forked from lijiext/lammps
55 lines
1.0 KiB
Groff
55 lines
1.0 KiB
Groff
LAMMPS (21 Aug 2012)
|
|
# Tethered nanorods
|
|
|
|
atom_style molecular
|
|
|
|
read_data data.rigid.tnr
|
|
1 = max bonds/atom
|
|
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
|
|
1 by 2 by 2 MPI processor grid
|
|
5600 atoms
|
|
1600 bonds
|
|
2 = max # of 1-2 neighbors
|
|
1 = max # of 1-3 neighbors
|
|
1 = max # of 1-4 neighbors
|
|
2 = max # of special neighbors
|
|
|
|
# Specify bond parameters
|
|
|
|
bond_style fene
|
|
bond_coeff 1 30.0 1.5 1.0 1.0
|
|
|
|
special_bonds fene
|
|
2 = max # of 1-2 neighbors
|
|
2 = max # of special neighbors
|
|
|
|
# Specify initial velocities
|
|
|
|
velocity all create 1.4 109345
|
|
|
|
# Specify rigid components
|
|
|
|
group rods type 2
|
|
4000 atoms in group rods
|
|
group tethers subtract all rods
|
|
1600 atoms in group tethers
|
|
|
|
neigh_modify exclude molecule rods delay 0 every 1
|
|
|
|
# Specify the pair potentials
|
|
|
|
pair_style lj/cut 2.5
|
|
pair_modify shift yes
|
|
pair_coeff * * 1.0 1.0 1.122
|
|
pair_coeff 2 2 1.0 1.0 2.5
|
|
|
|
# Specify output
|
|
|
|
thermo 100
|
|
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
|
|
thermo_modify flush yes lost warn
|
|
|
|
timestep 0.005
|
|
|
|
log log.tnr
|