# LAMMPS input script for a DPD simulation

units lj
atom_style bond
read_data box.lmps
pair_style hybrid dpd 1.0 1.0 34387 srp 0.8 * mid
bond_style harmonic
pair_coeff   1   1 dpd    25.000000     4.500000     1.000000
pair_coeff   1   2 dpd    80.956240     4.500000     1.000000
pair_coeff   1   3 dpd    77.679700     4.500000     1.000000
pair_coeff   1   4 dpd    27.001240     4.500000     1.000000
pair_coeff   1   5 dpd   147.952000     4.500000     1.000000
pair_coeff   2   2 dpd    25.000000     4.500000     1.000000
pair_coeff   2   3 dpd    27.001240     4.500000     1.000000
pair_coeff   2   4 dpd    39.999490     4.500000     1.000000
pair_coeff   2   5 dpd    29.002480     4.500000     1.000000
pair_coeff   3   3 dpd    20.000170     4.500000     1.000000
pair_coeff   3   4 dpd    32.004340     4.500000     1.000000
pair_coeff   3   5 dpd    29.999830     4.500000     1.000000
pair_coeff   4   4 dpd    25.000000     4.500000     1.000000
pair_coeff   4   5 dpd    45.012400     4.500000     1.000000
pair_coeff   5   5 dpd    25.000000     4.500000     1.000000
pair_coeff   1    6  none
pair_coeff   2    6  none
pair_coeff   3    6  none
pair_coeff   4    6  none
pair_coeff   5    6  none
pair_coeff   6    6  srp 100 0.8

bond_coeff   1     2.000000     0.000000
bond_coeff   2     2.000000     0.000000
bond_coeff   3     2.000000     0.000000
bond_coeff   4     2.000000     0.000000
bond_coeff   5     2.000000     0.000000


# system definition
# create initial velocities
velocity all create 1.0 4928459 dist gaussian
special_bonds lj 1.0 0.0 0.0

# change neighbor list parameters to avoid dangerous builds
neighbor 3.0 bin
neigh_modify delay 2

# specify simulation parameters
timestep 0.04
thermo 100
thermo_style custom step temp etotal pxx pyy pzz
# make sure ghost atoms used in parallelization receive velocity information
# velocities are needed for DPD force calculations
comm_modify cutoff 5.0 vel yes

# define molecule groups
group water molecule 1:3300
group toluene2 molecule 3301:9975
group asphaltene molecule 9976:9977

# define rigid/non-rigid groups and fixes
group fixGroup1 id 1:9975 9982:9983 9988:9989 9993:9994 9998:10000 10007:10008 10013:10014 10018:10019 10023:10025
group fixGroup2 id 9976:9981 9984:9987 9990:9992 9995:9997 10001:10006 10009:10012 10015:10017 10020:10022
fix 1 fixGroup1 nve
fix 2 fixGroup2 rigid/nve/small molecule

# setup data dumps
dump 1 all custom 200000 traj0.lammpstrj id mol type xu yu zu

# run the simulation
run 200000

# write restart file
write_restart restart_0.dpd