WIP

examples/PACKAGES/alchemy/h2o.mol

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+# Water molecule. SPC/E model.
+
+3 atoms
+2 bonds
+1 angles
+
+Coords
+
+1    1.12456   0.09298   1.27452
+2    1.53683   0.75606   1.89928
+3    0.49482   0.56390   0.65678
+
+Types
+
+1        1
+2        2
+3        2
+
+Charges
+
+1       -0.8472
+2        0.4236
+3        0.4236
+
+Bonds
+
+1   1      1      2
+2   1      1      3
+
+Angles
+
+1   1      2      1      3
+
+Shake Flags
+
+1 1
+2 1
+3 1
+
+Shake Atoms
+
+1 1 2 3
+2 1 2 3
+3 1 2 3
+
+Shake Bond Types
+
+1 1 1 1
+2 1 1 1
+3 1 1 1
+
+Special Bond Counts
+
+1 2 0 0
+2 1 1 0
+3 1 1 0
+
+Special Bonds
+
+1 2 3
+2 1 3
+3 1 2

examples/PACKAGES/alchemy/h3o+.mol

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+# Hydronium ion. SPC/E model.
+
+4 atoms
+3 bonds
+3 angles
+
+Coords
+
+1    0.00000   1.00000   0.00000
+2    0.00000   0.00000   0.00000
+3    0.00000  -0.50000  -0.8660
+4    0.00000  -0.50000   0.8660
+
+Types
+
+1        2
+2        1
+3        2
+4        2
+
+Charges
+
+1        0.56775
+2       -0.70305
+3        0.56775
+4        0.56775
+
+Bonds
+
+1   1      2      1
+2   1      2      3
+3   1      2      4
+
+Angles
+
+1   1      1      2      3
+1   1      3      2      4
+1   1      1      2      4
+

examples/PACKAGES/alchemy/in.twowater

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

examples/PACKAGES/alchemy/oh-.mol

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+# Hydroxyl ion. SPC/E model.
+
+2 atoms
+1 bonds
+
+Coords
+
+1    0.5   0.0   0.0
+2   -0.5   0.0   0.0
+
+Types
+
+1        1
+2        2
+
+Charges
+
+1       -1.1354
+2        0.1354
+
+Bonds
+
+1   1      1      2
+