From dima at xenon.spb.ru Wed Oct 1 06:44:37 2003 From: dima at xenon.spb.ru (Dmitry Rozmanov) Date: Wed, 01 Oct 2003 08:44:37 +0400 Subject: [CPMD-list] How can I get the CPMD code? Message-ID: <3F7A5BB5.1060304@xenon.spb.ru> Hello. I left several times request for code of CPMD on the web site and nothing happend. No responce at all. Is there any bug or problem with on-line requests? How can I get the code? Is it still possible? Thank you in advance. Best wishes. ---Dmitry Rozmanov. From hutter at pci.unizh.ch Wed Oct 1 08:44:54 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Wed, 1 Oct 2003 08:44:54 +0200 (MEST) Subject: [CPMD-list] g compilers In-Reply-To: <200309241258.h8OCwSr15274@kntu.ac.ir> References: <200309241258.h8OCwSr15274@kntu.ac.ir> Message-ID: Hi unfortunately CPMD can not be compiled with g77. As far as I know the Intel IFC compiler is the only free compiler that will work with CPMD. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Wed, 24 Sep 2003, sahand wrote: > > Dear CPMD users; > > Is it possible to compile CPMD source using gnom compilers, g77 and ggc? > any help will be appreciated. > > Best regards > Sahand > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From atte.sillanpaa at oulu.fi Wed Oct 1 12:27:50 2003 From: atte.sillanpaa at oulu.fi (=?ISO-8859-1?Q?Atte_Sillanp=E4=E4?=) Date: Wed, 1 Oct 2003 13:27:50 +0300 (EEST) Subject: [CPMD-list] g-vector ordering Message-ID: Hello all, I've run to a mysterious problem. An MD run crashed because of some unexplicable reason during writing the restart file possibly due to the platform related problems. I had, however, successfully already calculated thousands of steps. Now it seems, that I can neither restart nor start from scratch the run. I keep getting the following lines: PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES 0 1111 8895 9 102 414 16 1 1 1110 8880 9 104 412 16 1 2 1108 8884 9 104 412 16 1 3 1106 8880 9 104 412 16 1 4 1110 8878 9 104 412 16 1 5 1110 8840 9 103 411 16 1 6 1118 8874 9 104 412 16 1 7 1114 8874 9 104 412 16 1 GORDER| PROGRAMING ERROR. INFORM THE PROGRAMER GORDER| PROGRAMING ERROR. INFORM THE PROGRAMER G=0 COMPONENT ON PROCESSOR : 5 PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA after which the program proceeds a few lines and crashes: INITIALIZATION TIME: 60.95 SECONDS *** WFOPTS| THE NEW SIZE OF THE PROGRAM IS 89595 kBYTES *** *** PHFAC| THE NEW SIZE OF THE PROGRAM IS 89595 kBYTES *** *** ATOMWF| THE NEW SIZE OF THE PROGRAM IS 89595 kBYTES *** Abort (core dumped) Abort (core dumped) Abort (core dumped) Any ideas what this is about? I have two other similar runs in the same machine (alpha cluster) running without problems. Actually, the same calculation using 4 nodes works ok. Cheers, Atte atte.sillanpaa at oulu.fi +358 (0)8 553 1681 (work), KE 368 Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm) PO-BOX 3000 FIN-90014 University of Oulu FINLAND | Entropy requires no maintenance. | From cdy2000 at vip.sina.com Thu Oct 9 10:54:34 2003 From: cdy2000 at vip.sina.com (cdy2000 at vip.sina.com) Date: Thu, 09 Oct 2003 16:54:34 +0800 Subject: [CPMD-list] about RAMAN Message-ID: <20031009085434.19418.qmail@vip.sina.com.cn> Hello Everybody! I have computed RAMAN by LINEAR RESPONSE, and get two files: APT and POLARIZABILITY, lots of data in these files. I want to know the meaning of the data, please give me some answer in detail. Thanks for any help. Sincerely Cao Dayong ______________________________________ =================================================================== From J.C.Wojdel at tnw.tudelft.nl Thu Oct 9 11:39:58 2003 From: J.C.Wojdel at tnw.tudelft.nl (J.C.Wojdel at tnw.tudelft.nl) Date: Thu, 9 Oct 2003 11:39:58 +0200 Subject: [CPMD-list] Vanderbilt uspp transferability Message-ID: <20031009113958.B30165@dct7243.dct.tudelft.nl> Dear CPMD users, I recently stumbled on a problem when using uspps for transition metal complexes: the uspps do not seem to be transferable between configurations that differ in the spin state. Is anyone aware of some literature concerning transferability of uspps for hi/lo-spin states (like in weak/strong ligand field), or on influence of pseudization method (number of beta-functions etc) on recapturing the proper spin state of the complex? Any pointers even remotely related would be appreciated. Regards, Jacek Wojdel P.S. My apologies if you've got this e-mail twice via CCL as well. -- +-------------------------------------+ |from: J.C.Wojdel | | J.C.Wojdel at tnw.tudelft.nl | +-------------------------------------+ From vuilleum at lptl.jussieu.fr Thu Oct 9 11:42:13 2003 From: vuilleum at lptl.jussieu.fr (Rodolphe VUILLEUMIER) Date: Thu, 09 Oct 2003 11:42:13 +0200 Subject: [CPMD-list] about RAMAN In-Reply-To: <20031009085434.19418.qmail@vip.sina.com.cn> References: <20031009085434.19418.qmail@vip.sina.com.cn> Message-ID: <3F852D75.6030204@lptl.jussieu.fr> Dear all, The POLARIZABILITY file simply contains the polarizability tensor of the whole system in atomic units. As of the file APT, it contains the atomic polar tensors for each atoms in the system. The atomic polar tensor is the derivative of the forces on the atoms with respect to an applied external electric field. Equivalently it is, from a Maxwell relation, the derivative of the total dipole of the system with respect to the nuclei positions. It is thus an important ingredient of the calculation of infrared spectra intensities, for example used in an harmonic approximation. The trace of this tensor is the so-called Born charge of the considered atom. The data are arranged in the following order (still in AU): the APT tensor is dF_I,i/dE_j where F_I,i is the force on atom I along i=x,y,z and E_j is the electric field along j=x,y,z. (I,i) are the index of the 3Natoms lines in the APT file, one atom after the other, and j is the column index in the APT file. Best regards, Rodolphe Vuilleumier -- Rodolphe Vuilleumier Laboratoire de Physique Theorique de Liquides Universite Pierre et Marie Curie - Tour 16-15 - 5eme etage 4 place Jussieu - 75005 Paris - France Tel: 33-(0)1-44-27-72-39 Fax: 33-(0)1-44-27-51-00 Email:vuilleum at lptl.jussieu.fr From jiten at postech.ac.kr Fri Oct 10 03:23:05 2003 From: jiten at postech.ac.kr (N. Jiten Singh) Date: Fri, 10 Oct 2003 10:23:05 +0900 Subject: [CPMD-list] =?iso-8859-1?B?UGFpciBEaWlzdHJpYnV0aW9uIGZ1bmN0aW9uIGNhbGN1bGF0aW9u?= Message-ID: <20031010.AAA1065748688@postech.ac.kr> Could anybody tell if it is possible to calculate Pair Distribution function between a Wannier center and atoms in the system during the CPMD dynamics run. If not possible, how could I do that. It would be highly appreciated if someone could provide me the code of doing the same. Thanking in advance, Jiten N. Jiten Singh Center for Superfunctional Materials Department of Chemistry Pohang University of Science and Technology San 31, Hyojadong, Namgu Pohang 790-784, Korea Phone : 82-54-279-5853 ( Lab ) Fax : 82-54-279-8137 (or +82-54-279-3399) Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e From c00ycl00 at nchc.gov.tw Fri Oct 10 04:34:54 2003 From: c00ycl00 at nchc.gov.tw (c00ycl00) Date: Fri, 10 Oct 2003 10:34:54 +0800 Subject: [CPMD-list] Simulation under static external electric field Message-ID: <3F861ACE30C.27B6C00YCL00@smtp.nchc.gov.tw> Dear all, Could anybody tell if CPMD can calculate the characteristics of nanostructure (like carbon nanotube) under a static external electric field? Can anybody teach me how to do it using CPMD? Thank you for your help. Yung-Chiang Lan ************************************************* ?? ?? ?j, Yung-Chiang Lan, Ph. D. Associate Researcher, National Center for High-performance Computing, P.O. Box 19-136, Hsinchu, Taiwan, R.O.C. Tel: +886-3-5776085 Ext:316 Fax: +886-3-5773538 E-mail: YCLan at nchc.org.tw, c00ycl00 at nchc.org.tw ************************************************** From jwh at ciam.unibo.it Fri Oct 10 09:30:40 2003 From: jwh at ciam.unibo.it (Jan-Willem Handgraaf) Date: Fri, 10 Oct 2003 09:30:40 +0200 Subject: [CPMD-list] Pair Diistribution function calculation In-Reply-To: <20031010.AAA1065748688@postech.ac.kr> References: <20031010.AAA1065748688@postech.ac.kr> Message-ID: <200310100930.40653.jwh@ciam.unibo.it> Dear N. Jiten Singh, On Friday 10 October 2003 03:23, N. Jiten Singh wrote: > Could anybody tell if it is possible to calculate Pair Distribution > function between a Wannier center and atoms in the system during the CPMD > dynamics run. Of course it is possible. However your distribution will be quite narrow, see e.g. phys. rev. lett. 82, 3308 (1999). > If not possible, how could I do that. It would be highly appreciated if > someone could provide me the code of doing the same. I have done it in the past, but I am afraid I have thrown away the source code. I any case, it is quite simple and very similar to a calculation of an atom-atom radial distribution. Hope this helps, Jan-Willem -- Jan-Willem Handgraaf Dipartimento di Chimica "G. Ciamician" Universit? di Bologna Via F. Selmi 2 40126 Bologna, Italy Tel: +39-051-2099596 Email: jwh at ciam.unibo.it Web: http://www.ciam.unibo.it/sitcon/ From jiten at postech.ac.kr Fri Oct 10 11:38:27 2003 From: jiten at postech.ac.kr (N. Jiten Singh) Date: Fri, 10 Oct 2003 18:38:27 +0900 Subject: [CPMD-list] =?iso-8859-1?B?RGVuc2l0eSBvZiBzdGF0ZSBvZiBhIGxldmVsID8=?= Message-ID: <20031010.AAA1065778119@postech.ac.kr> Hello CPMD Members, During the MOLECULAR DYNAMICS CP run I would like to save the Density of state of a particular electronic level. Would it be possible? I also would like to print eigenvalues of this particular level for each step of the dynamics run. Unfortunately the PRINT ON EIGENVALUES gives the eigenvalues of all the levels and only at the beginning of the run, not for every steps. My intensition is that I would like draw DOS of few levels for a CP molecular dynamics run. It would be highly appreciated if someone could me suggestions regarding this. Thanking you in advance. Sincerely, N. Jiten Singh N. Jiten Singh Center for Superfunctional Materials Department of Chemistry Pohang University of Science and Technology San 31, Hyojadong, Namgu Pohang 790-784, Korea Phone : 82-54-279-5853 ( Lab ) Fax : 82-54-279-8137 (or +82-54-279-3399) Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e From r.meier at wxs.nl Sat Oct 11 09:32:28 2003 From: r.meier at wxs.nl (robert meier) Date: Sat, 11 Oct 2003 09:32:28 +0200 Subject: [CPMD-list] mertal surfaces, efficiently? Message-ID: <006401c38fc9$efb52350$685479c3@DSMF7HJCHW21SK> Hi, Does the CPMD code efficiently handle metal surfaces, e.g., is it capable of dealing with partial occupation numbers in orbitals (bands). I can not remember seeing many papers with CPMD on metal surfaces (any references?). I do remember that when partial occupancies were built in VASP some years ago this led to a vast speed-up in the convergence. Thanks for any help/suggestions, Rob Meier -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20031011/916bfe82/attachment.html From jiten at postech.ac.kr Sat Oct 11 13:27:18 2003 From: jiten at postech.ac.kr (N. Jiten Singh) Date: Sat, 11 Oct 2003 20:27:18 +0900 Subject: [CPMD-list] =?iso-8859-1?B?V0FOTklFUiBDT0RFIFdBUk5JTkc=?= Message-ID: <20031011.AAA1065871319@postech.ac.kr> To CMPD community, Could anybody tell me the follwing error in the *.out file during CP Molecular Dynamics run with WANNIER WFNOUT LIST DENSITY WANNIER CODE WARNING: GRADIENT FOR RESTA FUNCTIONAL IS GMAX=0.118E-02 Does it mean any serous error in the calculation. Thanking in advance, Sincerely, N. Jiten Singh N. Jiten Singh Center for Superfunctional Materials Department of Chemistry Pohang University of Science and Technology San 31, Hyojadong, Namgu Pohang 790-784, Korea Phone : 82-54-279-5853 ( Lab ) Fax : 82-54-279-8137 (or +82-54-279-3399) Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Sat Oct 11 14:03:18 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Sat, 11 Oct 2003 14:03:18 +0200 Subject: [CPMD-list] =?iso-8859-1?B?V0FOTklFUiBDT0RFIFdBUk5JTkc=?= In-Reply-To: <20031011.AAA1065871319@postech.ac.kr> Message-ID: <200310111203.h9BC3I926433@yello.theochem.ruhr-uni-bochum.de> On Sat, 11 Oct 2003 20:27:18 +0900 "N. Jiten Singh" wrote: > To CMPD community, > > Could anybody tell me the follwing error in the *.out file during CP Molecular Dynamics run with WA NNIER WFNOUT LIST DENSITY > > WANNIER CODE WARNING: GRADIENT FOR RESTA FUNCTIONAL IS GMAX=0.118E-02 > > Does it mean any serous error in the calculation. hi! are you using vanderbilt pseudopotentials? if yes, then - to the best of my knowledge - your wannier density is bogus, as the non-local contributions to the density are not accounted for properly. at least, this is the information i got, when i tried to calculate wannier centers from a simulation with vanderbilt USPPs. hope this helps, axel kohlmeyer. > > Thanking in advance, > > Sincerely, > > N. Jiten Singh > > N. Jiten Singh > Center for Superfunctional Materials > Department of Chemistry > Pohang University of Science and Technology > San 31, Hyojadong, Namgu > Pohang 790-784, Korea > Phone : 82-54-279-5853 ( Lab ) > Fax : 82-54-279-8137 (or +82-54-279-3399) > Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From jiten at postech.ac.kr Sat Oct 11 15:48:16 2003 From: jiten at postech.ac.kr (Jiten) Date: Sat, 11 Oct 2003 22:48:16 +0900 Subject: [CPMD-list] WANNIER CODE WARNING References: <200310111203.h9BC3I926433@yello.theochem.ruhr-uni-bochum.de> Message-ID: <018701c38ffe$532dee10$447fdf8d@theo68> Hai Alex, Thanks a lot for your comment. I use the Trouller Martin PP with BLYP. Does the WARNING still have serious problem in my calculations. It seems that the WANNIER TYPE is taken by default RESTA instead of VADERBILT though VANDERBILT is the default options as per the mannual. Could I use WANNIER TYPE VADERBILT with Trouller Martin PP type. Any more comments, Sincerely, Jiten ----- Original Message ----- From: "Axel Kohlmeyer" To: ; "N. Jiten Singh" Sent: Saturday, October 11, 2003 9:03 PM Subject: Re: [CPMD-list] WANNIER CODE WARNING > On Sat, 11 Oct 2003 20:27:18 +0900 "N. Jiten Singh" wrote: > > > To CMPD community, > > > > Could anybody tell me the follwing error in the *.out file during CP Molecular Dynamics run with WA > NNIER WFNOUT LIST DENSITY > > > > WANNIER CODE WARNING: GRADIENT FOR RESTA FUNCTIONAL IS GMAX=0.118E-02 > > > > Does it mean any serous error in the calculation. > > hi! > > are you using vanderbilt pseudopotentials? > if yes, then - to the best of my knowledge - > your wannier density is bogus, as the non-local > contributions to the density are not accounted > for properly. at least, this is the information > i got, when i tried to calculate wannier centers > from a simulation with vanderbilt USPPs. > > hope this helps, > axel kohlmeyer. > > > > > Thanking in advance, > > > > Sincerely, > > > > N. Jiten Singh > > > > N. Jiten Singh > > Center for Superfunctional Materials > > Department of Chemistry > > Pohang University of Science and Technology > > San 31, Hyojadong, Namgu > > Pohang 790-784, Korea > > Phone : 82-54-279-5853 ( Lab ) > > Fax : 82-54-279-8137 (or +82-54-279-3399) > > Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e > > > > > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > > -- > > ======================================================================= > Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de > Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 > Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 > D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > From hutter at pci.unizh.ch Sat Oct 11 16:55:52 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Sat, 11 Oct 2003 16:55:52 +0200 (MEST) Subject: [CPMD-list] =?iso-8859-1?B?V0FOTklFUiBDT0RFIFdBUk5JTkc=?= In-Reply-To: <20031011.AAA1065871319@postech.ac.kr> References: <20031011.AAA1065871319@postech.ac.kr> Message-ID: Hi The default spreadfunctional used in CPMD is the Vandebilt type. At the end of the calculation the convergence wrt the Resta type functional is also checked. For large cells both should be converged at the same time. However, for typical applicayion this is not the case and you get the warning. This is not serious and you can ignore it. 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 Sat, 11 Oct 2003, N. Jiten Singh wrote: > To CMPD community, > > Could anybody tell me the follwing error in the *.out file during CP Molecular Dynamics run with WANNIER WFNOUT LIST DENSITY > > WANNIER CODE WARNING: GRADIENT FOR RESTA FUNCTIONAL IS GMAX=0.118E-02 > > Does it mean any serous error in the calculation. > > Thanking in advance, > > Sincerely, > > N. Jiten Singh > > N. Jiten Singh > Center for Superfunctional Materials > Department of Chemistry > Pohang University of Science and Technology > San 31, Hyojadong, Namgu > Pohang 790-784, Korea > Phone : 82-54-279-5853 ( Lab ) > Fax : 82-54-279-8137 (or +82-54-279-3399) > Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From ncooper at physics.usyd.edu.au Wed Oct 15 07:17:44 2003 From: ncooper at physics.usyd.edu.au (Nick Cooper) Date: Wed, 15 Oct 2003 15:17:44 +1000 (EST) Subject: [CPMD-list] Energy conservation Message-ID: Hello all, I am simulating covalent materials at relatively high temperatures (3500K) and I have noticed that the conserved quantity in a canonical ensemble is monotonically decreasing, though admittedly the absolute change is small. I have tried decreasing the timestep (from 3au down to 1au) but all this does is decrease the gradient of the drop in energy. The systems I am looking at have significant metallic character at this temperature, so I have used a Nose-Hoover themostat for the ions and wavefunctions. The monotonic nature is what has me worried- am I just being paranoid? Any advice you can offer would be gratefully received. Yours sincerely, Nicholas Cooper PhD Student, The University of Sydney, NSW 2006 AUSTRALIA From hutter at pci.unizh.ch Wed Oct 15 14:03:48 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Wed, 15 Oct 2003 14:03:48 +0200 (MEST) Subject: [CPMD-list] Energy conservation In-Reply-To: References: Message-ID: Hi Nick the problem with energy conservation with systems of this type is often related to the thermostats. Instead of reducing the timestep you should try to increase the order of the integrator and the decomposition ratio for the thermostats. You do this by setting NOSE PARAMETERS 4 4 4 6 125 4 other choices for the Suzuki integrator are 3,5,7,9,15,25,125,625 The decomposition ratio is by default 1 (last number) and I did set it to 4. I don't have too much experience with that. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Wed, 15 Oct 2003, Nick Cooper wrote: > Hello all, > > I am simulating covalent materials at relatively high temperatures (3500K) > and I have noticed that the conserved quantity in a canonical ensemble is > monotonically decreasing, though admittedly the absolute change is small. > I have tried decreasing the timestep (from 3au down to 1au) but all this > does is decrease the gradient of the drop in energy. The systems I am > looking at have significant metallic character at this temperature, so I > have used a Nose-Hoover themostat for the ions and wavefunctions. > > The monotonic nature is what has me worried- am I just being paranoid? > > Any advice you can offer would be gratefully received. > > Yours sincerely, > > Nicholas Cooper > > PhD Student, > The University of Sydney, > NSW 2006 AUSTRALIA > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From ct at chemie.hu-berlin.de Wed Oct 15 15:00:16 2003 From: ct at chemie.hu-berlin.de (Christian Tuma) Date: Wed, 15 Oct 2003 15:00:16 +0200 Subject: [CPMD-list] calculation of deprotonation energies Message-ID: <20031015130016.GB95179@uranus.chemie.hu-berlin.de> Dear CPMD experts, I have a question which concerns plane wave pseudopotential calculations in general. The problem I have is the following: For the calculation of the electronic deprotonation energy of a system "X-H" one usually calculates the total energy of the neutral system "X-H", E(X-H), and the total energy of the negatively charged system "X-", E(X-). The energy difference between E(X-H) and E(X-) is the deprotonation energy since the energy of the removed proton itself is zero (no electrons present). Now, the chosen type of pseudo- potential for hydrogen in "X-H" affects the total energy of "X-H", whereas for "X-" this doesn't matter since this pseudopotential is absent there. That means, the deprotonation energy depends on the chosen pseudopotential for hydrogen in "X-H". The thing that worries me now is that the error introduced by the pseudopotential approach for hydrogen is present in E(X-H) but not in E(H+). So there is no kind of cancelation of this error in the deprotonation energy, in other words: the deprotonation energy contains an inherent error caused by the "disappearing" hydrogen pseudopotential (not by the special nature of the type of chosen pseudopotential itself). Is there a way to correct this error in the deprotonation energy? I think that this error is not big enough to be considered important, so my question has a rather theoretical and general background. Comments or help are welcome. Thanks, Christian Tuma. -- Christian Tuma Humboldt-Universitaet Berlin ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer From massimo.celino at casaccia.enea.it Wed Oct 15 15:56:49 2003 From: massimo.celino at casaccia.enea.it (Massimo Celino) Date: Wed, 15 Oct 2003 15:56:49 +0200 Subject: [CPMD-list] Pseudopotential for Ge Message-ID: <4.3.2.7.0.20031015155102.00d1e760@casaccia.enea.it> Dear CPMDer, does anybody have a reliable pseudopotential for Germanium ? Thank you very much. Sincerely Massimo Celino -------------------------------------------------------------- Massimo Celino ENEA - Calcolo e Modellistica (CAMO) C.R. Casaccia - SP103 Via Anguillarese 301, 00060 S.Maria di Galeria (Roma), Italy Tel.: +39-06-30483871 Fax: +39-06-30484230 From bala at jncasr.ac.in Thu Oct 16 05:31:07 2003 From: bala at jncasr.ac.in (Dr. Balasubramanian Sundaram) Date: Thu, 16 Oct 2003 09:01:07 +0530 Subject: [CPMD-list] Energy conservation References: Message-ID: <3F8E10FB.D6F55C78@jncasr.ac.in> Hi Nick, In addition, a couple of things came to my mind. Sorry if you have thought/taken care of these before. -- Has the system been "equilibrated" using MD with empirical potentials, prior to the CPMD run? That might help. Since the operating temperature is reasonably large, I am assuming that the system is not crystalline, and that you have an initial configuration that is not obtained from experiments. Hence, my concern about equilibration being a possible reason for relatively poorer energy conservation. -- Is the total potential energy (E_{KS}?) of the system too exhibiting a monotonic decrease? If yes, then the monotonic decrease in the conserved energy may not be from "improper" choice of timestep/thermostat parameters. May be, the system is just relaxing. Regards, Bala Juerg Hutter wrote: > > Hi Nick > > the problem with energy conservation with systems of this > type is often related to the thermostats. > Instead of reducing the timestep you should try to > increase the order of the integrator and the > decomposition ratio for the thermostats. > You do this by setting > > NOSE PARAMETERS > 4 4 4 6 125 4 > > other choices for the Suzuki integrator are > 3,5,7,9,15,25,125,625 > > The decomposition ratio is by default 1 (last number) > and I did set it to 4. I don't have too much experience > with that. > > regards > > Juerg > > ---------------------------------------------------------- > Juerg Hutter Phone : ++41 1 635 4491 > Physical Chemistry Institute FAX : ++41 1 635 6838 > University of Zurich E-mail: hutter at pci.unizh.ch > Winterthurerstrasse 190 > CH-8057 Zurich, Switzerland > ---------------------------------------------------------- > > On Wed, 15 Oct 2003, Nick Cooper wrote: > > > Hello all, > > > > I am simulating covalent materials at relatively high temperatures (3500K) > > and I have noticed that the conserved quantity in a canonical ensemble is > > monotonically decreasing, though admittedly the absolute change is small. > > I have tried decreasing the timestep (from 3au down to 1au) but all this > > does is decrease the gradient of the drop in energy. The systems I am > > looking at have significant metallic character at this temperature, so I > > have used a Nose-Hoover themostat for the ions and wavefunctions. > > > > The monotonic nature is what has me worried- am I just being paranoid? > > > > Any advice you can offer would be gratefully received. > > > > Yours sincerely, > > > > Nicholas Cooper > > > > PhD Student, > > The University of Sydney, > > NSW 2006 AUSTRALIA > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list From WANGYI at engr.sc.edu Thu Oct 16 21:54:23 2003 From: WANGYI at engr.sc.edu (WANG, YIXUAN ) Date: Thu, 16 Oct 2003 15:54:23 -0400 Subject: [CPMD-list] Energy conservation Message-ID: <99296F29E0A01A40A0503EB30507ECF91E9A7D@mail1.engr.sc.edu> Dear all, I do agree the point from Juerg that the problem of energy conservation with systems is often related to the thermostats. I have no experience that if the decomposition ratio in nose parameters(default 1) is responsible much for it, however the energy conservation is really sensitive to the set kinetic energy of electron. If it is too small, the energy usually monotonically decrease. Yixuan -----Original Message----- From: cpmd-list-admin at cpmd.org [mailto:cpmd-list-admin at cpmd.org]On Behalf Of Dr. Balasubramanian Sundaram Sent: Wednesday, October 15, 2003 11:31 PM Cc: Nick Cooper; cpmd-list at cpmd.org Subject: Re: [CPMD-list] Energy conservation Hi Nick, In addition, a couple of things came to my mind. Sorry if you have thought/taken care of these before. -- Has the system been "equilibrated" using MD with empirical potentials, prior to the CPMD run? That might help. Since the operating temperature is reasonably large, I am assuming that the system is not crystalline, and that you have an initial configuration that is not obtained from experiments. Hence, my concern about equilibration being a possible reason for relatively poorer energy conservation. -- Is the total potential energy (E_{KS}?) of the system too exhibiting a monotonic decrease? If yes, then the monotonic decrease in the conserved energy may not be from "improper" choice of timestep/thermostat parameters. May be, the system is just relaxing. Regards, Bala Juerg Hutter wrote: > > Hi Nick > > the problem with energy conservation with systems of this > type is often related to the thermostats. > Instead of reducing the timestep you should try to > increase the order of the integrator and the > decomposition ratio for the thermostats. > You do this by setting > > NOSE PARAMETERS > 4 4 4 6 125 4 > > other choices for the Suzuki integrator are > 3,5,7,9,15,25,125,625 > > The decomposition ratio is by default 1 (last number) > and I did set it to 4. I don't have too much experience > with that. > > regards > > Juerg > > ---------------------------------------------------------- > Juerg Hutter Phone : ++41 1 635 4491 > Physical Chemistry Institute FAX : ++41 1 635 6838 > University of Zurich E-mail: hutter at pci.unizh.ch > Winterthurerstrasse 190 > CH-8057 Zurich, Switzerland > ---------------------------------------------------------- > > On Wed, 15 Oct 2003, Nick Cooper wrote: > > > Hello all, > > > > I am simulating covalent materials at relatively high temperatures (3500K) > > and I have noticed that the conserved quantity in a canonical ensemble is > > monotonically decreasing, though admittedly the absolute change is small. > > I have tried decreasing the timestep (from 3au down to 1au) but all this > > does is decrease the gradient of the drop in energy. The systems I am > > looking at have significant metallic character at this temperature, so I > > have used a Nose-Hoover themostat for the ions and wavefunctions. > > > > The monotonic nature is what has me worried- am I just being paranoid? > > > > Any advice you can offer would be gratefully received. > > > > Yours sincerely, > > > > Nicholas Cooper > > > > PhD Student, > > The University of Sydney, > > NSW 2006 AUSTRALIA > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list From Magali.BENOIT at LDV.univ-montp2.fr Fri Oct 17 11:42:23 2003 From: Magali.BENOIT at LDV.univ-montp2.fr (Magali BENOIT) Date: Fri, 17 Oct 2003 11:42:23 +0200 Subject: [CPMD-list] energy conservation Message-ID: <3F8FB97F.4030602@ldv.univ-montp2.fr> Dear all, I do agree with all the comments that have been done previously. My experience in simulating high temperature (3500 K) silicate melts (SiO2, SiO2-Na2O etc.) with thermostats is that you have to "tune" your electronic thermostat parameters such that the total energy drift becomes small. The most important parameters are: - the kinetic energy of the electrons: if it is too small (compared to the kinetic energy that the electrons would normally have, without the thermostats) then you will have a large drift. - the number of electronic degrees of freedom (the 4th number in the Nose-Hoover parameters). You can try to increase the scaling. - the suzuki integrator (5th number) - the decomposition ratio (6th number) - if you use "MASSIVE" thermostats for the ions, you will generally undergo a larger drift. I was never able to totally remove the drift but only to make it small enough to live with it...You can help to cure the drift also by "refreshing" the thermostats (do not restart with the old ones) from time to time. Good luck, Magali From jiten at postech.ac.kr Sun Oct 19 05:44:36 2003 From: jiten at postech.ac.kr (Jiten) Date: Sun, 19 Oct 2003 12:44:36 +0900 Subject: [CPMD-list] Density pf state !! Message-ID: <04ee01c395f3$516215c0$447fdf8d@theo68> Dear CPMD community, I am new user in CPMD. Could anybody give me cetain guideline on how to generate desity of state of the electronic levels of a CPMD dynamics run. I am interested in plotting DOS of few electronic levels of my working system. You help would be highly appreciated, Sincerely, N. Jiten Singh C/O Prof. Kwang S. KIm Department of Chemistry Pohang University of Science and Technology San 31, Hyojadong, Namgu Pohang 790-784, Korea Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt ) Fax : 82-54-279-8137 (or +82-54-279-3399) Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e Home Page : http://www.geocities.com/njs_19 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20031019/dad5cd4f/attachment.html From dima at xenon.spb.ru Wed Oct 22 07:35:34 2003 From: dima at xenon.spb.ru (Dmitry Rozmanov) Date: Wed, 22 Oct 2003 09:35:34 +0400 Subject: [CPMD-list] How can I get the CPMD code? In-Reply-To: <200310010814.KAA27056@cpmd.org> References: <200310010814.KAA27056@cpmd.org> Message-ID: <3F961726.6010109@xenon.spb.ru> Dear Alessandro. I have sent a message with the statements you required as soon as I read this answer. And mentioned tree e-mail accounts for farther correspondence. It is a week passed since that time and I still have no responce from CPMD team. I believe that there is a severe problem on the way of our mailing systems then. Could you check, please, if you got my message? Thank you in advance. --- Dmitry. Alessandro Curioni wrote: > Dear Sir > > I am a little puzzled as to why you feel that you have had no reply from us > since our records show that we emailed you on 10th and 18th of September 2003. > > In both emails we requested that you returned to us the following declaration: > > We require you to declare (e-mail is OK) that you and your organization > will not use neither this code nor its derivatives for nuclear research > related activities. > > On both occasions we had no reply from you. > > Before we can issue you with a user ID and password, you are required to > agree to the above declaration and email it to us. > > Once we receive this we will send you your user ID etc. within c. 1-2 days. > > Looking forward to hearing from you, > > The CPMD Team > > > >>Hello. >> >>I left several times request for code of CPMD on the web site and >>nothing happend. No responce at all. >> >>Is there any bug or problem with on-line requests? >> >>How can I get the code? Is it still possible? >> >>Thank you in advance. >> >>Best wishes. >> >> ---Dmitry Rozmanov. >> >> >> >>_______________________________________________ >>CPMD-list mailing list >>CPMD-list at cpmd.org >>http://www.cpmd.org/mailman/listinfo/cpmd-list >> > > > From ncooper at physics.usyd.edu.au Thu Oct 23 02:55:30 2003 From: ncooper at physics.usyd.edu.au (Nick Cooper) Date: Thu, 23 Oct 2003 10:55:30 +1000 (EST) Subject: [CPMD-list] Energy conservation continued... Message-ID: Firstly, thank you very much to those who replied to my initial question regarding achieving energy conservation at elevated temperatures. However, having increased the order of the Suzuki integrator and decomposition ratio using NOSE PARAMETERS 4 4 4 6 125 4 a constant downwards drift of the "conserved" quantity was observed. Given this, I suspect that I have set the fictitious kinetic energy for the electrons (the first number in the NOSE ELECTRONS keyword of CPMD) too small. Having read "Adiabaticity in first-principles molecular dynamics" by Blochl and Parrinello: PRB 45, 9413 (1992), I came upon their expression for E_kin,ad (eqn 6 in the paper), which provides an estimate for the transition point between two regimes. However, I have a couple of questions regarding this expession: 1) I assume mu (EMASS in CPMD) is in electron mass units and M proton mass units? 2) How do I determine the value of the of what's contained in the sigma_i? Sorry for asking such a basic question but I haven't got anyone to ask at present, so I was hoping someone here could enlighten me. Thank you for your time. Regards, Nick Cooper From ncooper at physics.usyd.edu.au Thu Oct 23 06:38:17 2003 From: ncooper at physics.usyd.edu.au (Nick Cooper) Date: Thu, 23 Oct 2003 14:38:17 +1000 (EST) Subject: [CPMD-list] Energy conservation continued... (fwd) Message-ID: Dear all, Please disregard the message I posted below, as I have found that mu is in units of energy.time^2 by dimensional analysis and the sigma_i is just the EKINC in the output file produced by CPMD. Sorry for wasting your time, though I'm sure posting the question helped me to find a solution! Best Regards, Nick Cooper ---------- Forwarded message ---------- Date: Thu, 23 Oct 2003 10:55:30 +1000 (EST) From: Nick Cooper To: cpmd-list at cpmd.org Subject: Energy conservation continued... Firstly, thank you very much to those who replied to my initial question regarding achieving energy conservation at elevated temperatures. However, having increased the order of the Suzuki integrator and decomposition ratio using NOSE PARAMETERS 4 4 4 6 125 4 a constant downwards drift of the "conserved" quantity was observed. Given this, I suspect that I have set the fictitious kinetic energy for the electrons (the first number in the NOSE ELECTRONS keyword of CPMD) too small. Having read "Adiabaticity in first-principles molecular dynamics" by Blochl and Parrinello: PRB 45, 9413 (1992), I came upon their expression for E_kin,ad (eqn 6 in the paper), which provides an estimate for the transition point between two regimes. However, I have a couple of questions regarding this expession: 1) I assume mu (EMASS in CPMD) is in electron mass units and M proton mass units? 2) How do I determine the value of the of what's contained in the sigma_i? Sorry for asking such a basic question but I haven't got anyone to ask at present, so I was hoping someone here could enlighten me. Thank you for your time. Regards, Nick Cooper From ncooper at physics.usyd.edu.au Thu Oct 23 10:44:40 2003 From: ncooper at physics.usyd.edu.au (Nick Cooper) Date: Thu, 23 Oct 2003 18:44:40 +1000 (EST) Subject: [CPMD-list] Lack of energy conservation... Message-ID: Hello once again, I am still having problems getting any sort of energy conservation for an elevated temperature run of Si, C and H. This is meant to be the equilibration of a liquid obtained by melting a random collection of atoms but I think there must be something drastic wrong. I utilised the NOSE PARAMETERS to increase the order of the Suzuki integrator and the decomposition ratio for the thermostat but the energy drift was still of the order of 0.1eV/ps, when I believe that one should be looking at a drift of no more than 10E-5eV/ps? The relevant part of my input file is: &CPMD MOLECULAR DYNAMICS COMPRESS READ WRITE RESTART WAVEFUNCTION COORDINATES CELL LATEST QUENCH BO TEMPERATURE 3500 NOSE IONS 3500 3000 NOSE ELECTRONS 0.035 10000 NOSE PARAMETERS 4 4 4 6 125 4 MAXSTEP 13780 TIMESTEP 3. EMASS 200. &END I noticed that the ion temperature was fluctuating by +/- 1000 of so (which is VERY large for a 64 atom sample, as here), so I thought my choice of frequency for the ions (3000cm-1, which is the characteristic frequency for a C-H stretch) might not be coupling paticularly well. Thus I performed a VIBRATIONAL ANALYSIS run to find the harmonic frequencies, only to discover that the maximum frequency is 4636cm-1, which is well below the characteristic freqency for the electron thermostat. Finally, I decreased the timestep to 1a.u. but all this did was decrease the gradient of the monotonically decreases conserved quantity. Any ideas of what I'm doing wrong or suggestions for what to try next!? Help would be very much appreciated. Regards, Nick Cooper PhD Student, University of Sydney From jglee at nemo.physics.ncsu.edu Fri Oct 31 02:25:59 2003 From: jglee at nemo.physics.ncsu.edu (Jung Goo Lee) Date: Thu, 30 Oct 2003 20:25:59 -0500 Subject: [CPMD-list] combination of PBE USPP with BLYP DFT Message-ID: <3FA1BA27.1050601@nemo.physics.ncsu.edu> Hi everyone, I would like to know whether the combination of PBE uspp in ATOMS option and BLYP in DFT option (the example of partial input is shown below)makes sense or not, especially, for calculations of free energy (constraint). This is because BLYP method underestimate the dissociation free energy compared with experiment. For example, water dissociation in 32 water molecules with MT PP/ BLYP method gave 17 kcal/mol in free energy while experimental value is 21 kcal/mol(Trout and Parrinello, Chem. Phys. Lett, 288(1998)343. I tried the same calculation with PBE uspp and BLYP method. I got about 20 kcal/mol althogh I tried with a few hundred fs (instead of 1 ps) MD at each point of O-H bond constraint. So, this combination (PBE uspp/BLYP) seems to be o.k. in free energy calculations. Is this a reasonable and cheap(computationally) way to get out of the problem with free energy calculations with gbl uspp/BLYP? Does any one have any rationalization or contradiction with reasonable explanation? Jung-Goo Lee Example -- -- &ATOMS *008-O-gpbe--bm.uspp NEWF BINARY LMAX=P 1 4.3728 4.5000 4.5000 1 8 *001-H-gpbe--bm.uspp NEWF BINARY LMAX=S 2 5.5172 4.5000 5.9238 1 1 5.5172 4.5000 3.0761 1 1 &END &DFT OLDCODE FUNCTIONAL BLYP GRADIENT CORRECTION BECKE88 LYP LDA CORRELATION LYP &END -- -- From eesantis at unity.ncsu.edu Fri Oct 31 03:14:26 2003 From: eesantis at unity.ncsu.edu (Erik Emilio Santiso) Date: Thu, 30 Oct 2003 21:14:26 -0500 (EST) Subject: [CPMD-list] combination of PBE USPP with BLYP DFT In-Reply-To: <3FA1BA27.1050601@nemo.physics.ncsu.edu> References: <3FA1BA27.1050601@nemo.physics.ncsu.edu> Message-ID: Hi! Well, this looks more like a coincidence than anything else. I don't think it makes any sense to find a PP with one xc functional and then do the calculation with another one. What happens if you use the PBE PP's with the PBE functional? Erik. On Thu, 30 Oct 2003, Jung Goo Lee wrote: > Hi everyone, > > I would like to know whether the combination of PBE uspp in ATOMS option > and BLYP in DFT > option (the example of partial input is shown below)makes sense or not, > especially, for calculations > of free energy (constraint). This is because BLYP method underestimate > the dissociation free energy > compared with experiment. For example, water dissociation in 32 water > molecules with MT PP/ > BLYP method gave 17 kcal/mol in free energy while experimental value is > 21 kcal/mol(Trout and > Parrinello, Chem. Phys. Lett, 288(1998)343. > I tried the same calculation with PBE uspp and BLYP method. > I got about 20 kcal/mol althogh I tried with a few hundred fs (instead > of 1 ps) MD at each point of > O-H bond constraint. So, this combination (PBE uspp/BLYP) seems to be > o.k. in free energy > calculations. > > Is this a reasonable and cheap(computationally) way to get out of the > problem with free energy > calculations with gbl uspp/BLYP? > Does any one have any rationalization or contradiction with reasonable > explanation? > > Jung-Goo Lee > > Example > -- > -- > &ATOMS > *008-O-gpbe--bm.uspp NEWF BINARY > LMAX=P > 1 > 4.3728 4.5000 4.5000 1 8 > > *001-H-gpbe--bm.uspp NEWF BINARY > LMAX=S > 2 > 5.5172 4.5000 5.9238 1 1 > 5.5172 4.5000 3.0761 1 1 > &END > > &DFT > OLDCODE > FUNCTIONAL BLYP > GRADIENT CORRECTION BECKE88 LYP > LDA CORRELATION LYP > &END > -- > -- > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Fri Oct 31 09:34:37 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Fri, 31 Oct 2003 09:34:37 +0100 Subject: [CPMD-list] combination of PBE USPP with BLYP DFT In-Reply-To: Your message of "Thu, 30 Oct 2003 21:14:26 EST." Message-ID: <200310310834.h9V8Yb109122@yello.theochem.ruhr-uni-bochum.de> >>> "ES" == Erik Emilio Santiso writes: ES> Hi! Well, this looks more like a coincidence than anything else. I don't ES> think it makes any sense to find a PP with one xc functional and then do ES> the calculation with another one. yep. please have a look the documentation that comes along with the vanderbilt pseudopotential generation software. it says, you first run an all-electron calculation for the reference configuration where you have to specify the exchange-correlation type and then generate a pseudopotential from the results of that calculation. the best first order approximation you probably could do, is to generate the pseudopotential with the same parameters, but for BLYP (look for the parameter 'exfact' in the all electron input file) instead of PBE, and repeat your calculations with these potentials. but before using them for anything serious, you should _carefully_ test those 'new' pseudopotentials on some simple and representative examples. hope this helps, axel. ES> Erik. ES> On Thu, 30 Oct 2003, Jung Goo Lee wrote: >> Hi everyone, >> >> I would like to know whether the combination of PBE uspp in ATOMS option >> and BLYP in DFT >> option (the example of partial input is shown below)makes sense or not, >> especially, for calculations >> of free energy (constraint). This is because BLYP method underestimate >> the dissociation free energy >> compared with experiment. For example, water dissociation in 32 water >> molecules with MT PP/ >> BLYP method gave 17 kcal/mol in free energy while experimental value is >> 21 kcal/mol(Trout and >> Parrinello, Chem. Phys. Lett, 288(1998)343. >> I tried the same calculation with PBE uspp and BLYP method. >> I got about 20 kcal/mol althogh I tried with a few hundred fs (instead >> of 1 ps) MD at each point of >> O-H bond constraint. So, this combination (PBE uspp/BLYP) seems to be >> o.k. in free energy >> calculations. >> >> Is this a reasonable and cheap(computationally) way to get out of the >> problem with free energy >> calculations with gbl uspp/BLYP? >> Does any one have any rationalization or contradiction with reasonable >> explanation? >> >> Jung-Goo Lee >> >> Example >> -- >> -- >> &ATOMS >> *008-O-gpbe--bm.uspp NEWF BINARY >> LMAX=P >> 1 >> 4.3728 4.5000 4.5000 1 8 >> >> *001-H-gpbe--bm.uspp NEWF BINARY >> LMAX=S >> 2 >> 5.5172 4.5000 5.9238 1 1 >> 5.5172 4.5000 3.0761 1 1 >> &END >> >> &DFT >> OLDCODE >> FUNCTIONAL BLYP >> GRADIENT CORRECTION BECKE88 LYP >> LDA CORRELATION LYP >> &END >> -- >> -- >> >> >> _______________________________________________ >> CPMD-list mailing list >> CPMD-list at cpmd.org >> http://www.cpmd.org/mailman/listinfo/cpmd-list >> ES> _______________________________________________ ES> CPMD-list mailing list ES> CPMD-list at cpmd.org ES> http://www.cpmd.org/mailman/listinfo/cpmd-list -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From yliu252 at uwo.ca Fri Oct 31 20:15:50 2003 From: yliu252 at uwo.ca (Yi Liu) Date: Fri, 31 Oct 2003 14:15:50 -0500 Subject: [CPMD-list] combination of PBE USPP with BLYP DFT References: <3FA1BA27.1050601@nemo.physics.ncsu.edu> Message-ID: <001c01c39fe3$68fcdae0$de0aa8c0@theory.net> ----- Original Message ----- From: "Erik Emilio Santiso" To: "Jung Goo Lee" Cc: Sent: Thursday, October 30, 2003 9:14 PM Subject: Re: [CPMD-list] combination of PBE USPP with BLYP DFT > > Hi! Well, this looks more like a coincidence than anything else. I don't > think it makes any sense to find a PP with one xc functional and then do > the calculation with another one. What happens if you use the PBE PP's > with the PBE functional? > > Erik. > > On Thu, 30 Oct 2003, Jung Goo Lee wrote: > > > Hi everyone, > > > > I would like to know whether the combination of PBE uspp in ATOMS option > > and BLYP in DFT > > option (the example of partial input is shown below)makes sense or not, > > especially, for calculations > > of free energy (constraint). This is because BLYP method underestimate > > the dissociation free energy > > compared with experiment. For example, water dissociation in 32 water > > molecules with MT PP/ > > BLYP method gave 17 kcal/mol in free energy while experimental value is > > 21 kcal/mol(Trout and > > Parrinello, Chem. Phys. Lett, 288(1998)343. > > I tried the same calculation with PBE uspp and BLYP method. > > I got about 20 kcal/mol althogh I tried with a few hundred fs (instead > > of 1 ps) MD at each point of > > O-H bond constraint. So, this combination (PBE uspp/BLYP) seems to be > > o.k. in free energy > > calculations. > > > > Is this a reasonable and cheap(computationally) way to get out of the > > problem with free energy > > calculations with gbl uspp/BLYP? > > Does any one have any rationalization or contradiction with reasonable > > explanation? > > > > Jung-Goo Lee > > > > Example > > -- > > -- > > &ATOMS > > *008-O-gpbe--bm.uspp NEWF BINARY > > LMAX=P > > 1 > > 4.3728 4.5000 4.5000 1 8 > > > > *001-H-gpbe--bm.uspp NEWF BINARY > > LMAX=S > > 2 > > 5.5172 4.5000 5.9238 1 1 > > 5.5172 4.5000 3.0761 1 1 > > &END > > > > &DFT > > OLDCODE > > FUNCTIONAL BLYP > > GRADIENT CORRECTION BECKE88 LYP > > LDA CORRELATION LYP > > &END > > -- > > -- > > > > > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list From yliu252 at uwo.ca Fri Oct 31 20:18:40 2003 From: yliu252 at uwo.ca (Yi Liu) Date: Fri, 31 Oct 2003 14:18:40 -0500 Subject: [CPMD-list] combination of PBE USPP with BLYP DFT References: <3FA1BA27.1050601@nemo.physics.ncsu.edu> Message-ID: <002a01c39fe3$cf18afc0$de0aa8c0@theory.net> Sorry. I just forgot to paste contents. Please delete the previous one. Hi, I had ever calculated the binding energy (BE) of water dimmer using different PPs and xc functionals (they were always consistent in my test though). I did realize that PBE PP/xc combination gives larger BE(closer to experimental value) than BLYP PP/xc. Moreover, BE is much more sensitive to xc functional than PP, though Martin-Troullier type PP always gives slightly larger value than Godecker type. My results below support this statement, PP xc BE(KJ/mol) Godecker BLYP 18 MT BLYP 19 Godecker PBE 21 MT PBE 23 Expt. 22 I also found the same trends in Benzene-Water complex. Several points should be noted: 1. DFT do has difficulty to predict BE very accuratedly for weak bound system(eg. hydrogen bonded system), then DFT BE is not always satisfied for hydrogen bonding. 2. Even for same type PP, the parameters are somewhat different. So above comparison might depend on details of PPs. 3. Though BLYP has poor BE, it did give a better OH bond length and HOH angle for water than PBE. My experience shows that PBE is better than BLYP in describing weak binding energy, however, BLYP is better in geometry structure (or dipole moment etc.). I am not sure if this conclusion is general. I'd like to listern to other experience about that. Therefore, above discussion may answer your question, that is, PBE PP/xc will still give larger dissociation energy than BLYP. In addition, it is not necessary to use different xc functionals in generating PP and DFT calculation. Hope this helps! Yi ----- Original Message ----- From: "Erik Emilio Santiso" To: "Jung Goo Lee" Cc: Sent: Thursday, October 30, 2003 9:14 PM Subject: Re: [CPMD-list] combination of PBE USPP with BLYP DFT > > Hi! Well, this looks more like a coincidence than anything else. I don't > think it makes any sense to find a PP with one xc functional and then do > the calculation with another one. What happens if you use the PBE PP's > with the PBE functional? > > Erik. > > On Thu, 30 Oct 2003, Jung Goo Lee wrote: > > > Hi everyone, > > > > I would like to know whether the combination of PBE uspp in ATOMS option > > and BLYP in DFT > > option (the example of partial input is shown below)makes sense or not, > > especially, for calculations > > of free energy (constraint). This is because BLYP method underestimate > > the dissociation free energy > > compared with experiment. For example, water dissociation in 32 water > > molecules with MT PP/ > > BLYP method gave 17 kcal/mol in free energy while experimental value is > > 21 kcal/mol(Trout and > > Parrinello, Chem. Phys. Lett, 288(1998)343. > > I tried the same calculation with PBE uspp and BLYP method. > > I got about 20 kcal/mol althogh I tried with a few hundred fs (instead > > of 1 ps) MD at each point of > > O-H bond constraint. So, this combination (PBE uspp/BLYP) seems to be > > o.k. in free energy > > calculations. > > > > Is this a reasonable and cheap(computationally) way to get out of the > > problem with free energy > > calculations with gbl uspp/BLYP? > > Does any one have any rationalization or contradiction with reasonable > > explanation? > > > > Jung-Goo Lee > > > > Example > > -- > > -- > > &ATOMS > > *008-O-gpbe--bm.uspp NEWF BINARY > > LMAX=P > > 1 > > 4.3728 4.5000 4.5000 1 8 > > > > *001-H-gpbe--bm.uspp NEWF BINARY > > LMAX=S > > 2 > > 5.5172 4.5000 5.9238 1 1 > > 5.5172 4.5000 3.0761 1 1 > > &END > > > > &DFT > > OLDCODE > > FUNCTIONAL BLYP > > GRADIENT CORRECTION BECKE88 LYP > > LDA CORRELATION LYP > > &END > > -- > > -- > > > > > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list From vence at status-m.ru Sun Oct 19 12:47:09 2003 From: vence at status-m.ru (V.Sokolov) Date: Sun, 19 Oct 2003 14:47:09 +0400 Subject: [CPMD-list] about RAMAN In-Reply-To: <20031009085434.19418.qmail@vip.sina.com.cn> References: <20031009085434.19418.qmail@vip.sina.com.cn> Message-ID: <3F926BAD.7080503@status-m.ru> cdy2000 at vip.sina.com wrote: >I have computed RAMAN by LINEAR RESPONSE, and get two files: >APT and POLARIZABILITY, lots of data in these files. I want >to know the meaning of the data, please give me some answer in detail. > > > Dear CPMD experts, Wouldn't you give an advice how to get Raman intensities from these data? Thanking you in advance, -- V.Sokolov From nisanth at theochem.uni-hannover.de Wed Oct 22 11:29:28 2003 From: nisanth at theochem.uni-hannover.de (Nisanth Nair) Date: Wed, 22 Oct 2003 11:29:28 +0200 Subject: [CPMD-list] PROGRAM STOPS IN SUBROUTINE SOLVE Message-ID: <200310221129.28556.nisanth@theochem.uni-hannover.de> Dear cpmd users, I have a problem during the geometry optimization of TiO2 bulk. The program stops in SOLVE during wavefunction optimization after a few geometry optimization steps. I have used preconditioned DIIS for the wavefunction optimization. The error message looks like as below. Can you please help me in finding why it happens? 39 2.935E-05 1.860E-06 -180.627420 -2.193E-07 0.82 SOLVE! INFO= 10 PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 0] SOLVE! INFO= 10 PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 1] SOLVE! INFO= 10 PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 2] SOLVE! INFO= 10 PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 3] SOLVE! INFO= 10 PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 4] SOLVE! INFO= 10 PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 5] SOLVE! INFO= 10 PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 6] SOLVE! INFO= 10 PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 7] Thanking you, Nisanth From resumes at workwondersstaffing.net Fri Oct 31 20:06:30 2003 From: resumes at workwondersstaffing.net (Khristine Anderson) Date: Fri, 31 Oct 2003 12:06:30 -0700 Subject: [CPMD-list] (job) Senior Computational Chemist - northern New York state Message-ID: Senior Computational Chemist - New York state A client of ours in northern New York state is seeking a Senior Computational Chemist. The candidate should be willing to provide molecular modeling support for discovery projects by applying state-of-the-art computational techniques, with the goal of identifying and optimizing novel drug leads. This could be a management position with one to three direct reports. 3 or more years industrial experience in de-novo ligand design, pharmacophore analyses, ligand docking, library design and analysis, homology modeling and protein-ligand simulations is REQUIRED. Additional requirements include a Ph.D. in Chemistry, Biochemistry, Biophysics, or a related discipline, and excellent communication skills. If you are interested in pursuing this opportunity, please forward your CV, salary requirement, relocation considerations and references to resumes at workwondersstaffing.net. It is important to use the position title as the subject of your email to allow your resume to reach the appropriate recruiter as quickly as possible. If you feel you are not qualified or are not interested in the opportunity, do you know anyone who might be a good fit? Thank you for your time - have a great day! --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.530 / Virus Database: 325 - Release Date: 10/22/2003 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20031031/b25fc2c9/attachment.html