# Coulomb Crystal trapped by RF

# Steps
firststep 0
numsteps  100000

# System/topology
boundaryConditions vacuum
cellManager        Cubic
cellsize           500000
exclude            none

# Positions
posfile 309ca.pos.xyz

# Velocities
temperature 1e-3
#velfile 309ca.vel.xyz

# Molecular topology/atom definitions
psffile 309ca.psf

# Force field
parfile 309ca.par

# Random generator
seed 1234

# Modifications
#removeAngularMomentum 0
#removeLinearMomentum 0

#
# Output
#

# General/Screen output frequency
outputfreq 100

# PaulTrap relative output
PAULFILE          309ca.out.paul           # Write PaulTrap output
PAULLOWFILE       309ca.out.paul.low.xyz   # Write minimal positions and output
PAULOutputFreq    10
PAULCACHEFREQ     100                      # Cache 100 output lines before writing
#PAULOMEGA        2.6e-09                  # commented out to use values defined by force def.


# Trajectory position file
DCDOutputFreq 100
DCDFile       309ca.out.dcd

# Integration scheme
Integrator {
  level 0 PaulTrap {
      timestep 1e+08      # [fs]
      temperature 1e-28   # Temperature [K] if not defined by (t , time)
      thermal 1e-7        # 1.0 => instantly, 0.0 => Leapfrog
      scheme berendsen    # thermostat scheme

      force Coulomb -algorithm NonbondedSimpleFull #-blocksize 64
      # Multi-grid replacement for NonbondedSimpleFull
      #    force Coulomb -algorithm MultiGrid -interpolation Hermite -kernel C2 
      #          -s 500000 -levels 3 -h 250000 250000 250000  -order 6 -ratio 2

      force PaulTrap -omegaR 2.6e-09 -omegaZ 2.6e-09
  }
}