CP2K Open Source Molecular Dynamics

Here is the example file for KCl from the lecture

@SET METHOD = QMMM # FIST all classical treatment # QS all quantum treatment
 
&GLOBAL
  FLUSH_SHOULD_FLUSH
  PRINT_LEVEL LOW
  PROJECT KCl
  RUN_TYPE GEO_OPT
&END GLOBAL
 
&FORCE_EVAL
  METHOD $METHOD
  @include QS.inc
  @include MM.inc
  &QMMM
    #this defines the QS cell in the QMMM calc
    &CELL
      ABC 12.6 15.0 12.6
      PERIODIC XZ
    &END CELL
    ECOUPL GAUSS # use GEEP method
    NOCOMPATIBILITY
    USE_GEEP_LIB 6  # use GEEP method
    &PERIODIC # apply periodic potential
      #in this case QM box = MM box in XZ so turn
      #off coupling/recoupling of the QM multipole
      &MULTIPOLE OFF
      &END
    &END PERIODIC
    #these are just the ionic radii of K Cl
    #but should be treated as parameters in general
    #fit to some physical property
    &MM_KIND K
      RADIUS 1.52
    &END MM_KIND
    &MM_KIND Cl
      RADIUS 1.67
    &END MM_KIND
    #define the model
    &QM_KIND K
      MM_INDEX 25..32 41..48
    &END QM_KIND
        &MM_KIND Cl
      RADIUS 1.67
    &END MM_KIND
    #define the model
    &QM_KIND K
      MM_INDEX 25..32 41..48
    &END QM_KIND
    &QM_KIND Cl
      MM_INDEX 17..24 33..40
    &END QM_KIND
  &END QMMM
 
  &SUBSYS
    #this defines the cell of the whole system
    #must be orthorhombic, I think
    &CELL
      ABC 12.6 100.0 12.6
    &END CELL
    &TOPOLOGY
      COORD_FILE_NAME kcl.xyz
      COORD_FILE_FORMAT XYZ
      &GENERATE
         &ISOLATED_ATOMS
         #ignores bonds dihedrals etc in classical part
            LIST 1..48
         &END
      &END
    &END
    &KIND K
      ELEMENT K
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q9
    &END KIND
    &KIND Cl
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q7
    &END
  &END SUBSYS
&END FORCE_EVAL
 
#should be able to use most motion sections
#analytic stress tensor not available, I think
@include motion.inc

and includes as separate files, using the @include macro, for the QS, MM and motion sections

  &DFT
    BASIS_SET_FILE_NAME BASIS_MOLOPT
    POTENTIAL_FILE_NAME GTH_POTENTIALS
    &MGRID
      COMMENSURATE
      CUTOFF 150
    &END MGRID
    &QS
      EPS_DEFAULT 1.0E-12
    &END QS
    &SCF
      EPS_SCF 1.0E-06
      MAX_SCF 26
      SCF_GUESS RESTART
      &OT
        MINIMIZER CG
        PRECONDITIONER FULL_SINGLE_INVERSE
        ENERGY_GAP 0.001
      &END OT
      &OUTER_SCF
        EPS_SCF 1.0E-05
      &END OUTER_SCF
    &END SCF
    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC
    &PRINT
       &MO_CUBES
           NLUMO 10
           WRITE_CUBE T
       &END MO_CUBES
       &V_HARTREE_CUBE
           STRIDE 2 2 2
       &END
    &END PRINT
  &END DFT

  &MM
    &FORCEFIELD
      &CHARGE
         ATOM K
         CHARGE 1.0
      &END CHARGE
      &CHARGE
         ATOM Cl
         CHARGE -1.0
      &END CHARGE
      &NONBONDED
        &WILLIAMS
          atoms K   Cl
          A [eV] 4117.9
          B [angstrom^-1] 3.2808
          C [eV*angstrom^6] 0.0
          RCUT [angstrom] 3.0
        &END WILLIAMS
        &WILLIAMS
          atoms Cl  Cl
          A [eV] 1227.2
          B [angstrom^-1] 3.1114
          C [eV*angstrom^6] 124.0
          RCUT [angstrom] 3.0
        &END WILLIAMS
        &WILLIAMS
          atoms K   K
          A [eV] 3796.9
          B [angstrom^-1] 3.84172
          C [eV*angstrom^6] 124.0
          RCUT [angstrom] 3.0
        &END WILLIAMS
      &END NONBONDED
    &END FORCEFIELD
    &POISSON
      &EWALD
        EWALD_TYPE spme
        ALPHA .44
        GMAX  40
      &END EWALD
    &END POISSON
  &END MM

&GEO_OPT
     OPTIMIZER LBFGS
  &END
  &CONSTRAINT
     &FIXED_ATOMS
     LIST 1..16
     EXCLUDE_MM .FALSE.
     EXCLUDE_QM .TRUE.
     &END FIXED_ATOMS
  &END CONSTRAINT
&END MOTION