forked from lijiext/lammps
57 lines
1.3 KiB
Plaintext
57 lines
1.3 KiB
Plaintext
# sample surface deposition script for molecules
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units lj
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atom_style bond
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boundary p p f
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lattice fcc 1.0
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region box block 0 5 0 5 0 10
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create_box 3 box bond/types 1 extra/bond/per/atom 1
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region substrate block INF INF INF INF INF 3
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create_atoms 1 region substrate
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0
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pair_coeff 1 2 1.0 1.0 5.0
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mass * 1.0
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bond_style harmonic
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bond_coeff 1 5.0 1.0
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neigh_modify delay 0
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group addatoms type 2
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region mobile block 0 5 0 5 2 INF
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group mobile region mobile
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compute add addatoms temp
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compute_modify add dynamic/dof yes extra/dof 0
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fix 1 addatoms nve
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fix 2 mobile langevin 0.1 0.1 0.1 587283
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fix 3 mobile nve
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molecule dimer molecule.dimer.shake
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region slab block 0 5 0 5 8 9
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fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 &
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mol dimer vz -1.0 -1.0 shake 6
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fix 5 addatoms wall/reflect zhi EDGE
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fix 6 all shake 0.0001 20 1000 b 1 mol dimer
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thermo_style custom step atoms temp epair etotal press
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thermo 100
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thermo_modify temp add lost/bond ignore lost warn
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#dump 1 all atom 50 dump.deposit.atom
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#dump 2 all image 50 image.*.jpg type type &
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# axes yes 0.8 0.02 view 80 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 50 tmp.mpg type type &
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# axes yes 0.8 0.02 view 80 -30
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#dump_modify 3 pad 5
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run 10000
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