# Polymer Beads Calculation - DPD + FENE

# Reduced units
units		lj
# DPD forcefield with molecule (TP)
atom_style	hybrid dpd bond

# Read the input file (Atom positions, types and Bonds)
read_data	topo.dat

# Assign names to atom types
group TP type     1
group Solvent1 type  2
group Solvent2 type   3
group Solvent3 type  4


###########################################################
#Start the smothing procedure to release overlapping atoms#
###########################################################

# Change the weighting coeff (Bonds)
special_bonds 0 1 1

# Special pair interaction calculation. Very smooth. Exist even if distance=0
pair_style soft 1.12
pair_coeff * * 1.0 20.0 1.12

# Bond style
bond_style 	fene
bond_coeff	* 120.0 1.5 1.0 1.0

# Integration scheme. Prevent atoms from moving more than 1.0 of the unit
# distance between two timestep
fix		1 all nve/limit 1.0

# Save files to disk every 1000 timesteps. Unwrap positions. It yields a nice
# view of the bonds in VMD
dump custinit all custom 1000 DPD.unwrap.init.lammpstrj tag type xu yu zu

# Write thermo results to screen
thermo 1000


# Save restart files
restart 50000 restart


# Smoothing cycle. Increasing timestep lenght
timestep 0.00001
run 100000 start 0 stop 200000
timestep 0.00005
run 100000  start 0 stop 200000


############################################################
#End of the smothing procedure to release overlapping atoms#
############################################################
 
# Assign the DPD forcefield coefficients to atoms
pair_style	dpd 1 2.5 34567
# TP-TP
pair_coeff	1 1 25.0  4.5
# TGMDA-TGMDA
pair_coeff	2 2 25.0  4.5
# Solvent2-Solvent2 
pair_coeff	3 3 25.0  4.5
# Solvent3-Solvent3
pair_coeff	4 4 25.0  4.5

#PKHB-Solvent1
pair_coeff	1 2 22.32 4.5
#PKHB-Solvent2
pair_coeff	1 3 35.98 4.5
#PKHB-Solvent3
pair_coeff	1 4 34.61 4.5

#Solvent1-Solvent2
pair_coeff	2 3 37.75 4.5
#Solvent1-Sovent3
pair_coeff	2 4 39.48 4.5

#Solvent2-Solvent3
pair_coeff	3 4 25.01 4.5


# Remove the previous nve/limit integration scheme
unfix 1

# Perform mean-square displacement calculation for diffusion calculation
fix 2 TP msd 1000 diff_TP.dat


# Integration scheme.
fix		3 all nve

# Update the neighbors list every 5 timestep
neigh_modify delay 5

# Write thermodynamic data to screen every 1000 timestep
thermo		1000

# Force thermo prperties to be writen to disk
thermo_modify lost warn flush yes

# Save files to disk every 1000 timesteps. Unwrap positions. It yields a nice
# view of the bonds in VMD
dump cust all custom 1000 DPD.unwrap.lammpstrj tag type xu yu zu

# Force output files to be writen to disk
dump_modify cust flush yes


# Change the timestep to a larger value
timestep 0.0001

# Start the dynamics
run		1000000