update example so we can use the simpler communication pattern
This commit is contained in:
Axel Kohlmeyer
@ -1,39 +0,0 @@
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# Hydronium ion. SPC/E model.
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4 atoms
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3 bonds
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3 angles
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Coords
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1 0.00000 1.00000 0.00000
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2 0.00000 0.00000 0.00000
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3 0.00000 -0.50000 -0.8660
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4 0.00000 -0.50000 0.8660
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Types
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1 2
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2 1
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3 2
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4 2
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Charges
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1 0.56775
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2 -0.70305
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3 0.56775
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4 0.56775
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Bonds
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1 1 2 1
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2 1 2 3
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3 1 2 4
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Angles
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1 1 1 2 3
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1 1 3 2 4
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1 1 1 2 4
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@ -1,12 +1,16 @@
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# set up names for two partitions with different topologies
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# Example for alchemical transformation of two water molecules into a hydronium and hydroxyl ion
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# WARNING: This input is for demonstrating the method.
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# Force field parameters are made up and not suitable for production simulations.
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# set up names for two partitions with different topologies for output files.
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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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region box block -5 5 -5 5 -5 5
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boundary p p p
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create_box 2 box bond/types 2 angle/types 2 &
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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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@ -18,36 +22,65 @@ 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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bond_coeff * 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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angle_coeff * 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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# create the two molecules we want to transform ...
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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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timestep 0.1
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# ... and put them in a group
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group transform id 1:6
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# now fill the box with more water
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create_atoms 0 random 32 34564 NULL mol water 25367 overlap 1.4
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# change topology and settings for the two states
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# we cannot simply create a different topology directly or
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# load a different data file because the order and position
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# of all atoms must be maintained across both replica
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# for that we first have to remove everything.
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delete_bonds transform bond 1
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delete_bonds transform angle 1 remove
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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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"create_bonds single/bond 2 1 2" &
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"create_bonds single/bond 2 1 3" &
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"create_bonds single/bond 2 4 5" &
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"create_bonds single/bond 2 4 6" &
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"create_bonds single/angle 2 2 1 3" &
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"create_bonds single/angle 2 5 4 6" &
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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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"create_bonds single/bond 2 1 2" &
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"create_bonds single/bond 2 3 4" &
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"create_bonds single/bond 2 4 5" &
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"create_bonds single/bond 2 4 6" &
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"create_bonds single/angle 2 3 4 5" &
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"create_bonds single/angle 2 5 4 6" &
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"create_bonds single/angle 2 3 4 6" &
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"set atom 1 charge -1.1354" &
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"set atom 2 charge 0.1354" &
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"set atom 3 charge 0.56775" &
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"set atom 4 charge -0.70305" &
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"set atom 5*6 charge 0.56775"
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velocity all create 100 5463576
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velocity all create 300.0 5463576
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timestep 0.2
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fix 1 all nve
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fix 1 all nvt temp 300 300 1.0
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fix 2 all alchemy
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fix 3 all shake 0.0001 50 1000 b 1 a 1
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dump 1 all atom 100 ${name}.lammpstrj
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dump_modify 1 sort id
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if "${name} == twowater" then &
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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_style custom step temp press etotal density 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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run 20000
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@ -1,24 +0,0 @@
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# Hydroxyl ion. SPC/E model.
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2 atoms
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1 bonds
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Coords
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1 0.5 0.0 0.0
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2 -0.5 0.0 0.0
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Types
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1 1
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2 2
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Charges
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1 -1.1354
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2 0.1354
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Bonds
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1 1 1 2
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