Montecarlo

Matt obfis... at gmail.com
Wed Sep 15 10:53:20 CEST 2010


Hello Francesco.

One of the quirks with MC in CP2K is that it needs topology files
defined for every molecule type.  The reason is because we noticed
that the code would crash sometimes during a regular NVT run when CP2K
found that the number of molecules had changed (the automatic
molecular determination).

I have everything working with the following .psf file and topology
section:

    &TOPOLOGY
      CONNECTIVITY MOL_SET
      &MOL_SET
        &MOLECULE
          NMOL 1
          CONN_FILE_NAME topology_atoms_ETH.psf
        &END
      &END
    &END

Make sure that the coordinates in the input file match the order in
the topology file (i.e. hydrogens 3,4,5 are bonded to carbon 1).  This
is a rather clumsy way to do it, but it's the best I could come up
with when designing the routines.  The most difficult part of this is
creating the psf file: the formatting is VERY strict (number of
spaces), and a slight mistake will cause a seg fault (as I discovered
when creating this file).  I took the format from cp2k/tests/Fist/
sample_psf/solute1.psf.  Good luck!

                                  Cheers, Matt

 PSF EXT

         1 !NTITLE
     Topology file for ethane

         8 !NATOM
         1 ETH             1 ETH      C       C       0.000000
12.000000        0
         2 ETH             1 ETH      C       C       0.000000
12.000000        0
         3 ETH             1 ETH      H       H       0.000000
1.008000        0
         4 ETH             1 ETH      H       H       0.000000
1.008000        0
         5 ETH             1 ETH      H       H       0.000000
1.008000        0
         6 ETH             1 ETH      H       H       0.000000
1.008000        0
         7 ETH             1 ETH      H       H       0.000000
1.008000        0
         8 ETH             1 ETH      H       H       0.000000
1.008000        0

         7 !NBOND
         1         2         1         3         1         4
1         5
         2         6         2         7         2         8

         6 !NTHETA
         3         1         2         4         1         2
5         1         2
         6         2         1         7         2         1
8         2         1

         9 !NPHI
         3         1         2         6         4         1
2         6
         5         1         2         6         3         1
2         7
         4         1         2         7         5         1
2         7
         3         1         2         8         4         1
2         8
         5         1         2         8

         0 !NIMPHI

         0 !NDON

         0 !NACC

         0 !NNB

         0 !NGRP


On Sep 14, 7:38 pm, Francesco <francesc... at gmail.com> wrote:
> Hi to all,
>
> I would like to use the CP2K-Montecarlo module in order to do a
> conformational analysis test, with DFT.
>
> In order to understand what to do, I have started with ethane (and
> other small molecules), but any attempt failed till now. I've used the
> file in the regtest as a template, but in the best case I obtained the
> error attached below.
>
> After some tests, it seems to me that the Number of molecule types
> vary as the number of atoms: I tried also to define a psf file, but
> with other errors. By the way with "CONN_FILE_FORMAT OFF" should
> overcome this request. Or am I wrong?
>
> Has anybody of you done something similar?
> Any help will be appreciated.
>
> Thanks in advance,
> Francesco
>
> --------------------------------------------------------------------------- -----
>  Number of molecule types            8
>  &MOLECULE sections found            1
>
>  *
>  *** ERROR in mc_types.F/mc_input_file_create  ***
>  *
>
>  *** Did not find MOLECULE sections for every molecule in the
> simulation  ***
>  *** (make sure both input files have all
> types)                          ***
>
> --------------------------------------------------------------------------- -------
> &FORCE_EVAL
>   METHOD Quickstep
>   &DFT
>     &MGRID
>       CUTOFF 100
>     &END MGRID
>     &QS
>       EXTRAPOLATION USE_PREV_WF
>     &END QS
>     &SCF
>       SCF_GUESS ATOMIC
>     &END SCF
>     &XC
>       &XC_FUNCTIONAL Pade
>       &END XC_FUNCTIONAL
>       &XC_GRID
>         XC_DERIV SPLINE2
>         XC_SMOOTH_RHO NONE
>       &END XC_GRID
>     &END XC
>   &END DFT
>   &SUBSYS
>     &CELL
>       ABC 5.04977 5.04977 5.04977
>     &END CELL
>     &COORD
>  C     0.000000     0.000000     0.000000
>  C     0.000000     0.000000     1.450000
>  H     1.026720     0.000000     1.812996
>  H    -0.513360     0.889165     1.813000
>  H    -0.513360    -0.889165     1.813000
>  H    -1.026719     0.000000    -0.363000
>  H     0.513360     0.889165    -0.363000
>  H     0.513360    -0.889165    -0.363000
>     &END COORD
>     &KIND H
>       BASIS_SET DZVP-GTH-Pade
>       POTENTIAL GTH-BLYP-q1
>     &END KIND
>     &KIND C
>       BASIS_SET DZVP-GTH-Pade
>       POTENTIAL GTH-BLYP-q4
>     &END KIND
>     &TOPOLOGY
>       &MOL_SET
>         &MOLECULE
>           NMOL 1
>           CONN_FILE_FORMAT OFF
>         &END MOLECULE
>       &END MOL_SET
>       CONNECTIVITY MOL_SET
>     &END TOPOLOGY
>   &END SUBSYS
> &END FORCE_EVAL
> &GLOBAL
>   PROJECT ethane_MC
>   RUN_TYPE MC
>   PRINT_LEVEL LOW
> &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 1.013
>     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
>     TEMPERATURE 398.0
>     AVBMC_RMIN 1.0
>     AVBMC_RMAX 5.0
>     AVBMC_ATOM 1
>     PBIAS 0.5
>     ETA 0.0
>     PMAVBMC_MOL 1.0
>     PMSWAP_MOL 1.0
>     PMROT_MOL 1.0
>     PMTRANS_MOL 1.0
>     PMTRAION_MOL 1.0
>     VIRIAL_TEMPS 300.0
>   &END MC
> &END MOTION


More information about the CP2K-user mailing list