From asabir at nemo.physics.ncsu.edu Mon Apr 1 20:00:02 2002 From: asabir at nemo.physics.ncsu.edu (sabir) Date: Mon, 01 Apr 2002 13:00:02 -0500 Subject: [CPMD-list] Need Help Message-ID: <3CA8A022.E9337BD8@nemo.physics.ncsu.edu> 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 From phd15 at keele.ac.uk Thu Apr 4 17:33:36 2002 From: phd15 at keele.ac.uk (Zak) Date: Thu, 4 Apr 2002 16:33:36 +0100 Subject: [CPMD-list] program grid.x Message-ID: <001701c1dbee$1672b480$ae5005a0@phys.keele.ac.uk> Dear all, Can anyone let me know where I might be able to aquire Vanderbilt PP's for Carbon and Hydrogen, also I don't seem to have the program grid.x mentioned at the beginning of chapter 7 in the source code. Is there anywhere i can get this program ? Any assistance will be greatly appreciated. Zak -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020404/66959601/attachment.html From troya at chem.northwestern.edu Thu Apr 4 18:03:38 2002 From: troya at chem.northwestern.edu (Diego Troya) Date: Thu, 4 Apr 2002 10:03:38 -0600 (CST) Subject: [CPMD-list] Velocities in CPMD Message-ID: Hi all, I've been recently trying to use the VELOCITIES keyword in a molecular dynamics run. I want to collide fast atoms against surfaces. Despite the code seems to read the input velocities properly, when the run starts the initial velocities are always the same (apparently coming from a thermal distribution), no matter what is the velocity you specify for the incoming atom. I'm not using QUENCH IONS, so I don't understand why the input initial velocities are not considered in the calculation. Has anybody any experience with this? Thanks in advance, Diego. Dr. Diego Troya Chemistry Department, Northwestern University 2145 Sheridan Road, 60208 Evanston, Il. Phone: 847 491 7189 Fax: 847 491 7713 From hutter at pci.unizh.ch Fri Apr 5 09:41:14 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Fri, 5 Apr 2002 09:41:14 +0200 (MEST) Subject: [CPMD-list] Velocities in CPMD In-Reply-To: Message-ID: Hi there is no straightforward way in CPMD to achieve what you want. I suggest to follow this procedure. 1) Run a single step of MD with the following set up MOLELCULAR DYNAMICS MAXSTEP 1 RESTART WAVEFUNCTION COORDINATES TEMPERATURE 300 <- or whatever your surface should be This generates RESTART and GEOMETRY files. Now edit the GEOMETRY file to change the velocities of the particles according to your experiment. Now restart the MD with the options MOLELCULAR DYNAMICS MAXSTEP 1000 RESTART WAVEFUNCTION COORDINATES VELOCITIES GEOFILE QUENCH ELECTRONS The effect of this is: IONIC coordinates are read from GEOMETRY IONIC velocities are read from GEOMETRY ELECTRON wavefunctions and velocities are read from RESTART ELECTRON velocities are set to zero hope this helps 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, 4 Apr 2002, Diego Troya wrote: > Hi all, > > I've been recently trying to use the VELOCITIES keyword in a molecular > dynamics run. I want to collide fast atoms against surfaces. Despite the > code seems to read the input velocities properly, when the run starts the > initial velocities are always the same (apparently coming from a > thermal distribution), no matter what is the velocity you specify for the > incoming atom. I'm not using QUENCH IONS, so I don't understand why the > input initial velocities are not considered in the calculation. > > Has anybody any experience with this? > > Thanks in advance, > Diego. > > Dr. Diego Troya > Chemistry Department, Northwestern University > 2145 Sheridan Road, 60208 Evanston, Il. > Phone: 847 491 7189 > Fax: 847 491 7713 > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From M.A.Zwijnenburg at tnw.tudelft.nl Fri Apr 5 17:37:45 2002 From: M.A.Zwijnenburg at tnw.tudelft.nl (Martijn Zwijnenburg) Date: Fri, 05 Apr 2002 17:37:45 +0200 Subject: [CPMD-list] TRAJECTORY Message-ID: <3CADE0E2.12748.1A79A38F@localhost> Hi, I've understood that it's in principle possible to visualize the TRAJECTORY file ouputted by CPMD by standard packages like for instance Gopenmol. Now I was wondering if somebody has some scripts to convert the TRAJECTORY file into a file format which can be read by such a program. Thanx in advance, 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 jlr at che.utexas.edu Fri Apr 5 17:32:36 2002 From: jlr at che.utexas.edu (Jose Luis Rodriguez-Lopez) Date: Fri, 05 Apr 2002 09:32:36 -0600 Subject: [CPMD-list] program grid.x References: <001701c1dbee$1672b480$ae5005a0@phys.keele.ac.uk> Message-ID: <3CADC394.3BAEED50@che.utexas.edu> Zac, I got what i believe is the most updated version of the code, and there're only the following *grid* subrutines 2dgrid.F 3dgrid.F fnlgrid.F If you think one of this is useful for your purpose, i can send it to you. I'm afraid i can't help you with the other part of your question. JoseLuis Zak wrote: > Dear all, Can anyone let me know where I might be able to aquire > Vanderbilt PP's for Carbon and Hydrogen, also I don't seem to have the > program grid.x mentioned at the beginning of chapter 7 in the source > code. Is there anywhere i can get this program ? Any assistance will > be greatly appreciated. Zak -- J.L. Rodriguez-Lopez Texas Materials Institute The University of Texas at Austin ETC 8.180 Austin, Texas 78712-1063 Phone: (512) 471-3578 Fax: (512) 475-8482 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20020405/fa486392/attachment.html From aksabir1 at hotmail.com Wed Apr 10 05:06:28 2002 From: aksabir1 at hotmail.com (abdenour sabir) Date: Tue, 09 Apr 2002 20:06:28 -0700 Subject: [CPMD-list] HINTS Message-ID: Dear all Could anyone tell me what is missing in the Atoms section. The code just stops after getting through the pseudo-potential info.Thank you. A.Sabir HERE IS A PORTION OF THE INPUT FILE: &ATOMS *C_SGS LMAX=P 18 0.00000 0.00000 0.00000 2.32531 1.34252 0.00000 4.65062 0.00000 0.00000 6.97592 1.34252 0.00000 9.30123 0.00000 0.00000 11.62654 1.34252 0.00000 2.32531 4.02755 0.00000 4.65062 5.37007 0.00000 6.97592 4.02755 0.00000 9.30123 5.37007 0.00000 11.62654 4.02755 0.00000 13.95185 5.37007 0.00000 4.65062 8.05510 0.00000 6.97592 9.39762 0.00000 9.30123 8.05510 0.00000 11.62654 9.39762 0.00000 13.95185 8.05510 0.00000 16.27716 9.39762 0.00000 *LI_SGS LMAX=P 2 3.32531 1.34252 3.00000 4.05062 0.00000 3.00000 &END THIS IS THE ERROR MESSAGE I GET AT THE END OF THE OUTPUT: *** WFOPTS| THE NEW SIZE OF THE PROGRAM IS 3940 KBytes *** RV30! NUMBER OF SPECIES HAS CHANGED 1 2 RV30! INCONSISTENT NUMBER OF ATOMS. RV30| WARNING! CANNOT READ COORDINATES FROM SECTION 4 RV30| WARNING! NO INITIAL GEOMETRY RV30! CUTOFF HAS CHANGED 18.00 13.00 RV30! NUMBER OF ELECTRONS HAS CHANGED 72 74 RV30! X REAL SPACE MESH HAS CHANGED 40 36 RV30! Y REAL SPACE MESH HAS CHANGED 40 36 RV30! Z REAL SPACE MESH HAS CHANGED 18 16 RV30! NUMBER OF STATES HAS CHANGED 46 47 _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp. From Ari.P.Seitsonen at iki.fi Wed Apr 10 08:13:05 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Wed, 10 Apr 2002 08:13:05 +0200 Subject: [CPMD-list] HINTS In-Reply-To: (aksabir1@hotmail.com) References: Message-ID: <200204100613.g3A6D5129400@magadino.cscs.ch> Hi, From the output it seems that you have (drastically?) changed the system but still try to do a restart; can you try to initialise the wavefunctions again? Greetings, apsi > Could anyone tell me what is missing in the Atoms section. The code just > stops after getting through the pseudo-potential info.Thank you. > > A.Sabir > > HERE IS A PORTION OF THE INPUT FILE: > > &ATOMS > *C_SGS > LMAX=P > 18 > 0.00000 0.00000 0.00000 > 2.32531 1.34252 0.00000 > 4.65062 0.00000 0.00000 > 6.97592 1.34252 0.00000 > 9.30123 0.00000 0.00000 > 11.62654 1.34252 0.00000 > 2.32531 4.02755 0.00000 > 4.65062 5.37007 0.00000 > 6.97592 4.02755 0.00000 > 9.30123 5.37007 0.00000 > 11.62654 4.02755 0.00000 > 13.95185 5.37007 0.00000 > 4.65062 8.05510 0.00000 > 6.97592 9.39762 0.00000 > 9.30123 8.05510 0.00000 > 11.62654 9.39762 0.00000 > 13.95185 8.05510 0.00000 > 16.27716 9.39762 0.00000 > > *LI_SGS > LMAX=P > 2 > 3.32531 1.34252 3.00000 > 4.05062 0.00000 3.00000 > &END > > THIS IS THE ERROR MESSAGE I GET AT THE END OF THE OUTPUT: > > *** WFOPTS| THE NEW SIZE OF THE PROGRAM IS 3940 KBytes *** > RV30! NUMBER OF SPECIES HAS CHANGED 1 2 > RV30! INCONSISTENT NUMBER OF ATOMS. > RV30| WARNING! CANNOT READ COORDINATES FROM SECTION 4 > RV30| WARNING! NO INITIAL GEOMETRY > RV30! CUTOFF HAS CHANGED 18.00 13.00 > RV30! NUMBER OF ELECTRONS HAS CHANGED 72 74 > RV30! X REAL SPACE MESH HAS CHANGED 40 36 > RV30! Y REAL SPACE MESH HAS CHANGED 40 36 > RV30! Z REAL SPACE MESH HAS CHANGED 18 16 > RV30! NUMBER OF STATES HAS CHANGED 46 47 > > > _________________________________________________________________ > Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp. > > _______________________________________________ > 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 weiss at imo.physik.uni-muenchen.de Wed Apr 10 09:34:20 2002 From: weiss at imo.physik.uni-muenchen.de (Andreas Weiss) Date: Wed, 10 Apr 2002 09:34:20 +0200 (CEST) Subject: [CPMD-list] CPMD and Dual-Athlon Message-ID: Dear all, has anyone optimised CPMD for Dual-Athlon systems including - OPENMP - maybe making use of '3Dnow' options for FFT - Myrinet connected cluster Greetings, Andi Weiss +--------------------------------------------------------------+ | Andreas Weiss Tel. +49 089 2180-9228 | | LS BioMolekulare Optik Fax. +49 089 2180-9202 | | Oettingenstr. 67 andreas.weiss at physik.uni-muenchen.de | | D-80538 Muenchen http://www.imo.physik.uni-muenchen.de | +--------------------------------------------------------------+ From M.A.Zwijnenburg at tnw.tudelft.nl Thu Apr 11 18:11:03 2002 From: M.A.Zwijnenburg at tnw.tudelft.nl (Martijn Zwijnenburg) Date: Thu, 11 Apr 2002 18:11:03 +0200 Subject: [CPMD-list] MD on a molecule Message-ID: <3CB5D1B4.32569.574CF8E@localhost> Hi, I want to do a MD run on a isolated molecule in a periodic box but are not sure which keywords to include in the file. This is a list of the keywords which I thought were applicable. ISOLATED MOLECULE CENTER MOLECULE SYMMETRY 0 Are these keywords right? and are there other? Any advise is more then welcome. Furthermore, I wondered if CENTER MOLECULE just translates the center of origin of the input coordinates to the center of the box? Thanks in advance, Martijn Zwijnenburg ------------------------------------------------------------------------- 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 kresslists at kressworks.com Thu Apr 11 19:05:52 2002 From: kresslists at kressworks.com (Jim Kress) Date: Thu, 11 Apr 2002 13:05:52 -0400 Subject: [CPMD-list] CPMD on Windows NT References: <3CB5D1B4.32569.574CF8E@localhost> Message-ID: <005401c1e17b$22f086a0$0201a8c0@hppav> I'm preparing to try ro compile and link CPMD (using PGF77) on my Windows NT box. Has anyone done this? Does anyone have any tips or suggestions that will make this work? Thanks. Jim Kress From M.A.Zwijnenburg at tnw.tudelft.nl Fri Apr 12 10:44:50 2002 From: M.A.Zwijnenburg at tnw.tudelft.nl (Martijn Zwijnenburg) Date: Fri, 12 Apr 2002 10:44:50 +0200 Subject: [CPMD-list] Summary MD on a molecule Message-ID: <3CB6BA9F.6474.902A4AB@localhost> Hi, Herewith the answers I got on my question regarding MD on a single molecule. Thanx to Jan-Willem Handgraaf and Carme Rovira for their answers. cheers Martijn On 11 Apr 2002, at 18:41, Jan-Willem Handgraaf wrote: > If you use the option "SYMMETRY 0" you automatically also turn on the option > "ISOLATED MOLECULE". Now if you choose another symmetry and also the > "ISOLATED MOLECULE" option you can study an isolated molecule or cluster > within periodic boundary conditions. And if you choose your box big enough > the "CENTER MOLECULE" option is rather arbitrary, assuming that you start the > simulation with the molecule in the center of you box. > It all depends on the question if you want the molecules to 'feel each other' > or not? If yes, use the correct periodic symmetry of the system with the > "ISOLATED MOLECULE" option, if not "SYMMETRY 0" will suffice. This latter > option is more expensive, because the program uses a scheme to correct for > the periodic images (i.e. Hockney) which in principle should not be there. > > Jan-Willem Handgraaf > > > -- > Jan-Willem Handgraaf > Department of Chemical Engineering > University of Amsterdam > Nieuwe Achtergracht 166 > 1018 WV Amsterdam > The Netherlands > > Room: C6.18 > Tel: +31-20-5256492 > Fax: +31-20-5255604 > Email: jwh at science.uva.nl On 11 Apr 2002, at 19:44, Carme Rovira wrote: > Hello, > > I send you an input example for an isolated > water molecule in an isolated box (h2o_pbc.inp). > Alternatively you can also run it in a non-periodic > box (see h2o_isolated.inp) using together > ISOLATED MOLECULE and 0 for SYMMETRY. > > In general, the computed properties of the molecule > should be independent of the scheme used (either pbc or isolated > box) except in difficult cases such as charged molecules, > where the calculation in an isolated box is recommended. > The PBC calculation is always cheaper so for > a neutral molecule such as water molecule you would > save time and memory. > > In the case of a calculation in an isolated box, CPMD moves > the center of mass to the center of the box by default, > unless you use the keywords (CENTER MOLECULE OFF). I would > just use the default in your case. > > Good luck! > > Carme > > ==================================================== ===================== > Carme Rovira > Centre de Qu?mica Te?rica Tel: +34 93 4037112 > Parc Cient?fic de Barcelona Fax: +34 93 4037225 > Josep Samitier 1-5 Annex A. Pta 1 E-mail: crovira at pcb.ub.es > 08028 Barcelona, Spain (http://www.pcb.ub.es) > ----------- and ------------ > Departament de Qu?mica F?sica > Facultat de Qu?mica. Universitat de Barcelona > Mart? i Franqu?s 1. 08028 Barcelona. Spain > (http://www.qf.ub.es/personal/crovira) > ==================================================== ===================== > > ------------------------------------------------------------------------- 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 cur at zurich.ibm.com Tue Apr 16 09:39:22 2002 From: cur at zurich.ibm.com (Alessandro Curioni) Date: Tue, 16 Apr 2002 09:39:22 +0200 Subject: [CPMD-list] Test cases Message-ID: Following some requests, test cases to check the proper function of the program have been added under the contrib section of the cpmd distribution (contrib/test.tar.Z). 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 duaj at fudan.edu Wed Apr 17 07:42:46 2002 From: duaj at fudan.edu (duaj at fudan.edu) Date: 17 Apr 2002 05:42:46 -0000 Subject: [CPMD-list] Error on PC-Linux compilation Message-ID: <20020417054246.19438.qmail@s9.bn3.com> Dear all, I am trying to run CPMD v. 3.5 on an 1GHz Intel PC machine running Redhat 7.2. I am using the Portland Group Fortran 90 compiler. 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 Then while compiling, the following error message appears: PGF90-S-0021-Label field of continuation line is not blank (./cpmd.f:18) Such errors also exist in many other lines and other fortran source file, I open the cpmd.f and find all the errors come form "#" at the beginning of this line. But I don't know how to modify it! I hope you can help me. Many thanks, Best regards, A.J.Du ________________ Fudan University Alumni Email System, http://mail.fudan.edu, FREE Signup. From mit at uni.udm.ru Wed Apr 17 13:40:25 2002 From: mit at uni.udm.ru (mit) Date: Wed, 17 Apr 2002 16:40:25 +0500 (SAMST) Subject: [CPMD-list] Error on PC-Linux compilation In-Reply-To: <20020417054246.19438.qmail@s9.bn3.com> Message-ID: On 17 Apr 2002 duaj at fudan.edu wrote: > Dear all, > > I am trying to run CPMD v. 3.5 on an 1GHz Intel PC machine running > Redhat 7.2. I am using the Portland Group Fortran 90 compiler. 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 > > Then while compiling, the following error message appears: > > PGF90-S-0021-Label field of continuation line is not blank (./cpmd.f:18) > > Such errors also exist in many other lines and other fortran source file, > I open the cpmd.f and find all the errors come form "#" at the beginning > of this line. But I don't know how to modify it! I hope you can help me. > > Many thanks, > > Best regards, > > A.J.Du > > > > > > ________________ > Fudan University Alumni Email System, http://mail.fudan.edu, FREE Signup. > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > Dear A.J.Du, The simbol # in the beginig of the line meens the preprocessor must be used. It works automaticaly if such files have suffix *.F instead *.f. The Makefile must be adopted for using of the preprocessor in CPMD group. The main directivs is #ifdef and #endif for different options of platforms and compilers. 17 April 2002 Yuriy Mirtrokhin Udmirt State University, Izhevsk, Russia From aksabir1 at hotmail.com Wed Apr 17 15:25:03 2002 From: aksabir1 at hotmail.com (abdenour sabir) Date: Wed, 17 Apr 2002 06:25:03 -0700 Subject: [CPMD-list] Energy Bands Message-ID: Dear All I just want to know if it is necessary to run CPMD at a given k-points first then proceed with the band structure calculation at a chosen line using the restart file or is there a trick to calculate directly the band structure without having to use the Chadi-Cohen points. Regards _________________________________________________________________ Join the world?s largest e-mail service with MSN Hotmail. http://www.hotmail.com From francesco.filippone at mlib.cnr.it Wed Apr 17 16:26:13 2002 From: francesco.filippone at mlib.cnr.it (Francesco Filippone) Date: Wed, 17 Apr 2002 16:26:13 +0200 (CEST) Subject: [CPMD-list] Error on PC-Linux compilation In-Reply-To: <20020417054246.19438.qmail@s9.bn3.com> Message-ID: Dear A.J. Du, this error sounds like a preprocessor error. I can't reproduce it, but I rememeber I had something similar. The preprocessor is defined by the Configure script as /lib/cpp, which is part of gcc. Unfortunately RedHat 7.2 is shipped with un unsupported version of gcc, 2.96, while the stable and supported version is either 2.95.3 (at the time in which RH 7.2 was released) or 3.0.4 (now). Try cpp --version to figure out which version you have. It this is the problem, the solution is to download (gcc.gnu.org) the stable version, compile and install it. I kept the 2.96, installed in /usr/bin, version for consistency in any recompilation of the kernel and installed the stable release in /usr/local/bin. After installation you just need to relink /lib/cpp to /usr/local/bin/cpp. Try to recompile from scratch and it should work. 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 ---------------------------------------------------------------------------- From M.A.Zwijnenburg at tnw.tudelft.nl Wed Apr 17 18:17:29 2002 From: M.A.Zwijnenburg at tnw.tudelft.nl (Martijn Zwijnenburg) Date: Wed, 17 Apr 2002 18:17:29 +0200 Subject: [CPMD-list] SIGNAL: Floating point exception Message-ID: <3CBDBC34.30737.C15241D@localhost> Hi, When I try to perform a MD run on a isolated molecule (29 atoms, of which 10 H, NPT ensemble) on 8 processors of a Cray T-3E I get the following error message: SIGNAL: Floating point exception (floating point overflow) Beginning of Traceback (PE 0): Interrupt at address 0x80053a3e8 in routine 'SGEMM@'. Called from line 158 (address 0x80019d480) in routine 'RORTHO'. Called from line 35 (address 0x80019c8fc) in routine 'RORTOG'. Called from line 119 (address 0x80019aef4) in routine 'POSUPA'. Called from line 211 (address 0x80017c03c) in routine 'MDMAIN'. Called from line 123 (address 0x800179cf4) in routine 'MDPT'. Called from line 114 (address 0x800001774) in routine 'CPMD'. Called from line 3 (address 0x80000141c) in routine 'CPMD_STUTTGART'. Called from line 475 (address 0x800000c94) in routine '$START$'. End of Traceback. Floating exception (core dumped) I notticed that there is an influence of the cutoff. At a cutoff of 80 it runs 10 steps before crashing, while at 40 it runs 327 steps before crashing with the same error message. What could be the reason for this floating point overflow? The influence of the cutoff sugests something with lack of memory but I can not combibe that with a floating poitn overflow. Anyway, all sugestions are welcome. Regards, Martijn Zwijnenburg ------------------------------------------------------------------------- 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 weiz at mail.rochester.edu Thu Apr 18 03:50:36 2002 From: weiz at mail.rochester.edu (wei zhuang) Date: Wed, 17 Apr 2002 20:50:36 -0500 Subject: [CPMD-list] free energy calculation Message-ID: <200204180050.g3I0opsd3788021@mail.rochester.edu> Dear all: I wonder could one do a free energy calculation of a system with cpmd? wei zhuang weiz at mail.rochester.edu From hutter at pci.unizh.ch Thu Apr 18 09:26:52 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 18 Apr 2002 09:26:52 +0200 (MEST) Subject: [CPMD-list] SIGNAL: Floating point exception In-Reply-To: <3CBDBC34.30737.C15241D@localhost> Message-ID: Hi your problem is most likely related to the Nose thermostat for the electrons. The integrators are not able to handle your system and you get diverging values, depending on the cutoff this happens sooner or later during the job. The job stops in another part of the program because only then the large numbers cause an exception. This type of problem can usually be handled by adjusting the degrees of freedom for the thermostat. You have to change the 4th parameter in the NOSE PARAMETER list and it is probably also a good idea to crank up the integrators (parameter 5 and 6). Have a look in the manual at the HINTS section. BTW: NPT simulations for an isolated molecule, I assume this is only a test. 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 Wed, 17 Apr 2002, Martijn Zwijnenburg wrote: > Hi, > > When I try to perform a MD run on a isolated molecule (29 atoms, > of which 10 H, NPT ensemble) on 8 processors of a Cray T-3E I > get the following error message: > > SIGNAL: Floating point exception (floating point overflow) > > Beginning of Traceback (PE 0): > Interrupt at address 0x80053a3e8 in routine 'SGEMM@'. > Called from line 158 (address 0x80019d480) in routine 'RORTHO'. > Called from line 35 (address 0x80019c8fc) in routine 'RORTOG'. > Called from line 119 (address 0x80019aef4) in routine 'POSUPA'. > Called from line 211 (address 0x80017c03c) in routine 'MDMAIN'. > Called from line 123 (address 0x800179cf4) in routine 'MDPT'. > Called from line 114 (address 0x800001774) in routine 'CPMD'. > Called from line 3 (address 0x80000141c) in routine > 'CPMD_STUTTGART'. > Called from line 475 (address 0x800000c94) in routine '$START$'. > End of Traceback. > Floating exception (core dumped) > > I notticed that there is an influence of the cutoff. At a cutoff of 80 it > runs 10 steps before crashing, while at 40 it runs 327 steps before > crashing with the same error message. > What could be the reason for this floating point overflow? The > influence of the cutoff sugests something with lack of memory but I > can not combibe that with a floating poitn overflow. Anyway, all > sugestions are welcome. > > Regards, > > Martijn Zwijnenburg > > ------------------------------------------------------------------------- > 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 axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu Apr 18 18:21:38 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (axel.kohlmeyer at theochem.ruhr-uni-bochum.de) Date: Thu, 18 Apr 2002 18:21:38 +0200 Subject: [CPMD-list] Error on PC-Linux compilation In-Reply-To: Your message of "Wed, 17 Apr 2002 16:26:13 +0200." Message-ID: <200204181621.g3IGLcN29074@yello.theochem.ruhr-uni-bochum.de> >>> "FF" == Francesco Filippone writes: FF> Dear A.J. Du, FF> this error sounds like a preprocessor error. I can't reproduce it, but I FF> rememeber I had something similar. FF> The preprocessor is defined by the Configure script as /lib/cpp, which is FF> part of gcc. Unfortunately RedHat 7.2 is shipped with un unsupported FF> version of gcc, 2.96, while the stable and supported version is either FF> 2.95.3 (at the time in which RH 7.2 was released) or 3.0.4 (now). Try FF> cpp --version to figure out which version you have. FF> It this is the problem, the solution is to download (gcc.gnu.org) the FF> stable version, compile and install it. FF> I kept the 2.96, installed in /usr/bin, version for consistency in any FF> recompilation of the kernel and installed the stable release in FF> /usr/local/bin. After installation you just need to relink /lib/cpp to FF> /usr/local/bin/cpp. Try to recompile from scratch and it should work. FF> Ciao, FF> F. dear a.j. du, please verify that the makefile definition for CPP contains the '-traditional' flag. (e.g.CPP=/lib/cpp -P -C -traditional). omission of this flag with newer gcc's is the usual cause for the error you described, IIRC. 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 aksabir1 at hotmail.com Thu Apr 18 18:21:47 2002 From: aksabir1 at hotmail.com (abdenour sabir) Date: Thu, 18 Apr 2002 09:21:47 -0700 Subject: [CPMD-list] Hints On Energy Bands Message-ID: Dear All this is portion of my input file to calculate the band structure for graphite. So far I haven' been able to reproduce the results given in the literature. Is there anything wrong with it? Thanks in advance for your help. &CPMD KOHN-SHAM ENERGIES 0 RESTART WAVEFUNCTIONS COORDINATES LATEST LANCZOS DIAGONALIZATION ENERGYBANDS &END &SYSTEM SYMMETRY 4 CELL 13.9518 1.0 0.44000 0.0 0.0 -0.5 STATES 40 CUTOFF 13.00 KPOINTS BANDS 10 0.0 0.00000 0.0 0.5 0.28867 0.0 0 0. 0. 0. 0. 0. 0. &END _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx From mzapalow at mitr.p.lodz.pl Fri Apr 19 13:11:19 2002 From: mzapalow at mitr.p.lodz.pl (Michal Zapalowski) Date: Fri, 19 Apr 2002 13:11:19 +0200 Subject: [CPMD-list] DENSITY during MD run Message-ID: <02fb01c1e793$62eafa60$28d633d4@MITRMZ> Dear CPMD experts, is there any way to force CPMD to dump DENSITY files every N steps of molecular dynamics run instead (or except) of the end of the job? If yes, how? Thanks in advance, Michal --- Michal Zapalowski IARC, Technical University of Lodz 93-590 Lodz, Poland (+48 42) 631-31-77 mzapalow at mitr.p.lodz.pl From tdeutsch at cea.fr Tue Apr 23 13:43:52 2002 From: tdeutsch at cea.fr (Thierry Deutsch) Date: Tue, 23 Apr 2002 13:43:52 +0200 (MET DST) Subject: [CPMD-list] Energy Bands In-Reply-To: References: Message-ID: <15557.18680.5859.903766@ras-el-hanout.ceng.cea.fr> Hi everybody, To calculate a band structure with CPMD, You first calculate the correct density for your system with a Monkhorst-Pack Mesh. Then you use : OPTIMIZE WAVEFUNCTIONS with MAXSTEP 1 (no self-consistency) and RESTART DENSITY. In the section KPOINTS, you should use for instance a bcc: KPOINTS BANDS 51 0 0 0 0 0 1 Gamma to H 51 0 0 1 0 .5 .5 H to N 51 0 .5 .5 .5 .5 .5 N to P 51 .5 .5 .5 0 0 0 P to Gamma 51 0 0 0 .5 .5 0 Gamma to N 51 0 0 1 .5 .5 .5 H to P 0 0 0 0 0 0 0 You say that you want 51 points from (0,0,0) and (0,0,1) and so on. The last line with many zeros is to stop. If the memory of your computer is not enough, you can add in the line KPOINTS the option BLOCK=50 that means you want to have only 50 kpoints in memory. This options worked some times ago. Bye, Thierry Deutsch -- ----------------------------------------------------------------------- Thierry Deutsch Laboratoire de simulation atomistique (L_Sim) DRFMC/SP2M T?l:(33) 04 38 78 34 06 C.E.A.Grenoble Fax:(33) 04 38 78 51 97 17, Avenue des Martyrs mailto:TDeutsch at cea.fr 38054 GRENOBLE CEDEX 9 FRANCE http://www-drfmc.cea.fr/SP2M ----------------------------------------------------------------------- From mzapalow at mitr.p.lodz.pl Thu Apr 25 15:15:19 2002 From: mzapalow at mitr.p.lodz.pl (Michal Zapalowski) Date: Thu, 25 Apr 2002 15:15:19 +0200 Subject: [CPMD-list] cpmd2cube on Sun Message-ID: <050b01c1ec5b$48063530$28d633d4@MITRMZ> Dear all, I wonder if there is anybody who compiled the cpmd2cube utility on Sun machine and could share the working Makefile? Regards, Michal --- Michal Zapalowski IARC, Technical University of Lodz 93-590 Lodz, Poland (+48 42) 631-31-77 mzapalow at mitr.p.lodz.pl