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in.initialize
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#trying to just see how one polymer chain moves
dimension 3
units lj
atom_style hybrid full ellipsoid
boundary p p p
bond_style hybrid harmonic eldihedral
angle_style harmonic
dihedral_style none
improper_style none
pair_style gayberne 1.0 1.0 1.0 4.0
fix prop all property/atom i_coreid
read_data "v5_nosc.data" fix prop NULL CoreIDs
special_bonds lj 0.0 1.0 1.0
pair_coeff 1 1 1.0 1.0 0.1 1.0 0.25 0.1 1.0 0.25
pair_coeff 2 2 0.0 1.0 1 1 1 1 1 1
pair_coeff * 2 0 1.0 0 0 0 0 0 0
bond_coeff 1 harmonic 0.0 0.5
bond_coeff 2 harmonic 20.0 0.2
bond_coeff 3 eldihedral 0 3.0 0 0
angle_coeff 1 3.0 180.0
group disks type 1 2
group ell type 1
group bondSites type 2
neigh_modify delay 0 every 1 check no
fix 1 all rigid/nve/small custom i_coreid
fix 2 ell langevin 1.5 1.5 2 1 angmom 1.0
fix drift all momentum 10000 linear 1 1 1 angular rescale
restart 1000000 restarts_v5/equil.*.rst
compute ta ell temp/asphere dof all
compute rot all erotate/rigid 1
compute kin all ke/rigid 1
compute op ell property/atom quati quatj quatk quatw
compute shape ell property/atom shapex shapey shapez
dump 1 ell custom 100000 ovito.dump id type xu yu zu c_op[1] c_op[2] c_op[3] c_op[4] c_shape[1] c_shape[2] c_shape[3]
dump 2 all custom 100000 ovito_all.dump id type xu yu zu
timestep 0.001
thermo_style custom step temp c_ta epair ebond eangle etotal press pe ke c_rot c_kin
thermo 10000
run 20000000