@SET cp2k_tutorial_path /users/marcella/D07/CP2K_TUTORIAL
@SET LIBPATH  ${cp2k_tutorial_path}/MTD1/LIB_TOOLS
@SET XYZPATH  ${cp2k_tutorial_path}/MTD1/XYZ
@SET RESPATH  ${cp2k_tutorial_path}/MTD1/SI6_CLU/MTD_L_H0_P3
@SET RUNPATH  ${cp2k_tutorial_path}/MTD1/SI6_CLU/MTD_L_H0_P3

@SET METHOD_TO_USE DFT
@SET DO_RESTART   NO


&FORCE_EVAL
  METHOD Quickstep
@IF ( ${METHOD_TO_USE} == DFT )
  &DFT
    BASIS_SET_FILE_NAME ${LIBPATH}/BASIS_MOLOPT
    POTENTIAL_FILE_NAME ${LIBPATH}/GTH_POTENTIALS
    LSD
    &MGRID
      NGRIDS 5
      CUTOFF 200
    &END MGRID
    &QS
      METHOD GPW
      MAP_CONSISTENT
      EXTRAPOLATION ASPC
      EXTRAPOLATION_ORDER 3
    &END QS

    &SCF
      MAX_SCF 30
      EPS_SCF 1.0E-5
      SCF_GUESS ATOMIC
      &OT
        PRECONDITIONER FULL_SINGLE_INVERSE
        MINIMIZER DIIS
        N_DIIS 7
      &END OT

      &OUTER_SCF
        MAX_SCF 3
        EPS_SCF 1.0E-05
      &END OUTER_SCF

     &END SCF

     &XC
      &XC_FUNCTIONAL PADE
      &END XC_FUNCTIONAL
     &END XC

     &POISSON
       POISSON_SOLVER MT
       PERIODIC NONE
       &MT
       &END
     &END
  &END DFT
@ENDIF
@IF ( ${METHOD_TO_USE} == SE )
  &DFT
    CHARGE 0
    &QS
      METHOD PM6
      &SE
       RC_INTERACTION [angstrom] 50.0
       RC_COULOMB     [angstrom] 50.0
       RC_RANGE       [angstrom]  0.0
      &END
    &END QS
    &SCF
      MAX_SCF 30
      EPS_SCF 1.0E-6
      SCF_GUESS ATOMIC
      &OT 
        MINIMIZER DIIS
        PRECONDITIONER FULL_SINGLE_INVERSE
      &END
      &OUTER_SCF
        EPS_SCF 1.0E-6
        MAX_SCF 5
      &END
      &PRINT
        &RESTART OFF
        &END
        &RESTART_HISTORY OFF
        &END
      &END
    &END SCF
  &END DFT
@ENDIF
  &SUBSYS
    &CELL
      ABC   12.0  12.0  12.0
      PERIODIC NONE
    &END CELL

    &COORD
Si  0.0    1.7   -2.2
Si  1.25   1.25   0.0
Si  1.25  -1.25   0.0
Si -1.25  -1.25   0.0
Si -1.25   1.25   0.0 
Si  0.0    -1.7   2.2
H   2.0    1.25   1.29
H  -2.0    1.25   1.29
H   2.0   -1.25  -1.29
H  -2.0   -1.25  -1.29  
H   0.0    2.99  -2.95 
H   0.0    0.41  -2.95
H   0.0   -2.99   2.95
H   0.0   -0.41   2.95
    &END COORD

@IF ( ${METHOD_TO_USE} == DFT )
    &KIND Si
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q4
    &END KIND

    &KIND H
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q1
    &END KIND
@ENDIF

    &COLVAR
       &COORDINATION
          KINDS_FROM  Si
          KINDS_TO   Si
          R_0 [angstrom]  2.6
          NN  16
          ND  20
       &END COORDINATION
    &END COLVAR

    &COLVAR
       &COORDINATION
          KINDS_FROM  Si
          KINDS_TO   H
          R_0 [angstrom]  2.0
          NN  8
          ND  14
       &END COORDINATION
    &END COLVAR
    &COLVAR
       &COORDINATION
          KINDS_FROM  H
          KINDS_TO    H
          R_0 [angstrom]  1.8
          NN  8
          ND  14
       &END COORDINATION
    &END COLVAR
  &END SUBSYS

&END FORCE_EVAL

&GLOBAL
  PROJECT si6_clu_mtd_l_h0_p3
  RUN_TYPE MD
  PRINT_LEVEL LOW
&END GLOBAL

&MOTION
  &MD
    ENSEMBLE NVT
    STEPS  80000
    TIMESTEP 0.8
    TEMPERATURE 300.0
    TEMP_TOL   50
    &THERMOSTAT
      &NOSE
        LENGTH 3
        YOSHIDA 3
        TIMECON 1000.0
        MTS 2
      &END NOSE
    &END
    ANGVEL_ZERO
    COMVEL_TOL  2.0E-7

    &PRINT
      &ENERGY
        &EACH
           MD 1
        &END
      &END

      &PROGRAM_RUN_INFO
        &EACH
           MD 1
        &END
      &END
      FORCE_LAST
    &END PRINT
  &END MD

  &FREE_ENERGY
    &METADYN
      DO_HILLS .FALSE.
      LAGRANGE
      TEMPERATURE 100.
      TEMP_TOL  10.
      &METAVAR
        LAMBDA  2.5
        MASS   30.
        COLVAR 1
      &END METAVAR
      &METAVAR
        LAMBDA 3.0
        MASS 30.0
        COLVAR 2
      &END METAVAR
      &METAVAR
        LAMBDA 3.0
        MASS 30.0
        COLVAR 3
        &WALL
            POSITION 0.0
            TYPE QUARTIC
            &QUARTIC
               DIRECTION WALL_MINUS
               K  100.0
            &END
        &END
      &END METAVAR
      
      &PRINT
        &COLVAR
           COMMON_ITERATION_LEVELS 3
           &EACH
             MD 1
           &END
        &END
        &HILLS
           COMMON_ITERATION_LEVELS 3
           &EACH
             MD 1
           &END
        &END
      &END
    &END METADYN
  &END

  &PRINT
    &TRAJECTORY
      &EACH
        MD 1
      &END
    &END
    &VELOCITIES OFF
    &END
    &RESTART
      &EACH
         MD 100
      &END
      ADD_LAST NUMERIC
    &END
    &RESTART_HISTORY 
      &EACH
         MD 2000
      &END
    &END
  &END
&END MOTION

@IF ( ${DO_RESTART} == YES )
&EXT_RESTART
  RESTART_FILE_NAME  ${RESPATH}/si6_clu_mtd_l_h0_p3-1.restart
  RESTART_COUNTERS   T
  RESTART_POS        T
  RESTART_VEL        T
  RESTART_THERMOSTAT T
  RESTART_METADYNAMICS T
&END EXT_RESTART
@ENDIF