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Commit 0a32eed2 authored by Adam Fekete's avatar Adam Fekete
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more test examples

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LAMMPS (14 May 2016)
# input script for topotools tutorial step 2a
units real
boundary p p p
atom_style full
read_data data.1_methyl_naphthalene
orthogonal box = (-13.4569 -14.6313 -12.4476) to (13.25 14.1743 12.4476)
1 by 1 by 1 MPI processor grid
reading atoms ...
1134 atoms
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
reading bonds ...
1188 bonds
reading angles ...
1944 angles
reading dihedrals ...
2700 dihedrals
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
18 = max # of special neighbors
kspace_style pppm 1.0e-6
# interaction styles
pair_style lj/cut/coul/long 12.0 20.0 6.0 6.0
ERROR: Illegal pair_style command (../pair_lj_cut_coul_long.cpp:600)
LAMMPS (14 May 2016)
# input script for topotools tutorial step 2d
units real
boundary p p p
atom_style full
read_data data.hexane_cyclohexane
orthogonal box = (-18.2312 -11.4993 -15.9471) to (19.2106 10.9242 17.3543)
2 by 1 by 2 MPI processor grid
reading atoms ...
684 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
reading bonds ...
666 bonds
reading angles ...
1296 angles
reading dihedrals ...
1782 dihedrals
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
16 = max # of special neighbors
# interaction styles
pair_style lj/cut/coul/cut 12.0
bond_style harmonic
angle_style harmonic
dihedral_style opls
pair_modify mix geometric tail yes
# OPLS considers 1-4 interactions with 50%.
special_bonds lj/coul 0.0 0.0 0.5
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
16 = max # of special neighbors
# force field parameters
# missing nonbonded parameters are inferred from mixing.
pair_coeff 1 1 0.066 3.50 # CT
pair_coeff 2 2 0.03 2.50 # HC
bond_coeff 1 268.0 1.529 # CT-CT
bond_coeff 2 340.0 1.090 # CT-HC
angle_coeff 1 58.35 112.7 # CT-CT-CT
angle_coeff 2 37.5 110.7 # CT-CT-HC
angle_coeff 3 33.0 107.8 # HC-CT-HC
dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT
dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC
dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC
timestep 0.25
reset_timestep 0
neigh_modify every 10 delay 20 check yes
thermo 400
thermo_style multi
fix 1 all nvt temp 300.0 300.0 100.0
# equilibration trajectory
dump 1 all custom 400 hexane_cyclohexane_nvt_20ps.lammpstrj id type x y z ix iy iz
# dump_modify 1 unwrap yes
log log.hexane_cyclohexane_nvt-thermo_style_multi
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