umbrella sampling

caozhe... at gmail.com caozhe... at gmail.com
Tue Oct 13 09:23:49 CEST 2015


Dear all,

There is a problem regarding to the umbrella sampling

I am using the CP2K 2.6

The following is my input file. I would like to add harmonic constraint to 
sample the free energy as a function of distance between geometry center of 
atoms 1270..1276 and a plane (can be defined from atoms 91..93). However, 
it always gives me segmentation fault...

I have defined the collective variable (COLVAR) in &subsys section, and try 
to add constraint in &MOTION&CONSTRAINT&COLLECTIVE

Any suggestions/help are warm welcomed.

Thank you guys in advance!

Best Regards,
CZ


                     FRONTIERS IN SIMULATION TECHNOLOGY    
                                                           
                        C.J. Mundy, S. Balasubramanian,    
                     Ken Bagchi, J. Hutter, Ari Seitsonen  
                      IFW Kuo, T. Laino, J. VandeVondele   
                                 Version 1.0               

                                                           


Program received signal SIGSEGV: Segmentation fault - invalid memory 
reference.

Backtrace for this error:
#0  0x1DB74DD in _gfortrani_show_backtrace at backtrace.c:260
#1  0x1D93CA6 in _gfortrani_backtrace_handler at compile_options.c:129
#2  0x40BAEF in _L_unlock_16 at bar.c:0
#3  0xBFA720 in __colvar_types_MOD_colvar_setup at colvar_types.F:1138
#4  0xBE6B2A in __colvar_methods_MOD_colvar_read at colvar_methods.F:1100
#5  0xC8588D in __cp_subsys_methods_MOD_cp_subsys_read_colvar at 
cp_subsys_methods.F:90
#6  0xD254CF in __fist_environment_MOD_fist_init at fist_environment.F:171
#7  0x46F042 in __fist_main_MOD_fist_create_force_env at fist_main.F:92
#8  0x68C7A3 in __qmmm_main_MOD_qmmm_create_force_env_low at qmmm_main.F:466
#9  0x68FA7B in __qmmm_main_MOD_qmmm_create_force_env at qmmm_main.F:178
#10  0x449AE9 in __f77_interface_MOD_create_force_env at f77_interface.F:854
#11  0x41304B in __cp2k_runs_MOD_cp2k_run at cp2k_runs.F:318
#12  0x416F6B in __cp2k_runs_MOD_run_input at cp2k_runs.F:1161
#13  0x40D7B7 in cp2k at cp2k.F:307




!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!    setting variables for short
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@SET DIR /home/caoz/qmmm/test
@SET VAR PhosphateOnPt

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       global variables to do the general control
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
&GLOBAL
  PRINT_LEVEL MEDIUM
  PREFERRED_FFT_LIBRARY  FFTSG
  PROJECT ${VAR}
  RUN_TYPE MD
&END GLOBAL

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       start from "restart" file
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!&EXT_RESTART
!  RESTART_FILE_NAME ${DIR}/${VAR}.restart
!  RESTART_DEFAULT .TRUE.
!
!  RESTART_COUNTERS .FALSE.
!  RESTART_AVERAGES .FALSE.
!&END EXT_RESTART

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       propagate your system
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
&MOTION

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       the moving part
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
  &MD
    ENSEMBLE   NVT
    STEPS      1000000
    TIMESTEP   0.1
    TEMPERATURE 300.0
!   TEMP_TOL  50.0

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       thermostat for NVT
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &THERMOSTAT
      TYPE NOSE
      REGION GLOBAL
      &NOSE
        TIMECON  1.
      &END NOSE
    &END THERMOSTAT

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       output general info. for your system
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &PRINT
      &ENERGY
        FILENAME =${DIR}/${VAR}.ener
        &EACH
          MD 1
        &END EACH
      &END ENERGY
      &PROGRAM_RUN_INFO
        &EACH
          MD 1
        &END EACH
      &END PROGRAM_RUN_INFO
    &END PRINT
  &END MD

  &CONSTRAINT
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       these atoms will not move, but they contribute to force and energy
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &FIXED_ATOMS
      LIST 1..120
    &END FIXED_ATOMS

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       define umbrella spring constant
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &COLLECTIVE
      COLVAR 2000
      MOLECULE 1
      TARGET 6.4
      &RESTRAINT
        K  .05
      &END
    &END

  &END CONSTRAINT

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       output detailed dynamics of your system
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
  &PRINT

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       coordinates
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &TRAJECTORY
      FILENAME =${DIR}/${VAR}.xyz
      FORMAT XYZ
      &EACH
        MD 1
      &END EACH
    &END TRAJECTORY

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       velocities
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &VELOCITIES
      FILENAME =${DIR}/${VAR}.vel
      FORMAT XYZ
      &EACH
        MD 1
      &END EACH
    &END VELOCITIES

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       forces
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &FORCES
      FILENAME =${DIR}/${VAR}.for
      FORMAT XYZ
      &EACH
        MD 1
      &END EACH
    &END FORCES

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       restart
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &RESTART
      FILENAME =${DIR}/${VAR}.restart
      BACKUP_COPIES 1
      &EACH
        MD 10
      &END EACH
    &END RESTART
    &RESTART_HISTORY OFF
    &END RESTART_HISTORY

  &END PRINT
&END MOTION


!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       define how to calculate force
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
&FORCE_EVAL
  METHOD QMMM
  &MM
    &FORCEFIELD

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       empirical force field
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
      PARM_FILE_NAME ${DIR}/par
      PARMTYPE CHM
      VDW_SCALE14     0.0000000000000000E+00
      EI_SCALE14      0.0000000000000000E+00
      &SPLINE
        RCUT_NB     0.7000000000000009E+01
        EMAX_SPLINE 1.0000000000000000E+1000
      &END SPLINE
      &NONBONDED

        &GENPOT
          ATOMS OT Pt
          RCUT    26.4562
          RMIN  0.188973
          RMAX  26.4562
          VARIABLES R
          PARAMETERS A alpha
          VALUES 64.74957 11
          FUNCTION A*(R**(-alpha))
        &END GENPOT

        &GENPOT
          ATOMS OT Pt
          RCUT  26.4562
          RMIN  0.188973
          RMAX  26.4562
          VARIABLES R
          PARAMETERS C
          VALUES 0.6474957
          FUNCTION C*(R**(-6))
        &END GENPOT

        &SIEPMANN
          ATOMS OT Pt
          B     0.6
          BETA  10.
          D     0.54656
          E     0.0156
          F     13.3
          RCUT  6.04712
        &END SIEPMANN
      &END NONBONDED
    &END FORCEFIELD

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       electrostatic part
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &POISSON
      &EWALD
        EWALD_TYPE spme
        ALPHA .5
        GMAX  14 15 80
      &END EWALD
    &END POISSON
  &END MM



  &DFT
    CHARGE -1
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       pseudo-potential 
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    BASIS_SET_FILE_NAME  ${DIR}/GTH_BASIS_SETS 
    POTENTIAL_FILE_NAME  ${DIR}/GTH_POTENTIALS

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       wave function used for initial guess
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    WFN_RESTART_FILE_NAME  ${DIR}/RESTART


    &MGRID
      CUTOFF 300
      COMMENSURATE T
    &END MGRID

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       iteration methods and criteria
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &SCF
      MAX_SCF     10
      EPS_SCF     1.0E-5
      SCF_GUESS   RESTART

      &OUTER_SCF
        EPS_SCF 1.0E-5
        MAX_SCF 1
      &END

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       orbital transformation
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
      &OT 
        PRECONDITIONER    FULL_ALL
        MINIMIZER         CG
        STEPSIZE      0.15
      &END OT

      &PRINT
        &RESTART
          FILENAME =${DIR}/RESTART
        &END RESTART
      &END PRINT
    &END SCF

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       Ab initio/Quickstep parameters
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &QS
      METHOD GAPW
      EPS_GVG 1.0E-5
      EPS_PGF_ORB 1.0E-5
      EXTRAPOLATION ASPC
      EXTRAPOLATION_ORDER 3
      PW_GRID NS-FULLSPACE
      PW_GRID_BLOCKED FREE
    &END QS

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       exchange
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &XC
      &XC_GRID
        XC_SMOOTH_RHO    NN50
        XC_DERIV  SPLINE2_SMOOTH
      &END XC_GRID

       &XC_FUNCTIONAL  NO_SHORTCUT
         &PBE T
       PARAMETRIZATION PBESOL
         &END PBE
       &END XC_FUNCTIONAL

       &VDW_POTENTIAL
         POTENTIAL_TYPE  PAIR_POTENTIAL
         &PAIR_POTENTIAL
           TYPE  DFTD3
           PARAMETER_FILE_NAME ${DIR}/dftd3.dat
           REFERENCE_FUNCTIONAL PBE
         &END PAIR_POTENTIAL
       &END VDW_POTENTIAL
    &END XC

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       electrostatic for QM part
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &POISSON
       PERIODIC  XYZ
       &EWALD
     ALPHA 0.5
         GMAX   14 15 80
         EWALD_TYPE  SPME
       &END EWALD
    &END POISSON
  &END DFT

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       coupling between QM and MM
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
  &QMMM
    E_COUPL GAUSS
    USE_GEEP_LIB  12
    NOCOMPATIBILITY  T
    &CELL
      ABC 13.8741420 14.4184314 80.
      PERIODIC xyz
    &END CELL

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       this is recommended to maintain the hydrogen bond...
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &MM_KIND OT
      RADIUS     1.2000000000000000E+00
    &END MM_KIND

    &MM_KIND HT
      RADIUS     4.0000000000000002E-01
    &END MM_KIND


!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       define your QM atoms
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!   &QM_KIND Pt
!     MM_INDEX      1..120
!   &END QM_KIND

    &QM_KIND P
      MM_INDEX    1270
    &END QM_KIND

    &QM_KIND O
      MM_INDEX 1271 1272 1273 1274
    &END QM_KIND

    &QM_KIND H
      MM_INDEX 1275 1276
    &END QM_KIND

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       image charge method
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &IMAGE_CHARGE
      DETERM_COEFF ITERATIVE
      EXT_POTENTIAL -1
      IMAGE_RESTART_FILE_NAME ${DIR}/${VAR}.image
      MM_ATOM_LIST 91..120
    &END IMAGE_CHARGE

  &END QMMM

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       define your system
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
  &SUBSYS

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       PBC
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &CELL
      ABC 13.8741420 14.4184314 80.
      PERIODIC xyz
    &END CELL

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       coordinates
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &COORD
      @include 'coord.xyz'
    &END COORD

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       topology
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &TOPOLOGY
      CONN_FILE_FORMAT    PSF
      CONN_FILE_NAME      ${DIR}/${VAR}.psf
    &END TOPOLOGY


!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       define your collective variable
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &COLVAR
      &DISTANCE_POINT_PLANE
    ATOM_POINT 2000
    &POINT
      ATOMS 1270..1276
      TYPE GEO_CENTER
      WEIGHTS 31./97. 16./97. 16./97. 16./97. 16./97. 1./97. 1./97.
     &END POINT
    ATOMS_PLANE 91 92 93
      &END DISTANCE_POINT_PLANE
    &END

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!       pseudo-potential
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    &KIND O
      BASIS_SET DZVP-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND

    &KIND H
      BASIS_SET DZVP-GTH
      POTENTIAL GTH-PBE-q1
    &END KIND

    &KIND P
      BASIS_SET DZVP-GTH
      POTENTIAL GTH-PBE-q5
    &END KIND

    &KIND Pt
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q10
    &END KIND

  &END SUBSYS

  &PRINT
    &PROGRAM_RUN_INFO
      &EACH
        MD 1
      &END EACH
    &END PROGRAM_RUN_INFO
  &END PRINT
&END FORCE_EVAL
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20151013/6d26b540/attachment.html>


More information about the CP2K-user mailing list