From bala at jncasr.ac.in Mon Mar 1 06:41:43 2004 From: bala at jncasr.ac.in (Dr. Balasubramanian Sundaram) Date: Mon, 01 Mar 2004 11:11:43 +0530 Subject: [CPMD-list] IFC: "undefined reference" References: <200402261155.i1QBtGU29141@yello.theochem.ruhr-uni-bochum.de> Message-ID: <4042CD17.7D02EB6@jncasr.ac.in> Dear All, The last problem was related to the fact that -DPARALLEL flag was missing in CPPFLAGS. This is why lam's mpirun could not sense the executable as a parallel one, and was complaining that the process died before a MPI_INIT instruction came. With that fix, everything worked fine. Thanks! Best, Bala Axel Kohlmeyer wrote: > > On Thu, 26 Feb 2004 17:14:56 +0530 "Dr. Balasubramanian Sundaram" wrote: > > > Dear Axel, > > Thanks for your interest and helpful suggestions. My previous mail > > has to some extent, overtaken your reply. Now, I lamboot only one node. > > I run the parallel executable as, > > > > mpirun -vv -np 1 ../CPMD-3.7.2/SOURCE/cpmd.x system.in > ^^^^^ > are you _positive_, that you are pointing to the parallel executable? > try using an absolute path here. > > a. > > > > > and the output is: > > ------------------------ > > mpirun: waiting for MPI_INIT from 1 processes... > > mpirun: someone died before MPI_INIT -- rank 0 > > ----------------------------------------------------------------------------- > > It seems that [at least] one of the processes that was started with > > mpirun did not invoke MPI_INIT before quitting (it is possible that > > more than one process did not invoke MPI_INIT -- mpirun was only > > notified of the first one, which was on node n0). > > > > mpirun can *only* be used with MPI programs (i.e., programs that > > invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program > > to run non-MPI programs over the lambooted nodes. > > ----------------------------------------------------------------------------- > > mpirun: receiving 0 useless MPI_INIT/MPI_FINALIZE messages... > > ---------------------------------------- > > > > So, in this case I am not even trying to use node2. Incidentally, my > > cluster > > is a diskless one, and every filesystem is exported from the master to > > the > > nodes, and the nodes "see" them in a seamless fashion. Hence, this seems > > not > > to be due to differing versions/paths. > > > > My Makefile is: > > FFLAGS = -c -r8 -w90 -w95 -O3 -pc64 -axM -ip -tpp7 > > LFLAGS = \ > > -L/opt/intel/mkl61/lib/32 -lmkl_lapack \ > > -lmkl_ia32 -lguide \ > > -static-libcxa -Xlinker -Bstatic -lsvml \ > > -Vaxlib -Xlinker -Bdynamic -static > > > > CFLAGS = -c -O2 -Wall > > CPP = /lib/cpp -P -C -traditional > > CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT \ > > -DMP_LIBRARY=__MPI -DMYRINET -DLINUX_IFC > > NOOPT_FLAG = > > CC = mpicc > > FC = mpif77 > > LD = mpif77 > > -------------------------------------------------- > > > > Here are some more details of my "env" output: > > > > LD_LIBRARY_PATH=/usr/local/intel_fc_80/lib:/opt/intel/mkl61/lib/32 > > PP_LIBRARY_PATH=/home/bala/cpmd/CPMD-3.7.2/PPLIBNEW > > > > Thanks again, > > > > Regards, > > Bala > > > > > > > > Axel Kohlmeyer wrote: > > > > > > On Thu, 26 Feb 2004, Dr. Balasubramanian Sundaram wrote: > > > > > > [...] > > > > > > BS> LFLAGS, I get an undefined reference for s_copy. The following is the > > > BS> error message. > > > BS> ==================== > > > BS> /opt/intel/mkl60/lib/32/libmkl_lapack.a(ilaenv.o)(.text+0x52a): In > > > BS> function `__MKL_SERV_ilaenv': > > > BS> : undefined reference to `s_copy' > > > > > > ok, so the intel people either seem to compile parts of their lapack > > > libraries with g77 or use the f2c runtime (conventions). ;-). > > > should be rather easy for them to include a stripped down run-time > > > in their library. > > > > > > BS> =================== > > > BS> > > > BS> Strangely, cpmd.x give a runtime error. I have lambooted 2 nodes > > > BS> properly, and actually tried to run a job only on one node. This job > > > BS> runs fine for a serial cpmd executable that was compiled with IFC and > > > BS> MKL. > > > BS> So, the input file seems to be fine. > > > BS> I get the following runtime error. > > > BS> ----------------------------- > > > BS> PROGRAM CPMD STARTED AT: Thu Feb 26 12:31:44 2004 > > > BS> forrtl: severe (174): SIGSEGV, segmentation fault occurred > > > BS> Image PC Routine Line > > > BS> Source > > > BS> cpmd.x 08677134 Unknown Unknown Unknown > > > BS> cpmd.x 08243965 Unknown Unknown Unknown > > > BS> cpmd.x 00000000 Unknown Unknown Unknown > > > BS> ----------------------------------------------------------------------------- > > > BS> It seems that [at least] one of the processes that was started with > > > BS> mpirun did not invoke MPI_INIT before quitting (it is possible that > > > BS> more than one process did not invoke MPI_INIT -- mpirun was only > > > BS> notified of the first one, which was on node n0). > > > BS> > > > BS> mpirun can *only* be used with MPI programs (i.e., programs that > > > BS> invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program > > > BS> to run non-MPI programs over the lambooted nodes. > > > BS> ----------------------------------------------------------------------------- > > > BS> > > > > > > there are two likely causes: you have not installed the same version of > > > LAM on all nodes that you are using, or the network does not work > > > properly. > > > > > > so please try running the parallel executable only with one node, > > > and - if that works - lamboot only one node, but run two copies and > > > if that works too, please carefully whether the new lam on the additional > > > nodes is really in the search path and of the same version. > > > > > > hope this helps, > > > axel kohlmeyer. > > > > > > BS> Thanks again for your considerable help, > > > BS> > > > BS> Best Regards, > > > BS> Bala > > > BS> > > > BS> > > > BS> > > > BS> > > > BS> > > > BS> > > > BS> > > > BS> Axel Kohlmeyer wrote: > > > BS> > > > > BS> > On Wed, 25 Feb 2004, Dr. Balasubramanian Sundaram wrote: > > > BS> > > > > BS> > BS> Dear All, > > > BS> > BS> > > > BS> > BS> I have been having this trivial, yet nagging problem, and thought > > > BS> > BS> I should seek help to preserve my sanity! > > > BS> > BS> > > > BS> > BS> Details: CPMD 3.7.2, IFORT (IFC's new name): version 8.0, > > > BS> > BS> P4 at 3.0 GHz (with HT), Mandrake Linux 9.2 (kernel 2.4.22), with > > > BS> > BS> Intel's MKL version 6.0, gcc, lam-mpi version 7.0.4 > > > BS> > BS> > > > BS> > BS> I compiled lam-mpi using ifort compiler, using "FFLAGS=-us" option > > > BS> > BS> (i.e., equivalent of "-assume underscore"). lam-mpi compiled fine, > > > BS> > BS> and I could compile and run their examples/pi/fpi code properly > > > BS> > BS> on two nodes. > > > BS> > > > > BS> > dear bala, > > > BS> > > > > BS> > stupid question: why are you messing with the underscoring, when > > > BS> > you are compiling cpmd _and_ lam with the intel compiler anyway? > > > BS> > > > > BS> > BS> > > > BS> > BS> I have problems at the link stage for CPMD. I provide at the end of thi > s > > > BS> > BS> mail, my Makefile. Here, I give the output of the command, > > > BS> > BS> > > > BS> > BS> /home/bala/lam-7.0.4/tools/wrappers/mpif77 -showme > > > BS> > BS> > > > BS> > BS> OUTPUT: > > > BS> > BS> ifort -I/usr/include -llammpio -llamf77mpi -lmpi -llam -lutil > > > BS> > > > > BS> > hmm. you seem to be running lam from the compilation directory. > > > BS> > most likely you are not picking up the new libraries, but > > > BS> > an old set, that is installed in the default library search > > > BS> > path. if my assertion is correct, than you would have to run > > > BS> > 'make install' first. alternatively, you may be able to get > > > BS> > away with telling the linker via -L/home/bala/lam-7.0.4/and/so/on... > > > BS> > where to pick up the new libraries. but then again, you will > > > BS> > run into trouble when you start the lam daemons, since lamboot > > > BS> > will not find the matching executables. > > > BS> > > > > BS> > BS> > > > BS> > BS> All CPMD routines compile fine, but at the linker stage, I get the > > > BS> > BS> error message, > > > BS> > BS> ================= > > > BS> > BS> my_para.o(.text+0x6): In function `my_start_': > > > BS> > BS> : undefined reference to `mpi_init_' > > > BS> > BS> my_para.o(.text+0xbe5): In function `my_end_': > > > BS> > BS> : undefined reference to `mpi_finalize_' > > > BS> > BS> ================= > > > BS> > BS> > > > BS> > BS> I appreciate your help, > > > BS> > BS> > > > BS> > BS> Thanks, > > > BS> > BS> > > > BS> > BS> Regards, > > > BS> > BS> Bala > > > BS> > BS> -------------------------MAKEFILE HEADER-------------------------- > > > BS> > BS> > > > BS> > BS> FFLAGS = -c -r8 -w90 -w95 -O3 -pc64 -axM -ip -tpp7 -us > > > BS> > BS> > > > BS> > BS> LFLAGS = \ > > > BS> > BS> -L/opt/intel/mkl60/lib/32 -lmkl_lapack \ > > > BS> > BS> -lmkl_ia32 -lmkl_p4 -lguide \ > > > BS> > BS> -static-libcxa -Xlinker -Bstatic -lsvml \ > > > BS> > BS> /usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.1/libg2c.a \ > > > BS> > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > > BS> > > > > BS> > you should not need this. this is the g77 runtime. in fact it > > > BS> > may collide with the intel fortran runtime. > > > BS> > > > > BS> > hope this helps, > > > BS> > axel kohlmeyer. > > > BS> > > > > BS> > BS> -Vaxlib -Xlinker -Bdynamic > > > BS> > BS> CFLAGS = -c -O2 -Wall > > > BS> > BS> CPP = /lib/cpp -P -C -traditional > > > BS> > BS> > > > BS> > BS> CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT \ > > > BS> > BS> -DMP_LIBRARY=__MPI -DMYRINET -DLINUX_IFC > > > BS> > BS> NOOPT_FLAG = > > > BS> > BS> > > > BS> > BS> CC = /home/bala/lam-7.0.4/tools/wrappers/mpicc > > > BS> > BS> FC = /home/bala/lam-7.0.4/tools/wrappers/mpif77 > > > BS> > BS> LD = /home/bala/lam-7.0.4/tools/wrappers/mpif77 > > > BS> > BS> --------------------------------------------------------------------- > > > BS> > BS> _______________________________________________ > > > BS> > BS> CPMD-list mailing list > > > BS> > BS> CPMD-list at cpmd.org > > > BS> > BS> http://www.cpmd.org/mailman/listinfo/cpmd-list > > > BS> > BS> > > > BS> > BS> > > > BS> > > > > BS> > -- > > > BS> > > > > BS> > ======================================================================= > > > BS> > Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de > > > BS> > Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 > > > BS> > Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 > > > BS> > D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ > > > BS> > ======================================================================= > > > BS> > > > BS> > > > > > > -- > > > > > > ======================================================================= > > > Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de > > > Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 > > > Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 > > > D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ > > > ======================================================================= > > > > -- > > ======================================================================= > 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 radbalu at comcast.net Fri Mar 5 00:06:54 2004 From: radbalu at comcast.net (rad) Date: Thu, 4 Mar 2004 18:06:54 -0500 Subject: [CPMD-list] Compilation Issues Message-ID: <005e01c4023d$62955170$6501a8c0@H12009.ecpm.com> Hi , I am try to get CPMD running on my m/c that is a AMD 64 athlon based running suse linux 9.0 professional. I figured out from this site, that I have to use IFC to compile the code. (Please let me know if there is another free fortran compiler that I can be used for this purpose). While installing IFC I had to select the IA32 architecture, that means I may not be using the 64 bit features of my processor. After instllation, when I tried to compile and link edit, the "ld" component was trying to use 32 bit libraries from /usr/lib/crt1.o. So I created a link for usr/lib to point to /usr/lib64 libraries. Now the libifort module of IFC is complaining that it is incompatible. Could somebody suggest me a way to compile and link edit CPMD for my environment where there is a combination of 32 bit and 64 bit libraries producing inconsistencies. I have to add that I downloaded libatlas_athlon64.a binary from Dr. Axel Kohlmeyer's web site and here is a portion of my Makefile: #---------------------------------------------------------------------------- # Makefile for cpmd.x (plane wave electronic calculation) # Configuration: PC-IFC # Creation of Makefile: Feb 27 2004 # Author: root #---------------------------------------------------------------------------- # SHELL = /bin/sh # #--------------- Default Configuration for PC-IFC --------------- SRC = . DEST = . BIN = . #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = -c -O3 -pc64 -axN -unroll -cm pn4 -w95 LFLAGS = -L. -latlas_athlon64 -Vaxlib CFLAGS = -c -O2 -Wall CPP = /lib/cpp -P -C -traditional CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DLINUX_IFC NOOPT_FLAG = CC = gcc FC = ifort LD = ifort AR = #---------------------------------------------------------------------------- # I would appreciate if cpmd.org makes the binary version of CPMD available so that beginners like me can get started with the software easily. Any help from this group would be appreciated. Thanks Rad Graduate Student, Hopkins -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20040304/0bb7466b/attachment.html From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Fri Mar 5 13:31:16 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Fri, 5 Mar 2004 13:31:16 +0100 (CET) Subject: [CPMD-list] Compilation Issues In-Reply-To: <005e01c4023d$62955170$6501a8c0@H12009.ecpm.com> Message-ID: On Thu, 4 Mar 2004, rad wrote: > Hi , > > I am try to get CPMD running on my m/c that is a AMD 64 athlon based running suse linux 9.0 professional. I figured out from this site, that I have to use IFC to compile the code. (Please let me know if there is another free fortran compiler that I can be used for this purpose). > > While installing IFC I had to select the IA32 architecture, that means I may not be using the 64 bit features of my processor. After instllation, when I tried to compile and link edit, the "ld" component was trying to use 32 bit libraries from /usr/lib/crt1.o. So I created a link for usr/lib to point to /usr/lib64 libraries. Now the libifort module of IFC is complaining that it is incompatible. hi, if you want to compile a 32bit executable, you need a 32bit library. the x86_64/athlon64 libraries on my homepage are 64bit libraries. please use the athlon library (in 32-bit mode an opteron/athlon64 is very much like a 32-bit athlon). please note, that you should be able to download an evaluation version with a 2-week test license of the 64-bit pgi compiler for opteron/athlon64 from the portland group homepage. good luck, axel. [...] > Could somebody suggest me a way to compile and link edit CPMD for my environment where there is a combination of 32 bit and 64 bit libraries producing inconsistencies. I have to add that I downloaded libatlas_athlon64.a binary from Dr. Axel Kohlmeyer's web site and here is a portion of my Makefile: > #---------------------------------------------------------------------------- > # Makefile for cpmd.x (plane wave electronic calculation) > # Configuration: PC-IFC > # Creation of Makefile: Feb 27 2004 > # Author: root > #---------------------------------------------------------------------------- > # > SHELL = /bin/sh > # > #--------------- Default Configuration for PC-IFC --------------- > SRC = . > DEST = . > BIN = . > #QMMM_FLAGS = -D__QMECHCOUPL > #QMMM_LIBS = -L. -lmm > FFLAGS = -c -O3 -pc64 -axN -unroll -cm pn4 -w95 > LFLAGS = -L. -latlas_athlon64 -Vaxlib > CFLAGS = -c -O2 -Wall > CPP = /lib/cpp -P -C -traditional > CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DLINUX_IFC > NOOPT_FLAG = > CC = gcc > FC = ifort > LD = ifort > AR = > #---------------------------------------------------------------------------- > # > > I would appreciate if cpmd.org makes the binary version of CPMD available so that beginners like me can get started with the software easily. > > Any help from this group would be appreciated. > > Thanks > Rad > Graduate Student, Hopkins -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Fri Mar 5 16:23:05 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Fri, 05 Mar 2004 16:23:05 +0100 Subject: [CPMD-list] memory problems Linux/x86 In-Reply-To: Your message of "Tue, 24 Feb 2004 13:26:11 GMT." Message-ID: <200403051523.i25FN5B18622@yello.theochem.ruhr-uni-bochum.de> >>> "CD" == Carmen Domene writes: CD> Hi. CD> I have some memory problems with CPMD and the Linux/x86 implememtation. CD> When the program tries to allocate memory, the procedure returns a pointer CD> to the location of the memory allocated, that value that is returned is an CD> integer*4, meaning that it can only specify a maximum of 1Gb of memory. CD> Hence any problem that requires more than 1Gb per process fails. this is not totally correct. with a signed 32-bit integer you can store numbers as big a 2^31 = 2GB. since there is no point in using more memory per process on an 32-bit x86 machine, anyway, this should be ok. if you want to run problems, that need more memory, you should either run cpmd on a 64-bit machine or use a (MPI) parallel binary. CD> Has anyone managed to allocate more than 1Gb of memory per process on an CD> x86 system, and if so, how they do it? ================================================================ BIG MEMORY ALLOCATIONS PME 63991740 CATOM 17064432 GDE 15997935 SCR 8564196 C0 8532224 C2 8532224 SC0 8532216 EIGR 4266108 YF 1507142 PSI 1507142 ---------------------------------------------------------------- [PEAK NUMBER 72] PEAK MEMORY 143505865 = 1148.0 MBytes ================================================================ this is definitely more than a 1GByte. upon closer inspection, though, it seems as if cpmd is occasionaly overly careful when allocating scratch memory areas. e.g. the job, where i copied the memory allocation statistics from, needs only about 300MB resident. again, most of the time you can work around it by using a 64-bit machine or running in parallel. hope this helps, axel kohlmeyer. CD> Many thanks, CD> Carmen CD> *********************************************** CD> Carmen Domene CD> Physical and Theoretical Chemistry Laboratory CD> University of Oxford CD> South Parks Road CD> Oxford OX1 3QZ CD> UK CD> Tel: (0)1865 285401 CD> FAX: (0)1865 275410 CD> e-mail: carmen.domene at chem.ox.ac.uk CD> *********************************************** CD> _______________________________________________ CD> CPMD-list mailing list CD> CPMD-list at cpmd.org CD> http://www.cpmd.org/mailman/listinfo/cpmd-list -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From Joseph.Curtis at nist.gov Sun Mar 7 03:20:50 2004 From: Joseph.Curtis at nist.gov (Joseph E. Curtis, Ph. D.) Date: Sat, 6 Mar 2004 21:20:50 -0500 Subject: [CPMD-list] p4_error Message-ID: <1078626050.404a8702e8f74@webmail.nist.gov> Hi, I have been using CPMD extensively on Blue Horizon without any problems for a few years now and I would like to run some jobs here in-house on our cluster. I have installed Alex's LAM RPM and successfully compilied serial, open-mp and MPI versions of cpmd 3.7.2 using the PGI compilers. The serial and open-mp binaries run fine. Other LAM binaries work fine on this system (e.g. CHARMM) and MPI programs work as well (PINY-MD). When I run the MPI version (using lamexec -np 2 cpmd-mpi.exe input) it starts to run normally on both processors (SMP Xeon, RedHat 7.X, 2.4.7-10smp), using up only a fraction of the available 2 GB of RAM, then I get the following crash message: *** ATOMWF| THE NEW SIZE OF THE PROGRAM IS 65796 kBYTES *** *** ATOMWF| THE NEW SIZE OF THE PROGRAM IS 65796 kBYTES *** ATRHO| CHARGE(R-SPACE): 168.000000 (G-SPACE): 168.000000 ATRHO| CHARGE(R-SPACE): 168.000000 (G-SPACE): 168.000000 p0_25286: p4_error: interrupt SIGSEGV: 11 25286 (n0) exited with status 1 Here is the "TOP" output taken at the moment of the crash: 174 processes: 168 sleeping, 3 running, 0 zombie, 3 stopped CPU0 states: 94.3% user, 5.1% system, 0.0% nice, 0.0% idle CPU1 states: 98.1% user, 1.2% system, 0.0% nice, 0.1% idle Mem: 2059028K av, 1480184K used, 578844K free, 192K shrd, 127340K buff Swap: 2040244K av, 148880K used, 1891364K free 657048K cached PID USER PRI NI SIZE RSS SHARE STAT %CPU %MEM TIME COMMAND 25286 maduser 14 0 164M 164M 2032 R 97.5 8.1 1:42 cpmd_mpi.x 25287 maduser 15 0 164M 164M 2032 R 97.3 8.1 1:42 cpmd_mpi.x HERE is the meat of the Makefile: #--------------- Default Configuration for PC-PGI-MPI --------------- SRC = . DEST = . BIN = . #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = -Mr8 -pc 64 -byteswapio -Msignextend LFLAGS = ./libatlas_p4.a /usr/pgi/linux86/lib/libmpich.a -byteswapio $(QMMM_LIBS) CFLAGS = CPP = /lib/cpp -P -C -traditional CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT \ -DPARALLEL -DMP_LIBRARY=__MPI NOOPT_FLAG = CC = mpicc -O2 -Wall FC = pgf77 -c -fast LD = pgf77 -fast AND HERE is the simple wavefunction minimization file: &CPMD INITIALIZE WAVEFUNCTION OPTIMIZE WAVEFUNCTION STRUCTURE BOND ANGLES &END &SYSTEM SYMMETRY 14 POISSON SOLVER TUCKERMAN ANGSTROM CELL ABSOLUTE DEGREE 7.872 6.055 13.415 101.097 113.385 85.944 CUTOFF 70. CHARGE 0.0 &END &DFT FUNCTIONAL BLYP &END &ATOMS *C_MT_BLYP KLEINMAN-BYLANDER LMAX=P LOC=P 36 0.866970 0.190720 4.855890 -3.319740 -2.541300 7.012450 -3.776450 -1.837650 5.921350 -3.632690 -2.430090 4.637230 -4.048020 -1.749260 3.475660 -3.893360 -2.264650 2.155260 -4.318850 -1.608070 1.022770 -3.080120 -3.747820 4.455200 -2.682220 -4.391760 5.583730 -2.796940 -3.912830 6.844880 1.084800 0.920810 3.721730 0.588870 0.425690 2.429670 0.794350 1.121460 1.294870 0.339090 0.643870 0.022730 0.501740 1.318560 -1.153410 -0.025410 -0.833400 2.377240 0.501740 1.318560 -1.153410 -0.025410 -0.833400 2.377240 -0.274470 -1.568030 3.589240 0.193870 -1.088160 4.826930 -0.339090 -0.643870 -0.022730 0.025410 0.833400 -2.377240 -0.501740 -1.318560 1.153410 -0.794350 -1.121460 -1.294870 -0.588870 -0.425690 -2.429670 0.274470 1.568030 -3.589240 -1.084800 -0.920810 -3.721730 -0.193870 1.088160 -4.826930 -0.866970 -0.190720 -4.855890 -3.367660 -3.620760 2.035060 -4.180890 -2.137590 -0.264890 -2.942160 -4.277340 3.167550 -3.213000 -4.136150 0.714660 -3.628330 -3.455320 -0.446910 -4.578800 -1.493650 -1.393410 -3.484560 -4.047760 -1.731040 -4.464070 -1.972580 -2.654560 -3.941280 -3.344110 -2.822140 *H_MT_BLYP KLEINMAN-BYLANDER LMAX=P LOC=P 24 1.219850 0.585320 5.728440 -3.405420 -2.054250 7.979580 -4.175080 -0.850790 6.075700 -4.458260 -0.742150 3.593440 -4.712400 -0.639640 1.167450 -2.287220 -5.389870 5.385630 -2.505050 -4.456990 7.636880 1.539340 1.870650 3.720410 1.277940 2.091880 1.303040 0.972980 2.295580 -1.133020 -0.689800 -2.516950 3.486940 0.079870 -1.655780 5.678580 -0.972980 -2.295580 1.133020 -1.277940 -2.091880 -1.303040 0.689800 2.516950 -3.486940 -1.539340 -1.870650 -3.720410 -0.079870 1.655780 -5.678580 -1.219850 -0.585320 -5.728440 -2.548620 -5.245770 3.022860 -2.802750 -5.143260 0.596880 -4.973790 -0.495540 -1.195320 -3.085930 -5.034620 -1.885380 -4.755960 -1.428420 -3.446570 -3.855600 -3.831160 -3.789260 &END Any ideas? Thanks for ALL of your help! Cheers, j ******************************************************************************** Joseph E. Curtis, Ph. D. (301) 975-3959 joseph.curtis at nist.gov ******************************************************************************** From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Sun Mar 7 10:14:34 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Sun, 07 Mar 2004 10:14:34 +0100 Subject: [CPMD-list] p4_error In-Reply-To: Your message of "Sat, 06 Mar 2004 21:20:50 EST." <1078626050.404a8702e8f74@webmail.nist.gov> Message-ID: <200403070914.i279EYf31323@yello.theochem.ruhr-uni-bochum.de> >>> "JC" == Joseph E Curtis writes: JC> Hi, JC> I have been using CPMD extensively on Blue Horizon without any problems for a JC> few years now and I would like to run some jobs here in-house on our cluster. JC> I have installed Alex's LAM RPM and successfully compilied serial, open-mp and JC> MPI versions of cpmd 3.7.2 using the PGI compilers. The serial and open-mp JC> binaries run fine. Other LAM binaries work fine on this system (e.g. CHARMM) JC> and MPI programs work as well (PINY-MD). JC> When I run the MPI version (using lamexec -np 2 cpmd-mpi.exe input) it starts to JC> run normally on both processors (SMP Xeon, RedHat 7.X, 2.4.7-10smp), using up JC> only a fraction of the available 2 GB of RAM, then I get the following crash JC> message: JC> *** ATOMWF| THE NEW SIZE OF THE PROGRAM IS 65796 kBYTES *** JC> *** ATOMWF| THE NEW SIZE OF THE PROGRAM IS 65796 kBYTES *** JC> ATRHO| CHARGE(R-SPACE): 168.000000 (G-SPACE): 168.000000 JC> ATRHO| CHARGE(R-SPACE): 168.000000 (G-SPACE): 168.000000 JC> p0_25286: p4_error: interrupt SIGSEGV: 11 dear joseph, this error message is from an MPICH binary. are you positive, that you have linked the proper mpi library? also the fact, that output appears twice indicates, that the parallel infrastructure was not properly initialized, which would be the case, if you start an MPICH binary with lam. hope this helps, axel kohlmeyer. JC> 25286 (n0) exited with status 1 [...] -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From wyin at mail.unomaha.edu Mon Mar 8 22:54:13 2004 From: wyin at mail.unomaha.edu (Weiguo Yin) Date: Mon, 8 Mar 2004 15:54:13 -0600 Subject: [CPMD-list] calculate atomic charges Message-ID: Dear list, I tried to calculate atomic charges and met the following error. Could somebody tell me how to fix it? Your help would be appreciated very much. >>>> Output <<<< ESP CHARGES| NUMBER OF FITTING POINTS 0 ESP CHARGES| NOT ENOUGH FITTING POINTS PROGRAM STOPS IN SUBROUTINE SELECTP| NR OF POINTS [PROC= 0] >>>> Input <<<< &CPMD RESTART WAVEFUNCTION LATEST PROPERTIES CALCULATION &END &PROPERTIES PROJECT WAVEFUNCTION CHARGES &END &SYSTEM ... &END &ATOMS ... &END &DFT ... &END &BASIS PSEUDO AO 2 0 1 PSEUDO AO 2 0 1 PSEUDO AO 2 0 1 &END Sincerely, Dr. Weiguo Yin Department of Physics University of Nebraska at Omaha Omaha, NE 68182 U.S.A. TEL: (402) 554 3730 FAX: (402) 554 3100 E-mail: wyin at mail.unomaha.edu From hutter at pci.unizh.ch Wed Mar 10 14:51:11 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Wed, 10 Mar 2004 14:51:11 +0100 (MET) Subject: [CPMD-list] calculate atomic charges In-Reply-To: References: Message-ID: Hi CPMD trys to select ESP fitting points in the range of 2-4 times the vdW radius of all atoms. This will only work for molecules and if there is enough space between the molecule and the edge of the simulation box. 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 Mon, 8 Mar 2004, Weiguo Yin wrote: > > > > > Dear list, > > I tried to calculate atomic charges and met the following error. Could > somebody tell me how to fix it? Your help would be appreciated very much. > > >>>> Output <<<< > > ESP CHARGES| NUMBER OF FITTING POINTS 0 > ESP CHARGES| NOT ENOUGH FITTING POINTS > PROGRAM STOPS IN SUBROUTINE SELECTP| NR OF POINTS [PROC= 0] > > >>>> Input <<<< > &CPMD > RESTART WAVEFUNCTION LATEST > PROPERTIES CALCULATION > &END > &PROPERTIES > PROJECT WAVEFUNCTION > CHARGES > &END > &SYSTEM > ... > &END > > &ATOMS > ... > &END > > &DFT > ... > &END > &BASIS > PSEUDO AO 2 > 0 1 > PSEUDO AO 2 > 0 1 > PSEUDO AO 2 > 0 1 > &END > > Sincerely, > > Dr. Weiguo Yin > Department of Physics > University of Nebraska at Omaha > Omaha, NE 68182 > U.S.A. > TEL: (402) 554 3730 > FAX: (402) 554 3100 > E-mail: wyin at mail.unomaha.edu > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From wyin at mail.unomaha.edu Thu Mar 11 17:19:41 2004 From: wyin at mail.unomaha.edu (Weiguo Yin) Date: Thu, 11 Mar 2004 10:19:41 -0600 Subject: [CPMD-list] calculate atomic charges Message-ID: An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20040311/df0f39d0/attachment.html From hutter at pci.unizh.ch Fri Mar 12 13:53:14 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Fri, 12 Mar 2004 13:53:14 +0100 (MET) Subject: [CPMD-list] calculate atomic charges In-Reply-To: References: Message-ID: > > Hello, Juerg, > > Thank you very much. I was calculating the ESP charge of solid Na3PO4 using the periodic > boundary conditions. According to your message, the current version of CPMD does not work for > that purpose? That's correct. You can use the ESP procedure to calculate charges for solids. You have to use one of the other possibilities available in CPMD for this (Mulliken, Davidson, Hirschfeld). regards Juerg Hutter > > Sincerely > > Weiguo Yin > > ---- > Department of Physics > University of Nebraska at Omaha > Omaha, NE 68182 > U.S.A. > TEL: (402) 554 3730 > FAX: (402) 554 3100 > E-mail: wyin at mail.unomaha.edu > > ? > Juerg Hutter > 03/10/2004 02:51 PM CET > > To ? Weiguo Yin > cc ?cpmd-list at cpmd.org > bcc ? > Subject ?Re: [CPMD-list] calculate atomic charges > ? > > Hi > > CPMD trys to select ESP fitting points in the range > of 2-4 times the vdW radius of all atoms. > This will only work for molecules and if there is enough > space between the molecule and the edge of the > simulation box. > > 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 Mon, 8 Mar 2004, Weiguo Yin wrote: > > > > > > > > > > > Dear list, > > > > I tried to calculate atomic charges and met the following error. Could > > somebody tell me how to fix it? ?Your help would be appreciated very much. > > > > ? ? ? ? ? ?>>>> Output <<<< > > > > ESP CHARGES| NUMBER OF FITTING POINTS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 > > ?ESP CHARGES| NOT ENOUGH FITTING POINTS > > ?PROGRAM STOPS IN SUBROUTINE SELECTP| NR OF POINTS [PROC= ? 0] > > > > ? ? ? ? ? ?>>>> Input <<<< > > &CPMD > > ? RESTART WAVEFUNCTION LATEST > > ? PROPERTIES CALCULATION > > &END > > &PROPERTIES > > ? PROJECT WAVEFUNCTION > > ? CHARGES > > &END > > &SYSTEM > > ... > > &END > > > > &ATOMS > > ... > > &END > > > > &DFT > > ... > > &END > > &BASIS > > ? PSEUDO AO 2 > > ? 0 1 > > ? PSEUDO AO 2 > > ? 0 1 > > ? PSEUDO AO 2 > > ? 0 1 > > &END > > > > Sincerely, > > > > Dr. Weiguo Yin > > Department of Physics > > University of Nebraska at Omaha > > Omaha, NE 68182 > > U.S.A. > > TEL: (402) 554 3730 > > FAX: (402) 554 3100 > > E-mail: wyin at mail.unomaha.edu > > > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list > > > > > From wyin at mail.unomaha.edu Fri Mar 12 18:48:09 2004 From: wyin at mail.unomaha.edu (Weiguo Yin) Date: Fri, 12 Mar 2004 11:48:09 -0600 Subject: [CPMD-list] RESTART ... LATEST fails Message-ID: Dear members of CPMD-List, The following is an example of the failure of the LASTEST option of RESTART: Firstly, I performed a two-step MD run for two hydrogen atoms to generate two restart files, namely RESTART.1 and RESTART.2. The resulting LATEST file reads ./RESTART.2 2 Seondly, I tried to perform an one-step MD run with the "RESTART WAVEFUNCTION COORDINATES LATEST" command. Unfortunately, I got the following error message: "ZHRWF| RESTART FILE NOT FOUND: ./RESTART" The input files for this procedure are enclosed in the end. The user guide (CPMD 3.7.0, p 73) is telling us that the use of the LATEST option is dangerous. The saftest way is to manually copy the RESTART.? file to RESTART and not to use LATEST. Good luck, Weiguo Yin ==== Physics Department University of Nebraska at Omaha Omaha, NE 68182 E-mail: wgyin at yahoo.com ===== Input file for the first run ===== &CPMD MOLECULAR DYNAMICS RESTART WAVEFUNCTION COORDINATES LASTEST EMASS 500 TIMESTEP 0.0000001 MAXSTEP 2 STORE 1 RESTFILE 2 &END &SYSTEM SYMMETRY 1 CELL 10.000 1.0 1.0 0.0 0.0 0.0 CUTOFF 10 &END &ATOMS *H_MT_LDA LMAX=S 2 0.5 0. 0. -0.5 0. 0. &END &DFT NEWCODE FUNCTIONAL LDA &END ===== Input file for the second run ===== &CPMD MOLECULAR DYNAMICS RESTART WAVEFUNCTION COORDINATES LASTEST EMASS 500 TIMESTEP 0.0000001 MAXSTEP 1 &END &SYSTEM SYMMETRY 1 CELL 10.000 1.0 1.0 0.0 0.0 0.0 CUTOFF 10 &END &ATOMS *H_MT_LDA LMAX=S 2 1.0 0. 0. -1.0 0. 0. &END &DFT NEWCODE FUNCTIONAL LDA &END From ct at chemie.hu-berlin.de Sat Mar 13 09:00:21 2004 From: ct at chemie.hu-berlin.de (Christian Tuma) Date: Sat, 13 Mar 2004 09:00:21 +0100 Subject: [CPMD-list] RESTART ... LATEST fails In-Reply-To: References: Message-ID: <20040313080021.GA285925@uranus.chemie.hu-berlin.de> Hello Weiguo Yin, it was just a typo - try "LATEST" instead of "LASTEST". Good luck, Christian. On Fri, Mar 12, 2004 at 11:48:09AM -0600, Weiguo Yin wrote: > The following is an example of the failure of the LASTEST option of > RESTART: > ... > > ===== Input file for the second run ===== > &CPMD > MOLECULAR DYNAMICS > RESTART WAVEFUNCTION COORDINATES LASTEST > ... -- Christian Tuma Humboldt-Universitaet Berlin ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer From ketajone at yahoo.com Sat Mar 13 13:39:42 2004 From: ketajone at yahoo.com (Keta Jones) Date: Sat, 13 Mar 2004 04:39:42 -0800 (PST) Subject: [CPMD-list] VMD1.8(latest) with RedHat9.0 In-Reply-To: Message-ID: <20040313123942.83992.qmail@web13124.mail.yahoo.com> Please help me how to install the latest vmd version(1.8) in RedHat9.0. regards, keta ===== Keta ************************************************************************************** __________________________________ Do you Yahoo!? Yahoo! Mail - More reliable, more storage, less spam http://mail.yahoo.com From lajiapo at hotmail.com Sat Mar 6 22:58:44 2004 From: lajiapo at hotmail.com (=?gb2312?B?s8Igt+c=?=) Date: Sun, 07 Mar 2004 05:58:44 +0800 Subject: [CPMD-list] running error in CPMD Message-ID: Dear all, I am new for using CPMD. My running platform is RedHat9.0. I am using Intel Fortran Compiler8.0. First, I use -------------------------------------------------------- Configure LINUX_IA64_INTEL > Makefile -------------------------------------------------------- to generate the Makefile. Then I modified some parameters in Makefile because I have not installed Intel MKL yet (Is that necessary?). Now the Makefile looks like: ################################################################# SHELL = /bin/sh # #--------------- Default Configuration for LINUX_IA64_INTEL --------------- SRC = . DEST = . BIN = . #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = #LFLAGS = -L/opt/intel/mkl/lib/64 -lmkl_itp -lmkl_lapack -lmkl_itp \ # -lPEPCF90 -lm -lpthread $(QMMM_LIBS) LFLAGS = -llapack /usr/lib/gcc-lib/i386-redhat-linux/3.2.2/libg2c.a\ -lm -lpthread $(QMMM_LIBS) CFLAGS = -D__alpha CPP = /lib/cpp -P -C -traditional CPPFLAGS = -D__alpha -DPOINTER8 -DLAPACK -DFFT_DEFAULT -DALPHALINUX \ -DMYRINET -DLINUX_IA64_INTEL NOOPT_FLAG = CC = gcc -c -O FC = /opt/intel/bin/ifort -c LD = /opt/intel/bin/ifort AR = /usr/bin/ar -r ###################################################################### The compiling process looks fine except the following message appears ----------------------------------------------------------------------------------------------------------------------------------- fortcom: Info: ./swap.inc, line 28: Symbol in BLOCK DATA program unit is not in a COMMON block. [ISWRES] INTEGER ISWFIRST,NSWBLOCK,IUNITSW,ISIDISW,ISWRES .....................................................^ fortcom: Info: ./swap.inc, line 51: Symbol in BLOCK DATA program unit is not in a COMMON block. [ISWMEM] INTEGER ISWMEM,ISWPOS,ISWSIZE,ISWACCE,ISWCUR,ISWEND,ISWREC ..................^ ------------------------------------------------------------------------------------------------------------------------------------ But still the executive file cpmd.x is finally generated without any other problems. Now when I try to run the problem with some test input file(from the link: http://homepage.mac.com/mbsullivan/prog/cpmdtut.html) I get the following error info: --------------------------------------------------------------------------------------------------------------------------------- cpmd.x: error while loading shared libraries: libcxa.so.5: cannot open shared object file: No such file or directory --------------------------------------------------------------------------------------------------------------------------------- This means I need specify some path in the program? I appreciate if you can give me any comments or suggestion to make CPMD runs successfully. Thanks, lajiapo _________________________________________________________________ ???????? MSN Explorer: http://explorer.msn.com/lccn/ From simo_dragich at hotmail.com Mon Mar 8 15:52:27 2004 From: simo_dragich at hotmail.com (simo dragich) Date: Mon, 08 Mar 2004 19:52:27 +0500 Subject: [CPMD-list] Goedecker BLYP Message-ID: Hi, For a single point calculation of 10 atom organic molecule within CPMD, using Goedecker BLYP pseudos and relatively large box I get KS energy about 50 Hartrees. An all electron calculation using BLYP functional within Gaussian98 yields KS energy about 189 Hartrees. I am sure that Gaussian calculation is OK. Please help me - where things might have gone wrong with CPMD? Are there benchmark calculations comparing CPMD energy results with all-electron calculations for molecules? Thanks _________________________________________________________________ Add photos to your messages with MSN 8. Get 2 months FREE*. http://join.msn.com/?page=features/featuredemail From apu at veccal.ernet.in Sun Mar 14 12:34:25 2004 From: apu at veccal.ernet.in (apu at veccal.ernet.in) Date: Sun, 14 Mar 2004 16:34:25 +0500 Subject: [CPMD-list] New to CPMD Message-ID: <86b39150.915086b3@veccal.ernet.in> Hi, I am new to CPMD. I have downloaded CPMD version 3.7.2. I am not getting the idea of configure. Please explain this thing to me. Suggest what should be my initial steps to learn this software. Thanking you, Apu Sarkar **************************************************** Apu Sarkar Research Fellow Variable Energy Cyclotron Centre Kolkata 700 064 phone: 91-33-2337-1230 (extn. 3190) Fax: 91-33-2334-6871 INDIA **************************************************** -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: InterScan_Disclaimer.txt Url: http://cpmd.org/pipermail/cpmd-list/attachments/20040314/1e3d8143/attachment.txt From g0306324 at nus.edu.sg Mon Mar 15 10:11:04 2004 From: g0306324 at nus.edu.sg (Dai Ling) Date: Mon, 15 Mar 2004 17:11:04 +0800 Subject: [CPMD-list] Questions on K-points setting with VANDERBILT pseudopotential Message-ID: <16995C828ADE054BA57ABEC32E7B3F377B4841@MBXSRV26.stu.nus.edu.sg> Dear Sir: I am running a program conatining Tantalum and C,H atoms. I created VANDERBILT pseudopotential ( use uspp735) for Ta and use the GOEDECKER Norm-conserving pseudopotentials for C and H. Now I have three equiries as following: 1. I found the VANDERBILT pseudopotential are not applicable to K-points settings (Monkhorst-pack etc). It can only run after I delete the K-points Keywrods, ( that is with Gamma points?). I wonder whether there is a way to set k-points both applicable for VANDERBILT and other kinds of pseudopotentials? 2. I have also tried to generate Norm-conserving pseudopotentials via fhi98PP, but it cannot be read by CPMD. I have tired the script on http://www.cpmd.org/pipermail/cpmd-list/2002-February/000023.html, but it fails ( I tried to run it as a excutable file as well as add the scripts to the psgen file, but both failed). Is there other any source for generating Norm-conserving pseudopotentials that can be read via CPMD? 3. In the output file of CPMD, all the length, mass & energy are in A.U. unit. I think A.U. represents bohr for length &mass of one proton for the mass. But for the energy, is it in eV? The question seems too simple as I am a novice in this area. Thanks & Best Regards! Scott From apu at veccal.ernet.in Mon Mar 15 15:14:45 2004 From: apu at veccal.ernet.in (apu at veccal.ernet.in) Date: Mon, 15 Mar 2004 19:14:45 +0500 Subject: [CPMD-list] New to CPMD Message-ID: <966f7cdb.7cdb966f@veccal.ernet.in> Hi everybody, I am new to CPMD. I have downloaded CPMD 3.7.2 but I can't configure it. Please help me. Regards, Apu Sarkar **************************************************** Apu Sarkar Research Fellow Variable Energy Cyclotron Centre Kolkata 700 064 phone: 91-33-2337-1230 (extn. 3190) Fax: 91-33-2334-6871 INDIA **************************************************** -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: InterScan_Disclaimer.txt Url: http://cpmd.org/pipermail/cpmd-list/attachments/20040315/59ae8644/attachment.txt From cpmd at kressworks.com Mon Mar 15 15:10:24 2004 From: cpmd at kressworks.com (Jim Kress) Date: Mon, 15 Mar 2004 09:10:24 -0500 Subject: [CPMD-list] Goedecker BLYP References: Message-ID: <001101c40a97$433f5520$0901a8c0@mmserver> There are no core electrons in CPMD. Jim ----- Original Message ----- From: "simo dragich" To: Sent: Monday, March 08, 2004 9:52 AM Subject: [CPMD-list] Goedecker BLYP > Hi, > > For a single point calculation of 10 atom organic molecule within CPMD, > using Goedecker BLYP pseudos and relatively large box I get KS energy about > 50 Hartrees. > > An all electron calculation using BLYP functional within Gaussian98 yields > KS energy about 189 Hartrees. > > I am sure that Gaussian calculation is OK. > > > Please help me - where things might have gone wrong with CPMD? > > Are there benchmark calculations comparing CPMD energy results with > all-electron calculations > for molecules? > > > Thanks > > _________________________________________________________________ > Add photos to your messages with MSN 8. Get 2 months FREE*. > http://join.msn.com/?page=features/featuredemail > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Mon Mar 15 15:38:36 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 15 Mar 2004 15:38:36 +0100 (MET) Subject: [CPMD-list] Goedecker BLYP In-Reply-To: References: Message-ID: Hi > Hi, > > For a single point calculation of 10 atom organic molecule within CPMD, > using Goedecker BLYP pseudos and relatively large box I get KS energy about > 50 Hartrees. > > An all electron calculation using BLYP functional within Gaussian98 yields > KS energy about 189 Hartrees. You can't compare total energies of all-electron and pseudopotential calculations. > > I am sure that Gaussian calculation is OK. > > > Please help me - where things might have gone wrong with CPMD? > > Are there benchmark calculations comparing CPMD energy results with > all-electron calculations > for molecules? See for example the papers PRB 58 3641 (1998) PRB 54 1703 (1996) regrads Juerg Hutter > > > Thanks > > _________________________________________________________________ > Add photos to your messages with MSN 8. Get 2 months FREE*. > http://join.msn.com/?page=features/featuredemail > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From eesantis at unity.ncsu.edu Mon Mar 15 17:00:51 2004 From: eesantis at unity.ncsu.edu (Erik Santiso) Date: Mon, 15 Mar 2004 11:00:51 -0500 (EST) Subject: [CPMD-list] P-RFO Message-ID: <3064.24.74.147.174.1079366451.squirrel@webmail.ncsu.edu> Hi, I'm having a little trouble running a P-RFO search with CPMD. I'm trying to follow one of the eigenmodes starting from an equilibrium geometry. The input I'm using is: &CPMD OPTIMIZE GEOMETRY ISOLATED MOLECULE MEMORY BIG PRFO PRFO PRJHES PRFO MODE 3 RESTART WAVEFUNCTION COORDINATES LATEST &END &SYSTEM SYMMETRY 0 CELL 30.0000 1.0 1.0 0.0 0.0 0.0 CUTOFF 35 &END &ATOMS *006-C-gbl-n-erik.uspp FORMATTED NEWF NLCC LMAX=P 1 1.634613 0.961493 0.000000 *008-O-gbl-n-erik.uspp FORMATTED NEWF NLCC LMAX=P 1 1.634613 2.884667 0.000000 *001-H-gbl--erik.uspp FORMATTED NEWF LMAX=S 2 0.000000 0.000000 0.000000 3.269226 0.096187 0.000000 &END &DFT FUNCTIONAL BLYP GC-CUTOFF 5.D-5 &END I've also tried to just follow the first mode, and to do a vibrational analysis first and use "RESTART HESSIAN". In all cases the result is the same: the molecule does not move. Am I missing something? Thanks for your help! Erik. From ZRLSRB at ch.ibm.com Mon Mar 15 18:24:55 2004 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Mon, 15 Mar 2004 18:24:55 +0100 Subject: [CPMD-list] P-RFO Message-ID: Hi, before the transition-state search, it is very helpful to shift the atoms most directly involved in the reaction towards the products. This has mainly two reasons: - Avoid starting from near a stationary point. The convergence criteria are already met. If the system leaves the initial "stationary point" at all, the direction you go is co-determined by the (random) residual gradient. - At a reactant (or product) configuration, you cannot expect the curvature along a reaction coordinate to be particularly small; if bond breaking is involved, it's even quite unlikely that a reaction coordinate has a low frequency there (stretching vs. bending modes). The coordinate you are looking for could be almost anywhere in the spectrum. Otherwise, your approach is fine for smaller systems: - Do a vibrational analysis - Determine the mode to follow - Re-use the Hessian A small technical hint: it's not enough to specify RESTART HESSIAN This will only affect the system Hessian which is different from the 'partial Hessian' used by P-RFO. This is required for the linear-scaling microiterative scheme (variational decoupling: P-RFO for core / L-BFGS for environment) where P-RFO handles only a fraction of the degrees of freedom. However, you can copy the relevant part of the system Hessian to the partial Hessian using PRFO HESSTYPE 1 Also the opposite is possible if you want to use the Powell-updated Hessian for subsequent vibrational analysis (partial Hessian to Hessian): VIBRATIONAL ANALYSIS IN RESTART PHESS HESSIAN PARTIAL [UNIT,SCHLEGEL,DISCO] Hope this helps. Best regards Salomon From ivan_van_van at yahoo.com Tue Mar 16 22:31:11 2004 From: ivan_van_van at yahoo.com (Ivan Ivanov) Date: Tue, 16 Mar 2004 13:31:11 -0800 (PST) Subject: [CPMD-list] cpmd equilibrium In-Reply-To: Message-ID: <20040316213111.77734.qmail@web20422.mail.yahoo.com> Dear CPMD Experts, I am doing CPMD calculation of CH3OH hydrogen bonded to CH3NH2. I have achieved 1e-6 Ha accuracy for this system but 1e-2 Ha is the fluctuation for the system in external electrostatic field (EXTERNAL POTENTIAL keyword). In fact there is no systematic drift of EHAM - just large fluctuation. Is this trajectory reliable for blue-moon free energy calculation? I am using large box, 300K, 0.01 electronic fictitious temp. Without external potential everything is OK. Thanks Ivan Do you Yahoo!? Yahoo! Mail - More reliable, more storage, less spam -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20040316/3cddf5a8/attachment.html From weiqiao at wag.caltech.edu Tue Mar 16 23:11:20 2004 From: weiqiao at wag.caltech.edu (weiqiao Deng) Date: Tue, 16 Mar 2004 14:11:20 -0800 Subject: [CPMD-list] QMMM functional in CPMD Message-ID: <000801c40ba3$9d8f5e50$0d1ad783@citrix> Dear list, I tried to use QMMM function in CPMD. But I can't find any manual or example of input of this function. Can anybody do me a favor to give a brief introduction? Thanks in advance. Weiqiao -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20040316/9eed26fe/attachment.html From ketajone at yahoo.com Wed Mar 17 16:28:03 2004 From: ketajone at yahoo.com (Keta Jones) Date: Wed, 17 Mar 2004 07:28:03 -0800 (PST) Subject: [CPMD-list] constructing hydrated aluminium layers In-Reply-To: Message-ID: <20040317152803.4663.qmail@web13124.mail.yahoo.com> Dear CPMD users, I want to study some water molecules between two layers of hydrated aluminium.I have the water co-ordinates, but my problem is to cinstruct the hydrated aluminium layers. Would someone help me how to construct the aluminium layers for study.Is there any package available for constructing this type of two layers. Thanks in advance keta ===== Keta ************************************************************************************** __________________________________ Do you Yahoo!? Yahoo! Mail - More reliable, more storage, less spam http://mail.yahoo.com From ct at chemie.hu-berlin.de Wed Mar 17 18:46:00 2004 From: ct at chemie.hu-berlin.de (Christian Tuma) Date: Wed, 17 Mar 2004 18:46:00 +0100 Subject: [CPMD-list] problems with point group recognition and symmetrisation of coordinates Message-ID: <20040317174600.GH291346@uranus.chemie.hu-berlin.de> Dear CPMD developers, using CPMD 3.7.2 (Linux-PC, Redhat 9.0, ifort 8.0, ATLAS 3.6.0) I encountered problems with the recognition of molecular point groups and subsequent symmetrisation of coordinates. For the case of the methane molecule (CH4, symmetry point group "Td") I used two different orientations of the molecule in a cartesian coordinate system. Depending on which orientation I have chosen, I got quite different results concerning the recognition of a number of subgroups of "Td" and "Td" itself: A) one C2-axis corresponds to the z-axis, and the x-axis is orthogonal to a mirror plane ... &ATOMS *TM/C_TM_PBE_pade_110 KLEINMAN-BYLANDER LMAX=P 1 0.0000 0.0000 0.0000 *TM/H_TM_PBE_pade_070 KLEINMAN-BYLANDER LMAX=S 4 0.0035 -0.8952 0.6336 -0.8988 -0.0005 -0.6284 0.0031 0.8958 0.6327 0.8920 0.0000 -0.6379 &END ... C2, C2v : recognition and symmetrisation ok S4 : recognition ok, symmetrisation problem "ATOMS ARE VERY CLOSE" Td : recognition ok, symmetrisation problems DELTA=0.01 : bonds far too short DELTA=0.1 : loss of 4 symmetry operations D2d, D2 : not recognised B) all C2-axes correspond to cartesian axes ... &ATOMS *TM/C_TM_PBE_pade_110 KLEINMAN-BYLANDER LMAX=P 1 0.0000 0.0000 0.0000 *TM/H_TM_PBE_pade_070 KLEINMAN-BYLANDER LMAX=S 4 0.6355 -0.6304 0.6336 -0.6352 -0.6359 -0.6286 -0.6312 0.6356 0.6327 0.6307 0.6308 -0.6379 &END ... C2, D2 : recognition and symmetrisation ok C2v, Td : not recognised S4 : recognition ok, symmetrisation problem "ATOMS ARE VERY CLOSE" D2d : recognition ok, symmetrisation problems (bonds far too short) The rest of the input was as follows (with different Schoenfliess symbols): ! CH4 &CPMD OPTIMIZE GEOMETRY MAXSTEP 1 STRUCTURE BONDS ANGLES &END &SYSTEM ANGSTROM POINT GROUP MOLECULE DELTA=0.01 DND 2 sYMMETRIZE COORDINATES SYMMETRY 0 CUTOFF 50 CELL 5.0 1.0 1.0 0.0 0.0 0.0 &END &ATOMS ... &END &DFT NEWCODE FUNCTIONAL PBE &END These observations for (A) and (B) are somehow complementary, especially concerning the "D" point subgroups. That's why I think there is no way to put the CH4-molecule such that everything goes fine with all these symmetry point subgroups. So what's wrong? I took a look into the source code, but at some point I was unable to follow the programmers' ideas. My only vague idea is that the generation of the symmetry operators might not be sufficiently flexible, i.e. some of them could be excluded from each other. Do the CPMD developers know where the problem is hidden and how it can be fixed? Thanks a lot, Christian Tuma. PS: Another example for the failure in symmetry recognition is the case of the staggered ethane molecule C2H6. Although being aligned along the z-axis, CPMD doesn't recognise it as "D3d". -- Christian Tuma Humboldt-Universitaet Berlin ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer From weiqiao at wag.caltech.edu Wed Mar 17 23:37:35 2004 From: weiqiao at wag.caltech.edu (Weiqiao Deng) Date: Wed, 17 Mar 2004 14:37:35 -0800 (PST) Subject: [CPMD-list] Where to find more examples? Message-ID: Dear list, I am a beginner to use CPMD and hope to find more examples to repeat and learn CPMD simulation. Here is the special example I am interested at repeating. Anyone has that input file of that example? Thanks in advance. Tuckerman ME, Marx D, Parrinello M The nature and transport mechanism of hydrated hydroxide ions in aqueous solution NATURE 417 (6892): 925-929 JUN 27 2002 Weiqiao From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu Mar 18 08:29:23 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 18 Mar 2004 08:29:23 +0100 (CET) Subject: [CPMD-list] QMMM functional in CPMD In-Reply-To: <000801c40ba3$9d8f5e50$0d1ad783@citrix> Message-ID: On Tue, 16 Mar 2004, weiqiao Deng wrote: WD> Dear list, WD> WD> I tried to use QMMM function in CPMD. But I can't find any manual or WD> example of input of this function. Can anybody do me a favor to give a WD> brief introduction? dear weiqioa, to use QM/MM with CPMD you need additional software. assuming you are referring to the CPMD/Gromos interface, please have a look at the homepage of prof. ursula roethlisberger or more specifically at to learn what you need to do to get access to that code. regargs, axel. WD> WD> Thanks in advance. WD> WD> Weiqiao WD> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu Mar 18 08:40:41 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 18 Mar 2004 08:40:41 +0100 (CET) Subject: [CPMD-list] Where to find more examples? In-Reply-To: Message-ID: On Wed, 17 Mar 2004, Weiqiao Deng wrote: WD> Dear list, WD> WD> I am a beginner to use CPMD and hope to find more examples to repeat and WD> learn CPMD simulation. WD> WD> Here is the special example I am interested at repeating. Anyone has that WD> input file of that example? Thanks in advance. WD> WD> Tuckerman ME, Marx D, Parrinello M WD> The nature and transport mechanism of hydrated hydroxide ions in aqueous WD> solution NATURE 417 (6892): 925-929 JUN 27 2002 dear weiqiao, there is a 32-bulk water example in the cpmd-test archive, using MT pseudopotentials, you could use that as a starting point. i suggest you first equilibrate a suitable configuration with a classical MD simulation (i found the SPC/E water potential seems to yield structures, that are very close to the CP-MD structures with the BLYP functional). this way you would have a comparatively short equilibration time for the CP-MD run (compared to, e.g. removing a hydrogen atom from a bulk water system). btw: don't forget to set the charge or you will get very surprising results. good luck, axel. WD> WD> Weiqiao WD> WD> _______________________________________________ WD> CPMD-list mailing list WD> CPMD-list at cpmd.org WD> http://www.cpmd.org/mailman/listinfo/cpmd-list WD> WD> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu Mar 18 08:44:12 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 18 Mar 2004 08:44:12 +0100 (CET) Subject: [CPMD-list] New to CPMD In-Reply-To: <966f7cdb.7cdb966f@veccal.ernet.in> Message-ID: On Mon, 15 Mar 2004 apu at veccal.ernet.in wrote: AS> AS> Hi everybody, AS> AS> I am new to CPMD. AS> I have downloaded CPMD 3.7.2 AS> but I can't configure it. please be a bit more specific. the basic procedure of configuring (which means creating a suitable makefile) and compiling cpmd is described in the manual. which part of the steps do you have problems with? axel kohlmeyer. AS> AS> Please help me. AS> AS> Regards, AS> AS> Apu Sarkar AS> **************************************************** AS> Apu Sarkar AS> Research Fellow AS> Variable Energy Cyclotron Centre AS> Kolkata 700 064 AS> phone: 91-33-2337-1230 (extn. 3190) AS> Fax: 91-33-2334-6871 AS> INDIA AS> **************************************************** AS> AS> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu Mar 18 08:54:10 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 18 Mar 2004 08:54:10 +0100 (CET) Subject: [CPMD-list] running error in CPMD In-Reply-To: Message-ID: On Sun, 7 Mar 2004, [gb2312] ?? ?? wrote: > Dear all, > > I am new for using CPMD. > My running platform is RedHat9.0. I am using Intel Fortran > Compiler8.0. > First, I use > -------------------------------------------------------- > Configure LINUX_IA64_INTEL > Makefile > -------------------------------------------------------- > to generate the Makefile. > Then > I modified some parameters in Makefile because I have not installed > Intel MKL yet (Is that necessary?). Now the Makefile looks like: no, you can use ATLAS instead. see . > ################################################################# > SHELL = /bin/sh > # > #--------------- Default Configuration for LINUX_IA64_INTEL > --------------- > SRC = . > DEST = . > BIN = . > #QMMM_FLAGS = -D__QMECHCOUPL > #QMMM_LIBS = -L. -lmm > FFLAGS = > #LFLAGS = -L/opt/intel/mkl/lib/64 -lmkl_itp -lmkl_lapack -lmkl_itp \ > # -lPEPCF90 -lm -lpthread $(QMMM_LIBS) > LFLAGS = -llapack /usr/lib/gcc-lib/i386-redhat-linux/3.2.2/libg2c.a\ > -lm -lpthread $(QMMM_LIBS) > CFLAGS = -D__alpha > CPP = /lib/cpp -P -C -traditional > CPPFLAGS = -D__alpha -DPOINTER8 -DLAPACK -DFFT_DEFAULT -DALPHALINUX \ > -DMYRINET -DLINUX_IA64_INTEL > NOOPT_FLAG = > CC = gcc -c -O > FC = /opt/intel/bin/ifort -c > LD = /opt/intel/bin/ifort > AR = /usr/bin/ar -r > ###################################################################### > > The compiling process looks fine except the following message > appears > ----------------------------------------------------------------------------------------------------------------------------------- > > fortcom: Info: ./swap.inc, line 28: Symbol in BLOCK DATA program > unit is not in a COMMON block. [ISWRES] > INTEGER ISWFIRST,NSWBLOCK,IUNITSW,ISIDISW,ISWRES > .....................................................^ > fortcom: Info: ./swap.inc, line 51: Symbol in BLOCK DATA program > unit is not in a COMMON block. [ISWMEM] > INTEGER ISWMEM,ISWPOS,ISWSIZE,ISWACCE,ISWCUR,ISWEND,ISWREC > ..................^ > ------------------------------------------------------------------------------------------------------------------------------------ this is not exactly good programming practice, but not a problem. the intel fortran compilers version 8 use the fortran front end from the compaq fortran compiler, which is very picky about programming style. > > But still the executive file cpmd.x is finally generated without any > other problems. > > Now when I try to run the problem with some test input file(from the > link: http://homepage.mac.com/mbsullivan/prog/cpmdtut.html) > I get the following error info: > --------------------------------------------------------------------------------------------------------------------------------- > > cpmd.x: error while loading shared libraries: libcxa.so.5: cannot > open shared object file: No such file or directory your cpmd executable does not find the intel compiler runtime (shared) library you need to either link it statically or modify your shared linker path to find the intel libraries. see: for more information on that (i does not cover intel fortran 8 yet, but all the stuff for intel fortran 7 applies with the exception that intel fortran 8 supports NPT-glibc based distributions natively without any weird workarounds. hope this helps, axel kohlmeyer. > --------------------------------------------------------------------------------------------------------------------------------- > > This means I need specify some path in the program? > I appreciate if you can give me any comments or suggestion to make > CPMD runs successfully. > > Thanks, > > lajiapo > > _________________________________________________________________ > ???????? MSN Explorer: http://explorer.msn.com/lccn/ > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > > -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= From tangxin at student.dlut.edu.cn Thu Mar 18 09:12:31 2004 From: tangxin at student.dlut.edu.cn (tangxin at student.dlut.edu.cn) Date: Thu, 18 Mar 2004 16:12:31 +0800 Subject: [CPMD-list] bond energy Message-ID: <1079597551.405959ef92a35@mailb.dlut.edu.cn> Dear all: I am new to CPMD. I want to know whether CPMD code can calculate the bond energy. If it can do it ,which keyword should I use? thanks Xin Tang ------------------------------------------------- ????????????????????web????????: http://mail.dlut.edu.cn From eesantis at unity.ncsu.edu Thu Mar 18 18:20:12 2004 From: eesantis at unity.ncsu.edu (Erik Santiso) Date: Thu, 18 Mar 2004 12:20:12 -0500 (EST) Subject: [CPMD-list] bond energy In-Reply-To: <1079597551.405959ef92a35@mailb.dlut.edu.cn> References: <1079597551.405959ef92a35@mailb.dlut.edu.cn> Message-ID: <1839.152.14.40.160.1079630412.squirrel@webmail.ncsu.edu> Hi, This is what I do to get bond energies: (1) Run a geometry optimization with the molecule. (2) Run a wavefunction optimization with each atom separately (you're going to need to use LSD and maybe specify the spin multiplicity). (3) Substract the energies you got in (2) from the energy you got in (1). (4) Do a vibrational analysis on the molecule. (5) Use the frequencies to get the zero-point energy. Substract this from the energy you got in (3) and you have the bond energy. Erik. ------------------------------------- Vir prudens non contra ventum mingit. > > > Dear all: > I am new to CPMD. > I want to know whether CPMD code can calculate the bond energy. > If it can do it ,which keyword should I use? > > thanks > Xin Tang > > ------------------------------------------------- > ????????????????????web????????: http://mail.dlut.edu.cn > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From weiqiao at wag.caltech.edu Thu Mar 18 22:13:52 2004 From: weiqiao at wag.caltech.edu (Weiqiao Deng) Date: Thu, 18 Mar 2004 13:13:52 -0800 (PST) Subject: [CPMD-list] Where to find more examples? In-Reply-To: Message-ID: Dear Axel, Many thanks for your message. I have one more question. 32-bulk water is a neutral system. If we have extra OH- or H+ in the system, we set the charge as -1 or +1 for whole system? Do we have a way to set the particle extra H's charge as +1? Thanks. Weiqiao On Thu, 18 Mar 2004, Axel Kohlmeyer wrote: > On Wed, 17 Mar 2004, Weiqiao Deng wrote: > > WD> Dear list, > WD> > WD> I am a beginner to use CPMD and hope to find more examples to repeat and > WD> learn CPMD simulation. > WD> > WD> Here is the special example I am interested at repeating. Anyone has that > WD> input file of that example? Thanks in advance. > WD> > WD> Tuckerman ME, Marx D, Parrinello M > WD> The nature and transport mechanism of hydrated hydroxide ions in aqueous > WD> solution NATURE 417 (6892): 925-929 JUN 27 2002 > > dear weiqiao, > > there is a 32-bulk water example in the cpmd-test archive, > using MT pseudopotentials, you could use that as a starting point. > > i suggest you first equilibrate a suitable configuration with > a classical MD simulation (i found the SPC/E water potential > seems to yield structures, that are very close to the > CP-MD structures with the BLYP functional). this way you > would have a comparatively short equilibration time > for the CP-MD run (compared to, e.g. removing a hydrogen > atom from a bulk water system). > > btw: don't forget to set the charge or you > will get very surprising results. > > good luck, > axel. > > WD> > WD> Weiqiao > WD> > WD> _______________________________________________ > WD> CPMD-list mailing list > WD> CPMD-list at cpmd.org > WD> http://www.cpmd.org/mailman/listinfo/cpmd-list > WD> > WD> > > From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu Mar 18 22:50:48 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 18 Mar 2004 22:50:48 +0100 Subject: [CPMD-list] Where to find more examples? In-Reply-To: Message-ID: <200403182150.i2ILomD25479@yello.theochem.ruhr-uni-bochum.de> On Thu, 18 Mar 2004 13:13:52 -0800 (PST) Weiqiao Deng wrote: > Dear Axel, > > > Many thanks for your message. > I have one more question. 32-bulk water is a neutral system. If we have > extra OH- or H+ in the system, we set the charge as -1 or +1 for whole > system? Do we have a way to set the particle extra H's charge as +1? > Thanks. you can only set the charge for the whole system (CHARGE keyword, &SYSTEM section). cpmd uses that information in combination with the (effective) charges of the atoms from the pseudopotential files to compute the total number of electrons in the system. the actual charge distribution will be calculated, when you do the wavefunction optimization. please note that the keyword ATOMIC CHARGES (&ATOMS section) is only used to calculate the initial guess for the electron structure and has no effect on the total number of electrons. you may also have a look at which might be helpful to contruct the &ATOMS and &SYSTEM section of for your simulations if you feed it an xyz-file with your pre-equlibrated restart. you may have to adapt it for your choice of pseudopotentials. axel > > Weiqiao > > > On Thu, 18 Mar 2004, Axel Kohlmeyer wrote: > > > On Wed, 17 Mar 2004, Weiqiao Deng wrote: > > > > WD> Dear list, > > WD> > > WD> I am a beginner to use CPMD and hope to find more examples to repeat and > > WD> learn CPMD simulation. > > WD> > > WD> Here is the special example I am interested at repeating. Anyone has that > > WD> input file of that example? Thanks in advance. > > WD> > > WD> Tuckerman ME, Marx D, Parrinello M > > WD> The nature and transport mechanism of hydrated hydroxide ions in aqueous > > WD> solution NATURE 417 (6892): 925-929 JUN 27 2002 > > > > dear weiqiao, > > > > there is a 32-bulk water example in the cpmd-test archive, > > using MT pseudopotentials, you could use that as a starting point. > > > > i suggest you first equilibrate a suitable configuration with > > a classical MD simulation (i found the SPC/E water potential > > seems to yield structures, that are very close to the > > CP-MD structures with the BLYP functional). this way you > > would have a comparatively short equilibration time > > for the CP-MD run (compared to, e.g. removing a hydrogen > > atom from a bulk water system). > > > > btw: don't forget to set the charge or you > > will get very surprising results. > > > > good luck, > > axel. > > > > WD> > > WD> Weiqiao > > WD> > > WD> _______________________________________________ > > WD> CPMD-list mailing list > > WD> CPMD-list at cpmd.org > > WD> http://www.cpmd.org/mailman/listinfo/cpmd-list > > WD> > > WD> > > > > > -- ======================================================================= 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 eesantis at unity.ncsu.edu Fri Mar 19 05:09:40 2004 From: eesantis at unity.ncsu.edu (Erik Santiso) Date: Thu, 18 Mar 2004 23:09:40 -0500 (EST) Subject: [CPMD-list] P-RFO In-Reply-To: References: Message-ID: <3754.24.74.147.174.1079669380.squirrel@webmail.ncsu.edu> Hi again, I've tried this, and it works in several of the cases I'm looking at. However, for the formaldehyde example (the one I sent originally) I'm still having trouble. It seems that, no matter what I try (i.e. specifying different modes with PRFO mode, or moving the atoms along an eigenmode and start the optimization), P-RFO always wants to go to the minimum instead of the transition state. Here's the input file I'm using now: &CPMD GEOMETRY OPTIMIZATION xyz ISOLATED MOLECULE MEMORY BIG CONVERGENCE ENERGY 0.05 RESTART WAVEFUNCTION COORDINATES HESSIAN LATEST PRFO PRFO PRJHES PRFO MODE 1 PRFO HESSTYPE 1 &END &SYSTEM SYMMETRY 0 CELL 15.0000 1.0 1.0 0.0 0.0 0.0 CUTOFF 35 &END &ATOMS *C_BLYP.uspp FORMATTED NEWF LMAX=P 1 2.096865 1.778271 2.100213 *O_BLYP.uspp FORMATTED NEWF LMAX=P 1 3.098650 1.778271 2.100213 *H_BLYP.uspp FORMATTED NEWF LMAX=S 2 1.658508 1.490827 2.100130 2.655409 1.446718 2.100386 &END &DFT FUNCTIONAL BLYP GC-CUTOFF 5.D-5 &END This is after running a geometry optimization on a molecule where the atoms where displaced along the reactive mode (the same that is now mode 1). I've also tried using a transition state from the literature (JPCA 102,10805) as a starting point, running a vibrational analysis on it, and following the reactive mode, but CPMD converges to the minimum structure again. Is there anything that looks wrong on my input file? I can send the GEOMETRY, HESSIAN, etc. files if necessary if that may help pinpointing what the problem is. Thanks a lot for your help again, Erik. ------------------------------------- Vir prudens non contra ventum mingit. > > > > > Hi, > > before the transition-state search, it is very helpful to shift the atoms > most directly involved in the reaction towards the products. This has > mainly two reasons: > > - Avoid starting from near a stationary point. The convergence criteria > are > already met. If the system leaves the initial "stationary point" at all, > the direction you go is co-determined by the (random) residual gradient. > - At a reactant (or product) configuration, you cannot expect the > curvature > along a reaction coordinate to be particularly small; if bond breaking is > involved, it's even quite unlikely that a reaction coordinate has a low > frequency there (stretching vs. bending modes). The coordinate you are > looking for could be almost anywhere in the spectrum. > > Otherwise, your approach is fine for smaller systems: > - Do a vibrational analysis > - Determine the mode to follow > - Re-use the Hessian > > A small technical hint: it's not enough to specify > > RESTART HESSIAN > > This will only affect the system Hessian which is different from the > 'partial Hessian' used by P-RFO. This is required for the linear-scaling > microiterative scheme (variational decoupling: P-RFO for core / L-BFGS for > environment) where P-RFO handles only a fraction of the degrees of > freedom. > However, you can copy the relevant part of the system Hessian to the > partial Hessian using > > PRFO HESSTYPE > 1 > > Also the opposite is possible if you want to use the Powell-updated > Hessian > for subsequent vibrational analysis (partial Hessian to Hessian): > > VIBRATIONAL ANALYSIS IN > RESTART PHESS > HESSIAN PARTIAL [UNIT,SCHLEGEL,DISCO] > > Hope this helps. > > Best regards > Salomon > > From ZRLSRB at ch.ibm.com Fri Mar 19 09:38:51 2004 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Fri, 19 Mar 2004 09:38:51 +0100 Subject: [CPMD-list] P-RFO Message-ID: Hi, possibly, this is caused by the size of your box. It looks much too small. This could cause a problem especially if you are studying molecular decompositiion where the space between the molecules you are forming is very important. The Hockney Poisson solver (default for isolated system) requires the density to disappear at the border. For practical hints on the box size, you can have a look at the posting of 17 Aug 2002 by J. Hutter in this list. Do you see any negative eigenvalue of the Hessian at the transition state geometry from the literature? Best regards, Salomon From hutter at pci.unizh.ch Fri Mar 19 13:55:01 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Fri, 19 Mar 2004 13:55:01 +0100 (MET) Subject: [CPMD-list] problems with point group recognition and symmetrisation of coordinates In-Reply-To: <20040317174600.GH291346@uranus.chemie.hu-berlin.de> References: <20040317174600.GH291346@uranus.chemie.hu-berlin.de> Message-ID: Hi There are several possible sources of errors using the point group molecule functionality. - you need to position the molecule according the following rules C - Positioning of the molecule: C z-axis is the principal axis C x-axis is the two-fold axis C xz-plane is the sigma-v plane C xy-plane is the sigma-h or the Cs symmetry plane C origin is the center of inversion This means for example that for certain subgroups of Td you have to rotate the molecule in the input. - The parser has a rather strange format for the Schoenfliess symbols SYMBOL NAXIS where SYMBOL is C,CNH,CS,CNV,S,D,DNH,DND,DN,T,TD,O,OH,I,IH and NAXIS the value of the principle axis N. Put NAXIS=0 where there is no priciple axis. It's still possible that there are some bugs for certain point groups. I can't remember how seriously this was checked at the time. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Wed, 17 Mar 2004, Christian Tuma wrote: > Dear CPMD developers, > > using CPMD 3.7.2 (Linux-PC, Redhat 9.0, ifort 8.0, ATLAS 3.6.0) I encountered > problems with the recognition of molecular point groups and subsequent > symmetrisation of coordinates. > For the case of the methane molecule (CH4, symmetry point group "Td") I used > two different orientations of the molecule in a cartesian coordinate system. > Depending on which orientation I have chosen, I got quite different results > concerning the recognition of a number of subgroups of "Td" and "Td" itself: > > A) one C2-axis corresponds to the z-axis, and the x-axis is orthogonal to > a mirror plane > > ... > &ATOMS > *TM/C_TM_PBE_pade_110 KLEINMAN-BYLANDER > LMAX=P > 1 > 0.0000 0.0000 0.0000 > *TM/H_TM_PBE_pade_070 KLEINMAN-BYLANDER > LMAX=S > 4 > 0.0035 -0.8952 0.6336 > -0.8988 -0.0005 -0.6284 > 0.0031 0.8958 0.6327 > 0.8920 0.0000 -0.6379 > &END > ... > > C2, C2v : recognition and symmetrisation ok > S4 : recognition ok, symmetrisation problem "ATOMS ARE VERY CLOSE" > Td : recognition ok, symmetrisation problems > DELTA=0.01 : bonds far too short > DELTA=0.1 : loss of 4 symmetry operations > D2d, D2 : not recognised > > > B) all C2-axes correspond to cartesian axes > > ... > &ATOMS > *TM/C_TM_PBE_pade_110 KLEINMAN-BYLANDER > LMAX=P > 1 > 0.0000 0.0000 0.0000 > *TM/H_TM_PBE_pade_070 KLEINMAN-BYLANDER > LMAX=S > 4 > 0.6355 -0.6304 0.6336 > -0.6352 -0.6359 -0.6286 > -0.6312 0.6356 0.6327 > 0.6307 0.6308 -0.6379 > &END > ... > > C2, D2 : recognition and symmetrisation ok > C2v, Td : not recognised > S4 : recognition ok, symmetrisation problem "ATOMS ARE VERY CLOSE" > D2d : recognition ok, symmetrisation problems (bonds far too short) > > > The rest of the input was as follows (with different Schoenfliess symbols): > > ! CH4 > &CPMD > OPTIMIZE GEOMETRY > MAXSTEP > 1 > STRUCTURE BONDS ANGLES > &END > &SYSTEM > ANGSTROM > POINT GROUP MOLECULE DELTA=0.01 > DND 2 > sYMMETRIZE COORDINATES > SYMMETRY > 0 > CUTOFF > 50 > CELL > 5.0 1.0 1.0 0.0 0.0 0.0 > &END > &ATOMS > ... > &END > &DFT > NEWCODE > FUNCTIONAL PBE > &END > > > These observations for (A) and (B) are somehow complementary, especially > concerning the "D" point subgroups. That's why I think there is no way to > put the CH4-molecule such that everything goes fine with all these symmetry > point subgroups. > So what's wrong? I took a look into the source code, but at some point I > was unable to follow the programmers' ideas. My only vague idea is that > the generation of the symmetry operators might not be sufficiently flexible, > i.e. some of them could be excluded from each other. Do the CPMD developers > know where the problem is hidden and how it can be fixed? > > Thanks a lot, > > Christian Tuma. > > PS: Another example for the failure in symmetry recognition is the case > of the staggered ethane molecule C2H6. Although being aligned along > the z-axis, CPMD doesn't recognise it as "D3d". > > -- > Christian Tuma Humboldt-Universitaet Berlin > ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) > phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY > fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From ct at chemie.hu-berlin.de Fri Mar 19 15:50:40 2004 From: ct at chemie.hu-berlin.de (Christian Tuma) Date: Fri, 19 Mar 2004 15:50:40 +0100 Subject: [CPMD-list] problems with point group recognition and symmetrisation of coordinates In-Reply-To: References: <20040317174600.GH291346@uranus.chemie.hu-berlin.de> Message-ID: <20040319145040.GB294719@uranus.chemie.hu-berlin.de> Hello, On Fri, Mar 19, 2004 at 01:55:01PM +0100, Juerg Hutter wrote: > C - Positioning of the molecule: > C z-axis is the principal axis > C x-axis is the two-fold axis > C xz-plane is the sigma-v plane > C xy-plane is the sigma-h or the Cs symmetry plane > C origin is the center of inversion These conditions cannot be fulfilled completely in the case of the Td-group. Here the three C2-axes are orthogonal to each other, and the (four) principal axes (C3) are not orthogonal to any of the C2-axes. For some reason, however, using one of my two examples (the one with the z-axis corresponding to a C2-axis and the xz-plane as a mirror-plane, see previous posting), the point group Td was recognised, but, the symmetrisation failed. Some years ago I used CPMD 3.0h (!) for a molecule in C3v-symmetry, at that time the symmetrisation worked well (at least for this case of C3v). Using the same input and CPMD 3.7.2 the symmetrisation fails. This might be an indication that at least the problem of the symmetrisation of coordinates could be related to a bug which might have arisen in the development towards version 3.7.2. > It's still possible that there are some bugs for certain > point groups. Yes, e.g. systems in D3d are not recognised as such. I carefully tested it according to the rules you mentioned. At least C3v was working here, maybe the problems are connected to the three C2-axes in the xy-plane. Is there a chance that these problems might get fixed in the next CPMD release? With best regards, Christian Tuma. -- Christian Tuma Humboldt-Universitaet Berlin ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer From eesantis at unity.ncsu.edu Fri Mar 19 18:15:23 2004 From: eesantis at unity.ncsu.edu (Erik Santiso) Date: Fri, 19 Mar 2004 12:15:23 -0500 (EST) Subject: [CPMD-list] P-RFO In-Reply-To: References: Message-ID: <3030.24.74.147.174.1079716523.squirrel@webmail.ncsu.edu> Hi, Yes, I get actually two negative eigenvalues at the TS from the paper. The one for CHHO->CO+H2 is the second mode in that case. These negative eigenvalues also appear when I displace the atoms along the reactive mode starting from the equilibrium geometry. But I didn't think of the size of the box. I will take a look at the post and try a larger size. Many thanks again for your help! Erik. ------------------------------------- Vir prudens non contra ventum mingit. > > > > > Hi, > > possibly, this is caused by the size of your box. It looks much too small. > This could cause a problem especially if you are studying molecular > decompositiion where the space between the molecules you are forming is > very important. The Hockney Poisson solver (default for isolated system) > requires the density to disappear at the border. For practical hints on > the > box size, you can have a look at the posting of 17 Aug 2002 by J. Hutter > in > this list. Do you see any negative eigenvalue of the Hessian at the > transition state geometry from the literature? > > Best regards, > Salomon > > From weiqiao at wag.caltech.edu Mon Mar 22 04:02:33 2004 From: weiqiao at wag.caltech.edu (Weiqiao Deng) Date: Sun, 21 Mar 2004 19:02:33 -0800 (PST) Subject: [CPMD-list] Where to find more examples? In-Reply-To: <200403182150.i2ILomD25479@yello.theochem.ruhr-uni-bochum.de> Message-ID: Many thanks for your message. I checked your website. It is indeed helful. Weiqiao On Thu, 18 Mar 2004, Axel Kohlmeyer wrote: > On Thu, 18 Mar 2004 13:13:52 -0800 (PST) Weiqiao Deng wrote: > > > Dear Axel, > > > > > > Many thanks for your message. > > I have one more question. 32-bulk water is a neutral system. If we have > > extra OH- or H+ in the system, we set the charge as -1 or +1 for whole > > system? Do we have a way to set the particle extra H's charge as +1? > > Thanks. > > you can only set the charge for the whole system > (CHARGE keyword, &SYSTEM section). cpmd uses that > information in combination with the (effective) > charges of the atoms from the pseudopotential files > to compute the total number of electrons in the system. > > the actual charge distribution > will be calculated, when you do the wavefunction > optimization. please note that the keyword ATOMIC CHARGES > (&ATOMS section) is only used to calculate the initial > guess for the electron structure and has no effect on > the total number of electrons. > > you may also have a look at > > which might be helpful to contruct the &ATOMS and &SYSTEM section > of for your simulations if you feed it an xyz-file with your pre-equlibrated > restart. you may have to adapt it for your choice of pseudopotentials. > > axel > > > > > Weiqiao > > > > > > On Thu, 18 Mar 2004, Axel Kohlmeyer wrote: > > > > > On Wed, 17 Mar 2004, Weiqiao Deng wrote: > > > > > > WD> Dear list, > > > WD> > > > WD> I am a beginner to use CPMD and hope to find more examples to repeat and > > > WD> learn CPMD simulation. > > > WD> > > > WD> Here is the special example I am interested at repeating. Anyone has that > > > WD> input file of that example? Thanks in advance. > > > WD> > > > WD> Tuckerman ME, Marx D, Parrinello M > > > WD> The nature and transport mechanism of hydrated hydroxide ions in aqueous > > > WD> solution NATURE 417 (6892): 925-929 JUN 27 2002 > > > > > > dear weiqiao, > > > > > > there is a 32-bulk water example in the cpmd-test archive, > > > using MT pseudopotentials, you could use that as a starting point. > > > > > > i suggest you first equilibrate a suitable configuration with > > > a classical MD simulation (i found the SPC/E water potential > > > seems to yield structures, that are very close to the > > > CP-MD structures with the BLYP functional). this way you > > > would have a comparatively short equilibration time > > > for the CP-MD run (compared to, e.g. removing a hydrogen > > > atom from a bulk water system). > > > > > > btw: don't forget to set the charge or you > > > will get very surprising results. > > > > > > good luck, > > > axel. > > > > > > WD> > > > WD> Weiqiao > > > WD> > > > WD> _______________________________________________ > > > WD> CPMD-list mailing list > > > WD> CPMD-list at cpmd.org > > > WD> http://www.cpmd.org/mailman/listinfo/cpmd-list > > > WD> > > > WD> > > > > > > > > > > -- > > ======================================================================= > 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 audrius.alkauskas at unibas.ch Mon Mar 22 14:35:33 2004 From: audrius.alkauskas at unibas.ch (Audrius Alkauskas) Date: Mon, 22 Mar 2004 14:35:33 +0100 Subject: [CPMD-list] cpmd2cube is not working properly Message-ID: <405EEBA5.2070105@unibas.ch> Hello I have problems with cpmd2cube. It was compiled with the same options as cpmd (intel compiler V8 and the MKL library mkl60). If I run just cpmd2cube -dens DENSITY I get negative densities sometimes, like: 0.93180E-09 0.63883E-05 -0.22307E-04 -0.87219E-06 0.18121E-04 -0.95568E-04 0.92963E-04 0.82842E-05 -0.14464E-04 0.77029E-04 -0.73099E-04 -0.14575E-04 -0.49348E-04 0.18838E-05 0.37324E-04 0.47154E-04 0.29103E-04 -0.27480E-04 -0.26917E-05 -0.73552E-04 0.40827E-05 0.27440E-04 -0.21607E-04 0.80581E-04 -0.34046E-04 -0.10135E-04 0.36526E-04 -0.53954E-04 0.53740E-04 -0.89581E-04 which I suppose should not be the case. But I also tried to run to read the data with double precision, like: cpmd2cube -dens -double DENSITY and I got the messsage: > .read input file ... forrtl: severe (67): input statement requires too much data, unit 99, file (...)/DENSITY > Image PC Routine Line Source > cpmd2cube 0809C82D Unknown Unknown Unknown ..... > Stack trace terminated abnormally. What is wrong? Regards Audrius Alkauskas From g0306324 at nus.edu.sg Mon Mar 22 14:59:03 2004 From: g0306324 at nus.edu.sg (Dai Ling) Date: Mon, 22 Mar 2004 21:59:03 +0800 Subject: [CPMD-list] FAILED TO CONVERGE WHEN DIAGONALIZING A with Ta pseudopotential created with fhi98PP Message-ID: <16995C828ADE054BA57ABEC32E7B3F377B485D@MBXSRV26.stu.nus.edu.sg> Dear Sir: I created a pseudopotential for Ta with fhi98PP and found that the obtained file is in the MT_GIA_BLYP format. Accoring to the message in http://www.cpmd.org/pipermail/cpmd-list/2002-November/000537.html, I set "xc= 1312 .666667" in the Ta pseudopotential file. However, when I want to run a program with the Ta potential, It stops with output as follows. I have tried to change the value for "xc" in pseudopotential file, but results a waring message with "inconsistant of the XC energy" and failed in the same reason. I have once suspected the improper coordinates of Ta atoms and tried with only one Ta atom, but it still fails with the same reason. The input file are showed at the end of this message. Who can be so kind to offer me a help? Thanks in advance! Scott Outputfile: **************************************************************** * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * * C 12.0112 1.2000 NO GOEDECKER S NONLOCAL * * P LOCAL * * Ta 180.9480 1.2000 NOGAUSS-HERMIT S NONLOCAL * * P NONLOCAL * * D NONLOCAL * * F LOCAL * * GH INTEGRATION POINTS: 0 * **************************************************************** .............................................. ................... ................ INITIALIZATION TIME: .64 SECONDS *** GMOPTS| THE NEW SIZE OF THE PROGRAM IS 5228 KBytes *** *** PHFAC| THE NEW SIZE OF THE PROGRAM IS 5288 KBytes *** *** ATOMWF| THE NEW SIZE OF THE PROGRAM IS 5652 KBytes *** ATRHO| CHARGE(R-SPACE): 69.000000 (G-SPACE): 69.000000 ZSYGVX| INFO= 69 ZSYGVX| FAILED TO CONVERGE WHEN DIAGONALIZING A PROGRAM STOPS IN SUBROUTINE ZSYGVX| FAILED TO DIAGONALIZE [PROC= 0] Input file: &CPMD OPTIMIZE GEOMETRY SPLINE POINTS 500 TEMPERATURE 300.0 &END &SYSTEM ANGSTROM CELL ABSOLUTE DEGREE 5 5 5 90.0000 90.0000 90.0000 SYMMETRY 0 POINT GROUP DELTA=1.E-02 1 CUTOFF 29.4009555 400eV KPOINT MONKHORST-PACK 2 2 2 &END &DFT FUNCTIONAL BLYP &END &ATOMS Carbon *C_SG_BLYP LMAX=P 16 21.0108496 -35.40563575 -0.923629535 17.80501588 -33.26484866 0.395581986 19.16222312 -37.08828644 0.008990563 &CPMD OPTIMIZE GEOMETRY SPLINE POINTS 500 TEMPERATURE 300.0 &END &SYSTEM ANGSTROM CELL ABSOLUTE DEGREE 5 5 5 90.0000 90.0000 90.0000 SYMMETRY 0 POINT GROUP DELTA=1.E-02 1 CUTOFF 29.4009555 400eV KPOINT MONKHORST-PACK 2 2 2 &END &DFT FUNCTIONAL BLYP &END &ATOMS Carbon *C_SG_BLYP LMAX=P 16 21.0108496 -35.40563575 -0.923629535 17.80501588 -33.26484866 0.395581986 19.16222312 -37.08828644 0.008990563 19.62800856 -35.65065562 -0.291730294 21.48037302 -38.03209773 -0.910654519 20.08846189 -38.2793244 -0.29993637 21.93910709 -36.59612085 -1.228806564 18.71403958 -34.45885315 0.047746502 23.50653436 -35.13026081 1.37732926 20.65602699 -32.22497109 1.169968455 21.12762272 -36.19616092 1.941380538 21.9872704 -34.97315637 1.572434346 23.30427385 -37.73574717 1.90840725 21.78521484 -37.5781868 2.10577794 24.16539838 -36.51137632 1.546667792 21.32283936 -33.59813889 1.372931083 Tantalum *TA_MT_GIA_BLYP LMAX=F 1 21.35352203 -34.34253924 -1.151599451 &END From audrius.alkauskas at unibas.ch Mon Mar 22 16:23:04 2004 From: audrius.alkauskas at unibas.ch (Audrius Alkauskas) Date: Mon, 22 Mar 2004 16:23:04 +0100 Subject: [CPMD-list] cpmd2cube is not working properly References: <405EEBA5.2070105@unibas.ch> Message-ID: <405F04D8.3020501@unibas.ch> Hello Yes, this file I got with RHOOUT. I attach the density picutre (if I succed). Sometimes there are some "wiggles", though the common picture is allright. And negatvie values bother me a litlle bit. Audrius -------------- next part -------------- A non-text attachment was scrubbed... Name: s7xs7.jpg Type: image/jpeg Size: 91805 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20040322/716aedc0/attachment.jpg From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Mon Mar 22 19:10:29 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Mon, 22 Mar 2004 19:10:29 +0100 (CET) Subject: [CPMD-list] cpmd2cube is not working properly In-Reply-To: <405EEBA5.2070105@unibas.ch> Message-ID: On Mon, 22 Mar 2004, Audrius Alkauskas wrote: AA> Hello AA> AA> I have problems with cpmd2cube. AA> AA> It was compiled with the same options as cpmd (intel compiler V8 and the AA> MKL library mkl60). AA> AA> If I run just AA> AA> cpmd2cube -dens DENSITY AA> AA> I get negative densities sometimes, like: AA> hi, this is to be expected to some degree. the DENSITY file stores the density in g-space and cpmd2cube does the fourier transform back to real space. since you did not use an infinitely large grid in g-space, some noise (= negative density values) is to be expected. on top of that, the cpmd2cube version, that you are using, uses only half the grid points in each direction, for the backward fft than your simulation used. which makes gives you nice small but _much_ noisier cube files. this has been fixed recently in the development tree and will (hopefully) be released on cpmd.org soon. axel kohlmeyer. AA> 0.93180E-09 0.63883E-05 -0.22307E-04 -0.87219E-06 0.18121E-04 -0.95568E-04 AA> 0.92963E-04 0.82842E-05 -0.14464E-04 0.77029E-04 -0.73099E-04 -0.14575E-04 AA> -0.49348E-04 0.18838E-05 0.37324E-04 0.47154E-04 0.29103E-04 AA> -0.27480E-04 AA> -0.26917E-05 -0.73552E-04 0.40827E-05 0.27440E-04 -0.21607E-04 AA> 0.80581E-04 AA> -0.34046E-04 -0.10135E-04 0.36526E-04 -0.53954E-04 0.53740E-04 AA> -0.89581E-04 AA> AA> which I suppose should not be the case. AA> AA> But I also tried to run to read the data with double precision, like: AA> AA> cpmd2cube -dens -double DENSITY AA> AA> and I got the messsage: AA> AA> > .read input file ... forrtl: severe (67): input statement requires AA> too much data, unit 99, file (...)/DENSITY AA> > Image PC Routine AA> Line Source AA> > cpmd2cube 0809C82D Unknown Unknown Unknown AA> ..... AA> > Stack trace terminated abnormally. AA> AA> What is wrong? AA> AA> Regards AA> AA> Audrius Alkauskas AA> AA> _______________________________________________ AA> CPMD-list mailing list AA> CPMD-list at cpmd.org AA> http://www.cpmd.org/mailman/listinfo/cpmd-list AA> AA> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Mon Mar 22 19:29:09 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Mon, 22 Mar 2004 19:29:09 +0100 (CET) Subject: [CPMD-list] FAILED TO CONVERGE WHEN DIAGONALIZING A with Ta pseudopotential created with fhi98PP In-Reply-To: <16995C828ADE054BA57ABEC32E7B3F377B485D@MBXSRV26.stu.nus.edu.sg> Message-ID: On Mon, 22 Mar 2004, Dai Ling wrote: DL> Dear Sir: DL> DL> I created a pseudopotential for Ta with fhi98PP and found that the obtained file is in the MT_GIA_BLYP format. Accoring to the message in http://www.cpmd.org/pipermail/cpmd-list/2002-November/000537.html, I set "xc= 1312 .666667" in the Ta pseudopotential file. DL> DL> However, when I want to run a program with the Ta potential, It stops with output as follows. I have tried to change the value for "xc" in pseudopotential file, but results a waring message with "inconsistant of the XC energy" and failed in the same reason. I have once suspected the improper coordinates of Ta atoms and tried with only one Ta atom, but it still fails with the same reason. The input file are showed at the end of this message. DL> DL> Who can be so kind to offer me a help? Thanks in advance! DL> DL> Scott DL> DL> Outputfile: DL> DL> **************************************************************** DL> * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * DL> * C 12.0112 1.2000 NO GOEDECKER S NONLOCAL * DL> * P LOCAL * DL> * Ta 180.9480 1.2000 NOGAUSS-HERMIT S NONLOCAL * ^^^^^^^^^^^^^^^^^^^^ hi, i don't know how you have created the pseudopotential. but there is a high chance, that you want to use the kleinman-bylander formalism to treat the non-local parts of the pseudopotentials. unfortunately, cpmd v3.7 defaults to gauss-hermite with 0 (!) integration points, which might explain your error message. please check the pseudopotential section of the cpmd manual and the manual of your pseudopotential generation program for more details. axel kohlmeyer. DL> * P NONLOCAL * DL> * D NONLOCAL * DL> * F LOCAL * DL> * GH INTEGRATION POINTS: 0 * DL> **************************************************************** DL> DL> .............................................. DL> ................... DL> ................ DL> DL> DL> INITIALIZATION TIME: .64 SECONDS DL> DL> *** GMOPTS| THE NEW SIZE OF THE PROGRAM IS 5228 KBytes *** DL> *** PHFAC| THE NEW SIZE OF THE PROGRAM IS 5288 KBytes *** DL> *** ATOMWF| THE NEW SIZE OF THE PROGRAM IS 5652 KBytes *** DL> ATRHO| CHARGE(R-SPACE): 69.000000 (G-SPACE): 69.000000 DL> DL> ZSYGVX| INFO= 69 DL> ZSYGVX| FAILED TO CONVERGE WHEN DIAGONALIZING A DL> DL> DL> PROGRAM STOPS IN SUBROUTINE ZSYGVX| FAILED TO DIAGONALIZE [PROC= 0] DL> DL> Input file: DL> &CPMD DL> OPTIMIZE GEOMETRY DL> SPLINE POINTS DL> 500 DL> TEMPERATURE DL> 300.0 DL> &END DL> DL> &SYSTEM DL> ANGSTROM DL> CELL ABSOLUTE DEGREE DL> 5 5 5 90.0000 90.0000 90.0000 DL> DL> SYMMETRY DL> 0 DL> POINT GROUP DELTA=1.E-02 DL> 1 DL> DL> CUTOFF DL> 29.4009555 DL> 400eV DL> DL> KPOINT MONKHORST-PACK DL> 2 2 2 DL> DL> &END DL> DL> &DFT DL> FUNCTIONAL BLYP DL> DL> &END DL> DL> &ATOMS DL> Carbon DL> *C_SG_BLYP DL> LMAX=P DL> 16 DL> 21.0108496 -35.40563575 -0.923629535 DL> 17.80501588 -33.26484866 0.395581986 DL> 19.16222312 -37.08828644 0.008990563 DL> &CPMD DL> OPTIMIZE GEOMETRY DL> SPLINE POINTS DL> 500 DL> TEMPERATURE DL> 300.0 DL> &END DL> DL> &SYSTEM DL> ANGSTROM DL> CELL ABSOLUTE DEGREE DL> 5 5 5 90.0000 90.0000 90.0000 DL> DL> SYMMETRY DL> 0 DL> POINT GROUP DELTA=1.E-02 DL> 1 DL> DL> CUTOFF DL> 29.4009555 DL> 400eV DL> DL> KPOINT MONKHORST-PACK DL> 2 2 2 DL> DL> &END DL> DL> &DFT DL> FUNCTIONAL BLYP DL> DL> &END DL> DL> &ATOMS DL> Carbon DL> *C_SG_BLYP DL> LMAX=P DL> 16 DL> 21.0108496 -35.40563575 -0.923629535 DL> 17.80501588 -33.26484866 0.395581986 DL> 19.16222312 -37.08828644 0.008990563 DL> 19.62800856 -35.65065562 -0.291730294 DL> 21.48037302 -38.03209773 -0.910654519 DL> 20.08846189 -38.2793244 -0.29993637 DL> 21.93910709 -36.59612085 -1.228806564 DL> 18.71403958 -34.45885315 0.047746502 DL> 23.50653436 -35.13026081 1.37732926 DL> 20.65602699 -32.22497109 1.169968455 DL> 21.12762272 -36.19616092 1.941380538 DL> 21.9872704 -34.97315637 1.572434346 DL> 23.30427385 -37.73574717 1.90840725 DL> 21.78521484 -37.5781868 2.10577794 DL> 24.16539838 -36.51137632 1.546667792 DL> 21.32283936 -33.59813889 1.372931083 DL> DL> DL> Tantalum DL> *TA_MT_GIA_BLYP DL> LMAX=F DL> 1 DL> 21.35352203 -34.34253924 -1.151599451 DL> &END DL> _______________________________________________ DL> CPMD-list mailing list DL> CPMD-list at cpmd.org DL> http://www.cpmd.org/mailman/listinfo/cpmd-list DL> DL> -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= From audrius.alkauskas at unibas.ch Mon Mar 22 20:55:59 2004 From: audrius.alkauskas at unibas.ch (Audrius Alkauskas) Date: Mon, 22 Mar 2004 20:55:59 +0100 Subject: [CPMD-list] FAILED TO CONVERGE WHEN DIAGONALIZING A with Ta pseudopotential created with fhi98PP References: <200403221527.QAA20172@cpmd.org> Message-ID: <405F44CF.1070304@unibas.ch> Hello I guess, KLEINMAN-BYLANDER form should be used. I think, Ari Seitsonen has written a script psgen to convert fhi98PP output to CPMD form. Audrius Alkauskas From radbalu at comcast.net Tue Mar 23 04:24:24 2004 From: radbalu at comcast.net (Rad Balu) Date: Mon, 22 Mar 2004 22:24:24 -0500 Subject: [CPMD-list] MEMORY ALLOCATION FAILED Message-ID: <200403222224.24130.radbalu@comcast.net> Dear All, I am having some issues in running the test programs that is provided at the cpmd.org site. When I ran the code using the test inputs I get, "MEMORY| ALLOCATION FAILED" error message. My machine is an AMD64 based running suse linux 9.0 professional and I compiled the code using portland group compiler. Here is my make file: #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = -Mr8 -pc64 -Msignextend -Msecond_underscore -byteswapio LFLAGS = -L. -latlas_athlon64 -L/usr/pgi/linux86-64/5.1/lib -byteswapio $(QMMM_LIBS) CFLAGS = CPP = /lib/cpp -P -C -traditional CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT NOOPT_FLAG = CC = gcc -O2 -Wall FC = pgf90 -c -fast LD = pgf90 -fast AR = Here is the error message: **************************************************************** PROCESSOR 0 ALLOCATION OF 20080 WORDS OF MEMORY FAILED **************************************************************** *** MEMORY| THE NEW SIZE OF THE PROGRAM IS 1348 kBYTES *** ================================================================ BIG MEMORY ALLOCATIONS TAU0 189 VELP 189 NGHCOM 100 WSG 100 NGHTOL 100 RGH 100 WGH 100 LVELINI 64 BL 12 RCL 12 ---------------------------------------------------------------- [PEAK NUMBER 11] PEAK MEMORY 978 = 0.0 MBytes ================================================================ PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (GNL) 999 Here is my shell parameters: core file size (blocks, -c) unlimited data seg size (kbytes, -d) unlimited file size (blocks, -f) unlimited max locked memory (kbytes, -l) unlimited max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 stack size (kbytes, -s) unlimited cpu time (seconds, -t) unlimited max user processes (-u) 8191 virtual memory (kbytes, -v) unlimite Any suggestions to help me resolve this issue will be appreciated. Thanks Rad Graduate Student From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Wed Mar 24 09:06:59 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Wed, 24 Mar 2004 09:06:59 +0100 Subject: [CPMD-list] MEMORY ALLOCATION FAILED In-Reply-To: Your message of "Mon, 22 Mar 2004 22:24:24 EST." <200403222224.24130.radbalu@comcast.net> Message-ID: <200403240806.i2O86xH16460@yello.theochem.ruhr-uni-bochum.de> >>> "RB" == Rad Balu writes: RB> Dear All, hi, RB> I am having some issues in running the test programs that is provided at the RB> cpmd.org site. When I ran the code using the test inputs I get, "MEMORY| RB> ALLOCATION FAILED" error message. RB> My machine is an AMD64 based running suse linux 9.0 professional and I RB> compiled the code using portland group compiler. Here is my make file: RB> $(QMMM_LIBS) RB> CFLAGS = RB> CPP = /lib/cpp -P -C -traditional RB> CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT RB> NOOPT_FLAG = RB> CC = gcc -O2 -Wall RB> FC = pgf90 -c -fast RB> LD = pgf90 -fast RB> AR = you are missing the POINTER8 define. you need that on all 64-bit machines, that have 32bit integers. for your reference these are my settings: FFLAGS = -r8 -pc=64 -Msignextend LFLAGS = -Bstatic -L. -latlas_x86-64 $(QMMM_LIBS) #LFLAGS = -Bstatic -L/opt/acml/pgi64/lib/ -lacml $(QMMM_LIBS) -lpgmp -lpthread CFLAGS = CPP = /lib/cpp -P -C -traditional CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DPOINTER8 -D__pgf90 NOOPT_FLAG = CC = cc FC = pgf90 -c -fastsse -tp k8-64 LD = pgf90 -fastsse -tp k8-64 AR = hope this helps, axel kohlmeyer. RB> Here is the error message: RB> **************************************************************** RB> PROCESSOR 0 ALLOCATION OF 20080 WORDS OF MEMORY FAILED RB> **************************************************************** RB> *** MEMORY| THE NEW SIZE OF THE PROGRAM IS 1348 kBYTES *** RB> ================================================================ RB> BIG MEMORY ALLOCATIONS RB> TAU0 189 VELP 189 RB> NGHCOM 100 WSG 100 RB> NGHTOL 100 RGH 100 RB> WGH 100 LVELINI 64 RB> BL 12 RCL 12 RB> ---------------------------------------------------------------- RB> [PEAK NUMBER 11] PEAK MEMORY 978 = 0.0 MBytes RB> ================================================================ RB> PROGRAM STOPS IN SUBROUTINE MEMORY| ALLOCATION FAILED (GNL) RB> 999 RB> Here is my shell parameters: RB> core file size (blocks, -c) unlimited RB> data seg size (kbytes, -d) unlimited RB> file size (blocks, -f) unlimited RB> max locked memory (kbytes, -l) unlimited RB> max memory size (kbytes, -m) unlimited RB> open files (-n) 1024 RB> pipe size (512 bytes, -p) 8 RB> stack size (kbytes, -s) unlimited RB> cpu time (seconds, -t) unlimited RB> max user processes (-u) 8191 RB> virtual memory (kbytes, -v) unlimite RB> Any suggestions to help me resolve this issue will be appreciated. RB> Thanks RB> Rad RB> Graduate Student RB> _______________________________________________ RB> CPMD-list mailing list RB> CPMD-list at cpmd.org RB> http://www.cpmd.org/mailman/listinfo/cpmd-list -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From hutter at pci.unizh.ch Wed Mar 24 14:47:06 2004 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Wed, 24 Mar 2004 14:47:06 +0100 (MET) Subject: [CPMD-list] problems with point group recognition and symmetrisation of coordinates In-Reply-To: <20040319145040.GB294719@uranus.chemie.hu-berlin.de> References: <20040317174600.GH291346@uranus.chemie.hu-berlin.de> <20040319145040.GB294719@uranus.chemie.hu-berlin.de> Message-ID: Hi > Hello, > > On Fri, Mar 19, 2004 at 01:55:01PM +0100, Juerg Hutter wrote: > > C - Positioning of the molecule: > > C z-axis is the principal axis > > C x-axis is the two-fold axis > > C xz-plane is the sigma-v plane > > C xy-plane is the sigma-h or the Cs symmetry plane > > C origin is the center of inversion These rules are of course only to be applied if possible, with the first one having highest priority. > > These conditions cannot be fulfilled completely in the case of the Td-group. > Here the three C2-axes are orthogonal to each other, and the (four) principal > axes (C3) are not orthogonal to any of the C2-axes. > For some reason, however, using one of my two examples (the one with the z-axis > corresponding to a C2-axis and the xz-plane as a mirror-plane, see previous > posting), the point group Td was recognised, but, the symmetrisation failed. > > Some years ago I used CPMD 3.0h (!) for a molecule in C3v-symmetry, at that > time the symmetrisation worked well (at least for this case of C3v). Using > the same input and CPMD 3.7.2 the symmetrisation fails. This might be an > indication that at least the problem of the symmetrisation of coordinates > could be related to a bug which might have arisen i