From aijun_du at hotmail.com Tue Apr 1 16:05:00 2003 From: aijun_du at hotmail.com (Du Aijun) Date: Tue, 01 Apr 2003 22:05:00 +0800 Subject: [CPMD-list] Qestions on MD simulation! Message-ID: Dear all, In the process of MD simulation of NH3 molecule, I met the follwing wrong messages: PGFIO-F-201/OPEN/unit=4/illegal value for specifier. File name = ./TRAJECTORY In source file ./fileopen.f, at line number 20 p1_19095: (10.086610) net_recv failed for fd = 3 p1_19095: p4_error: net_recv read, errno = : 104 bm_list_13860: p4_error: lookup_slave_index_by_pid: %d not found: 13859 It seems okay when running the first MD step and the problem happens on writing the TRAJECTORY, MOVIE and ENERGIES files again! Could anyone please tell me how to solve it? Many thanks in advance! With regards, Aijun Du _________________________________________________________________ ?????????????????????????????? MSN Hotmail?? http://www.hotmail.com From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Tue Apr 1 16:55:11 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Tue, 01 Apr 2003 16:55:11 +0200 Subject: [CPMD-list] Qestions on MD simulation! In-Reply-To: Message-ID: <200304011455.h31EtB307869@yello.theochem.ruhr-uni-bochum.de> On Tue, 01 Apr 2003 22:05:00 +0800 "Du Aijun" wrote: > Dear all, > > In the process of MD simulation of NH3 molecule, I met the follwing wrong > messages: > > PGFIO-F-201/OPEN/unit=4/illegal value for specifier. > File name = ./TRAJECTORY > In source file ./fileopen.f, at line number 20 > p1_19095: (10.086610) net_recv failed for fd = 3 > p1_19095: p4_error: net_recv read, errno = : 104 > bm_list_13860: p4_error: lookup_slave_index_by_pid: %d not found: 13859 > > It seems okay when running the first MD step and the problem happens on > writing the TRAJECTORY, MOVIE and ENERGIES files again! Could anyone please > tell me how to solve it? yep. add -D__pgf90 to CPPFLAGS and recompile (make clean; make). cheers, axel kohlmeyer. > > Many thanks in advance! > > With regards, > Aijun Du > > > > > _________________________________________________________________ > ?????????????????????????????? MSN Hotmail?? http://www.hotmail.com > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From aijun_du at hotmail.com Wed Apr 2 11:24:13 2003 From: aijun_du at hotmail.com (Du Aijun) Date: Wed, 02 Apr 2003 17:24:13 +0800 Subject: [CPMD-list] Problems on running cpmd2cube!! Message-ID: Dear all, I met the following problems when running cpmd2cube: .read input file ... done I think you stored a density (sum^2 = 0.12959468E-02) ERROR in file DENSITY Wannier-functions stored as density, you can not create a cube-file with the wavefunction FORTRAN STOP Could anyone tell me how to how to choose the proper option? Many thanks! With regards, Aijun Du _________________________________________________________________ ???????????????????????????? MSN Messenger: http://messenger.msn.com/cn From hakan.hugosson at inorg.chem.ethz.ch Wed Apr 2 11:50:02 2003 From: hakan.hugosson at inorg.chem.ethz.ch (Hakan Hugosson) Date: Wed, 02 Apr 2003 11:50:02 +0200 Subject: [CPMD-list] Problems on running cpmd2cube!! References: Message-ID: <3E8AB24A.55FBE764@inorg.chem.ethz.ch> Du Aijun wrote: > > Dear all, > > I met the following problems when running cpmd2cube: > > .read input file ... done > I think you stored a density (sum^2 = 0.12959468E-02) > ERROR in file DENSITY > Wannier-functions stored as density, you can not > create a cube-file with the wavefunction > FORTRAN STOP > > Could anyone tell me how to how to choose the proper option? Many thanks! > > With regards, > Aijun Du > > _________________________________________________________________ > ???????????????????????????? MSN Messenger: http://messenger.msn.com/cn > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list Dear Aijun, It sounds as though you have forgot to put the flag -dens. If you have a DENSITY file: cpmd2cube.x -dens DENSITY should work (works when I try it). Yours, /haakan -- ________________________________________________________ Dr. Hakan Wilhelm Hugosson || work : +41 (0)21-6930322 Laboratory of Computational || home : +41 (0)21-6010239 Chemistry and Biochemistry || mobile: +41 (0)79-7724691 EPF Lausanne, Switzerland || www.rac.ethz.ch/hugosson/ -------------------------------------------------------- From c00ycl00 at nchc.gov.tw Wed Apr 2 16:07:18 2003 From: c00ycl00 at nchc.gov.tw (c00ycl00) Date: Wed, 02 Apr 2003 22:07:18 +0800 Subject: [CPMD-list] Some problems on restart CPMD Message-ID: <3E8AEE963DE.514DC00YCL00@smtp.nchc.gov.tw> Dear all, I met a problem when I run CPMD with RESTART on our IBM sp2. Originally, I run the following input and get the RESTART file. Then I change the line: OPTIMIZE WAVEFUNCTION to RESTART ALL KOHN-SHAM ENERGIES 8 RHOOUT. But when I run it again, the program stop with an error message: Segmentation fault. Does anyone met this before? Can anyone help me to solve it? Thank you very much. Best regards, Yung-Chiang Lan -------------------------------------------------------------------- &CPMD OPTIMIZE WAVEFUNCTION MAXSTEP 1000 STRUCTURE BONDS ANGLES &END &DFT NEWCODE FUNCTIONAL LDA GC-CUTOFF 0.1E-06 &END &SYSTEM SYMMETRY 0 CELL 15.0000 1.0 1.0 0 0 0 CUTOFF 70.0 &END &PROPERTIES DIPOLE MOMENT &END &ATOMS *O_SG_LDA KLEINMAN-BYLANDER LMAX=P 1 7.5000 7.5000 7.5000 *H_SG_LDA LMAX=S 2 7.5000 7.5000 9.3011 7.5000 7.5000 5.6989 &END ---------------------------------------------------------- From mkosmows at mailbox.syr.edu Wed Apr 2 23:27:45 2003 From: mkosmows at mailbox.syr.edu (mkosmows) Date: Wed, 2 Apr 2003 16:27:45 -0500 Subject: [CPMD-list] How to compile for Sun machine Message-ID: <3E9695F4@OrangeMail> Dear CPMD community: I've recently put CPMD (3.7.1) on an old Sun Ultra30 and compiled using ForteDev 7 (now called Sun Studio 7 I believe). I used the Conifgure SUN option to generate the makefile. I can run a job, but get a bit different result than with PC Linux, and the following warning: Note: IEEE floating point exception flags raised: Inexact, Underflow; Nonstandard floating point mode enabled See the Numerical Computation Guide, ieee_flags(3M), ieee_sun(3M) I am assuming that I need to do something to the makefile. If anyone knows, please inform me. Also, I am planning on purchasing a Sun Blade 150 workstaion soon, will the makefile need to be modified for that as well? Thank you very much, Mark Kosmowski Chemistry Department Syracuse University mkosmows at syr.edu From mkosmows at mailbox.syr.edu Thu Apr 3 05:00:45 2003 From: mkosmows at mailbox.syr.edu (mkosmows) Date: Wed, 2 Apr 2003 22:00:45 -0500 Subject: [CPMD-list] Using SCALE with a triclinic crystal Message-ID: <3E989144@OrangeMail> Dear CPMD community: I received the following message while doing a geometry optimization: MULTTB| SUPERCELL ATOMS FORM NO BASIS FOR THIS POINT GROUP. I think this is because I tried to invoke the SCALE keyword while using a triclinic crystal lattice. Is there a way to use fractional coordinates in crystals where alpha, beta and gamma are not all 90 degrees? Or does one simply need to enter in cartesian coordinates in these cases? Thank you, Mark Kosmowski Chemistry Department Syracuse University mkosmows at syr.edu From cdy2000 at vip.sina.com Thu Apr 3 11:24:28 2003 From: cdy2000 at vip.sina.com (cdy2000 at vip.sina.com) Date: Thu, 03 Apr 2003 17:24:28 +0800 Subject: [CPMD-list] PROGRAM STOPS IN SUBROUTINE RGMOPT Message-ID: <20030403092428.3114.qmail@vip.sina.com> Hello, every CPMDer! Thank Isaev's help. Another question, when I optimize the geometry and the wavefunction of a cluster, error output, the info is: PROGRAM STOPS IN SUBROUTINE RGMOPT | SIMUL NOT WORKING What's meaning? What is the RGMOPT? How should I do? Thanks for any help. ______________________________________ =================================================================== From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu Apr 3 11:58:08 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 03 Apr 2003 11:58:08 +0200 Subject: [CPMD-list] How to compile for Sun machine In-Reply-To: <3E9695F4@OrangeMail> Message-ID: <200304030958.h339w8l04259@yello.theochem.ruhr-uni-bochum.de> On Wed, 2 Apr 2003 16:27:45 -0500 mkosmows wrote: > Dear CPMD community: hi mark, > > I've recently put CPMD (3.7.1) on an old Sun Ultra30 and compiled using > ForteDev 7 (now called Sun Studio 7 I believe). I used the Conifgure SUN > option to generate the makefile. you are probably better off using the SUN-ULTRA3-32BIT configuration(s) and then change the -xtarget=ultra3 and -xarch=v8plusb flags to the appropriate values. > > I can run a job, but get a bit different result than with PC Linux, and the small(!) differences (especially in the gradients and forces) due to different rounding errors in optimized libraries and optimizing strategies in different compilers are to be expected. > following warning: > > Note: IEEE floating point exception flags raised: > Inexact, Underflow; > Nonstandard floating point mode enabled > See the Numerical Computation Guide, ieee_flags(3M), ieee_sun(3M) this one can be ignored. nonstandard floating point was a big win with _very_ old sun cpus (according to the manpage) so it is automatically turned on with -fast. with cpus currently in use you can safely set -fns=no and get rid of the warning (IIRC it is still printed once at the end of the job, but not all the time). > > I am assuming that I need to do something to the makefile. If anyone knows, > please inform me. Also, I am planning on purchasing a Sun Blade 150 > workstaion soon, will the makefile need to be modified for that as well? see above. please note that you should only compile in 64-bit mode, if you use more than 2GB memory. 32bit is from my experience significantly faster. > > Thank you very much, > > Mark Kosmowski hope this helps, axel kohlmeyer. > > Chemistry Department > Syracuse University > mkosmows at syr.edu > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From hutter at pci.unizh.ch Thu Apr 3 12:00:13 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 3 Apr 2003 12:00:13 +0200 (MEST) Subject: [CPMD-list] Some problems on restart CPMD In-Reply-To: <3E8AEE963DE.514DC00YCL00@smtp.nchc.gov.tw> References: <3E8AEE963DE.514DC00YCL00@smtp.nchc.gov.tw> Message-ID: Hi This is most likely due to the RESTART ALL option. Try to sepcify only RESTART WAVEFUNCTION COORDINATES Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Wed, 2 Apr 2003, c00ycl00 wrote: > Dear all, > > I met a problem when I run CPMD with RESTART > on our IBM sp2. > Originally, I run the following input and get the > RESTART file. Then I change the line: > > OPTIMIZE WAVEFUNCTION > > to > > RESTART ALL > KOHN-SHAM ENERGIES > 8 > RHOOUT. > > But when I run it again, the program stop with an error > message: Segmentation fault. Does anyone met this before? > Can anyone help me to solve it? Thank you very much. > > Best regards, > Yung-Chiang Lan > > -------------------------------------------------------------------- > &CPMD > OPTIMIZE WAVEFUNCTION > MAXSTEP > 1000 > STRUCTURE BONDS ANGLES > &END > > &DFT > NEWCODE > FUNCTIONAL LDA > GC-CUTOFF > 0.1E-06 > &END > > &SYSTEM > SYMMETRY > 0 > CELL > 15.0000 1.0 1.0 0 0 0 > CUTOFF > 70.0 > &END > > &PROPERTIES > DIPOLE MOMENT > &END > > &ATOMS > *O_SG_LDA KLEINMAN-BYLANDER > LMAX=P > 1 > 7.5000 7.5000 7.5000 > *H_SG_LDA > LMAX=S > 2 > 7.5000 7.5000 9.3011 > 7.5000 7.5000 5.6989 > &END > ---------------------------------------------------------- > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Thu Apr 3 12:04:10 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 3 Apr 2003 12:04:10 +0200 (MEST) Subject: [CPMD-list] How to compile for Sun machine In-Reply-To: <3E9695F4@OrangeMail> References: <3E9695F4@OrangeMail> Message-ID: Hi you might want to try the follwoing additional compiler flags -fast -fns=no Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Wed, 2 Apr 2003, mkosmows wrote: > Dear CPMD community: > > I've recently put CPMD (3.7.1) on an old Sun Ultra30 and compiled using > ForteDev 7 (now called Sun Studio 7 I believe). I used the Conifgure SUN > option to generate the makefile. > > I can run a job, but get a bit different result than with PC Linux, and the > following warning: > > Note: IEEE floating point exception flags raised: > Inexact, Underflow; > Nonstandard floating point mode enabled > See the Numerical Computation Guide, ieee_flags(3M), ieee_sun(3M) > > I am assuming that I need to do something to the makefile. If anyone knows, > please inform me. Also, I am planning on purchasing a Sun Blade 150 > workstaion soon, will the makefile need to be modified for that as well? > > Thank you very much, > > Mark Kosmowski > > Chemistry Department > Syracuse University > mkosmows at syr.edu > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Thu Apr 3 12:07:34 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 3 Apr 2003 12:07:34 +0200 (MEST) Subject: [CPMD-list] Using SCALE with a triclinic crystal In-Reply-To: <3E989144@OrangeMail> References: <3E989144@OrangeMail> Message-ID: Hi you can use SCALE with the triclinic cell. The problem seems to be that you have specified a point group and the program couldn't verify that the input is compatible with this group. Have you specified the coordinates with enough accuracy? Are you sure that you have picked the correct point group, maybe you want to try also POINT GROUP AUTO Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Wed, 2 Apr 2003, mkosmows wrote: > Dear CPMD community: > > I received the following message while doing a geometry > optimization: MULTTB| SUPERCELL ATOMS FORM NO BASIS FOR THIS > POINT GROUP. > > I think this is because I tried to invoke the SCALE keyword > while using a triclinic crystal lattice. Is there a way to > use fractional coordinates in crystals where alpha, beta and > gamma are not all 90 degrees? Or does one simply need to > enter in cartesian coordinates in these cases? > > Thank you, > > Mark Kosmowski > > Chemistry Department > Syracuse University > mkosmows at syr.edu > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Thu Apr 3 12:09:29 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 3 Apr 2003 12:09:29 +0200 (MEST) Subject: [CPMD-list] PROGRAM STOPS IN SUBROUTINE RGMOPT In-Reply-To: <20030403092428.3114.qmail@vip.sina.com> References: <20030403092428.3114.qmail@vip.sina.com> Message-ID: Hi It seems that you are using OPTIMIZE COMBINED as you can read in the manual, this options is not operational. With other words, it's not implemented. Use OPTIMIZE GEOMETRY instead, or if you want to do simulated annealing, do a MOLECULAR DYNAMICS with ANNEALING IONS Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Thu, 3 Apr 2003 cdy2000 at vip.sina.com wrote: > Hello, every CPMDer! > > Thank Isaev's help. > > Another question, when I optimize the geometry and the wavefunction of a cluster, error output, the info is: > > PROGRAM STOPS IN SUBROUTINE RGMOPT | SIMUL NOT WORKING > > What's meaning? What is the RGMOPT? How should I do? > > Thanks for any help. > ______________________________________ > > =================================================================== > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From mkosmows at mailbox.syr.edu Thu Apr 3 15:36:03 2003 From: mkosmows at mailbox.syr.edu (mkosmows) Date: Thu, 3 Apr 2003 08:36:03 -0500 Subject: [CPMD-list] Using SCALE with a triclinic crystal Message-ID: <3E9A0685@OrangeMail> Dear Juerg: I am using POINT GROUP AUTO with DELTA=.001 When I input cartesian coordinates, I do not get the error warning. I only get the error warning when I put in fractional coordinates and the SCALE keyword. My literature structure gives coordinates to 4 places (.xxxx) and I use rpluto to pack the cell and save the coordinates of the cell, which continue to have 4 places. I then just cut and paste into the input file. I can send an input file if that would be helpful. Thank you, Mark Kosmowski >===== Original Message From Juerg Hutter ===== >Hi > >you can use SCALE with the triclinic cell. >The problem seems to be that you have specified >a point group and the program couldn't verify that >the input is compatible with this group. >Have you specified the coordinates with enough >accuracy? Are you sure that you have picked >the correct point group, maybe you want to try also >POINT GROUP >AUTO > >Juerg > >---------------------------------------------------------- >Juerg Hutter Phone : ++41 1 635 4491 >Physical Chemistry Institute FAX : ++41 1 635 6838 >University of Zurich E-mail: hutter at pci.unizh.ch >Winterthurerstrasse 190 >CH-8057 Zurich, Switzerland >---------------------------------------------------------- > > >On Wed, 2 Apr 2003, mkosmows wrote: > >> Dear CPMD community: >> >> I received the following message while doing a geometry >> optimization: MULTTB| SUPERCELL ATOMS FORM NO BASIS FOR THIS >> POINT GROUP. >> >> I think this is because I tried to invoke the SCALE keyword >> while using a triclinic crystal lattice. Is there a way to >> use fractional coordinates in crystals where alpha, beta and >> gamma are not all 90 degrees? Or does one simply need to >> enter in cartesian coordinates in these cases? >> >> Thank you, >> >> Mark Kosmowski >> >> Chemistry Department >> Syracuse University >> mkosmows at syr.edu >> >> _______________________________________________ >> CPMD-list mailing list >> CPMD-list at cpmd.org >> http://www.cpmd.org/mailman/listinfo/cpmd-list >> Chemistry Department Syracuse University mkosmows at syr.edu From aijun_du at hotmail.com Thu Apr 3 16:42:34 2003 From: aijun_du at hotmail.com (Du Aijun) Date: Thu, 03 Apr 2003 22:42:34 +0800 Subject: [CPMD-list] Convergence is still too bad !! Message-ID: Dear all, When I performed a geomertry optimization on methane(CH4) molecule using Vanderbilt ultrasoft pseudopotential and PCG MINIMIZE, I found the maximum gradient of wavefunction grows bigger at first serveral steps, but keep constant later. The problems are as following: LINE SEARCH : LAMBDA=.281 ENERGY = -7.9000653 1 2.752E-02 4.714E-03 -7.897058 -7.897E+00 25.17 LINE SEARCH : LAMBDA=.422 ENERGY = -7.9589492 2 2.887E-02 4.662E-03 -7.900065 -3.008E-03 25.24 LINE SEARCH : LAMBDA=.107 ENERGY = -7.9773182 3 6.313E-02 3.395E-03 -7.958926 -5.886E-02 25.22 LINE SEARCH : LAMBDA=.176E-02 ENERGY = -7.9760463 4 9.486E-02 2.432E-03 -7.977438 -1.851E-02 25.18 LINE SEARCH : LAMBDA=.330E-03 ENERGY = -7.9757286 5 9.847E-02 2.356E-03 -7.976233 1.205E-03 25.21 LINE SEARCH : LAMBDA=.618E-04 ENERGY = -7.9755948 6 9.922E-02 2.343E-03 -7.975730 5.031E-04 25.21 LINE SEARCH : LAMBDA=.116E-04 ENERGY = -7.9755623 7 9.937E-02 2.340E-03 -7.975595 1.354E-04 25.14 LINE SEARCH : LAMBDA=.217E-05 ENERGY = -7.9755550 8 9.940E-02 2.339E-03 -7.975562 3.244E-05 25.11 LINE SEARCH : LAMBDA=.407E-06 ENERGY = -7.9755533 9 9.941E-02 2.339E-03 -7.975555 7.374E-06 25.26 LINE SEARCH : LAMBDA=.764E-07 ENERGY = -7.9755530 10 9.941E-02 2.339E-03 -7.975553 1.623E-06 25.10 ................................................................. ................................................................. 997 9.941E-02 2.339E-03 -7.975552 -8.882E-16 25.23 LINE SEARCH : LAMBDA=.525-157 ENERGY = -7.9755518 998 9.941E-02 2.339E-03 -7.975552 8.882E-16 25.21 LINE SEARCH : LAMBDA=.262-157 ENERGY = -7.9755518 999 9.941E-02 2.339E-03 -7.975552 -8.882E-16 25.15 LINE SEARCH : LAMBDA=.590-157 ENERGY = -7.9755518 1000 9.941E-02 2.339E-03 -7.975552 8.882E-16 25.17 ================================================================ = END OF GEOMETRY OPTIMIZATION = ================================================================ The following is my first time input file: &CPMD OPTIMIZE GEOMETRY HESSIAN UNIT BFGS PCG MINIMIZE CONVERGENCE 1.0D-4 5.0D-4 CENTER MOLECULE MAXSTEP 1000 &END &DFT NEWCODE FUNCTIONAL PBE GC_CUTOFF 0.2E-07 &END &SYSTEM ANGSTROM pOSSION SOLVER TUCKERMAN SYMMETRY 0 CELL 13.0 1.0 1.0 0 0 0 CUTOFF 30.0 STATES 5 CHARGE 0.0 TESR 2 &END &ATOMS *006-C-gpbe--bm.uspp NEWF BINARY LMAX=P 1 -4.3985 1.5414 0.0000 *001-H-gpbe--bm.uspp BINARY NEWF LMAX=S 4 -3.3985 1.5414 0.0000 -4.7323 2.4840 0.0000 -4.7323 1.0701 0.8164 -4.7323 1.0701 -0.8164 &END Then I made some changes on my input file according to the suggestion from others: Adding INITIALIZE WAVEFUNCTION RANDOM in the section of $CPMD..... $END! Increasing GC-CUTOFF to 5.D-5. But problem still exists and the only difference is that the gradient become a new constant! I also changed the Convergence standard to 1.D-3 and 1.D-3 to pass several Geometry steps first.Then I restart the calculation with 1.D-5 and 5.D-5. But the same Problems still met! In addition, bad convergence were also observed when using another Vanderbilt potential(pw91 not PBE). All the uspps inputfile are from inputfile http://www.physics.rutgers.edu/~dhv/uspp/uspp-cur/Work/ When I use other pseudopotential in the PP_LIBRARY provide by www.cpmd.org, such as BLYP. It is very fast to reach convergence. Could anyone help me solve this problem? Any comments and suggestions would be highly appreciated! With regards, A.J.Du _________________________________________________________________ ???????? MSN Explorer: http://explorer.msn.com/lccn/ From hwsheng at jhu.edu Thu Apr 3 19:17:29 2003 From: hwsheng at jhu.edu (HW Sheng) Date: Thu, 03 Apr 2003 12:17:29 -0500 Subject: [CPMD-list] PROGRAM STOPS IN SUBROUTINE RGMOPT References: <20030403092428.3114.qmail@vip.sina.com> Message-ID: <008101c2fa04$e7ced420$a567dc80@mrs.jhu.edu> Hi there. It means the error occurred during geometry optimization, specifically, in the subroutine rgmopt.F. (line 538, version 3.7). Most likely, the method of using simulated annealing to optimize geometry has not been implemented yet. You may want to modify your input file accordingly. Howard ----- Original Message ----- From: To: Sent: Thursday, April 03, 2003 4:24 AM Subject: [CPMD-list] PROGRAM STOPS IN SUBROUTINE RGMOPT > Hello, every CPMDer! > > Thank Isaev's help. > > Another question, when I optimize the geometry and the wavefunction of a cluster, error output, the info is: > > PROGRAM STOPS IN SUBROUTINE RGMOPT | SIMUL NOT WORKING > > What's meaning? What is the RGMOPT? How should I do? > > Thanks for any help. > ______________________________________ > > =================================================================== > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From audrius.alkauskas at unibas.ch Fri Apr 4 14:05:44 2003 From: audrius.alkauskas at unibas.ch (Audrius Alkauskas) Date: Fri, 04 Apr 2003 14:05:44 +0200 Subject: [CPMD-list] Ewald Message-ID: <001601c2faa2$8514e420$51669883@audrius> Dear colleagues I am writing a small molecular mechanics program, and wanted to implement Ewald summation. The numbers I got were not good, so I was looking for some mistake. In the article of Hutter and Marx ( in "Modern Methods and Algorithms of Quantum Chemistry") they say that Fourier transform of a Gaussian charge distribution A \exp (-\frac{r^2}{a^2}) is B \exp (-frac{1}{2} \frac{G^{2}}{a^{2}}) but according to my calculations it surely must be B \exp (-frac{1}{4} \frac{G^{2}}{a^{2}}) (one-fourth instead of one- secondth). Now my code is working properly. Is it some trick or is it something I don't understand or is it just a mistake in the book? Thank you ================================================= Audrius Alkauskas, PhD student Condensed Matter Theory Group & NCCR for Nanoscale Science Institute of Physics, University of Basel, Switzerland http://monet.physik.unibas.ch/~audrius/ Tel.: +41-61-267-3708 ================================================= From audrius.alkauskas at unibas.ch Fri Apr 4 14:09:43 2003 From: audrius.alkauskas at unibas.ch (Audrius Alkauskas) Date: Fri, 04 Apr 2003 14:09:43 +0200 Subject: [CPMD-list] Ewald corrected Message-ID: <001101c2faa3$13c0f060$51669883@audrius> Dear colleagues I am writing a small molecular mechanics program, and wanted to implement Ewald summation. The numbers I got were not good, so I was looking for some mistake. In the article of Hutter and Marx ( in "Modern Methods and Algorithms of Quantum Chemistry") they say that Fourier transform of a Gaussian charge distribution A \exp (-\frac{r^2}{a^2}) is B \exp (-frac{1}{2} G^2 a^2) but according to my calculations it surely must be B \exp (-frac{1}{4}G^2 a^2) (one-fourth instead of one- secondth). Now my code is working properly. Is it some trick or is it something I don't understand or is it just a mistake in the book? Thank you ================================================= Audrius Alkauskas, PhD student Condensed Matter Theory Group & NCCR for Nanoscale Science Institute of Physics, University of Basel, Switzerland http://monet.physik.unibas.ch/~audrius/ Tel.: +41-61-267-3708 ================================================= From hutter at pci.unizh.ch Fri Apr 4 14:43:53 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Fri, 4 Apr 2003 14:43:53 +0200 (MEST) Subject: [CPMD-list] Convergence is still too bad !! In-Reply-To: References: Message-ID: Hi if in a PCG MINIMIZE optimisation Lambda for the line search is smaller than 10**-2 there is a severe problem and the job should be stopped. I can't see exactly what the problem in your case is, but to set GC-CUTOFF to 10**-6 in a USPP calculation of an isolated molecule is certainly a good idea. I also see that you have set STATES to 5, one more than required. This introduces an additional state not needed in the optimisation. It's possible that this confuses the optimiser. On the other hand you say that it worked without problems using other PP. Still I would only use occupied states in a standard optimisation. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Thu, 3 Apr 2003, Du Aijun wrote: > Dear all, > > When I performed a geomertry optimization on methane(CH4) molecule using > Vanderbilt ultrasoft pseudopotential and PCG MINIMIZE, I found the maximum > gradient of wavefunction grows bigger at first serveral steps, but keep > constant later. The problems are as following: > > LINE SEARCH : LAMBDA=.281 ENERGY = -7.9000653 > 1 2.752E-02 4.714E-03 -7.897058 -7.897E+00 25.17 > LINE SEARCH : LAMBDA=.422 ENERGY = -7.9589492 > 2 2.887E-02 4.662E-03 -7.900065 -3.008E-03 25.24 > LINE SEARCH : LAMBDA=.107 ENERGY = -7.9773182 > 3 6.313E-02 3.395E-03 -7.958926 -5.886E-02 25.22 > LINE SEARCH : LAMBDA=.176E-02 ENERGY = -7.9760463 > 4 9.486E-02 2.432E-03 -7.977438 -1.851E-02 25.18 > LINE SEARCH : LAMBDA=.330E-03 ENERGY = -7.9757286 > 5 9.847E-02 2.356E-03 -7.976233 1.205E-03 25.21 > LINE SEARCH : LAMBDA=.618E-04 ENERGY = -7.9755948 > 6 9.922E-02 2.343E-03 -7.975730 5.031E-04 25.21 > LINE SEARCH : LAMBDA=.116E-04 ENERGY = -7.9755623 > 7 9.937E-02 2.340E-03 -7.975595 1.354E-04 25.14 > LINE SEARCH : LAMBDA=.217E-05 ENERGY = -7.9755550 > 8 9.940E-02 2.339E-03 -7.975562 3.244E-05 25.11 > LINE SEARCH : LAMBDA=.407E-06 ENERGY = -7.9755533 > 9 9.941E-02 2.339E-03 -7.975555 7.374E-06 25.26 > LINE SEARCH : LAMBDA=.764E-07 ENERGY = -7.9755530 > 10 9.941E-02 2.339E-03 -7.975553 1.623E-06 25.10 > ................................................................. > ................................................................. > 997 9.941E-02 2.339E-03 -7.975552 -8.882E-16 25.23 > LINE SEARCH : LAMBDA=.525-157 ENERGY = -7.9755518 > 998 9.941E-02 2.339E-03 -7.975552 8.882E-16 25.21 > LINE SEARCH : LAMBDA=.262-157 ENERGY = -7.9755518 > 999 9.941E-02 2.339E-03 -7.975552 -8.882E-16 25.15 > LINE SEARCH : LAMBDA=.590-157 ENERGY = -7.9755518 > 1000 9.941E-02 2.339E-03 -7.975552 8.882E-16 25.17 > ================================================================ > = END OF GEOMETRY OPTIMIZATION = > ================================================================ > > The following is my first time input file: > > &CPMD > OPTIMIZE GEOMETRY > HESSIAN UNIT > BFGS > PCG MINIMIZE > CONVERGENCE > 1.0D-4 5.0D-4 > CENTER MOLECULE > MAXSTEP > 1000 > &END > > > &DFT > NEWCODE > FUNCTIONAL PBE > GC_CUTOFF > 0.2E-07 > &END > > &SYSTEM > ANGSTROM > pOSSION SOLVER TUCKERMAN > SYMMETRY > 0 > CELL > 13.0 1.0 1.0 0 0 0 > CUTOFF > 30.0 > STATES > 5 > CHARGE > 0.0 > TESR > 2 > &END > &ATOMS > *006-C-gpbe--bm.uspp NEWF BINARY > LMAX=P > 1 > -4.3985 1.5414 0.0000 > *001-H-gpbe--bm.uspp BINARY NEWF > LMAX=S > 4 > -3.3985 1.5414 0.0000 > -4.7323 2.4840 0.0000 > -4.7323 1.0701 0.8164 > -4.7323 1.0701 -0.8164 > &END > > Then I made some changes on my input file according to the suggestion from > others: > > Adding INITIALIZE WAVEFUNCTION RANDOM in the section of $CPMD..... $END! > Increasing GC-CUTOFF to 5.D-5. But problem still exists and the only > difference is that the gradient become a new constant! > > I also changed the Convergence standard to 1.D-3 and 1.D-3 to pass several > Geometry steps first.Then I restart the calculation with 1.D-5 and 5.D-5. > But the same Problems still met! In addition, bad convergence were also > observed when using another Vanderbilt potential(pw91 not PBE). All the > uspps inputfile are from inputfile > http://www.physics.rutgers.edu/~dhv/uspp/uspp-cur/Work/ > > When I use other pseudopotential in the PP_LIBRARY provide by www.cpmd.org, > such as BLYP. It is very fast to reach convergence. > > Could anyone help me solve this problem? Any comments and suggestions would > be highly appreciated! > > With regards, > A.J.Du > > > > _________________________________________________________________ > ???????? MSN Explorer: http://explorer.msn.com/lccn/ > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Fri Apr 4 14:51:19 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Fri, 4 Apr 2003 14:51:19 +0200 (MEST) Subject: [CPMD-list] Using SCALE with a triclinic crystal In-Reply-To: <3E9A0685@OrangeMail> References: <3E9A0685@OrangeMail> Message-ID: Hi have you checked that CPMD generates the correct cartesian coordinates from the scaled coordinates input? Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Thu, 3 Apr 2003, mkosmows wrote: > Dear Juerg: > > I am using POINT GROUP AUTO with DELTA=.001 > > When I input cartesian coordinates, I do not get the error warning. I only > get the error warning when I put in fractional coordinates and the SCALE > keyword. > > My literature structure gives coordinates to 4 places (.xxxx) and I use rpluto > to pack the cell and save the coordinates of the cell, which continue to have > 4 places. I then just cut and paste into the input file. > > I can send an input file if that would be helpful. > > Thank you, > > Mark Kosmowski > > >===== Original Message From Juerg Hutter ===== > >Hi > > > >you can use SCALE with the triclinic cell. > >The problem seems to be that you have specified > >a point group and the program couldn't verify that > >the input is compatible with this group. > >Have you specified the coordinates with enough > >accuracy? Are you sure that you have picked > >the correct point group, maybe you want to try also > >POINT GROUP > >AUTO > > > >Juerg > > > >---------------------------------------------------------- > >Juerg Hutter Phone : ++41 1 635 4491 > >Physical Chemistry Institute FAX : ++41 1 635 6838 > >University of Zurich E-mail: hutter at pci.unizh.ch > >Winterthurerstrasse 190 > >CH-8057 Zurich, Switzerland > >---------------------------------------------------------- > > > > > >On Wed, 2 Apr 2003, mkosmows wrote: > > > >> Dear CPMD community: > >> > >> I received the following message while doing a geometry > >> optimization: MULTTB| SUPERCELL ATOMS FORM NO BASIS FOR THIS > >> POINT GROUP. > >> > >> I think this is because I tried to invoke the SCALE keyword > >> while using a triclinic crystal lattice. Is there a way to > >> use fractional coordinates in crystals where alpha, beta and > >> gamma are not all 90 degrees? Or does one simply need to > >> enter in cartesian coordinates in these cases? > >> > >> Thank you, > >> > >> Mark Kosmowski > >> > >> Chemistry Department > >> Syracuse University > >> mkosmows at syr.edu > >> > >> _______________________________________________ > >> CPMD-list mailing list > >> CPMD-list at cpmd.org > >> http://www.cpmd.org/mailman/listinfo/cpmd-list > >> > > Chemistry Department > Syracuse University > mkosmows at syr.edu > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From audrius.alkauskas at unibas.ch Fri Apr 4 15:08:35 2003 From: audrius.alkauskas at unibas.ch (Audrius Alkauskas) Date: Fri, 04 Apr 2003 15:08:35 +0200 Subject: [CPMD-list] Hockney Message-ID: <001001c2faab$4ce653f0$51669883@audrius> Hello A question about structure of CPMD. Would it be difficult to implement by myslef Ewald summation just in 2D and doing Hockney stuff in perpendicular direction (slab calculation). Is it already implemented? Regards ================================================= Audrius Alkauskas, PhD student Condensed Matter Theory Group & NCCR for Nanoscale Science Institute of Physics, University of Basel, Switzerland http://monet.physik.unibas.ch/~audrius/ Tel.: +41-61-267-3708 ================================================= -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20030404/65dde23c/attachment.html From audrius.alkauskas at unibas.ch Fri Apr 4 15:11:03 2003 From: audrius.alkauskas at unibas.ch (Audrius Alkauskas) Date: Fri, 04 Apr 2003 15:11:03 +0200 Subject: [CPMD-list] Hockney no html Message-ID: <000901c2faab$a52a0020$51669883@audrius> I keep forgeting that no html is allowed Hello A question about structure of CPMD. Would it be difficult to implement by myslef Ewald summation just in 2D and doing Hockney stuff in perpendicular direction (slab calculation). Is it already implemented? Regards ================================================= Audrius Alkauskas, PhD student Condensed Matter Theory Group & NCCR for Nanoscale Science Institute of Physics, University of Basel, Switzerland http://monet.physik.unibas.ch/~audrius/ Tel.: +41-61-267-3708 ================================================= From cdy2000 at vip.sina.com Sat Apr 5 13:34:17 2003 From: cdy2000 at vip.sina.com (cdy2000 at vip.sina.com) Date: Sat, 05 Apr 2003 19:34:17 +0800 Subject: [CPMD-list] "ODIIS| Insufficient progress; reset!" Message-ID: <20030405113417.20281.qmail@vip.sina.com> Hello,all CPMDer! Thanks for Hutter's and HW Sheng's help. Pinilla Castellanos Carlos has asked a question about "ODIIS| Insufficient progress; reset!" being in output file, someone give him two suggestions: a. a higher cutoff; b. using the keyword ODIIS NO_RESET=50. I met the same question, but the two methods is no useful to me. I want to know why and how to solve the question in other methods. Thanks for any help. Best regards Sincerely Cao Dayong ______________________________________ =================================================================== From hutter at pci.unizh.ch Sun Apr 6 19:59:18 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Sun, 6 Apr 2003 19:59:18 +0200 (MEST) Subject: [CPMD-list] Ewald corrected In-Reply-To: <001101c2faa3$13c0f060$51669883@audrius> References: <001101c2faa3$13c0f060$51669883@audrius> Message-ID: Hi this is obviously a mistake in the paper. regards Juerg Hutter ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Fri, 4 Apr 2003, Audrius Alkauskas wrote: > Dear colleagues > > I am writing a small molecular mechanics program, and wanted to implement > Ewald summation. The numbers I got were not good, so I was looking for some > mistake. In the article of Hutter and Marx ( in "Modern Methods and > Algorithms of Quantum Chemistry") they say that Fourier transform of a > Gaussian charge distribution A \exp (-\frac{r^2}{a^2}) is B \exp > (-frac{1}{2} G^2 a^2) but according to my calculations it surely > must be B \exp (-frac{1}{4}G^2 a^2) (one-fourth instead of > one- secondth). Now my code is working properly. Is it some trick or is it > something I don't understand or is it just a mistake in the book? > > Thank you > > ================================================= > Audrius Alkauskas, PhD student > Condensed Matter Theory Group & NCCR for Nanoscale Science > Institute of Physics, University of Basel, Switzerland > http://monet.physik.unibas.ch/~audrius/ > Tel.: +41-61-267-3708 > ================================================= > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Sun Apr 6 20:00:24 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Sun, 6 Apr 2003 20:00:24 +0200 (MEST) Subject: [CPMD-list] Hockney In-Reply-To: <001001c2faab$4ce653f0$51669883@audrius> References: <001001c2faab$4ce653f0$51669883@audrius> Message-ID: Hi The 2-dimensional Hockney solver has been implemented, but never tested. I'm also not sure if the implementation is really 100% done. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Fri, 4 Apr 2003, Audrius Alkauskas wrote: > Hello > > A question about structure of CPMD. Would it be difficult to implement by myslef Ewald summation just in 2D and doing Hockney stuff in perpendicular direction (slab calculation). Is it already implemented? > > Regards > ================================================= > Audrius Alkauskas, PhD student > Condensed Matter Theory Group & NCCR for Nanoscale Science > Institute of Physics, University of Basel, Switzerland > http://monet.physik.unibas.ch/~audrius/ > Tel.: +41-61-267-3708 > ================================================= > From hutter at pci.unizh.ch Sun Apr 6 20:02:20 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Sun, 6 Apr 2003 20:02:20 +0200 (MEST) Subject: [CPMD-list] "ODIIS| Insufficient progress; reset!" In-Reply-To: <20030405113417.20281.qmail@vip.sina.com> References: <20030405113417.20281.qmail@vip.sina.com> Message-ID: Hi PCG MINIMIZE TIMESTEP 20 is usually the most stable optimizer. See also earlyer mails where I outlined some strategies to converge difficult systems. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Sat, 5 Apr 2003 cdy2000 at vip.sina.com wrote: > Hello,all CPMDer! > > Thanks for Hutter's and HW Sheng's help. > > Pinilla Castellanos Carlos has asked a question about "ODIIS| Insufficient progress; reset!" being in output file, someone give him two suggestions: a. a higher cutoff; b. using the keyword ODIIS NO_RESET=50. > > I met the same question, but the two methods is no useful to me. I want to know why and how to solve the question in other methods. > > Thanks for any help. > > Best regards > > Sincerely Cao Dayong > ______________________________________ > > =================================================================== > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From mkosmows at mailbox.syr.edu Mon Apr 7 04:23:02 2003 From: mkosmows at mailbox.syr.edu (mkosmows) Date: Sun, 6 Apr 2003 22:23:02 -0400 Subject: [CPMD-list] Using SCALE with a triclinic crystal Message-ID: <3E9A2A9F@OrangeMail> Dear Juerg: The coordinates generated with SCALE are in fact not correct. Specifically, some of the x coordinates are too big. Any idea as to why this is? To get both sets of coordinates, I enter the literature coordinates into rpluto, pack a unit cell, remove the excess molecules thusly generated, and then save the resulting set of coordinates as either fractional or cartesian. Thank you for your assistance, Mark Kosmowski >===== Original Message From Juerg Hutter ===== >Hi > >have you checked that CPMD generates the correct >cartesian coordinates from the scaled coordinates >input? > >Juerg > > >On Thu, 3 Apr 2003, mkosmows wrote: > >> Dear Juerg: >> >> I am using POINT GROUP AUTO with DELTA=.001 >> >> When I input cartesian coordinates, I do not get the error warning. I only >> get the error warning when I put in fractional coordinates and the SCALE >> keyword. >> >> My literature structure gives coordinates to 4 places (.xxxx) and I use rpluto >> to pack the cell and save the coordinates of the cell, which continue to have >> 4 places. I then just cut and paste into the input file. >> >> I can send an input file if that would be helpful. >> >> Thank you, >> >> Mark Kosmowski >> >> >===== Original Message From Juerg Hutter ===== >> >Hi >> > >> >you can use SCALE with the triclinic cell. >> >The problem seems to be that you have specified >> >a point group and the program couldn't verify that >> >the input is compatible with this group. >> >Have you specified the coordinates with enough >> >accuracy? Are you sure that you have picked >> >the correct point group, maybe you want to try also >> >POINT GROUP >> >AUTO >> > >> >Juerg >> > >> >On Wed, 2 Apr 2003, mkosmows wrote: >> > >> >> Dear CPMD community: >> >> >> >> I received the following message while doing a geometry >> >> optimization: MULTTB| SUPERCELL ATOMS FORM NO BASIS FOR THIS >> >> POINT GROUP. >> >> >> >> I think this is because I tried to invoke the SCALE keyword >> >> while using a triclinic crystal lattice. Is there a way to >> >> use fractional coordinates in crystals where alpha, beta and >> >> gamma are not all 90 degrees? Or does one simply need to >> >> enter in cartesian coordinates in these cases? >> >> >> >> Thank you, >> >> >> >> Mark Kosmowski From aijun_du at hotmail.com Mon Apr 7 09:37:40 2003 From: aijun_du at hotmail.com (Du Aijun) Date: Mon, 07 Apr 2003 15:37:40 +0800 Subject: [CPMD-list] Problem on abnormal stop! Message-ID: Dear all, I met a problem on abnormal stop. The wrong message is as following: PROGRAM STOPS IN SUBROUTINE STACK_DO_SCHED| CANNOT RECOVER [PROC= 1] p1_24537: p4_error: : 999 bm_list_31729: p4_error: lookup_slave_index_by_pid: %d not found: 31728 Could someone give me some explanation? Many thanks in advance! With regards, A.J.Du _________________________________________________________________ ???????????????????????????? MSN Messenger: http://messenger.msn.com/cn From aijun_du at hotmail.com Mon Apr 7 18:41:56 2003 From: aijun_du at hotmail.com (Du Aijun) Date: Tue, 08 Apr 2003 00:41:56 +0800 Subject: [CPMD-list] Geometry optimization! Message-ID: Dear all, I perform a geometry optimization of Si(001) slab with 4 layers(9 atoms per layer)using LBFGS. I set the orbital and geometry convergence 1.E-5 and 5.E-5, respectively. The wavefunction convergence is okay, but the GNMAX sometimes still becomes a little bigger when 21 geometry steps passed. Is it normal? Any tricks to improve the geometry convergence? Any comments will be highly appreciated! With regards, A.J.Du _________________________________________________________________ ?????????????????????????????? MSN Hotmail?? http://www.hotmail.com From ZRLSRB at ch.ibm.com Mon Apr 7 19:28:11 2003 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Mon, 7 Apr 2003 19:28:11 +0200 Subject: [CPMD-list] Geometry optimization! Message-ID: Dear Aijun Du, transitory energy increases are a normal behavior of the L-BFGS implementation in CPMD. In order to avoid the extra effort associated with a proper line search algorithm and the robustness and performance problems of a fixed trust radius, this optimizer tries to predict the optimum step length along the new search direction based on the quality of the previous step in terms of the Wolfe criteria. Sometimes, such a step can be too large, and the energy can increase. This is no problem since the optimizer rejects that step and tries a smaller displacement starting from the last good geometry. Even the wavefunction is restored. However, if the fraction of rejected steps is large, there is a problem. L-BFGS reacts quite sensitively to an inaccurate gradient which can be caused by poor convergence of the wavefunction, etc. In order to see what is going on, I would recommend using PRINT LSCAL ON which turns on the diagnostics of the linear scaling optimizers. You might also want to use CONVERGENCE ADAPT 0.02 to save unnecessary wavefunction optimization cycles for the early part of the optimization, and to use CONVERGENCE ENERGY 0.05 to enforce more consistent energy changes for the late part of the optimization (you can change these parameters, of course). Best regards, Salomon Billeter From sidney at dqf.ufpe.br Tue Apr 8 16:44:46 2003 From: sidney at dqf.ufpe.br (Sidney Ramos de Santana) Date: Tue, 08 Apr 2003 11:44:46 -0300 Subject: [CPMD-list] Some examples of CPMD input Message-ID: <3E92E05E.4040508@dqf.ufpe.br> Dear CPMD Users, Please, could someone send me CPMD input examples ? Best Regards, Sidney Ramos Garduate Program of Material Science DQF - CCE N - UFPE From hwsheng at jhu.edu Thu Apr 10 22:34:58 2003 From: hwsheng at jhu.edu (HW Sheng) Date: Thu, 10 Apr 2003 16:34:58 -0400 Subject: [CPMD-list] cpmd2cube bug References: <20030403092428.3114.qmail@vip.sina.com> Message-ID: <004701c2ffa0$a7c745a0$a567dc80@mrs.jhu.edu> Dear all. I report a bug when invoking cpmd2cube -inbox -dens DENSITY The function of -inbox is mean to put atoms into box according periodic boundary condition. And the box size was read from the density file dumped by CPMD. Note here, only the initial cell dimension (CELLDM) rather than the cell metric tensor HT is dumped into DENSITY. After runing NPT md simulations, the cell size is alterted, and this result is not recorded in DENSITY files. Consequently, the use of -inbox is erraneous. Corret me if I am mistaken, please. Thank you. Howard From hwsheng at jhu.edu Thu Apr 10 22:45:53 2003 From: hwsheng at jhu.edu (HW Sheng) Date: Thu, 10 Apr 2003 16:45:53 -0400 Subject: [CPMD-list] cpmd2cube bug Message-ID: <006001c2ffa2$2df34e20$a567dc80@mrs.jhu.edu> Dear all. I report a bug when invoking cpmd2cube -inbox -dens DENSITY The function of -inbox is meant to put atoms back into box according to periodic boundary condition. And the box size was read from the density file dumped by CPMD. Note here, only the initial cell dimension (CELLDM) rather than the cell metric tensor HT is dumped into DENSITY. After running NPT md simulations, the cell size is altered, and this result is NOT recorded in DENSITY files. Consequently, the use of -inbox is erroneous. Correct me if I am mistaken, please. Thank you. Howard -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20030410/1468fa13/attachment.html From weiz at mail.rochester.edu Sat Apr 12 00:07:19 2003 From: weiz at mail.rochester.edu (wei) Date: Fri, 11 Apr 2003 18:07:19 -0400 Subject: [CPMD-list] QM/MM simulation Message-ID: <200304111807.19387.weiz@mail.rochester.edu> Dear All: I want to use cpmd to do some QM/MM simulation. I do have GROMOS by hand. but I couldn't find any detailed instruction in cpmd manual about how to compile the cpmd package for doing QM/MM calculation, also, there is no instruction about how to do QM/MM using cpmd. can anybody give me some hint about how to do this? thank you very much!! All the Best Wei Zhuang From aijun_du at hotmail.com Sat Apr 12 14:09:27 2003 From: aijun_du at hotmail.com (Du Aijun) Date: Sat, 12 Apr 2003 20:09:27 +0800 Subject: [CPMD-list] Help on obtaining a buckled Si(001) surface? Message-ID: Dear all, Recently, I performed a geometry optimization from a clean si(001) unreconstruced surface to obtain a bulckled dimer surface. The convergence is very slow and it seems the geometry don't changed too much after 20 geometry steps. Here is my imput file. I hope someone can check it for me! Any comments and suggestions will be highly appreciated! &CPMD OPTIMIZE GEOMETRY HESSIAN UNIT LBFGS MEMORY BIG PCG MINIMIZE CONVERGENCE 1.D-5 5.D-5 MAXSTEP 500 STRUCTURE BONDS ANGLES &END &SYSTEM ANGSTROM POINT GROUP AUTO SYMMETRY 6 CELL 15.358868 1.0 1.3 0.0 0.0 0.0 CUTOFF 30.0 STATES 128 TESR 1 1 1 &END &ATOMS *014-Si-gpw-n-campos.uspp BINARY NEWF NLCC LMAX=D 64 -6.7205 -6.7205 5.4310 ... ... ... ... 2.8802 4.8004 9.5043 6.7205 4.8004 9.5043 CONSTRAINTS FIX ATOMS 16 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 END CONSTRAINTS &END &DFT NEWCODE FUNCTIONAL GGA GC-CUTOFF 1.D-5 &END _________________________________________________________________ ???????? MSN Explorer: http://explorer.msn.com/lccn/ From yoo at phase6b.unl.edu Sat Apr 12 17:08:08 2003 From: yoo at phase6b.unl.edu (Soohaeng Yoo) Date: Sat, 12 Apr 2003 10:08:08 -0500 (CDT) Subject: [CPMD-list] QM/MM simulation In-Reply-To: <200304111807.19387.weiz@mail.rochester.edu> Message-ID: Dear Wei I recommand that you modify the GROMOS to use CPMD. The best example code is available from http://www.science.uva.nl/~bolhuis/tps. You can see how they use CPMD with Path Sampling Method. After you understand it, you can make how you use CPMD with GROMOS. Simple example code which should be addded in GROMOS to use CPMD === call write_cpmd_input(natoms, xq, yq, zq) call system ('cpmd.x exam.inp > exam.out') call read_cpmd_output(natoms, xq, yq, zq, vxq, vyq, vzq, potel) ===== Because I don't know what you want to do in detail, I will provide my code simply. Here 'call write_cpmd_input' makes the input file for CPMD program. After that, 'call system (....)' makes CPMD run using the input file and waits finishing of the job of CPMD. After finishing of CPMD, 'call read_cpmd_output' read the output file which cotains information of what you want to get. GROMOS will do the other parts for you. I hope that it help you. From Soohaeg Yoo. On Fri, 11 Apr 2003, wei wrote: > Dear All: > > I want to use cpmd to do some QM/MM simulation. I do have GROMOS by hand. but I couldn't find any detailed instruction in cpmd manual about how to compile the > cpmd package for doing QM/MM calculation, also, there is no instruction about how to do QM/MM using cpmd. can anybody give me some hint about how to do this? > thank you very much!! > > All the Best > > Wei Zhuang > > > From cdy2000 at vip.sina.com Sun Apr 13 10:10:21 2003 From: cdy2000 at vip.sina.com (cdy2000 at vip.sina.com) Date: Sun, 13 Apr 2003 16:10:21 +0800 Subject: [CPMD-list] two parts in h_ps.adat Message-ID: <20030413081041.23621.qmail@vip.sina.com> Thanks for Prof Hutter's help. Another question about uspp pseudopotential. When I make the PP files in 001-H-ca--bm directory, I find there are two parts in h_ps.adat: 0 2 1 1 3 ifae,ifpsp,ifprt,ifplw,ilogd (5i5) 1.2 -2.4 1.6 80 rlogd,emin,emax,nnt (3f10.5,i5) 1.0d-11 1.0d-09 0.5 0 thresh,tol,damp,maxit (2e10.1,f10.5,i5) hydrogen title (a20) 0 1 1 ncores,nvales,nang (3i5) 10.0 20.0 40.0 10.0 besrmax,besemin,besemax,besde (4f10.5) 3 0 0.8 keyps,ifpcor,rinner (2i5,f10.5) 1 0.8 nbeta,rcloc (i5,f10.5) 0.8 0.0 0.0 rc (3f10.5) 0 1 0.0 2 lll,keyee,eeread,iptype (2i5,f10.5,i5) 6 10.0 npf,ptryc (i5,f10.5) 1 0 0.0 1 lloc,keyee,eloc,iploctype (2i5,f10.5,i5) 2 8 10.0 ifqopt,nqf,qtryc (2i5,f10.5) Dominik King-Smith: 3 0 0.65 keyps,ifpcor,rinner (2i5,f10.5) 1 0.7 nbeta,rcloc (i5,f10.5) 0.8 0.0 0.0 rc (3f10.5) 0 1 0.0 2 lll,keyee,eeread,iptype (2i5,f10.5,i5) 8 10.0 npf,ptryc (i5,f10.5) 1 0 0.0 1 lloc,keyee,eloc,iploctype (2i5,f10.5,i5) 2 8 10.0 ifqopt,nqf,qtryc (2i5,f10.5) I want to know what's meaning in this file? If I want transform it form LDA to GGA, I should change the value of ifqopt from 2 to 3, But there are 2 values of ifqopt in the file, must I change all of them from 2 to 3?? Thanks for any help Cao Dayong ______________________________________ =================================================================== From hutter at pci.unizh.ch Sun Apr 13 16:13:45 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Sun, 13 Apr 2003 16:13:45 +0200 (MEST) Subject: [CPMD-list] QM/MM simulation In-Reply-To: <200304111807.19387.weiz@mail.rochester.edu> References: <200304111807.19387.weiz@mail.rochester.edu> Message-ID: Hi to use the full QM/MM implementation in CPMD you need additional code and a special version of Gromos. You can get this code from Prof. U. Rothlisberger EPF Lausanne upon request (provided you have a valid license of Gromos). They also have a short manual on how to use the codes. However, a good knowledge on how to use CPMD and Gromos on their own is needed in order to successfully use the QM/MM method. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Fri, 11 Apr 2003, wei wrote: > Dear All: > > I want to use cpmd to do some QM/MM simulation. I do have GROMOS by hand. but I couldn't find any detailed instruction in cpmd manual about how to compile the > cpmd package for doing QM/MM calculation, also, there is no instruction about how to do QM/MM using cpmd. can anybody give me some hint about how to do this? > thank you very much!! > > All the Best > > Wei Zhuang > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Sun Apr 13 16:18:45 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Sun, 13 Apr 2003 16:18:45 +0200 (MEST) Subject: [CPMD-list] Help on obtaining a buckled Si(001) surface? In-Reply-To: References: Message-ID: Hi a few observations regarding your input: - the optimized surface (most likely) will have lower symmetry than you initial clean surface. By using POINT GROUP AUTO you fix the symmetry. - Silicon is one of the few elements where normconserving PP can be used with cutoffs as low as 12 Ry. There is no need to use USPPs and a cutoff of 30 Ry. - NLCC is not needed either. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Sat, 12 Apr 2003, Du Aijun wrote: > Dear all, > > Recently, I performed a geometry optimization from a clean si(001) > unreconstruced surface to obtain a bulckled dimer surface. The convergence > is very slow and it seems the geometry don't changed too much after 20 > geometry steps. Here is my imput file. I hope someone can check it for me! > Any comments and suggestions will be highly appreciated! > > &CPMD > OPTIMIZE GEOMETRY > HESSIAN UNIT > LBFGS > MEMORY BIG > PCG MINIMIZE > CONVERGENCE > 1.D-5 5.D-5 > MAXSTEP > 500 > STRUCTURE BONDS ANGLES > &END > > &SYSTEM > ANGSTROM > POINT GROUP > AUTO > SYMMETRY > 6 > CELL > 15.358868 1.0 1.3 0.0 0.0 0.0 > CUTOFF > 30.0 > STATES > 128 > TESR > 1 1 1 > &END > > &ATOMS > *014-Si-gpw-n-campos.uspp BINARY NEWF NLCC > LMAX=D > 64 > -6.7205 -6.7205 5.4310 > ... > ... > ... > ... > 2.8802 4.8004 9.5043 > 6.7205 4.8004 9.5043 > CONSTRAINTS > FIX ATOMS > 16 > 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 > END CONSTRAINTS > &END > &DFT > NEWCODE > FUNCTIONAL GGA > GC-CUTOFF > 1.D-5 > &END > > > > > > > > > > _________________________________________________________________ > ???????? MSN Explorer: http://explorer.msn.com/lccn/ > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From tdeutsch at cea.fr Mon Apr 14 13:49:17 2003 From: tdeutsch at cea.fr (Thierry Deutsch) Date: Mon, 14 Apr 2003 13:49:17 +0200 Subject: [CPMD-list] Help on obtaining a buckled Si(001) surface? Message-ID: <200304141349.17298.tdeutsch@cea.fr> Hi, Some years ago I used CPMD to have the difference in energies for Si(001) surfaces : - c4x2 - p2x2 - p1x1 I have used k point and Goedecker pseudopotentials but other norm-consrving works well. I send you the input file in attached file. Bye, Thierry Deutsch -------------- next part -------------- &INFO Fichier ? d3 ? : Six4-001x4-rec.d3 Surfaces (001) reconstruites 2?2 (presque 2?1) de silicium &END INFO &CPMD OPTIMIZE GEOMETRY TIMESTEP 200 FREE ENERGY FUNCTIONAL LANCZOS PARAMETER N=5 50 8 0 1.D-10 0.01 1.D-12 0.005 1.D-14 0.001 1.D-16 0.0007 1.D-18 CONVERGENCE 5.D-4 1.D-3 BROYDEN MIXING W02BROY=0.01 IBRESET=3 BROYMIX=0.1 NFRBROY=3 MAXCPUTIME 200000 STORE 1000 SC=2 &END CPMD &SYSTEM ANGSTROM POINT GROUP AUTO SYMMETRY ORTHORHOMBIC CELL ABSOLUTE 7.6791796436859 7.6791796436859 31.720000000000 0. 0. 0. | cosinus des angles SPHERICAL CUTOFF 15.0 KPOINTS MONKHORST-PACK MESH 2 2 1 TESR 4 STATES 150 &END SYSTEM &ATOMS *GOEDECKER/Si_SG_Pade LMAX=P 64 | atomes Si 6.06928218822517 0.95989745546074 1.06875000000000 |n? 1 6.06928218822517 4.79948727730369 0.80875000000000 |n? 2 3.52969236638221 0.95989745546074 0.54875000000000 |n? 3 3.52969236638221 4.79948727730369 0.28875000000000 |n? 4 6.71928218822517 0.95989745546074 6.10875000000000 |n? 5 6.71928218822517 4.79948727730369 6.10875000000000 |n? 6 2.87969236638221 0.95989745546074 6.10875000000000 |n? 7 2.87969236638221 4.79948727730369 6.10875000000000 |n? 8 6.71928218822517 0.95989745546074 11.53875000000000 |n? 9 6.71928218822517 4.79948727730369 11.53875000000000 |n? 10 2.87969236638221 0.95989745546074 11.53875000000000 |n? 11 2.87969236638221 4.79948727730369 11.53875000000000 |n? 12 6.71928218822517 0.95989745546074 16.96875000000000 |n? 13 6.71928218822517 4.79948727730369 16.96875000000000 |n? 14 2.87969236638221 0.95989745546074 16.96875000000000 |n? 15 2.87969236638221 4.79948727730369 16.96875000000000 |n? 16 4.79948727730369 2.87969236638221 3.39375000000000 |n? 17 4.79948727730369 6.71928218822517 3.39375000000000 |n? 18 0.95989745546074 2.87969236638221 3.39375000000000 |n? 19 0.95989745546074 6.71928218822517 3.39375000000000 |n? 20 4.79948727730369 2.87969236638221 8.82375000000000 |n? 21 4.79948727730369 6.71928218822517 8.82375000000000 |n? 22 0.95989745546074 2.87969236638221 8.82375000000000 |n? 23 0.95989745546074 6.71928218822517 8.82375000000000 |n? 24 4.79948727730369 2.87969236638221 14.25375000000000 |n? 25 4.79948727730369 6.71928218822517 14.25375000000000 |n? 26 0.95989745546074 2.87969236638221 14.25375000000000 |n? 27 0.95989745546074 6.71928218822517 14.25375000000000 |n? 28 4.79948727730369 2.87969236638221 19.68375000000000 |n? 29 4.79948727730369 6.71928218822517 19.68375000000000 |n? 30 0.95989745546074 2.87969236638221 19.68375000000000 |n? 31 0.95989745546074 6.71928218822517 19.68375000000000 |n? 32 6.71928218822517 2.87969236638221 2.03625000000000 |n? 33 6.71928218822517 6.71928218822517 2.03625000000000 |n? 34 2.87969236638221 2.87969236638221 2.03625000000000 |n? 35 2.87969236638221 6.71928218822517 2.03625000000000 |n? 36 6.71928218822517 2.87969236638221 7.46625000000000 |n? 37 6.71928218822517 6.71928218822517 7.46625000000000 |n? 38 2.87969236638221 2.87969236638221 7.46625000000000 |n? 39 2.87969236638221 6.71928218822517 7.46625000000000 |n? 40 6.71928218822517 2.87969236638221 12.89625000000000 |n? 41 6.71928218822517 6.71928218822517 12.89625000000000 |n? 42 2.87969236638221 2.87969236638221 12.89625000000000 |n? 43 2.87969236638221 6.71928218822517 12.89625000000000 |n? 44 6.71928218822517 2.87969236638221 18.32625000000000 |n? 45 6.71928218822517 6.71928218822517 18.32625000000000 |n? 46 2.87969236638221 2.87969236638221 18.32625000000000 |n? 47 2.87969236638221 6.71928218822517 18.32625000000000 |n? 48 4.79948727730369 0.95989745546074 4.75125000000000 |n? 49 4.79948727730369 4.79948727730369 4.75125000000000 |n? 50 0.95989745546074 0.95989745546074 4.75125000000000 |n? 51 0.95989745546074 4.79948727730369 4.75125000000000 |n? 52 4.79948727730369 0.95989745546074 10.18125000000000 |n? 53 4.79948727730369 4.79948727730369 10.18125000000000 |n? 54 0.95989745546074 0.95989745546074 10.18125000000000 |n? 55 0.95989745546074 4.79948727730369 10.18125000000000 |n? 56 4.79948727730369 0.95989745546074 15.61125000000000 |n? 57 4.79948727730369 4.79948727730369 15.61125000000000 |n? 58 0.95989745546074 0.95989745546074 15.61125000000000 |n? 59 0.95989745546074 4.79948727730369 15.61125000000000 |n? 60 5.44948727730369 0.95989745546074 20.91125000000000 |n? 61 5.44948727730369 4.79948727730369 20.65125000000000 |n? 62 0.30989745546074 0.95989745546074 21.43125000000000 |n? 63 0.30989745546074 4.79948727730369 21.17125000000000 |n? 64 &END ATOMS From proffess at mail.ru Tue Apr 15 17:47:06 2003 From: proffess at mail.ru (Sergey) Date: Tue, 15 Apr 2003 19:47:06 +0400 Subject: [CPMD-list] Memory Message-ID: Dear CPMD users, I ran my example (120 atoms of carbon in unit cell). I got the message: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > CARBON LDA-PSEUDOPOTENTIAL (GOEDECKER TYPE) > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> **************************************************************** * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * * C 12.0112 1.2000 NO GOEDECKER S NONLOCAL * * P LOCAL * **************************************************************** PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES 0 220504 1763614 16 21089 84373 60 1 1 220506 1763741 16 21088 84374 60 1 2 220510 1763763 16 21088 84374 60 1 3 220512 1763868 16 21088 84372 60 1 G=0 COMPONENT ON PROCESSOR : 0 PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA *** LOADPA| PROGSIZE DATA= 83.38 MByte / STACK= 0.03 MByte *** RGGEN| PROGSIZE DATA= 122.88 MByte / STACK= 0.03 MByte ************************** SUPERCELL *************************** SYMMETRY: ORTHORHOMBIC POINT GROUP : [ORTHORHOMBIC] m (c1h) LATTICE CONSTANT(a.u.): 16.64849 CELL DIMENSION: 16.6485 8.6740 12.6010 0.0000 0.0000 0.0000 VOLUME(OMEGA IN BOHR^3): 504369.32080 LATTICE VECTOR A1(BOHR): 16.6485 0.0000 0.0000 LATTICE VECTOR A2(BOHR): 0.0000 144.4090 0.0000 LATTICE VECTOR A3(BOHR): 0.0000 0.0000 209.7876 RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0601 0.0000 0.0000 RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0069 0.0000 RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0048 REAL SPACE MESH: 64 576 800 WAVEFUNCTION CUTOFF(RYDBERG): 35.00000 DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 140.00000 NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 882032 NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 7054986 NUMBER OF PLANE WAVES FOR BROYDEN MIXING: 1763614 **************************************************************** *** RINFORCE| PROGSIZE DATA= 165.00 MByte / STACK= 0.03 MByte *** FFTPRP| PROGSIZE DATA= 409.75 MByte / STACK= 0.03 MByte GENERATE ATOMIC BASIS SET C SLATER ORBITALS 2S ALPHA= 1.6083 OCCUPATION= 2.00 2P ALPHA= 1.5679 OCCUPATION= 2.00 INITIALIZATION TIME: 353.36 SECONDS **************************************************************** PROCESSOR 0 ALLOCATION OF 105841920 WORDS OF MEMORY FAILED **************************************************************** *** MEMORY| PROGSIZE DATA= 437.94 MByte / STACK= 0.03 MByte ================================================================ BIG MEMORY ALLOCATIONS C2 105841928 C0 105841928 YF 15714018 XF 15714018 GK 5290842 SCG 3527228 INYH 3174745 HG 2116496 HO 1763868 HX 1763868 ---------------------------------------------------------------- [PEAK NUMBER 60] PEAK MEMORY 268654631 = 2149.2 MBytes ================================================================ PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (PME) [PROC= 0] **************************************************************** PROCESSOR 2 ALLOCATION OF 105844800 WORDS OF MEMORY FAILED **************************************************************** *** MEMORY| PROGSIZE DATA= 438.00 MByte / STACK= 0.02 MByte ================================================================ BIG MEMORY ALLOCATIONS C2 105844808 C0 105844808 YF 15714018 XF 15714018 GK 5291289 SCG 3527526 INYH 3174745 HG 2116496 HO 1763868 HX 1763868 ---------------------------------------------------------------- [PEAK NUMBER 62] PEAK MEMORY 268671913 = 2149.4 MBytes ================================================================ PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (PME) [PROC= 2] **************************************************************** PROCESSOR 3 ALLOCATION OF 52951680 WORDS OF MEMORY FAILED **************************************************************** *** MEMORY| PROGSIZE DATA= 438.38 MByte / STACK= 0.02 MByte ================================================================ BIG MEMORY ALLOCATIONS C2 105845768 C0 105845768 PME 105845760 PSI 15714018 YF 15714018 XF 15714018 RHOE 7857009 GK 5291604 SCG 3527736 INYH 3174745 ---------------------------------------------------------------- [PEAK NUMBER 69] PEAK MEMORY 398351620 = 3186.8 MBytes ================================================================ PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (SCR) [PROC= 3] mpid: MPI Application exited before MPI_Finalize() with status 231 mpirun exits with status: 231/users/sergey/CPMD-3.7.1/work/c120 5 % I have 4 processors and 16GB RAM. Is it not enough? Thanks. Sergey From Ari.P.Seitsonen at iki.fi Tue Apr 15 18:32:01 2003 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Tue, 15 Apr 2003 18:32:01 +0200 Subject: [CPMD-list] Memory In-Reply-To: (proffess@mail.ru) References: Message-ID: <200304151632.h3FGW1G14767@magadino.cscs.ch> Dear Sergey, If you look at the generated lattice vectors A1,A2,A3 you'll see that they are HUGE; the input for the keyword "CELL" in the orthorhombic case are a b/a c/a 0 0 0 Or you can give the absolute lattice vectors ("CELL ABSOLUTE"), please check up the exact syntax in the manual. BTW as a hint, you can see in 'latgen.F' how the lattice vectors are generated. Greetings from the sunny & warm Zurich!, apsi > From: "Sergey" > Reply-To: "Sergey" > Date: Tue, 15 Apr 2003 19:47:06 +0400 > > Dear CPMD users, > > I ran my example (120 atoms of carbon in unit cell). I got the message: > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > > CARBON LDA-PSEUDOPOTENTIAL (GOEDECKER TYPE) > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > > **************************************************************** > * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * > * C 12.0112 1.2000 NO GOEDECKER S NONLOCAL * > * P LOCAL * > **************************************************************** > > > PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA > NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES > 0 220504 1763614 16 21089 84373 60 1 > 1 220506 1763741 16 21088 84374 60 1 > 2 220510 1763763 16 21088 84374 60 1 > 3 220512 1763868 16 21088 84372 60 1 > G=0 COMPONENT ON PROCESSOR : 0 > PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA > > *** LOADPA| PROGSIZE DATA= 83.38 MByte / STACK= 0.03 MByte > *** RGGEN| PROGSIZE DATA= 122.88 MByte / STACK= 0.03 MByte > > ************************** SUPERCELL *************************** > SYMMETRY: ORTHORHOMBIC > POINT GROUP : [ORTHORHOMBIC] m (c1h) > LATTICE CONSTANT(a.u.): 16.64849 > CELL DIMENSION: 16.6485 8.6740 12.6010 0.0000 0.0000 0.0000 > VOLUME(OMEGA IN BOHR^3): 504369.32080 > LATTICE VECTOR A1(BOHR): 16.6485 0.0000 0.0000 > LATTICE VECTOR A2(BOHR): 0.0000 144.4090 0.0000 > LATTICE VECTOR A3(BOHR): 0.0000 0.0000 209.7876 > RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0601 0.0000 0.0000 > RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0069 0.0000 > RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0048 > REAL SPACE MESH: 64 576 800 > WAVEFUNCTION CUTOFF(RYDBERG): 35.00000 > DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 140.00000 > NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 882032 > NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 7054986 > NUMBER OF PLANE WAVES FOR BROYDEN MIXING: 1763614 > **************************************************************** > > *** RINFORCE| PROGSIZE DATA= 165.00 MByte / STACK= 0.03 MByte > *** FFTPRP| PROGSIZE DATA= 409.75 MByte / STACK= 0.03 MByte > > GENERATE ATOMIC BASIS SET > C SLATER ORBITALS > 2S ALPHA= 1.6083 OCCUPATION= 2.00 > 2P ALPHA= 1.5679 OCCUPATION= 2.00 > > > INITIALIZATION TIME: 353.36 SECONDS > > > **************************************************************** > PROCESSOR 0 ALLOCATION OF 105841920 WORDS OF MEMORY FAILED > **************************************************************** > > *** MEMORY| PROGSIZE DATA= 437.94 MByte / STACK= 0.03 MByte > > ================================================================ > BIG MEMORY ALLOCATIONS > C2 105841928 C0 105841928 > YF 15714018 XF 15714018 > GK 5290842 SCG 3527228 > INYH 3174745 HG 2116496 > HO 1763868 HX 1763868 > ---------------------------------------------------------------- > [PEAK NUMBER 60] PEAK MEMORY 268654631 = 2149.2 MBytes > ================================================================ > > > PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (PME) [PROC= 0] > > **************************************************************** > PROCESSOR 2 ALLOCATION OF 105844800 WORDS OF MEMORY FAILED > **************************************************************** > > *** MEMORY| PROGSIZE DATA= 438.00 MByte / STACK= 0.02 MByte > > ================================================================ > BIG MEMORY ALLOCATIONS > C2 105844808 C0 105844808 > YF 15714018 XF 15714018 > GK 5291289 SCG 3527526 > INYH 3174745 HG 2116496 > HO 1763868 HX 1763868 > ---------------------------------------------------------------- > [PEAK NUMBER 62] PEAK MEMORY 268671913 = 2149.4 MBytes > ================================================================ > > > PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (PME) [PROC= 2] > > **************************************************************** > PROCESSOR 3 ALLOCATION OF 52951680 WORDS OF MEMORY FAILED > **************************************************************** > > *** MEMORY| PROGSIZE DATA= 438.38 MByte / STACK= 0.02 MByte > > ================================================================ > BIG MEMORY ALLOCATIONS > C2 105845768 C0 105845768 > PME 105845760 PSI 15714018 > YF 15714018 XF 15714018 > RHOE 7857009 GK 5291604 > SCG 3527736 INYH 3174745 > ---------------------------------------------------------------- > [PEAK NUMBER 69] PEAK MEMORY 398351620 = 3186.8 MBytes > ================================================================ > > > PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (SCR) [PROC= 3] > mpid: MPI Application exited before MPI_Finalize() with status 231 > mpirun exits with status: 231/users/sergey/CPMD-3.7.1/work/c120 5 % > > I have 4 processors and 16GB RAM. Is it not enough? > > Thanks. > Sergey > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From proffess at mail.ru Tue Apr 15 19:19:46 2003 From: proffess at mail.ru (Sergey) Date: Tue, 15 Apr 2003 21:19:46 +0400 Subject: [CPMD-list] FAILED TO CONVERGE WHEN DIAGONALIZING A Message-ID: Dear Apsi and another users, I changed the lattice parameters you wrote. But I got the next error: **************************************************************** * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * * C 12.0112 1.2000 NO GOEDECKER S NONLOCAL * * P LOCAL * **************************************************************** *** RGGEN| PROGSIZE DATA= 7.50 MByte / STACK= 0.02 MByte ************************** SUPERCELL *************************** SYMMETRY: TRICLINIC POINT GROUP : [ORTHORHOMBIC] m (c1h) REFERENCE LATTICE CONSTANT(a.u.): 16.64849 REFERENCE CELL DIMENSION: 16.648 0.985 1.430 0.000 0.000 0.000 REFERENCE VOLUME(OMEGA0 IN BOHR^3): 6499.7477 INITIAL CELL DIMENSION: 16.648 0.985 1.430 0.000 0.000 0.000 INITIAL VOLUME(OMEGA IN BOHR^3): 6499.7477 REFERENCE STRESS TENSOR(KBAR): 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 LATTICE VECTOR A1(BOHR): 16.6485 0.0000 0.0000 LATTICE VECTOR A2(BOHR): 0.0000 16.3988 0.0000 LATTICE VECTOR A3(BOHR): 0.0000 0.0000 23.8073 RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0601 0.0000 0.0000 RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0610 0.0000 RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0420 REAL SPACE MESH: 64 64 90 WAVEFUNCTION CUTOFF(RYDBERG): 35.00000 DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 140.00000 NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 11393 NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 90900 NUMBER OF PLANE WAVES FOR BROYDEN MIXING: 90900 **************************************************************** *** RINFORCE| PROGSIZE DATA= 10.31 MByte / STACK= 0.02 MByte *** FFTPRP| PROGSIZE DATA= 22.06 MByte / STACK= 0.02 MByte GENERATE ATOMIC BASIS SET C SLATER ORBITALS 2S ALPHA= 1.6083 OCCUPATION= 2.00 2P ALPHA= 1.5679 OCCUPATION= 2.00 INITIALIZATION TIME: 1.53 SECONDS *** GMOPTS| PROGSIZE DATA= 24.50 MByte / STACK= 0.02 MByte *** PHFAC| PROGSIZE DATA= 25.81 MByte / STACK= 0.02 MByte *** ATOMWF| PROGSIZE DATA= 47.63 MByte / STACK= 0.02 MByte ATRHO| CHARGE(R-SPACE): 480.000000 (G-SPACE): 480.000000 DSYGVX| INFO= 479 DSYGVX| FAILED TO CONVERGE WHEN DIAGONALIZING A STOPGM! STACK OF MAIN CALLS: STOPGM! CALL ATOMWF PROGRAM STOPS IN SUBROUTINE DSYGVX| FAILED TO DIAGONALIZE STOP 999 What is problem? Thanks. Sergey From proffess at mail.ru Tue Apr 15 19:19:46 2003 From: proffess at mail.ru (Sergey) Date: Tue, 15 Apr 2003 21:19:46 +0400 Subject: [CPMD-list] FAILED TO CONVERGE WHEN DIAGONALIZING A Message-ID: <200304151729.TAA09214@internet-fence.zurich.ihost.com> Dear Apsi and another users, I changed the lattice parameters you wrote. But I got the next error: **************************************************************** * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * * C 12.0112 1.2000 NO GOEDECKER S NONLOCAL * * P LOCAL * **************************************************************** *** RGGEN| PROGSIZE DATA= 7.50 MByte / STACK= 0.02 MByte ************************** SUPERCELL *************************** SYMMETRY: TRICLINIC POINT GROUP : [ORTHORHOMBIC] m (c1h) REFERENCE LATTICE CONSTANT(a.u.): 16.64849 REFERENCE CELL DIMENSION: 16.648 0.985 1.430 0.000 0.000 0.000 REFERENCE VOLUME(OMEGA0 IN BOHR^3): 6499.7477 INITIAL CELL DIMENSION: 16.648 0.985 1.430 0.000 0.000 0.000 INITIAL VOLUME(OMEGA IN BOHR^3): 6499.7477 REFERENCE STRESS TENSOR(KBAR): 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 LATTICE VECTOR A1(BOHR): 16.6485 0.0000 0.0000 LATTICE VECTOR A2(BOHR): 0.0000 16.3988 0.0000 LATTICE VECTOR A3(BOHR): 0.0000 0.0000 23.8073 RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0601 0.0000 0.0000 RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0610 0.0000 RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0420 REAL SPACE MESH: 64 64 90 WAVEFUNCTION CUTOFF(RYDBERG): 35.00000 DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 140.00000 NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 11393 NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 90900 NUMBER OF PLANE WAVES FOR BROYDEN MIXING: 90900 **************************************************************** *** RINFORCE| PROGSIZE DATA= 10.31 MByte / STACK= 0.02 MByte *** FFTPRP| PROGSIZE DATA= 22.06 MByte / STACK= 0.02 MByte GENERATE ATOMIC BASIS SET C SLATER ORBITALS 2S ALPHA= 1.6083 OCCUPATION= 2.00 2P ALPHA= 1.5679 OCCUPATION= 2.00 INITIALIZATION TIME: 1.53 SECONDS *** GMOPTS| PROGSIZE DATA= 24.50 MByte / STACK= 0.02 MByte *** PHFAC| PROGSIZE DATA= 25.81 MByte / STACK= 0.02 MByte *** ATOMWF| PROGSIZE DATA= 47.63 MByte / STACK= 0.02 MByte ATRHO| CHARGE(R-SPACE): 480.000000 (G-SPACE): 480.000000 DSYGVX| INFO= 479 DSYGVX| FAILED TO CONVERGE WHEN DIAGONALIZING A STOPGM! STACK OF MAIN CALLS: STOPGM! CALL ATOMWF PROGRAM STOPS IN SUBROUTINE DSYGVX| FAILED TO DIAGONALIZE STOP 999 What is problem? Thanks. Sergey From Ari.P.Seitsonen at iki.fi Tue Apr 15 19:56:52 2003 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Tue, 15 Apr 2003 19:56:52 +0200 Subject: [CPMD-list] FAILED TO CONVERGE WHEN DIAGONALIZING A In-Reply-To: (proffess@mail.ru) References: Message-ID: <200304151756.h3FHuq215202@magadino.cscs.ch> Dear Sergey, I just guess, due to the limited amount of information available: Did you check that the coordinates of the atoms generated are reasonable? Greetings, apsi PS You try to optimised the lattice constant, right? > I changed the lattice parameters you wrote. But I got the next error: > > > > **************************************************************** > * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * > * C 12.0112 1.2000 NO GOEDECKER S NONLOCAL * > * P LOCAL * > **************************************************************** > > *** RGGEN| PROGSIZE DATA= 7.50 MByte / STACK= 0.02 MByte > > ************************** SUPERCELL *************************** > SYMMETRY: TRICLINIC > POINT GROUP : [ORTHORHOMBIC] m (c1h) > REFERENCE LATTICE CONSTANT(a.u.): 16.64849 > REFERENCE CELL DIMENSION: 16.648 0.985 1.430 0.000 0.000 0.000 > REFERENCE VOLUME(OMEGA0 IN BOHR^3): 6499.7477 > INITIAL CELL DIMENSION: 16.648 0.985 1.430 0.000 0.000 0.000 > INITIAL VOLUME(OMEGA IN BOHR^3): 6499.7477 > REFERENCE STRESS TENSOR(KBAR): 0.00 0.00 0.00 > 0.00 0.00 0.00 > 0.00 0.00 0.00 > LATTICE VECTOR A1(BOHR): 16.6485 0.0000 0.0000 > LATTICE VECTOR A2(BOHR): 0.0000 16.3988 0.0000 > LATTICE VECTOR A3(BOHR): 0.0000 0.0000 23.8073 > RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0601 0.0000 0.0000 > RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0610 0.0000 > RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0420 > REAL SPACE MESH: 64 64 90 > WAVEFUNCTION CUTOFF(RYDBERG): 35.00000 > DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 140.00000 > NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 11393 > NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 90900 > NUMBER OF PLANE WAVES FOR BROYDEN MIXING: 90900 > **************************************************************** > > *** RINFORCE| PROGSIZE DATA= 10.31 MByte / STACK= 0.02 MByte > *** FFTPRP| PROGSIZE DATA= 22.06 MByte / STACK= 0.02 MByte > > GENERATE ATOMIC BASIS SET > C SLATER ORBITALS > 2S ALPHA= 1.6083 OCCUPATION= 2.00 > 2P ALPHA= 1.5679 OCCUPATION= 2.00 > > > INITIALIZATION TIME: 1.53 SECONDS > > *** GMOPTS| PROGSIZE DATA= 24.50 MByte / STACK= 0.02 MByte > *** PHFAC| PROGSIZE DATA= 25.81 MByte / STACK= 0.02 MByte > *** ATOMWF| PROGSIZE DATA= 47.63 MByte / STACK= 0.02 MByte > ATRHO| CHARGE(R-SPACE): 480.000000 (G-SPACE): 480.000000 > > DSYGVX| INFO= 479 > DSYGVX| FAILED TO CONVERGE WHEN DIAGONALIZING A > STOPGM! STACK OF MAIN CALLS: > STOPGM! CALL ATOMWF > > > PROGRAM STOPS IN SUBROUTINE DSYGVX| FAILED TO DIAGONALIZE > STOP 999 > > What is problem? > > Thanks. > Sergey > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From ketajone at yahoo.com Fri Apr 18 12:41:30 2003 From: ketajone at yahoo.com (Keta Jones) Date: Fri, 18 Apr 2003 03:41:30 -0700 (PDT) Subject: [CPMD-list] System co-ordinates In-Reply-To: <200304151756.h3FHuq215202@magadino.cscs.ch> Message-ID: <20030418104130.31308.qmail@web13103.mail.yahoo.com> Dear All, I want to study some water molecules i.e. 30 water molecules, but for writing an input file for CPMD simulation, one needs the coordinates of 30 water molecules.I will appreciate if someone kindly help me how to get the coordinates.If classical MD is the solution,please tell me the alternate methods as I have no classical code for this.I am new to this area. Thanks in advance, Keta __________________________________________________ Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo http://search.yahoo.com From mkosmows at mailbox.syr.edu Fri Apr 18 16:28:17 2003 From: mkosmows at mailbox.syr.edu (mkosmows) Date: Fri, 18 Apr 2003 10:28:17 -0400 Subject: [CPMD-list] What effect do the assumed Hydrogen Bonds play? Message-ID: <3EA04E28@OrangeMail> Dear CPMD community: Do the assumed Hydrogen Bonds that CPMD determines have an effect on geometry optimization? If so, can they be changed? I have tried the CHANGE BONDS keyword, but that does not seem to work. Thank you, Mark Kosmowski Chemistry Department Syracuse University mkosmows at syr.edu From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Fri Apr 18 21:18:56 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Fri, 18 Apr 2003 21:18:56 +0200 Subject: [CPMD-list] System co-ordinates In-Reply-To: <20030418104130.31308.qmail@web13103.mail.yahoo.com> Message-ID: <200304181918.h3IJIuq00502@yello.theochem.ruhr-uni-bochum.de> On Fri, 18 Apr 2003 03:41:30 -0700 (PDT) Keta Jones wrote: > Dear All, > > I want to study some water molecules i.e. 30 water > molecules, but for writing an input file for CPMD > simulation, one needs the coordinates of 30 water > molecules.I will appreciate if someone kindly help > me how to get the coordinates.If classical MD is the > solution,please tell me the alternate methods as I > have no classical code for this.I am new to this area. well, there are several classical md codes available for free. some of them are fairly easy to use, come with good manuals and are a very good introduction to molecular dynamics (and you can learn much faster, since classical md is so much faster). just have a look at some of the chemistry link collections )or do a web search). from my experience, getting a reasonable, pre-equilibrated structure is a prerequisite for a meaningful cpmd simulation of a liquid, especially for a highly polar and structured liquid like water. btw, i recently prepared a introductory exercise for doing cpmd simulations of a hydronium ion in water. if you are interested, please get back to me. i can send you the exercise sheet and some example input files. cheers, axel. > > Thanks in advance, > Keta > > __________________________________________________ > Do you Yahoo!? > The New Yahoo! Search - Faster. Easier. Bingo > http://search.yahoo.com > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From adrainzhou at yahoo.com.cn Mon Apr 21 18:05:04 2003 From: adrainzhou at yahoo.com.cn (=?gb2312?q?Adrain=20Zhou?=) Date: Tue, 22 Apr 2003 00:05:04 +0800 (CST) Subject: [CPMD-list] Problems with the abnormal stop! Message-ID: <20030421160504.9234.qmail@web15305.mail.bjs.yahoo.com> Dear all, Sometimes I met the following problems when I am using LBFGS to optimize a geometry. PROGRAM STOPS IN SUBROUTINE STACK_DO_SCHED| CANNOT RECOVER [PROC= 2] p2_8299: p4_error: : 999 Can anyone tell me whether there is a solution to it? Any comments and suggestions would be highly appreciated! With regards,Adrain_Zhou --------------------------------- Do You Yahoo!? "????????????CCTV-2?????????????????????????????????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20030422/5c5f3e8a/attachment.html From hutter at pci.unizh.ch Mon Apr 21 18:08:06 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 21 Apr 2003 18:08:06 +0200 (MEST) Subject: [CPMD-list] What effect do the assumed Hydrogen Bonds play? In-Reply-To: <3EA04E28@OrangeMail> References: <3EA04E28@OrangeMail> Message-ID: Hi assumed hydrogen bonds are used in the initialization of the empirical Hessian only (see manual for the reference). Unfortunately, this part of the code is not well maintained and the algorithm to determine the H bonds is not very good. The same is true for the CHANGE BONDS option. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Fri, 18 Apr 2003, mkosmows wrote: > Dear CPMD community: > > Do the assumed Hydrogen Bonds that CPMD determines have an effect on > geometry optimization? If so, can they be changed? > > I have tried the CHANGE BONDS keyword, but that does not seem to work. > > Thank you, > > Mark Kosmowski > > Chemistry Department > Syracuse University > mkosmows at syr.edu > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From cur at zurich.ibm.com Tue Apr 22 11:05:02 2003 From: cur at zurich.ibm.com (Alessandro Curioni) Date: Tue, 22 Apr 2003 11:05:02 +0200 Subject: [CPMD-list] What effect do the assumed Hydrogen Bonds play? In-Reply-To: Message-ID: Hello everybody. In many of these cases, the HESSIAN UNIT keyword helps avoiding starting with spurious HESSIANS. Best Regards, Alessandro CURIONI, PhD Research Staff Member Computational Biochemistry and Material Science group IBM Research Division - Zurich Research Laboratory Saumerstrasse 4 8003 Rueschlikon - Switzerland e-mail: cur at zurich.ibm.com www: www.zurich.ibm.com Tel: +41-1-7248633 Fax: +41-1-7248958 Juerg Hutter Sent by: cc: cpmd-list at cpmd.org cpmd-list-admin at c Subject: Re: [CPMD-list] What effect pmd.org do the assumed Hydrogen Bonds play? 04/21/2003 06:08 PM Hi assumed hydrogen bonds are used in the initialization of the empirical Hessian only (see manual for the reference). Unfortunately, this part of the code is not well maintained and the algorithm to determine the H bonds is not very good. The same is true for the CHANGE BONDS option. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Fri, 18 Apr 2003, mkosmows wrote: > Dear CPMD community: > > Do the assumed Hydrogen Bonds that CPMD determines have an effect on > geometry optimization? If so, can they be changed? > > I have tried the CHANGE BONDS keyword, but that does not seem to work. > > Thank you, > > Mark Kosmowski > > Chemistry Department > Syracuse University > mkosmows at syr.edu > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > _______________________________________________ CPMD-list mailing list CPMD-list at cpmd.org http://www.cpmd.org/mailman/listinfo/cpmd-list From ZRLSRB at ch.ibm.com Tue Apr 22 11:32:10 2003 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Tue, 22 Apr 2003 11:32:10 +0200 Subject: [CPMD-list] Problems with the abnormal stop! Message-ID: Dear Adrain Zhou, you have found a bug. I assume you are having this problem when working with a 64-bit executable. Please apply the following patches to rlbfgs.F: Before line 538, insert this line: INCLUDE 'irat.inc' Change line 545 from MSGLEN = 4 to MSGLEN = 8/IRAT Best regards, Salomon From cdy2000 at vip.sina.com Sun Apr 27 12:35:07 2003 From: cdy2000 at vip.sina.com (cdy2000 at vip.sina.com) Date: Sun, 27 Apr 2003 18:35:07 +0800 Subject: [CPMD-list] PROGRAM STOPS IN SUBROUTINE UINV| ILLEGA Message-ID: <20030427103507.3034.qmail@vip.sina.com> Hello, every CPMDer! when I optimize the GEOMETRY of a oxide, there is the problem after many steps: 3485 3.416E-04 2.018E-05 -1447.214130 0.000E+00 185.50 LINE SEARCH: WARNING! 2*E0-4*E1+2*E2 == 0.0 LINE SEARCH : LAMBDA=.399-309 ENERGY = -1447.2141 3486 3.416E-04 2.018E-05 -1447.214130 0.000E+00 185.38 LINE SEARCH : LAMBDA=.797-308 ENERGY = -1447.2141 3487 3.416E-04 2.018E-05 -1447.214130 0.000E+00 185.56 LINE SEARCH: WARNING! 2*E0-4*E1+2*E2 == 0.0 LINE SEARCH : LAMBDA=.747-310 ENERGY = -1447.2141 3488 3.416E-04 2.018E-05 -1447.214130 2.274E-13 185.81 LINE SEARCH : LAMBDA=.747-309 ENERGY = -1447.2141 3489 3.416E-04 2.018E-05 -1447.214130 0.000E+00 186.19 UNIV| THE LEADING MINOR OF ORDER 1 IS NOT POSITIVE DEFINITE, UNIV| AND THE FACTORIZATION COULD NOT BE COMPLETED. PROGRAM STOPS IN SUBROUTINE UINV| ILLEGAL RESULTS DPOTRF then the process ends, I want to know how to solve the problem in modifying the parameters of the input code? Thanks for any help! Sincerely Cao Dayong ______________________________________ =================================================================== From zxdai at theory.issp.ac.cn Mon Apr 28 05:39:45 2003 From: zxdai at theory.issp.ac.cn (zxdai at theory.issp.ac.cn) Date: Mon, 28 Apr 2003 11:39:45 +0800 (CST) Subject: [CPMD-list] Compile question for PC-MPI Message-ID: <33308.202.127.203.187.1051501185.squirrel@202.127.203.201> Dear CPMDuser : I have downloaded CPMD-3.7.1,then I Configure PC-PGI >Makefile Default configuration for PC-PGI. Use standard output for the Makefile. The source directory is: . The object directory is: . The file ./irat.inc is correct. The file ./gromos.h is consistent with normal qm. Add OBJECTS (object files)...done. Add INCFILES (include files)...done. Add explicit rules...done. Create dependencies...done dep main. done. O.K. Then I run make,however,there is following message: pgf77 -c -fast -Mr8 -pc64 -Msignextend -Msecond_underscore ./my_para.f -o ./my_para.o PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 19) 0 inform, 0 warnings, 1 severes, 0 fatal for my_start PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 42) 0 inform, 0 warnings, 1 severes, 0 fatal for my_end PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 117) PGFTN-W-0038-Symbol, mpi_comm_world, has not been explicitly declared (./my_para.f: 119) 0 inform, 1 warnings, 1 severes, 0 fatal for my_group PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 138) PGFTN-W-0038-Symbol, mpi_comm_world, has not been explicitly declared (./my_para.f: 140) 0 inform, 1 warnings, 1 severes, 0 fatal for my_stopall PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 176) PGFTN-W-0038-Symbol, mpi_comm_world, has not been explicitly declared (./my_para.f: 178) 0 inform, 1 warnings, 1 severes, 0 fatal for my_environ PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 194) PGFTN-W-0038-Symbol, mpi_comm_world, has not been explicitly declared (./my_para.f: 194) 0 inform, 1 warnings, 1 severes, 0 fatal for my_task_query PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 211) PGFTN-W-0038-Symbol, mpi_byte, has not been explicitly declared (./my_para.f: 217) 0 inform, 1 warnings, 1 severes, 0 fatal for my_bcast PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 272) PGFTN-W-0038-Symbol, mpi_byte, has not been explicitly declared (./my_para.f: 278) PGFTN-W-0038-Symbol, mpi_comm_world, has not been explicitly declared (./my_para.f: 278) 0 inform, 2 warnings, 1 severes, 0 fatal for my_bsend PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 299) PGFTN-W-0038-Symbol, mpi_status_size, has not been explicitly declared (./my_para.f: 299) PGFTN-W-0038-Symbol, mpi_byte, has not been explicitly declared (./my_para.f: 305) PGFTN-W-0038-Symbol, mpi_comm_world, has not been explicitly declared (./my_para.f: 305) PGFTN-S-0050-Adjustable or assumed size array, status, is not a dummy argument (./my_para.f: 305) PGFTN-S-0084-Illegal use of symbol mpi_status_size - adjustable array bounds not dummy argument or in common (./my_para.f) 0 inform, 3 warnings, 3 severes, 0 fatal for my_brecv PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 325) PGFTN-W-0038-Symbol, mpi_byte, has not been explicitly declared (./my_para.f: 327) 0 inform, 1 warnings, 1 severes, 0 fatal for my_concat PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 350) PGFTN-W-0038-Symbol, mpi_byte, has not been explicitly declared (./my_para.f: 371) 0 inform, 1 warnings, 1 severes, 0 fatal for my_trans PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 397) PGFTN-W-0038-Symbol, mpi_double_precision, has not been explicitly declared (./my_para.f: 413) PGFTN-W-0038-Symbol, mpi_sum, has not been explicitly declared (./my_para.f: 413) PGFTN-W-0038-Symbol, mpi_integer, has not been explicitly declared (./my_para.f: 418) PGFTN-W-0038-Symbol, mpi_max, has not been explicitly declared (./my_para.f: 423) PGFTN-W-0038-Symbol, mpi_min, has not been explicitly declared (./my_para.f: 429) PGFTN-W-0038-Symbol, mpi_prod, has not been explicitly declared (./my_para.f: 435) 0 inform, 6 warnings, 1 severes, 0 fatal for my_combine PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 465) PGFTN-W-0038-Symbol, mpi_status_size, has not been explicitly declared (./my_para.f: 465) PGFTN-W-0038-Symbol, mpi_byte, has not been explicitly declared (./my_para.f: 478) PGFTN-S-0050-Adjustable or assumed size array, status, is not a dummy argument (./my_para.f: 481) PGFTN-S-0084-Illegal use of symbol mpi_status_size - adjustable array bounds not dummy argument or in common (./my_para.f) 0 inform, 2 warnings, 3 severes, 0 fatal for my_shift make: *** [my_para.o] Error 1 Could you help me compile it correctly?? From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Mon Apr 28 08:22:20 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Mon, 28 Apr 2003 08:22:20 +0200 Subject: [CPMD-list] Compile question for PC-MPI In-Reply-To: <33308.202.127.203.187.1051501185.squirrel@202.127.203.201> Message-ID: <200304280622.h3S6MKF27881@yello.theochem.ruhr-uni-bochum.de> On Mon, 28 Apr 2003 11:39:45 +0800 (CST) zxdai at theory.issp.ac.cn wrote: > Dear CPMDuser : > I have downloaded CPMD-3.7.1,then I > Configure PC-PGI >Makefile > Default configuration for PC-PGI. > Use standard output for the Makefile. > The source directory is: . > The object directory is: . > The file ./irat.inc is correct. > The file ./gromos.h is consistent with normal qm. > Add OBJECTS (object files)...done. > Add INCFILES (include files)...done. > Add explicit rules...done. > Create dependencies...done dep main. > done. > O.K. > Then I run make,however,there is following message: > pgf77 -c -fast -Mr8 -pc64 -Msignextend -Msecond_underscore ./my_para.f -o > ./my_para.o > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 19) > 0 inform, 0 warnings, 1 severes, 0 fatal for my_start > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 42) > 0 inform, 0 warnings, 1 severes, 0 fatal for my_end > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 117) > PGFTN-W-0038-Symbol, mpi_comm_world, has not been explicitly declared > (./my_para.f: 119) > 0 inform, 1 warnings, 1 severes, 0 fatal for my_group > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 138) > PGFTN-W-0038-Symbol, mpi_comm_world, has not been explicitly declared > (./my_para.f: 140) > 0 inform, 1 warnings, 1 severes, 0 fatal for my_stopall > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 176) > PGFTN-W-0038-Symbol, mpi_comm_world, has not been explicitly declared > (./my_para.f: 178) > 0 inform, 1 warnings, 1 severes, 0 fatal for my_environ > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 194) > PGFTN-W-0038-Symbol, mpi_comm_world, has not been explicitly declared > (./my_para.f: 194) > 0 inform, 1 warnings, 1 severes, 0 fatal for my_task_query > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 211) > PGFTN-W-0038-Symbol, mpi_byte, has not been explicitly declared > (./my_para.f: 217) > 0 inform, 1 warnings, 1 severes, 0 fatal for my_bcast > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 272) > PGFTN-W-0038-Symbol, mpi_byte, has not been explicitly declared > (./my_para.f: 278) > PGFTN-W-0038-Symbol, mpi_comm_world, has not been explicitly declared > (./my_para.f: 278) > 0 inform, 2 warnings, 1 severes, 0 fatal for my_bsend > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 299) > PGFTN-W-0038-Symbol, mpi_status_size, has not been explicitly declared > (./my_para.f: 299) > PGFTN-W-0038-Symbol, mpi_byte, has not been explicitly declared > (./my_para.f: 305) > PGFTN-W-0038-Symbol, mpi_comm_world, has not been explicitly declared > (./my_para.f: 305) > PGFTN-S-0050-Adjustable or assumed size array, status, is not a dummy > argument (./my_para.f: 305) > PGFTN-S-0084-Illegal use of symbol mpi_status_size - adjustable array > bounds not dummy argument or in common (./my_para.f) > 0 inform, 3 warnings, 3 severes, 0 fatal for my_brecv > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 325) > PGFTN-W-0038-Symbol, mpi_byte, has not been explicitly declared > (./my_para.f: 327) > 0 inform, 1 warnings, 1 severes, 0 fatal for my_concat > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 350) > PGFTN-W-0038-Symbol, mpi_byte, has not been explicitly declared > (./my_para.f: 371) > 0 inform, 1 warnings, 1 severes, 0 fatal for my_trans > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 397) > PGFTN-W-0038-Symbol, mpi_double_precision, has not been explicitly > declared (./my_para.f: > 413) > PGFTN-W-0038-Symbol, mpi_sum, has not been explicitly declared > (./my_para.f: 413) > PGFTN-W-0038-Symbol, mpi_integer, has not been explicitly declared > (./my_para.f: 418) > PGFTN-W-0038-Symbol, mpi_max, has not been explicitly declared > (./my_para.f: 423) > PGFTN-W-0038-Symbol, mpi_min, has not been explicitly declared > (./my_para.f: 429) > PGFTN-W-0038-Symbol, mpi_prod, has not been explicitly declared > (./my_para.f: 435) > 0 inform, 6 warnings, 1 severes, 0 fatal for my_combine > PGFTN-S-0017-Unable to open include file: mpif.h (./my_para.f: 465) > PGFTN-W-0038-Symbol, mpi_status_size, has not been explicitly declared > (./my_para.f: 465) > PGFTN-W-0038-Symbol, mpi_byte, has not been explicitly declared > (./my_para.f: 478) > PGFTN-S-0050-Adjustable or assumed size array, status, is not a dummy > argument (./my_para.f: 481) > PGFTN-S-0084-Illegal use of symbol mpi_status_size - adjustable array > bounds not dummy argument or in common (./my_para.f) > 0 inform, 2 warnings, 3 severes, 0 fatal for my_shift > make: *** [my_para.o] Error 1 > > > Could you help me compile it correctly?? hi! it seems, you have tried to compile a parallel cpmd version in the same directory before. try 'make clean ; make' regards, axel. > > > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From hutter at pci.unizh.ch Mon Apr 28 13:16:16 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 28 Apr 2003 13:16:16 +0200 (MEST) Subject: [CPMD-list] PROGRAM STOPS IN SUBROUTINE UINV| ILLEGA In-Reply-To: <20030427103507.3034.qmail@vip.sina.com> References: <20030427103507.3034.qmail@vip.sina.com> Message-ID: Hi your problem seems to be that the wavefunction optimization didn't converge. If this happens with PCG MINIMIZE you can see that the step size goes to zero (LAMBDA=10^-309 in your case). Experience tells us that this usually happens with systems that a far from equilibrium (e.g. at the beginning of a geometry optimization). It is therefore a good practise to start an optimisation with a relaxed convergence criteria and tighten it when approaching the minimum. There is an automatic scheme to do this with the LBFGS optimizer, have a look in the manual. In general, I would advice everybody to treat optimizations not as black box jobs. Have a look at the output and stop runs when irregularities appear. Then restart with an adapted set of options. This way a lot of computer time can be saved. regards Juerg Hutter ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Sun, 27 Apr 2003 cdy2000 at vip.sina.com wrote: > Hello, every CPMDer! > > when I optimize the GEOMETRY of a oxide, there is the problem after many steps: > > 3485 3.416E-04 2.018E-05 -1447.214130 0.000E+00 185.50 > LINE SEARCH: WARNING! 2*E0-4*E1+2*E2 == 0.0 > LINE SEARCH : LAMBDA=.399-309 ENERGY = -1447.2141 > 3486 3.416E-04 2.018E-05 -1447.214130 0.000E+00 185.38 > LINE SEARCH : LAMBDA=.797-308 ENERGY = -1447.2141 > 3487 3.416E-04 2.018E-05 -1447.214130 0.000E+00 185.56 > LINE SEARCH: WARNING! 2*E0-4*E1+2*E2 == 0.0 > LINE SEARCH : LAMBDA=.747-310 ENERGY = -1447.2141 > 3488 3.416E-04 2.018E-05 -1447.214130 2.274E-13 185.81 > LINE SEARCH : LAMBDA=.747-309 ENERGY = -1447.2141 > 3489 3.416E-04 2.018E-05 -1447.214130 0.000E+00 186.19 > UNIV| THE LEADING MINOR OF ORDER 1 IS NOT POSITIVE DEFINITE, > UNIV| AND THE FACTORIZATION COULD NOT BE COMPLETED. > > > PROGRAM STOPS IN SUBROUTINE UINV| ILLEGAL RESULTS DPOTRF > > then the process ends, I want to know how to solve the problem in modifying the parameters of the input code? > > Thanks for any help! > > Sincerely Cao Dayong > ______________________________________ > > =================================================================== > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From catic at fy.chalmers.se Mon Apr 28 16:11:25 2003 From: catic at fy.chalmers.se (Ermin Catic) Date: Mon, 28 Apr 2003 16:11:25 +0200 (MEST) Subject: [CPMD-list] Visualising unoccupied orbitals Message-ID: Hello, I have a problem with visualising unoccupied orbitals. When I use RHOOUT BANDS or CUBEFILE ORBITALS after wavefunction optimization I get only occupied orbitals. If I add one empty state when optimizing wavefunction the program never reaches convergence. It is the same problem several other users have had with Vanderbilt pseudopotentials (http://www.cpmd.org/pipermail/cpmd-list/2003-April/000879.html). I have tried PCG MINIMIZE, larger MESH, increased CUTOFF, decreased GC-CUTOFF and every other advice i could find in this mailing list but nothing helped. Is there any other way of visualising unoccupied orbitals? I should also add that visualising LUMO for a water molecule works well. Thank you for your help. Best regards, Ermin Catic From hutter at pci.unizh.ch Mon Apr 28 17:53:53 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 28 Apr 2003 17:53:53 +0200 (MEST) Subject: [CPMD-list] Visualising unoccupied orbitals In-Reply-To: References: Message-ID: Hi the most efficient way to calculate unoccupied orbitals is to first optimize the occupied orbitals and then restart the calculation using the run option KOHN-SHAM ENERGIES n where n ist the number of unoccupied orbitas. This will diagonalize the Kohn-Sham Potential (defined by the occupied orbitals alone). To test if everything goes fine, you can check the total energy printed at the beginning of this job, it should be exactly the one at the end of the optimization. In addition, if you don't change the default convergence criteria, the number of converged Kohn-Sham states should be equal to the number of occupied states in the first step. ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Mon, 28 Apr 2003, Ermin Catic wrote: > Hello, > > I have a problem with visualising unoccupied orbitals. When I use RHOOUT > BANDS or CUBEFILE ORBITALS after wavefunction optimization I get only > occupied orbitals. If I add one empty state when optimizing wavefunction > the program never reaches convergence. It is the same problem several > other users have had with Vanderbilt pseudopotentials > > (http://www.cpmd.org/pipermail/cpmd-list/2003-April/000879.html). > > I have tried PCG MINIMIZE, larger MESH, increased CUTOFF, decreased > GC-CUTOFF and every other advice i could find in this mailing list but > nothing helped. > > Is there any other way of visualising unoccupied orbitals? > > I should also add that visualising LUMO for a water molecule works well. > > Thank you for your help. > > Best regards, > Ermin Catic > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From cdy2000 at vip.sina.com Tue Apr 1 15:11:38 2003 From: cdy2000 at vip.sina.com (cdy2000 at vip.sina.com) Date: Tue, 01 Apr 2003 21:11:38 +0800 Subject: [CPMD-list] help Message-ID: <20030401131138.3241.qmail@vip.sina.com> Hello, every CPMDer! Thank Isaev's help. Another problem, when I optimize the geometry and the wavefunction of a cluster, error output, the info is: PROGRAM STOP IN SUBROUTINE RGMOPT| SIMUL NOT WORKING what's meaning? what is RGMOPT? How should I do? Thanks for any help. Sincerely Cao Dayong ______________________________________ =================================================================== From yamaki at sci.hokudai.ac.jp Fri Apr 4 17:42:23 2003 From: yamaki at sci.hokudai.ac.jp (Yamaki Takayoshi) Date: Sat, 5 Apr 2003 00:42:23 +0900 Subject: [CPMD-list] Install with Redhat 7.3 and ABSOFT compiler Message-ID: <07906A56-66B4-11D7-A649-000393488768@sci.hokudai.ac.jp> Dear all, I tried to install CPMD 3.7 to PC with Redhat 7.3, ABSOFT. I ran "Configure" as following: Configure PC-ABSOFT > Makefile Then, Makefile was modified in order to be refer to the libraries correctly. However, I got a error message, ........... .o mm_init.o mm_dim.o mm_qmmm_forcedr.o mm_mdmain.o mm_coninp.o mm_cpmd_add_MM_forces_f77.o mm_cpmd_esp_charges_f77.o mm_cpmd_ext_pot_f77.o vdwin.o vdw.o sysdepend.o shmemory.o -L/home/private2/prog/ABSOFT/opt/absoft/lib -llibf90math -llibimsl -llibimslblas -llibimslf90 -lblas -llibU77 /usr/bin/ld: cannot find -llibf90math collect2: ld returned 1 exit status make: *** [cpmd.x] Error 1 ............ and compile is not successful. I can not understand this message. Please help me solving this problem. Modified makefile is the following. #----------------------------------------------------------------------- ----- # Makefile for cpmd.x (plane wave electronic calculation) # Configuration: PC-ABSOFT # Creation of Makefile: Apr 4 2003 # on Linux soranuma 2.4.18-3smp #1 SMP Thu Apr 18 07:27:31 EDT 2002 i686 unknown # Author: soranuma!yamaki #----------------------------------------------------------------------- ----- # SHELL = /bin/sh # #--------------- Default Configuration for PC-ABSOFT ---------------SRC = . DEST = .BIN = . #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = #LFLAGS = -L/usr/absoft/lib -llapack -lblas -lU77 $(QMMM_LIBS) LFLAGS = -L/home/private2/prog/ABSOFT/opt/absoft/lib -llibf90math -llibimsl -llibimslblas -llibimslf90 -lblas -llibU77 $(QMMM_LIBS) #LFLAGS = -L/home/private2/prog/ABSOFT/opt/absoft/lib -llibf77math -llibimsl -llibimslblas -llibimslf90 -lblas -llibU77 $(QMMM_LIBS) CFLAGS = CPP = /lib/cpp -P -C CPPFLAGS = -D__NOINT8 -D__Linux -D__ABSOFT -DLAPACK -DFFT_DEFAULT NOOPT_FLAG = CC = cc -O FC = f90 -c -B108 -B100 -YEXT_NAMES=LCS -O LD = f90 -O -X-Bstatic AR = #----------------------------------------------------------------------- ----- # # LIST OF FILES # Thank you in advance. Sincerely yours. T.Yamaki