From shyma at imr.ac.cn Thu Dec 1 06:36:00 2005 From: shyma at imr.ac.cn (=?gb2312?B?U2hhbmd5aSBNYQ==?=) Date: Thu, 1 Dec 2005 13:36:00 +0800 (CST) Subject: [CPMD-list] some problems need your help Message-ID: <438E8BC0.000145.26949@app-01> Dear cpmd-user: I have some problems need your help: The first, I want to compute the energy of single Al atom, but it 's difficult converge through hundreds of steps or even two thousand! The following is my input-file, could you help me solve the problem: ************************************************* &CPMD OPTIMIZE WAVEFUNCTION RESTART WAVEFUNCTION COORDINATES CONVERGENCE ORBITALS 1.0D-5 FREE ENERGY FUNCTIONAL LANCZOS DIAGONALISATION LANCZOS PARAMETAERS N=5 50 6 20 1.0D-9 0.05 1.0D-10 0.01 1.0D-12 0.0025 1.0D-14 0.001 1.0D-16 LSD ANDERSON MIXING 0.2 BROYDEN MIXING BROYMIX=0.15 TEMPERATURE ELCECTRON 1000 CENTER MOLECULE ON MIRROR &END &SYSTEM SYMMETRY 0 MULTIPLICITY 2 #(for al atom, the 2S+1=2 ? or 4?) POISSON SOLVER TUCKERMAN ANGSTROM CELL 12.0 1.0 1.0 0.0 0.0 0.0 STATES 10 CUTOFF 60 &END &ATOMS *Al_SGS_LDA.psp KLEINMAN-BYLANDER LMAX=D 1 6.0 6.0 6.0 &END ********************************************************** Secondly, how can I get the Partial_DOS information of the system(for example, the al cluster) that i compute? Could someone teach me details? Thirdly, how can I get the information of HOMO and LUMO about the system that I compute? More details is better! Any comments and help is appreciated! Thanks in advance! Best wishes! shyma -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20051201/f5331e43/attachment.html From ari.p.seitsonen at iki.fi Fri Dec 2 08:40:20 2005 From: ari.p.seitsonen at iki.fi (Ari P Seitsonen) Date: Fri, 2 Dec 2005 08:40:20 +0100 (CET) Subject: [CPMD-list] some problems need your help In-Reply-To: <438E8BC0.000145.26949@app-01> References: <438E8BC0.000145.26949@app-01> Message-ID: Dear Shangyi, The easiest way to calculate the energy of the single atom is to use MULTIPLICITY of 4 (three unpaired electrons) and no FREE ENERGY FUNCTIONAL (and you can erase keyword 'STATES'). Please notice that you have a typo in 'TEMPERATURE ELCECTRON', however in this case it wouldn't matter because the default value is the same, but in case of molecular dynamics this would be interpreted as _ionic_ temperature. The cut-off energy of 60 Ry is probably much too high, maybe you used it just to find the problem in the convergence? Besides this, I also find the slow/missing convergence strange, as the initial guess of an atomic charge density with the atomic orbitals should be very close to the final solution. About partial DOS, I guess that you mean the projected density of states? You can check the keywords 'LDOS', and maybe 'POPULATION ANALYSIS' is interesting for you. About HOMO/LUMO, well for aluminium clusters they are probably not very important, but in general you get the eigenvalues directly printed out if using FREE ENERGY FUNCTIONAL, and if not you can perform a calculation with 'KOHN-SHAM ENERGIES'. For the wave functions, you can use either 'RHOOUT BANDS' + cpmd2cube or the 'PROPERTIES' and 'CUBEFILE'. Hopefully this helps at least a bit. Greetings from San Sebastian, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ CNRS & IMPMC, Universit? Pierre et Marie Curie 4 place Jussieu, case 115 / F-75252 Paris Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820 On Thu, 1 Dec 2005, Shangyi Ma wrote: > Dear cpmd-user: > I have some problems need your help: > The first, I want to compute the energy of single Al atom, but it 's difficult converge through hundreds of steps or even two thousand! The following is my input-file, could you help me solve the problem: > ************************************************* > &CPMD > OPTIMIZE WAVEFUNCTION > RESTART WAVEFUNCTION COORDINATES > CONVERGENCE ORBITALS > 1.0D-5 > FREE ENERGY FUNCTIONAL > LANCZOS DIAGONALISATION > LANCZOS PARAMETAERS N=5 > 50 6 20 1.0D-9 > 0.05 1.0D-10 > 0.01 1.0D-12 > 0.0025 1.0D-14 > 0.001 1.0D-16 > LSD > ANDERSON MIXING > 0.2 > BROYDEN MIXING > BROYMIX=0.15 > TEMPERATURE ELCECTRON > 1000 > CENTER MOLECULE ON > MIRROR > &END > > &SYSTEM > SYMMETRY > 0 > MULTIPLICITY > 2 #(for al atom, the 2S+1=2 ? or 4?) > POISSON SOLVER TUCKERMAN > ANGSTROM > CELL > 12.0 1.0 1.0 0.0 0.0 0.0 > STATES > 10 > CUTOFF > 60 > &END > > &ATOMS > *Al_SGS_LDA.psp KLEINMAN-BYLANDER > LMAX=D > 1 > 6.0 6.0 6.0 > &END > ********************************************************** > > Secondly, how can I get the Partial_DOS information of the system(for > example, the al cluster) that i compute? Could someone teach me details? > > Thirdly, how can I get the information of HOMO and LUMO about the system > that I compute? More details is better! > > Any comments and help is appreciated! > Thanks in advance! > Best wishes! > > shyma From yangzy at lnm.imech.ac.cn Fri Dec 2 13:10:26 2005 From: yangzy at lnm.imech.ac.cn (Yang Zhenyu) Date: Fri, 2 Dec 2005 20:10:26 +0800 Subject: [CPMD-list] Why convergence is so slow? Message-ID: <200512021211.NAA18276@internet-fence.zurich.ihost.com> Dear CPMD users: I try to calcluate a molecule adsorption on Ni surface with GH-pseudopotentials, but I find it is very hard to converge in the geometry optimization. So I post my input here, hoping anybody can give me some advices! ------------------------------- &CPMD OPTIMIZE GEOMETRY TRAJECTORY XYZ UNIT HESSIAN BFGS FREE ENERGY FUNCTIONAL LANCZOS DIAGONALISATION LANCZOS PARAMETERS 1 6 10 1.D-18 TROTTER FACTOR 0.001 BOGOLIUBOV CORRECTION OFF GRAM-SCHMIDT ORTHOGONALISATION CONVERGENCE 1.D-4 5.D-4 MAXSTEP 500 BROYDEN MIXING 0.3 200 0.01 0 8 ALEXANDER MIXING 1.1 ELECTRON TEMPERATURE 1000. COMPRESS WRITE32 STRUCTURE BONDS RHOOUT WANNIER WFNOUT ALL PRINT ON &END &SYSTEM POINT GROUP AUTO SYMMETRY 4 ANGSTROM CELL 7.3818 1.0 5.0 0.00 0.00 -0.5 CHARGE 0 CUTOFF 60 TESR 3 &END &DFT NEWCODE FUNCTIONAL PBE &END &ATOMS *Ni-q18-pbe KLEINMAN-BYLANDER LMAX=P ..................................... *N-q5-pbe KLEINMAN-BYLANDER LMAX=P ..................................... *C-q4-pbe KLEINMAN-BYLANDER LMAX=P ..................................... *H-q1-pbe KLEINMAN-BYLANDER ..................................... CONSTRAINTS FIX ATOMS 8 1 2 3 4 5 6 7 8 END CONSTRAINTS &END --------------------------------------------------- ?????????????? ??Best Regards ??Yang Zhenyu State Key Laboratory of Nonlinear Mechanics (LNM) Institute of Mechanics, Chinese Academy of Sciences No.15 Beisihuanxi Road Beijing 100080, P. R. China FAX: 010-62579511 ??yangzy at lnm.imech.ac.cn ??2005-12-02 From ara_1357_2416 at yahoo.com Sat Dec 3 06:19:55 2005 From: ara_1357_2416 at yahoo.com (Younes Ansari) Date: Fri, 2 Dec 2005 21:19:55 -0800 (PST) Subject: [CPMD-list] ATOMIC CHARGES Message-ID: <20051203051955.38881.qmail@web33207.mail.mud.yahoo.com> Dear cpmd-list: I want to use the keyword ATOMIC CHARGES in my input file .My system contains N,H,C,I . I want to apply some charges to N(+.5) and I(-1). Would you please tell me hoe could I insert it into the input file in &ATOMS section.(It is not clearly defined by cpmd manual.) --------------------------------- Yahoo! Personals Single? There's someone we'd like you to meet. Lots of someones, actually. Yahoo! Personals -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20051202/a0bfe2d8/attachment.html From ara_1357_2416 at yahoo.com Sat Dec 3 07:07:38 2005 From: ara_1357_2416 at yahoo.com (Younes Ansari) Date: Fri, 2 Dec 2005 22:07:38 -0800 (PST) Subject: [CPMD-list] 48 nodes super computer Message-ID: <20051203060738.54151.qmail@web33207.mail.mud.yahoo.com> Dear cpmd-list: I am trying to install cpmd into a system contain 48 nodes but only the main computer had Hard disk. So I have to use the system LAN to run cpmd. I have installed it but when I am trying to run cpmd for a small system of H2 This message appears: ALLOCATION MEMORY FAILED.(It appears just when I am trying to run that using LAN but the main computer runs my program. What would be helpful solving my problem.??????? --------------------------------- Yahoo! Shopping Find Great Deals on Gifts at Yahoo! Shopping -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20051202/31b8f502/attachment.html From akohlmey at vitae.cmm.upenn.edu Sat Dec 3 15:05:21 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Sat, 3 Dec 2005 09:05:21 -0500 (EST) Subject: [CPMD-list] 48 nodes super computer In-Reply-To: <20051203060738.54151.qmail@web33207.mail.mud.yahoo.com> Message-ID: On Fri, 2 Dec 2005, Younes Ansari wrote: YA> Dear cpmd-list: YA> I am trying to install cpmd into a system contain 48 nodes but YA> only the main computer had Hard disk. So I have to use the system YA> LAN to run cpmd. I have installed it but when I am trying to run YA> cpmd for a small system of H2 This message appears: YA> ALLOCATION MEMORY FAILED.(It appears just when I am trying to run YA> that using LAN but the main computer runs my program. YA> YA> What would be helpful solving my problem.??????? first you should provide more information about the hard- and software that you are using, the compiler flags and how you start the job and what kind of output you get _before_ the error message. none of us here is a psychic, so you have to help us to help you, and the quality of answer you get will depend on the quality of question you ask. please have a look at the mailing list archives, how others did report similar problems (and which kind of report prompted a helpful answer. there are also two nice webpages with guidelines for meaningful bug/problem reports: http://www.chiark.greenend.org.uk/~sgtatham/bugs.html http://www.catb.org/~esr/faqs/smart-questions.html axel YA> YA> YA> --------------------------------- YA> Yahoo! Shopping YA> Find Great Deals on Gifts at Yahoo! Shopping -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From k3135005 at guedu.cc.gifu-u.ac.jp Sun Dec 4 02:28:50 2005 From: k3135005 at guedu.cc.gifu-u.ac.jp (Hiroshi Amawashi) Date: Sun, 04 Dec 2005 10:28:50 +0900 Subject: [CPMD-list] geometry optimization of a carbon nanotube Message-ID: <200512040128.AA00024@motet.guedu.cc.gifu-u.ac.jp> Dear CPMD community, I'm a beginner of CPMD and trying to do a geometry optimization of an armchair-type carbon nanotube with chiral vector of (5,5). But the results were bizarre: 20-atom armchair ring in the unit cell had broken into two parts. When I set TESR = 8, the bond angles of armchir were `optimized' to around 100 degrees rather than the normal angle of 120 degrees. Obviously, these results are all wrong. Any useful suggestions would be greatly appreciated. I've included the input file that I'm using below, in case I'm making a stupid mistake...... Best wishes, Hiroshi Amawashi ------------------INPUT FILE &CPMD OPTIMIZE GEOMETRY XYZ ODIIS 4 TSDC SPLINE RANGE 5.0 BFGS STRUCTURE BONDS ANGLES MIRROR HESSIAN UNIT &END &SYSTEM SYMMETRY 6 ANGSTROM CELL 10.0 1.0 0.2494153 0.0 0.0 0.0 CUTOFF 80. TESR 8 POINT GROUP AUTO &END &ATOMS Carbon C_MT_GIA_BLYP KLEIMANN-BYLANDER LMAX=P LOC=P 20 3.4377467708 0.0000000000 0.0000000000 3.1405379470 1.3982575813 0.0000000000 2.7811955599 2.0206568530 1.2470765814 1.7188733854 2.9771760353 1.2470765814 1.0623221745 3.2694914677 -0.0000000000 -0.3593423871 3.4189144343 -0.0000000000 -1.0623221745 3.2694914677 1.2470765814 -2.3003015812 2.5547437240 1.2470765814 -2.7811955599 2.0206568530 -0.0000000000 -3.3626237558 0.7147477437 -0.0000000000 -3.4377467708 0.0000000000 1.2470765814 -3.1405379470 -1.3982575813 1.2470765814 -2.7811955599 -2.0206568530 -0.0000000000 -1.7188733854 -2.9771760353 -0.0000000000 -1.0623221745 -3.2694914677 1.2470765814 0.3593423871 -3.4189144343 1.2470765814 1.0623221745 -3.2694914677 -0.0000000000 2.3003015812 -2.5547437240 -0.0000000000 2.7811955599 -2.0206568530 1.2470765814 3.3626237558 -0.7147477437 1.2470765814 &END &DFT FUNCTIONAL BLYP &END ---------------------End of INPUT FILE ---------------------------------------------------------------- Hiroshi Amawashi University of Gifu 1-1 , yanagido , Gifu City, Gifu, Japan E-mail: k3135005 at guedu.cc.gifu-u.ac.jp ---------------------------------------------------------------- ---- Hiroshi Amawashi k3135005 at guedu.cc.gifu-u.ac.jp From akohlmey at vitae.cmm.upenn.edu Sun Dec 4 03:45:34 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Sat, 3 Dec 2005 21:45:34 -0500 (EST) Subject: [CPMD-list] geometry optimization of a carbon nanotube In-Reply-To: <200512040128.AA00024@motet.guedu.cc.gifu-u.ac.jp> Message-ID: On Sun, 4 Dec 2005, Hiroshi Amawashi wrote: HA> Dear CPMD community, dear hiroshi, HA> I'm a beginner of CPMD and trying to do a geometry optimization of HA> an armchair-type carbon nanotube with chiral vector of (5,5). may i suggest that you should first gain a little practice in using CPMD with a few smaller and less demanding problems. HA> But the results were bizarre: 20-atom armchair ring in the unit cell HA> had broken into two parts. When I set TESR = 8, the bond angles of HA> armchir were `optimized' to around 100 degrees rather than the normal angle HA> of 120 degrees. Obviously, these results are all wrong. HA> Any useful suggestions would be greatly appreciated. I've included the HA> input file that I'm using below, in case I'm making a stupid mistake...... thank you for the detailed description of your attempts. i have a few remarks about your input. i won't say that you are making a _stupid_ mistake, but it is more that you are not considering two factors that are important for a system like yours, and those are actually quite common mistakes for a beginner, hence my suggestion above. 1) your box in x-, and y- direction is too small. you have to keep in mind, that your system cell must be large enough to hold all atoms _and_ their electron density and that there should be enough distance from the atom centers to the wall of the unit cell, that the periodic images (of the density) does not touch or influence each other. so changing the cell keyword to: CELL ABSOLUTE 15.0 15.0 2.494153 0.0 0.0 0.0 should take care of that. 2) the second problem is more grave. you are doing a gamma-point only calculation with a very small cell dimension in z-direction and no k-points. this is all the worse, since your nanotube should be metallic and thus you would need a lot of them and/or do a free energy functional type calculation (which requires quite a bit of experience, since there are many parameters to fiddle with in order to get a good convergence). to some degree, you may be able to avoid the k-point issue, by replicating your your box in z-direction a few times. but you should carefully compare your results to what is published in the literature. there should be a ton of those. you can find some examples of using k-points (without the free energy functional) at: http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-tutor/part7.html#chap8 where you have different types and sizes of unit cells. unfortunately i did not have the time to add an explanation of the results. they should basically all give the same total energy per atom, but you need either a many k-points or a lot of atoms to get that, and doubling the unitcell (in all directions) should be equivalent to doubling the number of k-points (in all directions). the only good news i have is that you can probably 'get away' with a smaller plane wave cutoff (e.g. 60ry), but that won't by far compensate the additional effort from the other required changes. also in that case TESR would not matter and can be kept at the default (0). BTW: a fast and convenient way of testing whether your box is large enough, is doing a wavefunction optimization with RHOOUT using a plane wave cutoff of 10ry or even 5ry. you can then convert the resulting DENSITY file into cube format with: cpmd2cube -center -dens DENSITY and visualize the resulting density as an isosurface with a very low isovalue (0.0001 or lower). the isosurface should not touch the walls, or better there should be a small safety margin. it took me longer to write this mail than checking your input this way... ;-) best wishes from cold philadelphia, axel. HA> Best wishes, HA> HA> Hiroshi Amawashi HA> HA> ------------------INPUT FILE HA> HA> HA> &CPMD HA> OPTIMIZE GEOMETRY XYZ HA> ODIIS HA> 4 HA> TSDC HA> SPLINE RANGE HA> 5.0 HA> BFGS HA> STRUCTURE BONDS ANGLES HA> MIRROR HA> HESSIAN UNIT HA> &END HA> HA> &SYSTEM HA> SYMMETRY HA> 6 HA> ANGSTROM HA> CELL HA> 10.0 1.0 0.2494153 0.0 0.0 0.0 HA> CUTOFF HA> 80. HA> TESR HA> 8 HA> POINT GROUP HA> AUTO HA> &END HA> HA> &ATOMS HA> Carbon HA> C_MT_GIA_BLYP KLEIMANN-BYLANDER HA> LMAX=P LOC=P HA> 20 HA> 3.4377467708 0.0000000000 0.0000000000 HA> 3.1405379470 1.3982575813 0.0000000000 HA> 2.7811955599 2.0206568530 1.2470765814 HA> 1.7188733854 2.9771760353 1.2470765814 HA> 1.0623221745 3.2694914677 -0.0000000000 HA> -0.3593423871 3.4189144343 -0.0000000000 HA> -1.0623221745 3.2694914677 1.2470765814 HA> -2.3003015812 2.5547437240 1.2470765814 HA> -2.7811955599 2.0206568530 -0.0000000000 HA> -3.3626237558 0.7147477437 -0.0000000000 HA> -3.4377467708 0.0000000000 1.2470765814 HA> -3.1405379470 -1.3982575813 1.2470765814 HA> -2.7811955599 -2.0206568530 -0.0000000000 HA> -1.7188733854 -2.9771760353 -0.0000000000 HA> -1.0623221745 -3.2694914677 1.2470765814 HA> 0.3593423871 -3.4189144343 1.2470765814 HA> 1.0623221745 -3.2694914677 -0.0000000000 HA> 2.3003015812 -2.5547437240 -0.0000000000 HA> 2.7811955599 -2.0206568530 1.2470765814 HA> 3.3626237558 -0.7147477437 1.2470765814 HA> &END HA> HA> &DFT HA> FUNCTIONAL BLYP HA> &END HA> ---------------------End of INPUT FILE HA> HA> HA> ---------------------------------------------------------------- HA> Hiroshi Amawashi HA> University of Gifu HA> 1-1 , yanagido , Gifu City, Gifu, Japan HA> E-mail: k3135005 at guedu.cc.gifu-u.ac.jp HA> ---------------------------------------------------------------- HA> HA> ---- HA> Hiroshi Amawashi k3135005 at guedu.cc.gifu-u.ac.jp HA> _______________________________________________ HA> CPMD-list mailing list HA> CPMD-list at cpmd.org HA> http://cpmd.org/mailman/listinfo/cpmd-list HA> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From shyma at imr.ac.cn Sun Dec 4 14:20:01 2005 From: shyma at imr.ac.cn (=?gb2312?B?U2hhbmd5aSBNYQ==?=) Date: Sun, 4 Dec 2005 21:20:01 +0800 (CST) Subject: [CPMD-list] help, the problem still exist Message-ID: <4392ED01.000028.06968@app-01> Dear apsi: Thanks for your reply, but the problem is still exist! I'm troubled in getting the cohesive energy of Al. The cohesive energy calculation are performed by subtracting the total energy(E1) of the spin ploarized Al atom from the energy(E2) per atom in the bulk. So I must get the different energys E1 and E2 firstly. In your last letter, you said "The easiest way to calculate the energy of the single atom is to use MULTIPLICITY of 4 (three unpaired electrons) and no FREE ENERGY FUNCTIONAL (and you can erase keyword 'STATES'). Please notice that you have a typo in 'TEMPERATURE ELCECTRON', however in this case it wouldn't matter because the default value is the same, but in case of molecular dynamics this would be interpreted as _ionic_ temperature...", so need I use the FREE ENERGY FUNCTIONAL if I want to get the energy(E2) per atom in the bulk? The energy of spin ploarized Al atom I get is -1.95126380 A.U. and -1.82387924 A.U. when I specified MULTIPLICITY 2 and 4 respectively.(In my mind, the electron configuration of Al is 1s(2)2s(2)2p(6)3s(2)3p(1) and one unpair electron, so I think the multiplicity is 2*(1/2)+1=2.But you specified MULTIPLICITY 4 in your letter, does it means the electron configuration is 1s(2)2s(2)2p(6)3s(1)3P(2) and three unpair electrons, so what are the difference and which multiplicity value should I specified when I get the energy of spin ploarized Al atom?) The input file for the spin Al atom calculation is following: ******************************************************* &CPMD OPTIMIZE WAVEFUNCTION CONVERGENCE ORBITALS 1.0D-6 PCG MINIMIZE TIMESTEP 20 LSD MIRROR &END &SYSTEM SYMMETRY 0 MULTIPLICITY 2 (4 or 2?) POISSON SOLVER TUCKERMAN ANGSTROM CELL 10.0 1.0 1.0 0.0 0.0 0.0 CUTOFF 30 &END &ATOMS *Al_SGS_LDA.psp KLEINMAN-BYLANDER LMAX=D 1 5.0 5.0 5.0 &END &DFT FUNCTIONAL LDA &END ******************************************************* Then I calculate the energy per atom in bulk with FREE ENERGY FUNCTIONAL and without it, the E2 are -2.10337731 A.U. and -2.01913733 A.U. respectively, the following are the input files with and without free energy funcitonal: ****************************************************** &CPMD OPTIMIZE WAVEFUNCTION FREE ENERGY FUNCTIONAL CONVERGENCE ORBITALS 1.0D-6 MIRROR &END &SYSTEM SYMMETRY FCC ANGSTROM CELL 3.95 1.0 1.0 0 0 0 (#I get the equilibration lattice with the energy vs variety lattice) CUTOFF 60 TESR 3 STATES 4 KPOINTS MONKHORST-PACK 8 8 8 &END &ATOMS *Al_SGS_LDA.psp KLEINMAN-BYLANDER LMAX=D 1 0 0 0 &END &DFT FUNCTIONAL LDA &END ***************************************************** ****************************************************** &CPMD OPTIMIZE WAVEFUNCTION CONVERGENCE ORBITALS 1.0D-6 MIRROR &END &SYSTEM SYMMETRY FCC ANGSTROM CELL 3.95 1.0 1.0 0 0 0 CUTOFF 60 TESR 3 KPOINT MONKHORST-PACK 8 8 8 &END &ATOMS *Al_SGS_LDA.psp KLEINMAN-BYLANDER LMAX=D 1 0 0 0 &END &DFT FUNCTIONAL LDA &END ********************************************************** the cohesive energy I get with the above the values are far away the experiment values 3.45 ev. Could you help me solve the problem and get the calculation cohesive value approach the experiment values? Another problem about project-dos is that I want to get the information that the dos vs energy on s,p,d ...orbitals, I check the LDOS and PROJECT ANALYSIS and don't know how to get the information I need, could you explain it to me in details? I'm poor on the sphere of ab initio calculation and maybe some questions is stupid and not professional, but I really need your help thirstly! Thanks in advace! Best regards! shyma -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20051204/d35e0fa6/attachment.html From akohlmey at vitae.cmm.upenn.edu Sun Dec 4 17:59:22 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Sun, 4 Dec 2005 11:59:22 -0500 (EST) Subject: [CPMD-list] help, the problem still exist In-Reply-To: <4392ED01.000028.06968@app-01> Message-ID: On Sun, 4 Dec 2005, [gb2312] Shangyi Ma wrote: SM> Dear apsi: SM> Thanks for your reply, but the problem is still exist! dear shyma, SM> I'm troubled in getting the cohesive energy of Al. The cohesive SM> energy calculation are performed by subtracting the total energy(E1) SM> of the spin ploarized Al atom from the energy(E2) per atom in the SM> bulk. So I must get the different energys E1 and E2 firstly. first off, you should note, that you are digging into parts of the CPMD code, that are not so frequently used and thus there is less expertise available and the usage of that part of the code needs you to do have a deeper understanding of the underlying physics. or to put it differenty: in the old times people would have written 'here be dragons' (remember that in europe dragons are usually fear inspiring creatures). SM> In your last letter, you said "The easiest way to calculate the SM> energy of the single atom is to use MULTIPLICITY of 4 (three SM> unpaired electrons) and no FREE ENERGY FUNCTIONAL (and you can erase SM> keyword 'STATES'). Please notice that you have a typo in SM> 'TEMPERATURE ELCECTRON', however in this case it wouldn't matter SM> because the default value is the same, but in case of molecular SM> dynamics this would be interpreted as _ionic_ temperature...", so SM> need I use the FREE ENERGY FUNCTIONAL if I want to get the SM> energy(E2) per atom in the bulk? since you want to compute the _difference_ of energies, you have to use the same method. IIRC, using FEMD will shift the total energy depending on the electron temperature, so you have to use the same settings for both calculations. of course you need to run an open-shell calculation in both cases, too. SM> The energy of spin ploarized Al atom I get is -1.95126380 A.U. SM> and -1.82387924 A.U. when I specified MULTIPLICITY 2 and 4 SM> respectively.(In my mind, the electron configuration of Al is SM> 1s(2)2s(2)2p(6)3s(2)3p(1) and one unpair electron, so I think the SM> multiplicity is 2*(1/2)+1=2.But you specified MULTIPLICITY 4 in your SM> letter, does it means the electron configuration is SM> 1s(2)2s(2)2p(6)3s(1)3P(2) and three unpair electrons, so what are SM> the difference and which multiplicity value should I specified when SM> I get the energy of spin ploarized Al atom?) The input file for the SM> spin Al atom calculation is following: i have to disagree with ari, i think you are correct in using a multiplicity of 2. SM> ******************************************************* SM> &CPMD SM> OPTIMIZE WAVEFUNCTION SM> CONVERGENCE ORBITALS SM> 1.0D-6 SM> PCG MINIMIZE SM> TIMESTEP SM> 20 SM> LSD SM> MIRROR SM> &END SM> SM> &SYSTEM SM> SYMMETRY SM> 0 there is little need to use a poisson solver (symmetry 0) here. just make sure your box is large enough. SM> MULTIPLICITY SM> 2 (4 or 2?) SM> POISSON SOLVER TUCKERMAN SM> ANGSTROM SM> CELL SM> 10.0 1.0 1.0 0.0 0.0 0.0 SM> CUTOFF SM> 30 SM> Then I calculate the energy per atom in bulk with FREE ENERGY SM> FUNCTIONAL and without it, the E2 are -2.10337731 A.U. and SM> -2.01913733 A.U. respectively, the following are the input files SM> with and without free energy funcitonal: SM> SM> ****************************************************** SM> &CPMD SM> OPTIMIZE WAVEFUNCTION SM> FREE ENERGY FUNCTIONAL SM> CONVERGENCE ORBITALS SM> 1.0D-6 SM> MIRROR SM> &END SM> SM> &SYSTEM SM> SYMMETRY SM> FCC SM> ANGSTROM SM> CELL SM> 3.95 1.0 1.0 0 0 0 (#I get the equilibration lattice with the energy vs variety lattice) SM> CUTOFF SM> 60 whoa, there! why suddenly a cutoff of 60ry? SM> TESR SM> 3 SM> STATES SM> 4 SM> KPOINTS MONKHORST-PACK SM> 8 8 8 SM> &END SM> the cohesive energy I get with the above the values are far away the SM> experiment values 3.45 ev. Could you help me solve the problem and SM> get the calculation cohesive value approach the experiment values? well, you cannot compare two energies with different basis set sizes. in fact, there are a number of issues that you have to pay attention to, many of them related to using a plane wave basis set: a) you have to make sure, that your energy difference are converged with respect to the plain wave cutoff. mind you, the _differences_ not the total energy. due to error cancellation, the difference should converge much faster. converging the total energy would usually require a higher plane wave cutoff. feel free to do it, but you are wasting your (cpu) time. b) you have to make sure, that your bulk system's total energy is converged with respect to the number of k-points and the electron temperature. a higher electron temperature should correspond to a larger smearing of the electrons, which in turn should facilitate an easier k-point convergence, but in turn it will take you further away from the 'cold' real minimum. so you have to find a good compromise, that also represents other bulk properties well. c) you then have to make sure, that all relevant parameters for the two runs (single atom and bulk) are comparable. most importantly, plain wave cutoff (and density cutoff), but also the number of grid points per volume should be the same (note, that these numbers are chosen based on supported FFT-grids, and thus it is most likely that you get comparable grids when the lattice constant of the single atom box is an integer multiple of the bulk system). you can set the grid manually, but you have to double check, because the FFT-will use the smallest _supported_ grid, which may be larger that what you chose. SM> Another problem about project-dos is that I want to get the SM> information that the dos vs energy on s,p,d ...orbitals, I check the SM> LDOS and PROJECT ANALYSIS and don't know how to get the information SM> I need, could you explain it to me in details? i am sorry but, no. i know there is a tool in the pwscf package, that can do this, and perhaps somebody has dome something similar for cpmd. if yes, please speak up. otherwise, you probably have to figure it out for yourself. SM> I'm poor on the sphere of ab initio calculation and maybe some SM> questions is stupid and not professional, but I really need your SM> help thirstly! well, the best way to deal with it, is to use your thirst and _learn_ the method instead of letting others doing the work for you. there is a ton of textbooks, reviews, lecture notes, and you can learn a lot from reading the source code or by just figuring things out, using common sense and careful double checking of your results. at least on the last part, you have already come pretty far, so that should be encouraging. since there are many more people asking about these issues, than answering, you may even become the 'CPMD-expert' in this area pretty fast (all you need is to know a little more and have a bit experience). as i wrote before, chances are pretty slim that you'll get anything better than people like me mostly trying to guess, what is going on. with best regards, axel. SM> Thanks in advace! SM> Best regards! SM> shyma SM> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From Christopher.DeDobbelaere at student.ua.ac.be Mon Dec 5 10:04:26 2005 From: Christopher.DeDobbelaere at student.ua.ac.be (De Dobbelaere Christopher) Date: Mon, 5 Dec 2005 10:04:26 +0100 Subject: [CPMD-list] forces, convergence and gga Message-ID: Hi cpmd users, I've got 3 little questions.. 1) I'm doing a md run of a molecule surrounded by water molecules. In order to check if the forces acting on the molecules are not too large, i'd like to check out the forces acting on them (since i didn't do a geometry optimalization at the beginning). I checked out the manual and found that it is possible to print the acting forces during the trajectory in the TRAJECTORY file. Since the md run is 'finished' it seems to be a little late for that.. But now I was wondering what the initial forces acting on the atoms would be. Since they are listed in the output file that seemed not to be a problem. But what are the units of the forces? They are not mentioned in the manual, so i suppose it's a.u.? If it it, what's the conversion to convert them to dyne, Newton,.. or something else? 2) Before I did a md run, i checked out some dft functionals to describe the geometry of the molecule. I got convergence for C=C, C-H, more or less convergence for S-N but the C-S bound seems not to convergence at all (the C's from a aromatic system and C is attached to it). Does anyone have an idea why that could be? 3) In the manual, the GGA functional is mentioned. But what's the exact functional behind that GGA implemented in cpmd? Since GGA stands for Generalized-gradient-approximation, it doesnt give me any new information.. Thanks in advance! Christopher Undergrad. Student University of Antwerp -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20051205/0d91afce/attachment.html From hutter at pci.unizh.ch Mon Dec 5 11:15:11 2005 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 5 Dec 2005 11:15:11 +0100 (MET) Subject: [CPMD-list] ATOMIC CHARGES In-Reply-To: <20051203051955.38881.qmail@web33207.mail.mud.yahoo.com> References: <20051203051955.38881.qmail@web33207.mail.mud.yahoo.com> Message-ID: Hi the ATOMIC CHARGES keyword changes the total charge of the atoms for the "initial guess" (see also manual). The idea is that this allows for improved inital guesses for charged systems. This will NOT change the final result of the calculation! The syntax is &ATOMS ATOMIC CHARGES val1 val2 ... &END where val1, val2, ... are the charges for all the species in the same order as they are defined in the ATOMS section. regards Juerg Hutter ---------------------------------------------------------- Juerg Hutter Phone : ++41 44 635 4491 Physical Chemistry Institute FAX : ++41 44 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Fri, 2 Dec 2005, Younes Ansari wrote: > Dear cpmd-list: > I want to use the keyword ATOMIC CHARGES in my input file .My system contains N,H,C,I . I want to apply some charges to N(+.5) and I(-1). Would you please tell me hoe could I insert it into the input file in &ATOMS section.(It is not clearly defined by cpmd manual.) > > > --------------------------------- > Yahoo! Personals > Single? There's someone we'd like you to meet. > Lots of someones, actually. Yahoo! Personals From hutter at pci.unizh.ch Mon Dec 5 11:17:17 2005 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 5 Dec 2005 11:17:17 +0100 (MET) Subject: [CPMD-list] Why convergence is so slow? In-Reply-To: <200512021211.NAA18276@internet-fence.zurich.ihost.com> References: <200512021211.NAA18276@internet-fence.zurich.ihost.com> Message-ID: Hi the only improvement I can see right away would be to use the LBFGS optimizer. This usually works better for this type of systems. regards Juerg Hutter ---------------------------------------------------------- Juerg Hutter Phone : ++41 44 635 4491 Physical Chemistry Institute FAX : ++41 44 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Fri, 2 Dec 2005, Yang Zhenyu wrote: > Dear CPMD users: > > I try to calcluate a molecule adsorption on Ni surface with GH-pseudopotentials, but I find it is very hard to converge in the geometry optimization. So I post my input here, hoping anybody can give me some advices! > > ------------------------------- > &CPMD > OPTIMIZE GEOMETRY > TRAJECTORY XYZ > UNIT HESSIAN > BFGS > FREE ENERGY FUNCTIONAL > LANCZOS DIAGONALISATION > LANCZOS PARAMETERS > 1 6 10 1.D-18 > TROTTER FACTOR > 0.001 > BOGOLIUBOV CORRECTION OFF > GRAM-SCHMIDT ORTHOGONALISATION > CONVERGENCE > 1.D-4 5.D-4 > MAXSTEP > 500 > BROYDEN MIXING > 0.3 200 0.01 0 8 > ALEXANDER MIXING > 1.1 > ELECTRON TEMPERATURE > 1000. > COMPRESS WRITE32 > STRUCTURE BONDS > RHOOUT > WANNIER WFNOUT ALL > PRINT ON > &END > > &SYSTEM > POINT GROUP > AUTO > SYMMETRY > 4 > ANGSTROM > CELL > 7.3818 1.0 5.0 0.00 0.00 -0.5 > CHARGE > 0 > CUTOFF > 60 > TESR > 3 > &END > > &DFT > NEWCODE > FUNCTIONAL PBE > &END > > &ATOMS > *Ni-q18-pbe KLEINMAN-BYLANDER > LMAX=P > ..................................... > > *N-q5-pbe KLEINMAN-BYLANDER > LMAX=P > ..................................... > > *C-q4-pbe KLEINMAN-BYLANDER > LMAX=P > ..................................... > > *H-q1-pbe KLEINMAN-BYLANDER > ..................................... > CONSTRAINTS > FIX ATOMS > 8 > 1 2 3 4 5 6 7 8 > END CONSTRAINTS > &END > > --------------------------------------------------- > > > > > ?????????????? > ??Best Regards > > ??Yang Zhenyu > State Key Laboratory of Nonlinear Mechanics (LNM) > Institute of Mechanics, Chinese Academy of Sciences > No.15 Beisihuanxi Road > Beijing 100080, P. R. China > FAX: 010-62579511 > ??yangzy at lnm.imech.ac.cn > ??2005-12-02 > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Mon Dec 5 11:25:08 2005 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 5 Dec 2005 11:25:08 +0100 (MET) Subject: [CPMD-list] forces, convergence and gga In-Reply-To: References: Message-ID: Hi > I've got 3 little questions.. > > 1) I'm doing a md run of a molecule surrounded by water molecules. In order to check if the forces acting on the molecules are not too large, i'd like to check out the forces acting on them (since i didn't do a geometry optimalization at the beginning). I checked out the manual and found that it is possible to print the acting forces during the trajectory in the TRAJECTORY file. Since the md run is 'finished' it seems to be a little late for that.. > But now I was wondering what the initial forces acting on the atoms would be. Since they are listed in the output file that seemed not to be a problem. But what are the units of the forces? They are not mentioned in the manual, so i suppose it's a.u.? If it it, what's the conversion to convert them to dyne, Newton,.. or something else? Forces are in a.u., I'm sorry but I'm too lazy to do the work for converting into other units for you. BTW. You can calculate the forces on the atoms from the trajectory file using positions and velocities by inverting the velocity Verlet algorithm. > > 2) Before I did a md run, i checked out some dft functionals to describe the geometry of the molecule. I got convergence for C=C, C-H, more or less convergence for S-N but the C-S bound seems not to convergence at all (the C's from a aromatic system and C is attached to it). Does anyone have an idea why that could be? > What do you mean by convergence? All functionals give the same values? As there is no series of functionals that will give better and better results you cannot talk about convergence in this case. It might be a good idea to get a "correct" value for the problematic bond (e.g. by a large basis set CCSD(T) calculation) and then look for the functional that comes close to that value. > 3) In the manual, the GGA functional is mentioned. But what's the exact functional behind that GGA implemented in cpmd? Since GGA stands for Generalized-gradient-approximation, it doesnt give me any new information.. > The reference to the papers is usually written in the output for all functionals. You can also have a look into the file "functionals.F". regards Juerg Hutter > Thanks in advance! > > > > Christopher > Undergrad. Student > University of Antwerp > > > From akohlmey at vitae.cmm.upenn.edu Mon Dec 5 14:25:12 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Mon, 5 Dec 2005 08:25:12 -0500 (EST) Subject: [CPMD-list] forces, convergence and gga In-Reply-To: Message-ID: On Mon, 5 Dec 2005, De Dobbelaere Christopher wrote: CD> 3) In the manual, the GGA functional is mentioned. But what's the CD> exact functional behind that GGA implemented in cpmd? Since GGA CD> stands for Generalized-gradient-approximation, it doesnt give me any CD> new information.. GGA stands for PW91 a. CD> CD> Thanks in advance! CD> CD> CD> CD> Christopher CD> Undergrad. Student CD> University of Antwerp CD> CD> CD> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From Christopher.DeDobbelaere at student.ua.ac.be Mon Dec 5 15:49:27 2005 From: Christopher.DeDobbelaere at student.ua.ac.be (De Dobbelaere Christopher) Date: Mon, 5 Dec 2005 15:49:27 +0100 Subject: [CPMD-list] forces, convergence and gga Message-ID: Hi, Thanks for the replies (Axel also). Referring to question 2: Maybe i didn't formulate the problem as it should. What i did is the following: I want to use the VDB uspp and BLYP functional (because B3LYP describes the molecule relatively good in gaussian). So i tried different cutoff values (20 to 45) and looked for convergence for some 'important' bond lengths. I think the convergence for S-N and S-C is not really good, but C=C and C-H seem to converge nicely (cutoff values going from 20 Ry to 45 Ry). Values for S-N going from 20 to 45 Ry (steps of 5 Ry) in Angstrom: 1.72176 1.71772 1.71836 1.71851 1.71658 1.71772 Values for C-N: 1.81367 1.82001 1.81453 1.82000 1.81888 1.82267 Values for C=C: 1.42900 1.41553 1.41521 1.41571 1.41532 1.41554 The question now is either or not the S-N and C-N values may be considered as converged or not? And maybe someone knows why the S-N and C-N values are not as good converged as the C=C and C-H values. We do know from experience that C-N and S-N (in our molecule) are difficult to converge in gaussian calculations also, so maybe it's just an functional issue, but maybe i'm just doing something wrong with cpmd.. With kind regards, Christopher Undergrad. Student University of Antwerp ________________________________ From: Juerg Hutter [mailto:hutter at pci.unizh.ch] Sent: Mon 5/12/2005 11:25 To: De Dobbelaere Christopher Cc: cpmd-list at cpmd.org Subject: Re: [CPMD-list] forces, convergence and gga Hi > I've got 3 little questions.. > > 1) I'm doing a md run of a molecule surrounded by water molecules. In order to check if the forces acting on the molecules are not too large, i'd like to check out the forces acting on them (since i didn't do a geometry optimalization at the beginning). I checked out the manual and found that it is possible to print the acting forces during the trajectory in the TRAJECTORY file. Since the md run is 'finished' it seems to be a little late for that.. > But now I was wondering what the initial forces acting on the atoms would be. Since they are listed in the output file that seemed not to be a problem. But what are the units of the forces? They are not mentioned in the manual, so i suppose it's a.u.? If it it, what's the conversion to convert them to dyne, Newton,.. or something else? Forces are in a.u., I'm sorry but I'm too lazy to do the work for converting into other units for you. BTW. You can calculate the forces on the atoms from the trajectory file using positions and velocities by inverting the velocity Verlet algorithm. > > 2) Before I did a md run, i checked out some dft functionals to describe the geometry of the molecule. I got convergence for C=C, C-H, more or less convergence for S-N but the C-S bound seems not to convergence at all (the C's from a aromatic system and C is attached to it). Does anyone have an idea why that could be? > What do you mean by convergence? All functionals give the same values? As there is no series of functionals that will give better and better results you cannot talk about convergence in this case. It might be a good idea to get a "correct" value for the problematic bond (e.g. by a large basis set CCSD(T) calculation) and then look for the functional that comes close to that value. > 3) In the manual, the GGA functional is mentioned. But what's the exact functional behind that GGA implemented in cpmd? Since GGA stands for Generalized-gradient-approximation, it doesnt give me any new information.. > The reference to the papers is usually written in the output for all functionals. You can also have a look into the file "functionals.F". regards Juerg Hutter > Thanks in advance! > > > > Christopher > Undergrad. Student > University of Antwerp > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20051205/8bf24acb/attachment.html From shyma at imr.ac.cn Mon Dec 5 16:50:35 2005 From: shyma at imr.ac.cn (=?gb2312?B?U2hhbmd5aSBNYQ==?=) Date: Mon, 5 Dec 2005 23:50:35 +0800 (CST) Subject: [CPMD-list] help, the meaning of LDOS Message-ID: <439461CB.00000B.07576@app-01> Dear axel: Thanks for your reply! I check the keywords LDOS which's related with DOS in the manual and can't understand its explains clearly! It says: "LDOS : Calculate the layer projected density of states. The number of layers is read from the nest line ". But I don't know what's the meaning of the letter "L" , it means "local" or "layer"? And what's the meaning of "layer" in the explanation "The number of layers ..."? What information can we get from the LDOS in general? Thanks in advance! Best regards! shyma -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20051205/419d7fb1/attachment.html From akohlmey at vitae.cmm.upenn.edu Mon Dec 5 18:10:50 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Mon, 5 Dec 2005 12:10:50 -0500 (EST) Subject: [CPMD-list] forces, convergence and gga In-Reply-To: Message-ID: On Mon, 5 Dec 2005, De Dobbelaere Christopher wrote: CD> Hi, CD> CD> Thanks for the replies (Axel also). CD> CD> Referring to question 2: CD> Maybe i didn't formulate the problem as it should. What i did is the following: CD> I want to use the VDB uspp and BLYP functional (because B3LYP describes the molecule relatively good in gaussian). So i tried different cutoff values (20 to 45) and looked for convergence for some 'important' bond lengths. I think the convergence for S-N and S-C is not really good, but C=C and C-H seem to converge nicely (cutoff values going from 20 Ry to 45 Ry). please note, that there is a significant difference between BLYP and B3LYP, the former does not include the hartree-fock exchange. so you should first compare (in gaussian) how the values change when going from B3LYP to BLYP. CD> Values for S-N going from 20 to 45 Ry (steps of 5 Ry) in Angstrom: CD> 1.72176 1.71772 1.71836 1.71851 1.71658 1.71772 CD> Values for C-N: CD> 1.81367 1.82001 1.81453 1.82000 1.81888 1.82267 CD> Values for C=C: CD> 1.42900 1.41553 1.41521 1.41571 1.41532 1.41554 CD> CD> The question now is either or not the S-N and C-N values may be CD> considered as converged or not? And maybe someone knows why the S-N CD> and C-N values are not as good converged as the C=C and C-H values. CD> We do know from experience that C-N and S-N (in our molecule) are CD> difficult to converge in gaussian calculations also, so maybe it's CD> just an functional issue, but maybe i'm just doing something wrong CD> with cpmd.. what kind of _density_ cutoff did you use here? also what was the convergence for the geometry optimization and the corresponding wavefunction optimization convergence parameter? it may simply be, that you are a victim of 'ripples'. please note, that the pseudopotentials you are using were 'optimized' to give good results at a plane wave cutoff of 25ry. axel. CD> CD> With kind regards, CD> CD> Christopher CD> Undergrad. Student CD> University of Antwerp CD> CD> CD> CD> ________________________________ -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at vitae.cmm.upenn.edu Mon Dec 5 18:27:27 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Mon, 5 Dec 2005 12:27:27 -0500 (EST) Subject: [CPMD-list] help, the meaning of LDOS In-Reply-To: <439461CB.00000B.07576@app-01> Message-ID: On Mon, 5 Dec 2005, [gb2312] Shangyi Ma wrote: SM> Dear axel: SM> Thanks for your reply! SM> I check the keywords LDOS which's related with DOS in the manual and can't understand its explains clearly! SM> It says: SM> "LDOS : Calculate the layer projected density of states. The SM> number of layers is read from the nest line ". But I don't know SM> what's the meaning of the letter "L" , it means "local" or "layer"? layer. you even quoted the sentence right above your question: calculate the _L_ayer projected _D_ensity _O_f _S_tates: = LDOS. SM> And what's the meaning of "layer" in the explanation "The number of SM> layers ..."? What information can we get from the LDOS in general? you are about to learn a valueable lesson in using CPMD: if the manual does not provide the answer, have a look at the source code. so load the file ldos.F into your favorate text editor and try to figure out, what the code is doing. as you can see, the resulting file is the DOS projected on the electronic density written out in a loop over k-points, states, and 2d-planes (=layers) of the 3d-real space density grid. if you want something else, you most likely will have to program it. in that case, the file ldos.F may serve as a starting point. axel. SM> Thanks in advance! SM> Best regards! SM> shyma -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From lyuan at Princeton.EDU Tue Dec 6 08:48:14 2005 From: lyuan at Princeton.EDU (Lan-Feng Yuan (lyuan@Princeton.EDU)) Date: Tue, 06 Dec 2005 02:48:14 -0500 Subject: [CPMD-list] What are classic energies for CP MD and PI MD? Message-ID: Dear CPMD community, I am using CPMD to do path integral simulations and find it very useful, thanks! The total quantum energy in output corresponds to the total energy estimator, and by subtracting the nuclear ground state energy, I can get the vibrational energy at a given temperature. Well, what is the "ECLASSIC" in output? Also, in a classic CP MD simulation, "ECLASSIC" is also printed. Are they the same thing? I guess it's the sum of Kohn-Sham energy and classic nuclear kinetic energy (which is proportional to instant temperature). If this is correct, then ECLASSIC - EKS should be equal to 3/2*N*k_B*T (N is number of atoms) when average temperature reaches its target value, right? However, it seems that I never get it exact. What's the problem? Thank you very much! Best regards, Lan-Feng ---------------------------- Dr. Lan-Feng Yuan, Postdoctoral Associate, Department of Chemistry, Princeton University, Princeton, NJ 08544, USA Office Phone: 1-609-258-1834 Fax: 1-609-258-6746 ---------------------------- From akohlmey at vitae.cmm.upenn.edu Tue Dec 6 16:05:49 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Tue, 6 Dec 2005 10:05:49 -0500 (EST) Subject: [CPMD-list] What are classic energies for CP MD and PI MD? In-Reply-To: Message-ID: On Tue, 6 Dec 2005, Lan-Feng Yuan (lyuan at Princeton.EDU) wrote: LF> Dear CPMD community, dear lan-feng, LF> I am using CPMD to do path integral simulations and find it very LF> useful, thanks! The total quantum energy in output corresponds to LF> the total energy estimator, and by subtracting the nuclear ground LF> state energy, I can get the vibrational energy at a given LF> temperature. Well, what is the "ECLASSIC" in output? Also, in a i can't speak for the PI-MD case, but ... LF> classic CP MD simulation, "ECLASSIC" is also printed. Are they the LF> same thing? I guess it's the sum of Kohn-Sham energy and classic LF> nuclear kinetic energy (which is proportional to instant LF> temperature). If this is correct, then ECLASSIC - EKS should be LF> equal to 3/2*N*k_B*T (N is number of atoms) when average temperature LF> reaches its target value, right? However, it seems that I never get LF> it exact. What's the problem? Thank you very much! are you doing an isolated system (symmetry 0)? then you have only 3N-3 DOFs. axel. LF> LF> Best regards, LF> LF> Lan-Feng LF> LF> ---------------------------- LF> Dr. Lan-Feng Yuan, LF> Postdoctoral Associate, LF> Department of Chemistry, LF> Princeton University, LF> Princeton, NJ 08544, USA LF> Office Phone: 1-609-258-1834 LF> Fax: 1-609-258-6746 LF> ---------------------------- LF> _______________________________________________ LF> CPMD-list mailing list LF> CPMD-list at cpmd.org LF> http://cpmd.org/mailman/listinfo/cpmd-list LF> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From lyuan at Princeton.EDU Wed Dec 7 04:17:37 2005 From: lyuan at Princeton.EDU (Lan-Feng Yuan (lyuan@Princeton.EDU)) Date: Tue, 06 Dec 2005 22:17:37 -0500 Subject: [CPMD-list] how to do constraint optimization? Message-ID: Dear CPMD users, I want to optimize a structure under a constraint, e.g., the distance between atoms 1 and 2 must be 3 A. According to manual, the way is to add CONSTRAINTS ... END CONSTRAINTS in &ATOMS. Emm ... but how about the initial geometry? It seems that I don't need to make the input geometry satisfy the constraint, because in the output it prints the current value and its difference with the desired value. However, the program updates the structure by thousands of times, but never gets convergence. And the constraint is not reached neither. What's the algorithm to do constraint optimization? Is this feature kind of broken, or do I miss something? Thank you very much! Lan-Feng ---------------------------- Dr. Lan-Feng Yuan, Postdoctoral Associate, Department of Chemistry, Princeton University, Princeton, NJ 08544, USA Office Phone: 1-609-258-1834 Fax: 1-609-258-6746 ---------------------------- From lyuan at Princeton.EDU Wed Dec 7 04:46:22 2005 From: lyuan at Princeton.EDU (Lan-Feng Yuan (lyuan@Princeton.EDU)) Date: Tue, 06 Dec 2005 22:46:22 -0500 Subject: [CPMD-list] What are classic energies for CP MD and PI MD? In-Reply-To: References: Message-ID: Dear Axel, > LF> I am using CPMD to do path integral simulations and find it very > LF> useful, thanks! The total quantum energy in output corresponds to > LF> the total energy estimator, and by subtracting the nuclear ground > LF> state energy, I can get the vibrational energy at a given > LF> temperature. Well, what is the "ECLASSIC" in output? Also, in a > > i can't speak for the PI-MD case, but ... > > LF> classic CP MD simulation, "ECLASSIC" is also printed. Are they the > LF> same thing? I guess it's the sum of Kohn-Sham energy and classic > LF> nuclear kinetic energy (which is proportional to instant > LF> temperature). If this is correct, then ECLASSIC - EKS should be > LF> equal to 3/2*N*k_B*T (N is number of atoms) when average > temperatureLF> reaches its target value, right? However, it seems > that I never get > LF> it exact. What's the problem? Thank you very much! > > are you doing an isolated system (symmetry 0)? > then you have only 3N-3 DOFs. > > axel. > Yes, I am doing symmetry 0. 3N-3? Not 3N-6? Because translation is frozen, but rotation not? Anyway, it's still not quite right. For example, for a H2O molecule at 150 K, I get: MEAN VALUE +/- RMS DEVIATION [-^2]**(1/2) ELECTRON KINETIC ENERGY 0.382262E-04 0.289944E-04 IONIC TEMPERATURE 145.36 110.93 DENSITY FUNCTIONAL ENERGY -17.184344 0.132918E-03 CLASSICAL ENERGY -17.180351 0.289125E-04 CONSERVED ENERGY -17.180313 0.197829E-05 So ECLASSIC - EKS = 0.003993 Har = 0.1087 eV = 8.40 k_B*T (k_B*T = 0.01293 eV). I can't figure out how this 8.4 comes ... Thank you very much! Best regards, Lan-Feng From akohlmey at vitae.cmm.upenn.edu Wed Dec 7 16:30:14 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Wed, 7 Dec 2005 10:30:14 -0500 (EST) Subject: [CPMD-list] how to do constraint optimization? In-Reply-To: Message-ID: On Tue, 6 Dec 2005, Lan-Feng Yuan (lyuan at Princeton.EDU) wrote: LY> Dear CPMD users, dear lan-feng, LY> I want to optimize a structure under a constraint, e.g., the LY> distance between atoms 1 and 2 must be 3 A. According to manual, the LY> way is to add CONSTRAINTS ... END CONSTRAINTS in &ATOMS. Emm ... but LY> how about the initial geometry? It seems that I don't need to make LY> the input geometry satisfy the constraint, because in the output it LY> prints the current value and its difference with the desired value. LY> However, the program updates the structure by thousands of times, LY> but never gets convergence. And the constraint is not reached LY> neither. What's the algorithm to do constraint optimization? Is this LY> feature kind of broken, or do I miss something? Thank you very much! geometry optimization with constraints is somewhat tricky, compared to MD. how about, you start with an simulated annealing and then switch over to geometry optimization when you are close to the minimum? axel. LY> LY> Lan-Feng LY> LY> ---------------------------- LY> Dr. Lan-Feng Yuan, LY> Postdoctoral Associate, LY> Department of Chemistry, LY> Princeton University, LY> Princeton, NJ 08544, USA LY> Office Phone: 1-609-258-1834 LY> Fax: 1-609-258-6746 LY> ---------------------------- LY> _______________________________________________ LY> CPMD-list mailing list LY> CPMD-list at cpmd.org LY> http://cpmd.org/mailman/listinfo/cpmd-list LY> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From Christopher.DeDobbelaere at student.ua.ac.be Wed Dec 7 11:39:02 2005 From: Christopher.DeDobbelaere at student.ua.ac.be (De Dobbelaere Christopher) Date: Wed, 7 Dec 2005 11:39:02 +0100 Subject: [CPMD-list] forces, convergence and gga Message-ID: Hi cpmd users, Another few additions :) > CD> Hi, > CD> > CD> Thanks for the replies (Axel also). > CD> > CD> Referring to question 2: > CD> Maybe i didn't formulate the problem as it should. What i did is the following: > CD> I want to use the VDB uspp and BLYP functional (because B3LYP describes the molecule relatively good in gaussian). So i tried different cutoff values (20 to 45) and looked for convergence for some 'important' bond lengths. I think the convergence for S-N and S-C is not really good, but C=C and C-H seem to converge nicely (cutoff values going from 20 Ry to 45 Ry). > > please note, that there is a significant difference between BLYP > and B3LYP, the former does not include the hartree-fock exchange. > so you should first compare (in gaussian) how the values change > when going from B3LYP to BLYP. I know, but I'm not worried about the fact that the values are 'wrong', it's just that they do not converge when increasing cutoff values that worries me. > CD> Values for S-N going from 20 to 45 Ry (steps of 5 Ry) in Angstrom: > CD> 1.72176 1.71772 1.71836 1.71851 1.71658 1.71772 > CD> Values for C-N: > CD> 1.81367 1.82001 1.81453 1.82000 1.81888 1.82267 > CD> Values for C=C: > CD> 1.42900 1.41553 1.41521 1.41571 1.41532 1.41554 > CD> > > CD> The question now is either or not the S-N and C-N values may be > CD> considered as converged or not? And maybe someone knows why the S-N > CD> and C-N values are not as good converged as the C=C and C-H values. > CD> We do know from experience that C-N and S-N (in our molecule) are > CD> difficult to converge in gaussian calculations also, so maybe it's > CD> just an functional issue, but maybe i'm just doing something wrong > CD> with cpmd.. > > what kind of _density_ cutoff did you use here? also what was > the convergence for the geometry optimization and the > corresponding wavefunction optimization convergence parameter? I used the following parameters: CONVERGENCE ORBITALS 1.0d-7 CONVERGENCE GEOMETRY 4.5d-4 CONVERGENCE INITIAL 1.0d-4 CONVERGENCE ADAPT 0.02 CONVERGENCE ENERGY 0.05 and GC-CUTOFF 1.0d-06 > it may simply be, that you are a victim of 'ripples'. > please note, that the pseudopotentials you are using were > 'optimized' to give good results at a plane wave cutoff > of 25ry. I thought the best way to get a 'good' cutoff value is to try several ones and get use the one that gives convergence (more or less)? Thanks in advance, Christopher Undergrad. Student University of Antwerp -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20051207/eea0d3e0/attachment.html From lyuan at Princeton.EDU Wed Dec 7 22:53:02 2005 From: lyuan at Princeton.EDU (Lan-Feng Yuan (lyuan@Princeton.EDU)) Date: Wed, 07 Dec 2005 16:53:02 -0500 Subject: [CPMD-list] What are classic energies for CP MD and PI MD? In-Reply-To: References: Message-ID: ----- Original Message ----- From: Axel Kohlmeyer Date: Wednesday, December 7, 2005 10:35 am Subject: Re: [CPMD-list] What are classic energies for CP MD and PI MD? To: "Lan-Feng Yuan (lyuan at Princeton.EDU)" > On Tue, 6 Dec 2005, Lan-Feng Yuan (lyuan at Princeton.EDU) wrote: > > LY> > > > LY> Yes, I am doing symmetry 0. 3N-3? Not 3N-6? Because > translation is > > 3N-3 is what is used in DETDOF to compute the temperature. > > LY> frozen, but rotation not? Anyway, it's still not quite right. For > LY> example, for a H2O molecule at 150 K, I get: > > > LY> > LY> MEAN VALUE +/- RMS DEVIATION > LY> [-^2]**(1/2) > LY> ELECTRON KINETIC ENERGY 0.382262E-04 0.289944E-04 > LY> IONIC TEMPERATURE 145.36 110.93 > LY> DENSITY FUNCTIONAL ENERGY -17.184344 0.132918E-03 > LY> CLASSICAL ENERGY -17.180351 0.289125E-04 > LY> CONSERVED ENERGY -17.180313 0.197829E-05 > LY> > > LY> So ECLASSIC - EKS = 0.003993 Har = 0.1087 eV = 8.40 k_B*T > (k_B*T = > LY> 0.01293 eV). I can't figure out how this 8.4 comes ... > > hmm, i currently have no time to check this, but you may > have to factor in the DOFs from the nose-hoover chains, > if you used them. > > axel. > Well, I certainly use Nose-Hoover chains, otherwise the temperature cannot be fixed around 150 K (although its fluctuation is huge because the system is so small). In my understanding, the instant temperature is simply a constant times the total nuclear kinetic energy, and the constant has to do degree of freedoms (3N-3 here). The tricky thing is what's ECLASSIC? Just sum of EKS and nuclear KE? Or thermostat KE also included? If thermostat energy is also there, then it has not much use in calculating other properties. Thanks! Best regards, Lan-Feng From lyuan at Princeton.EDU Wed Dec 7 23:00:24 2005 From: lyuan at Princeton.EDU (Lan-Feng Yuan (lyuan@Princeton.EDU)) Date: Wed, 07 Dec 2005 17:00:24 -0500 Subject: [CPMD-list] how to do constraint optimization? In-Reply-To: References: Message-ID: ----- Original Message ----- From: Axel Kohlmeyer Date: Wednesday, December 7, 2005 10:32 am Subject: Re: [CPMD-list] how to do constraint optimization? To: "Lan-Feng Yuan (lyuan at Princeton.EDU)" Cc: cpmd-list at cpmd.org > On Tue, 6 Dec 2005, Lan-Feng Yuan (lyuan at Princeton.EDU) wrote: > > LY> Dear CPMD users, > > dear lan-feng, > > LY> I want to optimize a structure under a constraint, e.g., the > LY> distance between atoms 1 and 2 must be 3 A. According to > manual, the > LY> way is to add CONSTRAINTS ... END CONSTRAINTS in &ATOMS. Emm > ... but > LY> how about the initial geometry? It seems that I don't need to make > LY> the input geometry satisfy the constraint, because in the > output it > LY> prints the current value and its difference with the desired > value.LY> However, the program updates the structure by thousands > of times, > LY> but never gets convergence. And the constraint is not reached > LY> neither. What's the algorithm to do constraint optimization? > Is this > LY> feature kind of broken, or do I miss something? Thank you very > much! > geometry optimization with constraints is somewhat tricky, compared > to MD. how about, you start with an simulated annealing and then > switch over to geometry optimization when you are close to the > minimum? > axel. > Dear Axel, Do you propose to run a simulated annealing MD with constraint to find some nearly optimized structure, then run constraint optimization? First I didn't know simulated annealing MD can run with constraint, thank you ... But I doubt it's much helpful, because I already have the fully optimized structure (i.e., without constraint), then change the atom 1-2 distance a bit, so the start geometry should not be too far from constraint optimized structure. But it still runs for thousands of steps without a conclusion. Thanks! Regards, Lan-Feng From yangzy at lnm.imech.ac.cn Thu Dec 8 12:45:09 2005 From: yangzy at lnm.imech.ac.cn (Yang Zhenyu) Date: Thu, 8 Dec 2005 19:45:09 +0800 Subject: [CPMD-list] [help] Pseudopotential for Ni Message-ID: <200512081145.MAA11498@internet-fence.zurich.ihost.com> Dear CPMD users: Would you please recommend a working pseudo for Ni. And I need that it is impossible in FEMD/k points. Considering the capability of my computer, more smaller cutoff needed, more better! ?????????????? ??Best Regards ??Yang Zhenyu State Key Laboratory of Nonlinear Mechanics (LNM) Institute of Mechanics, Chinese Academy of Sciences No.15 Beisihuanxi Road Beijing 100080, P. R. China FAX: 010-62579511 ??yangzy at lnm.imech.ac.cn ??2005-12-08 From akohlmey at vitae.cmm.upenn.edu Thu Dec 8 15:23:47 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Thu, 8 Dec 2005 09:23:47 -0500 (EST) Subject: [CPMD-list] [help] Pseudopotential for Ni In-Reply-To: <200512081145.MAA11498@internet-fence.zurich.ihost.com> Message-ID: On Thu, 8 Dec 2005, Yang Zhenyu wrote: YZ> Dear CPMD users: YZ> YZ> Would you please recommend a working pseudo for Ni. YZ> And I need that it is impossible in FEMD/k points. do you mean, that you _want_ it to be _in_compatible with FEMD?? please rephrase. YZ> Considering the capability of my computer, more smaller YZ> cutoff needed, more better! for a smaller cutoff, you need ultra-soft pseudopotentials. which, are usually better suited for d-metals anyway. unfortunately, CPMD does not support k-points with ultra-soft pseudopotentials. so you have two options: try to get access on a larger/faster computer (or cluster), or try a code that does supports ultra-soft pps with k-points (there are several). axel YZ> YZ> YZ> YZ> ?????????????? YZ> ??Best Regards YZ> YZ> ??Yang Zhenyu YZ> State Key Laboratory of Nonlinear Mechanics (LNM) YZ> Institute of Mechanics, Chinese Academy of Sciences YZ> No.15 Beisihuanxi Road YZ> Beijing 100080, P. R. China YZ> FAX: 010-62579511 YZ> ??yangzy at lnm.imech.ac.cn YZ> ??2005-12-08 YZ> YZ> YZ> _______________________________________________ YZ> CPMD-list mailing list YZ> CPMD-list at cpmd.org YZ> http://cpmd.org/mailman/listinfo/cpmd-list YZ> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From ari.p.seitsonen at iki.fi Thu Dec 8 15:27:04 2005 From: ari.p.seitsonen at iki.fi (Ari P Seitsonen) Date: Thu, 8 Dec 2005 15:27:04 +0100 (CET) Subject: [CPMD-list] how to do constraint optimization? In-Reply-To: References: Message-ID: Dear Lan-Feng, In addition to Axel's recommendations I could maybe add that if the constraints that you want to fulfill are not very close to the wanted values in the optimised geometry you can use RESTRAINTS to bias the system to approach the wanted values. This option (please check the manual for the syntax and usage; it's almost identical to the case of CONSTRAINTS) adds a harmonic potential around the restrained value, and by increasing the force constant you can force your system closer and closer to the wanted value. This option, however, should only be used to approach a configuration since it doesn't lead to conserved dynamics (like the CONSTRAINTS do). Greetings from Garching bei Munich / Bavaria, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ CNRS & IMPMC, Universit? Pierre et Marie Curie 4 place Jussieu, case 115 / F-75252 Paris Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820 On Tue, 6 Dec 2005, Lan-Feng Yuan (lyuan at Princeton.EDU) wrote: > Dear CPMD users, > > I want to optimize a structure under a constraint, e.g., the distance between atoms 1 and 2 must be 3 A. According to manual, the way is to add CONSTRAINTS ... END CONSTRAINTS in &ATOMS. Emm ... but how about the initial geometry? It seems that I don't need to make the input geometry satisfy the constraint, because in the output it prints the current value and its difference with the desired value. However, the program updates the structure by thousands of times, but never gets convergence. And the constraint is not reached neither. What's the algorithm to do constraint optimization? Is this feature kind of broken, or do I miss something? Thank you very much! > > Lan-Feng > > ---------------------------- > Dr. Lan-Feng Yuan, > Postdoctoral Associate, > Department of Chemistry, > Princeton University, > Princeton, NJ 08544, USA > Office Phone: 1-609-258-1834 > Fax: 1-609-258-6746 > ---------------------------- > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://cpmd.org/mailman/listinfo/cpmd-list > From akohlmey at vitae.cmm.upenn.edu Thu Dec 8 15:28:08 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Thu, 8 Dec 2005 09:28:08 -0500 (EST) Subject: [CPMD-list] how to do constraint optimization? In-Reply-To: Message-ID: On Wed, 7 Dec 2005, Lan-Feng Yuan (lyuan at Princeton.EDU) wrote: LY> Dear Axel, LY> LY> Do you propose to run a simulated annealing MD with constraint to LY> find some nearly optimized structure, then run constraint LY> optimization? First I didn't know simulated annealing MD can run LY> with constraint, thank you ... But I doubt it's much helpful, LY> because I already have the fully optimized structure (i.e., without LY> constraint), then change the atom 1-2 distance a bit, so the start LY> geometry should not be too far from constraint optimized structure. LY> But it still runs for thousands of steps without a conclusion. do you want to say, that the geometry optimization does not converge? that may be simply due to the way the convergence is computed (i.e. it may not ignore the constraint forces properly). does the geometry change significantly? axel LY> LY> Thanks! Regards, LY> LY> Lan-Feng LY> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at vitae.cmm.upenn.edu Thu Dec 8 16:19:23 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Thu, 8 Dec 2005 10:19:23 -0500 (EST) Subject: [CPMD-list] What are classic energies for CP MD and PI MD? In-Reply-To: Message-ID: On Wed, 7 Dec 2005, Lan-Feng Yuan (lyuan at Princeton.EDU) wrote: LY> > LY> > axel. LY> > LY> Well, I certainly use Nose-Hoover chains, otherwise the LY> temperature cannot be fixed around 150 K (although its fluctuation LY> is huge because the system is so small). In my understanding, the LY> instant temperature is simply a constant times the total nuclear LY> kinetic energy, and the constant has to do degree of freedoms (3N-3 LY> here). The tricky thing is what's ECLASSIC? Just sum of EKS and LY> nuclear KE? Or thermostat KE also included? If thermostat energy is LY> also there, then it has not much use in calculating other LY> properties. well, here is the beauty of having the source code. you can see for yourself (and change it if needed). for a regular CP-MD you have to look into mdmain.F and there you have: ECONS=EKINP+ETOT+ENOSE+ENOSP+ECNSTR+EKINCV+VHARM C ... EHAM=ECONS+EKINC ECONS is ECLASSIC on output. as you can see ECLASSIC is EHAM - EKINC. axel. LY> LY> Thanks! Best regards, LY> LY> Lan-Feng LY> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From ZRLSRB at ch.ibm.com Thu Dec 8 22:10:02 2005 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Thu, 8 Dec 2005 22:10:02 +0100 Subject: [CPMD-list] how to do constraint optimization? In-Reply-To: Message-ID: Dear Lan-Feng, which optimizer and which version of CPMD do you use? Depending on the version of code and the type of optimizer, you could have hit a bug in the constraints code (which was fixed once) which caused the optimization not to converge. Also, playing around with the PENALTY parameters could help. For geometry optimization (except with RFO), CPMD does not calculate Lagrange multipliers to satisfy the constraints but rather harmonically penalizes the deviation from the target value. Could you please send the input? Best regards, Salomon From lyuan at Princeton.EDU Fri Dec 9 06:29:30 2005 From: lyuan at Princeton.EDU (Lan-Feng Yuan (lyuan@Princeton.EDU)) Date: Fri, 09 Dec 2005 00:29:30 -0500 Subject: [CPMD-list] how to do constraint optimization? In-Reply-To: References: Message-ID: ----- Original Message ----- From: Salomon Billeter Date: Thursday, December 8, 2005 4:10 pm Subject: Re: [CPMD-list] how to do constraint optimization? To: "Lan-Feng Yuan (lyuan at Princeton.EDU)" Cc: cpmd-list at cpmd.org > Dear Lan-Feng, > > which optimizer and which version of CPMD do you use? Depending on the > version of code and the type of optimizer, you could have hit a > bug in the > constraints code (which was fixed once) which caused the > optimization not > to converge. > Also, playing around with the PENALTY parameters could help. For > geometryoptimization (except with RFO), CPMD does not calculate > Lagrangemultipliers to satisfy the constraints but rather > harmonically penalizes > the deviation from the target value. > Could you please send the input? > > Best regards, > Salomon > Dear Salomon, Thank you. My version is 3.10 (yes, higher than the open source, I got it from a colleague who is a developer of CPMD). An example of my input is: &INFO (H2O)2 constraint optimization, O-O fixed at 3.25 A &END &CPMD CENTER MOLECULE ISOLATED MOLECULE OPTIMIZE GEOMETRY MAXSTEP 100000 CONJUGATE GRADIENTS IONS CONVERGENCE ORBITALS 1.D-8 CONVERGENCE GEOMETRY 5.D-5 &END &SYSTEM SYMMETRY 1 CELL 18.89725988578923203102406997093 1. 1. 0. 0. 0. CUTOFF 80. &END &DFT NEWCODE FUNCTIONAL PBE &END &ATOMS *O_MT_PBE KLEINMAN-BYLANDER LMAX=P 2 6.7455 9.6133 9.5180 12.2607 9.3529 9.2784 *H_MT_PBE.psp KLEINMAN-BYLANDER LMAX=S 4 6.1602 10.9878 8.4572 6.0122 8.0957 8.8010 10.3669 9.4438 9.4475 12.8311 9.4411 11.0165 CONSTRAINTS FIX STRUCTURE 1 DIST 1 2 6.1416094628815004100828227405521 END CONSTRAINTS &END Without constraint, I did get convergence and all 12 positive frequencies, so the fundamental feature of optimization is correct. With constraint, I never get convergence. Thank you very much! Best regards, Lan-Feng From ZRLSRB at ch.ibm.com Fri Dec 9 12:19:17 2005 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Fri, 9 Dec 2005 12:19:17 +0100 Subject: [CPMD-list] how to do constraint optimization? In-Reply-To: Message-ID: Dear Lan-Feng, version 3.10 is not affected by the bug. With the linear-scaling geometry optimizer, the optimization will converge quickly (it converged quickly here, while the conjugate gradient optimization did not converge either). To switch to L-BFGS, change the keyword 'CONJUGATE GRADIENTS IONS' to 'LBFGS' in the &CPMD section. You best also switch on diagnostics using PRINT LSCAL ON. May I comment on two other portions of your input: - You have an isolated system but not SYMMETRY=0. Your periodic images will be electrostatically coupled. Also, your cell size is rather at the lower limit. - You have very tight convergence criteria, espeically for the electrons. If you start with a large nuclear gradient (as you do), adaptive tolerance saves you many cycles (keywords CONVERGENCE ADAPT, CONVERGENCE INITIAL, and - in your case probably not too helpful - CONVERGENCE ENERGY, CONVERGENCE CALFOR, and CONVERGENCE RELAX). Values around 0.01 and 0.0001 for the first two options could speed up the calculation in your case. When reaching convergence, please make sure the constraint is maintained accurately enough. As written before, CPMD does not determine Lagrange multipliers during geometry optimization for most optimizers, and the penalty could be too small. Best regards, Salomon From ZRLSRB at ch.ibm.com Fri Dec 9 12:13:34 2005 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Fri, 9 Dec 2005 12:13:34 +0100 Subject: [CPMD-list] how to do constraint optimization? In-Reply-To: Message-ID: Dear Lan-Feng, version 3.10 is not affected by the bug. With the linear-scaling geometry optimizer, the optimization will converge quickly (it converged quickly here, while the conjugate gradient optimization did not converge either). To switch to L-BFGS, change the keyword 'CONJUGATE GRADIENTS IONS' to 'LBFGS' in the &CPMD section. You best also switch on diagnostics using PRINT LSCAL ON. May I comment on two other portions of your input: - You have an isolated system but not SYMMETRY=0. Your periodic images will be electrostatically coupled. Also, your cell size is rather at the lower limit. - You have very tight convergence criteria, espeically for the electrons. If you start with a large nuclear gradient (as you do), adaptive tolerance saves you many cycles (keywords CONVERGENCE ADAPT, CONVERGENCE INITIAL, and - in your case probably not too helpful - CONVERGENCE ENERGY, CONVERGENCE CALFOR, and CONVERGENCE RELAX). Values around 0.01 and 0.0001 for the first two options could speed up the calculation in your case. When reaching convergence, please make sure the constraint is maintained accurately enough. As written before, CPMD does not determine Lagrange multipliers during geometry optimization for most optimizers, and the penalty could be too small. Best regards, Salomon From lyuan at Princeton.EDU Sun Dec 11 04:03:00 2005 From: lyuan at Princeton.EDU (Lan-Feng Yuan (lyuan@Princeton.EDU)) Date: Sat, 10 Dec 2005 22:03:00 -0500 Subject: [CPMD-list] how to do constraint optimization? In-Reply-To: References: Message-ID: ----- Original Message ----- From: Salomon Billeter Date: Friday, December 9, 2005 6:13 am Subject: Re: [CPMD-list] how to do constraint optimization? To: "Lan-Feng Yuan (lyuan at Princeton.EDU)" Cc: cpmd-list at cpmd.org > Dear Lan-Feng, > > version 3.10 is not affected by the bug. With the linear-scaling > geometryoptimizer, the optimization will converge quickly (it > converged quickly > here, while the conjugate gradient optimization did not converge > either).To switch to L-BFGS, change the keyword 'CONJUGATE > GRADIENTS IONS' to > 'LBFGS' in the &CPMD section. You best also switch on diagnostics > usingPRINT LSCAL ON. > > May I comment on two other portions of your input: > - You have an isolated system but not SYMMETRY=0. Your periodic > images will > be electrostatically coupled. Also, your cell size is rather at > the lower > limit. > - You have very tight convergence criteria, espeically for the > electrons.If you start with a large nuclear gradient (as you do), > adaptive tolerance > saves you many cycles (keywords CONVERGENCE ADAPT, CONVERGENCE > INITIAL, and > - in your case probably not too helpful - CONVERGENCE ENERGY, > CONVERGENCECALFOR, and CONVERGENCE RELAX). Values around 0.01 and > 0.0001 for the first > two options could speed up the calculation in your case. > > When reaching convergence, please make sure the constraint is > maintainedaccurately enough. As written before, CPMD does not > determine Lagrange > multipliers during geometry optimization for most optimizers, and the > penalty could be too small. > > Best regards, > Salomon > Dear Salomon, Thank you very much. Adopting your suggestions, I indeed get convergence. Well, the output says: <<<<< CONSTRAINTS >>>>> FIXED STRUCTURE ELEMENTS TYPE ATOM ATOM ATOM ATOM VALUE DIFFERENCE DISTANCE 1 2 0 0 5.57361 -1.086070E-03 Therefore, the constraint is not exactly fulfilled, leaving a small difference (0.001 Bohr). I have no complaint on that. But is there any way to select the threshold of tolerance? Thanks! Best regards, Lan-Feng From shyma at imr.ac.cn Sun Dec 11 05:55:52 2005 From: shyma at imr.ac.cn (=?gb2312?B?U2hhbmd5aSBNYQ==?=) Date: Sun, 11 Dec 2005 12:55:52 +0800 (CST) Subject: [CPMD-list] help, draw ELECTROSTATIC POTENTIAL Message-ID: <439BB158.00009B.29176@app-01> Dear CPMD users: Does anyone has the experiences draw the 2D plane contour from the file elpot produced by the keyword ELECTROSTATIC POTENTIAL? I know the file can be display by converting it to the form of elpot.cube and using the VMD software, but I find it's not clearly to see the potential. So I think it's better to draw it in the form of 2D plane contour perpendicular x, y, or z direction and I don't know how to get the datas I needed to finish it. Do I can export the data from the elpot.cube file or from the VMD Volumetric data in other methods? Does anyone has good ideas on the question? Another question is that what's the meaning of "isovalue" when I visualize the Volumetric data in the form of isosurface? I find it shows different shapes in the different isovalue? So how can I get the appropriate isovalue? Thanks in advance! Best wishes! shyma -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20051211/1d863b8a/attachment.html From haiderabbasphy at yahoo.co.in Mon Dec 12 07:11:32 2005 From: haiderabbasphy at yahoo.co.in (haider abbas) Date: Mon, 12 Dec 2005 06:11:32 +0000 (GMT) Subject: [CPMD-list] cpmd2cube segmentation fault error Message-ID: <20051212061132.1563.qmail@web8403.mail.in.yahoo.com> Dear all cpmd user, running cpmd2cube shows the following error [haider at falcon1 cpmd2cube]$ cpmd2cube.x -rho -halfmesh ELPOT .read input file ... done I think you stored a density (sum^2 = 0.77965627E-03) .building g vectors ... done forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source cpmd2cube.x 08055F58 Unknown Unknown Unknown cpmd2cube.x 0805404E Unknown Unknown Unknown cpmd2cube.x 0805880F Unknown Unknown Unknown cpmd2cube.x 0806C9D8 Unknown Unknown Unknown cpmd2cube.x 00763E33 Unknown Unknown Unknown cpmd2cube.x 08049CE1 Unknown Unknown Unknown the makefile of cpmd2cube.x is #-----------------------------------------------------------------------------# # Makefile for cpmd2cube.x # Configuration: Linux-PC-IFC-P4 # Creation of Makefile: Nov 23 2005 # on Linux robin 2.4.21-15.EL #1 Sun May 16 02:45:06 EDT 2004 i686 athlon i386 GNU/Linux # Author: haider #---------------------------------------------------------------------------- # SHELL = /bin/sh # #--------------- Configuration FC = ifc FFLAGS = -FR -D__IFC -DFFT_DEFAULT -O -tpp7 -w90 -w95 -pc64 LFLAGS = -O -tpp7 -w90 -w95 -pc64 LIBS = -Vaxlib # uncomment and set only if needed #CC = cc #CFLAGS = #--------------- End of Configuration ############## EXE = cpmd2cube.x OBJECTS = \ kinds.o periodic_table.o util.o grids.o cpmd2cube.o \ main.o grid_types.o atom_types.o readwrites.o \ fftsg_lib.o fft_tools.o fftsg.o CFGDEST = . CFGMACH = Linux-PC-IFC-P4 SRC=. ############################# all: $(EXE) trimcube $(EXE): $(OBJECTS) $(FC) -o $(EXE) $(LFLAGS) $(OBJECTS) $(LIBS) trimcube: trimcube.o $(CC) $(CFLAGS) -o $@ trimcube.o ############################# clean: rm -f *.o *.mod *.L *~ # Create a new makefile with new dependencies but retain the configuration. reconfig: ( cd $(SRC) ; ./Configure -r -m -SRC=$(SRC) -DEST=$(CFGDEST) $(CFGMACH) ; cd $(CFGDEST) ) ############################# atom_types.o: $(SRC)/atom_types.F $(FC) -c $(FFLAGS) $(SRC)/$*.F cpmd2cube.o: $(SRC)/cpmd2cube.F $(FC) -c $(FFLAGS) $(SRC)/$*.F fft_tools.o: $(SRC)/fft_tools.F $(FC) -c $(FFLAGS) $(SRC)/$*.F grid_types.o: $(SRC)/grid_types.F $(FC) -c $(FFLAGS) $(SRC)/$*.F grids.o: $(SRC)/grids.F $(FC) -c $(FFLAGS) $(SRC)/$*.F main.o: $(SRC)/main.F $(FC) -c $(FFLAGS) $(SRC)/$*.F periodic_table.o: $(SRC)/periodic_table.F $(FC) -c $(FFLAGS) $(SRC)/$*.F readwrites.o: $(SRC)/readwrites.F $(FC) -c $(FFLAGS) $(SRC)/$*.F util.o: $(SRC)/util.F $(FC) -c $(FFLAGS) $(SRC)/$*.F kinds.o: $(SRC)/kinds.F $(FC) -c $(FFLAGS) $(SRC)/$*.F fftsg.o: $(SRC)/fftsg.F $(FC) -c $(FFLAGS) $(SRC)/$*.F fftsg_lib.o: $(SRC)/fftsg_lib.F $(FC) -c $(FFLAGS) $(SRC)/$*.F trimcube.o: $(SRC)/trimcube.c $(CC) -c $(CFLAGS) $(SRC)/$*.c # Dependencies atom_types.o: kinds.o \ periodic_table.o cpmd2cube.o: atom_types.o \ fft_tools.o \ grid_types.o \ grids.o \ kinds.o \ periodic_table.o \ readwrites.o \ util.o fft_tools.o: grid_types.o \ fftsg_lib.o \ kinds.o grid_types.o: kinds.o grids.o: grid_types.o \ kinds.o \ util.o main.o: cpmd2cube.o periodic_table.o: kinds.o readwrites.o: atom_types.o \ grid_types.o \ kinds.o util.o: kinds.o i have also tried it on a 1GB ram pc but its showing the same error could you please tell me what is wrong thanks yours sincerely Haider Abbas __________________________________________________________ Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com From ZRLSRB at ch.ibm.com Mon Dec 12 09:57:24 2005 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Mon, 12 Dec 2005 09:57:24 +0100 Subject: [CPMD-list] how to do constraint optimization? In-Reply-To: Message-ID: Dear Lan-Feng, > Therefore, the constraint is not exactly fulfilled, leaving a small difference (0.001 Bohr). I have no complaint > on that. But is there any way to select the threshold of tolerance? Thanks! Best regards, not directly, at least at this time (Lagrange multipliers are currently not implemented in CPMD for most geometry optimizers, and a variable transform such that the active space is orthogonal to the constraints, is not implemented for most types of constraints, either). However, if you increase the penalties, you'll get tighter control over the constraints. Best regards, Salomon From akohlmey at vitae.cmm.upenn.edu Mon Dec 12 16:05:01 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Mon, 12 Dec 2005 10:05:01 -0500 (EST) Subject: [CPMD-list] cpmd2cube segmentation fault error In-Reply-To: <20051212061132.1563.qmail@web8403.mail.in.yahoo.com> References: <20051212061132.1563.qmail@web8403.mail.in.yahoo.com> Message-ID: hi, this is most likely not a problem of the code. please try raising the stacksize using the ulimit command. the newer intel compilers allocate automatic arrays from the stack. axel. ======================================================================= Axel Kohlmeyer e-mail: akohlmey at cmm.upenn.edu, tel: ++1-215-898-1582 Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. On Mon, 12 Dec 2005, haider abbas wrote: > Dear all cpmd user, > > running cpmd2cube shows the following error > > [haider at falcon1 cpmd2cube]$ cpmd2cube.x -rho > -halfmesh ELPOT > > .read input file ... done > I think you stored a density (sum^2 = 0.77965627E-03) > .building g vectors ... done > forrtl: severe (174): SIGSEGV, segmentation fault > occurred > Image PC Routine Line > Source > cpmd2cube.x 08055F58 Unknown > Unknown Unknown > cpmd2cube.x 0805404E Unknown > Unknown Unknown > cpmd2cube.x 0805880F Unknown > Unknown Unknown > cpmd2cube.x 0806C9D8 Unknown > Unknown Unknown > cpmd2cube.x 00763E33 Unknown > Unknown Unknown > cpmd2cube.x 08049CE1 Unknown > Unknown Unknown > > > the makefile of cpmd2cube.x is > > #-----------------------------------------------------------------------------# > # Makefile for cpmd2cube.x > # Configuration: Linux-PC-IFC-P4 > # Creation of Makefile: Nov 23 2005 > # on Linux robin 2.4.21-15.EL #1 Sun May 16 02:45:06 > EDT 2004 i686 athlon i386 GNU/Linux > # Author: haider > #---------------------------------------------------------------------------- > # > SHELL = /bin/sh > # > #--------------- Configuration > FC = ifc > FFLAGS = -FR -D__IFC -DFFT_DEFAULT -O -tpp7 -w90 -w95 > -pc64 > LFLAGS = -O -tpp7 -w90 -w95 -pc64 > LIBS = -Vaxlib > # uncomment and set only if needed > #CC = cc > #CFLAGS = > #--------------- End of Configuration > ############## > > EXE = cpmd2cube.x > > OBJECTS = \ > kinds.o periodic_table.o util.o grids.o > cpmd2cube.o \ > main.o grid_types.o atom_types.o readwrites.o > \ > fftsg_lib.o fft_tools.o fftsg.o > > CFGDEST = . > CFGMACH = Linux-PC-IFC-P4 > SRC=. > > ############################# > > all: $(EXE) trimcube > > $(EXE): $(OBJECTS) > $(FC) -o $(EXE) $(LFLAGS) $(OBJECTS) $(LIBS) > > trimcube: trimcube.o > $(CC) $(CFLAGS) -o $@ trimcube.o > ############################# > clean: > rm -f *.o *.mod *.L *~ > > # Create a new makefile with new dependencies but > retain the configuration. > reconfig: > ( cd $(SRC) ; ./Configure -r -m -SRC=$(SRC) > -DEST=$(CFGDEST) $(CFGMACH) ; cd $(CFGDEST) ) > > ############################# > atom_types.o: $(SRC)/atom_types.F > $(FC) -c $(FFLAGS) $(SRC)/$*.F > > cpmd2cube.o: $(SRC)/cpmd2cube.F > $(FC) -c $(FFLAGS) $(SRC)/$*.F > > fft_tools.o: $(SRC)/fft_tools.F > $(FC) -c $(FFLAGS) $(SRC)/$*.F > > grid_types.o: $(SRC)/grid_types.F > $(FC) -c $(FFLAGS) $(SRC)/$*.F > > grids.o: $(SRC)/grids.F > $(FC) -c $(FFLAGS) $(SRC)/$*.F > > main.o: $(SRC)/main.F > $(FC) -c $(FFLAGS) $(SRC)/$*.F > > periodic_table.o: $(SRC)/periodic_table.F > $(FC) -c $(FFLAGS) $(SRC)/$*.F > > readwrites.o: $(SRC)/readwrites.F > $(FC) -c $(FFLAGS) $(SRC)/$*.F > > util.o: $(SRC)/util.F > $(FC) -c $(FFLAGS) $(SRC)/$*.F > > kinds.o: $(SRC)/kinds.F > $(FC) -c $(FFLAGS) $(SRC)/$*.F > > fftsg.o: $(SRC)/fftsg.F > $(FC) -c $(FFLAGS) $(SRC)/$*.F > > fftsg_lib.o: $(SRC)/fftsg_lib.F > $(FC) -c $(FFLAGS) $(SRC)/$*.F > > trimcube.o: $(SRC)/trimcube.c > $(CC) -c $(CFLAGS) $(SRC)/$*.c > > # Dependencies > atom_types.o: kinds.o \ > periodic_table.o > > cpmd2cube.o: atom_types.o \ > fft_tools.o \ > grid_types.o \ > grids.o \ > kinds.o \ > periodic_table.o \ > readwrites.o \ > util.o > > fft_tools.o: grid_types.o \ > fftsg_lib.o \ > kinds.o > > grid_types.o: kinds.o > > grids.o: grid_types.o \ > kinds.o \ > util.o > > main.o: cpmd2cube.o > > periodic_table.o: kinds.o > > readwrites.o: atom_types.o \ > grid_types.o \ > kinds.o > > util.o: kinds.o > > i have also tried it on a 1GB ram pc but its showing > the same error > could you please tell me what is wrong > thanks > yours sincerely > Haider Abbas > > > > > __________________________________________________________ > Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://cpmd.org/mailman/listinfo/cpmd-list > From akohlmey at vitae.cmm.upenn.edu Mon Dec 12 16:27:46 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Mon, 12 Dec 2005 10:27:46 -0500 (EST) Subject: [CPMD-list] help, draw ELECTROSTATIC POTENTIAL In-Reply-To: <439BB158.00009B.29176@app-01> References: <439BB158.00009B.29176@app-01> Message-ID: On Sun, 11 Dec 2005, [gb2312] Shangyi Ma wrote: > Dear CPMD users: > Does anyone has the experiences draw the 2D plane contour from the > file elpot produced by the keyword ELECTROSTATIC POTENTIAL? I know the yes. > file can be display by converting it to the form of elpot.cube and > using the VMD software, but I find it's not clearly to see the > potential. So I think it's better to draw it in the form of 2D plane > contour perpendicular x, y, or z direction and I don't know how to get > the datas I needed to finish it. Do I can export the data from the > elpot.cube file or from the VMD Volumetric data in other methods? Does > anyone has good ideas on the question? there are several ways to deal with that. the easiest way is probably, you write a small program that extracts the pice of data that you want to look at. the cube format is, e.g., described shortly in the first part of the file util_p.F from the cpmd sources. > Another question is that what's the meaning of "isovalue" when I > visualize the Volumetric data in the form of isosurface? I find it > shows different shapes in the different isovalue? So how can I get the > appropriate isovalue? an isosurface is a surface, where all points have the same value. this value is the isovalue. this is most easily understood in atoms or molecules, if you look at the density. a small (positive) isovalue will lead to an isosurface through the low (electron) density area, and will thus show the 'size' of the molecule. with the electrostatic potential, this is not that easy, since you usually have areas of high and low potential which in addition can be positive or negative. the appropriate isovalue is the value, that demonstrates, what you want to show, e.g. if you want to show areas of strong positive and negativ potentials, you use _two_ representations of different colors with isovalues of opposite sign. most commonly people 'map' the electrostatic potential on an isosurface of the 'outside' of a molecule, so you can see how the molecule is 'seen' from other molecules in terms of electrostatics, i.e. where the molecule is polarized. regards, axel. > Thanks in advance! > Best wishes! > shyma ======================================================================= Axel Kohlmeyer e-mail: akohlmey at cmm.upenn.edu, tel: ++1-215-898-1582 Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From ara_1357_2416 at yahoo.com Mon Dec 12 20:17:47 2005 From: ara_1357_2416 at yahoo.com (Younes Ansari) Date: Mon, 12 Dec 2005 11:17:47 -0800 (PST) Subject: [CPMD-list] want some PSP files Message-ID: <20051212191747.85358.qmail@web33215.mail.mud.yahoo.com> Dear cpmd-list: I will appreciate it if someone send me the: I_MT_PBE I_MT_BLYP Cl_MT_PBE Cl_MT_BLYP Br_MT_PBE Br_MT_BLYP F_MT_PBE F_MT_BLYP Pseudopotentials THANKS............... --------------------------------- Yahoo! Shopping Find Great Deals on Holiday Gifts at Yahoo! Shopping -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20051212/632cd120/attachment.html From akohlmey at vitae.cmm.upenn.edu Mon Dec 12 21:41:29 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Mon, 12 Dec 2005 15:41:29 -0500 (EST) Subject: [CPMD-list] want some PSP files In-Reply-To: <20051212191747.85358.qmail@web33215.mail.mud.yahoo.com> References: <20051212191747.85358.qmail@web33215.mail.mud.yahoo.com> Message-ID: On Mon, 12 Dec 2005, Younes Ansari wrote: > Dear cpmd-list: please check the available resources more carefully. the majority of the potentials are available from mauro boero's extendet pp library (should be in the cpmd download area or on juerg hutter's homepage in the 'information' section). > I will appreciate it if someone send me the: ...and i will appreciate it, if someone would send me a keg of beer, that never runs dry. ;-)) > I_MT_PBE > I_MT_BLYP here you are out of luck. but the rest should be available. greetings from snowy illinois, axel. > Cl_MT_PBE > Cl_MT_BLYP > > Br_MT_PBE > Br_MT_BLYP > > F_MT_PBE > F_MT_BLYP > > Pseudopotentials > THANKS............... > > > --------------------------------- > Yahoo! Shopping > Find Great Deals on Holiday Gifts at Yahoo! Shopping ======================================================================= Axel Kohlmeyer e-mail: akohlmey at cmm.upenn.edu, tel: ++1-215-898-1582 Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From shyma at imr.ac.cn Tue Dec 13 09:37:30 2005 From: shyma at imr.ac.cn (=?gb2312?B?U2hhbmd5aSBNYQ==?=) Date: Tue, 13 Dec 2005 16:37:30 +0800 (CST) Subject: [CPMD-list] help on the kohn-sham energies! Message-ID: <439E884A.00000F.25116@app-01> Dear axel and cpmd-users: Thanks for your kindly reply! Today I have other questions need your help! Firstly, I have optimized the wavefunction of the 5 atoms clusters and recalculated the kohn-sham energyes of it, but I find the final total energys is different,but I don't know what's the reason cause the difference. The following are the input and out files in different calculation respectively: input file for the wavefunction optimization: ********************************************* &CPMD OPTIMIZE WAVEFUNCTION CONVERGENCE ORBITALS 1.0D-5 FREE ENERGY FUNCTIONAL LANCZOS DIAGONALISATION LANCZOS PARAMETAERS N=5 1 6 20 1.0D-9 0.05 1.0D-10 0.01 1.0D-12 0.0025 1.0D-14 0.001 1.0D-16 ANDERSON MIXING 0.2 BROYDEN MIXING BROYMIX=0.15 TEMPERATURE ELCECTRON 1000 CENTER MOLECULE ON MAXSTEP 1000 STRUCTURE BONDS ANGLES MIRROR &END &SYSTEM SYMMETRY 0 POISSON SOLVER TUCKERMAN ANGSTROM CELL 18.0 1.0 1.0 0.0 0.0 0.0 STATES 12 CUTOFF 60 &END &ATOMS *Al_SGS_LDA.psp KLEINMAN-BYLANDER LMAX=D 5 9.627618698838 10.483425410635 8.869432662311 10.799305233317 8.197179013185 8.528215175287 8.342182486388 8.284268303325 7.708984912400 9.030290923963 8.232406355001 10.421762121950 7.200662913258 9.802781813240 9.471731059454 &END &DFT FUNCTIONAL LDA &END input for the khon-sham energies: ******************************** &CPMD KOHN-SHAM ENERGIES 8 RESTART WAVEFUNCTION COORDINATES FREE ENERGY FUNCTIONAL LANCZOS DIAGONALIZATION RHOOUT ELECTROSTATIC POTENTIAL ELF CONVERGENCE ORBITALS 1.0D-5 CENTER MOLECULE ON TEMPERATURE ELECTRON 1000 MIRROR &END &SYSTEM SYMMETRY 0 POISSON SOLVER TUCKERMAN ANGSTROM CELL 18.0 1.0 1.0 0.0 0.0 0.0 CUTOFF 60 &END &DFT FUNCTIONAL LDA &END &ATOMS *Al_SGS_LDA.psp KLEINMAN-BYLANDER LMAX=D 5 9.627618698838 10.483425410635 8.869432662311 10.799305233317 8.197179013185 8.528215175287 8.342182486388 8.284268303325 7.708984912400 9.030290923963 8.232406355001 10.421762121950 7.200662913258 9.802781813240 9.471731059454 &END the final results for the wavefunction optimization: **************************************************************** EIGENVALUES(EV) AND OCCUPATION: 1 -12.1696122 2.000 2 -8.8559503 2.000 3 -7.9476996 2.000 4 -7.9473935 2.000 5 -5.7240799 2.000 6 -4.7316987 1.988 7 -4.3800213 1.465 8 -4.3798610 1.464 9 -3.9610614 0.041 10 -3.9609183NC 0.041 11 -3.4441107NC 0.000 12 -1.4512370NC 0.000 CHEMICAL POTENTIAL = -4.2932170551 EV **************************************************************** ELECTRONIC GRADIENT: MAX. COMPONENT = 9.04632E-06 NORM = 2.01259E-06 TOTAL INTEGRATED ELECTRONIC DENSITY IN G-SPACE = 15.000000 IN R-SPACE = 15.000000 (F+E2+X-V+O) TOTAL ENERGY = -10.13365518 A.U. (F) ELECTRONIC FREE ENERGY = -3.97233193 A.U. (E2=I-H-S+R) ELECTROSTATIC ENERGY = -7.20586331 A.U. (S) ESELF = 14.96033552 A.U. (R) ESR = 0.00054749 A.U. (X) EXCHANGE-CORRELATION ENERGY = -3.45753883 A.U. (V) EXCHANGE-CORRELATION POTEN. = -4.50207656 A.U. (O) BOGOLIUBOV CORRECTION ENERGY = 0.00000233 A.U. ***************************************************************** and final results for the kohn-sham energies: **************************************************************** EIGENVALUES(EV) AND OCCUPATION: 1 -12.1738143 2.000 2 -8.8233432 2.000 3 -8.2125551 2.000 4 -7.7129732 2.000 5 -5.6818952 2.000 6 -4.8253746 1.999 7 -4.5739314 1.979 8 -4.1403639 0.761 9 -3.9798900 0.174 10 -3.9165498 0.087 11 -3.3955067 0.000 12 -1.5688794 0.000 13 -1.3219857 0.000 14 -0.8650114NC 0.000 15 -0.7020890NC 0.000 16 -0.3384448NC 0.000 CHEMICAL POTENTIAL = -4.1824507416 EV **************************************************************** ELECTRONIC GRADIENT: MAX. COMPONENT = 9.86609E-03 NORM = 2.54834E+00 TOTAL INTEGRATED ELECTRONIC DENSITY IN G-SPACE = 15.000000 IN R-SPACE = 15.000000 (F+E2+X-V+O) TOTAL ENERGY = -10.15535475 A.U. (F) ELECTRONIC FREE ENERGY = -3.97978925 A.U. (E2=I-H-S+R) ELECTROSTATIC ENERGY = -7.22134101 A.U. (S) ESELF = 14.96033552 A.U. (R) ESR = 0.00054749 A.U. (X) EXCHANGE-CORRELATION ENERGY = -3.46149018 A.U. (V) EXCHANGE-CORRELATION POTEN. = -4.50726336 A.U. (O) BOGOLIUBOV CORRECTION ENERGY = 0.00000233 A.U. **************************************************************** You can see the difference what I mean from the above files. The final results "TOTAL ENERGY" "EIGENVALUES(EV) AND OCCUPATION" and "CHEMICAL POTENTIAL(is it the Fermi energy?)" are all not the same for the wavefunction calculation and kohn-sham energies calculation. So what cause the difference and which results are more correct? Are there some faults in my 2 input files? Secondly, what's the meaning of "NC" in the "EIGENVALUES(EV) AND OCCUPATION" results if the results show the occupation stats? Does it mean "not converged"? Is there any difference between the "13 -1.3219857 0.000 " and "14 -0.8650114NC 0.000"? The occupation of all them are 0 and "14" indentfied NC and "13" is not. Any comments and advices are appreciated! Thanks in advance! Best regards! shyma -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20051213/29edf7e0/attachment.html From yangzy at lnm.imech.ac.cn Tue Dec 13 15:49:34 2005 From: yangzy at lnm.imech.ac.cn (Yang Zhenyu) Date: Tue, 13 Dec 2005 22:49:34 +0800 Subject: [CPMD-list] How to view the orbitals or density by Molekel? Message-ID: <200512131450.PAA12366@internet-fence.zurich.ihost.com> Dear CPMD users: Are there some comrades using Molekel(version 4.3 Win) to view the results of CPMD? I got problems when I read the cube file into Molekel. It tells me only coordinates read. And I click "compute>> Orbital" or "El. density" and the others, but it tells "Load an output-file first". I am confused. What output file do I need? Would please give me some directions? ?????????????? ??Best Regards ??Yang Zhenyu State Key Laboratory of Nonlinear Mechanics (LNM) Institute of Mechanics, Chinese Academy of Sciences No.15 Beisihuanxi Road Beijing 100080, P. R. China FAX: 010-62579511 ??yangzy at lnm.imech.ac.cn ??2005-12-13 From akohlmey at vitae.cmm.upenn.edu Tue Dec 13 16:09:26 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Tue, 13 Dec 2005 10:09:26 -0500 (EST) Subject: [CPMD-list] help on the kohn-sham energies! In-Reply-To: <439E884A.00000F.25116@app-01> References: <439E884A.00000F.25116@app-01> Message-ID: On Tue, 13 Dec 2005, [gb2312] Shangyi Ma wrote: > Dear axel and cpmd-users: > Thanks for your kindly reply! > Today I have other questions need your help! > Firstly, I have optimized the wavefunction of the 5 atoms clusters and recalculated the kohn-sham energyes of it, but I find the final total energys is different,but I don't know what's the reason cause the difference. The following are the input and out files in different calculation respectively: > > input file for the wavefunction optimization: > ********************************************* > &CPMD > OPTIMIZE WAVEFUNCTION > CONVERGENCE ORBITALS > 1.0D-5 > FREE ENERGY FUNCTIONAL > LANCZOS DIAGONALISATION if you are doing a diagonalization to optimize the wavefunction, there is little need to do a kohn-sham energies calculation. you already have the diagonalized orbitals. > LANCZOS PARAMETAERS N=5 > 1 6 20 1.0D-9 > 0.05 1.0D-10 > 0.01 1.0D-12 > 0.0025 1.0D-14 > 0.001 1.0D-16 > ANDERSON MIXING > input for the khon-sham energies: > ******************************** > &CPMD > KOHN-SHAM ENERGIES > 8 do you really need 8 _additional_ empty states. the majority of them will be meaningless. > > You can see the difference what I mean from the above files. The final > results "TOTAL ENERGY" "EIGENVALUES(EV) AND OCCUPATION" and "CHEMICAL > POTENTIAL(is it the Fermi energy?)" are all not the same for the > wavefunction calculation and kohn-sham energies calculation. So what > cause the difference and which results are more correct? Are there > some faults in my 2 input files? > Secondly, what's the meaning of "NC" in the "EIGENVALUES(EV) AND > OCCUPATION" results if the results show the occupation stats? Does it > mean "not converged"? Is there any difference between the "13 EXACTLY. so the KS energies run added one more diagonalization iteration to the not fully diagonal wavefunction, a few more got converged now. so you have to continue the wavefunction optimization for a bit, or change the lanzcos parameters, so you have a few more lanczos iterations before you update the wavefunction, not only one. regards, axel. > -1.3219857 0.000 " and "14 -0.8650114NC 0.000"? The occupation of all > them are 0 and "14" indentfied NC and "13" is not. > > Any comments and advices are appreciated! > Thanks in advance! > Best regards! > shyma > ======================================================================= Axel Kohlmeyer e-mail: akohlmey at cmm.upenn.edu, tel: ++1-215-898-1582 Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at vitae.cmm.upenn.edu Tue Dec 13 16:11:54 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Tue, 13 Dec 2005 10:11:54 -0500 (EST) Subject: [CPMD-list] How to view the orbitals or density by Molekel? In-Reply-To: <200512131450.PAA12366@internet-fence.zurich.ihost.com> References: <200512131450.PAA12366@internet-fence.zurich.ihost.com> Message-ID: On Tue, 13 Dec 2005, Yang Zhenyu wrote: > Dear CPMD users: > > Are there some comrades using Molekel(version 4.3 Win) to view > the results of CPMD? > I got problems when I read the cube file into Molekel. It tells > me only coordinates read. And I click "compute>> Orbital" or "El. > density" and the others, but it tells "Load an output-file first". I > am confused. What output file do I need? this is the normal behavior. please read the molekel documentation. you first read the coordinates and then read the density. note that cube files from cpmd2cube are _always_ 'density style' cubefiles, so if you want to load multiple orbitals, you have to load multiple cube files. > > Would please give me some directions? apart from the above: try VMD. ;-) cheers, axel. > > ?????????????? > ??Best Regards > > ??Yang Zhenyu > State Key Laboratory of Nonlinear Mechanics (LNM) > Institute of Mechanics, Chinese Academy of Sciences > No.15 Beisihuanxi Road > Beijing 100080, P. R. China > FAX: 010-62579511 > ??yangzy at lnm.imech.ac.cn > ??2005-12-13 > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://cpmd.org/mailman/listinfo/cpmd-list > ======================================================================= Axel Kohlmeyer e-mail: akohlmey at cmm.upenn.edu, tel: ++1-215-898-1582 Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From haiderabbasphy at yahoo.co.in Wed Dec 14 10:54:31 2005 From: haiderabbasphy at yahoo.co.in (haider abbas) Date: Wed, 14 Dec 2005 09:54:31 +0000 (GMT) Subject: [CPMD-list] still cpmd2cube segmentation fault error occurring In-Reply-To: Message-ID: <20051214095432.25719.qmail@web8403.mail.in.yahoo.com> Dear Axel, I have used the command haider at robin:~/cpmd2cube> ulimit -s unlimited haider at robin:~/cpmd2cube> cpmd2cube.x -dens DENSITY .read input file ... done I think you stored a density (sum^2 = 0.12582877E-03) .building g vectors ... done forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source cpmd2cube.x 08055F58 Unknown Unknown Unknown cpmd2cube.x 0805404E Unknown Unknown Unknown cpmd2cube.x 0805880F Unknown Unknown Unknown cpmd2cube.x 0806C9D8 Unknown Unknown Unknown cpmd2cube.x 40099768 Unknown Unknown Unknown cpmd2cube.x 08049CE1 Unknown Unknown Unknown but it is still there, i am using intel_fc_80 and White Box Enterprise Linux release 3.0 (Liberation Respin 1) Kernel 2.4.21-15.EL on an i686 now please guide me Thanks yours sincerely Haider Abbas --- Axel Kohlmeyer wrote: > > hi, > > this is most likely not a problem of the code. > please try raising the stacksize using the ulimit > command. > the newer intel compilers allocate automatic arrays > from > the stack. > > axel. > > ======================================================================= > Axel Kohlmeyer e-mail: akohlmey at cmm.upenn.edu, > tel: ++1-215-898-1582 > Center for Molecular Modeling -- > University of Pennsylvania > Department of Chemistry, 231 S.34th Street, > Philadelphia, PA 19104-6323 > ======================================================================= > If you make something idiot-proof, the universe > creates a better idiot. > > On Mon, 12 Dec 2005, haider abbas wrote: > > > Dear all cpmd user, > > > > running cpmd2cube shows the following error > > > > [haider at falcon1 cpmd2cube]$ cpmd2cube.x -rho > > -halfmesh ELPOT > > > > .read input file ... done > > I think you stored a density (sum^2 = > 0.77965627E-03) > > .building g vectors ... done > > forrtl: severe (174): SIGSEGV, segmentation fault > > occurred > > Image PC Routine > Line > > Source > > cpmd2cube.x 08055F58 Unknown > > Unknown Unknown > > cpmd2cube.x 0805404E Unknown > > Unknown Unknown > > cpmd2cube.x 0805880F Unknown > > Unknown Unknown > > cpmd2cube.x 0806C9D8 Unknown > > Unknown Unknown > > cpmd2cube.x 00763E33 Unknown > > Unknown Unknown > > cpmd2cube.x 08049CE1 Unknown > > Unknown Unknown > > > > > > the makefile of cpmd2cube.x is > > > > > #-----------------------------------------------------------------------------# > > # Makefile for cpmd2cube.x > > # Configuration: Linux-PC-IFC-P4 > > # Creation of Makefile: Nov 23 2005 > > # on Linux robin 2.4.21-15.EL #1 Sun May 16 >