# =========================================================================
# LAMMPS main parameter file and script                                    
#                                                                          
# Author: Paul J. Atzberger.               
#
# Based on script generated by the MANGO-SELM Model Builder.
#                                                                          
# =========================================================================

# == Setup variables for the script 

variable dumpfreq         equal    1
variable restart          equal    0
variable neighborSkinDist equal    1.0 # distance for bins beyond force cut-off (1.0 = 1.0 Ang for units = real) 
variable baseFilename     universe FENE_Dimer

# == Setup the log file
log         ${baseFilename}.LAMMPS_logFile

# == Setup style of the run

# type of units to use in the simulation (units used are in fact: amu, nm, ns, Kelvins)
units       real

# indicates possible types allowed for interactions between the atoms
atom_style  angle 

# indicates possible types allowed for bonds between the atoms 
bond_style  hybrid fene 

# indicates possible types allowed for bond angles between the atoms 
angle_style none 


# indicates type of boundary conditions in each direction (p = periodic) 
boundary p p p 

read_data ${baseFilename}.LAMMPS_read_data # file of atomic coordinates and topology
velocity all zero linear                   # initialize all atomic velocities initially to zero

# == Interactions 

#pair_style none
pair_style lj/cut 30.0                             # Lennard-Jones with cut-off
pair_coeff 1 1 2478959.87 22.5                    # epsilon and sigma : KBT and bead-size
atom_modify sort 1000 ${neighborSkinDist}          # setup sort data explicitly since no interactions to set this data. 

# == Setup neighbor list distance
neighbor ${neighborSkinDist} bin                   # first number gives a distance beyond the force cut-off ${neighborSkinDist}

# == Setup the SELM integrator
fix 1 all SELM ${baseFilename}.SELM_params

# == Setup output data write to disk
dump        1 all dcd ${dumpfreq} ${baseFilename}_LAMMPS_atomCoords.dcd
dump_modify 1 unwrap yes                   # indicates for periodic domains that unwrapped coordinate should be given

# == Run the simulation
timestep 100.0
run      10000 upto

# == Write restart data
write_restart ${baseFilename}.LAMMPS_restart_data