From hutter at oci.unizh.ch Fri Feb 1 13:26:53 2002 From: hutter at oci.unizh.ch (Juerg Hutter) Date: Fri, 1 Feb 2002 13:26:53 +0100 (MET) Subject: [CPMD-list] Error on HP compilation In-Reply-To: Message-ID: TRIM is a F90 intrinsic function that works on strings. As CPMD is a almost F77 Program, such F90 functions should not be used. However, I don't know why the HP F90 compiler has a problem with this. Work around: replace trim(converged) by converged regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Thu, 31 Jan 2002, Manh Nguyen wrote: > > Dear users, > > I compile the CPMD (version 3.5) package on our workstation with HP > Fortran 90 for HP-UX 10.20/11.x. I have noticed the following error > message: > > ------------------------------------------------------------------------- > ...... > trim(converged),abs(eigenvect(iter,i)),').' > ^ > Error 220 at (434:./lanc_phon_p.F) : This entity has not been given a type > > ------------------------------------------------------------------------- > > Have you ever encountered similar problem with > type of trim(converged)? > > Thank you in advance for any comment/suggestion. > > Yours sincerely, > Duc. > > ********************************************************************* > Dr. Duc Nguyen-Manh > Materials Modelling Laboratory Phone: 44 (0) 1865 283 326 > Fax : 44 (0) 1865 273 764 > Office: Room 30.23 Phone: 44 (0) 1865 273 672 > Holder Building > Department of Materials, Fax: 44 (0) 1865 273 789 > Oxford University, > Oxford, Parks Road, OX1 3PH, UK. Email:manh.nguyen at materials.ox.ac.uk > ********************************************************************** > > > > From hutter at oci.unizh.ch Fri Feb 1 13:39:23 2002 From: hutter at oci.unizh.ch (Juerg Hutter) Date: Fri, 1 Feb 2002 13:39:23 +0100 (MET) Subject: [CPMD-list] Goedecker-type pseudopotentials In-Reply-To: Message-ID: Hi it is understood in the CPMD community that PP were generated with the same functional as used in the calculation. I will ask Alessandro Curioni at IBM to upload the programs to generate Goedecker-type PP. A few words on PP - It's by no means trivial to generate Goedecker-type PP. Read carefully the README files - All new PP have to be tested - Another place to find PP is www.abinit.org but you will have to convert the formats regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Wed, 30 Jan 2002 jarek at elrond.chem.uni.wroc.pl wrote: > Dear CPMD Community, > > have you got any idea how to obtain the programs for generating / > adjusting Goedecker-type pseudopotential parameters? It seems this is the > advisable thing to do when changing from LDA to GGA functionals. > > With regards, > > Jaroslaw Panek > Faculty of Chemistry, University of Wroclaw, Poland > > From cur Tue Feb 5 07:14:45 2002 From: cur (Alessandro Curioni) Date: Tue, 5 Feb 2002 07:14:45 +0100 Subject: [CPMD-list] Change of configuration Message-ID: <200202050614.HAA19584@cpmd.org> Dear cpmd-list subscriber, following the suggestion of many subscribers, the default configuration of the mailing list has been modified to "regular" (not-digested) for all the subscribers. This will allow a much faster reactions to comments and/or problems. If you want to receive only digested messages, please change your configuration in www.cpmd.org/mailman/listinfo/cpmd-list Another section will be added soon to the web pages : "Known bugs" where we will report all the known bugs and relative corrections. Please be tuned! From huang_d at gold.cchem.berkeley.edu Tue Feb 5 17:33:28 2002 From: huang_d at gold.cchem.berkeley.edu (David Mark Huang) Date: Tue, 5 Feb 2002 08:33:28 -0800 (PST) Subject: [CPMD-list] runtime error with pgf90 Message-ID: I am trying to run CPMD v. 3.5 on an 800MHz AMD Athlon machine running Redhat 6.2. I am using the Portland Group Fortran 90 compiler v. 3.1. I have used the Configure script provided with the source code, with the "PC-PGI" option. I altered the Makefile so that I could compile it with pgf90, with the following lines being the only ones changed. LFLAGS = -llapack -lblas $(QMMM_LIBS) FC = pgf90 -c -fast LD = pgf90 -fast The code compiles OK, but after running for a while, I get the error message: PGFIO-F-201/OPEN/unit=4/illegal value for specifier. File name = ./TRAJECTORY In source file ./fileopen.f, at line number 17 This seems to happen after the program has already written to the TRAJECTORY file once. I have tried changing the unit value from "4" to something larger like "64" (making sure that it doesn't conflict with some other file) and the same error message results. Is there a simple solution to this? Thanks David Huang Department of Chemistry University of California, Berkeley From hutter at oci.unizh.ch Tue Feb 5 17:48:44 2002 From: hutter at oci.unizh.ch (Juerg Hutter) Date: Tue, 5 Feb 2002 17:48:44 +0100 (MET) Subject: [CPMD-list] runtime error with pgf90 Message-ID: Hi the problem is the different behavior of pgf77 and pgf90 with the OPEN statement. For the pgf77 compiler you need the current version of fileopen.F . If you want to use the pgf90 compiler you have to change fileopen.F on line 16. You have to add a "defined(__PGI)". C Old file (append). #if defined(__IBM) || defined(__PGI) || defined(__ABSOFT) Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- From huang_d at gold.cchem.berkeley.edu Wed Feb 6 23:13:39 2002 From: huang_d at gold.cchem.berkeley.edu (David Mark Huang) Date: Wed, 6 Feb 2002 14:13:39 -0800 (PST) Subject: [CPMD-list] equilibrated H3O+/OH- in H2O Message-ID: Hello I am looking for well equilibrated CPMD trajectories of H3O+ in water and trajectories of OH- in water. I would appreciate it very much if anyone who has such trajectories could send them to me. It would also be helpful to me, but not necessary, if the Wannier function centers along the trajectory were also available. Thanks David Huang Chandler Group Department of Chemistry University of California, Berkeley From fparnold at chem.northwestern.edu Thu Feb 7 20:47:39 2002 From: fparnold at chem.northwestern.edu (Fred P. Arnold) Date: Thu, 7 Feb 2002 13:47:39 -0600 (CST) Subject: [CPMD-list] BYLM_p.F Message-ID: Hello, This may be an odd question, but has anyone else noticed that on Sun / Linux (at least with the Intel Fortran compiler), that BYLM_p.F takes an inordinately long time and large amount of swap to compile? Is there some sensible way to break this file down into more manageable chunks? From cur Fri Feb 8 19:17:33 2002 From: cur (Alessandro Curioni) Date: Fri, 8 Feb 2002 19:17:33 +0100 Subject: [CPMD-list] Goedecker pseudo-potentials program and files Message-ID: <200202081817.TAA26236@cpmd.org> Dear all, thank to the courtesy of J. Hutter, we have added in the cpmd repository a directory "contrib" where the program to generate Goedecker pseudopotentials and the pseudopotentials reported in his papers are stored. Best Regards, Your cpmd.org team. From hutter at oci.unizh.ch Sat Feb 9 17:07:36 2002 From: hutter at oci.unizh.ch (Juerg Hutter) Date: Sat, 9 Feb 2002 17:07:36 +0100 (MET) Subject: [CPMD-list] BYLM_p.F In-Reply-To: Message-ID: Hi BYLM_p.F is part of an experimental section of the code. It will never be called in normal execution of the program. It's therefore save to replace the body of the subroutine by a stop statement. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Thu, 7 Feb 2002, Fred P. Arnold wrote: > Hello, > > This may be an odd question, but has anyone else noticed that on Sun / > Linux (at least with the Intel Fortran compiler), that BYLM_p.F takes an > inordinately long time and large amount of swap to compile? Is there some > sensible way to break this file down into more manageable chunks? > > >From the Sun side, it was under Solaris 8, Forte 6.2 development > environment. For IFC, it's version 5 (the first release for Linux/Intel), > on a SuSE 7.3 (2.4.9 kernel) system. > > Thanks. > > -Fred > > Frederick P. Arnold, Jr. > NUIT, Northwestern U. > f-arnold at northwestern.edu > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From gas5x at bancorp.ru Tue Feb 12 08:22:17 2002 From: gas5x at bancorp.ru (Gregory Shamov) Date: Tue, 12 Feb 2002 10:22:17 +0300 Subject: [CPMD-list] problem compiling CPMD with IFC Message-ID: <132142597861.20020212102217@bancorp.ru> Hello All, I have tryed to build CPMD with Intel Fortran on PC-Linux, but make reports to me the following error: make: *** No rule to make target `Gromos/toposz.h', needed by `mm_init.o'. Stop How to I fix it? -- Best regards, Gregory Shamov mailto:gas5x at bancorp.ru From mit at parc.uni.udm.ru Tue Feb 12 22:29:29 2002 From: mit at parc.uni.udm.ru (mit) Date: Tue, 12 Feb 2002 16:29:29 -0500 (EST) Subject: [CPMD-list] problem compiling CPMD with IFC In-Reply-To: <132142597861.20020212102217@bancorp.ru> Message-ID: I meens the make utility dosn't find file toposz.h. Shuch error occur in Intel compiler and you need use key -I in compilation step for findihg include file and *.h files. 11.02.2002 Izhevsk, Russia Yorus Yuri Mitrokhin mailto: mit at uni.udm.ru On Tue, 12 Feb 2002, Gregory Shamov wrote: > Hello All, > > I have tryed to build CPMD with Intel Fortran on PC-Linux, but > make reports to me the following error: > > make: *** No rule to make target `Gromos/toposz.h', needed by `mm_init.o'. Stop > > How to I fix it? > > -- > Best regards, > Gregory Shamov mailto:gas5x at bancorp.ru > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From weiz at mail.rochester.edu Tue Feb 12 17:32:28 2002 From: weiz at mail.rochester.edu (weizhuang) Date: Tue, 12 Feb 2002 11:32:28 -0500 Subject: [CPMD-list] the creation of pseudopotential Message-ID: <200202121618.g1CGINif1170395@mail.rochester.edu> Hi, guys: I need help in the creation of pseudopotential. seems that I need a executable "atomc.x", but I can only find "atomc.o", "atomc.F", "atomc.f " after compiling. the only executable is "cpmd.x". could anybody tell me what is the matter? I am using cpmd v.3.5 From pmothe at ig.com.br Tue Feb 12 14:29:09 2002 From: pmothe at ig.com.br (=?iso-8859-1?Q?Pierre_Moth=E9_Esteves?=) Date: Tue, 12 Feb 2002 10:29:09 -0300 Subject: [CPMD-list] The MOVIE program Message-ID: <004501c1b3c9$41b899e0$d43697c8@ig> Dear CPMD Community, I would like to ask you about the MOVIE program, by J. Shelly as cited in the Manual (ref. 15). Nevertheless, I could not find any information about where or how to get this program. Do you know if it is possible to download or to ask for this program? Thanks in advance Best wishes Pierre M. Esteves -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020212/3c3268c6/attachment.html From a.wander at dl.ac.uk Wed Feb 13 16:02:59 2002 From: a.wander at dl.ac.uk (Adrian Wander) Date: Wed, 13 Feb 2002 15:02:59 +0000 Subject: [CPMD-list] Problems in Compilation on the Cray T3E Message-ID: <3C6A8023.684FB211@dl.ac.uk> Dear All I've tried to compile CPMD on the T3E in Manchester. This produces a number of warnings regarding unitialised variables. It also produces a loader error with DSYSV being undefined. This can be cured by adding -DSYSV=SSYSV to the CPPFLAGS in the makefile. Has any one else seen similar behaviour, or managed to compile on the Manchester machine? The full log from the compilation showing the warnings is appended. Regards Adrian Wander --------------------------Log file------------------ CMIC$ DOALL PRIVATE(IR,RHO,SMOO,DSMOO,TEXP,GRHO,SX,SC, ^ cf90-801 f90: WARNING GCOLD, File = ./gcener.f, Line = 405, Column = 7 Unsupported compiler directive. CMIC$ GUARD ^ cf90-801 f90: WARNING GCOLD, File = ./gcener.f, Line = 421, Column = 7 Unsupported compiler directive. CMIC$ END GUARD ^ cf90-801 f90: WARNING GCOLD, File = ./gcener.f, Line = 424, Column = 7 Unsupported compiler directive. CMIC$ DOALL PRIVATE(IR,RHO,RHOA,RHOB,SMOO,DSMOO,TEXP,GRHO,SX,SC, ^ cf90-801 f90: WARNING GCLSDOLD, File = ./gcener.f, Line = 459, Column = 7 Unsupported compiler directive. CMIC$ GUARD ^ cf90-801 f90: WARNING GCLSDOLD, File = ./gcener.f, Line = 484, Column = 7 Unsupported compiler directive. CMIC$ END GUARD ^ cf90-801 f90: WARNING GCLSDOLD, File = ./gcener.f, Line = 487, Column = 7 Unsupported compiler directive. Cray Fortran: Version 3.4.0.2 (u12f41p34061m32027a14) Cray Fortran: Mon Feb 11, 2002 13:49:05 Cray Fortran: Compile time: 4.1141 seconds Cray Fortran: 2887 source lines Cray Fortran: 0 errors, 6 warnings, 0 other messages, 0 ansi Cray Fortran: "explain cf90-message number" gives more information about each message NDFNLB=LDFD cf90-7212 f90: WARNING FNL_SET, File = ./fnlalloc.f, Line = 114 Variable "LDFD" is used before it is defined. Cray Fortran: Version 3.4.0.2 (u12f41p34061m32027a14) Cray Fortran: Mon Feb 11, 2002 13:53:15 Cray Fortran: Compile time: 0.7190 seconds Cray Fortran: 1586 source lines Cray Fortran: 0 errors, 1 warnings, 0 other messages, 0 ansi Cray Fortran: "explain cf90-message number" gives more information about each message DETOT=ETOT-ETOTO cf90-7212 f90: WARNING OHLR, File = ./ohlr.f, Line = 184 Variable "ETOTO" is used before it is defined. Cray Fortran: Version 3.4.0.2 (u12f41p34061m32027a14) Cray Fortran: Mon Feb 11, 2002 14:00:50 Cray Fortran: Compile time: 9.5251 seconds Cray Fortran: 3454 source lines Cray Fortran: 0 errors, 1 warnings, 0 other messages, 0 ansi Cray Fortran: "explain cf90-message number" gives more information about each message LVHK = MAX(NNR1,NHG*2)*NLSX+LTGC+LTINLC !GCENER cf90-7212 f90: WARNING GIVE_SCR_VHK, File = ./vhk.f, Line = 123 Variable "LTINLC" is used before it is defined. Cray Fortran: Version 3.4.0.2 (u12f41p34061m32027a14) Cray Fortran: Mon Feb 11, 2002 14:01:24 Cray Fortran: Compile time: 1.0671 seconds Cray Fortran: 1248 source lines Cray Fortran: 0 errors, 1 warnings, 0 other messages, 0 ansi Cray Fortran: "explain cf90-message number" gives more information about each message CALL MY_CONCAT(IPAD,IPADDR(0),LENGTH,GID) ^ cf90-1615 f90: WARNING MPP_ALLTOALL, File = ./my_para.f, Line = 641, Column = 22 Procedure "MY_CONCAT" is defined at line 407 (./my_para.f). Dummy argument "OUTMSG" is an array argument. This argument is scalar. Cray Fortran: Version 3.4.0.2 (u12f41p34061m32027a14) Cray Fortran: Mon Feb 11, 2002 14:03:07 Cray Fortran: Compile time: 3.5843 seconds Cray Fortran: 3346 source lines Cray Fortran: 0 errors, 1 warnings, 0 other messages, 0 ansi Cray Fortran: "explain cf90-message number" gives more information about each message okay=okay+4 cf90-7212 f90: WARNING CHECK_LLC, File = ./nmr_util_p.f, Line = 306 Variable "OKAY" is used before it is defined. call lambda(c0(1,is),LC,1d0,is,iB,psi,scr) ^ cf90-1279 f90: WARNING MODIFIED_ORTHOGONALITY_NEW, File = ./nmr_util_p.f, Line = 430, Column = 30 Procedure "LAMBDA" is defined at line 358 (./nmr_util_p.f). The type of this argument does not agree with dummy argument "COUT". ^ cf90-1279 f90: WARNING MODIFIED_ORTHOGONALITY_NEW, File = ./nmr_util_p.f, Line = 430, Column = 43 Procedure "LAMBDA" is defined at line 358 (./nmr_util_p.f). The type of this argument does not agree with dummy argument "PSI". ^ cf90-1279 f90: WARNING MODIFIED_ORTHOGONALITY_NEW, File = ./nmr_util_p.f, Line = 430, Column = 47 Procedure "LAMBDA" is defined at line 358 (./nmr_util_p.f). The type of this argument does not agree with dummy argument "SCR". & -1.d0,is,iB,psi,scr) ^ cf90-1279 f90: WARNING ADD_ADDITIONAL_HAMILTONIAN, File = ./nmr_util_p.f, Line = 475, Column = 24 Procedure "LAMBDA" is defined at line 358 (./nmr_util_p.f). The type of this argument does not agree with dummy argument "PSI". ^ cf90-1279 f90: WARNING ADD_ADDITIONAL_HAMILTONIAN, File = ./nmr_util_p.f, Line = 475, Column = 28 Procedure "LAMBDA" is defined at line 358 (./nmr_util_p.f). The type of this argument does not agree with dummy argument "SCR". call lambda(c0(1,is), c2(1,is),1.d0,is,iB,psi,scr) ^ cf90-1279 f90: WARNING ADD_ADDITIONAL_HAMILTONIAN, File = ./nmr_util_p.f, Line = 483, Column = 51 Procedure "LAMBDA" is defined at line 358 (./nmr_util_p.f). The type of this argument does not agree with dummy argument "PSI". ^ cf90-1279 f90: WARNING ADD_ADDITIONAL_HAMILTONIAN, File = ./nmr_util_p.f, Line = 483, Column = 55 Procedure "LAMBDA" is defined at line 358 (./nmr_util_p.f). The type of this argument does not agree with dummy argument "SCR". call fftTOg(psi,psi,scr,nhg,.true.) ^ cf90-1279 f90: WARNING PRINT_ORBITAL_DENSITIES, File = ./nmr_util_p.f, Line = 1725, Column = 25 Procedure "FFTTOG" is defined at line 1514 (./nmr_util_p.f). The type of this argument does not agree with dummy argument "DEST". Cray Fortran: Version 3.4.0.2 (u12f41p34061m32027a14) Cray Fortran: Mon Feb 11, 2002 14:29:10 Cray Fortran: Compile time: 13.0779 seconds Cray Fortran: 20661 source lines Cray Fortran: 0 errors, 9 warnings, 0 other messages, 0 ansi Cray Fortran: "explain cf90-message number" gives more information about each message shift = shift - 2d0*alat*shift_factor * eigr_dot(isa,psi) ^ cf90-1279 f90: WARNING CALC_SHIFT_VIA_CURRENT, File = ./nmr_shift_p.f, Line = 756, Column = 60 Procedure "EIGR_DOT" is defined at line 577 (./nmr_shift_p.f). The type of this argument does not agree with dummy argument "FUNC". Cray Fortran: Version 3.4.0.2 (u12f41p34061m32027a14) Cray Fortran: Mon Feb 11, 2002 14:29:30 Cray Fortran: Compile time: 5.1672 seconds Cray Fortran: 8647 source lines Cray Fortran: 0 errors, 1 warnings, 0 other messages, 0 ansi Cray Fortran: "explain cf90-message number" gives more information about each message CC-9 cc: WARNING File = ./sysdepend.c, Line = 3 A "/*" appears inside a comment. /* Revision 1.11.2.2 2002/01/09 19:01:41 cpmd ^ CC-9 cc: WARNING File = ./sysdepend.c, Line = 4 A "/*" appears inside a comment. /* Added the option for Intel Fortran Compiler (IFC) according to the ^ CC-9 cc: WARNING File = ./sysdepend.c, Line = 5 A "/*" appears inside a comment. /* instructions by Axel Kohlmeyer ^ CC-9 cc: WARNING File = ./sysdepend.c, Line = 6 A "/*" appears inside a comment. /* ^ CC-9 cc: WARNING File = ./sysdepend.c, Line = 7 A "/*" appears inside a comment. /* Revision 1.11.2.1 2001/11/12 14:58:57 tdeutsch ^ CC-9 cc: WARNING File = ./sysdepend.c, Line = 8 A "/*" appears inside a comment. /* Correct with lint and define PID_MAX if not defined. ^ CC-9 cc: WARNING File = ./sysdepend.c, Line = 9 A "/*" appears inside a comment. /* ^ From kenneth at geisshirt.dk Thu Feb 14 10:37:26 2002 From: kenneth at geisshirt.dk (Kenneth Geisshirt) Date: Thu, 14 Feb 2002 10:37:26 +0100 (CET) Subject: [CPMD-list] Demo? Message-ID: Hi CPMD hackers, March 2nd, 2002 I will attend LinuxForum 2002 which is the annual Linux conference in Denmark. The organizers have faith in me (still wondering why), so I'm going to give demos on an 8-way Compaq server, 4-way Dell and maybe a HP Blade server - all running Linux. I'm would love to show CPMD to the participants, but I don't have other than the GNU Fortran 77 compiler and the source code for CPMD. Is there someone out there having a binary to share? And some cool simulations? I'll be happy to public benchmarks from the runs I do that day. Kneth -- Kenneth Geisshirt, M.Sc., Ph.D. http://kenneth.geisshirt.dk Gr?ndals Parkvej 2A, 3. sal kenneth at geisshirt.dk DK-2720 Vanl?se +45 38 87 78 38 From hutter at oci.unizh.ch Fri Feb 15 10:58:24 2002 From: hutter at oci.unizh.ch (Juerg Hutter) Date: Fri, 15 Feb 2002 10:58:24 +0100 (MET) Subject: [CPMD-list] The MOVIE program In-Reply-To: <004501c1b3c9$41b899e0$d43697c8@ig> Message-ID: Hi originally CPMD was interfaced with the MOVIE program. However, most groups use now the generally available programms from other sources for post-processing: gopenmol molden molekel are the ones that come to my mind. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Tue, 12 Feb 2002, Pierre Moth? Esteves wrote: > > Dear CPMD Community, > > > I would like to ask you about the MOVIE program, by J. Shelly as cited in the Manual (ref. 15). Nevertheless, I could not find any information about where or how to get this program. Do you know if it is possible to download or to ask for this program? Thanks in advance > > Best wishes > > Pierre M. Esteves > From hutter at oci.unizh.ch Fri Feb 15 10:58:58 2002 From: hutter at oci.unizh.ch (Juerg Hutter) Date: Fri, 15 Feb 2002 10:58:58 +0100 (MET) Subject: [CPMD-list] the creation of pseudopotentia Message-ID: Hi you need a special atomic code to generate pseudopotentials. These codes are not part of the CPMD program. The file atomc.F is a subroutine within CPMD and cannot be used for pseudopotentials. There are many PP programs available on the net. They differ in complexity and functionality. Here an incomplete list www.abinit.org http://leopardi.cmp.sns.it/~giannozz/ www.cpmd.org (for Goedecker type PP) regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Tue, 12 Feb 2002, weizhuang wrote: > Hi, guys: > > I need help in the creation of pseudopotential. seems that I need a > executable "atomc.x", but I can only find "atomc.o", "atomc.F", "atomc.f " > after compiling. the only executable is "cpmd.x". could anybody tell me what > is the matter? I am using cpmd v.3.5 > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at oci.unizh.ch Fri Feb 15 13:11:22 2002 From: hutter at oci.unizh.ch (Juerg Hutter) Date: Fri, 15 Feb 2002 13:11:22 +0100 (MET) Subject: [CPMD-list] Problems in Compilation on the Cray T3E In-Reply-To: <3C6A8023.684FB211@dl.ac.uk> Message-ID: Hi thanks a lot for the information on the warnings. I had a look at them and there should not be any problems for the standard options in the code. Some of the warnings do concern experimental code and we will fix them in the next release of the code. greetings Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- From weiz at mail.rochester.edu Tue Feb 19 22:40:46 2002 From: weiz at mail.rochester.edu (weizhuang) Date: Tue, 19 Feb 2002 16:40:46 -0500 Subject: [CPMD-list] about pseudopotential creation Message-ID: <200202192131.g1JLVSmA5575138@mail.rochester.edu> Dear Friends: I wonder if I use the package "fhi98PP" to create a Pseudopotential file. is it compatible with cpmd? I mean, can I use it directly as the input pseudo potential file of cpmd? what about the pseudopotential file created by other PP packages. what package could create PP file which could be used directly in cpmd? thanks wei zhuang From dyyang at po.iams.sinica.edu.tw Wed Feb 20 07:57:00 2002 From: dyyang at po.iams.sinica.edu.tw (dyyang) Date: Wed, 20 Feb 2002 14:57:00 +0800 Subject: [CPMD-list] questions of CPMD Message-ID: <3C7348BC.3B23D537@po.iams.sinica.edu.tw> Hi We have tested CPMD with several questions. Is there anybody can help? 1. Does the input coordinates with Bohr unit? 2. Our Linux system has physical memory 2062240 kB and swap 4096524 kB. However, when we test run our molecule, the memory is limited upper to 1GB. How to fix this problem? 3. How can we open the DENSITY file? 4. Does CPMD support QM/MM, i.e. CPMD/CHARMM, interface? If yes, where can we find this interface? Best regards. Dah-Yen Yang From langel at mail.uni-greifswald.de Wed Feb 20 10:58:02 2002 From: langel at mail.uni-greifswald.de (Walter Langel) Date: Wed, 20 Feb 2002 10:58:02 +0100 Subject: [CPMD-list] about pseudopotential creation References: <200202192131.g1JLVSmA5575138@mail.rochester.edu> Message-ID: <3C73732A.7090309@mail.uni-greifswald.de> Hello Wei, you only have to recast the fhi98PP .cpi files, which are the standard output, into another format, since wavefunctions and potentials are arranged in a way which is not compatible with cpmd, but in principle the fhi pseudopotentials work fine with cpmd. I add a scilab-script which should show how to do this. It writes the POTENTIAL and WAVEFUNCTION blocks of the cpmd pseudopotential format. The first two blocks, ATOMS and INFO, can be copied from another pseudopotential and edited by hand. Regards Walter Langel weizhuang wrote: >Dear Friends: > >I wonder if I use the package "fhi98PP" to create a Pseudopotential file. is >it compatible with cpmd? I mean, can I use it directly as the input pseudo >potential file of cpmd? what about the pseudopotential file created by other >PP packages. what package could create PP file which could be used directly >in cpmd? > >thanks > >wei zhuang >_______________________________________________ >CPMD-list mailing list >CPMD-list at cpmd.org >http://www.cpmd.org/mailman/listinfo/cpmd-list > > -- 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 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: fhi.sce Url: http://cpmd.org/pipermail/cpmd-list/attachments/20020220/17a33507/attachment.cc From cur at zurich.ibm.com Wed Feb 20 11:22:06 2002 From: cur at zurich.ibm.com (Alessandro Curioni) Date: Wed, 20 Feb 2002 11:22:06 +0100 Subject: [CPMD-list] questions of CPMD Message-ID: Hi! >Hi >We have tested CPMD with several questions. Is there anybody can help? Yes.! >1. Does the input coordinates with Bohr unit? The default coordinates are Bohr. You can switch to Angstrom with the ANGSTROM keyword in the input (see manual) >2. Our Linux system has physical memory 2062240 kB and swap 4096524 kB. >However, when we test run our molecule, the memory is limited upper to >1GB. How to fix this problem? This is probably due to the maximum data segment allocated; the default value depend on your compiler/linker and the same is true for the flag needed to change it. Which compiler are you using ? >3. How can we open the DENSITY file? There are many utility that can open and convert the DENSITY files. We will make on available on the web soon. >4. Does CPMD support QM/MM, i.e. CPMD/CHARMM, interface? If yes, where >can we find this interface? Several QM/MM interfaces have been built on top of CPMD. CPMD V3.5 contain only the basic routines of the QM/MM implementations, because most of the QM/MM work is in progress and differents implementation are actually tested. If you are interested in the available interfaces, please contact the people that are working on this namely : Prof. Tavan group - University of Munich ( QM/MM interface with the EGO program, SPLAM link atoms and ESP electrostatic), Prof. Roetlisberger group - ETH Zurich ( QM/MM interface with Gromos, pseudo link atom + full electrostatic), Dr. W. Andreoni group - IBM Zurich (QM/MM interface with Gromos, pseudo link atom + M-RESP electrostatic + reaction field correction). >Best regards. >Dah-Yen Yang 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 aps at cscs.ch Tue Feb 19 22:54:58 2002 From: aps at cscs.ch (Ari P Seitsonen (CSCS)) Date: Tue, 19 Feb 2002 22:54:58 +0100 (CET) Subject: [CPMD-list] about pseudopotential creation In-Reply-To: <200202192131.g1JLVSmA5575138@mail.rochester.edu> Message-ID: I have modified the script 'psgen' in order to generate the pseudo potential also in the format understood by CPMD; however I would be happy if someone would still check it (the four \pi's) by comparing to another code. I did it once, and I _hope_ that this was the final i.e. most current version. :*) On Tue, 19 Feb 2002, weizhuang wrote: > Dear Friends: > > I wonder if I use the package "fhi98PP" to create a Pseudopotential file. is > it compatible with cpmd? I mean, can I use it directly as the input pseudo > potential file of cpmd? what about the pseudopotential file created by other > PP packages. what package could create PP file which could be used directly > in cpmd? > > thanks > > wei zhuang > _______________________________________________ > 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 -------------- next part -------------- #!/bin/csh -f onintr INTERRUPT # #------ Generate pseudopotentials with fhipp code ----- # # "psgen -h" returns a list of options # set WORKDIR = `pwd` # working directory set SOURCES = . # path to package's resources set PROGRAM = ${SOURCES}/src/fhipp.x # executable set GRAPHIC = ${SOURCES}/lib/Xvgr # path for xvgr graphics header files set RESULTS = Tmp # directory where we save results set EDITOR = vi set scratch = ".scratch" # scratchfile set marker = $$.marker # used for listing # #--------------------------------------------------------- # aliases alias testinput 'set INFO = \!:1; if (! -e \!:1 || -z \!:1) goto \!:2' # default unset ONLYATOM #do all-electron and generate pseudopotentials unset DEBUG #remove all scratch files unset NONRELATIVISTIC #relativistic all-electron calculation unset NO_XVGR #grapics output in xmgr set OUT = 'ncpp' #prefix for outputfiles set INI = 'ncpp.ini' unset SAVE #do not save results in $HARDCOPY set OPTIONT = (x x x x x) set OPTIONR = (x x x x) # input if ($#argv == 0) goto SHORTHELP while ($#argv) switch ($1) case [-][hH]* : goto LONGHELP shift; breaksw case [a-zA-Z0-9]* : set INI = $1 shift; breaksw case -xv : set NO_XVGR shift; breaksw case -ao : set ONLYATOM shift; breaksw case -o : set OUT = $2 shift; shift; breaksw case -xc : set xctyp = $2 shift; shift; breaksw case -rc : set rcore = $2 shift; shift; breaksw case -r : set NONRELATIVISTIC shift; breaksw case -e : unset VIEW set EDIT shift; breaksw case -v : set VIEW shift; breaksw case [-][r][spdf] : switch ($2) case [0-9][.][0-9]* : set VALUE = $2; breaksw default : set VALUE = "0.0"; breaksw endsw switch ($1) case -rs: set OPTIONR[1] = ${VALUE}; breaksw case -rp: set OPTIONR[2] = ${VALUE}; breaksw case -rd: set OPTIONR[3] = ${VALUE}; breaksw case -rf: set OPTIONR[4] = ${VALUE}; breaksw endsw shift; shift; breaksw case [-][t][spdf] : switch ($2) case [tThH] : set VALUE = $2; breaksw default : set VALUE = "h"; breaksw endsw switch ($1) case -ts: set OPTIONT[1] = ${VALUE}; breaksw case -tp: set OPTIONT[2] = ${VALUE}; breaksw case -td: set OPTIONT[3] = ${VALUE}; breaksw case -tf: set OPTIONT[4] = ${VALUE}; breaksw endsw shift; shift; breaksw case -T : set VALUE = `echo $2 | awk '{print substr($1,1,1)}'` switch (${VALUE}) case [tThH]: set OPTIONT[5] = ${VALUE} ; shift; breaksw default : set OPTIONT[5] = "t"; breaksw endsw shift; breaksw case -s : set SAVE shift; breaksw case -ip : set INITIAL_POTENTIAL = $2 shift; shift; breaksw case -g : set DEBUG shift; breaksw case -fc : set CORE_FILE = $2 shift; shift; breaksw default : echo $0 - option $1 undefined shift; breaksw endsw end testinput $INI NOINPUT #cleanup rm -f fort.* >& $scratch ; date >! $marker # prepare input set default_input = ${INI} testinput ${default_input} NOINPUT set INI = ${default_input} # modifying input file from command line set IWC = `awk 'NR == 1 {print $2+$3+2}' $INI` if( ${OPTIONT[5]} !~ "x" ) then awk '{if (NR == '"${IWC}"') {print $1,"'${OPTIONT[5]}'"} else {print $0}}' $INI >! $scratch mv $scratch $INI endif set PP_TYPE = `awk < $INI 'NR == '"${IWC}"' {print $2}' ` if ( $?xctyp ) then awk 'NR == 1 {print $1,$2,$3,"'${xctyp}'",$5,$6,$7,$8,$9};\ NR > 1 {print $0}' ${INI} > $scratch mv $scratch ${INI} endif if ( $?rcore ) then awk 'NR == 1 {print $1,$2,$3,$4,"'${rcore}'",$6,$7,$8,$9};\ NR > 1 {print $0}' ${INI} > $scratch mv $scratch ${INI} endif @ N = 1 while ( $N < 5 ) if ( ${OPTIONT[$N]} !~ "x" ) then (head -${IWC} $INI ; \ awk 'BEGIN {g = 0; l = '$N'-1} \ NR > '"${IWC}"' {if ($1 == l) {print l,$2,$3,"'${OPTIONT[$N]}'"; g = 1} else {print $0} } \ END {if (g == 0) {print l,"0.0","0.0","'${OPTIONT[$N]}'"}}' $INI ) >! $scratch mv $scratch $INI endif if ( ${OPTIONR[$N]} !~ "x" ) then (head -${IWC} $INI ; \ awk 'BEGIN {g = 0; l = '$N'-1} \ NR > '"${IWC}"' {if ($1 == l) {print l,"'${OPTIONR[$N]}'",$3,$4; g = 1} else {print $0} } \ END {if (g == 0) {print l,"'${OPTIONR[$N]}'","0.0","'${PP_TYPE}'"}}' $INI ) >! $scratch mv $scratch $INI endif @ N++ end if ( $?CORE_FILE ) then testinput $CORE_FILE NOINPUT cp $CORE_FILE fort.18 endif if ( $?INITIAL_POTENTIAL ) then testinput $INITIAL_POTENTIAL NOINPUT cp $INITIAL_POTENTIAL fort.36 endif set LINE_1 = (.t. .f. : TDOPSP TNRL) if ( $?ONLYATOM ) set LINE_1[1] = ".f." if ( $?NONRELATIVISTIC ) set LINE_1[2] = ".t." echo $LINE_1 >! fort.20 if ( $?EDIT ) $EDITOR ${INI} if ( $?VIEW ) less ${INI} cp ${INI} fort.22 if ( -e $PROGRAM ) then ${PROGRAM} else echo $0 "- executable not found:" $PROGRAM goto INTERRUPT endif onintr - cp ${INI} $$.input rm -f ${OUT}.* xv.${OUT}.* mv $$.input ${INI} onintr INTERRUPT # output set DAT = ${OUT}.dat set STAMP = "$OUT `date +'"'%T %h %d %Y'"'` $USER" (echo "#info $0 $STAMP"; cat fort.23) >! ${DAT} if(-e fort.19) cp fort.19 ${OUT}.fc if(-e fort.24) fgrep -v "p " fort.24 >>! ${DAT} if(-e fort.37) cp fort.37 ${OUT}.aep # ======= begin graphics ======== if(! $?NO_XVGR ) then ( cat ${GRAPHIC}/xvgr.ae_wfct ;\ echo "@ title" '"'"Radial Wavefunctions \s\S"${STAMP}"\N\N"'"' ;\ awk < fort.38 'BEGIN {g = 0} \ {if ($1 == "#" && NR == 1) {print "@ legend string",g,"\""$2"\"";g++} \ else if ($1 == "#") {print "@ legend string",g,"\""$2"\"";print "&";g++}\ else {printf "%12.6e %12.6e \n", $1,$2} }' \ ) >! xv.${OUT}.ae_wfct if ( $?ONLYATOM ) goto TERMINATE ( cat ${GRAPHIC}/xvgr.pspot_i ;\ echo "@ title" '"'"Ionic Pseudopotentials \s\S"${STAMP}"\N\N"'"' ;\ grep xvgr ${DAT} | \ awk '{printf "@ world ymin %4.2f\n",$(NF-2); printf "@ world ymax %4.2f\n",$(NF-1) \ printf "@ yaxis tick major %4.2f\n",$NF; printf "@ yaxis tick minor %4.2f\n", $NF/4}' \ ) >! xv.${OUT}.pspot_i foreach PSEUDOPOTENTIAL ( fort.4[0-4] ) awk < $PSEUDOPOTENTIAL '{if (NR == 1) {print "@ legend string",$4,"\""$4,"\\6r\\sc\\N\\4="substr($5,1,5),"\""} \ else {printf "%12.6e %12.6e \n",$2,$4}} END {print "&"}' >>! xv.${OUT}.pspot_i # else {printf "%20.12e %20.12e \n",$2,$4}} END {print "&"}' >>! xv.${OUT}.pspot_i end ( cat ${GRAPHIC}/xvgr.pspot_i ;\ echo "@ title" '"'"Screened Pseudopotentials \s\S"${STAMP}"\N\N"'"' ;\ grep xvgr ${DAT} | \ awk '{printf "@ world ymin %4.2f\n",$(NF-2); printf "@ world ymax %4.2f\n",$(NF-1) \ printf "@ yaxis tick major %4.2f\n",$NF; printf "@ yaxis tick minor %4.2f\n", $NF/4}' \ ) >! xv.${OUT}.pspot_s foreach PSEUDOPOTENTIAL ( fort.4[5-9] ) awk < $PSEUDOPOTENTIAL '{if (NR == 1) {print "@ legend string",$4,"\""$4,"\\6r\\sc\\N\\4="substr($5,1,5),"\""} \ else {printf "%12.6e %12.6e \n",$1,$2}} END {print "&"}' >>! xv.${OUT}.pspot_s end ( cat ${GRAPHIC}/xvgr.ps_ae_wfct ;\ echo "@ title" '"'"Pseudo vs All-Electron Wavefunctions \s\S"${STAMP}"\N\N"'"'; \ awk < fort.39 'BEGIN {g = 0}; {if ($1 == "##" ) \ {{if (g > 0) print "&"} print "@ legend string",g,"\""$2,"\\6r\\sc\\N\\4="$NF,"\"";g++} \ else if ($1 == "#") {print "&"; print "@ legend string",g,"\""$2,"\"";g++} \ else {printf "%12.6e %12.6e \n", $1,$2}}' \ )>! xv.${OUT}.ps_ae_wfct ( cat ${GRAPHIC}/xvgr.density ;\ echo "@ title" '"'"Radial Densities \s\S"${STAMP}"\N\N"'"' ; \ awk 'BEGIN {print "@ legend string 0 \"pseudo valence\""} \ {printf "%12.6e %12.6e \n", $1,$2*$1^2} END {print "&"}' fort.25 ; \ if(-e fort.19) \ awk 'BEGIN {print "@ legend string 1 \"true core\""} \ NR > 1 {printf "%12.6e %12.6e \n", $1,$2*$1^2} END {print "&"}' fort.19 ; \ if(-e fort.27) \ awk 'BEGIN {print "@ legend string 2 \"model core\""} \ {printf "%12.6e %12.6e \n", $1,$2*$1^2} END {print "&"}' fort.27 \ ) >! xv.${OUT}.density ( cat ${GRAPHIC}/xvgr.unscreen ; \ awk < fort.28 'BEGIN {print "@WITH G0"; print "@G0 ON"} {printf "%12.6e %12.6e \n",$1,-$4} END {print "&"}' ; \ awk < fort.28 '{printf "%12.6e %12.6e \n",$1,$5} END {print "&"; print "@WITH G1"; print "@G1 ON"}' ; \ echo "@ title" '"'"Unscreening potentials \s\S"${STAMP}"\N\N"'"' ; \ awk < fort.28 '{print $1,$2} END {print "&"}' ; \ awk < fort.28 '{print $1,$3} END {print "&"}' \ ) >> xv.${OUT}.unscreen endif # ======= done with graphics ======== if ( $?ONLYATOM ) goto TERMINATE # ======= fhi94md output ====== # VALENCE total valence charge NOOFPOT number of pseudopotentials present echo `head -1 fort.40 | awk '{print $NF}'` " " `ls fort.4[0-4] | wc -l` >! ${OUT}.cpi cat << unused_fit_parameters >>! ${OUT}.cpi 0.0000 0.0000 0.0000 0.0000 0.0000 .00e+00 .00e+00 0.0000 .00e+00 .00e+00 0.0000 .00e+00 .00e+00 0.0000 .00e+00 .00e+00 0.0000 .00e+00 .00e+00 0.0000 .00e+00 .00e+00 0.0000 .00e+00 .00e+00 0.0000 .00e+00 .00e+00 0.0000 .00e+00 .00e+00 unused_fit_parameters foreach PSEUDOPOTENTIAL ( fort.4[0-4] ) (head -1 $PSEUDOPOTENTIAL | awk '{print $2," "$3}' ;\ tail +2 $PSEUDOPOTENTIAL ) >>! ${OUT}.cpi end if (-e fort.27) cat fort.27 >>! ${OUT}.cpi # append pseudocore # ======= done with fhi94md output ====== ##### output for CPMD set nmesh=`head -1 fort.40 | awk '{print $2}'` ### Atom echo '&ATOM' >> ${OUT}.pp cat > awkfile << EOF BEGIN { getline <"${INI}" printf " Z = %3d\n", \$1 xc = \$4 getline <"fort.40" printf " ZV = %9.5lf\n", \$NF # 3 = CA/PZ 4 = GGA91 5 = BP 6 = PBE 8 = CA/PW 9 = BLYP if ( xc == 3 ) { exch = 0; corr = 0 } if ( xc == 4 ) { exch = 2; corr = 3 } if ( xc == 5 ) { exch = 1; corr = 1 } if ( xc == 6 ) { exch = 3; corr = 4 } if ( xc == 8 ) { exch = 0; corr = 0 } if ( xc == 9 ) { exch = 1; corr = 2 } printf " XC = %1d%1d 0.666667\n", exch, corr } EOF awk -f awkfile /dev/null >> ${OUT}.pp echo " TYPE = NORMCONSERVING NUMERIC" >> ${OUT}.pp echo '&END' >> ${OUT}.pp ### Info echo '&INFO' >> ${OUT}.pp cat ${INI} >> ${OUT}.pp echo '&END' >> ${OUT}.pp ### Potential echo '&POTENTIAL' >> ${OUT}.pp echo "LOGSCALE" >> ${OUT}.pp cat > awkfile << EOF BEGIN { lines = ${nmesh}; print lines; getline <"fort.40"; getline <"fort.41"; getline <"fort.42"; getline <"fort.43"; getline <"fort.44"; for ( line = 0; line < lines; line++ ) { getline <"fort.40"; r = \$2; v_s = \$4 getline <"fort.41"; v_p = \$4; \$4 = "" getline <"fort.42"; v_d = \$4; \$4 = "" getline <"fort.43"; v_f = \$4; \$4 = "" getline <"fort.44"; v_g = \$4; \$4 = "" print r, v_s, v_p, v_d, v_f, v_g } } EOF awk -f awkfile /dev/null >> ${OUT}.pp echo '&END' >> ${OUT}.pp ### Wave function echo '&WAVEFUNCTION' >> ${OUT}.pp cat > awkfile << EOF BEGIN { sc = 1.0 / sqrt ( 12.566370614359172954 ) lines = ${nmesh}; print lines; getline <"fort.40"; getline <"fort.41"; getline <"fort.42"; getline <"fort.43"; getline <"fort.44"; for ( line = 0; line < lines; line++ ) { getline <"fort.40"; r = \$2; v_s = \$3 getline <"fort.41"; v_p = \$3; \$3 = "" getline <"fort.42"; v_d = \$3; \$3 = "" getline <"fort.43"; v_f = \$3; \$3 = "" getline <"fort.44"; v_g = \$3; \$3 = "" print r, v_s * sc, v_p * sc, v_d * sc, v_f * sc, v_g * sc } } EOF awk -f awkfile /dev/null >> ${OUT}.pp echo '&END' >> ${OUT}.pp ### NLCC if ( -e fort.27 ) then echo '&NLCC' >> ${OUT}.pp echo 'NUMERICAL' >> ${OUT}.pp cat > awkfile << EOF BEGIN { lines = ${nmesh}; print lines; for ( line = 0; line < lines; line++ ) { getline <"fort.27"; r = \$1; dens = \$2 printf "%15.10lf%25.10lf\n", r, dens / 12.566370614359172954 } } EOF awk -f awkfile /dev/null >> ${OUT}.pp rm -f awkfile #echo ${nmesh} >> ${OUT}.pp #cat fort.27 >> ${OUT}.pp echo '&END' >> ${OUT}.pp endif ##### end of output for CPMD # hardcopies if( $?SAVE ) then if(! -d ${RESULTS}) mkdir ${RESULTS} echo "psgen - copying results to" ${RESULTS} foreach i ( *${OUT}* ) cp -i $i ${RESULTS} end pushd ${RESULTS} >& $scratch ; chmod u-w *${OUT}* ; popd >& ${WORKDIR}/$scratch endif TERMINATE: rm -f $scratch if (! $?DEBUG) rm -f fort.* echo $0 - done: output ls -t -1 | awk '{if ($0 ~ /'$marker'/) {exit} else {print $0}'} | sort rm -f $marker exit 0 INTERRUPT: rm -f fort.* $scratch echo $0 - quit: output ls -t -1 | awk '{if ($0 ~ /'$marker'/) {exit 0} else {print $0}'} rm -f $marker exit 1 NOINPUT: echo $0 - missing input file $INFO rm -f $marker exit 0 SHORTHELP: cat << SYNTAX $0 -h -g -xv -e -v -s -ao [-xc Number] [-rc Number] [-r(spdf) Number] [-t(spdf) String] [-T String] [-fc File] [-ip File] [-o String] File SYNTAX exit 0 LONGHELP: less << INFO program $0 tool generate Hamann or Troullier-Martins pseudopotentials options -h help -g do not cleanup (debugging) -xv skip graphics output -e edit input file -v display input file -s take a hardcopy of the output -ao perform all-electron calculation only -xc number exchange(X)-correlation(C) type 1 LDA Wigner 2 LDA Hedin/Lundqvist 3 LDA Ceperley/Alder Perdew/Zunger (1980) 4 GGA Perdew/Wang (1991) 5 GGA Becke (1988) X, Perdew (1986) C 6 GGA Perdew/Burke/Ernzerhof (1996) 7 LDA like 8 + MacDonald/Vosko relativistic correction 8 LDA Ceperley/Alder Perdew/Wang (1991) 9 GGA Becke (1988) X, Lee/Yang/Parr (1988) C 10 GGA Perdew/Wang (1991) X, Lee/Yang/Parr (1988) C -rc number cutoff radius for pseudocore = 0 linearized core-valence XC, no core > 0 nonlinear core-valence XC, pseudo core inside cutoff radius -rs number cutoff radius for s-like pseudopotential, pdf channels likewise -ts string pseudopotential type for s-like pseudopotential, pdf channel likewise h Hamann scheme t Troullier-Martins scheme -T string default pseudopotential type, see above -fc file frozen core calculation, core density read from file -ip file initial potential read from file -o string identifying prefix for output files input file initialization file, generic format 14.0 3 2 8 0.0 : z nc nv iexc rnlc 1 0 2.0 : n l f 2 0 2.0 2 1 6.0 3 0 2.0 3 1 2.0 2 h : lmax s_pp_def 1 1.5 0.0 h : l rct et s_pp_type (optional) author Martin Fuchs Abteilung Theorie Fritz-Haber-Institut der MPG internet fuchs at fhi-berlin.mpg.de INFO exit 0 From s.meloni at caspur.it Fri Feb 22 16:19:37 2002 From: s.meloni at caspur.it (simonem) Date: Fri, 22 Feb 2002 16:19:37 +0100 Subject: [CPMD-list] Convergence on PC Message-ID: <3C766189.2020606@caspur.it> Dear CMPDer, I just installed V35 on my athlon pc using the default make file, that is the one created by Configure. I was testing the installation and the performances with a very simple calculation: geometry optimizaton of an H2O molecule, here is my input file: &SYSTEM SYMMETRY 1 CELL 15.0 1.0 1.0 0.0 0.0 0.0 CUTOFF 70. &END &ATOMS *O_SG_BLYP LMAX=P 1 0. 0. 0. *H_SG_BLYP KLEINMAN-BYLANDER LMAX=S 2 1.1299 1.4564 0.0000 1.1299 -1.4564 0.0000 &END &DFT NEWCODE FUNCTIONAL BLYP &END &CPMD OPTIMIZE GEOMETRY RESTART WAVEFUNCTION COORDINATES &END V35 miss convergy of ionic position while V33 fail also the convergency of WF. I never experienced this problem using other machines (IBM, COMPAQ, CRAY). I tested several optimization techniques (GDIIS and CG for ions and diis, pcg) but the results were always the same. Does anybody have some suggestion? 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 ilia at techunix.technion.ac.il Fri Feb 22 19:50:55 2002 From: ilia at techunix.technion.ac.il (Ilijah V. Kaganov) Date: Fri, 22 Feb 2002 19:50:55 Subject: [CPMD-list] (no subject) Message-ID: <3.0.6.16.20020222195055.46875e30@techunix.technion.ac.il> Hello! The CPMD demands RESTART file when started with MOLECULAR DYNAMICS BO option. It is not the case when MOLECULAR DYNAMICS CP option is used. What's wrong here? Yours sincerely, Ilijah V. Kaganov From hutter at oci.unizh.ch Sat Feb 23 13:45:24 2002 From: hutter at oci.unizh.ch (Juerg Hutter) Date: Sat, 23 Feb 2002 13:45:24 +0100 (MET) Subject: [CPMD-list] (no subject) In-Reply-To: <3.0.6.16.20020222195055.46875e30@techunix.technion.ac.il> Message-ID: Hi nothing is wrong here. The issue arises because the CP and BO option to MD result in the execution of totally different parts of the program. In the CP part the possibility to start from scratch was not excluded. However, it only makes sense to do so for very special purposes. On the other hand such starts of simulations would make sense for the BO dynamics but were excluded in the program. It is strongly recommended to start a new simulation always with an optimisation of the wavefunction and only then restart for MD. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Fri, 22 Feb 2002, Ilijah V. Kaganov wrote: > Hello! > The CPMD demands RESTART file when started with MOLECULAR DYNAMICS BO option. > It is not the case when MOLECULAR DYNAMICS CP option is used. What's wrong > here? > > Yours sincerely, Ilijah V. Kaganov > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From sahu at matter3.ph.utexas.edu Mon Feb 25 00:32:34 2002 From: sahu at matter3.ph.utexas.edu (Dr. B.R.Sahu) Date: Sun, 24 Feb 2002 17:32:34 -0600 (CST) Subject: [CPMD-list] hello Message-ID: hi all I am compiling cpmdv3.5 on CRAY T3E. I got the following error: WARNING The symbol `DSYSV' referenced in relocatable object `gndstate_p.o:GENERATE_GAUSSIAN' is not defined. cld-431 cld: WARNING The resulting output file `./cpmd.x' is not executable because of previous WARNING messages. any suggestions? best sahu From hutter at oci.unizh.ch Mon Feb 25 09:34:55 2002 From: hutter at oci.unizh.ch (Juerg Hutter) Date: Mon, 25 Feb 2002 09:34:55 +0100 (MET) Subject: [CPMD-list] hello In-Reply-To: Message-ID: Hi you have to add a -DDSYSV=SSYSV into the CPPFLAGS block in the Makefile. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Sun, 24 Feb 2002, Dr. B.R.Sahu wrote: > > hi all > > I am compiling cpmdv3.5 on CRAY T3E. I got the following error: > > WARNING > The symbol `DSYSV' referenced in relocatable object > `gndstate_p.o:GENERATE_GAUSSIAN' is not defined. > cld-431 cld: WARNING > The resulting output file `./cpmd.x' is not executable because of > previous WARNING messages. > > > any suggestions? > > best > sahu > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From mzapalow at mitr.p.lodz.pl Mon Feb 25 12:12:46 2002 From: mzapalow at mitr.p.lodz.pl (Michal Zapalowski) Date: Mon, 25 Feb 2002 12:12:46 +0100 Subject: [CPMD-list] Compilation error on SGI Message-ID: <084f01c1bdee$75370250$28d633d4@MITRMZ> Dear Readers, I've tried to compile v35 on SGI Power Challenge with MIPSPro F90. Unfortunetely, the compiler returned following error: ----- f90 -mips4 -64 -c -O3 -nocpp -r8 ./wr30wfn.f -o ./wr30wfn.o ZI=ABS(IMAG(C0(1,I))) ^ 90-232 mfef90: ERROR PUTCONJ, File = ./wr30wfn.f, Line = 733, Column = 18 IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for function "IMAG". ----- Any ideas how to fix it will be very appreciated... Sincerely, Michal --- Michal Zapalowski, MSc IARC, Technical University of Lodz 93-590 Lodz, Poland (+48 42) 631-31-77 mzapalow at mitr.p.lodz.pl From hutter at oci.unizh.ch Mon Feb 25 13:28:44 2002 From: hutter at oci.unizh.ch (Juerg Hutter) Date: Mon, 25 Feb 2002 13:28:44 +0100 (MET) Subject: [CPMD-list] Compilation error on SGI In-Reply-To: <084f01c1bdee$75370250$28d633d4@MITRMZ> Message-ID: Hi I'm using the same compiler and don't have this problem. Do you have an older version? Anyway, replacing IMAG by DIMAG should fix the problem. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Mon, 25 Feb 2002, Michal Zapalowski wrote: > Dear Readers, > > I've tried to compile v35 on SGI Power Challenge with MIPSPro F90. > Unfortunetely, the compiler returned following error: > > ----- > f90 -mips4 -64 -c -O3 -nocpp -r8 ./wr30wfn.f -o ./wr30wfn.o > > > ZI=ABS(IMAG(C0(1,I))) > ^ > 90-232 mfef90: ERROR PUTCONJ, File = ./wr30wfn.f, Line = 733, Column = 18 > IMPLICIT NONE is specified in the local scope, therefore an explicit type > must be specified for function "IMAG". > ----- > > Any ideas how to fix it will be very appreciated... > > Sincerely, Michal > > --- > Michal Zapalowski, MSc > IARC, Technical University of Lodz > 93-590 Lodz, Poland > (+48 42) 631-31-77 > mzapalow at mitr.p.lodz.pl > > > > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From huang_d at gold.cchem.berkeley.edu Tue Feb 26 07:23:00 2002 From: huang_d at gold.cchem.berkeley.edu (David Mark Huang) Date: Mon, 25 Feb 2002 22:23:00 -0800 (PST) Subject: [CPMD-list] DIPOLE file Message-ID: I was wondering what columns 2 to 7 in the DIPOLE file correspond to? When I run CPMD v.3.5.1, columns 2 to 4 come out identical to columns 5 to 7 respectively. when I run with CPMD v.3.4.1, the columns come out different. Is there an explanation for this? Thanks David Huang Chandler Group Department of Chemistry University of California at Berkeley From hutter at oci.unizh.ch Tue Feb 26 09:29:37 2002 From: hutter at oci.unizh.ch (Juerg Hutter) Date: Tue, 26 Feb 2002 09:29:37 +0100 (MET) Subject: [CPMD-list] DIPOLE file In-Reply-To: Message-ID: Hi columns 2 to 4 in the DIPOLE file are the electronic contribution to the dipole moment, columns 5 to 7 are the total (electronic + ionic) dipole moment. All dipole moments are divided by the volume of the box. In version 3.5.1 we have changed the reference point of the calculation. Now the ref. point is chosen such that the ionic contribution is zero and the electronic contribution minimal (=total dipole). This avoids a problem that occasionaly was seen in older versions. The electronic dipole is calculated modulo(2Pi/L). Now if the electronic dipole became to big, because the ionic contribution was big (bad choice of reference point) the total dipole made jumps of 2Pi. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4211 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Mon, 25 Feb 2002, David Mark Huang wrote: > I was wondering what columns 2 to 7 in the DIPOLE file correspond to? When > I run CPMD v.3.5.1, columns 2 to 4 come out identical to columns 5 to 7 > respectively. when I run with CPMD v.3.4.1, the columns come out > different. Is there an explanation for this? > > Thanks > > David Huang > Chandler Group > Department of Chemistry > University of California at Berkeley > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From langel at mail.uni-greifswald.de Thu Feb 28 19:17:06 2002 From: langel at mail.uni-greifswald.de (Walter Langel) Date: Thu, 28 Feb 2002 19:17:06 +0100 Subject: [CPMD-list] PhD vacancy Message-ID: <3C7E7422.2070001@mail.uni-greifswald.de> Hi, I am not sure that this list is for job vacancies, I will just try and would be glad if you could pass this message to the community: ________________________________________________________________________________ PhD Position Institute for Chemistry and Biochemistry University of Greifswald Position for PhD studies in biochemistry (24 months at the BAT IIa/2 level) to work with the Car-Parrinello method [1-4] and classical molecular dynamics simulation on the interaction of amino acids with titanium oxide surfaces [5]. The project is supported by the Deutsche Forschungsgemeinschaft (DFG). This position would suit someone with a chemical or biochemical background having strong interests in computational methods such as quantum chemistry and molecular dynamics. Some previous experiences with program packages on UNIX(Linux)-machines would be desirable but is not essential. Greifswald university has a history more than 500 years old. Today numerous institutions including the Institute for Chemistry and Biochemistry focus on life sciences. Please contact or submit an application to: Prof. Dr. Walter Langel, Institute for Chemistry and Biochemistry, University of Greifswald, Soldmannstra?e 23, 17489 Greifswald, Germany Tel +49 3834 86 4423 Fax +49 3834 86 4413 E-mail: langel at uni-greifswald.de http://www.chemie.uni-greifswald.de/~plasma [1] W.Langel and M.Parrinello, J.Chem.Phys. 103,3240(1995) [2] W.Langel and M.Parrinello, Phys.Rev.Lett.73,504-507(1994) [3] W.Langel, J.Mol.Struct.349,69(1995) [4] W.Langel, Chem.Phys.Lett. 259,7(1996) [5] W. Langel, Surf. Sci. 496,141-150(2001), Greifswald, 02/27/ 2002 _____________________________________________________________________________________ -- 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