From sacha at cermm.concordia.ca Wed Dec 1 20:27:09 2004 From: sacha at cermm.concordia.ca (sacha at cermm.concordia.ca) Date: Wed, 1 Dec 2004 14:27:09 -0500 (EST) Subject: [CPMD-list] troubles downloading v3.9 In-Reply-To: <200412011100.MAA34414@cpmd.org> Message-ID: Hi, Would anyone, please tell me what should I type as user name (my e-mail address doesn't work) in order to download CPMDv3.9 ? The only possible problem would be the browser I am using (Firefox), is it really because I am still not able to download the last release even if I use Internet Explorer? Thank you in advance, Sacha From cur at zurich.ibm.com Wed Dec 1 19:38:21 2004 From: cur at zurich.ibm.com (Alessandro Curioni) Date: Wed, 1 Dec 2004 19:38:21 +0100 Subject: [CPMD-list] troubles downloading v3.9 In-Reply-To: Message-ID: Yes - should have received an user-id and password in a separate note - I will check - if something went wrong - 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 wolfi at mittelerde.physik.uni-konstanz.de Wed Dec 1 20:35:36 2004 From: wolfi at mittelerde.physik.uni-konstanz.de (Wolfram Quester) Date: Wed, 1 Dec 2004 20:35:36 +0100 Subject: [CPMD-list] Au pseudopotentials In-Reply-To: References: Message-ID: <20041201193535.GA3516@halley.zuhause> Hi alltogether! While we are at the topic of pseudopotentials, I'd like to add a question, too. I'm a newbie in the field, so I'm still trying and experimenting with cpmd. At the moment I try to simulate Si-Clusters using the PSP Si_MT_PBE.psp contained in pseudo_ext.tar.gz available at www.cpmd.org. I was told that I should be able to read the LMAX= parameter from that file. But I don't know how and I did not see a not how the PSP was created. Could you please point me in the right direction to search? I tried LMAX=D which seems to be the right thing from my understanding, and I get more or less bond lengths, but bad values for the VDE. If I use LMAX=P as a shot in the dark, the agrrement with literature for VDE becomes better, but the bonding lengths are worse. The info-part of the PSP is &INFO ============================================================ | Pseudopotential Report | ------------------------------------------------------------ | Atomic Symbol : SI | | Atomic Number : 14 | | Number of core states : 3 | | Number of valence states : 2 | | Exchange-Correlation Functional : | | Slater exchange : 0.6667 | | LDA correlation : Ceperley-Alder | | Exchange GC : Perdew-Burke-Ernzerhof | | Correlation GC : Perdew-Burke-Ernzerhof | | Electron Configuration : N L Occupation | | 1 S 2.0000 | | 2 S 2.0000 | | 2 P 6.0000 | | 3 S 2.0000 | | 3 P 2.0000 | | Full Potential Total Energy = -289.201384 | | Trouiller-Martins normconserving PP | | n l rc energy | | 3 S 1.9000 -0.39594 | | 3 P 2.1000 -0.15055 | | 3 D 2.1000 -0.15055 | | Number of Mesh Points : 664 | | Pseudoatom Total Energy = -3.737242 | ============================================================ &END Thanks for your help, Wolfi -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: Digital signature Url : http://cpmd.org/pipermail/cpmd-list/attachments/20041201/6042676e/attachment.pgp From bohr123 at 163.com Thu Dec 2 02:10:29 2004 From: bohr123 at 163.com (=?gb2312?B?sqi2+w==?=) Date: Thu, 2 Dec 2004 09:10:29 +0800 (CST) Subject: [CPMD-list] subject Message-ID: <41AE6B85.00002B.23652@m222.163.com> help -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20041202/92b90c3e/attachment.html From piana at power.curtin.edu.au Thu Dec 2 04:51:17 2004 From: piana at power.curtin.edu.au (Stefano Piana) Date: Thu, 02 Dec 2004 11:51:17 +0800 Subject: [CPMD-list] Optimization with k-points Message-ID: <41AE9135.80606@power.curtin.edu.au> Just a quick question. Is it possible to optimize the lattice parameters with K-POINTS? I tried with steepest descent cell but seems not to be implemented. If I try with molecular dynamics it looks for a restart file even if I put no RESTART keyworkd in the input. If I try to generate a restart file with a single point wavefunction optimization it is not able to use it as it gives me an error like "wrong density" or somethig like this. I am a bit stuck... Stefano From Ari.P.Seitsonen at iki.fi Thu Dec 2 08:39:33 2004 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Thu, 2 Dec 2004 08:39:33 +0100 (CET) Subject: [CPMD-list] Optimization with k-points In-Reply-To: <41AE9135.80606@power.curtin.edu.au> References: <41AE9135.80606@power.curtin.edu.au> Message-ID: Dear Stefano, No, it is not possible to optimise the cell with k points, the stress tensor has not been implemented in the general case, only for the Gamma point. Keyword 'MOLECULAR DYNAMICS' should always require a previous calculation (irrespective of k points or Gamma-only), however sometimes it is possible to get around this (with 'QUENCH BO'...). Did you mean that you get the error message when you try to optimise the unit cell with k points, or in general? Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstrasse 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland On Thu, 2 Dec 2004, Stefano Piana wrote: > Just a quick question. > Is it possible to optimize the lattice parameters with K-POINTS? > I tried with steepest descent cell but seems not to be implemented. > If I try with molecular dynamics it looks for a restart file even if I > put no RESTART keyworkd in the input. If I try to generate a restart > file with a single point wavefunction optimization it is not able to use > it as it gives me an error like "wrong density" or somethig like this. I > am a bit stuck... > > > Stefano > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://cpmd.org/mailman/listinfo/cpmd-list > From D.Curulla.Ferre at TUE.NL Thu Dec 2 10:10:07 2004 From: D.Curulla.Ferre at TUE.NL (Curulla Ferre, D.) Date: Thu, 2 Dec 2004 10:10:07 +0100 Subject: [CPMD-list] I have not received yet my username and password Message-ID: Hi, I have applied several times for a license to use CPMD, but I have not received yet any reply. Can somebody help me? Thank-you very much, Daniel Curulla ========================= Dr. D. Curulla Ferre Technische Universiteit Eindhoven Den Dolech 2, 5600 MB Eindhoven The Netherlands Tel. +31 40 247 4997 Fax +31 40 247 3481 ========================= -----Original Message----- From: cpmd-list-bounces at cpmd.org on behalf of Alessandro Curioni Sent: Wed 12/1/2004 7:38 PM To: sacha at cermm.concordia.ca Cc: cpmd-list at cpmd.org; cpmd-list-bounces at cpmd.org Subject: Re: [CPMD-list] troubles downloading v3.9 Yes - should have received an user-id and password in a separate note - I will check - if something went wrong - 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 _______________________________________________ CPMD-list mailing list CPMD-list at cpmd.org http://cpmd.org/mailman/listinfo/cpmd-list From wolfi at mittelerde.physik.uni-konstanz.de Fri Dec 3 11:36:15 2004 From: wolfi at mittelerde.physik.uni-konstanz.de (Wolfram Quester) Date: Fri, 3 Dec 2004 11:36:15 +0100 Subject: [CPMD-list] Clearification in the manual In-Reply-To: References: <20040527135833.GB1863@halley.zuhause> Message-ID: <20041203103615.GA11439@halley.zuhause> Dear Juerg, long time ago we wrote: On Mon, May 31, 2004 at 10:48:26AM +0200, Juerg Hutter wrote: > Dear Wolfram > > thanks a lot for your suggestions for the manual. > We will make the changes you suggested in the next version. > [...snip...] > > > On Thu, 27 May 2004, Wolfram Quester wrote: > > > Dear Authors of CPMD! > > > > I am new to CPMD and some time ago, I took one of the examples and > > started to create an own input file. I wanted to calculate Mullican > > population analysis and created a &PROP ... END section in my input > > file. But that section was ignored. > > After some googling and reading I found out, that this section is only > > evaluated if the PROPERTIES keyword is present in the &CPMD ... END > > section. > > I think it would be nice if there was a hint for that in the manual, > > e.g. on page 9 in section 7 "Input Sections", or on page 15 in the > > beginning of section 8.2.6, like > > > > &PROP ... &END <-> Calculation of properties > > This section is only evaluated if the PROPERTIES keyword is present > > in the &CPMD ... END section. > > This was shortly before 3.9.1 was released, probably to short to make it into the release. Now I had a look at the mannal after a long time and thought that I could prepare a patch to simplify things for you. The patch is attached and fixes additionally two or three typos and changes the use of quotation marks in one section according to type setting rules. Thanks for consideration, Wolfi -------------- next part -------------- --- SOURCE/manual.tex.orig 2004-12-01 20:53:16.000000000 +0100 +++ SOURCE/manual.tex 2004-12-02 11:11:05.000000000 +0100 @@ -673,12 +673,14 @@ \\ \> \&ATOMS ... \> \&END \> $\leftrightarrow$ \> Atoms and Pseudopotentials\\ +\> Section \ref{S_Pseudopotentials} explains the usage of Pseudopotentials in more detail.\\ \\ \> \&DFT ... \> \&END \> $\leftrightarrow$ \> Exchange and Correlation Functional\\ \\ \> \&PROP ... \> \&END \> $\leftrightarrow$ \> Calculation of properties\\ +\> This section is only evaluated if the \refkeyword{PROPERTIES} keyword is given in the \&CPMD section.\\ \\ \> \&BASIS ... \> \&END \> $\leftrightarrow$ \> Basis sets for properties or initial guess\\ @@ -935,6 +937,11 @@ % \subsubsection[\&ATOMS ... \&END]{\&ATOMS $\ldots$ \&END} % +This section also contains information on the pseudopotentials to be used. See +section \ref{S_Pseudopotentials} for more details on this. +%The following \options gives proper indentation, but it is a bad solution + +\options{}{}{} \refkeyword{ATOMIC CHARGES}\options{}{}{} \refkeyword{CHANGE BONDS}\options{}{}{} \refkeyword{CONFINEMENT POTENTIAL}\options{}{}{} @@ -969,11 +976,16 @@ % \subsubsection[\&PROP ... \&END]{\&PROP $\ldots$ \&END} % +The keyword \refkeyword{PROPERTIES} has to be present in the \&CPMD-section of +the input-file if this section shall be evaluated. +%The following \options gives proper indentation, but it is a bad solution + +\options{}{}{} \refkeyword{CHARGES}\options{}{}{} \refkeyword{CONDUCTIVITY}\options{}{}{} \refkeyword{CUBECENTER}\options{}{}{} \refkeyword{CUBEFILE}\options{\{ORBITALS,DENSITY\}}{[HALFMESH]}{} -\refkeyword{DIPOLE MOMENT}\options{\{BERRY,RS \}}{}{} +\refkeyword{DIPOLE MOMENT}\options{\{BERRY,RS\}}{}{} \refkeyword{EXCITED DIPOLE}\options{}{}{} \refkeyword{LDOS}\options{}{}{} \refkeyword{LOCALIZE}\options{}{}{} @@ -1306,7 +1318,7 @@ FUNCTIONAL keyword, since, in this functional form, both the occupation numbers $f_i$ and the empty/partially occupied states are taken properly into account. - This calculation is executed wihen the keyword PROPERTIES is + This calculation is executed when the keyword PROPERTIES is used in the section \&CPMD ... \&END. In the section \&PROP ... \&END the keyword CONDUCTIVITY must be present and the interval interval $\Delta \omega$ for the calculation of the spectrum @@ -3493,7 +3505,7 @@ The general format for entering the pseudo potentials in the input file is: \begin{itemize} \item The input for a {\bf new atom type} is started - with a "{\bf *}" in the first column. This line further contains: + with a ``{\bf *}'' in the first column. This line further contains: \begin{itemize} \item the {\bf file name} ({\sl ECPNAME}) where to find the {\bf pseudopotential} @@ -3505,7 +3517,7 @@ specifies the method to be used for the calculation of the {\bf nonlocal parts} of the {\bf pseudopotential}. It can be omitted for Vanderbilt pseudopotentials - and Stefan Goedecker's pseudopotentials. For seni-local + and Stefan Goedecker's pseudopotentials. For semi-local pseudopotentials the default is Gauss-Hermite integration with 20 special points. The number of integration points can be changed using {\bf GAUSS-HERMITE=xx}. @@ -3522,7 +3534,7 @@ file from Vanderbilts atomic code. \\ {\bf FORMATTED} indicates the formatted version of the Vanderbilt pseudopotential files after a conversion with - the program 'reform.f' from the + the program `reform.f' from the Vanderbilt atomic code package (see Section 1.1) \\ For Vanderbilt pseudopotentials the option NLCC is ignored. The nonlinear core correction will always be used if the @@ -3552,15 +3564,15 @@ can be given in two different styles: \begin{itemize} \item[-] You can specify the maximum $l$ - quantum number with - "{\bf LMAX}=$l$" where $l$ is S, P or D. \\ + ``{\bf LMAX}=$l$'' where $l$ is S, P or D. \\ If this is the only input, the program assumes that LMAX is the local potential (LOC). \\ - You can use another local function by specifying "{\bf LOC}=$l$".\\ + You can use another local function by specifying ``{\bf LOC}=$l$''.\\ In addition it is possible to assign the local potential to a - further potential with "{\bf SKIP}=$l$". + further potential with ``{\bf SKIP}=$l$''. \item[-] Alternatively you can specify these three angular quantum numbers by their numerical values (S=0, P=1, D=2) in the - order "LMAX LOC SKIP".\\ + order ``LMAX LOC SKIP''.\\ If values for LOC and SKIP are provided outside the range 0 - LMAX the program uses the default. \end{itemize} @@ -6756,7 +6768,7 @@ \faqquestion{gaussianbasis} I want to to run CPMD with basis sets equivalent to Gaussian -6-31+G(d) and 6-311+G(2d,p). How do i set up the \&BASIS section? +6-31+G(d) and 6-311+G(2d,p). How do I set up the \&BASIS section? \faqanswer You should be able to construct -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: Digital signature Url : http://cpmd.org/pipermail/cpmd-list/attachments/20041203/c112d35e/attachment.pgp From Davide.Provasi at mi.infn.it Fri Dec 3 12:33:42 2004 From: Davide.Provasi at mi.infn.it (Davide.Provasi at mi.infn.it) Date: Fri, 3 Dec 2004 12:33:42 +0100 (CET) Subject: [CPMD-list] CPMD2CUBE IFC Message-ID: <2971.193.205.78.74.1102073622.squirrel@193.205.78.74> dear cpmd users, I am trying to compile and use cpmd2cube on a linux xeon cluster with ifc. the compilation terminates successfully but the resulting executable gives a strange seg fault error on the gsort call. has anyone experienced the same problem? thank you in advance Davide From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Fri Dec 3 12:45:14 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Fri, 3 Dec 2004 12:45:14 +0100 (CET) Subject: [CPMD-list] Clearification in the manual In-Reply-To: <20041203103615.GA11439@halley.zuhause> Message-ID: On Fri, 3 Dec 2004, Wolfram Quester wrote: dear wolfram, thanks for the updates. i am currently working on updating the manual for the next release, so i will see to it, that it gets included this time. if anybody else has suggestions, changes, comments, etc. please send me your patches, texts, notes as soon as possible and i will try to include as much as possible. thanks in advance, axel kohlmeyer. WF> Dear Juerg, WF> WF> long time ago we wrote: WF> On Mon, May 31, 2004 at 10:48:26AM +0200, Juerg Hutter wrote: WF> > Dear Wolfram WF> > WF> > thanks a lot for your suggestions for the manual. WF> > We will make the changes you suggested in the next version. WF> > WF> [...snip...] WF> > WF> > WF> > On Thu, 27 May 2004, Wolfram Quester wrote: WF> > WF> > > Dear Authors of CPMD! WF> > > WF> > > I am new to CPMD and some time ago, I took one of the examples and WF> > > started to create an own input file. I wanted to calculate Mullican WF> > > population analysis and created a &PROP ... END section in my input WF> > > file. But that section was ignored. WF> > > After some googling and reading I found out, that this section is only WF> > > evaluated if the PROPERTIES keyword is present in the &CPMD ... END WF> > > section. WF> > > I think it would be nice if there was a hint for that in the manual, WF> > > e.g. on page 9 in section 7 "Input Sections", or on page 15 in the WF> > > beginning of section 8.2.6, like WF> > > WF> > > &PROP ... &END <-> Calculation of properties WF> > > This section is only evaluated if the PROPERTIES keyword is present WF> > > in the &CPMD ... END section. WF> > > WF> WF> This was shortly before 3.9.1 was released, probably to short to make it WF> into the release. Now I had a look at the mannal after a long time and WF> thought that I could prepare a patch to simplify things for you. The WF> patch is attached and fixes additionally two or three typos and changes WF> the use of quotation marks in one section according to type setting WF> rules. WF> WF> Thanks for consideration, WF> WF> Wolfi WF> WF> -- ======================================================================= Dr. 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Fri Dec 3 13:23:40 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Fri, 3 Dec 2004 13:23:40 +0100 (CET) Subject: [CPMD-list] CPMD2CUBE IFC In-Reply-To: <2971.193.205.78.74.1102073622.squirrel@193.205.78.74> Message-ID: On Fri, 3 Dec 2004 Davide.Provasi at mi.infn.it wrote: dear davide, please try updating to the lastest release of the intel compiler. you can also try lowering the optimization level. you didn't tell which version of the intel compiler you are using and what version of glibc. there are some incompatible or 'tricky' combinations. see: http://www.theochem.rub.de/~axel.kohlmeyer/cpmd-linux.html#mkl if you have the unsupported non-commercial version you should register for permier support (it comes without charge) to get access to the latest updates. finally, there were some bugs fixed (especially with the -inbox, -shift, and -center flags) since the latest release available from cpmd.org, so you should try applying the attached patch. apropos optimization levels. contrary to the claims of the intel compiler manuals, cpmd seems to run the fastest when compiled with '-O2 -unroll', without SSE support (-ax... flag), and without -ipo. especially on pentium-4 or xeon machines, i found a speed gain of over 15% by disabling these "optimizations". for cpmd2cube optimization is of no importance, anyways. best regards, axel. DP> dear cpmd users, DP> I am trying to compile and use cpmd2cube on a linux xeon cluster with ifc. DP> the compilation terminates successfully but the resulting executable gives DP> a strange seg fault error on the gsort call. DP> DP> has anyone experienced the same problem? DP> DP> thank you in advance DP> DP> DP> Davide DP> DP> DP> _______________________________________________ DP> CPMD-list mailing list DP> CPMD-list at cpmd.org DP> http://cpmd.org/mailman/listinfo/cpmd-list DP> DP> -- ======================================================================= Dr. 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. -------------- next part -------------- A non-text attachment was scrubbed... Name: cpmd2cube-update.patch.gz Type: application/x-gzip Size: 4367 bytes Desc: Url : http://cpmd.org/pipermail/cpmd-list/attachments/20041203/3b5bd9f0/attachment.gz From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Sat Dec 4 13:21:48 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Sat, 04 Dec 2004 13:21:48 +0100 Subject: [CPMD-list] list of know problems, workarounds and missing/wanted features Message-ID: <200412041221.iB4CLmt20657@yello.theochem.ruhr-uni-bochum.de> hello everybody, another piece of information, i'd like to collect for the next CPMD release is a list of known problems (with workarounds if available), incomplete implementations, inconsistencies and so on. thanks in advance, axel kohlmeyer. -- ======================================================================= 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From wkhan at wow.hongik.ac.kr Sat Dec 4 16:32:52 2004 From: wkhan at wow.hongik.ac.kr (Wone Keun Han) Date: Sat, 4 Dec 2004 10:32:52 -0500 Subject: [CPMD-list] CPMD-Linux Message-ID: <009a01c4da16$864067c0$9d3c9480@physics.brown.edu> HI! I am trying to install CPMD on a Linux machine-Intel Pentium 3.4 GHz/ 4GB memory and Mandrake Linux v.10.1. I am using Intel Fortran compiler and MKL. I put library atlas on ~/SOURCE directory. I made Makefile using BOCHUM-P4. After typing make, it starts compiling. But it stops and gives me an error message: "ld cannot find -lm" Does anyone know what it means and how I can fix? Thank you, Wone Keun Han -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20041204/853ed6d0/attachment.html From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Sun Dec 5 16:05:22 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Sun, 5 Dec 2004 16:05:22 +0100 (CET) Subject: [CPMD-list] CPMD-Linux In-Reply-To: <009a01c4da16$864067c0$9d3c9480@physics.brown.edu> Message-ID: On Sat, 4 Dec 2004, Wone Keun Han wrote: WKH> HI! WKH> hi! WKH> WKH> WKH> I am trying to install CPMD on a Linux machine-Intel Pentium 3.4 GHz/ 4GB WKH> memory and Mandrake Linux v.10.1. WKH> WKH> I am using Intel Fortran compiler and MKL. which version, i assume version 8.1, right? in that case, please update to the latest version (intel-ifort8-8.1-020.i386.rpm) from the intel support website. WKH> I put library atlas on ~/SOURCE directory. well, if you want to use MKL, you don't need atlas. both packages provide the same functionality (optimized LAPACK and BLAS), though. WKH> WKH> I made Makefile using BOCHUM-P4. ok, this one uses atlas. btw: for optimal performance and reusability of the binary you should probably replace: '-O3 -pc64 -axiKMWN' with '-O2 -pc64' and '-static' with '-i-static'. WKH> After typing make, it starts compiling. WKH> WKH> But it stops and gives me an error message: WKH> WKH> "ld cannot find -lm" WKH> WKH> Does anyone know what it means and how I can fix? yes. the linker is looking for a file libm.so or libm.a this means, that you either have not installed the glibc-devel package or made an incorrect installatio of the intel compiler. regards, axel kohlmeyer. WKH> WKH> WKH> Thank you, WKH> WKH> WKH> WKH> Wone Keun Han WKH> WKH> WKH> WKH> -- ======================================================================= Dr. 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From chokosabe at yahoo.co.uk Mon Dec 6 13:30:39 2004 From: chokosabe at yahoo.co.uk (Abraham Alaka) Date: Mon, 6 Dec 2004 12:30:39 +0000 (GMT) Subject: Fwd: Re: [CPMD-list] Clearification in the manual Message-ID: <20041206123039.34308.qmail@web25707.mail.ukl.yahoo.com> Note: forwarded message attached. ___________________________________________________________ Win a castle for NYE with your mates and Yahoo! Messenger http://uk.messenger.yahoo.com -------------- next part -------------- An embedded message was scrubbed... From: Wolfram Quester Subject: Re: [CPMD-list] Clearification in the manual Date: Sat, 4 Dec 2004 17:16:21 +0100 Size: 3315 Url: http://cpmd.org/pipermail/cpmd-list/attachments/20041206/0efef588/attachment.mht From cur at zurich.ibm.com Mon Dec 6 12:26:17 2004 From: cur at zurich.ibm.com (Alessandro Curioni) Date: Mon, 6 Dec 2004 12:26:17 +0100 Subject: [CPMD-list] New release soon - Message-ID: Dear colleagues, we are planning a new CPMD minor release to be released soon (probably just atfter Xmas- mainly bug fixes and new supported platforms). In the meantime we are already working on the next major release - which will include several interesting new stuff - (among them tuned code for IBM BG/L - where we were able to scale to more than 4000 processors). If you have some interesting development that you would like to share with the community, scripts, or also only idea or suggestions - it is the right time to send them - and we will try to include them in the next major release. Thank you for your collaboration , Best Regards, Alessandro Curioni for the CPMD team. 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 p.hunt at imperial.ac.uk Mon Dec 6 11:30:31 2004 From: p.hunt at imperial.ac.uk (Patricia Hunt) Date: Mon, 6 Dec 2004 10:30:31 +0000 Subject: [CPMD-list] noprint of wavefunctions larger than 100 Message-ID: Hi, When using CPMD-3.9.1 and printing wavefunctions (RHOOUT BANDS) with values greater than 2 digits eg request print out of wavefunction for orbitals 125,126,127 & 128 RHOOUT BANDS 4 -125 -126 -127 -128 ONLY output file is WAVEFUNCTION.12 yet when I request print out of wavefunctions for orbitals 15,16,17, & 18 I get the expected 4 files: WAVEFUNCTION.15 WAVEFUNCTION.16 WAVEFUNCTION.17 WAVEFUNCTION.18 I couldn't find a mention in the lists? Is there a work around? Tricia. --------------------------------------------------------- Dr Patricia Hunt Department of Chemistry Imperial College London South Kensington London, SW7 2AZ Tel: 44 (0)20759-41219 e-mail: p.hunt at imperial.ac.uk web-page: http://www.ch.ic.ac.uk/hunt/ -------------------------------------------------------------- From eduard.schreiner at theochem.ruhr-uni-bochum.de Mon Dec 6 15:09:06 2004 From: eduard.schreiner at theochem.ruhr-uni-bochum.de (Eduard Schreiner) Date: Mon, 06 Dec 2004 15:09:06 +0100 Subject: [CPMD-list] noprint of wavefunctions larger than 100 In-Reply-To: References: Message-ID: <41B46802.6040709@theochem.ruhr-uni-bochum.de> Patricia Hunt wrote: > Hi, > > When using CPMD-3.9.1 and printing wavefunctions (RHOOUT BANDS) with > values greater than 2 digits > > eg request print out of wavefunction for orbitals 125,126,127 & 128 > > RHOOUT BANDS > 4 > -125 > -126 > -127 > -128 > > ONLY output file is WAVEFUNCTION.12 > > yet when I request print out of wavefunctions for orbitals 15,16,17, & > 18 I get the expected 4 files: > > WAVEFUNCTION.15 > WAVEFUNCTION.16 > WAVEFUNCTION.17 > WAVEFUNCTION.18 > > I couldn't find a mention in the lists? Is there a work around? > > Tricia. > > --------------------------------------------------------- > Dr Patricia Hunt > Department of Chemistry > Imperial College London > South Kensington > London, SW7 2AZ > Tel: 44 (0)20759-41219 > e-mail: p.hunt at imperial.ac.uk > web-page: http://www.ch.ic.ac.uk/hunt/ > -------------------------------------------------------------- > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://cpmd.org/mailman/listinfo/cpmd-list > > Hello Tricia, this problem is known. In the current version it should be fixed. Here a part from the ChangeLog: ##################### 2004-07-14 18:42 hutter * densrd.F, densto.F: adjust string length 2004-07-14 18:42 hutter * densrd.F, densto.F: Adjust string length ##################### Try to set in the file densrd.F: CHARACTER FILEN*100 CHARACTER FILIN*25 and in densto.F: CHARACTER FILEN*100 CHARACTER FILIN*(*) This should do it. Eddi -- -- ======================================================================= Eduard Schreiner e-mail: eduard.schreiner at rub.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-22121 Ruhr-Universitaet Bochum - NC 03/52 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.rub.de ======================================================================= From ewald.pauwels at UGent.be Mon Dec 6 15:33:26 2004 From: ewald.pauwels at UGent.be (Ewald Pauwels) Date: Mon, 06 Dec 2004 15:33:26 +0100 Subject: [CPMD-list] Problems optimizing monoclinic unit cell In-Reply-To: <41401A0B.4050302@UGent.be> References: <41401A0B.4050302@UGent.be> Message-ID: <41B46DB6.2060301@UGent.be> Dear all, A few months ago, I posted a question regarding a problem with optimizing the molecules in a monoclinic unit cell (original message below). After some helpfull comments (for which I am very grateful, btw), I did some further testing on this matter. I now suspect that there is a bug in the CPMD code (both in 3.7.2 and in 3.9.1)! The problem apparently lies in the treatment of the CELL keyword, as I will try to discuss. I first started out with the definition for my molecular system using the keywords SYMMETRY and CELL: &SYSTEM ANGSTROM SYMMETRY 12 CELL 5.0872 2.314338 1.073321 0.0 -0.374493314 0.0 As Bala Sundaram pointed out to me, this specific format (as given in the manual) was incorrect and should be replaced by: &SYSTEM ANGSTROM SYMMETRY 12 CELL 5.0872 2.314338 1.073321 -0.374493314 0.0 0.0 That is, the format of the CELL keyword for a monoclinic system is: a b/a c/a cos(beta) 0 0 A notification of this format is also implemented in version 3.9.1 of cpmd, although I think some mention in the manual would be helpfull. Anyhow, the calculation still failed and the reason is quite apparent in the output: ************************** SUPERCELL *************************** SYMMETRY: MONOCLINIC LATTICE CONSTANT(a.u.): 9.61341 CELL DIMENSION: 9.6134 2.3143 1.0733 -0.3745 0.0000 0.0000 VOLUME(OMEGA IN BOHR^3): 2046.33461 LATTICE VECTOR A1(BOHR): 9.6134 0.0000 0.0000 LATTICE VECTOR A2(BOHR): -8.3320 20.6296 0.0000 LATTICE VECTOR A3(BOHR): 0.0000 0.0000 10.3183 As the lattice vectors point out, the a and c axis are perpendicular!! This is obviously not in accordance with the monoclinic symmetry! As this did not solve my problem, I redid my calculation, this time with the CELL VECTORS keyword: &SYSTEM ANGSTROM CELL VECTORS 5.087 0.0 0.0 0.0 11.773 0.0 -2.04447 0.0 5.062781 This calculation was succesfull, but now in the output it appears that my molecular symmetry is TRICLINIC!! ************************** SUPERCELL *************************** SYMMETRY: TRICLINIC LATTICE CONSTANT(a.u.): 9.61304 CELL DIMENSION: 9.6130 2.3143 1.0733 0.0000 -0.3744 0.0000 VOLUME(OMEGA IN BOHR^3): 2046.13616 LATTICE VECTOR A1(BOHR): 9.6130 0.0000 0.0000 LATTICE VECTOR A2(BOHR): 0.0000 22.2477 0.0000 LATTICE VECTOR A3(BOHR): -3.8635 0.0000 9.5673 Eventually, my calculations succeeded but I hope you agree that there are certain issues with regard to the SYMMETRY and CELL keywords that need to be looked at. Sincerely, Ewald Pauwels. Ewald Pauwels wrote: > Dear all, > > Does anybody have any experience with applying CPMD on monoclinic > crystals? > The system I am studying contains four (organic) molecules in the unit > cell. When I optimize these molecules (only the atomic coordinates - > not the cell constants), I find that the unit cell no longer satisfies > the original symmetry. I.e. all four molecules have a substantially > different conformation! > > I suspect that I must be doing something wrong here. Below is my > inputfile. > > > Thanks in advance, > Ewald. > > > > ------------------------------------------------------- > inputfile > ------------------------------------------------------- > &CPMD > RESTART LATEST GEOFILE WAVEFUNCTION > OPTIMIZE GEOMETRY > LSD > ODIIS NO_RESET=50 > 10 > TIMESTEP > 20 > PRINT > 10 > STRUCTURE BONDS ANGLES > &END > > &SYSTEM > ANGSTROM > SYMMETRY > 12 > CELL > 5.0872 2.314338 1.073321 0.0 -0.374493314 0.0 > CUTOFF > 25. > MULTIPLICITY > 1 > &END > > &ATOMS > *C_VDB_U BINARY NEWF > LMAX=P > 8 > 0.218182218417937 1.473520453 0.333090471110274 > 0.732546560623109 1.717103823 -1.08374897292691 > 1.30308357695184 7.360020453 2.1982999039374 > 0.788719234746671 7.603603823 3.61513934797459 > -0.218182218417937 -1.473520453 -0.333090471110274 > -0.732546560623109 -1.717103823 1.08374897292691 > 1.73944801378772 4.412979547 2.86448084615795 > 2.25381235599289 4.169396177 1.44764140212077 > *N_VDB_U BINARY NEWF > LMAX=P > 4 > 2.03113800324446 1.040509513 -1.31410549705625 > -0.509872207874679 6.927009513 3.84549587210393 > -2.03113800324446 -1.040509513 1.31410549705625 > 3.55240379861424 4.845990487 1.21728487799143 > *O_VDB_U BINARY NEWF > LMAX=P > 8 > 1.05333382374583 1.104201443 1.19695275049904 > -1.00750738194352 1.676251513 0.53944941448416 > 0.467931971623952 6.990701443 1.33443762454863 > 2.5287731773133 7.562751513 1.99194096056352 > -1.05333382374583 -1.104201443 -1.19695275049904 > 1.00750738194352 -1.676251513 -0.53944941448416 > 2.57459961911561 4.782298557 3.72834312554672 > 0.513758413426261 4.210248487 3.07083978953184 > *H_VDB_U BINARY NEWF > LMAX=S > 20 > 2.33817143317496 1.18130282 -2.29299415508719 > 2.75812420631155 1.37791192 -0.67745575495101 > 1.93653355901116 0.03473035 -1.14763114043162 > 0.875530385150063 2.77889892 -1.22357285168305 > 0.0131007466085907 1.35318862 -1.81758891709173 > -0.816905637805185 7.06780282 4.82438453013487 > -1.23685841094177 7.26441192 3.20884612999869 > -0.415267763641377 5.92123035 3.67902151547929 > 0.645735410219716 8.66539892 3.75496322673072 > 1.50816504876119 7.23968862 4.34897929213941 > -2.33817143317496 -1.18130282 2.29299415508719 > -2.75812420631155 -1.37791192 0.67745575495101 > -1.93653355901116 -0.03473035 1.14763114043162 > -0.875530385150063 -2.77889892 1.22357285168305 > -0.0131007466085907 -1.35318862 1.81758891709173 > 3.85943722854474 4.70519718 0.23839621996049 > 4.27939000168133 4.50858808 1.85393462009667 > 3.45779935438094 5.85176965 1.38375923461606 > 2.39679618051984 3.10760108 1.30781752336463 > 1.53436654197837 4.53331138 0.713801457955944 > &END > > &DFT > LDA CORRELATION PZ > FUNCTIONAL BP > GC-CUTOFF > 5.D-5 > &END > ------------------------------------------------------------------ > > > > > > -- Ewald Pauwels Centre for Molecular Modelling Laboratory of Theoretical Physics Ghent University Proeftuinstraat 86 B-9000 Gent Belgium ewald.pauwels at UGent.be +32 9 264 65 76 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20041206/40810341/attachment.html From martin.konopka at stuba.sk Mon Dec 6 15:13:39 2004 From: martin.konopka at stuba.sk (Martin Konopka) Date: Mon, 6 Dec 2004 15:13:39 +0100 (CET) Subject: [CPMD-list] convergence perfect with OLDCODE, fails with NEWCODE Message-ID: Dear CPMD developers and users, I would like just to report that sometime the NEWCODE option (which is the default) is not working while the OLDCODE one works fine in CPMD 3.9.1. I found it when calculating wavefunctions of both O and S atoms in triplet states. I was not able to achieve convergence with the NEWCODE. I used ultrasoft pseudopotentials from David Vanderbilt's web page. Below is my NEWCODE input file. The succesful run used the same input file except that the NEWCODE keyword was replaced by the OLDCODE one. &CPMD RESTFILE 2 STORE 100 OPTIMIZE WAVEFUNCTIONS PCG CONVERGENCE ORBITALS 1.0D-7 CENTER MOLECULE OFF SPLINE POINTS QFUNCTIONS 2001 MEMORY BIG LSD &END &DFT NEWCODE GRADIENT CORRECTION PBEX PBEC GC-CUTOFF 5.0D-5 &END &SYSTEM SYMMETRY 0 POISSON SOLVER TUCKERMAN ANGSTROM CELL 13.0D0 1.0D0 1.0D0 0.0D0 0.0D0 0.0D0 TESR 4 CUTOFF 25.0D0 MULTIPLICITY 3 &END &ATOMS *O.uspp BINARY NEWF TPSEU LMAX=D 1 5.8D0 5.5D0 7.1D0 &END On the output I am getting enormous quantities like NFI GEMAX CNORM ETOT DETOT TCPU 1 4.424E+05 6.544E+04 -15.263055 0.000E+00 3.04 2 6.100E+06 1.889E+06 23.493112 3.876E+01 2.98 3 4.057E+06 1.120E+06 23.215886 -2.772E-01 2.99 4 3.780E+06 1.230E+06 23.008182 -2.077E-01 3.02 It persists when using the default optimization method or starting from random wavefunctions. Thanks for your attention to CPMD development. Best regards Martin Konopka. ------------------------------------------------------------------------ Dr. Martin Konopka http://www.ccms.elf.stuba.sk/konopka.html Department of Physics, CCMS tel: +421 (0)2 60291714 Slovak University of Technology (FEI STU) fax: +421 (0)2 65411483 Ilkovicova 3, 812 19 Bratislava, Slovakia ------------------------------------------------------------------------ From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Mon Dec 6 16:48:56 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Mon, 6 Dec 2004 16:48:56 +0100 (CET) Subject: [CPMD-list] Problems optimizing monoclinic unit cell In-Reply-To: <41B46DB6.2060301@UGent.be> Message-ID: On Mon, 6 Dec 2004, Ewald Pauwels wrote: dear ewald, [...] EW> This calculation was succesfull, but now in the output it appears that EW> my molecular symmetry is TRICLINIC!! this is to be expected. if you use CELL VECTORS, cpmd does not even try to detect cell symmetry and thus assumes a triclinic cell (and cannot take advantage of the symmetry). EW> ************************** SUPERCELL *************************** EW> SYMMETRY: TRICLINIC EW> LATTICE CONSTANT(a.u.): 9.61304 EW> CELL DIMENSION: 9.6130 2.3143 1.0733 0.0000 -0.3744 0.0000 EW> VOLUME(OMEGA IN BOHR^3): 2046.13616 EW> LATTICE VECTOR A1(BOHR): 9.6130 0.0000 0.0000 EW> LATTICE VECTOR A2(BOHR): 0.0000 22.2477 0.0000 EW> LATTICE VECTOR A3(BOHR): -3.8635 0.0000 9.5673 EW> EW> Eventually, my calculations succeeded but I hope you agree that there EW> are certain issues with regard to the SYMMETRY and CELL keywords that EW> need to be looked at. as far as i understand it - please correct me anybody, if i am mistaken, i'd really like to be certain about this - you have give the cell dimensions for the _conventional_ cell (but only the atom positions for the primitive cell). i know at least one more code, that uses the exact same conventions, so i am pretty sure, that this is intentionally so. best regards, axel. EW> EW> EW> Sincerely, EW> Ewald Pauwels. EW> EW> EW> EW> EW> Ewald Pauwels wrote: EW> EW> > Dear all, EW> > EW> > Does anybody have any experience with applying CPMD on monoclinic EW> > crystals? EW> > The system I am studying contains four (organic) molecules in the unit EW> > cell. When I optimize these molecules (only the atomic coordinates - EW> > not the cell constants), I find that the unit cell no longer satisfies EW> > the original symmetry. I.e. all four molecules have a substantially EW> > different conformation! EW> > EW> > I suspect that I must be doing something wrong here. Below is my EW> > inputfile. EW> > EW> > EW> > Thanks in advance, EW> > Ewald. EW> > EW> > EW> > EW> > ------------------------------------------------------- EW> > inputfile EW> > ------------------------------------------------------- EW> > &CPMD EW> > RESTART LATEST GEOFILE WAVEFUNCTION EW> > OPTIMIZE GEOMETRY EW> > LSD EW> > ODIIS NO_RESET=50 EW> > 10 EW> > TIMESTEP EW> > 20 EW> > PRINT EW> > 10 EW> > STRUCTURE BONDS ANGLES EW> > &END EW> > EW> > &SYSTEM EW> > ANGSTROM EW> > SYMMETRY EW> > 12 EW> > CELL EW> > 5.0872 2.314338 1.073321 0.0 -0.374493314 0.0 EW> > CUTOFF EW> > 25. EW> > MULTIPLICITY EW> > 1 EW> > &END EW> > EW> > &ATOMS EW> > *C_VDB_U BINARY NEWF EW> > LMAX=P EW> > 8 EW> > 0.218182218417937 1.473520453 0.333090471110274 EW> > 0.732546560623109 1.717103823 -1.08374897292691 EW> > 1.30308357695184 7.360020453 2.1982999039374 EW> > 0.788719234746671 7.603603823 3.61513934797459 EW> > -0.218182218417937 -1.473520453 -0.333090471110274 EW> > -0.732546560623109 -1.717103823 1.08374897292691 EW> > 1.73944801378772 4.412979547 2.86448084615795 EW> > 2.25381235599289 4.169396177 1.44764140212077 EW> > *N_VDB_U BINARY NEWF EW> > LMAX=P EW> > 4 EW> > 2.03113800324446 1.040509513 -1.31410549705625 EW> > -0.509872207874679 6.927009513 3.84549587210393 EW> > -2.03113800324446 -1.040509513 1.31410549705625 EW> > 3.55240379861424 4.845990487 1.21728487799143 EW> > *O_VDB_U BINARY NEWF EW> > LMAX=P EW> > 8 EW> > 1.05333382374583 1.104201443 1.19695275049904 EW> > -1.00750738194352 1.676251513 0.53944941448416 EW> > 0.467931971623952 6.990701443 1.33443762454863 EW> > 2.5287731773133 7.562751513 1.99194096056352 EW> > -1.05333382374583 -1.104201443 -1.19695275049904 EW> > 1.00750738194352 -1.676251513 -0.53944941448416 EW> > 2.57459961911561 4.782298557 3.72834312554672 EW> > 0.513758413426261 4.210248487 3.07083978953184 EW> > *H_VDB_U BINARY NEWF EW> > LMAX=S EW> > 20 EW> > 2.33817143317496 1.18130282 -2.29299415508719 EW> > 2.75812420631155 1.37791192 -0.67745575495101 EW> > 1.93653355901116 0.03473035 -1.14763114043162 EW> > 0.875530385150063 2.77889892 -1.22357285168305 EW> > 0.0131007466085907 1.35318862 -1.81758891709173 EW> > -0.816905637805185 7.06780282 4.82438453013487 EW> > -1.23685841094177 7.26441192 3.20884612999869 EW> > -0.415267763641377 5.92123035 3.67902151547929 EW> > 0.645735410219716 8.66539892 3.75496322673072 EW> > 1.50816504876119 7.23968862 4.34897929213941 EW> > -2.33817143317496 -1.18130282 2.29299415508719 EW> > -2.75812420631155 -1.37791192 0.67745575495101 EW> > -1.93653355901116 -0.03473035 1.14763114043162 EW> > -0.875530385150063 -2.77889892 1.22357285168305 EW> > -0.0131007466085907 -1.35318862 1.81758891709173 EW> > 3.85943722854474 4.70519718 0.23839621996049 EW> > 4.27939000168133 4.50858808 1.85393462009667 EW> > 3.45779935438094 5.85176965 1.38375923461606 EW> > 2.39679618051984 3.10760108 1.30781752336463 EW> > 1.53436654197837 4.53331138 0.713801457955944 EW> > &END EW> > EW> > &DFT EW> > LDA CORRELATION PZ EW> > FUNCTIONAL BP EW> > GC-CUTOFF EW> > 5.D-5 EW> > &END EW> > ------------------------------------------------------------------ EW> > EW> > EW> > EW> > EW> > EW> > EW> EW> EW> -- ======================================================================= Dr. 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From eunggun.kim at chemistry.gatech.edu Mon Dec 6 20:22:22 2004 From: eunggun.kim at chemistry.gatech.edu (Eung-Gun Kim) Date: Mon, 6 Dec 2004 14:22:22 -0500 Subject: [CPMD-list] Discrepancy between MORTENSEN and TUCKERMAN Message-ID: <1102360942.41b4b16eaa2bc@webmail.mail.gatech.edu> Dear List Subscribers, I was comparing results from three different methods, namely, PBC, TUCKERMAN, and MORTENSEN, for calculating an isolated molecule and noticed a significant deviation with the choice of MORTENSEN. Test conditions and observations are summarized below: 1) CPMD 3.9.1 on IBM SP4 2) box size: 25 x 25 x 25 A for all three methods spatial dimension of the molecule ~ 10 A 3) Geometry optimization was performed first under PBC, and the resulting geometry was used as input for TUCKERMAN and MORTENSEN. 4) Geometry optimization finished in one step with TUCKERMAN while it took additional *160* geometry optimization steps with MORTENSEN. 5) The optimized geometry from MORTENSEN is different--but not unphysical-- from either PBC or TUCKERMAN. 6) The total energy is also quite different for MORTENSEN: -158.02613142: PBC -158.02596806: TUCKERMAN -158.08337274: MORTENSEN I've attached a portion of my input for MORTENSEN below for your reference. For TUCKERMAN, I simply replaced the keyword MORTENSEN with TUCKERMAN. Thanks very much for reading. Best regards, EG Kim ############################################################################### &CPMD RESTART LATEST COORDINATES HESSIAN WAVEFUNCTION OPTIMIZE GEOMETRY LBFGS ODIIS 5 CONVERGENCE ORBITALS 1.D-6 ELECTROSTATIC POTENTIAL STORE 50 RESTFILE 2 &END &DFT FUNCTIONAL BLYP &END &SYSTEM ANGSTROM POINT GROUP AUTO SYMMETRY ISOLATED POISSON SOLVER MORTENSEN CELL ABSOLUTE DEGREE 25.0 25.0 25.0 90.0 90.0 90.0 CUTOFF 70 CHARGE 0 &END From mkosmows at mailbox.syr.edu Wed Dec 1 12:54:22 2004 From: mkosmows at mailbox.syr.edu (mkosmows) Date: Wed, 1 Dec 2004 06:54:22 -0500 Subject: [CPMD-list] Phonon linear response calculation question Message-ID: <41C30B2C@OrangeMail> Dear CPMD Community: I have been studying a system that gives a good geometry optimization, without negative frequencies using finite differences for vibrational analysis. However, when I try to perform a vibrational analysis by linear response, I see several messages: WARNING! First order density integral (R space) n.xxxEdd, where dd ranges from -6 to -8, and the system fails to converge. What should I try to do to get the linear response to converge? Thank you, Mark Kosmowski Graduate Student Chemistry Department Syracuse University From ewald.pauwels at UGent.be Tue Dec 7 11:20:04 2004 From: ewald.pauwels at UGent.be (Ewald Pauwels) Date: Tue, 07 Dec 2004 11:20:04 +0100 Subject: [CPMD-list] Problems optimizing monoclinic unit cell In-Reply-To: References: Message-ID: <41B583D4.8050308@UGent.be> Dear Axel, First of all I would to thank you for your swift response. >this is to be expected. if you use CELL VECTORS, cpmd does not even >try to detect cell symmetry and thus assumes a triclinic cell (and >cannot take advantage of the symmetry). > > > In retrospect, this is indeed quite logical. So, whatever the original symmetry, using CELL VECTORS would result in a "triclinic" cell in the CPMD output? >as far as i understand it - please correct me anybody, if i am mistaken, >i'd really like to be certain about this - you have give the cell dimensions >for the _conventional_ cell (but only the atom positions for the primitive cell). >i know at least one more code, that uses the exact same conventions, so >i am pretty sure, that this is intentionally so. > > Actually, I have given the cell dimensions for the _primitive_ unit cell (which is monoclinic). This cell contains four glycine molecules, for which I have specified all atom positions explicitly. So, I might have misunderstood, but I don't think I have used a conventional cell in any way. Sincerely, Ewald. -- Ewald Pauwels Centre for Molecular Modelling Laboratory of Theoretical Physics Ghent University Proeftuinstraat 86 B-9000 Gent Belgium ewald.pauwels at UGent.be +32 9 264 65 76 From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Tue Dec 7 11:40:06 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Tue, 07 Dec 2004 11:40:06 +0100 Subject: [CPMD-list] Problems optimizing monoclinic unit cell In-Reply-To: Your message of "Tue, 07 Dec 2004 11:20:04 +0100." <41B583D4.8050308@UGent.be> Message-ID: <200412071040.iB7Ae6S19809@yello.theochem.ruhr-uni-bochum.de> >>> "EP" == Ewald Pauwels writes: EP> Dear Axel, dear ewald, EP> First of all I would to thank you for your swift response. you're welcome. >> this is to be expected. if you use CELL VECTORS, cpmd does not even >> try to detect cell symmetry and thus assumes a triclinic cell (and >> cannot take advantage of the symmetry). >> >> >> EP> In retrospect, this is indeed quite logical. So, whatever the original EP> symmetry, using CELL VECTORS would result in a "triclinic" cell in the EP> CPMD output? exactly. you can see this from the source code. please have a look at the files sysin.F around lines 415 and 820 and the file setsc.F around lines 30, 73, and especially 193 (line numbers correspond to my current version, which may be a little different from the released version). >> as far as i understand it - please correct me anybody, if i am mistaken, >> i'd really like to be certain about this - you have give the cell dimensions >> for the _conventional_ cell (but only the atom positions for the primitive cell). >> i know at least one more code, that uses the exact same conventions, so >> i am pretty sure, that this is intentionally so. >> >> EP> Actually, I have given the cell dimensions for the _primitive_ unit cell EP> (which is monoclinic). This cell contains four glycine molecules, for EP> which I have specified all atom positions explicitly. So, I might have EP> misunderstood, but I don't think I have used a conventional cell in any way. this is ok, but you simply need to give the cell dimensions for the conventional cell corresponding to your primitive cell. example: bulk ZnS. which is fcc. in &SYSTEM i have: SYMMETRY FCC ANGSTROM SCALE CELL 5.42 1.0 1.0 0.0 0.0 0.0 and specify the atom coordinates as (due to SCALE in fractional coordinates): *Zn_MT_PBE_NLCC.psp KLEINMAN-BYLANDER NLCC LMAX=D LOC=S 1 0.0 0.0 0.0 *S_MT_PBE.psp KLEINMAN-BYLANDER LMAX=D 1 0.2500000000 0.2500000000 0.2500000000 best regards, axel. EP> Sincerely, EP> Ewald. EP> -- EP> Ewald Pauwels EP> Centre for Molecular Modelling EP> Laboratory of Theoretical Physics EP> Ghent University EP> Proeftuinstraat 86 EP> B-9000 Gent EP> Belgium EP> ewald.pauwels at UGent.be EP> +32 9 264 65 76 -- ======================================================================= 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From ZRLSRB at ch.ibm.com Tue Dec 7 12:33:36 2004 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Tue, 7 Dec 2004 12:33:36 +0100 Subject: [CPMD-list] Discrepancy between MORTENSEN and TUCKERMAN Message-ID: Dear Eung-Gun, is there also a difference between single-point energies (same geometry, same or random initial wavefunction)? What system do you calculate? I cannot reproduce such a large difference (i.e., I get the same numbers for both Poisson solvers for your settings with ethylene up to 10^-5 atomic units and very parallel evolution of the optimization). It's possible that you are converging to two slightly separated local minima. Did you make sure there is enough empty space in each direction? Just a hint for easier convergence: If you are using quite a tough convergence criterion such as 10^-6 AU and have a healthy system, I'd strongly recommend using CONVERGENCE ADAPT (e.g. 0.02) and (if not restarting from a good wavefunction) CONVERGENCE INITIAL (e.g. 0.02 times the gradient on ions you expect for the first step). Could you please tell us more about your system? Best regards, Salomon From hjsongmoru at hotmail.com Tue Dec 7 14:59:25 2004 From: hjsongmoru at hotmail.com (Song Huajie) Date: Tue, 7 Dec 2004 21:59:25 +0800 Subject: [CPMD-list] Qusestion about the functionality of &VDW References: <200411270454.FAA38094@cpmd.org> Message-ID: Dear CPMD experters, To study the dispersion bound systems (organic clusters and solids), I intend to use the functionality (&VDW) of CPMD that adds van der Waals (dispersion) term to DFT. Unfortunately, The Manual of CPMD does not offer more information about it. I would like to know whether or not to activate the &VDW when performing energy minimization and (or) molecular dynamics. I am very hopeful that he who has been used this &VDW can response or offer some input files for carring out this functionality. Your help will be appreciated. With best regards, H.-J. Song From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Tue Dec 7 16:13:27 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Tue, 7 Dec 2004 16:13:27 +0100 (CET) Subject: [CPMD-list] Qusestion about the functionality of &VDW In-Reply-To: Message-ID: On Tue, 7 Dec 2004, Song Huajie wrote: HS> Dear CPMD experters, dear hj song, please have a look at the 'vdw' subdirectory of the CPMD-test archive. it contains two examples for the use of this feature. you may also want to have a look at chem. phys. lett. 331(2000), 339-345 and chem. phys. lett. 360(2002), 487-493 for two successful applications of the VDW correction. HS> To study the dispersion bound systems (organic clusters and solids), I HS> intend to use the functionality (&VDW) of CPMD that adds van der Waals HS> (dispersion) term to DFT. Unfortunately, The Manual of CPMD does not HS> offer more information about it. I would like to know whether or not HS> to activate the &VDW when performing energy minimization and (or) HS> molecular dynamics. I am very hopeful that he who has been used this HS> &VDW can response or offer some input files for carring out this i have not used the feature myself, but i only makes sense to me, to use it consistently for all calculations. best regards, axel kohlmeyer. HS> functionality. Your help will be appreciated. HS> With best regards, HS> H.-J. Song HS> HS> HS> HS> HS> _______________________________________________ HS> CPMD-list mailing list HS> CPMD-list at cpmd.org HS> http://cpmd.org/mailman/listinfo/cpmd-list HS> HS> -- ======================================================================= Dr. 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From eunggun.kim at chemistry.gatech.edu Tue Dec 7 17:06:23 2004 From: eunggun.kim at chemistry.gatech.edu (Eung-Gun Kim) Date: Tue, 7 Dec 2004 11:06:23 -0500 Subject: [CPMD-list] Discrepancy between MORTENSEN and TUCKERMAN In-Reply-To: References: Message-ID: <1102435583.41b5d4ff20b2d@webmail.mail.gatech.edu> Dear Salomon, Thanks very much for kindly replying to my posted message. The system I tested is a rod-like molecule aligned along a body diagonal. I used the body diagonal orientation in order to accommodate this 18 A long molecule within the maximum box size (25x25x25) I could run without G-Vec ordering errors. This molecular orientation reduces the spatial dimensions of the molecule down to 10 A in all three directions, leaving about 7.5 A space between the molecule and the closest box surface. I've attached a complete input and output geometry file from a MORTENSEN run for your reference. The input geometry is very close to a structure that I get from PBC or TUCKERMAN. In the output geometry, however, you will find MORTENSEN has changed the torsion angle at a phenyl-phenyl bond by almost 180 deg. Thanks again for your help and also the suggestion on the use of CONVERGENCE ADAPT. Regards, Eung-Gun Quoting Salomon Billeter : > > > > > Dear Eung-Gun, > > is there also a difference between single-point energies (same geometry, > same or random initial wavefunction)? What system do you calculate? I > cannot reproduce such a large difference (i.e., I get the same numbers for > both Poisson solvers for your settings with ethylene up to 10^-5 atomic > units and very parallel evolution of the optimization). It's possible that > you are converging to two slightly separated local minima. Did you make > sure there is enough empty space in each direction? > Just a hint for easier convergence: If you are using quite a tough > convergence criterion such as 10^-6 AU and have a healthy system, I'd > strongly recommend using CONVERGENCE ADAPT (e.g. 0.02) and (if not > restarting from a good wavefunction) CONVERGENCE INITIAL (e.g. 0.02 times > the gradient on ions you expect for the first step). > Could you please tell us more about your system? > > Best regards, > Salomon > > -------------- next part -------------- A non-text attachment was scrubbed... Name: bfo.inp Type: application/octet-stream Size: 2515 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20041207/31c43c60/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: GEOMETRY.xyz Type: chemical/x-xyz Size: 5849 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20041207/31c43c60/attachment.xyz From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Tue Dec 7 18:19:32 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Tue, 07 Dec 2004 18:19:32 +0100 Subject: [CPMD-list] Postdoc and PhD positions Message-ID: <200412071719.iB7HJWe03788@yello.theochem.ruhr-uni-bochum.de> dear cpmd-list subscribers, on behalf of prof. dominik marx i'd like to post the following announcement. regards, axel kohlmeyer. ========================================================================== Center of Theoretical Chemistry, Ruhr-Universitaet Bochum, Germany Applications are invited for one Research Associate and two PhD positions, please check http://www.theochem.rub.de/go/jobs.html for details. Candidates should send a detailed resume including an outline of their achievements and interests as well as contact information for academic references to office at theochem.rub.de Professor Dominik Marx Lehrstuhl fuer Theoretische Chemie Ruhr-Universitaet Bochum 44780 Bochum, Germany Email: office at theochem.rub.de Fax: ++49 234 32 14045 URL: http://www.theochem.rub.de/ Consideration of candidates will begin immediately and continue until the position is filled. The University particularly welcomes applications from women. ========================================================================== -- ======================================================================= 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From hutter at pci.unizh.ch Tue Dec 7 18:42:10 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Tue, 7 Dec 2004 18:42:10 +0100 (MET) Subject: [CPMD-list] convergence perfect with OLDCODE, fails with NEWCODE In-Reply-To: References: Message-ID: Hi this problem occurs because the two implementation of functionals use a different approach for the low density and low gradient limit. The PBE functional was specially affected (see also some older postings). In the upcomming release the behavior of OLDCODE and NEWCODE should also for PBE be comparable. The difference of the two implementation is mainly speed. Newcode should always be faster (on some computer architectures much faster). regards Juerg Hutter > Dear CPMD developers and users, > > I would like just to report that sometime the NEWCODE option (which is the > default) is not working while the OLDCODE one works fine in CPMD 3.9.1. > I found it when calculating wavefunctions of both O and S atoms in triplet > states. I was not able to achieve convergence with the NEWCODE. I used > ultrasoft pseudopotentials from David Vanderbilt's web page. Below is my > NEWCODE input file. The succesful run used the same input file except that > the NEWCODE keyword was replaced by the OLDCODE one. > > > &CPMD > RESTFILE > 2 > STORE > 100 > OPTIMIZE WAVEFUNCTIONS > PCG > CONVERGENCE ORBITALS > 1.0D-7 > CENTER MOLECULE OFF > SPLINE POINTS QFUNCTIONS > 2001 > MEMORY BIG > LSD > &END > > &DFT > NEWCODE > GRADIENT CORRECTION PBEX PBEC > GC-CUTOFF > 5.0D-5 > &END > > &SYSTEM > SYMMETRY > 0 > POISSON SOLVER TUCKERMAN > ANGSTROM > CELL > 13.0D0 1.0D0 1.0D0 0.0D0 0.0D0 0.0D0 > TESR > 4 > CUTOFF > 25.0D0 > MULTIPLICITY > 3 > &END > > &ATOMS > *O.uspp BINARY NEWF TPSEU > LMAX=D > 1 > 5.8D0 5.5D0 7.1D0 > &END > > > On the output I am getting enormous quantities like > > NFI GEMAX CNORM ETOT DETOT TCPU > 1 4.424E+05 6.544E+04 -15.263055 0.000E+00 3.04 > 2 6.100E+06 1.889E+06 23.493112 3.876E+01 2.98 > 3 4.057E+06 1.120E+06 23.215886 -2.772E-01 2.99 > 4 3.780E+06 1.230E+06 23.008182 -2.077E-01 3.02 > > It persists when using the default optimization method or starting from > random wavefunctions. > > Thanks for your attention to CPMD development. > Best regards > Martin Konopka. > > > ------------------------------------------------------------------------ > Dr. Martin Konopka http://www.ccms.elf.stuba.sk/konopka.html > Department of Physics, CCMS tel: +421 (0)2 60291714 > Slovak University of Technology (FEI STU) fax: +421 (0)2 65411483 > Ilkovicova 3, 812 19 Bratislava, Slovakia > ------------------------------------------------------------------------ > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Wed Dec 8 09:56:59 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Wed, 8 Dec 2004 09:56:59 +0100 (MET) Subject: [CPMD-list] Discrepancy between MORTENSEN and TUCKERMAN Message-ID: Hi some words on the Poisson solver for isolated systems. There are three solvers for isolated systems implemented in CPMD: Hockney, Tuckerman, Mortensen The Hockney solver is the most thorough method, but it's not working with all options (especially linear response). Requirements are that the molecule is in the middle of the box and that the electron density falls off to zero within the box. The 1/r interaction is correctly included for the full box. The Tuckerman solver works in Fourier space alone using a numerical approximation to 1/r. The maximum extend is L/2 (L is the box length). To be exact this requires that L is twice the extend of the charge distribution of the molecule. With oder words the box should be twice the size of the Hockney box. In real application this requirement is relaxed and a smaller box can be used with good accuracy. Finally the Mortensen solver is just an analytic solver in Fourier space for spherical boundary conditions. The same restrictions as for the Tuckerman solver hold. In addition, using smaller boxes is restricted by the fact that the 1/r term works only within a sphere inscribed within the box. Comming back to the problem described in the original posting I would guess that the box size was large enough for the Tuckerman solver but not for the Mortensen solver. regards Juerg Hutter ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- From nevil at fermi.kaist.ac.kr Wed Dec 8 14:14:24 2004 From: nevil at fermi.kaist.ac.kr (Nevil) Date: Wed, 8 Dec 2004 22:14:24 +0900 Subject: [CPMD-list] the problem of MD simulation of H2O molecular Message-ID: <001d01c4dd27$d6787ca0$333ef88f@nurapt69oqv9ii> Hi everyone: I download the input file of H2O molecular at this website: http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part5.html#chap7_sect1 After the wavefuntion optimization, I wanted to continue the MD simulation of the H2O molecular. But I failed to get the result. The program seemed it couldn't converge. Is there anybody who have met this kind of problem? Please give me some advise. Thank you all very much. Good luck and happy new year. ^^ The input file of MD simulation and the output are following: Input file: &CPMD MOLECULAR DYNAMICS CP RESTART WAVEFUNCTION COORDINATES LATEST TRAJECTORY XYZ MAXSTEP 100 TIMESTEP 4.0 TEMOCONTROL IONS 300 ELECTROSTATIC POTENTIAL RHOOUT &END &DFT FUNCTIONAL PBE &END &SYSTEM SYMMETRY 0 CUTOFF 120.0 ANGSTROM CELL 6.0 1.0 1.0 0.0 0.0 0.0 &END &ATOMS *O_MT_PBE KLEINMAN-BYLANDER LMAX=P 1 2.904516 3.000000 2.926732 *H_MT_PBE KLEINMAN-BYLANDER LMAX=S 2 2.900437 3.000000 3.897528 3.841176 3.000000 2.671532 &END And the output file: NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU 1 0.00000 0.0 -17.21135 -17.21135 -17.21135 0.108E-09 1.89 2 0.00000 0.0 -17.21135 -17.21135 -17.21135 0.171E-08 1.87 3 0.00000 0.1 -17.21135 -17.21135 -17.21135 0.857E-08 1.88 4 0.00000 0.1 -17.21135 -17.21135 -17.21135 0.267E-07 1.88 5 0.00000 0.2 -17.21135 -17.21135 -17.21135 0.643E-07 1.87 6 0.00000 0.3 -17.21135 -17.21135 -17.21135 0.131E-06 1.88 7 0.00000 0.3 -17.21136 -17.21135 -17.21135 0.240E-06 1.88 8 0.00000 0.4 -17.21136 -17.21135 -17.21135 0.403E-06 1.88 9 0.00000 0.5 -17.21136 -17.21135 -17.21135 0.635E-06 1.87 10 0.00000 0.6 -17.21136 -17.21135 -17.21135 0.952E-06 1.88 11 0.00000 0.8 -17.21136 -17.21135 -17.21135 0.137E-05 1.87 12 0.00000 0.9 -17.21134 -17.21134 -17.21133 0.191E-05 1.88 13 0.00002 1.0 -17.21127 -17.21127 -17.21125 0.260E-05 1.88 14 0.00009 1.1 -17.21089 -17.21088 -17.21079 0.343E-05 1.88 15 0.00050 1.2 -17.20877 -17.20876 -17.20826 0.447E-05 1.88 16 0.00278 1.5 -17.19707 -17.19705 -17.19428 0.563E-05 1.88 17 0.01544 1.4 -17.13222 -17.13221 -17.11676 0.719E-05 1.89 18 0.08574 2.0 -16.77173 -16.77171 -16.68598 0.851E-05 1.90 19 0.47317 0.8 -14.76271 -14.76270 -14.28953 0.112E-04 1.90 20 2.51965 2.6 -3.39605 -3.39602 -0.87638 0.109E-04 1.90 21 9.54015 77.3 68.11950 68.12023 77.66038 0.154E-04 1.91 22 NaN NaN NaN NaN NaN 0.685E-05 403.49 23 NaN NaN NaN NaN NaN NaN 410.48 24 NaN NaN NaN NaN NaN NaN 410.67 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20041208/d47e878f/attachment.html From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Wed Dec 8 14:56:57 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Wed, 8 Dec 2004 14:56:57 +0100 (CET) Subject: [CPMD-list] the problem of MD simulation of H2O molecular In-Reply-To: <001d01c4dd27$d6787ca0$333ef88f@nurapt69oqv9ii> Message-ID: On Wed, 8 Dec 2004, Nevil wrote: hello nevil, your time step is too large, so your CP-MD diverges after a while. try using TIMESTEP 3.0 or less. alternatively you can increase the fictitious electron mass, but that may take you further away from the BO-surface and give a larger 'dragging' effect. btw: it has to be TEMPCONTROL IONS 300.0 30.0 or so (i.e. 'TEMP' and not 'TEMO', and two numbers, the target temperature and the delta for when to rescale the velocities.) btw^2: you won't really need a cutoff of 120ry for those pseudopotentials for MD. about 85ry should do about as well. the 120ry was mainly needed to get nicer/smoother cubefiles. regards, axel. N> Hi everyone: N> N> I download the input file of H2O molecular at this website: N> N> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part5.html#chap7_sect1 N> N> After the wavefuntion optimization, I wanted to continue the MD simulation of the H2O molecular. But I failed to get the result. The program seemed it couldn't converge. N> N> Is there anybody who have met this kind of problem? Please give me some advise. N> N> Thank you all very much. Good luck and happy new year. ^^ N> N> The input file of MD simulation and the output are following: N> N> Input file: N> N> &CPMD N> MOLECULAR DYNAMICS CP N> RESTART WAVEFUNCTION COORDINATES LATEST N> TRAJECTORY XYZ N> MAXSTEP N> 100 N> TIMESTEP N> 4.0 N> TEMOCONTROL IONS N> 300 N> ELECTROSTATIC POTENTIAL N> RHOOUT N> &END N> N> &DFT N> FUNCTIONAL PBE N> &END N> N> &SYSTEM N> SYMMETRY N> 0 N> CUTOFF N> 120.0 N> ANGSTROM N> CELL N> 6.0 1.0 1.0 0.0 0.0 0.0 N> &END N> N> &ATOMS N> N> *O_MT_PBE KLEINMAN-BYLANDER N> LMAX=P N> 1 N> 2.904516 3.000000 2.926732 N> N> *H_MT_PBE KLEINMAN-BYLANDER N> LMAX=S N> 2 N> 2.900437 3.000000 3.897528 N> 3.841176 3.000000 2.671532 N> N> &END N> N> And the output file: N> N> NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU N> 1 0.00000 0.0 -17.21135 -17.21135 -17.21135 0.108E-09 1.89 N> 2 0.00000 0.0 -17.21135 -17.21135 -17.21135 0.171E-08 1.87 N> 3 0.00000 0.1 -17.21135 -17.21135 -17.21135 0.857E-08 1.88 N> 4 0.00000 0.1 -17.21135 -17.21135 -17.21135 0.267E-07 1.88 N> 5 0.00000 0.2 -17.21135 -17.21135 -17.21135 0.643E-07 1.87 N> 6 0.00000 0.3 -17.21135 -17.21135 -17.21135 0.131E-06 1.88 N> 7 0.00000 0.3 -17.21136 -17.21135 -17.21135 0.240E-06 1.88 N> 8 0.00000 0.4 -17.21136 -17.21135 -17.21135 0.403E-06 1.88 N> 9 0.00000 0.5 -17.21136 -17.21135 -17.21135 0.635E-06 1.87 N> 10 0.00000 0.6 -17.21136 -17.21135 -17.21135 0.952E-06 1.88 N> 11 0.00000 0.8 -17.21136 -17.21135 -17.21135 0.137E-05 1.87 N> 12 0.00000 0.9 -17.21134 -17.21134 -17.21133 0.191E-05 1.88 N> 13 0.00002 1.0 -17.21127 -17.21127 -17.21125 0.260E-05 1.88 N> 14 0.00009 1.1 -17.21089 -17.21088 -17.21079 0.343E-05 1.88 N> 15 0.00050 1.2 -17.20877 -17.20876 -17.20826 0.447E-05 1.88 N> 16 0.00278 1.5 -17.19707 -17.19705 -17.19428 0.563E-05 1.88 N> 17 0.01544 1.4 -17.13222 -17.13221 -17.11676 0.719E-05 1.89 N> 18 0.08574 2.0 -16.77173 -16.77171 -16.68598 0.851E-05 1.90 N> 19 0.47317 0.8 -14.76271 -14.76270 -14.28953 0.112E-04 1.90 N> 20 2.51965 2.6 -3.39605 -3.39602 -0.87638 0.109E-04 1.90 N> 21 9.54015 77.3 68.11950 68.12023 77.66038 0.154E-04 1.91 N> 22 NaN NaN NaN NaN NaN 0.685E-05 403.49 N> 23 NaN NaN NaN NaN NaN NaN 410.48 N> 24 NaN NaN NaN NaN NaN NaN 410.67 N> N> -- ======================================================================= Dr. 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From archilles02 at gmail.com Wed Dec 8 17:46:15 2004 From: archilles02 at gmail.com (Archilles) Date: Wed, 8 Dec 2004 11:46:15 -0500 Subject: [CPMD-list] How to rerun the same job for statistical purpose? Message-ID: Dear all, I tried to rerun the same CPMD simulation job several times to obtain statistical sense of multiple simulations. By "the same CPMD simulation job ", I mean the identical input file. But what I got is the identical output files. After changing the temperature by 1 K, each step KS energy remains the same with two different runs. The trajectory also remains the same for two runs. What I expected is that each run are simillar, but quite different from each other. Maybe each run the program use the same random seed to start the simulation, which leads to the same results. Is there any way to change it each time? Therefore, I can run the same job more than once, and get different results to inspect the statistical properties of the system. Thank you very much. Peng From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Wed Dec 8 18:36:26 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Wed, 8 Dec 2004 18:36:26 +0100 (CET) Subject: [CPMD-list] How to rerun the same job for statistical purpose? In-Reply-To: Message-ID: On Wed, 8 Dec 2004, Archilles wrote: dear peng, AP> Dear all, AP> AP> AP> I tried to rerun the same CPMD simulation job several times to obtain AP> statistical sense of multiple simulations. By "the same CPMD AP> simulation job ", I mean the identical input file. But what I got is AP> the identical output files. well, if you start every time from the same coordinates and electron structure (i.e. the same RESTART file), you should get the same trajectory for quite a while until some numerical noise kicks in and the trajectories will gradually diverge. if you use the restart written at the end of each simulation to start the next run, there should be differences. AP> After changing the temperature by 1 K, each step KS energy remains the AP> same with two different runs. that depends on what kind of thermostatting you use. with TEMPCONTROL IONS for example, the change by 1K will only affect the simulation, if the instantaneous temperature with be outside of the given bounds. it may be helpful, if you'd post your input (or at least the part up to the coordinates section, if you have a large system). AP> The trajectory also remains the same for two runs. AP> AP> What I expected is that each run are simillar, but quite different AP> from each other. Maybe each run the program use the same random seed AP> to start the simulation, which leads to the same results. Is there any why a random seed? you are doing molecular dynamics, in which the new positions are determined from the old positions of the atoms and the forces on them. AP> way to change it each time? Therefore, I can run the same job more AP> than once, and get different results to inspect the statistical AP> properties of the system. due to ergodicity hypothesis, you only have to run the MD long enough to sample phase space, povided you are in equilibrium, and the average over them. of course you could also use different starting coordinates and thus have independent trajectories, but those you'd have to create yourself. regards, axel kohlmeyer. AP> AP> Thank you very much. AP> AP> Peng AP> _______________________________________________ AP> CPMD-list mailing list AP> CPMD-list at cpmd.org AP> http://cpmd.org/mailman/listinfo/cpmd-list AP> AP> -- ======================================================================= Dr. 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From cur at zurich.ibm.com Thu Dec 9 10:53:32 2004 From: cur at zurich.ibm.com (Alessandro Curioni) Date: Thu, 9 Dec 2004 10:53:32 +0100 Subject: [CPMD-list] How to rerun the same job for statistical purpose? In-Reply-To: Message-ID: Some clarifications: -the first time you start an MD after a wfn optimization you have positions assigned but not velocities - the velocity are assigned randomly using a Maxwell distribution for the ions for a temperature T - the seed for this depends on timec() so you will get different velocity distributions for different runs - Of course this is not true if you start your dynamics with T=0 - all the initial velocities will be zero - and you will have identical dynamics (divergences only on very long runs)- small changes of the temperature (1K) (this dipends however on the temperature control chosen) could remain hidden for many steps since the coupled electrons-ions system has a finite relaxation time. Moreover - if you want to have independent trajectories to calculate ensemble averages - you can create them using the randomize coordinates keyword (see manual) followed by a quench bo (see manual) - without having to randomize the initial coordinates by hand. Ciao. 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 Axel Kohlmeyer Archilles , Sent by: cpmd-list-bounces cc @cpmd.org Subject Re: [CPMD-list] How to rerun the 12/08/2004 06:36 same job for statistical purpose? PM On Wed, 8 Dec 2004, Archilles wrote: dear peng, AP> Dear all, AP> AP> AP> I tried to rerun the same CPMD simulation job several times to obtain AP> statistical sense of multiple simulations. By "the same CPMD AP> simulation job ", I mean the identical input file. But what I got is AP> the identical output files. well, if you start every time from the same coordinates and electron structure (i.e. the same RESTART file), you should get the same trajectory for quite a while until some numerical noise kicks in and the trajectories will gradually diverge. if you use the restart written at the end of each simulation to start the next run, there should be differences. AP> After changing the temperature by 1 K, each step KS energy remains the AP> same with two different runs. that depends on what kind of thermostatting you use. with TEMPCONTROL IONS for example, the change by 1K will only affect the simulation, if the instantaneous temperature with be outside of the given bounds. it may be helpful, if you'd post your input (or at least the part up to the coordinates section, if you have a large system). AP> The trajectory also remains the same for two runs. AP> AP> What I expected is that each run are simillar, but quite different AP> from each other. Maybe each run the program use the same random seed AP> to start the simulation, which leads to the same results. Is there any why a random seed? you are doing molecular dynamics, in which the new positions are determined from the old positions of the atoms and the forces on them. AP> way to change it each time? Therefore, I can run the same job more AP> than once, and get different results to inspect the statistical AP> properties of the system. due to ergodicity hypothesis, you only have to run the MD long enough to sample phase space, povided you are in equilibrium, and the average over them. of course you could also use different starting coordinates and thus have independent trajectories, but those you'd have to create yourself. regards, axel kohlmeyer. AP> AP> Thank you very much. AP> AP> Peng AP> _______________________________________________ AP> CPMD-list mailing list AP> CPMD-list at cpmd.org AP> http://cpmd.org/mailman/listinfo/cpmd-list AP> AP> -- ======================================================================= Dr. 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. _______________________________________________ CPMD-list mailing list CPMD-list at cpmd.org http://cpmd.org/mailman/listinfo/cpmd-list From hutter at pci.unizh.ch Thu Dec 9 13:10:36 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 9 Dec 2004 13:10:36 +0100 (MET) Subject: [CPMD-list] Phonon linear response calculation question In-Reply-To: <41C30B2C@OrangeMail> References: <41C30B2C@OrangeMail> Message-ID: Hi did you use VIBRATIONAL ANALYSIS LR ? This option seems to be brocken and has at least one known bug when used together with Goedecker PP. Please use either finite differences or the linear response code with the Keyword LINEAR RESPONSE (see manual) regards Juerg Hutter ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Wed, 1 Dec 2004, mkosmows wrote: > Dear CPMD Community: > > I have been studying a system that gives a good geometry optimization, without > negative frequencies using finite differences for vibrational analysis. > However, when I try to perform a vibrational analysis by linear response, I > see several messages: WARNING! First order density integral (R space) > n.xxxEdd, where dd ranges from -6 to -8, and the system fails to converge. > > What should I try to do to get the linear response to converge? > > Thank you, > > Mark Kosmowski > Graduate Student > Chemistry Department > Syracuse University > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://cpmd.org/mailman/listinfo/cpmd-list > From archilles02 at gmail.com Thu Dec 9 17:13:54 2004 From: archilles02 at gmail.com (Archilles) Date: Thu, 9 Dec 2004 11:13:54 -0500 Subject: [CPMD-list] How to rerun the same job for statistical purpose? In-Reply-To: References: Message-ID: Thank you all for your help. After reading all the replies, I think I have the following options to do what I want: 1) Run a certain LONG time, I will get good enough statistical simulation results 2) Change the default random number generator DURAND to a different one, then recompile the CPMD code. 3) Use RANDOMIZE COORDINATES combined with QUENCH BO keywords to randomize the optimized initial position Since I am interested in selectivity of epoxide ring openning (two possible positions), once the ring openned, I cannot afford to run it until the reaction reverse and happen again: it take about 80 hours to see the ring openning, and even after 200 hours running the system remained as product. Here I would like to try RANDOMIZE COORDINATES with QUENCH BO method. Here is the input file I am using. With "# New Line", it means I just added these lines. Thanks again for all of you. Best regards, Peng &CPMD MOLECULAR DYNAMICS CP RESTART WAVEFUNCTION COORDINATES LATEST RANDOMIZE COORDINATES #New Line 0.03 #New Line QUENCH BO #New Line TEMPERATURE 401.0 NOSE IONS MASSIVE 300.0 2500.0 NOSE ELECTRONS 0.02 10000.0 TRAJECTORY SAMPLE 10 TIMESTEP 4.0 EMASS 600.0 STORE 1000 &END &SYSTEM ANGSTROM SYMMETRY 0 CHARGE 0.0 CELL 15.0 1.0 1.0 0.0 0.0 0.0 CUTOFF 70.0 &END &DFT NEWCODE FUNCTIONAL BLYP GC-CUTOFF 5.0E-06 &END &ATOMS *C_SG_BLYP LMAX=P 22 -6.9130 1.3380 -1.9970 -5.7840 2.2900 -1.5960 -6.9190 3.7400 0.0690 -7.3940 5.1700 0.3920 -8.4160 5.5820 -0.6650 -6.2570 6.2120 0.5080 -6.7610 7.5060 1.1690 -5.6270 8.5220 1.3030 -5.0740 8.8240 -0.0890 -7.6830 1.9180 -3.1830 -8.2440 3.2810 -2.7830 -7.1100 4.2350 -2.3700 -7.6660 5.6270 -1.9930 -6.5990 6.7350 -1.9070 -4.5670 7.5340 -0.7380 -3.9110 5.5590 -4.9450 -2.1500 4.7170 -3.5660 -1.3830 6.0130 -3.3180 -0.6140 5.7760 -1.8780 -1.0240 4.3720 -1.4430 -1.5720 4.3780 -0.0050 2.3010 5.2530 -4.7730 *O_SG_BLYP LMAX=P 4 -3.5560 4.9740 -3.6850 -1.6790 6.5400 -2.1270 -2.0690 3.9290 -2.3520 1.2320 5.0660 -3.9860 *N_SG_BLYP LMAX=P 3 -6.2870 3.6510 -1.2740 -5.6240 6.4910 -0.8120 -2.6290 3.3550 0.1640 *Li_SG_BLYP LMAX=P 1 -4.0840 4.6790 -1.3450 *H_SG_BLYP LMAX=S 40 -5.2530 1.8710 -0.7400 -5.0860 2.3580 -2.4320 -6.2030 3.4310 0.8320 -7.7790 3.0730 0.1250 -7.9050 5.1240 1.3560 -8.8470 6.5570 -0.4430 -9.2360 4.8660 -0.6940 -5.4970 5.7960 1.1700 -7.1450 7.2790 2.1650 -7.5590 7.9680 0.5910 -6.0100 9.4400 1.7510 -4.8380 8.1180 1.9390 -5.8470 9.2870 -0.7030 -4.2450 9.5270 0.0040 -6.4860 0.3770 -2.2880 -7.5920 1.1710 -1.1600 -7.0190 2.0260 -4.0420 -8.5020 1.2490 -3.4490 -8.7790 3.7010 -3.6360 -8.9550 3.1290 -1.9730 -6.4720 4.3620 -3.2450 -8.3720 5.9270 -2.7700 -7.1080 7.6870 -1.7520 -6.0730 6.7870 -2.8610 -4.1900 7.7630 -1.7360 -3.7380 7.1600 -0.1370 -3.4340 6.5330 -5.0640 -4.9920 5.6920 -4.9880 -3.6080 4.9060 -5.7650 -1.7440 4.1560 -4.4180 -0.9720 6.5860 -4.1590 0.3790 6.1700 -1.6240 -0.1740 3.6820 -1.5260 -1.9880 5.3560 0.2410 -0.7480 4.1770 0.6830 -2.7600 3.2050 1.1620 -2.2520 2.4810 -0.1980 3.3160 5.1330 -4.2670 2.3840 6.2830 -5.2580 2.3850 4.5490 -5.6690 &END On Thu, 9 Dec 2004 10:53:32 +0100, Alessandro Curioni wrote: > > > Some clarifications: > > -the first time you start an MD after a wfn optimization you have > positions assigned but not velocities - the velocity are assigned > randomly using a Maxwell distribution for the ions for a temperature T - > the seed for this depends on timec() so you will get different velocity > distributions for different runs - Of course this is not true if you > start your dynamics with T=0 - all the initial velocities will be zero - > and you will have identical dynamics (divergences only on very long > runs)- small changes of the temperature (1K) (this dipends however on > the temperature control chosen) could remain hidden for many steps since > the coupled electrons-ions system has a finite relaxation time. > Moreover - if you want to have independent trajectories to calculate > ensemble averages - you can create them using the randomize coordinates > keyword (see manual) followed by a quench bo (see manual) - without having > to randomize the initial coordinates by hand. > > Ciao. > > 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 > > Axel Kohlmeyer > heochem.ruhr-uni- To > bochum.de> Archilles , > Sent by: > cpmd-list-bounces cc > @cpmd.org > Subject > Re: [CPMD-list] How to rerun the > 12/08/2004 06:36 same job for statistical purpose? > PM > > > > > On Wed, 8 Dec 2004, Archilles wrote: > > dear peng, > > AP> Dear all, > AP> > AP> > AP> I tried to rerun the same CPMD simulation job several times to obtain > AP> statistical sense of multiple simulations. By "the same CPMD > AP> simulation job ", I mean the identical input file. But what I got is > AP> the identical output files. > > well, if you start every time from the same coordinates and > electron structure (i.e. the same RESTART file), you should get > the same trajectory for quite a while until some numerical > noise kicks in and the trajectories will gradually diverge. > > if you use the restart written at the end of each simulation > to start the next run, there should be differences. > > AP> After changing the temperature by 1 K, each step KS energy remains the > AP> same with two different runs. > > that depends on what kind of thermostatting you use. > with TEMPCONTROL IONS for example, the change by 1K will > only affect the simulation, if the instantaneous temperature > with be outside of the given bounds. > > it may be helpful, if you'd post your input (or at least the > part up to the coordinates section, if you have a large system). > > AP> The trajectory also remains the same for two runs. > AP> > AP> What I expected is that each run are simillar, but quite different > AP> from each other. Maybe each run the program use the same random seed > AP> to start the simulation, which leads to the same results. Is there any > > why a random seed? you are doing molecular dynamics, in which the > new positions are determined from the old positions of the atoms > and the forces on them. > > AP> way to change it each time? Therefore, I can run the same job more > AP> than once, and get different results to inspect the statistical > AP> properties of the system. > > due to ergodicity hypothesis, you only have to run the MD long > enough to sample phase space, povided you are in equilibrium, > and the average over them. of course you could also use different > starting coordinates and thus have independent trajectories, but > those you'd have to create yourself. > > regards, > axel kohlmeyer. > > AP> > AP> Thank you very much. > AP> > AP> Peng > AP> _______________________________________________ > AP> CPMD-list mailing list > AP> CPMD-list at cpmd.org > AP> http://cpmd.org/mailman/listinfo/cpmd-list > AP> > AP> > > -- > > ======================================================================= > Dr. 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/~axel.kohlmeyer/ > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://cpmd.org/mailman/listinfo/cpmd-list > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > > > http://cpmd.org/mailman/listinfo/cpmd-list > From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu Dec 9 18:59:27 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 9 Dec 2004 18:59:27 +0100 (CET) Subject: [CPMD-list] How to rerun the same job for statistical purpose? In-Reply-To: Message-ID: On Thu, 9 Dec 2004, Archilles wrote: dear peng, a few remarks to your post. - there are more ways to achieve what you want: a) you could run a normal MD and use constraints to keep your reaction from happening and then start an MD from several selected, decorrelated coordinate snapshots along the trajectory. b) you could use metadynamics to determine the free energy profiles for both reaction pathways. - 200 hours (is this serial or parallel?) is not exactly excessive for cpmd calculations of larger systems. i know of simulations that have been running over a large number (20-200) processors for weeks and months. - there are some problems with your input: a) your supercell is much too small. you are using SYMMETRY 0 yet your electron density is not zero at the box border (in fact it 'wraps around', as can be easily seen from creating a DENSITY.cube file, and then visualize it ). please see the manual for the requirements of the HOCKNEY poisson solver. b) i assume you use pseudopotentials from the goedecker-hartwigsen library. a plane wave cutoff of 70.0 is (far) too small for those. AFAICT, you need at least 120ry, probably 150ry (thanks to the oxygen being rather 'hard'). c) a high GC-CUTOFF of 5.0e-6 is only needed for low CUTOFF calculations (e.g. for vanderbilt ultra-soft pseudopotentials with 25ry cutoff). for high cutoff calculations a much lower value can/should be used. AP> Thank you all for your help. AP> AP> After reading all the replies, I think I have the following options to AP> do what I want: AP> 1) Run a certain LONG time, I will get good enough statistical AP> simulation results AP> AP> 2) Change the default random number generator DURAND to a different AP> one, then recompile the CPMD code. AP> AP> 3) Use RANDOMIZE COORDINATES combined with QUENCH BO keywords to AP> randomize the optimized initial position AP> AP> Since I am interested in selectivity of epoxide ring openning (two AP> possible positions), once the ring openned, I cannot afford to run it AP> until the reaction reverse and happen again: it take about 80 hours to AP> see the ring openning, and even after 200 hours running the system AP> remained as product. Here I would like to try RANDOMIZE COORDINATES AP> with QUENCH BO method. AP> AP> Here is the input file I am using. With "# New Line", it means I just AP> added these lines. AP> AP> Thanks again for all of you. AP> AP> Best regards, AP> Peng [...] -- ======================================================================= Dr. 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From wolfi at mittelerde.physik.uni-konstanz.de Thu Dec 9 22:34:40 2004 From: wolfi at mittelerde.physik.uni-konstanz.de (Wolfram Quester) Date: Thu, 9 Dec 2004 22:34:40 +0100 Subject: [CPMD-list] Clearification in the manual In-Reply-To: References: <20041203103615.GA11439@halley.zuhause> Message-ID: <20041209213439.GA3691@halley.zuhause> Dear Axel, On Fri, Dec 03, 2004 at 12:45:14PM +0100, Axel Kohlmeyer wrote: > On Fri, 3 Dec 2004, Wolfram Quester wrote: > > dear wolfram, > > thanks for the updates. i am currently working on updating the > manual for the next release, so i will see to it, that it gets > included this time. I attach an additional update which adds a fix for a typo and a link from the explanation of "POISSON SOLVER" to the section about "Cell Size for Cluster Calculations". Since this section is quite general I'd suggest to rename it into "Calculations of isolated systems or something like this. Another thing is that "POISSON SOLVER" mentions references to the literature for HOCKNEY and TUCKERMAN but not for MORTENSEN. I guess this is not deliberate. > > if anybody else has suggestions, changes, comments, etc. > please send me your patches, texts, notes as soon as possible > and i will try to include as much as possible. > > thanks in advance, > > axel kohlmeyer. Thanks for considering, Wolfi -------------- next part -------------- --- manual.tex.orig 2004-12-03 19:30:13.000000000 +0100 +++ manual.tex 2004-12-09 22:12:33.664753632 +0100 @@ -1379,7 +1379,7 @@ wavefunction optimization cycles, the convergence criteria for the wavefunction are relaxed by a factor of two. A geometry optimization step resets the criteria to the unrelaxed values. By default, the criteria for - wavefunction convergence are never relaxed.} + wavefunction convergence are never relaxed.\\ % When starting a geometry optimization from an unconverged wavefunction, the nuclear gradient and therefore the adaptive tolerance of the electronic @@ -1387,7 +1387,7 @@ applied at the beginning, a convergence criterion for the wavefunction of the initial geometry can be supplied with {\bf CONVERGENCE INITIAL}. By default, the initial convergence criterion is equal to the full - convergence criterion. + convergence criterion.} \spekeyword{CONVERGENCE}{}{[ORBITALS, GEOMETRY, CELL]}{}{\&CPMD}{CONVERGENCE 2} \desc{The convergence criteria for optimization runs is specified. \\ @@ -2566,7 +2566,11 @@ method~\cite{Hockney70} or Martyna and Tuckerman's method~\cite{Martyna99} is used. The smoothing parameter (for Hockney's method) or $L \times \alpha$ for Tuckerman's method can be read from the - next line using the {\bf PARAMETER} keyword.} + next line using the {\bf PARAMETER} keyword. + + For more information about the usage of this parameter see also + section \ref{hints:symm0}.} + \keyword{POLAK}{}{}{}{\&RESP} \desc{ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: Digital signature Url : http://cpmd.org/pipermail/cpmd-list/attachments/20041209/d31c6360/attachment.pgp From Reinout.Declerck at UGent.be Fri Dec 10 00:24:53 2004 From: Reinout.Declerck at UGent.be (Reinout Declerck) Date: Fri, 10 Dec 2004 00:24:53 +0100 Subject: [CPMD-list] Looking for TM pseudos for Kalium (Potassium) PBE and Blyp Message-ID: <1102634693.41b8dec55a861@mail.ugent.be> Hi all, I am looking for the TM pseudos of Kalium (Potassium), using PBE and using BLYP. They are not included in de CPMD nor in the contrib section. I would be very grateful if anyone would want to share them with me. Many thanks in advance, Reinout Declerck -- From piana at power.curtin.edu.au Thu Dec 9 20:03:49 2004 From: piana at power.curtin.edu.au (Stefano Piana) Date: Fri, 10 Dec 2004 03:03:49 +0800 Subject: [CPMD-list] Gold pseudopotentials and cell parameters Message-ID: <41B8A195.1000802@power.curtin.edu.au> Dear CPMD users, I am still generating MT PBE gold pseudopotentials with not a lot of success so far. At the moment I am able to generate pseudopotentials that give a reasonable geometry for the gold dimer but that have serious convergence problems when I try to simulate the bulk gold. I tried to generate the pseudos from the Au and Au+ atom, but they do not differ much. I tried with and without NLCC but, again, not much difference there. I tried both LOC=S;P and D. LOC=S seems to give the best results. I also played a bit with the cutoff (from 50 to 80) and with the GC-CUTOFF (from 1e-6 to 5e-5) but these do not seem to change things much, a cutoff of 50 and a GC-CUTOFF of 5e-6 seem to be reasonable. Somebody suggested me that I should use a _LARGE_ number of K-Points for the bulk gold. Although I tried to run with up to 40 K-Points, I still have convergence problems and moreover it is not possible to optimize the cell with K-POints, therefore I cannot calculate the bulk properties of gold with my pseudo. An alternative is to use a bigger cell. I tried to run with 2x2x2 supercell containing 32 gold atoms, but still convergence problems arise (i.e. the wavefunction never converges). I tried also INITIALIZE WAVEFUNCTION RANDOM and to run a few steps of PCG MINIMIZE before switching to ODIIS. The second method sometimes works, but convergence seems to be a bit erratic. At the moment I am including only the 6S and 5D in the valence. IF I include the 5P as well I get very good results for the gold dimer (as expected from the literature), but the calculation is more expensive and it looks like the convergence problems for the solid state worsen. I would like to have some suggestions. If anybody has already generated a MT pseudopotential for gold could he send it to me so that I can compare with my pseudos? Stefano -- Nanochemistry Research Institute Curtin University of Technology GPO Box U1987 Perth 6845 - Western Australia tel. +61 8 9266 2687 piana at power.curtin.edu.au From ejl7240 at chemail.tamu.edu Fri Dec 10 04:46:13 2004 From: ejl7240 at chemail.tamu.edu (Eduardo J. Lamas) Date: Thu, 9 Dec 2004 21:46:13 -0600 Subject: [CPMD-list] Gold pseudopotentials and cell parameters In-Reply-To: <41B8A195.1000802@power.curtin.edu.au> Message-ID: <001401c4de6a$cb3b5760$0ee35ba5@ch0316> Dear Stefano: In the cpmd download are (contrib directory, file pseudo_ext.tar.gz) there is a Au MT pseudopotential. It is also nice because it has information about the reference states (one for s and d channels and the other for the p channel) used to build it so you can use Haman PP code in case you want to reproduce it. If I were you I will use GAUSS-HERMIT=15 instead of KLEINMAN-BYLANDER for the calculation of the non local part of the PP as it is in general recommended for transition metals. Regards, Eduardo -----Original Message----- From: cpmd-list-bounces at cpmd.org [mailto:cpmd-list-bounces at cpmd.org] On Behalf Of Stefano Piana Sent: Thursday, December 09, 2004 1:04 PM To: cpmd-list at cpmd.org Subject: [CPMD-list] Gold pseudopotentials and cell parameters Dear CPMD users, I am still generating MT PBE gold pseudopotentials with not a lot of success so far. At the moment I am able to generate pseudopotentials that give a reasonable geometry for the gold dimer but that have serious convergence problems when I try to simulate the bulk gold. I tried to generate the pseudos from the Au and Au+ atom, but they do not differ much. I tried with and without NLCC Au+ but, again, not much difference there. I tried both LOC=S;P and D. LOC=S seems to give the best results. I also played a bit with the cutoff (from 50 to 80) and with the GC-CUTOFF (from 1e-6 to 5e-5) but these do not seem to change things much, a cutoff of 50 and a GC-CUTOFF of 5e-6 seem to be reasonable. Somebody suggested me that I should use a _LARGE_ number of K-Points for the bulk gold. Although I tried to run with up to 40 K-Points, I still have convergence problems and moreover it is not possible to optimize the cell with K-POints, therefore I cannot calculate the bulk properties of gold with my pseudo. An alternative is to use a bigger cell. I tried to run with 2x2x2 supercell containing 32 gold atoms, but still convergence problems arise (i.e. the wavefunction never converges). I tried also INITIALIZE WAVEFUNCTION RANDOM and to run a few steps of PCG MINIMIZE before switching to ODIIS. The second method sometimes works, but convergence seems to be a bit erratic. At the moment I am including only the 6S and 5D in the valence. IF I include the 5P as well I get very good results for the gold dimer (as expected from the literature), but the calculation is more expensive and it looks like the convergence problems for the solid state worsen. I would like to have some suggestions. If anybody has already generated a MT pseudopotential for gold could he send it to me so that I can compare with my pseudos? Stefano -- Nanochemistry Research Institute Curtin University of Technology GPO Box U1987 Perth 6845 - Western Australia tel. +61 8 9266 2687 piana at power.curtin.edu.au _______________________________________________ CPMD-list mailing list CPMD-list at cpmd.org http://cpmd.org/mailman/listinfo/cpmd-list From Ari.P.Seitsonen at iki.fi Fri Dec 10 13:46:01 2004 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Fri, 10 Dec 2004 13:46:01 +0100 (CET) Subject: [CPMD-list] Gold pseudopotentials and cell parameters In-Reply-To: <41B8A195.1000802@power.curtin.edu.au> References: <41B8A195.1000802@power.curtin.edu.au> Message-ID: Dear Stefano, Not much about pseudo (well, you CERTAINLY shouldn't use LOC=D, you get ghosts!), your pseudo is probably okay (otherwise I can give you one). However bulk gold is METALLIC, you'll certainly have problems with ODIIS and PCG; there are too many states around the Fermi energy. You have to use broadening (FREE ENERGY FUNCTIONAL), or if you only want to dynamics, you can try using a thermostat for the electrons. Or maybe I misunderstood your problem. Greetings from Zurich, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstrasse 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland On Fri, 10 Dec 2004, Stefano Piana wrote: > Dear CPMD users, > I am still generating MT PBE gold pseudopotentials with not a lot of success > so far. > At the moment I am able to generate pseudopotentials that give a reasonable > geometry for the gold dimer but that have serious convergence problems when I > try to simulate the bulk gold. I tried to generate the pseudos from the Au and > Au+ atom, but they do not differ much. I tried with and without NLCC but, > again, not much difference there. > I tried both LOC=S;P and D. LOC=S seems to give the best results. I also > played a bit with the cutoff (from 50 to 80) and with the GC-CUTOFF (from 1e-6 > to 5e-5) but these do not seem to change things much, a cutoff of 50 and a > GC-CUTOFF of 5e-6 seem to be reasonable. > > Somebody suggested me that I should use a _LARGE_ number of K-Points for the > bulk gold. Although I tried to run with up to 40 K-Points, I still have > convergence problems and moreover it is not possible to optimize the cell with > K-POints, therefore I cannot calculate the bulk properties of gold with my > pseudo. An alternative is to use a bigger cell. I tried to run with 2x2x2 > supercell containing 32 gold atoms, but still convergence problems arise (i.e. > the wavefunction never converges). I tried also INITIALIZE WAVEFUNCTION RANDOM > and to run a few steps of PCG MINIMIZE before switching to ODIIS. The second > method sometimes works, but convergence seems to be a bit erratic. > > At the moment I am including only the 6S and 5D in the valence. IF I include > the 5P as well I get very good results for the gold dimer (as expected from > the literature), but the calculation is more expensive and it looks like the > convergence problems for the solid state worsen. > I would like to have some suggestions. If anybody has already generated a MT > pseudopotential for gold could he send it to me so that I can compare with my > pseudos? > > Stefano > -- > Nanochemistry Research Institute > Curtin University of Technology > GPO Box U1987 > Perth 6845 - Western Australia > tel. +61 8 9266 2687 > piana at power.curtin.edu.au > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://cpmd.org/mailman/listinfo/cpmd-list > From bob at bob.usuhs.mil Fri Dec 10 15:26:08 2004 From: bob at bob.usuhs.mil (Robert Williams) Date: Fri, 10 Dec 2004 09:26:08 -0500 Subject: [CPMD-list] Qusestion about the functionality of &VDW In-Reply-To: References: Message-ID: <41B9B200.4020102@bob.usuhs.mil> Dear List, With respect to VDW CORRECTION, it is not clear from the manual or from the examples how the parameters should be chosen. Of the parameters: type, i, j, \alpha_{ij}, R^{ij}_m, \beta_{ij} only the "type" of C6 is explained. (My notation is in TeX.) i,j: I gather from the source that i and j are the indexes of the atom types in the order that they are listed in the &ATOMS section. \alpha_{ij}: has to be calculated by hand using tables I and II and equation 7 from Elstner et al., I gather. However, when I do this I do not get values that are close to the values used in the cpmd/contrib/CPMD-test/vdw examples. Please someone correct me if I've made a dumb mistake. It would be very useful to know what units are expected, since three of the papers I've read all use different units for the C_6 coefficients, J nm^6 mol^{-1} (S. Grimme), \AA^6 kcal/mol (S. Serra et al. Chem. Phys. Let. 331 (2000) 339-345, one of the references Axel refers to below), and in the Elstner paper, eV/\AA^6 (!? This must surely be a typographical error in this paper. It should be eV \AA^6/mol.) The source is not informative here. The reference, M. Elstner et al., gives a damping term in equation 8 that appears to be different from that given in the cpmd manual under "VDW CORRECTION", so it is not clear how R^{ij}_m is determined. Likewise, \beta_{ij} (Elstner's "d*" in his eqn. 8), is also in question because the form of the damping terms is quite different in the manual compared to Elstner et al., a source of concern. After a cursory reading of the cpmd source, and running the examples, I am a little confused about how to choose atom types (i,j), since the types chosen for the ch4-ch4 calculation in the example both appear to be for carbon, where i and j are 1. Should not the dispersion terms here be for H? I'm waiting for an interlibrary loan to read the references by Le Sar (1984, 1987), and Elstner does refer to several other earlier papers that I've not seen yet, so perhaps I'm a little premature to submit this question to the list. Still, the manual should probably contain a little more guidance about the parameters, and about the difference between the implemented damping term and the one given in the reference. Can anyone clarify this issue? The most comprehensive recent VDW paper I've read is: S. Grimme, J Comput Chem 25: 1463-1473, 2004. Best regards, Bob Williams Axel Kohlmeyer wrote: > On Tue, 7 Dec 2004, Song Huajie wrote: > > HS> Dear CPMD experters, > > dear hj song, > > please have a look at the 'vdw' subdirectory of the > CPMD-test archive. it contains two examples for the > use of this feature. > > you may also want to have a look at > > chem. phys. lett. 331(2000), 339-345 > and > chem. phys. lett. 360(2002), 487-493 > > for two successful applications of the VDW correction. > > HS> To study the dispersion bound systems (organic clusters and solids), I > HS> intend to use the functionality (&VDW) of CPMD that adds van der Waals > HS> (dispersion) term to DFT. Unfortunately, The Manual of CPMD does not > HS> offer more information about it. I would like to know whether or not > HS> to activate the &VDW when performing energy minimization and (or) > HS> molecular dynamics. I am very hopeful that he who has been used this > HS> &VDW can response or offer some input files for carring out this > > i have not used the feature myself, but i only makes sense to me, > to use it consistently for all calculations. > > best regards, > axel kohlmeyer. > > HS> functionality. Your help will be appreciated. > > HS> With best regards, > HS> H.-J. Song > HS> > HS> > HS> > HS> > HS> _______________________________________________ > HS> CPMD-list mailing list > HS> CPMD-list at cpmd.org > HS> http://cpmd.org/mailman/listinfo/cpmd-list > HS> > HS> > -- Dr. Robert Williams Dept. of Biomedical Informatics Uniformed Services University 301-295-3568 From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Fri Dec 10 16:34:14 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Fri, 10 Dec 2004 16:34:14 +0100 (CET) Subject: [CPMD-list] Gold pseudopotentials and cell parameters In-Reply-To: <41B8A195.1000802@power.curtin.edu.au> Message-ID: On Fri, 10 Dec 2004, Stefano Piana wrote: dear stefano, what about the goedecker pbe pseudopotential i sent you? does it not work for you? is it much worse or only slightly? it has been used successfully with a cutoff as little as 45ryd. as a benefit, you don't have to worry about the treatment of the non-local part, as it is already included in the pseudopotential. SP> Somebody suggested me that I should use a _LARGE_ number of K-Points for the SP> bulk gold. Although I tried to run with up to 40 K-Points, I still have SP> convergence problems and moreover it is not possible to optimize the cell with SP> K-POints, therefore I cannot calculate the bulk properties of gold with my to be frank, the k-point support in CPMD is not as good as the support for gamma-point calculations and the direct minimizers don't work as well with k-points. convergence is (sometimes) better when using lanczos, but then again, lanczos is much slower. SP> pseudo. An alternative is to use a bigger cell. I tried to run with 2x2x2 SP> supercell containing 32 gold atoms, but still convergence problems arise (i.e. SP> the wavefunction never converges). I tried also INITIALIZE WAVEFUNCTION RANDOM SP> and to run a few steps of PCG MINIMIZE before switching to ODIIS. The second SP> method sometimes works, but convergence seems to be a bit erratic. you can also switch to lanczos for a few rounds and then go back to odiis. for the gamma point case, this can be automated with the following input: ODIIS NO_RESET=50 5 LANCZOS DIAGONALIZATION RESET=2 which will run a round of lanczos after you had two successive diis resets (which are set to happen not earlier than 50 steps apart). what also happens occasionally, is that you converge to the wrong state. one way to get out of this, is to do a car-parrinello run with a high electron mass, ANNEALING ELECTRONS and _all_ atom positions fixed to get the electron structure optimized. i've tried that recently quite successfully on some otherwise pathological cases. SP> At the moment I am including only the 6S and 5D in the valence. IF I include SP> the 5P as well I get very good results for the gold dimer (as expected from SP> the literature), but the calculation is more expensive and it looks like the SP> convergence problems for the solid state worsen. yep, that is to be expected. as ari already pointed out: gold is a metal, and using the free energy functional is a method implemented in cpmd to deal with that. however, there have been meaningful simulations of metals (e.g. gold, check out the mailing list archives), but you need to carefully tune your thermostats and watch your simulation like a raw egg. as for optimizing the cell: generally the best way of calculating the equilibrium lattice constant and the bulk modulus, is to perform a series of single point calculations with varying lattice constant and then do a Murnaghan fit. with a variable cell calculation in CPMD you don't have (in general) a constant cutoff, but constant number of plane waves, so when the cell changes, your 'effective' cutoff changes. which in turn requires that the stress tensor is not only reasonably converged (which already requires a much higher cutoff than for converged forces) but also _very_ well converged, so that the change in the effective cutoff has no side effect. in short: don't do it unless you really, really need it. there is a CONSTANT CUTOFF keyword, that tries to avoid that constant plane wave problem, but i don't know where and how well this works. you may want to check out the referred literature. but the requirement of having a converged stress tensor still holds. try it out for a simple case (e.g. bulk silicon), you will be surprised (i was). best regards, axel. SP> I would like to have some suggestions. If anybody has already generated a MT SP> pseudopotential for gold could he send it to me so that I can compare with my SP> pseudos? SP> SP> Stefano SP> -- ======================================================================= Dr. 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/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From nevil at fermi.kaist.ac.kr Sat Dec 11 14:31:49 2004 From: nevil at fermi.kaist.ac.kr (Nevil) Date: Sat, 11 Dec 2004 22:31:49 +0900 Subject: [CPMD-list] Questions of potential function and the visualization of bulk system Message-ID: <001901c4df85$c500b9a0$333ef88f@nurapt69oqv9ii> Hi everyone: I have two questions one is about the potential function and another for the visualization of bulk system. 1,For the potential function: CPMD uses the Busing potential function which doesn't include the cation-anion interactions. Is it possible to use Morse potential function which first has the same form as Busing function but then has one Morse-type potential more in it. 2,For the visualization of the bulk system: I want to follow the example for the visualization of the bulk system in this website: http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part5.html#chap7_sect5 But I don't know how to get the .cube file which has many moleculars in it. My .cube file just has one isolated molecular. Is there anyone can help me? Thank you very much. Merry Christmas. ^^ Regards. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20041211/5471a140/attachment.html From nevil at fermi.kaist.ac.kr Sun Dec 12 05:26:32 2004 From: nevil at fermi.kaist.ac.kr (Nevil) Date: Sun, 12 Dec 2004 13:26:32 +0900 Subject: [CPMD-list] How to get physical parameters of material from the result of cpmd? Message-ID: <001001c4e002$c2192240$333ef88f@nurapt69oqv9ii> Hi everyone: I am a beginner of CPMD. I want to use CPMD to simulate the thermal parameters of material. So I need the physical parameters of material after MD simulation, such as volume (m*3/mol), density (g/mol), lattice parameter, and MSD. But in the standard output file of CPMD, i just can find the final result of energies. I think the following part of ouput is from the restart file before MD simulation. And also it's not enough for the parameters. So how can I get the physical parameters of material from the final result? It's a simple question but i can't find solution in cpmd manual. Is there anyone can help me? Thank you very much. ************************** SUPERCELL *************************** THIS IS AN ISOLATED SYSTEM CALCULATION POISSON EQUATION SOLVER : HOCKNEY COULOMB SMOOTHING RADIUS : 0.810 SYMMETRY: SIMPLE CUBIC LATTICE CONSTANT(a.u.): 11.33836 CELL DIMENSION: 11.3384 1.0000 1.0000 0.0000 0.0000 0.0000 VOLUME(OMEGA IN BOHR^3): 1457.63994 LATTICE VECTOR A1(BOHR): 11.3384 0.0000 0.0000 LATTICE VECTOR A2(BOHR): 0.0000 11.3384 0.0000 LATTICE VECTOR A3(BOHR): 0.0000 0.0000 11.3384 RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0882 0.0000 0.0000 RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0882 0.0000 RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000