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update local/density examples to follow conventions more closely

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This commit is contained in:
Axel Kohlmeyer
2021-12-10 08:50:58 -05:00
parent 14fc42833f
commit 6140503158
6 changed files with 19 additions and 20 deletions
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2
examples/PACKAGES/local_density/benzene_water/benzene_water.localdensity.table
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@ -1,4 +1,4 @@
# local density potentials: (B,B), (W,W), (B,W), (W,B) # local density potentials: (B,B), (W,W), (B,W), (W,B) UNITS: real
4 500 4 500

2
examples/PACKAGES/local_density/benzene_water/benzene_water.pair.table
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@ -1,4 +1,4 @@
# UNITS: real
PairBB PairBB
N 500 R 2.00000e-02 1.32500e+01 N 500 R 2.00000e-02 1.32500e+01

14
examples/PACKAGES/local_density/benzene_water/in.benzene_water
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@ -11,7 +11,7 @@
# Initialize simulation box # Initialize simulation box
dimension 3 dimension 3
boundary p p p boundary p p p
units real units real
atom_style molecular atom_style molecular
@ -32,7 +32,7 @@ pair_coeff * * local/density benzene_water.localdensity.table
fix recentering all recenter 0.0 0.0 0.0 units box fix recentering all recenter 0.0 0.0 0.0 units box
# Thermostat & time integration # Thermostat & time integration
timestep 2.0 timestep 2.0
thermo 100 thermo 100
thermo_style custom temp ke pe etotal ebond eangle edihed evdwl thermo_style custom temp ke pe etotal ebond eangle edihed evdwl
@ -49,14 +49,14 @@ run 5000
# Turn off recentering during production phase # Turn off recentering during production phase
unfix recentering unfix recentering
reset_timestep 0
# Setup trajectory output # Setup trajectory output
dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element #dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
dump_modify myDump element B W #dump_modify myDump element B W
dump_modify myDump sort id #dump_modify myDump sort id
# Production (for realistic results, run for 10000000 steps) # Production (for realistic results, run for 10000000 steps)
reset_timestep 0 run 1000
run 1000

17
examples/PACKAGES/local_density/methanol_implicit_water/in.methanol_implicit_water
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@ -1,6 +1,6 @@
# LAMMPS input file for 50.0% methanol mole fraction solution # LAMMPS input file for 50.0% methanol mole fraction solution
# with 2500 methanol molecules in implicit water. # with 2500 methanol molecules in implicit water.
# #
# #
# Author: David Rosenberger, van der Vegt Group, TU Darmstadt # Author: David Rosenberger, van der Vegt Group, TU Darmstadt
# #
@ -9,7 +9,7 @@
# Initialize simulation box # Initialize simulation box
dimension 3 dimension 3
boundary p p p boundary p p p
units real units real
atom_style molecular atom_style molecular
@ -17,7 +17,7 @@ atom_style molecular
pair_style hybrid/overlay table spline 500 local/density pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities # Read molecule data and set initial velocities
read_data methanol_implicit_water.data read_data methanol_implicit_water.data
velocity all create 3.0000e+02 12142 rot yes dist gaussian velocity all create 3.0000e+02 12142 rot yes dist gaussian
# Assign potentials # Assign potentials
@ -31,7 +31,7 @@ pair_coeff * * local/density methanol_implicit_water.localdensity.t
fix recentering all recenter 0.0 0.0 0.0 units box fix recentering all recenter 0.0 0.0 0.0 units box
#Thermostat & time integration #Thermostat & time integration
timestep 1.0 timestep 1.0
thermo 100 thermo 100
thermo_style custom etotal ke pe temp evdwl thermo_style custom etotal ke pe temp evdwl
@ -52,15 +52,14 @@ run 2000
#turn off recentering during production run #turn off recentering during production run
unfix recentering unfix recentering
reset_timestep 0
#setup trajectory output #setup trajectory output
dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element #dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
dump_modify myDump element M #dump_modify myDump element M
dump_modify myDump sort id #dump_modify myDump sort id
#run production (for realistic results, run for 10000000 steps) #run production (for realistic results, run for 10000000 steps)
reset_timestep 0
thermo 1000 thermo 1000
thermo_style custom etotal ke pe temp evdwl thermo_style custom etotal ke pe temp evdwl
run 10000 run 10000

2
examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table
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@ -1,4 +1,4 @@
#LOCAL DENSITY POTENTIALS #LOCAL DENSITY POTENTIALS UNITS: real
1 500 1 500

2
examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.pair.table
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@ -1,4 +1,4 @@
# UNITS: real
PairMM PairMM
N 500 R 2.00000e-02 1.50000e+01 N 500 R 2.00000e-02 1.50000e+01