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Copy pathcoll_pol_deform.in
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coll_pol_deform.in
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#BD of a 60 particle + 615 chain in total
#VARIABLES
variable eq_steps equal 0
variable run_steps equal 1e7
variable xyz_steps equal 1e4
variable nevery equal 10
variable thermo_steps equal 1e3
variable dt equal 0.001
variable eq_dt equal 0.001
variable mass_bead equal 1.0
variable mass_part equal 100.0
variable damp_coeff equal 1.0
variable eps equal 8.0
variable Kuhn equal 60.00
variable K_Kuhn equal 1.50
variable R0_Kuhn equal 30.00
variable n_every equal 1e2
variable n_repeat equal 1e4
variable n_freq equal 1e6
variable partsize equal 0.88 #radius
units lj
boundary p p p
atom_style bond
pair_style hybrid lj/cut 1.12 lj/expand 2.5
bond_style fene
special_bonds fene
#ATOM DEFINITION
read_data micelle.data
#read_restart restart.poly
mass 1 ${mass_bead}
mass 2 ${mass_part}
group polymer type 1
group coll type 2
# COEFFICIENTS
pair_coeff 1 1 lj/cut 1.0 1.0 1.12 #HYD-HYD
pair_modify shift yes
pair_coeff 1 2 lj/expand ${eps} 1.0 ${partsize} 2.5 #HYD-PAR
pair_coeff 2 2 lj/expand 2.0 2.0 6.5 2.24 #PART-PART
pair_modify shift yes
bond_coeff 1 ${K_Kuhn} ${R0_Kuhn} 0.0 1.0
#pair_write 1 1 501 r 0.97 10 table_11.txt LJ
#pair_write 1 2 501 r 0.98 10 table_12.txt LJ
#pair_write 2 2 501 r 6.3 10 table_22.txt LJ
neighbor 10.00 multi
neigh_modify delay 1 every 1
min_style cg
minimize 1.0e-4 1.0e-6 100 1000
fix 1 all nve
fix 2 all langevin 1.0 1.0 ${damp_coeff} 485048
fix 3 all deform 1 x final 0.0 50.0 y final 0.0 50.0 z final 0.0 50.0
#compute firstrdf all rdf 100 1 1
#compute secondrdf all rdf 100 2 1
#fix myfix1 all ave/time ${n_every} ${n_repeat} ${n_freq} c_firstrdf[*] file rdf_11.txt mode vector
#fix myfix2 all ave/time ${n_every} ${n_repeat} ${n_freq} c_secondrdf[*] file rdf_12.txt mode vector
# PRE-RUN SIMULATIONS
#reset_timestep 0
#timestep ${eq_dt}
thermo ${thermo_steps}
#run ${eq_steps}
# RUN SIMULATIONS
#reset_timestep 0
dump 1 all custom ${xyz_steps} dump.lammpstrj id type x y z
dump_modify 1 sort id
compute press all pressure thermo_temp bond
#fix fly_corr_xy all ave/correlate/long ${nevery} ${run_steps} c_press[4] file corr_xy.txt title1 "time" title2 "corr" ncorr 30 nlen 16 ncount 2
#fix fly_corr_xz all ave/correlate/long ${nevery} ${run_steps} c_press[5] file corr_xz.txt title1 "time" title2 "corr" ncorr 30 nlen 16 ncount 2
#fix fly_corr_yz all ave/correlate/long ${nevery} ${run_steps} c_press[6] file corr_yz.txt title1 "time" title2 "corr" ncorr 30 nlen 16 ncount 2
thermo_style custom step pe ke etotal temp c_press[4] density emol epair
timestep ${dt}
thermo ${thermo_steps}
print "Run Simulations"
run ${run_steps}
write_restart restart.poly2
write_data restart-1a.data2 nocoeff