From Veronique.VanSpeybroeck at rug.ac.be Fri Mar 1 10:03:03 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Fri, 1 Mar 2002 10:03:03 +0100 (MET) Subject: [CPMD-list] Vanderbilt pseudopotentials Message-ID: Is there anyone who has any experience with the use of Vanderbilt pseudopotentials with the CPMD code. I do have a library of Vanderbilt pseudopotentials which I used with another AIMD package. When trying to use these potentials with the CPMD code, the program reads the pseudopotential right, a correct pseudopotential report is written. Due to some reason the program stops somewhat further after reporting the atomic coordinates. The last output I get is (for a simple example of one C atom) **************************************************************** * ATOMIC COORDINATES * **************************************************************** 1 C 0.000000 0.000000 0.000000 **************************************************************** CPU TIME FOR WAVEFUNCTION INITIALIZATION: 0.41 SECONDS *** RWFOPT| THE NEW SIZE OF THE PROGRAM IS 10716 KBytes *** EWALD SUM IN REAL SPACE OVER 1* 1* 1 CELLS ** On entry to DSYRK parameter number 10 had an illegal value FORTRAN STOP The program works well when using other pseudopotentials, like Martin Trouiller, ... Is there anyone who knows how to resolve this problem? 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 langel at mail.uni-greifswald.de Fri Mar 1 10:53:30 2002 From: langel at mail.uni-greifswald.de (Walter Langel) Date: Fri, 01 Mar 2002 10:53:30 +0100 Subject: [CPMD-list] formatting RESTART-files Message-ID: <3C7F4F9A.506@mail.uni-greifswald.de> Hello, is there a routine around for formatting the binary cpmd RESTART files into ASCII and back into binary? This would be necessary to move a cpmd-job between different systems which have different binary formats (such as AIX and Linux). Regards Walter Langel -- Prof. Dr. Walter Langel Institut fuer Chemie und Biochemie Universitaet Greifswald Soldmannstrasse 23 D-17487 Greifswald Germany Tel +49 3834 86 4423 Fax +49 3834 86 4413 http://www.chemie.uni-greifswald.de/~plasma From huang_d at gold.cchem.berkeley.edu Fri Mar 1 22:56:58 2002 From: huang_d at gold.cchem.berkeley.edu (David Mark Huang) Date: Fri, 1 Mar 2002 13:56:58 -0800 (PST) Subject: [CPMD-list] MOLVIB Message-ID: The MOLVIB output file from a VIBRATIONAL ANALYSIS calculation is used by the MOLVIB program to visualize the normal modes. Is there a way of getting MOLVIB for free? Or are there alternative freeware programs (preferably for Unix) that will do the same job? Thanks David Huang Chandler Group Department of Chemistry University of California at Berkeley From vuilleum at lptl.jussieu.fr Mon Mar 4 09:58:26 2002 From: vuilleum at lptl.jussieu.fr (Rodolphe VUILLEUMIER) Date: Mon, 04 Mar 2002 09:58:26 +0100 Subject: [CPMD-list] Re: MOLVIB References: <200203021101.MAA20984@cpmd.org> Message-ID: <3C833732.5020803@lptl.jussieu.fr> I have slightly modified a program called xvibs and made a cp2xvib program which I hope could help you. cp2xvib takes the MOLVIB file and creates an input file for xvibs; just run cp2xvib in the directory wher e the MOLVIB file is. It also calculates the frequency and normal modes (you can specify to clean them of rotations and translations if you want). The xvibs program which is free software of Bradley A. Smith then plots out movies in the xyz format of desired normal modes. I attached both programs; hoping that they still work, since I didn't use them for some time. Greetings, R. Vuilleumier -- Rodolphe Vuilleumier Laboratoire de Physique Theorique de Liquides Universite Pierre et Marie Curie - Tour 16-15 - 5eme etage 4 place Jussieu - 75005 Paris - France Tel: 33-(0)1-44-27-72-39 Fax: 33-(0)1-44-27-51-00 Email:vuilleum at lptl.jussieu.fr -------------- next part -------------- A non-text attachment was scrubbed... Name: cp2xvibs.f Type: application/acroread Size: 6405 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20020304/ac4b7096/attachment.bin -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: xvibs.c Url: http://cpmd.org/pipermail/cpmd-list/attachments/20020304/ac4b7096/attachment.c From mzapalow at mitr.p.lodz.pl Mon Mar 4 15:48:53 2002 From: mzapalow at mitr.p.lodz.pl (Michal Zapalowski) Date: Mon, 4 Mar 2002 15:48:53 +0100 Subject: [CPMD-list] CPMDv35 crash on SGI Message-ID: <03fe01c1c38b$d41dae70$28d633d4@MITRMZ> Dear All, after successful compilation on SGI Power Challenge I've tried to run the test job: wavefunction optimization, taken from manual (see attached files). Unfortunately CPMD crashed at the beginning of the job after the following: [..complete output in the attachement...] GENERATE ATOMIC BASIS SET Si SLATER ORBITALS 3S ALPHA= 1.6344 OCCUPATION= 2.00 3P ALPHA= 1.4284 OCCUPATION= 2.00 Bus error (core dumped) Was it my fault or CPMD feature? Or, maybe, something else?? Any help will be very appreciated, Michal --- Michal Zapalowski IARC, Technical University of Lodz 93-590 Lodz, Poland (+48 42) 631-31-77 mzapalow at mitr.p.lodz.pl -------------- next part -------------- A non-text attachment was scrubbed... Name: test.in Type: application/octet-stream Size: 394 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20020304/c10ce00a/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: test.out Type: application/octet-stream Size: 5783 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20020304/c10ce00a/attachment-0001.obj From cur at zurich.ibm.com Tue Mar 5 13:26:03 2002 From: cur at zurich.ibm.com (Alessandro Curioni) Date: Tue, 5 Mar 2002 13:26:03 +0100 Subject: [CPMD-list] CPMDv35 crash on SGI Message-ID: Hi. in some version of the SGI compiler the -O3 optimization flag doesn't work properly. Please recompile with -O. Regards 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 From zucco at dipteris.unige.it Tue Mar 5 14:06:49 2002 From: zucco at dipteris.unige.it (marino vetuschi zuccolini) Date: Tue, 5 Mar 2002 14:06:49 +0100 Subject: [CPMD-list] CPMD and ATLAS libs Message-ID: <200203051301.NAA25433@hpe35.dipteris.unige.it> Hello to all, I try to compile CPMD on a dual proc, based on RH7.2, and the Intel Fortran. Atlas3.2.1 for PIII are the blas/lapack libs compiled for my system. During compilation I have this kind of message with two ATLAS subroutines dlamch and xerbla. Does anyone knows if I have a wrong version of ATLAS lib or what ? Thanks marino ######################################################################## rm -f cpmd.x if [ "." != "." ]; then ln -s ./cpmd.x cpmd.x; fi ifc -tp p6 -axiM -o ./cpmd.x timetag.o cpmd.o softex. ... ... mm_cpmd_ext_pot_f77.o sysdepend.o shmemory.o -llapack -lf77blas -latlas -Vaxlib /usr/lib/liblapack.a(dlamch.o): In function `dlamc2_': dlamch.o(.text+0xbbf): undefined reference to `s_wsfe' dlamch.o(.text+0xbd3): undefined reference to `do_fio' dlamch.o(.text+0xbd8): undefined reference to `e_wsfe' /usr/lib/liblapack.a(xerbla.o): In function `xerbla_': xerbla.o(.text+0x14): undefined reference to `s_wsfe' xerbla.o(.text+0x24): undefined reference to `do_fio' xerbla.o(.text+0x34): undefined reference to `do_fio' xerbla.o(.text+0x39): undefined reference to `e_wsfe' make: *** [cpmd.x] Error 1 [zucco at qed SOURCE]$ -- Marino Vetuschi Zuccolini PESTO Group http://ugo.dipteris.unige.it DIPTERIS - Genova University Corso Europa 26 - 16132 - Italy email: zucco at dipteris.unige.it From cur at zurich.ibm.com Tue Mar 5 14:49:28 2002 From: cur at zurich.ibm.com (Alessandro Curioni) Date: Tue, 5 Mar 2002 14:49:28 +0100 Subject: [CPMD-list] cpmd2grid Message-ID: Dear all, thank to J. Hutter, I have put in the contrib directory the program cpmd2grid that is the most updated version of the grid utility (utility that converts DENSITY files to pdb and cube files to visualize the electronic density distributions). This utility has been rewritten by W. Silvestri and A. Seitsonen based on older versions of this program originally written by J. Hutter, P. Giannozzi and myself. Best Regards, 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 From paulsen at troubadix.physik.mu-luebeck.de Tue Mar 5 15:16:00 2002 From: paulsen at troubadix.physik.mu-luebeck.de (paulsen at troubadix.physik.mu-luebeck.de) Date: Tue, 5 Mar 2002 15:16:00 +0100 Subject: [CPMD-list] Re: CPMD and ATLAS libs Message-ID: <3C84E130.6565.1488701@localhost> Dear Marino, I had similar problems with the compilation, but I can not tell you what is wrong. I used the Intel Math Kernel Library (MKL) instead, which can be downloaded from www.intel.com. It looks to me that the cpmd program has a good performance if linked with this library. I am quite curious if anyone knows which of the two libraries (LAPACK + ATLAS or MKL) has the better performance. Best regards, Hauke From sebastia at mpip-mainz.mpg.de Tue Mar 5 15:24:54 2002 From: sebastia at mpip-mainz.mpg.de (Daniel Sebastiani) Date: Tue, 5 Mar 2002 15:24:54 +0100 (CET) Subject: [CPMD-list] cubefiles In-Reply-To: Message-ID: Dear all, I just want to draw your attention to the fact that there is already an option in CPMD that prints out selected orbitals or the density in .CUBE format. It is in the &PROPerties section and simply called CUBEFILE { DENSITY | ORBITALS }, followed by the total number and indices of the orbitals. Regards, Daniel. -------------------------------------------------------------- Daniel Sebastiani mobile +41 7 65 92 04 79 ETH Z?rich Dept. Prof. R?thlisberger HCI H 111 Phone +41 1 63 34546 CH-8093 Z?rich Fax +41 1 63 21090 -------------------------------------------------------------- Max-Planck-Institut Dept. Prof. Spiess f?r Polymerforschung Phone +49 6131 379 126 Ackermannweg 10 Fax +49 6131 379 100 D-55128 Mainz, Germany sebastia at mpip-mainz.mpg.de -------------------------------------------------------------- From cur at zurich.ibm.com Tue Mar 5 15:45:58 2002 From: cur at zurich.ibm.com (Alessandro Curioni) Date: Tue, 5 Mar 2002 15:45:58 +0100 Subject: [CPMD-list] cubefiles Message-ID: One remark: the cpmd2grid utility is very useful to change the resolution of your grid, to shift the density or to have at high resolution only one portion of the density, all things that you cannot do directly from CPMD. Moreover, if you want to save several DENSITY files it is always much more convenient to store that in G-space than to have directly in real space, especially if you want to store a series of densities from MD. Regards, 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 From frank at blue.cup.uni-muenchen.de Tue Mar 5 17:22:14 2002 From: frank at blue.cup.uni-muenchen.de (Irmgard Frank) Date: Tue, 5 Mar 2002 17:22:14 +0100 (CET) Subject: [CPMD-list] CPMD and ATLAS libs In-Reply-To: <200203051301.NAA25433@hpe35.dipteris.unige.it> Message-ID: Hi, a helpful command to find out what is contained in a library file is objdump, e.g: objdump -t /usr/lib/libXXXX.a | grep dlamch There may be slight differences like additional underscores in subroutine names. Best wishes, Irmgard On Tue, 5 Mar 2002, marino vetuschi zuccolini wrote: > Hello to all, > I try to compile CPMD on a dual proc, based on RH7.2, and the Intel Fortran. > Atlas3.2.1 for PIII are the blas/lapack libs compiled for my system. > During compilation I have this kind of message with two ATLAS subroutines > dlamch and xerbla. > Does anyone knows if I have a wrong version of ATLAS lib or what ? > > Thanks > > marino > > ######################################################################## > > rm -f cpmd.x > if [ "." != "." ]; then ln -s ./cpmd.x cpmd.x; fi > ifc -tp p6 -axiM -o ./cpmd.x timetag.o cpmd.o softex. > ... > ... > mm_cpmd_ext_pot_f77.o sysdepend.o shmemory.o -llapack -lf77blas -latlas > -Vaxlib > /usr/lib/liblapack.a(dlamch.o): In function `dlamc2_': > dlamch.o(.text+0xbbf): undefined reference to `s_wsfe' > dlamch.o(.text+0xbd3): undefined reference to `do_fio' > dlamch.o(.text+0xbd8): undefined reference to `e_wsfe' > /usr/lib/liblapack.a(xerbla.o): In function `xerbla_': > xerbla.o(.text+0x14): undefined reference to `s_wsfe' > xerbla.o(.text+0x24): undefined reference to `do_fio' > xerbla.o(.text+0x34): undefined reference to `do_fio' > xerbla.o(.text+0x39): undefined reference to `e_wsfe' > make: *** [cpmd.x] Error 1 > [zucco at qed SOURCE]$ > -- > Marino Vetuschi Zuccolini > PESTO Group > http://ugo.dipteris.unige.it > DIPTERIS - Genova University > Corso Europa 26 - 16132 - Italy > email: zucco at dipteris.unige.it > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From Ari.P.Seitsonen at iki.fi Tue Mar 5 19:10:17 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Tue, 5 Mar 2002 19:10:17 +0100 Subject: [CPMD-list] CPMD and ATLAS libs In-Reply-To: (message from Irmgard Frank on Tue, 5 Mar 2002 17:22:14 +0100 (CET)) References: Message-ID: <200203051810.g25IAHG30331@magadino.cscs.ch> Hi, > a helpful command to find out what is contained in a library file > is objdump, e.g: > > objdump -t /usr/lib/libXXXX.a | grep dlamch > > There may be slight differences like additional underscores in > subroutine names. And if 'objdump' doesn't exist on your favourite operating system, you can try 'nm'. # > nm /apps/lapack/lib/liblapack_32.a (If you happen to look at 64-bit libraries on an IBM Regatta/p690/SP4/PWR4 machine, then...) # > nm -X 64 /apps/lapack/lib/liblapack_64.a Ciao, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- ____ ____ ____ ____ Ari Paavo Seitsonen / __// _// __// __/ fax +41 91 610 82 82 tel +41 91 610 82 59 / /_ _\ \ / /_ _\ \ Ari.P.Seitsonen at iki.fi gsm +41 79 719 09 35 \__/\___/ \__/\___/ http://www.iki.fi/~apsi/ Indirizzo: CSCS (Centro Svizzero di Calcolo Scientifico) Anschrift: Via Cantonale, CH-6928 Manno Address: Svizzera / Schweiz / Suisse / Svizra / Switzerland From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Wed Mar 6 14:00:44 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (axel.kohlmeyer at theochem.ruhr-uni-bochum.de) Date: Wed, 06 Mar 2002 14:00:44 +0100 Subject: [CPMD-list] CPMD and ATLAS libs In-Reply-To: <200203051301.NAA25433@hpe35.dipteris.unige.it> Message-ID: <200203061300.g26D0iO02938@yello.theochem.ruhr-uni-bochum.de> On Tue, 5 Mar 2002 14:06:49 +0100 marino vetuschi zuccolini wrote: > Hello to all, > I try to compile CPMD on a dual proc, based on RH7.2, and the Intel Fortran. > Atlas3.2.1 for PIII are the blas/lapack libs compiled for my system. > During compilation I have this kind of message with two ATLAS subroutines > dlamch and xerbla. > Does anyone knows if I have a wrong version of ATLAS lib or what ? > > Thanks > > marino > > ######################################################################## > > rm -f cpmd.x > if [ "." != "." ]; then ln -s ./cpmd.x cpmd.x; fi > ifc -tp p6 -axiM -o ./cpmd.x timetag.o cpmd.o softex. > ... > ... > mm_cpmd_ext_pot_f77.o sysdepend.o shmemory.o -llapack -lf77blas -latlas > -Vaxlib > /usr/lib/liblapack.a(dlamch.o): In function `dlamc2_': > dlamch.o(.text+0xbbf): undefined reference to `s_wsfe' > dlamch.o(.text+0xbd3): undefined reference to `do_fio' > dlamch.o(.text+0xbd8): undefined reference to `e_wsfe' > /usr/lib/liblapack.a(xerbla.o): In function `xerbla_': > xerbla.o(.text+0x14): undefined reference to `s_wsfe' > xerbla.o(.text+0x24): undefined reference to `do_fio' > xerbla.o(.text+0x34): undefined reference to `do_fio' > xerbla.o(.text+0x39): undefined reference to `e_wsfe' hello! the undefined references presumably belong to the f2c (or g2c) GNU fortran runtime library. that means, your lapack library has been compiled with g77 rather than intel ifc. you have to either compile all fortran libraries (including lapack) with the _same_ compiler or try to link the gnu fortran runtime as well (i.e. add the output of gcc -print-libgcc-file-name | sed -e 's,gcc.a,g2c.a,' to the linker command line). but keep in mind, that mixing objects of different fortran compilers can result in unexpected behavior of the final execuable. take care, axel. > make: *** [cpmd.x] Error 1 > [zucco at qed SOURCE]$ > -- > Marino Vetuschi Zuccolini > PESTO Group > http://ugo.dipteris.unige.it > DIPTERIS - Genova University > Corso Europa 26 - 16132 - Italy > email: zucco at dipteris.unige.it > > --__--__-- > -- ======================================================================= 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 s.meloni at caspur.it Thu Mar 7 10:00:30 2002 From: s.meloni at caspur.it (simonem) Date: Thu, 07 Mar 2002 10:00:30 +0100 Subject: [CPMD-list] constant pressure run Message-ID: <3C872C2E.7040808@caspur.it> Hi all, do you know meaningfull values for the parameter AKIN,SKIN,ECKIN to be read by the option CONSTANT CUTOFF during a constant pressure run? Grazie El Simon -- +-----------------------------------------+ | Simone Meloni | | CASPUR | | c/o Universita' di Roma "La Sapienza" | | P.le A. Moro 5, 00185 Roma, Italy | | Phone + 39 (0)6 4991 3064 | | Fax + 39 (0)6 5134864 | | E-mail s.meloni at caspur.it | +-----------------------------------------+ From mqtan0610 at mail.hz.zj.cn Thu Mar 7 15:04:47 2002 From: mqtan0610 at mail.hz.zj.cn (Mingqiu Tan) Date: Thu, 7 Mar 2002 22:4:47 +0800 Subject: [CPMD-list] uspp Message-ID: <200203071403.PAA11448@internet-fence.zurich.ibm.com> Dear all, please tell me which version of uspp generator from Vanderbilt is compatible with present CPMD v3.5. Regards. Mingqiu Tan mqtan at css.zju.edu.cn --------------------------------- Department of Physics Zhejiang University Hangzhou 310027 P. R. China Tel: +86-571-87951594(O) +86-571-88858360(H) Fax: +86-571-87951328 --------------------------------- From weiz at mail.rochester.edu Thu Mar 7 17:38:06 2002 From: weiz at mail.rochester.edu (weizhuang) Date: Thu, 7 Mar 2002 11:38:06 -0500 Subject: [CPMD-list] choosing the energy cutoff Message-ID: <200203071626.g27GQDTM2964628@mail.rochester.edu> Dear all: could anybody tell me how to choose the energy cut-off in &SYSTEM section? for example, if I want to find out the energy cutoff for Hydrogen Fluoride in isolated state. where can I look for it. is there any papers that I can refer to? regards wei zhuang From weiz at mail.rochester.edu Thu Mar 7 22:34:51 2002 From: weiz at mail.rochester.edu (weizhuang) Date: Thu, 7 Mar 2002 16:34:51 -0500 Subject: [CPMD-list] one question Message-ID: <200203072122.g27LMv6o3280221@mail.rochester.edu> a warning message appeared in the output file: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ?WARNING! XC FUNCTIONALS INCONSISTENT FOR h.pp ?!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! does it mean that my pseudopotential file is wrong? I used fhi98PP to create this pp file, and just recast it. so if it is wrong, what more should I do to the output file of fhi98PP? regards wei zhuang From Ari.P.Seitsonen at iki.fi Thu Mar 7 23:28:38 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Thu, 7 Mar 2002 23:28:38 +0100 Subject: [CPMD-list] one question In-Reply-To: <200203072122.g27LMv6o3280221@mail.rochester.edu> (message from weizhuang on Thu, 7 Mar 2002 16:34:51 -0500) References: <200203072122.g27LMv6o3280221@mail.rochester.edu> Message-ID: <200203072228.g27MSc715057@magadino.cscs.ch> > a warning message appeared in the output file: > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?WARNING! XC FUNCTIONALS INCONSISTENT FOR h.pp > ?!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > does it mean that my pseudopotential file is wrong? I used fhi98PP > to create this pp file, and just recast it. so if it is wrong, what > more should I do to the output file of fhi98PP? It means that the XC functional used to generate the pseudo potential and the functional which you want to use in CPMD are not the same; it could be more or less serious: Some of the XC functionals in CPMD are just minor variations of each others, e.g. the LDA part is evaluated using Perdew-Wang'92, Perdew-Zunger'7? or the Pade-interpolation formula. If this is the case, the resulting error is usually small, however if your pseudos were generated e.g. with PBE and you try to use BLYP, the error might become serious. I suggest you to see what are the two functionals (pp & CPMD-input), and look if the difference is significant or not. (Sorry for not making the added lines for 'psgen' not 100 % and maybe also not 100 % operational/full-proof!) Ciao, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- ____ ____ ____ ____ Ari Paavo Seitsonen / __// _// __// __/ fax +41 91 610 82 82 tel +41 91 610 82 59 / /_ _\ \ / /_ _\ \ Ari.P.Seitsonen at iki.fi gsm +41 79 719 09 35 \__/\___/ \__/\___/ http://www.iki.fi/~apsi/ Indirizzo: CSCS (Centro Svizzero di Calcolo Scientifico) Anschrift: Via Cantonale, CH-6928 Manno Address: Svizzera / Schweiz / Suisse / Svizra / Switzerland From hutter at pci.unizh.ch Fri Mar 8 10:18:34 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Fri, 8 Mar 2002 10:18:34 +0100 (MET) Subject: [CPMD-list] choosing the energy cutoff In-Reply-To: <200203071626.g27GQDTM2964628@mail.rochester.edu> Message-ID: The best way to choose the cutoff for a CPMD calculations is by running first a series of tests. Select a test system and a representative quantity (bond length, reaction energy, etc.), perform a series of calculations with increasing cutoff, pick the lowest cutoff with satisfactory results. It's always a good idea to make checks at some critical points of the calculations by increasing the cutoff. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 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, 7 Mar 2002, weizhuang wrote: > Dear all: > > could anybody tell me how to choose the energy cut-off in &SYSTEM section? > for example, if I want to find out the energy cutoff for Hydrogen Fluoride in > isolated state. where can I look for it. is there any papers that I can refer > to? > > regards > wei zhuang > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Fri Mar 8 10:27:27 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Fri, 8 Mar 2002 10:27:27 +0100 (MET) Subject: [CPMD-list] uspp/ Vanderbilt pp In-Reply-To: <200203071403.PAA11448@internet-fence.zurich.ibm.com> Message-ID: Hi there is a problem with the current status of the implementation of Vandebilt ultra soft PP in CPMD. This version of the code has not been actively maintained over the past years. The two formats supported by CPMD correspond to the output of USPP-atomic codes that are from before 1995. The implemented versions only support a very special kind of pseudization of the Q-functions (the atomic augmentation charges). Another problem is, that most of the properties and additional features of the code are not implemented for USPP (e.g. Wannier functions, all linear response properties, k-points). Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 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, 7 Mar 2002, Mingqiu Tan wrote: > Dear all, > > please tell me which version of uspp generator from Vanderbilt is compatible with present CPMD v3.5. > > > Regards. > Mingqiu Tan > mqtan at css.zju.edu.cn > > --------------------------------- > Department of Physics > Zhejiang University > Hangzhou 310027 > P. R. China > > Tel: +86-571-87951594(O) > +86-571-88858360(H) > Fax: +86-571-87951328 > --------------------------------- > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From Ari.P.Seitsonen at iki.fi Fri Mar 8 11:07:29 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Fri, 8 Mar 2002 11:07:29 +0100 Subject: [CPMD-list] uspp/ Vanderbilt pp In-Reply-To: (message from Juerg Hutter on Fri, 8 Mar 2002 10:27:27 +0100 (MET)) References: Message-ID: <200203081007.g28A7Tr19884@magadino.cscs.ch> Ciao, I might add to the reply of J?rg that we (here at Manno, CSCS; we'll set it available on the web in the near future) have the copy of the Vb generator prepared by Mauro Boero but it's somewhat out-of-date, as J?rg says. We are also going to adapt Mauro's changes to the newest version of Prof. Vanderbilt's own generator - which is downloadable in the web -, so that it could be used to generate potentials compatible with CPMD. Greetings, apsi > there is a problem with the current status of the implementation > of Vandebilt ultra soft PP in CPMD. This version of the > code has not been actively maintained over the past years. > The two formats supported by CPMD correspond to the output > of USPP-atomic codes that are from before 1995. > The implemented versions only support a very special kind > of pseudization of the Q-functions (the atomic augmentation > charges). > > Another problem is, that most of the properties and additional > features of the code are not implemented for USPP (e.g. Wannier > functions, all linear response properties, k-points). > > Juerg > > ---------------------------------------------------------- > Juerg Hutter Phone : ++41 1 635 4211 > 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, 7 Mar 2002, Mingqiu Tan wrote: > > > Dear all, > > > > please tell me which version of uspp generator from Vanderbilt is compatible with present CPMD v3.5. > > > > > > Regards. > > Mingqiu Tan > > mqtan at css.zju.edu.cn > > > > --------------------------------- > > Department of Physics > > Zhejiang University > > Hangzhou 310027 > > P. R. China > > > > Tel: +86-571-87951594(O) > > +86-571-88858360(H) > > Fax: +86-571-87951328 > > --------------------------------- > > > > _______________________________________________ > > 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 > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- ____ ____ ____ ____ Ari Paavo Seitsonen / __// _// __// __/ fax +41 91 610 82 82 tel +41 91 610 82 59 / /_ _\ \ / /_ _\ \ Ari.P.Seitsonen at iki.fi gsm +41 79 719 09 35 \__/\___/ \__/\___/ http://www.iki.fi/~apsi/ Indirizzo: CSCS (Centro Svizzero di Calcolo Scientifico) Anschrift: Via Cantonale, CH-6928 Manno Address: Svizzera / Schweiz / Suisse / Svizra / Switzerland From Veronique.VanSpeybroeck at rug.ac.be Fri Mar 8 11:12:15 2002 From: Veronique.VanSpeybroeck at rug.ac.be (Veronique Van Speybroeck) Date: Fri, 8 Mar 2002 11:12:15 +0100 (MET) Subject: [CPMD-list] uspp/ Vanderbilt pp In-Reply-To: Message-ID: On Fri, 8 Mar 2002, Juerg Hutter wrote: > Hi > > there is a problem with the current status of the implementation > of Vandebilt ultra soft PP in CPMD. This version of the > code has not been actively maintained over the past years. > The two formats supported by CPMD correspond to the output > of USPP-atomic codes that are from before 1995. > The implemented versions only support a very special kind > of pseudization of the Q-functions (the atomic augmentation > charges). About a week ago I stated a problem that I had with the use of VDB pseudopotentials. Has this anything to do with the above explanation. In my case it seems that the pseudopotential is read correctly. I have written an own program that converts the output of the original vanderbilt code to the right format and this seems to work. However somewhat further the program stills stops with an error message : On entry to DSYRK parameter number 10 had an illegal value Do you have an example VDB pseudopotential file, with which that program properly works. I would like to figure out what the problem is Thanks in advance veornique > > Another problem is, that most of the properties and additional > features of the code are not implemented for USPP (e.g. Wannier > functions, all linear response properties, k-points). > > Juerg > > ---------------------------------------------------------- > Juerg Hutter Phone : ++41 1 635 4211 > 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, 7 Mar 2002, Mingqiu Tan wrote: > > > Dear all, > > > > please tell me which version of uspp generator from Vanderbilt is compatible with present CPMD v3.5. > > > > > > Regards. > > Mingqiu Tan > > mqtan at css.zju.edu.cn > > > > --------------------------------- > > Department of Physics > > Zhejiang University > > Hangzhou 310027 > > P. R. China > > > > Tel: +86-571-87951594(O) > > +86-571-88858360(H) > > Fax: +86-571-87951328 > > --------------------------------- > > > > _______________________________________________ > > 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 sasha at photonics.ru Mon Mar 18 22:35:28 2002 From: sasha at photonics.ru (Alexander Bagatur'yants) Date: Tue, 19 Mar 2002 00:35:28 +0300 Subject: [CPMD-list] Nano&Giga Challenges in Microelectronics Message-ID: <027001c1cec4$d2dfd1c0$77df55c2@Orion> Dear Colleagues, I would like to inform you about the Symposium and Summer School on Nano and Giga Challenges in Microelectronics Research and Opportunities in Russia Moscow, September 11-13, 2002 http://www.AtomicScaleDesign.Net/Moscow The section on Atomic Scale Design: Modeling and Simulation will be devoted to various aspects of Computational materials science. The last updates of the 2nd Call and the section program are attached. Prof. Alexander Bagatur'yants Photochemistry Center, Russian Academy of Sciences ul. Novatorov 7a, Moscow, 117421 Russia Phone: (007-095)-936-2588 Fax: (007-095)-936-1255 E-mail: sasha at photonics.ru Home page: http://www.photonics.ru/eng/bagat/bagat.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: NGCM_2nd Call_March7.pdf Type: application/pdf Size: 32834 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20020319/b5a51386/attachment.pdf -------------- next part -------------- A non-text attachment was scrubbed... Name: AtomicScale_program.pdf Type: application/pdf Size: 59439 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20020319/b5a51386/attachment-0001.pdf From aksabir1 at hotmail.com Wed Mar 20 16:55:37 2002 From: aksabir1 at hotmail.com (abdenour sabir) Date: Wed, 20 Mar 2002 08:55:37 -0700 Subject: [CPMD-list] (no subject) Message-ID: To The CPMD Team I would like to know if there is someone that could give some hints or advice on how to run CPMD for a graphene sheet, say 18 atoms of carbon,. The goal here is to find the minimum lattice constant (z-direction) and do a band structure plot. Many authors that dealt with Carbon have claimed that ab initio code (DFT) usually over estimate the lattice contstant or total energy. On the other hand I would like to see to what extent is the CPMD code reliable,i.e by directly comparing the results to those given by the experiments. Thank you in advance for your kind cooperation. A.Sabir _________________________________________________________________ Chat with friends online, try MSN Messenger: http://messenger.msn.com From M.A.Zwijnenburg at tnw.tudelft.nl Mon Mar 25 16:37:25 2002 From: M.A.Zwijnenburg at tnw.tudelft.nl (Martijn Zwijnenburg) Date: Mon, 25 Mar 2002 16:37:25 +0100 (MET) Subject: [CPMD-list] examples Message-ID: <6807A45E75@stm-ltc2.dct.tudelft.nl> Hi, I've just setup CPMD on our local Cray T3E and ran a number of the examples from the manual. Now I wonder of somebody could send me some working inputfiles for Molecular Dynamics runs (preferably molecular systems/ H2O). In my experience you can learn a lot more from running examples then from just reading the manual. Any links to hands-on tutorials would be also more then welcomed. 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