POINTS MONKHORST PACK 8 8 8 The calculation crashes with a SIGSEGV error when it does the ewald sumation in real space. The last line printed in the output is "EWALD SUMATION IN REAL SPACE OVER 1* 1* 1 CELLS". No other error messages apear in the output and lowering the amount of k-points to 1 1 1 doesn't change what happens. Anybody any clue what might be the problem?? CPMD runs on a linux beowulf (both tested on multiple (MPI/mpich) and single processor). cheers, Martijn ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg at tnw.tudelft.nl web page: http://come.to/tock From vb at chemie.hu-berlin.de Mon Sep 23 15:05:40 2002 From: vb at chemie.hu-berlin.de (Veronika Brazdova) Date: Mon, 23 Sep 2002 14:05:40 +0100 Subject: [CPMD-list] Re: k-points & SIGSEGV In-Reply-To: <3D8F1D29.28669.43AE22B9@localhost>; from M.A.Zwijnenburg@tnw.tudelft.nl on Mon, Sep 23, 2002 at 01:55:03PM +0200 References: <3D8F1D29.28669.43AE22B9@localhost> Message-ID: <20020923140540.D452399@ceres.chemie.hu-berlin.de> Hi Martijn, You need to specify the k-point mesh in this way: KPOINTS MONKHORST-PACK 8 8 8 so that CPMD recognizes the keyword. Otherwise it will just use the Gamma point - and it will not issue any warning. I don't know if this is the reason for the crash, since I was not able to reproduce it (CPMD 3.5.2 on SUSE linux, PC cluster, Intel compiler). Cheers Veronika > perfectly. However, when we include k-points by means of adding > the following lines: > POINT GROUP > AUTO > K-POINTS MONKHORST PACK > 8 8 8 > The calculation crashes with a SIGSEGV error when it does the > ewald sumation in real space. The last line printed in the output is > "EWALD SUMATION IN REAL SPACE OVER 1* 1* 1 CELLS". No > other error messages apear in the output and lowering the amount > of k-points to 1 1 1 doesn't change what happens. > Anybody any clue what might be the problem?? CPMD runs on a > linux beowulf (both tested on multiple (MPI/mpich) and single > processor). > > cheers, > > Martijn > ------------------------------------------------------------------------- > Martijn Zwijnenburg > Lab. of Applied Organic Chemistry and Catalysis > Delft University of Technology > Julianalaan 136 > 2628 BL Delft > The Netherlands > Tel: 0031-(0)152782691 > Fax: 0031-(0)152784700 > e-mail: M.A.Zwijnenburg at tnw.tudelft.nl > web page: http://come.to/tock > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list -- _______________________________________________________________________________ Veronika Brazdova Humboldt University, Institute of Chemistry, Brook-Taylor-Strasse 2, 12489, Berlin vb at chemie.hu-berlin.de http://atrey.karlin.mff.cuni.cz/~verunka phone: +49 30 2093 7140 fax: +49 03 2093 7136 _______________________________________________________________________________ From hutter at pci.unizh.ch Mon Sep 23 15:24:34 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 23 Sep 2002 15:24:34 +0200 (MEST) Subject: [CPMD-list] k-points & SIGSEGV In-Reply-To: <3D8F1D29.28669.43AE22B9@localhost> Message-ID: Hi Martijn when you want to use k-points you have to use the diagonalization schemes for optimization. Currently, the direct optimizations (ODIIS, PCG) do not work with k-points. Unfortunately, the default is ODIIS and the program does not check for the correct combination DIAGONALIZATION/KPOINTS. 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 Mon, 23 Sep 2002, Martijn Zwijnenburg wrote: > Hi, > > We are having a problem with CPMD v3.5.1 (we haven't come > round to installing the latest release yet). When we do the simple > wavefunction optimization of a eight silicon periodic system > (example 1 on page 49 of the manual) everything proceeds > perfectly. However, when we include k-points by means of adding > the following lines: > POINT GROUP > AUTO > K-POINTS MONKHORST PACK > 8 8 8 > The calculation crashes with a SIGSEGV error when it does the > ewald sumation in real space. The last line printed in the output is > "EWALD SUMATION IN REAL SPACE OVER 1* 1* 1 CELLS". No > other error messages apear in the output and lowering the amount > of k-points to 1 1 1 doesn't change what happens. > Anybody any clue what might be the problem?? CPMD runs on a > linux beowulf (both tested on multiple (MPI/mpich) and single > processor). > > cheers, > > Martijn > ------------------------------------------------------------------------- > Martijn Zwijnenburg > Lab. of Applied Organic Chemistry and Catalysis > Delft University of Technology > Julianalaan 136 > 2628 BL Delft > The Netherlands > Tel: 0031-(0)152782691 > Fax: 0031-(0)152784700 > e-mail: M.A.Zwijnenburg at tnw.tudelft.nl > web page: http://come.to/tock > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From masroor at chemie.uni-siegen.de Thu Sep 26 16:29:23 2002 From: masroor at chemie.uni-siegen.de (Masroor Ahmad) Date: Thu, 26 Sep 2002 16:29:23 +0200 Subject: [CPMD-list] About QM/MM in CPMD References: <200209171000.MAA20970@cpmd.org> Message-ID: <3D9319C3.6070304@chemie.uni-siegen.de> Hi I needed your help in figuring out this problem. While compiling cpmd on CRAY-T3E with -qmmm flag of Configure ,compilation gives error message for f90 -O 3 -c -dp ./mm_detsp.f -o ./mm_detsp.o Data type logical is not allowed with INTEGER for the operation "and" on the following line (118) of mm_detsp.f IF (NPROC.GT.1.and. mm_split) then .............................................................. Thanks in advance Your's truly Masroor Ahmad Universit?t Siegen From hutter at pci.unizh.ch Thu Sep 26 17:24:13 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 26 Sep 2002 17:24:13 +0200 (MEST) Subject: [CPMD-list] About QM/MM in CPMD In-Reply-To: <3D9319C3.6070304@chemie.uni-siegen.de> Message-ID: Hi this looks ok to me. mm_split is logical and so is NPROC.GT.1. Maybe the Cray f90 compiler is special about the order of statements, try IF ( (NPROC.GT.1) .and. mm_split) then 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, 26 Sep 2002, Masroor Ahmad wrote: > Hi > I needed your help in figuring out this problem. > While compiling cpmd on CRAY-T3E with -qmmm flag of Configure > ,compilation gives error message for f90 -O 3 -c -dp ./mm_detsp.f -o > ./mm_detsp.o > Data type logical is not allowed with INTEGER for the operation "and" > on the following line (118) of mm_detsp.f > IF (NPROC.GT.1.and. mm_split) then > .............................................................. > > Thanks in advance > Your's truly > Masroor Ahmad > Universit?t Siegen > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From masroor at chemie.uni-siegen.de Thu Sep 26 19:01:03 2002 From: masroor at chemie.uni-siegen.de (Masroor Ahmad) Date: Thu, 26 Sep 2002 19:01:03 +0200 Subject: [CPMD-list] About QM/MM in CPMD References: Message-ID: <3D933D4F.3020508@chemie.uni-siegen.de> Hi Thanks for help. But problem persists even with this recipie..any other hint please? Masroor Juerg Hutter wrote: >Hi > >this looks ok to me. mm_split is logical and so is >NPROC.GT.1. Maybe the Cray f90 compiler is special about >the order of statements, try > >IF ( (NPROC.GT.1) .and. mm_split) then > >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, 26 Sep 2002, Masroor Ahmad wrote: > > > >>Hi >>I needed your help in figuring out this problem. >>While compiling cpmd on CRAY-T3E with -qmmm flag of Configure >>,compilation gives error message for f90 -O 3 -c -dp ./mm_detsp.f -o >>./mm_detsp.o >>Data type logical is not allowed with INTEGER for the operation "and" >>on the following line (118) of mm_detsp.f >>IF (NPROC.GT.1.and. mm_split) then >>.............................................................. >> >>Thanks in advance >>Your's truly >>Masroor Ahmad >>Universit?t Siegen >> >>_______________________________________________ >>CPMD-list mailing list >>CPMD-list at cpmd.org >>http://www.cpmd.org/mailman/listinfo/cpmd-list >> >> >> > > > From hutter at pci.unizh.ch Thu Sep 26 20:23:35 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 26 Sep 2002 20:23:35 +0200 (MEST) Subject: [CPMD-list] About QM/MM in CPMD In-Reply-To: <3D933D4F.3020508@chemie.uni-siegen.de> Message-ID: Hi I checked on a newer version where this error had been fixed. The problem is that in V3.5 mm_split is defined as an integer not as a logical. As you are using this QM/MM code I suppose you have a contact in the group of Prof. Roethlisberger. They should know how to fix this bug in V3.5 . An easy workaround is to delete the part ".and. mm_split" This disables the option and allows to compile. Of course this is only a valid if you don't need this option. 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, 26 Sep 2002, Masroor Ahmad wrote: > Hi > Thanks for help. > But problem persists even with this recipie..any other hint please? > > Masroor > > > Juerg Hutter wrote: > > >Hi > > > >this looks ok to me. mm_split is logical and so is > >NPROC.GT.1. Maybe the Cray f90 compiler is special about > >the order of statements, try > > > >IF ( (NPROC.GT.1) .and. mm_split) then > > > >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, 26 Sep 2002, Masroor Ahmad wrote: > > > > > > > >>Hi > >>I needed your help in figuring out this problem. > >>While compiling cpmd on CRAY-T3E with -qmmm flag of Configure > >>,compilation gives error message for f90 -O 3 -c -dp ./mm_detsp.f -o > >>./mm_detsp.o > >>Data type logical is not allowed with INTEGER for the operation "and" > >>on the following line (118) of mm_detsp.f > >>IF (NPROC.GT.1.and. mm_split) then > >>.............................................................. > >> > >>Thanks in advance > >>Your's truly > >>Masroor Ahmad > >>Universit?t Siegen > >> > >>_______________________________________________ > >>CPMD-list mailing list > >>CPMD-list at cpmd.org > >>http://www.cpmd.org/mailman/listinfo/cpmd-list > >> > >> > >> > > > > > > > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From Veronique.VanSpeybroeck at rug.ac.be Fri Sep 27 10:06:40 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Fri, 27 Sep 2002 10:06:40 +0200 (MEST) Subject: [CPMD-list] Rh pseudopotentials Message-ID: Hi again, I still can't run the uspp of Rh : My pseudopotential looks as follows ============================================================ | pseudopotential report: version 7.3.3 date 9-20-2002 | ------------------------------------------------------------ | rhodium ceperley-alder exchange-corr | | z = 45.00 zv = 17.00 exfact = 0.00000 | | etot =-221.70348 | | index orbital occupation energy | | 1 400 2.00 -5.65 | | 2 410 6.00 -3.61 | | 3 420 8.00 -0.48 | | 4 500 1.00 -0.31 | | keyps = 3 ifpcor = 0 | | rinner = 1.30 for L= 1 | | rinner = 1.30 for L= 2 | | rinner = 1.30 for L= 3 | | rinner = 1.30 for L= 4 | | rinner = 1.30 for L= 5 | | new generation scheme: | | nbeta = 6 kkbeta = 475 rcloc = 1.9000 | | ibeta l epsilon rcut iptype | | 1 0 -5.65 2.00 0 | | 2 0 -0.31 2.00 0 | | 3 1 -3.61 2.00 0 | | 4 1 -5.65 2.00 0 | | 5 2 -0.48 2.00 0 | | 6 2 -5.65 2.00 0 | | lloc =-1 eloc = 0.000 | | ifqopt = 0 nqf = 8 qtryc = 10.000 | | all electron calculation used schroedinger equation | | ************logarithmic mesh************ | ============================================================ In the output I get : !!! ERROR !!! AP(ILP,IL,IK) = -6.27356 7.03722 1 4 9 PROGRAM STOPS IN SUBROUTINE AAINIT| Does anybody knows how to solve this problem. If not does anybody has a hard pseudopotential for Rh available? 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 rug.ac.be http://inwfaxp2.rug.ac.be/~web/onderzoek/proj_3.html ----------------------------------------------------------------------- From WANGYI at engr.sc.edu Sun Sep 29 01:03:10 2002 From: WANGYI at engr.sc.edu (WANG, YIXUAN ) Date: Sat, 28 Sep 2002 19:03:10 -0400 Subject: [CPMD-list] IR and RDF Message-ID: Dear all, Two questions need your help. 1) I failed to find the way to extract radial distribution function (rdf) from CPMD manual. Could you tell me how to do this? 2) I am trying to calculate IR for (salt+ solvent ) system in CPMD simulation. Is it possible to do this with CPMD? If so, please describe it. Thanks in advance. Yixuan Wang Chem. Engineering Univ. S. Carolina From lghiring at science.uva.nl Fri Sep 20 13:53:59 2002 From: lghiring at science.uva.nl (Luca UvA) Date: Fri, 20 Sep 2002 13:53:59 +0200 Subject: [CPMD-list] On periodic boundary conditions Message-ID: <008101c2609d$20ebee20$0201a8c0@SonyLuca> Dear all, it is clear that the TRAJECTORY file does not apply PBC, for good reason (e.g. calculation of RMS displacement). I am working with an fcc cell, and recovering the PBC (e.g. for pair-correlation function), in NVT ensemble, is easy, applying an algorithm based on Allen-Tildesley one, found at CCP5 library. But, for NPT ensemble (since I am working on liquid phase I allow only isotropic deformations), to compare data I am trying to simulate still in a fcc cell, just setting the proper triclinic parameters (a 1. 1. 0.5 0.5 0.5). Clearly the cell is defined by only one parameter. Then, trying to recover the minimum image, still applying the former algorithm, I find only crazy results. Any suggestion? Luca Ghiringhelli. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020920/daf70d95/attachment.html From gary.martin at physics.org Sat Sep 21 20:47:45 2002 From: gary.martin at physics.org (Gary Martin) Date: Sat, 21 Sep 2002 19:47:45 +0100 Subject: [CPMD-list] Energies Message-ID: <3D8CBED1.7010207@physics.org> A simple question here I hope! I just wanted to check, for my peace of mind, what the energy unit "A.U." refers to in the output of CPMD. I don't think that I have missed anything completely obvious that states this unequivocally but sorry if I missed something! Cheers Gary From gary.martin at ucl.ac.uk Mon Sep 30 15:09:08 2002 From: gary.martin at ucl.ac.uk (Gary Martin) Date: Mon, 30 Sep 2002 14:09:08 +0100 Subject: [CPMD-list] Energies References: <3D8CBED1.7010207@physics.org> Message-ID: <3D984CF4.5040205@ucl.ac.uk> Dear all, Now that this email has turned up, I might as well take the opportunity of thanking Ari Seitsonen for his answer to my question. Cheers, Gary Gary Martin wrote: > A simple question here I hope! > > I just wanted to check, for my peace of mind, what the energy unit > "A.U." refers to in the output of CPMD. I don't think that I have missed > anything completely obvious that states this unequivocally but sorry if > I missed something! > > Cheers > Gary From francesco.filippone at mlib.cnr.it Mon Sep 30 16:04:40 2002 From: francesco.filippone at mlib.cnr.it (Francesco Filippone) Date: Mon, 30 Sep 2002 16:04:40 +0200 (CEST) Subject: [CPMD-list] IR and RDF In-Reply-To: Message-ID: On Sat, 28 Sep 2002, WANG, YIXUAN wrote: Dear Yixuan, I try to help you. > Dear all, > > Two questions need your help. > > 1) I failed to find the way to extract radial distribution function > (rdf) from CPMD > manual. Could you tell me how to do this? There is no keyword for this. Radial distribution function is to be calculated from a statistics, for instance from a Molecular Dynamics run. In CPMD you can extract (in post processing!) all the relevant information from the TRAJECTORY file; refer to the manual for the keywords MOLECULAR DYNAMICS and TRAJECTORY SAMPLE. You can apply the algorithm given in textbooks on MD, like M.P. Allen and D.J. Tildesley, Computer simulation of liquids, Oxford Science Publications, 1987. > > 2) I am trying to calculate IR for (salt+ solvent ) system in CPMD > simulation. > Is it possible to do this with CPMD? If so, please describe it. I am not directly involved in CPMD development, so I don't know if the following point are completely up to date. You can either; a) perform a vibrational analysis (keyword VIBRATIONAL ANALYSIS; otherwise the keywords PHONONS, LANCZOS with the LINEAR RESPONSE calculations). In this way you have a harmonic spectrum of the system you are simulating. This does not mean IR bands. If you want to know whether the modes you obtain are IR active or not, you have to perform a group theoretical analysis on the eigenvectors. Procedures are described, in, e.g., Wilson Decius Cross, Molecular Vibrations, Dover reprint, 1980, F.A. Cotton, Chemical Applications of Group Theory, Wiley, 1990. If you want IR intensities you have to look deeper into Chap. 7 of Wilson DEcius Cross b) Calculate the power spectrum from a MD calculation. In this way you get rid of harmonic approximation, but you need a very very very long run to have a sufficient accuracy in numerical data. You can calculate the velocity-velocity autocorrelation function using the information in the TRAJECTORY file and perform a FT transform on it. Refer to Allen-Tildesley for all details. Again, you do not get the IR bands, rather all the vibrational degrees of freedom of the system. c) Perform a similar analysis on the dypole dynamics (keyword DIPOLE DYNAMICS in a MD simulation) that is recorded in the file DIPOLE. In this case you have the IR bands. Again you do not get the intensities. Hope could be useful (and not wrong :-)))), ciao, F. -- ---------------------------------------------------------------------------- Francesco Filippone | Tanto gentile e CNR - ISTITUTO DI STRUTTURA DELLA MATERIA | tant'onesta pare v. Salaria Km 29,300 - C.P. 10 | la donna mia quand'ella I 00016 - Monterotondo Stazione (RM) | altrui saluta... Tel + 39 06 90672342 - Fax +39 06 90672316 | e-mail: | Dante ----------------------------------------------------------------------------