#CPQA INCLUDE dimer.xyz
#CPQA INCLUDE topology_atoms.psf
!!cp2k!!
!! inp file by Alin M Elena
!! alinm.elena@gmail.com
!! http://alin.elenaworld.net
#global section sets what kind of calculations you want to do an general
! settings
@set pfreq 100 ! the frequency for printing .cube properties and restart files
@set name dimer
@set period T
@set method GPW ! use GAPW/ GPW for dft
@set zk 10.0  ! coupling constant for collective variables and atoms
@set zmass 100.0 ! mass for collective variables
@set zgamma 0.001 ! friction coefficient for lagrange equations for cvs
@set Tz  3000.0 ! temperature 
@set Nz 1   ! number of steps to integrate z
@set dtz 0.5 ! time step to integrate the z 
@set dt 1.0 ! time steps to integrate atoms
@set N 1 ! the length of the mini-trajectory
@set M 2 ! number of cycles/steps for the HMC part
@set Temp 25 ! physical system temperature

&Global
  Project ${name}
!   Run_type ENERGY_Force
  Run_type TAMC
!   Run_type MD
!  Run_type GEOMETRY_OPTIMIZATION
  Print_Level low
  Echo_input yes
  Preferred_FFT_library FFTSG
   &Print
    filename=./${name}
  &end print
  walltime 3600
&End Global
#defines how forces are evaluated
&Force_eval
  Method QS ! what is the method used for computing the energy
  Stress_tensor analytical
  &DFT ! dft settings
    Charge 0
    BASIS_SET_FILE_NAME ../../../data/BASIS_SET
    POTENTIAL_FILE_NAME ../../../data/POTENTIAL
    &QS
      Eps_default 1.0e-12
      Extrapolation ASPC
      Extrapolation_order 3
      Method ${method}

      &DFTB
        Self_consistent    T
        Dispersion         T
        Orthogonal_basis   F
        DO_EWALD           T
        &Parameter
          Param_file_path  params_scc
          Param_file_name  scc_parameter
          UFF_force_field  uff_table
        &End Parameter
      &End DFTB

    &End QS

    &XC ! exchange and correlation functionals
      &XC_Functional HCTH120
        &HCTH T
          Parameter_set 120
        &End HCTH
      &End XC_Functional
    &End XC

    &SCF ! the scf settings...
      Max_SCF 20
      Eps_SCF 1.e-1
      SCF_Guess Atomic
      &OT T ! orbital transformation settings
        Preconditioner Full_single_inverse
        Minimizer CG
      &End OT
      &Outer_SCF On
        Eps_scf 1.0E-1
        Max_scf 5
      &End Outer_SCF
      &Print
        &Restart
          &Each
           QS_SCF 0
           GEO_OPT 1
           MD ${pfreq}
          &End Each
          Add_last Numeric
        &End restart
      &End Print
      &Mixing
        Method Pulay_Mixing
        Pulay_alpha 0.3
        Pulay_beta 0.5
        NMixing 1
        NBuffer 5
      &end Mixing
    &End SCF
    &Mgrid
      Cutoff 50
    &end mgrid
    &Poisson
      Periodic None
      Poisson_Solver MT
      &MT
      &end MT
    &end poisson
    &Localize True
      Eps_localization 1.0e-4
      Eps_occupation 1.0e-6
      Min_or_Max SpreadMin
      Restart false
      States Occupied
      Use_History true
      &Print
        &Wannier_Centers
          Format xyz
          Ions+Centers true
          &each
            MD 1
          &end each
          Add_last numeric
        &end Wannier_Centers
        &Total_dipole On
          Periodic ${period}
          Reference zero
          reference_point 0.0 0.0 0.0
          &each
            MD 10
          &end each
          Add_last numeric
        &end total_dipole
        &molecular_dipoles Off
          Periodic ${period}
          Reference zero
          reference_point 0.0 0.0 0.0
          &each
            MD 10
          &end each
          Add_last numeric
        &end molecular_dipoles
        &wannier_states on
          &each
            MD 1
          &end each
          add_last numeric
        &end wannier_states
       &molecular_states off
          &each
            MD 10
          &end each
          add_last numeric
        &end molecular_states
      &end 
    &end Localize
    &Print
      &MO_Cubes Medium
        &each
          MD 1
        &end Each
        Add_last Numeric
      &end MO_Cubes
      &E_Density_Cube Medium
        &each
          MD ${pfreq}
        &end Each
        Add_last Numeric
      &end E_Density_Cube
      &Tot_density_cube Medium
        &each
          MD ${pfreq}
        &end Each
        Add_last Numeric
      &end tot_density_cube
      &V_Hartree_Cube Medium
        &each
          MD ${pfreq}
        &end Each
        Add_last Numeric
      &end V_Hartree_Cube
      &EFIELD_Cube Medium
        &each
          MD ${pfreq}
        &end Each
        Add_last Numeric
      &end EFIELD_Cube
    &end Print
  &End DFT
  &Subsys
    &cell
      ABC [angstrom] 6.0 6.0 6.0
      alpha_beta_gamma 90.0 90.0 90.0
      Periodic xyz
    &end cell
    &topology
      coord_file_format xyz
      coord_file_name dimer.xyz
     &center_coordinates off
     &end center_coordinates
     &MOL_SET
        &MOLECULE
          NMOL 1
          CONN_FILE_NAME topology_atoms.psf
        &END Molecule
      &END MOL_SET
      CONNECTIVITY MOL_SET
    &end topology

    &kind O
      Basis_set DZVP-GTH-PADE
      Potential GTH-HCTH120-q6
    &end kind
    &kind H
      Basis_set DZVP-GTH-PADE
      Potential GTH-HCTH120-q1
    &end kind
    &colvar
      &HBP
        NPOINTS 1
        ATOMS 4 5 1
      &end HBP
    &end colvar
 &end subsys
&End Force_eval
&Motion
  &Geo_Opt
    Max_Iter 1000
    Max_Force 4.5e-4
    Max_Dr 3.0e-3
    Optimizer LBFGS
  &end Geo_Opt
  &MD
    Timestep ${dt}
    Time_Start_Val 0.0
    Steps ${N}
    Ensemble NVE
    Temperature ${Temp}
    &Thermostat
      &Nose
        length 3
        yoshida 3
        Timecon 1000.0
        MTS 2
      &end Nose
    &End Thermostat
  &End MD
  &MC
    Ensemble Traditional
    Nstep ${M}
    Iprint 1
    RANDOMTOSKIP 0
  &End MC
  &Free_Energy Metadyn
    &Metadyn
      Lagrange true
      Langevin true
      Temperature ${Tz}
      Temp_Tol 2000.0
      TAMCSteps ${Nz}
      Timestep ${dtz}
      &Metavar
        Lambda ${zk}
        Mass  ${zmass}
        Gamma ${zgamma}
        Scale 1.0
        Colvar 1
      &end metavar
      &EXT_LAGRANGE_SS0                                                                                                                                                                                                                                                       
        0.44025202                                                                                                                                                                                                                                             
      &END EXT_LAGRANGE_SS0
      &Print
        &Colvar
          &Each
            MD 1
          &End each
        &end colvar
      &End print
    &End Metadyn
  &End Free_energy
  &print
    &Trajectory
      filename trajectory.xyz
      format xyz
      &Each
        MD 10
      &end each
    &end trajectory
    &Velocities
      filename velocity.xyz
      format xyz
      &Each
        MD 10
      &End each
    &end velocities
  &End print
&End Motion

