54 lines
1.2 KiB
Plaintext
54 lines
1.2 KiB
Plaintext
# set up names for two partitions with different topologies
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variable name world twowater twoions
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units real
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atom_style full
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atom_modify map array
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region box block -10 10 -10 10 -10 10
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boundary m m m
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create_box 2 box bond/types 1 angle/types 1 &
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extra/bond/per/atom 3 extra/angle/per/atom 3 extra/special/per/atom 3
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mass 1 15.9994
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mass 2 1.008
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pair_style lj/cut/coul/cut 10.0
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pair_coeff 1 1 0.1553 3.166
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pair_coeff 1 2 0.0 1.0
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pair_coeff 2 2 0.0 1.0
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bond_style harmonic
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bond_coeff 1 1000.0 1.0
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angle_style harmonic
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angle_coeff 1 100.0 109.47
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molecule water h2o.mol
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molecule hydronium h3o+.mol
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molecule hydroxyl oh-.mol
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timestep 0.1
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# generate different topologies with the same number of atoms
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if "${name} == twowater" then &
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"create_atoms 0 single -2.0 0.0 0.0 mol water 453624" &
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"create_atoms 0 single 2.0 0.0 0.0 mol water 767353" &
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else &
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"create_atoms 0 single 2.0 0.0 0.0 mol hydroxyl 767353" &
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"create_atoms 0 single -2.0 0.0 0.0 mol hydronium 453624"
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velocity all create 100 5463576
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fix 1 all nve
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fix 2 all alchemy
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dump 1 all atom 100 ${name}.lammpstrj
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dump_modify 1 sort id
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thermo_style custom step temp press etotal pe ke f_2[*]
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thermo 100
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reset_timestep 100
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run 10000 start 0 stop 20000
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