psf problems

Toon Toon.Ver... at gmail.com
Fri Jun 1 13:50:53 CEST 2007


Hi, I have a related question. Is it normal that

      COORDINATE XYZ
      COORD_FILE_NAME geometry.xyz

can not be used with MC simumations, or is this a problem with my
compilation of cp2k?

cheers,

Toon

On 30 mei, 08:12, Teodoro Laino <teodor... at gmail.com> wrote:
> PSF is a CHARMM standard format.. you won't find any place around
> where they specify the format..
> all the available programs reading PSF have +/- hacked the original
> format..
> so we do..
>
> teo
>
> On 30 May 2007, at 08:00, Toon wrote:
>
>
>
> > Hi Teo,
>
> > Thanks for your help. I'll update my copy of cp2k. Is there a standard
> > specification for the PSF format availlable on the internet? In the
> > (very) long run, I'd like to update my scripts to generate standard
> > psf files.
>
> > cheers,
>
> > Toon
>
> > On 29 mei, 19:40, Teodoro Laino <teodor... at gmail.com> wrote:
> >> Toon,
>
> >> from your input file I see you're using not an up2date version of
> >> cp2k.. at least 1-2 months old..
> >> I cannot offer any help for the code you are using..
>
> >> BUT if you update to the new one and use this section:
>
> >>      &TOPOLOGY
> >>        CONNECTIVITY MOL_SET
> >>        &MOL_SET
> >>          &MOLECULE
> >>            NMOL 8
> >>            CONN_FILE_NAME single.psf
> >>            CONNECTIVITY UPSF
> >>          &END
> >>        &END
> >>      &END TOPOLOGY
>
> >> your example works..
>
> >> Bytheway.. yours is not a standard PSF.. me and Axel were working
> >> for a couple of weeks and at the moment
> >> cp2k supports the EXT standard of the PSF.. everytime you have a psf
> >> that is not standard you need to specify
> >> that its connectivity is UPSF (mostly you don't care about the
> >> format..)
>
> >> teo
>
> >> On 29 May 2007, at 15:11, Toon wrote:
>
> >>> Hi,
>
> >>> I've been trying to run an mc simulation with the input given below.
> >>> I'm just trying to understand how this should work in cp2k. The
> >>> input
> >>> is just a dummy example. When I try to run this example (with
> >>> cp2k.sdbg), I got this error:
>
> >>> ...
> >>>  PSF_INFO| Parsing the NATOM section
> >>>  PSF_INFO| NATOM =        5
> >>>  PSF_INFO| Parsing the NBOND section
> >>>  PSF_INFO| NBOND =        4
> >>>  PSF_INFO| Parsing the NTHETA section
> >>>  PSF_INFO| NTHETA =        6
> >>>  PSF_INFO| Parsing the NPHI section
> >>>  PSF_INFO| NPHI =        0
> >>> At line 886 of file /home/toon/tmp/build/cp2k/makefiles/../src/
> >>> topology_util.F
> >>> Traceback: (Innermost first)
> >>>    Called from line 498 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/topology_psf.F
> >>>    Called from line 359 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/topology.F
> >>>    Called from line 206 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/topology.F
> >>>    Called from line 279 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/qs_environment.F
> >>>    Called from line 111 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/qs_main.F
> >>>    Called from line 729 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/f77_interface.F
> >>>    Called from line 268 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/cp2k_runs.F
> >>>    Called from line 847 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/cp2k_runs.F
> >>>    Called from line 248 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/cp2k.F
> >>> Fortran runtime error: Array element out of bounds: 31 in (1:5),
> >>> dim=1
>
> >>> The psf file is also given below. It describes the topology of
> >>> exactly
> >>> one of the eight methane molecules. I believe the psf file is
> >>> correct,
> >>> is it? I did take a look at the part of the code where the error
> >>> occurs but I don't really understand what it is expected to do. (It
> >>> reads the psf file, something goes wrong when processing the one-
> >>> four
> >>> pairs, but I don't get the details.) Is there something wrong in the
> >>> input/psf file or is this a bug? The examples from the regtests work
> >>> on my machine.
>
> >>> best regards,
>
> >>> Toon
>
> >>> the input file:
>
> >>> &FORCE_EVAL
>
> >>>   METHOD Quickstep
> >>>   &DFT
> >>>     &QS
> >>>       METHOD PM3
> >>>       EPS_DEFAULT 1.0E-12
> >>>       EPS_GVG 1.0E-6
> >>>       EPS_PGF_ORB 1.0E-6
> >>>     &END QS
> >>>     &SCF
> >>>       EPS_SCF 1.0E-6
> >>>       MAX_SCF 150
> >>>       SCF_GUESS atomic
> >>>     &END SCF
> >>>   &END DFT
>
> >>>   &SUBSYS
> >>>     &CELL
> >>>       ABC 7.800000 7.800000 7.800000
> >>>       UNIT ANGSTROM
> >>>     &END CELL
> >>>     &COORD
> >>>   C         7.1545135964        0.2916147406        0.6622232680
> >>>   H         6.6668950468        1.1504609369        1.1033507689
> >>>   H         7.6334667531        0.6233226102       -0.2564860726
> >>>   H         6.4208845485       -0.4795931637        0.4356274201
> >>>   H         7.9005900072       -0.1048244889        1.3410306662
> >>>   C         6.8528101393        3.6807499565        1.5744193983
> >>>   H         6.4514929741        2.8349587584        2.1188989803
> >>>   H         7.7679317225        3.4073223315        1.0559592149
> >>>   H         7.0709998781        4.4961704973        2.2881955953
> >>>   H         6.1341098685        4.0308814768        0.8225903997
> >>>   C         1.9813613499        6.7192653419        5.8763727299
> >>>   H         2.0321973418        7.4196170794        6.7046158757
> >>>   H         1.2903991153        7.1400631283        5.1330330349
> >>>   H         1.5834916118        5.7941607545        6.2462624125
> >>>   H         2.9782222352        6.5700588933        5.4382607646
> >>>   C         6.8935808834       10.9042343214        4.8896018240
> >>>   H         6.9090027651       10.0556726408        5.5732300957
> >>>   H         7.1082178538       11.7975226536        5.4836337927
> >>>   H         5.9106655806       10.9864139714        4.4468607567
> >>>   H         7.6585223681       10.7854616816        4.0984669623
> >>>   C         3.4097928887        4.5767446702        2.2242443860
> >>>   H         3.0529585247        4.4184677018        1.2009363529
> >>>   H         3.2785552112        3.6406911435        2.7889006394
> >>>   H         2.8302525350        5.3840010296        2.6917414739
> >>>   H         4.4528957985        4.8811323379        2.2007501082
> >>>   C         2.9805519373        8.2006034213        9.5372130039
> >>>   H         3.3335722902        9.0450868984       10.1155313292
> >>>   H         2.1188103649        7.7275659069       10.0272973693
> >>>   H         3.7804325728        7.4372375456        9.4173176654
> >>>   H         2.6890775746        8.5348163384        8.5285057129
> >>>   C         6.0352120743        6.4801397125        4.0960140077
> >>>   H         6.5874102060        7.3836880272        3.9041291362
> >>>   H         5.4489916745        6.2452884244        3.2172777054
> >>>   H         5.3670640659        6.6104228115        4.9504368037
> >>>   H         6.7521214494        5.6814792763        4.3123759997
> >>>   C         3.2928814788        2.5582719306        5.8498575291
> >>>   H         3.0860227820        2.3159397213        6.8922542536
> >>>   H         3.5005462509        3.6199393877        5.7655448415
> >>>   H         2.4455631533        2.3255776287        5.2113735329
> >>>   H         4.1684058503        1.9781743596        5.5368454612
> >>>     &END COORD
> >>>     &TOPOLOGY
> >>>       CONNECTIVITY MOL_SET
> >>>       &MOL_SET
> >>>         NMOL 8
> >>>         CONN_FILE_NAME single.psf
> >>>       &END
> >>>     &END TOPOLOGY
> >>>     &PRINT
> >>>       &TOPOLOGY_INFO
> >>>         EACH 1
> >>>         PSF_INFO T
> >>>       &END TOPOLOGY_INFO
> >>>     &END PRINT
> >>>   &END SUBSYS
> >>> &END FORCE_EVAL
>
> >>> &GLOBAL
> >>>   FFT_LIB FFTW3
> >>>   PROJECT mc
> >>>   RUN_TYPE MC
> >>> &END GLOBAL
>
> >>> &MOTION
> >>>   &MC
> >>>     IUPTRANS 6400000
> >>>     IUPVOLUME 3200000
> >>>     LBIAS no
> >>>     LSTOP yes
> >>>     NMOVES 8
> >>>     NSTEP 2
> >>>     PMSWAP 0.0
> >>>     PMTRAION 0.00
> >>>     PMTRANS 0.00
> >>>     PMVOLUME 1.00
> >>>     PMVOL_BOX 1.00
> >>>     PRESSURE 1
> >>>     ENSEMBLE traditional
> >>>     RESTART no
> >>>     RESTART_FILE_NAME mc_restart_1
> >>>     RMDIHEDRAL 3.0
> >>>     RMANGLE 3.0
> >>>     RMBOND 0.074
> >>>     RMROT 26.0
> >>>     RMTRANS 0.38
> >>>     RMVOLUME 0.5
> >>>     TEMP 101.055000
> >>>     AVBMC_RMIN 1.0
> >>>     AVBMC_RMAX 5.0
> >>>     AVBMC_ATOM 1
> >>>     PBIAS 0.5
> >>>     PMAVBMC_MOL 1.0
> >>>     PMSWAP_MOL 1.0
> >>>     PMROT_MOL 1.0
> >>>     PMTRANS_MOL 1.0
> >>>     PMTRAION_MOL 1.0
> >>>   &END MC
> >>>   &PRINT
> >>>     &TRAJECTORY
> >>>       EACH 5
> >>>     &END TRAJECTORY
> >>>   &END PRINT
> >>> &END MOTION
>
> >>> The file single.psf looks like this:
>
> >>> PSF
>
> >>>       1 !NTITLE
> >>> None
>
> >>>       5 !NATOM
> >>>       1 NAME    1 NAME  C     C 0.0    12.010700 0
> >>>       2 NAME    1 NAME  H     H 0.0     1.007940 0
> >>>       3 NAME    1 NAME  H     H 0.0     1.007940 0
> >>>       4 NAME    1 NAME  H     H 0.0     1.007940 0
> >>>       5 NAME    1 NAME  H     H 0.0     1.007940 0
>
> >>>       4 !NBOND
> >>>       2       1       3       1       4       1       5       1
>
> >>>       6 !NTHETA
> >>>       4      1      2      5      1      2      3      1      2
> >>>       5      1      4      4      1      3      5      1      3
>
> >>>       0 !NPHI
>
> >>>       0 !NIMPHI
>
> >>>       0 !NDON
>
> >>>       0 !NACC
>
> >>>       0 !NNB




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