add progress information to screen or universe logfile
This commit is contained in:
Axel Kohlmeyer
@ -73,18 +73,18 @@ else &
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velocity all create 300.0 5463576
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velocity all create 300.0 5463576
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timestep 0.2
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timestep 0.2
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# since the trajectory and forces are kept identical through fix alchemy
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# since the trajectory and forces are kept identical through fix alchemy,
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# we can even do fix npt simulations, but we need to use the "mixed" pressure
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# we can do fix npt simulations, but we must use the "mixed" pressure
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fix integrate all npt temp 300 300 1.0 iso 1.0 1.0 10.0
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fix integrate all npt temp 300 300 1.0 iso 1.0 1.0 10.0
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fix transform all alchemy
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fix transform all alchemy
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compute pressure all pressure/alchemy transform
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compute pressure all pressure/alchemy transform
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fix_modify integrate press pressure
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fix_modify integrate press pressure
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# only need to output a dump file form one partition
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# only need to output a dump file from one partition
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if "${name} == twowater" then &
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# if "${name} == twowater" then &
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"dump 1 all atom 100 ${name}.lammpstrj" &
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# "dump 1 all atom 100 ${name}.lammpstrj" &
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"dump_modify 1 sort id"
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# "dump_modify 1 sort id"
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thermo_style custom step temp press etotal density pe ke f_transform[1] f_transform[4]
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thermo_style custom step temp press etotal density pe ke f_transform[1] f_transform[4]
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thermo_modify colname f_transform[1] lambda colname f_transform[4] EPot_mixed
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thermo_modify colname f_transform[1] lambda colname f_transform[4] EPot_mixed
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13
examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4
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13
examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4
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@ -0,0 +1,13 @@
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LAMMPS (8 Feb 2023)
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Running on 2 partitions of processors
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Starting alchemical transformation at 0%
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Alchemical transformation progress: 10%
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Alchemical transformation progress: 20%
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Alchemical transformation progress: 30%
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Alchemical transformation progress: 40%
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Alchemical transformation progress: 50%
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Alchemical transformation progress: 60%
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Alchemical transformation progress: 70%
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Alchemical transformation progress: 80%
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Alchemical transformation progress: 90%
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Alchemical transformation progress: 100%
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408
examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.0
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408
examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.0
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@ -0,0 +1,408 @@
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LAMMPS (8 Feb 2023)
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Processor partition = 0
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using 1 OpenMP thread(s) per MPI task
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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 intended for demonstrating the method, only
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# The force field parameters are made up and NOT suitable for production simulations.
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# set up different names for two partitions
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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 -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 extra/bond/per/atom 3 extra/angle/per/atom 3 extra/special/per/atom 3
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Created orthogonal box = (-5 -5 -5) to (5 5 5)
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1 by 1 by 2 MPI processor grid
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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 * 1000.0 1.0
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angle_style harmonic
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angle_coeff * 100.0 109.47
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molecule water h2o.mol
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Read molecule template water:
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1 molecules
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0 fragments
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3 atoms with max type 2
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2 bonds with max type 1
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1 angles with max type 1
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0 dihedrals with max type 0
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0 impropers with max type 0
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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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Created 3 atoms
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using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
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create_atoms CPU = 0.003 seconds
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create_atoms 0 single 2.0 0.0 0.0 mol water 767353
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Created 3 atoms
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using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
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create_atoms CPU = 0.000 seconds
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# ... and put them in a group
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group transform id 1:6
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6 atoms in group transform
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# now fill the rest of the box with more water
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create_atoms 0 random 32 34564 NULL mol water 25367 overlap 1.33
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Created 96 atoms
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using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
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create_atoms CPU = 0.001 seconds
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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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# we first have to remove all topology data in the transform group
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delete_bonds transform bond 1
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System init for delete_bonds ...
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 2 2 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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Deleting bonds ...
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68 total bonds, 64 turned on, 4 turned off
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34 total angles, 34 turned on, 0 turned off
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0 total dihedrals, 0 turned on, 0 turned off
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0 total impropers, 0 turned on, 0 turned off
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delete_bonds transform angle 1 remove
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System init for delete_bonds ...
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Deleting bonds ...
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64 total bonds, 64 turned on, 0 turned off
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32 total angles, 32 turned on, 0 turned off
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0 total dihedrals, 0 turned on, 0 turned off
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0 total impropers, 0 turned on, 0 turned off
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# then generate different topologies for the two partitions. select by name.
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if "${name} == twowater" then "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 1 3" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 2 1 3" "create_bonds single/angle 2 5 4 6" else "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 3 4" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 3 4 5" "create_bonds single/angle 2 5 4 6" "create_bonds single/angle 2 3 4 6" "set atom 1 charge -1.1354" "set atom 2 charge 0.1354" "set atom 3 charge 0.56775" "set atom 4 charge -0.70305" "set atom 5*6 charge 0.56775"
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create_bonds single/bond 2 1 2
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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7 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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create_bonds single/bond 2 1 3
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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7 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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create_bonds single/bond 2 4 5
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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7 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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create_bonds single/bond 2 4 6
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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7 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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create_bonds single/angle 2 2 1 3
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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7 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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create_bonds single/angle 2 5 4 6
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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7 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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velocity all create 300.0 5463576
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timestep 0.2
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# since the trajectory and forces are kept identical through fix alchemy,
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# we can do fix npt simulations, but we must use the "mixed" pressure
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fix integrate all npt temp 300 300 1.0 iso 1.0 1.0 10.0
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fix transform all alchemy
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compute pressure all pressure/alchemy transform
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fix_modify integrate press pressure
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# only need to output a dump file from one partition
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# if "${name} == twowater" then # "dump 1 all atom 100 ${name}.lammpstrj" # "dump_modify 1 sort id"
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thermo_style custom step temp press etotal density pe ke f_transform[1] f_transform[4]
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thermo_modify colname f_transform[1] lambda colname f_transform[4] EPot_mixed
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thermo_modify press pressure
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thermo 100
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run 20000
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 7.535 | 7.535 | 7.535 Mbytes
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Step Temp Press TotEng Density PotEng KinEng lambda EPot_mixed
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0 300 184631.17 -802.19609 1.0171193 -892.51464 90.318545 1 -892.51464
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100 293.4335 -513.97927 189.09028 0.3029684 100.74865 88.341623 0.995 207.29243
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200 320.81838 1513.3 111.09325 0.64509407 14.507087 96.586165 0.99 46.402434
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300 261.53825 -3808.6942 -538.67351 0.88817871 -617.41269 78.739179 0.985 -614.76481
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400 308.32444 1375.0327 -804.08042 0.97694485 -896.90513 92.824715 0.98 -897.24386
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500 292.60623 -12843.384 -1141.5985 1.0140814 -1229.691 88.092563 0.975 -1221.948
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600 326.16112 91608.645 2882.4855 1.0263567 2784.2908 98.194659 0.97 2786.0743
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700 317.22811 -60420.408 -1517.0601 0.9919143 -1612.5654 95.505272 0.965 -1616.7677
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800 309.94673 -56793.931 -1549.4612 1.0024958 -1642.7743 93.313126 0.96 -1640.8606
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900 272.80718 -5076.2282 -1266.6775 1.0141078 -1348.8093 82.131824 0.955 -1357.1812
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1000 346.52557 -16919.192 -1406.675 1.0170322 -1511.0006 104.32562 0.95 -1514.1398
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1100 300.62984 -51826.972 -2469.2821 1.0063592 -2559.7903 90.508164 0.945 -2565.9668
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1200 293.72767 45222.698 2039.1938 1.0272336 1950.7636 88.430186 0.94 1951.1683
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1300 289.4971 94600.203 2184.5096 1.0298091 2097.3531 87.156524 0.935 2088.1011
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1400 328.98666 35468.53 1816.723 1.0198467 1717.6777 99.045321 0.93 1716.9268
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1500 392.9407 41220.21 1820.7312 1.0194044 1702.4317 118.29944 0.925 1690.6416
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1600 284.90093 -37995.141 -2439.9256 1.0068497 -2525.6984 85.772791 0.92 -2529.5874
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1700 267.67454 25275.255 1612.5912 1.0313556 1532.0046 80.586582 0.915 1520.9695
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1800 247.16495 -68222.994 -2699.1903 1.0018048 -2773.6022 74.41193 0.91 -2788.9545
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|
1900 328.41849 -51979.665 -2339.7432 1.0154952 -2438.6175 98.874268 0.905 -2461.3422
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2000 313.8715 21726.003 1473.9594 1.018831 1379.4647 94.494725 0.9 1363.0739
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2100 296.07341 66130.11 1379.1597 1.0224882 1290.0233 89.136398 0.895 1272.1884
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|
2200 282.67889 51746.464 2376.377 1.0362683 2291.2732 85.103821 0.89 2276.1488
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2300 281.04207 -71937.759 -2791.0867 1.0111968 -2875.6977 84.611035 0.885 -2892.2526
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2400 321.00806 -51658.758 -2507.6376 1.0168161 -2604.2809 96.643269 0.88 -2622.9732
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|
2500 288.95906 49645.753 2361.024 1.0355648 2274.0295 86.99454 0.875 2275.0348
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|
2600 303.0064 -48470.216 -1973.9561 1.000439 -2065.1798 91.223657 0.87 -2082.5895
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|
2700 361.7083 54973.584 1929.0772 1.0223169 1820.1806 108.89656 0.865 1817.1972
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|
2800 289.27827 33564.017 1783.5154 1.0257088 1696.4248 87.090642 0.86 1682.9162
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|
2900 283.94365 -47190.274 -2286.9529 1.0059224 -2372.4375 85.484591 0.855 -2395.9575
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|
3000 337.10996 61988.686 2289.363 1.0258 2187.8721 101.49094 0.85 2168.1085
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|
3100 305.28249 -50123.109 -1913.7375 1.0143567 -2005.6464 91.9089 0.845 -2040.3453
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|
3200 270.19471 -18114.265 -1961.3048 1.0132413 -2042.6502 81.345309 0.84 -2076.9595
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|
3300 263.39996 -109301.89 -2351.6647 0.99956867 -2430.9643 79.299671 0.835 -2471.0269
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|
3400 249.01722 -37585.949 -2423.3849 1.0080932 -2498.3544 74.969576 0.83 -2537.734
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|
3500 267.88868 65528.865 2164.3882 1.0390872 2083.7372 80.651054 0.825 2061.6421
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|
3600 351.46458 -67583.574 -2861.4561 1.0059621 -2967.2687 105.81256 0.82 -3004.5028
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|
3700 332.82565 -61204.843 -2275.2765 1.0053485 -2375.4776 100.20109 0.815 -2415.4435
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|
3800 298.0279 61123.085 1951.1943 1.020672 1861.4695 89.724819 0.81 1831.9734
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|
3900 317.04715 43210.045 1848.3875 1.0287838 1752.9367 95.450792 0.805 1721.1961
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|
4000 261.75174 -111920.72 -3274.707 0.99457106 -3353.5105 78.803455 0.8 -3394.3528
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|
4100 338.34245 89763.083 2115.4809 1.0318272 2013.6189 101.86199 0.795 1973.419
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|
4200 288.52623 19989.792 1758.0617 1.0204119 1671.1975 86.86423 0.79 1633.1439
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|
4300 322.05593 -33791.403 -2107.1643 1.0155065 -2204.1231 96.958741 0.785 -2246.4353
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|
4400 280.59054 -27839.599 -1534.3265 1.0123506 -1618.8016 84.475096 0.78 -1672.1425
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|
4500 296.08336 75206.112 2789.7494 1.0329133 2700.61 89.139393 0.775 2670.4908
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|
4600 288.02094 -67445.101 -2983.5242 0.99579107 -3070.2363 86.712106 0.77 -3132.6352
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|
4700 332.21641 -83964.647 -2746.0748 1.0053915 -2846.0925 100.01768 0.765 -2916.6652
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|
4800 305.52557 -93111.682 -2354.6562 0.99824941 -2446.6383 91.982082 0.76 -2514.039
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|
4900 272.82262 -53664.198 -2790.1342 0.99527907 -2872.2707 82.136472 0.755 -2947.2062
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|
5000 288.96388 39846.089 1975.7895 1.0371205 1888.7935 86.99599 0.75 1833.3716
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||||||
|
5100 293.25543 -71819.425 -2916.8817 0.99452016 -3005.1697 88.288011 0.745 -3069.7618
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||||||
|
5200 296.16486 -64484.821 -2416.0381 1.0153125 -2505.2021 89.163931 0.74 -2589.6878
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||||||
|
5300 342.07246 60255.985 1749.8984 1.0306374 1646.9134 102.98496 0.735 1608.5673
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||||||
|
5400 295.53315 61421.189 1620.6432 1.0334762 1531.6695 88.973746 0.73 1492.0969
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||||||
|
5500 285.1755 24845.113 1144.9009 1.0335035 1059.0454 85.855455 0.725 1014.0263
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||||||
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5600 276.79246 66244.072 1523.3405 1.0251134 1440.0089 83.331641 0.72 1390.9078
|
||||||
|
5700 288.43485 14629.129 1208.7278 1.02997 1121.8911 86.836719 0.715 1074.3779
|
||||||
|
5800 276.64233 59262.97 914.26981 1.0332305 830.98336 83.286443 0.71 763.27415
|
||||||
|
5900 358.25384 -111203.23 -3370.7104 1.006331 -3478.567 107.85655 0.705 -3561.6283
|
||||||
|
6000 327.82233 -62936.335 -1881.2426 1.0106476 -1979.9373 98.694786 0.7 -2062.107
|
||||||
|
6100 309.86553 -59110.381 -2698.4147 1.0076375 -2791.7034 93.28868 0.695 -2870.9566
|
||||||
|
6200 294.95752 -58011.845 -1819.201 1.0161986 -1908.0014 88.800448 0.69 -1971.2586
|
||||||
|
6300 307.27252 59016.127 1186.0709 1.0225343 1093.5629 92.508022 0.685 1032.9616
|
||||||
|
6400 292.21611 -118857.83 -2992.9227 1.0031304 -3080.8978 87.975114 0.68 -3175.9068
|
||||||
|
6500 332.21108 97132.547 2290.2726 1.0349752 2190.2565 100.01607 0.675 2121.4674
|
||||||
|
6600 321.93985 -50017.836 -2484.5919 1.0076385 -2581.5157 96.923796 0.67 -2673.6819
|
||||||
|
6700 299.07231 -98136.241 -3013.1584 1.0106261 -3103.1976 90.039252 0.665 -3194.0694
|
||||||
|
6800 285.33731 28487.407 455.68104 1.017186 369.77687 85.904169 0.66 294.02418
|
||||||
|
6900 296.41387 50054.533 2028.1018 1.0445934 1938.8629 89.238897 0.655 1851.1397
|
||||||
|
7000 318.34109 -71579.897 -3114.0324 1.007304 -3209.8728 95.840345 0.65 -3305.5715
|
||||||
|
7100 317.2192 12370.315 1139.7687 1.0177238 1044.2661 95.502589 0.645 961.68146
|
||||||
|
7200 289.91091 43944.333 1213.4685 1.0302599 1126.1874 87.281105 0.64 1039.3329
|
||||||
|
7300 324.81227 42859.173 1288.5297 1.0300698 1190.7411 97.788572 0.635 1083.5764
|
||||||
|
7400 305.72634 76516.72 2404.9462 1.0580673 2312.9036 92.042527 0.63 2218.3674
|
||||||
|
7500 283.77479 -87225.247 -3401.4354 0.9936609 -3486.8692 85.433754 0.625 -3581.9003
|
||||||
|
7600 318.72048 16084.995 1848.3396 1.0296163 1752.385 95.954566 0.62 1653.5125
|
||||||
|
7700 307.36895 74007.024 1754.8928 1.0363553 1662.3558 92.537054 0.615 1572.8568
|
||||||
|
7800 297.44704 28693.429 1261.5958 1.0206402 1172.0459 89.549946 0.61 1093.5903
|
||||||
|
7900 288.47173 -94644.76 -2455.4369 1.0095244 -2542.2847 86.847823 0.605 -2648.2974
|
||||||
|
8000 280.5001 63255.987 1584.7287 1.020587 1500.2808 84.44787 0.6 1418.7144
|
||||||
|
8100 320.23351 68383.584 2300.142 1.0419027 2203.7319 96.410082 0.595 2111.2616
|
||||||
|
8200 354.86765 50012.316 1350.3752 1.0292074 1243.5381 106.8371 0.59 1149.0631
|
||||||
|
8300 278.8859 24200.145 772.82478 1.0232468 688.86288 83.961894 0.585 569.83331
|
||||||
|
8400 295.95754 -12010.401 1078.6687 1.0200526 989.56716 89.101514 0.58 872.63254
|
||||||
|
8500 289.57525 -64114.236 -3017.5291 1.0062613 -3104.7091 87.18005 0.575 -3227.8592
|
||||||
|
8600 329.23192 15948.893 1427.4791 1.0271511 1328.3599 99.119161 0.57 1211.3868
|
||||||
|
8700 327.45998 39407.811 1697.908 1.0343756 1599.3223 98.585695 0.565 1480.9482
|
||||||
|
8800 296.99753 18017.036 871.11717 1.0178295 781.70256 89.414616 0.56 657.09357
|
||||||
|
8900 289.10016 79527.35 2536.8041 1.0462904 2449.7671 87.037018 0.555 2338.4742
|
||||||
|
9000 260.53308 -51430.717 -2680.1664 1.0040128 -2758.603 78.436561 0.55 -2894.7913
|
||||||
|
9100 314.17867 40043.249 2043.6144 1.0361707 1949.0272 94.5872 0.545 1836.5399
|
||||||
|
9200 362.21236 -55153.163 -2232.4614 1.0102652 -2341.5097 109.04831 0.54 -2497.8765
|
||||||
|
9300 266.62049 -72193.959 -2980.9254 1.0063615 -3061.1946 80.269248 0.535 -3225.2604
|
||||||
|
9400 259.59316 7674.9295 1378.2484 1.0326879 1300.0948 78.153588 0.53 1171.7119
|
||||||
|
9500 278.72962 -33127.835 -2581.8908 1.0163553 -2665.8057 83.914845 0.525 -2805.1711
|
||||||
|
9600 299.09039 24570.664 1839.3275 1.025317 1749.2828 90.044695 0.52 1631.8392
|
||||||
|
9700 336.65655 37767.059 1415.9074 1.0245842 1314.5529 101.35443 0.515 1218.4022
|
||||||
|
9800 279.68112 -55007.939 -2548.4947 1.0129837 -2632.696 84.201305 0.51 -2775.6909
|
||||||
|
9900 300.55694 14964.424 1332.287 1.0176315 1241.8008 90.486218 0.505 1127.7276
|
||||||
|
10000 276.77193 -75638.817 -3100.7483 1.0019055 -3184.0738 83.325459 0.5 -3341.663
|
||||||
|
10100 316.26926 61548.301 2406.8933 1.0427988 2311.6767 95.216598 0.495 2206.7159
|
||||||
|
10200 297.28171 56814.839 2073.2348 1.0270036 1983.7347 89.500171 0.49 1859.0176
|
||||||
|
10300 276.84774 83572.576 1920.2202 1.0322243 1836.8719 83.348283 0.485 1704.2233
|
||||||
|
10400 263.28687 -16549.994 1144.9186 1.0177296 1065.6529 79.265623 0.48 940.36339
|
||||||
|
10500 332.79252 47379.311 1538.8168 1.0223403 1438.6257 100.19112 0.475 1301.3762
|
||||||
|
10600 329.01105 39299.248 1330.9914 1.0230094 1231.9387 99.052663 0.47 1077.5639
|
||||||
|
10700 339.21335 -4217.0313 981.9193 1.0235915 879.79511 102.12419 0.465 741.87272
|
||||||
|
10800 297.11192 -80013.424 -3682.9794 1.0009566 -3772.4285 89.449054 0.46 -3958.8283
|
||||||
|
10900 299.63096 47783.864 1833.1832 1.0435283 1742.9757 90.207441 0.455 1620.9328
|
||||||
|
11000 363.58243 67370.65 1769.9236 1.0450565 1660.4628 109.46079 0.45 1543.803
|
||||||
|
11100 306.04664 50246.004 1323.7676 1.0341876 1231.6287 92.138957 0.445 1063.5345
|
||||||
|
11200 255.68488 43750.967 2205.2392 1.0530607 2128.2623 76.976955 0.44 1986.9636
|
||||||
|
11300 271.71957 -40289.299 -3083.4093 1.0168497 -3165.2137 81.804388 0.435 -3344.1558
|
||||||
|
11400 291.74007 -115249.24 -3319.2153 1.0067921 -3407.0471 87.831795 0.43 -3569.0256
|
||||||
|
11500 270.22077 28235.119 596.78348 1.0195886 515.43032 81.353155 0.425 373.78255
|
||||||
|
11600 297.08506 29790.701 1031.3514 1.0317561 941.91046 89.440969 0.42 803.92835
|
||||||
|
11700 295.33119 -101140.58 -3068.1166 1.0107252 -3157.0295 88.912943 0.415 -3348.5652
|
||||||
|
11800 308.77287 -120312.75 -3553.1266 0.99681611 -3646.0863 92.95972 0.41 -3835.4663
|
||||||
|
11900 293.86337 82287.969 1847.0953 1.0331446 1758.6242 88.47104 0.405 1625.4846
|
||||||
|
12000 279.9866 27919.689 2249.3175 1.0384909 2165.0242 84.293273 0.4 2028.6311
|
||||||
|
12100 292.19439 47035.018 1220.3593 1.0210948 1132.3908 87.968573 0.395 976.68113
|
||||||
|
12200 317.78325 46886.483 2039.3721 1.0310567 1943.6997 95.672401 0.39 1763.6359
|
||||||
|
12300 357.44038 51492.35 1898.3396 1.0414835 1790.7279 107.61165 0.385 1638.1905
|
||||||
|
12400 288.16042 -50528.478 -2837.5599 1.0130798 -2924.314 86.7541 0.38 -3115.1383
|
||||||
|
12500 300.37356 -114034.29 -3091.586 1.0130272 -3182.017 90.431009 0.375 -3364.511
|
||||||
|
12600 265.4402 73960.28 1297.3012 1.0343798 1217.3873 79.913907 0.37 1094.544
|
||||||
|
12700 287.07994 22722.337 1711.9055 1.0268893 1625.4767 86.428809 0.365 1490.443
|
||||||
|
12800 315.39745 46072.191 926.21362 1.0205906 831.25949 94.954129 0.36 662.83753
|
||||||
|
12900 307.48549 -120472.73 -3181.5418 1.005689 -3274.1139 92.57214 0.355 -3469.7834
|
||||||
|
13000 291.00577 -59154.878 -2652.0402 1.012821 -2739.6509 87.610727 0.35 -2966.2448
|
||||||
|
13100 318.37718 86703.775 2087.145 1.036209 1991.2938 95.851211 0.345 1819.7078
|
||||||
|
13200 280.41509 -107033.79 -2683.9682 1.0135499 -2768.3905 84.422277 0.34 -2953.8355
|
||||||
|
13300 275.01919 112086.85 2632.1169 1.0437945 2549.3192 82.797775 0.335 2394.6707
|
||||||
|
13400 299.46547 -111959.62 -3475.4354 0.98732074 -3565.593 90.157617 0.33 -3792.6798
|
||||||
|
13500 275.65631 17625.49 1762.6531 1.0255473 1679.6636 82.989588 0.325 1521.2745
|
||||||
|
13600 302.63525 122466.63 2853.8095 1.0438137 2762.6976 91.111917 0.32 2611.7188
|
||||||
|
13700 302.21323 -94399.663 -3003.7573 1.0068914 -3094.7422 90.984863 0.315 -3328.4539
|
||||||
|
13800 305.70483 30039.825 1792.3286 1.0225478 1700.2926 92.036052 0.31 1502.8476
|
||||||
|
13900 273.15564 -27822.597 -2346.6702 1.0131002 -2428.9069 82.236732 0.305 -2683.7804
|
||||||
|
14000 257.14635 -1821.0012 1378.2522 1.0172653 1300.8352 77.416947 0.3 1067.8821
|
||||||
|
14100 323.74174 -76139.363 -2747.4152 1.0139806 -2844.8814 97.466276 0.295 -3052.598
|
||||||
|
14200 274.99913 54440.943 983.27131 1.0186356 900.47957 82.791736 0.29 767.64274
|
||||||
|
14300 291.8774 1281.7286 1258.7881 1.0214356 1170.915 87.873139 0.285 1042.8585
|
||||||
|
14400 308.97245 -47961.551 -2680.7892 1.0155221 -2773.809 93.019806 0.28 -3007.3204
|
||||||
|
14500 311.05309 86026.739 2115.2413 1.0311818 2021.5951 93.646208 0.275 1830.5463
|
||||||
|
14600 269.27432 -12972.747 971.48792 1.0172239 890.41971 81.068214 0.27 711.81484
|
||||||
|
14700 262.20739 -77722.459 -3215.6796 1.0029421 -3294.6202 78.940634 0.265 -3537.1929
|
||||||
|
14800 300.33592 -107332.8 -2798.6664 1.0126785 -2889.086 90.419677 0.26 -3125.8439
|
||||||
|
14900 307.0173 -73204.94 -2652.7275 1.016875 -2745.1587 92.431185 0.255 -3016.0143
|
||||||
|
15000 334.08711 64440.709 1615.3385 1.0369481 1514.7576 100.58087 0.25 1323.9179
|
||||||
|
15100 293.46703 35179.395 2020.1996 1.0331703 1931.8479 88.351717 0.245 1768.9681
|
||||||
|
15200 307.80546 54006.291 1111.7619 1.0246134 1019.0935 92.668471 0.24 822.22754
|
||||||
|
15300 336.59792 33832.907 1282.8271 1.0242407 1181.4903 101.33678 0.235 956.25285
|
||||||
|
15400 285.46526 -99629.94 -2336.7535 1.0041261 -2422.6962 85.942688 0.23 -2730.1887
|
||||||
|
15500 269.15938 122546.45 3012.0792 1.0318941 2931.0456 81.033612 0.225 2695.4331
|
||||||
|
15600 294.50818 -104733.19 -1914.0242 1.0017241 -2002.6894 88.665166 0.22 -2281.5773
|
||||||
|
15700 321.05125 -40438.501 -1721.9536 1.0125007 -1818.6099 96.656271 0.215 -2084.0893
|
||||||
|
15800 303.22185 -42224.408 -2145.481 1.0090867 -2236.7695 91.288521 0.21 -2506.3355
|
||||||
|
15900 281.65025 78652.063 2791.9418 1.0460521 2707.1477 84.794136 0.205 2500.7128
|
||||||
|
16000 286.5056 63174.412 1725.0409 1.0185277 1638.785 86.255897 0.2 1442.2427
|
||||||
|
16100 271.74574 -75051.584 -2101.5778 1.0091727 -2183.3901 81.812265 0.195 -2447.1967
|
||||||
|
16200 266.40007 -64120.09 -2223.3693 1.0064388 -2303.5722 80.202888 0.19 -2525.4243
|
||||||
|
16300 330.67137 46204.124 1837.3168 1.0271037 1737.7643 99.552523 0.185 1529.8186
|
||||||
|
16400 310.94573 18510.676 1531.823 1.0188695 1438.2091 93.613887 0.18 1195.3041
|
||||||
|
16500 270.29191 79005.409 1989.9392 1.0354088 1908.5646 81.374574 0.175 1678.7342
|
||||||
|
16600 334.24108 17143.221 1644.1483 1.0230561 1543.521 100.62723 0.17 1379.3215
|
||||||
|
16700 292.28721 -78618.031 -2768.3997 0.99940789 -2856.3962 87.996518 0.165 -3087.379
|
||||||
|
16800 346.09157 -69398.937 -2647.1375 1.0153026 -2751.3325 104.19496 0.16 -3011.3476
|
||||||
|
16900 284.37042 39314.526 2287.7061 1.0343186 2202.093 85.613074 0.155 2045.8316
|
||||||
|
17000 281.69389 86032.163 1817.9125 1.0237583 1733.1052 84.807275 0.15 1528.8391
|
||||||
|
17100 297.2629 55128.393 2617.4156 1.0419182 2527.9211 89.494508 0.145 2369.0347
|
||||||
|
17200 328.81472 47063.86 1880.9768 1.0364627 1781.9832 98.993555 0.14 1526.7115
|
||||||
|
17300 313.41363 -46685.063 -2310.803 1.008117 -2405.1599 94.356878 0.135 -2685.8034
|
||||||
|
17400 288.17114 68721.523 2771.6788 1.0429105 2684.9215 86.757326 0.13 2490.5845
|
||||||
|
17500 260.01702 -23324.539 -1436.6738 1.0100415 -1514.955 78.281195 0.125 -1812.4813
|
||||||
|
17600 297.6633 72795.463 2635.741 1.0362827 2546.126 89.615054 0.12 2336.0152
|
||||||
|
17700 301.02937 93833.118 2690.518 1.0276466 2599.8896 90.628448 0.115 2364.8751
|
||||||
|
17800 238.92837 -78317.212 -2175.2589 1.0084077 -2247.1911 71.932208 0.11 -2579.4429
|
||||||
|
17900 299.27724 -65278.891 -2589.1173 1.0034773 -2679.2182 90.10095 0.105 -2987.498
|
||||||
|
18000 315.15753 -72437.481 -2338.6068 1.0136139 -2433.4887 94.881898 0.1 -2718.125
|
||||||
|
18100 268.39411 -42194.209 -2285.3824 1.0108104 -2366.1856 80.803219 0.095 -2656.3853
|
||||||
|
18200 284.91941 40905.162 2045.1299 1.0266185 1959.3515 85.778354 0.09 1723.6803
|
||||||
|
18300 329.41629 -56526.814 -2104.8386 1.0137784 -2204.0133 99.174667 0.085 -2540.6829
|
||||||
|
18400 293.16732 -22085.551 -1652.5444 1.0163557 -1740.8059 88.261484 0.08 -2052.7864
|
||||||
|
18500 276.28141 29367.359 2314.5497 1.0270087 2231.3719 83.177784 0.075 1971.9405
|
||||||
|
18600 331.18031 94669.124 2466.3928 1.0225403 2366.6871 99.705745 0.07 2081.8675
|
||||||
|
18700 265.4491 49872.536 2571.9864 1.0255308 2492.0698 79.916587 0.065 2260.4261
|
||||||
|
18800 314.51042 60758.629 2560.3258 1.0300818 2465.6387 94.687078 0.06 2219.6547
|
||||||
|
18900 317.70309 66345.835 1768.2041 1.0248229 1672.5558 95.648268 0.055 1410.3087
|
||||||
|
19000 291.39831 -96336.931 -2448.6251 1.0100498 -2536.354 87.728905 0.05 -2805.9396
|
||||||
|
19100 303.37353 -21421.495 -2012.0929 0.99771284 -2103.4271 91.334186 0.045 -2436.2173
|
||||||
|
19200 293.92948 36383.881 2042.0163 1.0251299 1953.5254 88.490944 0.04 1633.579
|
||||||
|
19300 287.24409 -46691.027 -2399.698 1.0112067 -2486.1762 86.478228 0.035 -2811.3506
|
||||||
|
19400 333.42205 21152.63 1524.8699 1.0189912 1424.4893 100.38065 0.03 1118.2463
|
||||||
|
19500 309.17989 60445.761 2298.6966 1.0338543 2205.6144 93.082259 0.025 1928.6181
|
||||||
|
19600 255.92246 -32795.547 -1724.7933 1.0157044 -1801.8418 77.04848 0.02 -2213.9484
|
||||||
|
19700 342.62332 33538.746 2439.138 1.0225905 2335.9872 103.1508 0.015 2081.9185
|
||||||
|
19800 295.68946 81474.342 2308.3249 1.0240743 2219.3041 89.020804 0.01 1910.5545
|
||||||
|
19900 306.4947 43488.052 2330.4958 1.0222707 2238.222 92.27385 0.005 1957.4368
|
||||||
|
20000 313.31679 -25133.284 -1161.6979 1.0163289 -1256.0256 94.327722 0 -1649.7551
|
||||||
|
Loop time of 11.8252 on 2 procs for 20000 steps with 102 atoms
|
||||||
|
|
||||||
|
Performance: 29.226 ns/day, 0.821 hours/ns, 1691.296 timesteps/s, 172.512 katom-step/s
|
||||||
|
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 6.8298 | 8.6298 | 10.43 | 61.3 | 72.98
|
||||||
|
Bond | 0.045072 | 0.045296 | 0.045519 | 0.1 | 0.38
|
||||||
|
Neigh | 0.10567 | 0.10572 | 0.10577 | 0.0 | 0.89
|
||||||
|
Comm | 0.73714 | 2.5381 | 4.3392 | 113.0 | 21.46
|
||||||
|
Output | 0.0032977 | 0.0035468 | 0.003796 | 0.4 | 0.03
|
||||||
|
Modify | 0.43872 | 0.44155 | 0.44438 | 0.4 | 3.73
|
||||||
|
Other | | 0.06121 | | | 0.52
|
||||||
|
|
||||||
|
Nlocal: 51 ave 51 max 51 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 3317 ave 3317 max 3317 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 18320 ave 21941 max 14699 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 36640
|
||||||
|
Ave neighs/atom = 359.21569
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 181
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:11
|
||||||
433
examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.1
Normal file
433
examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.1
Normal file
@ -0,0 +1,433 @@
|
|||||||
|
LAMMPS (8 Feb 2023)
|
||||||
|
Processor partition = 1
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Example for alchemical transformation of two water molecules into a hydronium and hydroxyl ion
|
||||||
|
# WARNING: This input is intended for demonstrating the method, only
|
||||||
|
# The force field parameters are made up and NOT suitable for production simulations.
|
||||||
|
|
||||||
|
# set up different names for two partitions
|
||||||
|
variable name world twowater twoions
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
atom_modify map array
|
||||||
|
region box block -5 5 -5 5 -5 5
|
||||||
|
boundary p p p
|
||||||
|
create_box 2 box bond/types 2 angle/types 2 extra/bond/per/atom 3 extra/angle/per/atom 3 extra/special/per/atom 3
|
||||||
|
Created orthogonal box = (-5 -5 -5) to (5 5 5)
|
||||||
|
1 by 1 by 2 MPI processor grid
|
||||||
|
|
||||||
|
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 * 1000.0 1.0
|
||||||
|
|
||||||
|
angle_style harmonic
|
||||||
|
angle_coeff * 100.0 109.47
|
||||||
|
|
||||||
|
molecule water h2o.mol
|
||||||
|
Read molecule template water:
|
||||||
|
1 molecules
|
||||||
|
0 fragments
|
||||||
|
3 atoms with max type 2
|
||||||
|
2 bonds with max type 1
|
||||||
|
1 angles with max type 1
|
||||||
|
0 dihedrals with max type 0
|
||||||
|
0 impropers with max type 0
|
||||||
|
|
||||||
|
# create the two molecules we want to transform ...
|
||||||
|
create_atoms 0 single -2.0 0.0 0.0 mol water 453624
|
||||||
|
Created 3 atoms
|
||||||
|
using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
|
||||||
|
create_atoms CPU = 0.004 seconds
|
||||||
|
create_atoms 0 single 2.0 0.0 0.0 mol water 767353
|
||||||
|
Created 3 atoms
|
||||||
|
using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
# ... and put them in a group
|
||||||
|
group transform id 1:6
|
||||||
|
6 atoms in group transform
|
||||||
|
|
||||||
|
# now fill the rest of the box with more water
|
||||||
|
create_atoms 0 random 32 34564 NULL mol water 25367 overlap 1.33
|
||||||
|
Created 96 atoms
|
||||||
|
using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
# change topology and settings for the two states
|
||||||
|
# we cannot simply create a different topology directly or
|
||||||
|
# load a different data file because the order and position
|
||||||
|
# of all atoms must be maintained across both replica
|
||||||
|
|
||||||
|
# we first have to remove all topology data in the transform group
|
||||||
|
delete_bonds transform bond 1
|
||||||
|
System init for delete_bonds ...
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 12
|
||||||
|
ghost atom cutoff = 12
|
||||||
|
binsize = 6, bins = 2 2 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut/coul/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Deleting bonds ...
|
||||||
|
68 total bonds, 64 turned on, 4 turned off
|
||||||
|
34 total angles, 34 turned on, 0 turned off
|
||||||
|
0 total dihedrals, 0 turned on, 0 turned off
|
||||||
|
0 total impropers, 0 turned on, 0 turned off
|
||||||
|
delete_bonds transform angle 1 remove
|
||||||
|
System init for delete_bonds ...
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Deleting bonds ...
|
||||||
|
64 total bonds, 64 turned on, 0 turned off
|
||||||
|
32 total angles, 32 turned on, 0 turned off
|
||||||
|
0 total dihedrals, 0 turned on, 0 turned off
|
||||||
|
0 total impropers, 0 turned on, 0 turned off
|
||||||
|
|
||||||
|
# then generate different topologies for the two partitions. select by name.
|
||||||
|
if "${name} == twowater" then "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 1 3" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 2 1 3" "create_bonds single/angle 2 5 4 6" else "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 3 4" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 3 4 5" "create_bonds single/angle 2 5 4 6" "create_bonds single/angle 2 3 4 6" "set atom 1 charge -1.1354" "set atom 2 charge 0.1354" "set atom 3 charge 0.56775" "set atom 4 charge -0.70305" "set atom 5*6 charge 0.56775"
|
||||||
|
create_bonds single/bond 2 1 2
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
1 = max # of 1-4 neighbors
|
||||||
|
7 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
create_bonds single/bond 2 3 4
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
1 = max # of 1-4 neighbors
|
||||||
|
7 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
create_bonds single/bond 2 4 5
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
1 = max # of 1-4 neighbors
|
||||||
|
7 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
create_bonds single/bond 2 4 6
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
3 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
2 = max # of 1-4 neighbors
|
||||||
|
7 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
create_bonds single/angle 2 3 4 5
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
3 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
2 = max # of 1-4 neighbors
|
||||||
|
7 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
create_bonds single/angle 2 5 4 6
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
3 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
2 = max # of 1-4 neighbors
|
||||||
|
7 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
create_bonds single/angle 2 3 4 6
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
3 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
2 = max # of 1-4 neighbors
|
||||||
|
7 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
set atom 1 charge -1.1354
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for charge
|
||||||
|
set atom 2 charge 0.1354
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for charge
|
||||||
|
set atom 3 charge 0.56775
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for charge
|
||||||
|
set atom 4 charge -0.70305
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for charge
|
||||||
|
set atom 5*6 charge 0.56775
|
||||||
|
Setting atom values ...
|
||||||
|
2 settings made for charge
|
||||||
|
|
||||||
|
velocity all create 300.0 5463576
|
||||||
|
timestep 0.2
|
||||||
|
|
||||||
|
# since the trajectory and forces are kept identical through fix alchemy,
|
||||||
|
# we can do fix npt simulations, but we must use the "mixed" pressure
|
||||||
|
|
||||||
|
fix integrate all npt temp 300 300 1.0 iso 1.0 1.0 10.0
|
||||||
|
fix transform all alchemy
|
||||||
|
compute pressure all pressure/alchemy transform
|
||||||
|
fix_modify integrate press pressure
|
||||||
|
|
||||||
|
# only need to output a dump file from one partition
|
||||||
|
# if "${name} == twowater" then # "dump 1 all atom 100 ${name}.lammpstrj" # "dump_modify 1 sort id"
|
||||||
|
|
||||||
|
thermo_style custom step temp press etotal density pe ke f_transform[1] f_transform[4]
|
||||||
|
thermo_modify colname f_transform[1] lambda colname f_transform[4] EPot_mixed
|
||||||
|
thermo_modify press pressure
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
run 20000
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 7.535 | 7.535 | 7.535 Mbytes
|
||||||
|
Step Temp Press TotEng Density PotEng KinEng lambda EPot_mixed
|
||||||
|
0 300 184631.17 10769.267 1.0171193 10678.948 90.318545 0 -892.51464
|
||||||
|
100 293.4335 -513.97927 21497.846 0.3029684 21409.505 88.341623 0.005 207.29243
|
||||||
|
200 320.81838 1513.3 3300.6279 0.64509407 3204.0418 96.586165 0.01 46.402434
|
||||||
|
300 261.53825 -3808.6942 -362.14861 0.88817871 -440.88779 78.739179 0.015 -614.76481
|
||||||
|
400 308.32444 1375.0327 -821.01681 0.97694485 -913.84152 92.824715 0.02 -897.24386
|
||||||
|
500 292.60623 -12843.384 -831.87625 1.0140814 -919.96881 88.092563 0.025 -1221.948
|
||||||
|
600 326.16112 91608.645 2941.9339 1.0263567 2843.7393 98.194659 0.03 2786.0743
|
||||||
|
700 317.22811 -60420.408 -1637.1259 0.9919143 -1732.6311 95.505272 0.035 -1616.7677
|
||||||
|
800 309.94673 -56793.931 -1501.6195 1.0024958 -1594.9326 93.313126 0.04 -1640.8606
|
||||||
|
900 272.80718 -5076.2282 -1452.719 1.0141078 -1534.8508 82.131824 0.045 -1357.1812
|
||||||
|
1000 346.52557 -16919.192 -1469.4601 1.0170322 -1573.7857 104.32562 0.05 -1514.1398
|
||||||
|
1100 300.62984 -51826.972 -2581.5818 1.0063592 -2672.09 90.508164 0.055 -2565.9668
|
||||||
|
1200 293.72767 45222.698 2045.9381 1.0272336 1957.5079 88.430186 0.06 1951.1683
|
||||||
|
1300 289.4971 94600.203 2042.1709 1.0298091 1955.0144 87.156524 0.065 2088.1011
|
||||||
|
1400 328.98666 35468.53 1805.9965 1.0198467 1706.9512 99.045321 0.07 1716.9268
|
||||||
|
1500 392.9407 41220.21 1663.5291 1.0194044 1545.2297 118.29944 0.075 1690.6416
|
||||||
|
1600 284.90093 -37995.141 -2488.5372 1.0068497 -2574.31 85.772791 0.08 -2529.5874
|
||||||
|
1700 267.67454 25275.255 1482.7666 1.0313556 1402.18 80.586582 0.085 1520.9695
|
||||||
|
1800 247.16495 -68222.994 -2869.7712 1.0018048 -2944.1832 74.41193 0.09 -2788.9545
|
||||||
|
1900 328.41849 -51979.665 -2578.9515 1.0154952 -2677.8258 98.874268 0.095 -2461.3422
|
||||||
|
2000 313.8715 21726.003 1310.0519 1.018831 1215.5571 94.494725 0.1 1363.0739
|
||||||
|
2100 296.07341 66130.11 1209.3035 1.0224882 1120.1671 89.136398 0.105 1272.1884
|
||||||
|
2200 282.67889 51746.464 2238.8823 1.0362683 2153.7785 85.103821 0.11 2276.1488
|
||||||
|
2300 281.04207 -71937.759 -2935.0422 1.0111968 -3019.6532 84.611035 0.115 -2892.2526
|
||||||
|
2400 321.00806 -51658.758 -2663.4071 1.0168161 -2760.0503 96.643269 0.12 -2622.9732
|
||||||
|
2500 288.95906 49645.753 2369.0667 1.0355648 2282.0722 86.99454 0.125 2275.0348
|
||||||
|
2600 303.0064 -48470.216 -2107.8769 1.000439 -2199.1005 91.223657 0.13 -2082.5895
|
||||||
|
2700 361.7083 54973.584 1906.9779 1.0223169 1798.0813 108.89656 0.135 1817.1972
|
||||||
|
2800 289.27827 33564.017 1687.0255 1.0257088 1599.9349 87.090642 0.14 1682.9162
|
||||||
|
2900 283.94365 -47190.274 -2449.1599 1.0059224 -2534.6445 85.484591 0.145 -2395.9575
|
||||||
|
3000 337.10996 61988.686 2157.6059 1.0258 2056.115 101.49094 0.15 2168.1085
|
||||||
|
3100 305.28249 -50123.109 -2137.6015 1.0143567 -2229.5104 91.9089 0.155 -2040.3453
|
||||||
|
3200 270.19471 -18114.265 -2175.7381 1.0132413 -2257.0834 81.345309 0.16 -2076.9595
|
||||||
|
3300 263.39996 -109301.89 -2594.4684 0.99956867 -2673.7681 79.299671 0.165 -2471.0269
|
||||||
|
3400 249.01722 -37585.949 -2655.0291 1.0080932 -2729.9987 74.969576 0.17 -2537.734
|
||||||
|
3500 267.88868 65528.865 2038.1308 1.0390872 1957.4797 80.651054 0.175 2061.6421
|
||||||
|
3600 351.46458 -67583.574 -3068.3126 1.0059621 -3174.1251 105.81256 0.18 -3004.5028
|
||||||
|
3700 332.82565 -61204.843 -2491.3087 1.0053485 -2591.5097 100.20109 0.185 -2415.4435
|
||||||
|
3800 298.0279 61123.085 1795.9521 1.020672 1706.2273 89.724819 0.19 1831.9734
|
||||||
|
3900 317.04715 43210.045 1685.6151 1.0287838 1590.1643 95.450792 0.195 1721.1961
|
||||||
|
4000 261.75174 -111920.72 -3478.9188 0.99457106 -3557.7223 78.803455 0.2 -3394.3528
|
||||||
|
4100 338.34245 89763.083 1919.3836 1.0318272 1817.5216 101.86199 0.205 1973.419
|
||||||
|
4200 288.52623 19989.792 1576.8543 1.0204119 1489.99 86.86423 0.21 1633.1439
|
||||||
|
4300 322.05593 -33791.403 -2303.9654 1.0155065 -2400.9242 96.958741 0.215 -2246.4353
|
||||||
|
4400 280.59054 -27839.599 -1776.7852 1.0123506 -1861.2603 84.475096 0.22 -1672.1425
|
||||||
|
4500 296.08336 75206.112 2655.8862 1.0329133 2566.7468 89.139393 0.225 2670.4908
|
||||||
|
4600 288.02094 -67445.101 -3254.8238 0.99579107 -3341.5359 86.712106 0.23 -3132.6352
|
||||||
|
4700 332.21641 -83964.647 -3046.3841 1.0053915 -3146.4017 100.01768 0.235 -2916.6652
|
||||||
|
4800 305.52557 -93111.682 -2635.4926 0.99824941 -2727.4747 91.982082 0.24 -2514.039
|
||||||
|
4900 272.82262 -53664.198 -3095.9932 0.99527907 -3178.1297 82.136472 0.245 -2947.2062
|
||||||
|
5000 288.96388 39846.089 1754.1018 1.0371205 1667.1058 86.99599 0.25 1833.3716
|
||||||
|
5100 293.25543 -71819.425 -3170.1841 0.99452016 -3258.4721 88.288011 0.255 -3069.7618
|
||||||
|
5200 296.16486 -64484.821 -2740.9832 1.0153125 -2830.1471 89.163931 0.26 -2589.6878
|
||||||
|
5300 342.07246 60255.985 1605.1961 1.0306374 1502.2111 102.98496 0.265 1608.5673
|
||||||
|
5400 295.53315 61421.189 1474.0782 1.0334762 1385.1045 88.973746 0.27 1492.0969
|
||||||
|
5500 285.1755 24845.113 981.19505 1.0335035 895.3396 85.855455 0.275 1014.0263
|
||||||
|
5600 276.79246 66244.072 1347.9794 1.0251134 1264.6478 83.331641 0.28 1390.9078
|
||||||
|
5700 288.43485 14629.129 1042.0147 1.02997 955.17799 86.836719 0.285 1074.3779
|
||||||
|
5800 276.64233 59262.97 680.78976 1.0332305 597.50331 83.286443 0.29 763.27415
|
||||||
|
5900 358.25384 -111203.23 -3652.2742 1.006331 -3760.1307 107.85655 0.295 -3561.6283
|
||||||
|
6000 327.82233 -62936.335 -2155.1414 1.0106476 -2253.8362 98.694786 0.3 -2062.107
|
||||||
|
6100 309.86553 -59110.381 -2958.2613 1.0076375 -3051.5499 93.28868 0.305 -2870.9566
|
||||||
|
6200 294.95752 -58011.845 -2023.2564 1.0161986 -2112.0569 88.800448 0.31 -1971.2586
|
||||||
|
6300 307.27252 59016.127 993.68575 1.0225343 901.17773 92.508022 0.315 1032.9616
|
||||||
|
6400 292.21611 -118857.83 -3289.8257 1.0031304 -3377.8009 87.975114 0.32 -3175.9068
|
||||||
|
6500 332.21108 97132.547 2078.6137 1.0349752 1978.5976 100.01607 0.325 2121.4674
|
||||||
|
6600 321.93985 -50017.836 -2763.8832 1.0076385 -2860.807 96.923796 0.33 -2673.6819
|
||||||
|
6700 299.07231 -98136.241 -3284.4174 1.0106261 -3374.4566 90.039252 0.335 -3194.0694
|
||||||
|
6800 285.33731 28487.407 232.87902 1.017186 146.97485 85.904169 0.34 294.02418
|
||||||
|
6900 296.41387 50054.533 1773.8315 1.0445934 1684.5926 89.238897 0.345 1851.1397
|
||||||
|
7000 318.34109 -71579.897 -3387.4573 1.007304 -3483.2977 95.840345 0.35 -3305.5715
|
||||||
|
7100 317.2192 12370.315 907.13585 1.0177238 811.63326 95.502589 0.355 961.68146
|
||||||
|
7200 289.91091 43944.333 972.20602 1.0302599 884.92492 87.281105 0.36 1039.3329
|
||||||
|
7300 324.81227 42859.173 994.92755 1.0300698 897.13897 97.788572 0.365 1083.5764
|
||||||
|
7400 305.72634 76516.72 2149.4427 1.0580673 2057.4002 92.042527 0.37 2218.3674
|
||||||
|
7500 283.77479 -87225.247 -3654.8517 0.9936609 -3740.2855 85.433754 0.375 -3581.9003
|
||||||
|
7600 318.72048 16084.995 1588.1487 1.0296163 1492.1941 95.954566 0.38 1653.5125
|
||||||
|
7700 307.36895 74007.024 1522.4279 1.0363553 1429.8909 92.537054 0.385 1572.8568
|
||||||
|
7800 297.44704 28693.429 1060.4277 1.0206402 970.87774 89.549946 0.39 1093.5903
|
||||||
|
7900 288.47173 -94644.76 -2723.8234 1.0095244 -2810.6712 86.847823 0.395 -2648.2974
|
||||||
|
8000 280.5001 63255.987 1380.8125 1.020587 1296.3647 84.44787 0.4 1418.7144
|
||||||
|
8100 320.23351 68383.584 2071.8202 1.0419027 1975.4101 96.410082 0.405 2111.2616
|
||||||
|
8200 354.86765 50012.316 1119.9483 1.0292074 1013.1112 106.8371 0.41 1149.0631
|
||||||
|
8300 278.8859 24200.145 486.00653 1.0232468 402.04464 83.961894 0.415 569.83331
|
||||||
|
8400 295.95754 -12010.401 800.25292 1.0200526 711.1514 89.101514 0.42 872.63254
|
||||||
|
8500 289.57525 -64114.236 -3307.2939 1.0062613 -3394.4739 87.18005 0.425 -3227.8592
|
||||||
|
8600 329.23192 15948.893 1155.4486 1.0271511 1056.3294 99.119161 0.43 1211.3868
|
||||||
|
8700 327.45998 39407.811 1425.7837 1.0343756 1327.198 98.585695 0.435 1480.9482
|
||||||
|
8800 296.99753 18017.036 587.91493 1.0178295 498.50031 89.414616 0.44 657.09357
|
||||||
|
8900 289.10016 79527.35 2286.7077 1.0462904 2199.6707 87.037018 0.445 2338.4742
|
||||||
|
9000 260.53308 -51430.717 -2982.8072 1.0040128 -3061.2437 78.436561 0.45 -2894.7913
|
||||||
|
9100 314.17867 40043.249 1796.3896 1.0361707 1701.8024 94.5872 0.455 1836.5399
|
||||||
|
9200 362.21236 -55153.163 -2572.3893 1.0102652 -2681.4376 109.04831 0.46 -2497.8765
|
||||||
|
9300 266.62049 -72193.959 -3333.755 1.0063615 -3414.0242 80.269248 0.465 -3225.2604
|
||||||
|
9400 259.59316 7674.9295 1105.0933 1.0326879 1026.9397 78.153588 0.47 1171.7119
|
||||||
|
9500 278.72962 -33127.835 -2875.2917 1.0163553 -2959.2065 83.914845 0.475 -2805.1711
|
||||||
|
9600 299.09039 24570.664 1594.6533 1.025317 1504.6086 90.044695 0.48 1631.8392
|
||||||
|
9700 336.65655 37767.059 1217.6584 1.0245842 1116.3039 101.35443 0.485 1218.4022
|
||||||
|
9800 279.68112 -55007.939 -2840.321 1.0129837 -2924.5223 84.201305 0.49 -2775.6909
|
||||||
|
9900 300.55694 14964.424 1101.8362 1.0176315 1011.35 90.486218 0.495 1127.7276
|
||||||
|
10000 276.77193 -75638.817 -3415.9268 1.0019055 -3499.2523 83.325459 0.5 -3341.663
|
||||||
|
10100 316.26926 61548.301 2199.0502 1.0427988 2103.8336 95.216598 0.505 2206.7159
|
||||||
|
10200 297.28171 56814.839 1828.6916 1.0270036 1739.1915 89.500171 0.51 1859.0176
|
||||||
|
10300 276.84774 83572.576 1662.6501 1.0322243 1579.3018 83.348283 0.515 1704.2233
|
||||||
|
10400 263.28687 -16549.994 903.97712 1.0177296 824.71149 79.265623 0.52 940.36339
|
||||||
|
10500 332.79252 47379.311 1277.3892 1.0223403 1177.1981 100.19112 0.525 1301.3762
|
||||||
|
10600 329.01105 39299.248 1039.7181 1.0230094 940.66548 99.052663 0.53 1077.5639
|
||||||
|
10700 339.21335 -4217.0313 724.12043 1.0235915 621.99624 102.12419 0.535 741.87272
|
||||||
|
10800 297.11192 -80013.424 -4028.1643 1.0009566 -4117.6134 89.449054 0.54 -3958.8283
|
||||||
|
10900 299.63096 47783.864 1609.2512 1.0435283 1519.0437 90.207441 0.545 1620.9328
|
||||||
|
11000 363.58243 67370.65 1557.8148 1.0450565 1448.354 109.46079 0.55 1543.803
|
||||||
|
11100 306.04664 50246.004 1020.8953 1.0341876 928.75637 92.138957 0.555 1063.5345
|
||||||
|
11200 255.68488 43750.967 1952.9201 1.0530607 1875.9431 76.976955 0.56 1986.9636
|
||||||
|
11300 271.71957 -40289.299 -3400.121 1.0168497 -3481.9254 81.804388 0.565 -3344.1558
|
||||||
|
11400 291.74007 -115249.24 -3603.3881 1.0067921 -3691.2199 87.831795 0.57 -3569.0256
|
||||||
|
11500 270.22077 28235.119 350.43952 1.0195886 269.08637 81.353155 0.575 373.78255
|
||||||
|
11600 297.08506 29790.701 793.45124 1.0317561 704.01027 89.440969 0.58 803.92835
|
||||||
|
11700 295.33119 -101140.58 -3395.5279 1.0107252 -3484.4409 88.912943 0.585 -3348.5652
|
||||||
|
11800 308.77287 -120312.75 -3874.1096 0.99681611 -3967.0693 92.95972 0.59 -3835.4663
|
||||||
|
11900 293.86337 82287.969 1623.3312 1.0331446 1534.8602 88.47104 0.595 1625.4846
|
||||||
|
12000 279.9866 27919.689 2021.9956 1.0384909 1937.7024 84.293273 0.6 2028.6311
|
||||||
|
12100 292.19439 47035.018 962.98803 1.0210948 875.01946 87.968573 0.605 976.68113
|
||||||
|
12200 317.78325 46886.483 1744.1855 1.0310567 1648.5131 95.672401 0.61 1763.6359
|
||||||
|
12300 357.44038 51492.35 1650.3113 1.0414835 1542.6996 107.61165 0.615 1638.1905
|
||||||
|
12400 288.16042 -50528.478 -3145.341 1.0130798 -3232.0951 86.7541 0.62 -3115.1383
|
||||||
|
12500 300.37356 -114034.29 -3383.5763 1.0130272 -3474.0074 90.431009 0.625 -3364.511
|
||||||
|
12600 265.4402 73960.28 1102.3119 1.0343798 1022.398 79.913907 0.63 1094.544
|
||||||
|
12700 287.07994 22722.337 1499.2541 1.0268893 1412.8252 86.428809 0.635 1490.443
|
||||||
|
12800 315.39745 46072.191 663.05431 1.0205906 568.10018 94.954129 0.64 662.83753
|
||||||
|
12900 307.48549 -120472.73 -3484.9054 1.005689 -3577.4775 92.57214 0.645 -3469.7834
|
||||||
|
13000 291.00577 -59154.878 -3000.6461 1.012821 -3088.2569 87.610727 0.65 -2966.2448
|
||||||
|
13100 318.37718 86703.775 1825.1817 1.036209 1729.3305 95.851211 0.655 1819.7078
|
||||||
|
13200 280.41509 -107033.79 -2964.9455 1.0135499 -3049.3678 84.422277 0.66 -2953.8355
|
||||||
|
13300 275.01919 112086.85 2399.5628 1.0437945 2316.765 82.797775 0.665 2394.6707
|
||||||
|
13400 299.46547 -111959.62 -3814.3709 0.98732074 -3904.5286 90.157617 0.67 -3792.6798
|
||||||
|
13500 275.65631 17625.49 1528.0027 1.0255473 1445.0131 82.989588 0.675 1521.2745
|
||||||
|
13600 302.63525 122466.63 2631.7819 1.0438137 2540.67 91.111917 0.68 2611.7188
|
||||||
|
13700 302.21323 -94399.663 -3344.9423 1.0068914 -3435.9271 90.984863 0.685 -3328.4539
|
||||||
|
13800 305.70483 30039.825 1506.1765 1.0225478 1414.1404 92.036052 0.69 1502.8476
|
||||||
|
13900 273.15564 -27822.597 -2713.3946 1.0131002 -2795.6313 82.236732 0.695 -2683.7804
|
||||||
|
14000 257.14635 -1821.0012 1045.462 1.0172653 968.04508 77.416947 0.7 1067.8821
|
||||||
|
14100 323.74174 -76139.363 -3042.0486 1.0139806 -3139.5149 97.466276 0.705 -3052.598
|
||||||
|
14200 274.99913 54440.943 796.17718 1.0186356 713.38545 82.791736 0.71 767.64274
|
||||||
|
14300 291.8774 1281.7286 1079.6881 1.0214356 991.81498 87.873139 0.715 1042.8585
|
||||||
|
14400 308.97245 -47961.551 -3005.1106 1.0155221 -3098.1304 93.019806 0.72 -3007.3204
|
||||||
|
14500 311.05309 86026.739 1851.7257 1.0311818 1758.0795 93.646208 0.725 1830.5463
|
||||||
|
14600 269.27432 -12972.747 726.82371 1.0172239 645.7555 81.068214 0.73 711.81484
|
||||||
|
14700 262.20739 -77722.459 -3545.7104 1.0029421 -3624.651 78.940634 0.735 -3537.1929
|
||||||
|
14800 300.33592 -107332.8 -3118.6094 1.0126785 -3209.0291 90.419677 0.74 -3125.8439
|
||||||
|
14900 307.0173 -73204.94 -3016.2921 1.016875 -3108.7233 92.431185 0.745 -3016.0143
|
||||||
|
15000 334.08711 64440.709 1360.8856 1.0369481 1260.3047 100.58087 0.75 1323.9179
|
||||||
|
15100 293.46703 35179.395 1804.4648 1.0331703 1716.1131 88.351717 0.755 1768.9681
|
||||||
|
15200 307.80546 54006.291 852.72781 1.0246134 760.05934 92.668471 0.76 822.22754
|
||||||
|
15300 336.59792 33832.907 988.39905 1.0242407 887.06227 101.33678 0.765 956.25285
|
||||||
|
15400 285.46526 -99629.94 -2736.0944 1.0041261 -2822.0371 85.942688 0.77 -2730.1887
|
||||||
|
15500 269.15938 122546.45 2708.063 1.0318941 2627.0294 81.033612 0.775 2695.4331
|
||||||
|
15600 294.50818 -104733.19 -2271.5729 1.0017241 -2360.238 88.665166 0.78 -2281.5773
|
||||||
|
15700 321.05125 -40438.501 -2060.144 1.0125007 -2156.8002 96.656271 0.785 -2084.0893
|
||||||
|
15800 303.22185 -42224.408 -2486.7037 1.0090867 -2577.9922 91.288521 0.79 -2506.3355
|
||||||
|
15900 281.65025 78652.063 2532.2753 1.0460521 2447.4812 84.794136 0.795 2500.7128
|
||||||
|
16000 286.5056 63174.412 1479.3631 1.0185277 1393.1072 86.255897 0.8 1442.2427
|
||||||
|
16100 271.74574 -75051.584 -2429.2879 1.0091727 -2511.1002 81.812265 0.805 -2447.1967
|
||||||
|
16200 266.40007 -64120.09 -2497.2609 1.0064388 -2577.4638 80.202888 0.81 -2525.4243
|
||||||
|
16300 330.67137 46204.124 1582.1688 1.0271037 1482.6162 99.552523 0.815 1529.8186
|
||||||
|
16400 310.94573 18510.676 1235.5974 1.0188695 1141.9835 93.613887 0.82 1195.3041
|
||||||
|
16500 270.29191 79005.409 1711.3568 1.0354088 1629.9822 81.374574 0.825 1678.7342
|
||||||
|
16600 334.24108 17143.221 1446.3175 1.0230561 1345.6903 100.62723 0.83 1379.3215
|
||||||
|
16700 292.28721 -78618.031 -3045.0258 0.99940789 -3133.0223 87.996518 0.835 -3087.379
|
||||||
|
16800 346.09157 -69398.937 -2956.6793 1.0153026 -3060.8742 104.19496 0.84 -3011.3476
|
||||||
|
16900 284.37042 39314.526 2102.7814 1.0343186 2017.1683 85.613074 0.845 2045.8316
|
||||||
|
17000 281.69389 86032.163 1577.5995 1.0237583 1492.7922 84.807275 0.85 1528.8391
|
||||||
|
17100 297.2629 55128.393 2431.5835 1.0419182 2342.089 89.494508 0.855 2369.0347
|
||||||
|
17200 328.81472 47063.86 1584.1492 1.0364627 1485.1556 98.993555 0.86 1526.7115
|
||||||
|
17300 313.41363 -46685.063 -2635.2463 1.008117 -2729.6032 94.356878 0.865 -2685.8034
|
||||||
|
17400 288.17114 68721.523 2548.303 1.0429105 2461.5456 86.757326 0.87 2490.5845
|
||||||
|
17500 260.01702 -23324.539 -1776.7039 1.0100415 -1854.9851 78.281195 0.875 -1812.4813
|
||||||
|
17600 297.6633 72795.463 2396.9788 1.0362827 2307.3638 89.615054 0.88 2336.0152
|
||||||
|
17700 301.02937 93833.118 2424.9649 1.0276466 2334.3364 90.628448 0.885 2364.8751
|
||||||
|
17800 238.92837 -78317.212 -2548.5755 1.0084077 -2620.5077 71.932208 0.89 -2579.4429
|
||||||
|
17900 299.27724 -65278.891 -2933.564 1.0034773 -3023.6649 90.10095 0.895 -2987.498
|
||||||
|
18000 315.15753 -72437.481 -2654.8693 1.0136139 -2749.7512 94.881898 0.9 -2718.125
|
||||||
|
18100 268.39411 -42194.209 -2606.045 1.0108104 -2686.8482 80.803219 0.905 -2656.3853
|
||||||
|
18200 284.91941 40905.162 1786.1505 1.0266185 1700.3722 85.778354 0.91 1723.6803
|
||||||
|
18300 329.41629 -56526.814 -2472.7835 1.0137784 -2571.9582 99.174667 0.915 -2540.6829
|
||||||
|
18400 293.16732 -22085.551 -1991.6537 1.0163557 -2079.9152 88.261484 0.92 -2052.7864
|
||||||
|
18500 276.28141 29367.359 2034.0833 1.0270087 1950.9056 83.177784 0.925 1971.9405
|
||||||
|
18600 331.18031 94669.124 2160.1352 1.0225403 2060.4295 99.705745 0.93 2081.8675
|
||||||
|
18700 265.4491 49872.536 2324.2391 1.0255308 2244.3225 79.916587 0.935 2260.4261
|
||||||
|
18800 314.51042 60758.629 2298.6407 1.0300818 2203.9536 94.687078 0.94 2219.6547
|
||||||
|
18900 317.70309 66345.835 1490.6939 1.0248229 1395.0457 95.648268 0.945 1410.3087
|
||||||
|
19000 291.39831 -96336.931 -2732.3994 1.0100498 -2820.1283 87.728905 0.95 -2805.9396
|
||||||
|
19100 303.37353 -21421.495 -2360.5644 0.99771284 -2451.8986 91.334186 0.955 -2436.2173
|
||||||
|
19200 293.92948 36383.881 1708.7388 1.0251299 1620.2479 88.490944 0.96 1633.579
|
||||||
|
19300 287.24409 -46691.027 -2736.6663 1.0112067 -2823.1445 86.478228 0.965 -2811.3506
|
||||||
|
19400 333.42205 21152.63 1209.1556 1.0189912 1108.7749 100.38065 0.97 1118.2463
|
||||||
|
19500 309.17989 60445.761 2014.5979 1.0338543 1921.5157 93.082259 0.975 1928.6181
|
||||||
|
19600 255.92246 -32795.547 -2145.3103 1.0157044 -2222.3587 77.04848 0.98 -2213.9484
|
||||||
|
19700 342.62332 33538.746 2181.2002 1.0225905 2078.0494 103.1508 0.985 2081.9185
|
||||||
|
19800 295.68946 81474.342 1996.4567 1.0240743 1907.4359 89.020804 0.99 1910.5545
|
||||||
|
19900 306.4947 43488.052 2048.2997 1.0222707 1956.0258 92.27385 0.995 1957.4368
|
||||||
|
20000 313.31679 -25133.284 -1555.4274 1.0163289 -1649.7551 94.327722 1 -1649.7551
|
||||||
|
Loop time of 11.8253 on 2 procs for 20000 steps with 102 atoms
|
||||||
|
|
||||||
|
Performance: 29.226 ns/day, 0.821 hours/ns, 1691.295 timesteps/s, 172.512 katom-step/s
|
||||||
|
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 6.8508 | 8.6272 | 10.404 | 60.5 | 72.96
|
||||||
|
Bond | 0.045829 | 0.046542 | 0.047256 | 0.3 | 0.39
|
||||||
|
Neigh | 0.10781 | 0.10791 | 0.108 | 0.0 | 0.91
|
||||||
|
Comm | 0.75178 | 2.5281 | 4.3045 | 111.7 | 21.38
|
||||||
|
Output | 0.0032916 | 0.0035722 | 0.0038527 | 0.5 | 0.03
|
||||||
|
Modify | 0.44867 | 0.45212 | 0.45556 | 0.5 | 3.82
|
||||||
|
Other | | 0.05976 | | | 0.51
|
||||||
|
|
||||||
|
Nlocal: 51 ave 51 max 51 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 3317 ave 3317 max 3317 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 18319.5 ave 21940 max 14699 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 36639
|
||||||
|
Ave neighs/atom = 359.20588
|
||||||
|
Ave special neighs/atom = 2.0196078
|
||||||
|
Neighbor list builds = 181
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:11
|
||||||
@ -45,6 +45,7 @@ FixAlchemy::FixAlchemy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
|
|||||||
if (narg != 3) error->all(FLERR, "Incorrect number of arguments for fix alchemy");
|
if (narg != 3) error->all(FLERR, "Incorrect number of arguments for fix alchemy");
|
||||||
|
|
||||||
lambda = epot[0] = epot[1] = 0.0;
|
lambda = epot[0] = epot[1] = 0.0;
|
||||||
|
progress = 0;
|
||||||
for (int i = 0; i < 6; ++i) pressure[i] = 0.0;
|
for (int i = 0; i < 6; ++i) pressure[i] = 0.0;
|
||||||
|
|
||||||
no_change_box = 1;
|
no_change_box = 1;
|
||||||
@ -125,6 +126,13 @@ void FixAlchemy::setup(int vflag)
|
|||||||
} else {
|
} else {
|
||||||
post_force(vflag);
|
post_force(vflag);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (universe->me == 0) {
|
||||||
|
progress = static_cast<int>(100.0 - lambda * 100.0);
|
||||||
|
auto msg = fmt::format("Starting alchemical transformation at {:>3d}%\n", progress);
|
||||||
|
if (universe->uscreen) fmt::print(universe->uscreen, msg);
|
||||||
|
if (universe->ulogfile) fmt::print(universe->ulogfile, msg);
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -164,6 +172,17 @@ void FixAlchemy::post_force(int /*vflag*/)
|
|||||||
for (int i = 0; i < 6; ++i) commbuf[i] = lambda * scalefac * press->vector[i];
|
for (int i = 0; i < 6; ++i) commbuf[i] = lambda * scalefac * press->vector[i];
|
||||||
MPI_Allreduce(commbuf, pressure, 6, MPI_DOUBLE, MPI_SUM, universe->uworld);
|
MPI_Allreduce(commbuf, pressure, 6, MPI_DOUBLE, MPI_SUM, universe->uworld);
|
||||||
press->addstep(update->ntimestep + 1);
|
press->addstep(update->ntimestep + 1);
|
||||||
|
|
||||||
|
// print progress info
|
||||||
|
if (universe->me == 0) {
|
||||||
|
int status = static_cast<int>(100.0 - lambda * 100.0);
|
||||||
|
if ((status / 10) > (progress / 10)) {
|
||||||
|
progress = status;
|
||||||
|
auto msg = fmt::format(" Alchemical transformation progress: {:>3d}%\n", progress);
|
||||||
|
if (universe->uscreen) fmt::print(universe->uscreen, msg);
|
||||||
|
if (universe->ulogfile) fmt::print(universe->ulogfile, msg);
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -45,6 +45,7 @@ class FixAlchemy : public Fix {
|
|||||||
double lambda; // changes from 0 to 1 during run
|
double lambda; // changes from 0 to 1 during run
|
||||||
double epot[3]; // last (unscaled) potential energy from each replica and combined energy
|
double epot[3]; // last (unscaled) potential energy from each replica and combined energy
|
||||||
double pressure[6]; // joined pressure
|
double pressure[6]; // joined pressure
|
||||||
|
int progress; // for progress indicator
|
||||||
int ilevel_respa;
|
int ilevel_respa;
|
||||||
int nmax;
|
int nmax;
|
||||||
};
|
};
|
||||||
|
|||||||
Reference in New Issue
Block a user