psf problems

Toon Toon.Ver... at gmail.com
Fri Jun 1 15:18:41 CEST 2007


My apologies for the inconveinience. This is a more complete
description of the problem: I'm now running a cp2k compilation checked
out this morning. I have a problem that seems to be related to these
two input lines:

      COORDINATE XYZ
      COORD_FILE_NAME geometry.xyz

The error given by cp2k looks like this:

...
 MC| The moves will not be biased,
 MC| A full energy calculation will be done at every step.
 MC|    4 swap insertions will be attempted per molecular swap move

 File name mc.inp


 ************************************************
 *** ERROR in mc_types.F/mc_input_file_create ***
 ************************************************

 *** Could not find &END after &COORD (make sure & is the first in the
***
 *** same column after &COORD)
***


 ===== Routine Calling Stack =====

            1 CP2K

 CP2K| Stopped by process
number                                               0
 CP2K| Abnormal program termination

Aborted


It appears that the MC code requires the COORD section to be used
instead of other means of defining the molecular geometry. These are
all the input files:

mc.inp:

&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
    &TOPOLOGY
      COORDINATE XYZ
      COORD_FILE_NAME init.xyz
      CONNECTIVITY MOL_SET
      &MOL_SET
        &MOLECULE
          NMOL 8
          CONN_FILE_NAME single.psf
          CONNECTIVITY UPSF
        &END
      &END
    &END TOPOLOGY
    &PRINT
      &TOPOLOGY_INFO
        EACH 1
        PSF_INFO T
      &END TOPOLOGY_INFO
    &END PRINT
  &END SUBSYS
&END FORCE_EVAL

&GLOBAL
  FFT_LIB FFTSG
  PROJECT mc
  RUN_TYPE MC
&END GLOBAL

&MOTION
  &MC
    IUPTRANS 100
    IUPVOLUME 100
    LBIAS no
    LSTOP no
    NMOVES 1
    NSTEP 10
    PMSWAP 0.0
    PMSWAP_MOL 1.0
    PMTRAION 0.00
    PMTRAION_MOL 1.0
    PMTRANS 0.5
    PMTRANS_MOL 1.0
    PMROT_MOL 1.0
    PMVOLUME 0.2
    PMVOL_BOX 1.0
    PRESSURE 1.013
    ENSEMBLE traditional
    RESTART no
    RESTART_FILE_NAME mc_restart_1
    RMDIHEDRAL 1.0
    RMANGLE 3.0
    RMBOND 0.074
    RMROT 26.0
    RMTRANS 0.38
    RMVOLUME 1.0
    TEMPERATURE 298.0
    IPRINT 1
    AVBMC_ATOM 1
    NSWAPMOVES 4
    PMAVBMC 0.5
    PMAVBMC_MOL 1.0
    AVBMC_RMIN 2.0
    AVBMC_RMAX 4.0
    PBIAS 0.5
    VIRIAL_TEMPS 300.0
  &END MC
  &PRINT
    &TRAJECTORY
      EACH 5
    &END TRAJECTORY
  &END PRINT
&END MOTION

This is single.psf

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


This is init.xyz

      40
 i =     200, E =       22.6433415965
  C         6.9039075582        2.2556748672        0.6684090906
  H         7.5807042939        2.9514646584        0.1778234170
  H         6.4359114825        1.6148018511       -0.0751255788
  H         6.1411834553        2.8077213762        1.2123856443
  H         7.4649087760        1.6437421117        1.3661103663
  C         6.9115470203        6.1425921064        2.1589360246
  H         7.6276416557        6.8618026951        2.5486690023
  H         7.4061522809        5.4950308617        1.4429986121
  H         6.1001618632        6.6677780946        1.6615302422
  H         6.5170086641        5.5418353691        2.9752995498
  C         0.8124559617        6.2174060423        6.1085385115
  H         0.9682759157        6.3527520522        5.0415332216
  H        -0.0050460555        6.8521178205        6.4438165561
  H         1.7204472263        6.4844467269        6.6359163451
  H         0.5776741793        5.1779744893        6.3188571695
  C         4.6568183079        8.5306984679        4.5589000442
  H         5.4014171220        8.0383130247        5.1798098710
  H         4.0720357993        7.7856805661        4.0247749152
  H         5.1510519252        9.1888538100        3.8480745892
  H         3.9962925018        9.1156867542        5.1893066759
  C         3.0026367985        4.6804958145        2.1341762406
  H         2.5872117262        5.3961909512        2.8398055744
  H         3.5973758287        3.9441956718        2.6702281645
  H         3.6343783322        5.2012588593        1.4230404511
  H         2.1983186479        4.1851221980        1.5958594440
  C         3.0357598254        8.6354879819        8.5015934277
  H         2.2355644284        8.1192114793        9.0268620523
  H         3.7132001125        7.9084963590        8.0584302518
  H         3.5842911872        9.2497091821        9.2067104274
  H         2.6159490587        9.2689729491        7.7228475826
  C         8.5668539873        2.2952643674        4.5588139458
  H         9.3584593729        2.7884860822        5.1172331341
  H         9.0003049169        1.6000473260        3.8438410104
  H         7.9715191708        3.0389332591        4.0342037810
  H         7.9309384985        1.7492402764        5.2468924719
  C         4.7102978422        4.6594015643        6.0167776096
  H         5.5013143603        4.2000713116        5.4279574197
  H         5.1427927774        5.3339687406        6.7519655838
  H         4.1333208145        3.8893804981        6.5228756168
  H         4.0540983796        5.2195783822        5.3595115407






More information about the CP2K-user mailing list