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examples/PACKAGES/interlayer/ilp_water_2dm/COH.ILP Symbolic link
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../../../../potentials/COH.ILP

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examples/PACKAGES/interlayer/ilp_water_2dm/gra_water.data Normal file
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examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water Normal file
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# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data
mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
group water molecule 2
######################## Potential defition ##############################
# Interlayer potential
pair_style hybrid/overlay ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * ilp/water/2dm COH.ILP C Ow Hw # C-water
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
# define kspace calculation
kspace_style pppm/tip4p 1E-5
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair ilp/water/2dm
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt
############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100
thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000

51
examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water.opt Normal file
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# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data
mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
group water molecule 2
######################## Potential defition ##############################
# Interlayer potential
pair_style hybrid/overlay ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * ilp/water/2dm/opt COH.ILP C Ow Hw # C-water
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
# define kspace calculation
kspace_style pppm/tip4p 1E-5
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair ilp/water/2dm/opt
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt
############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100
thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000

234
examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.1 Normal file
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LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data
Reading data file ...
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
1 by 1 by 1 MPI processor grid
reading atoms ...
936 atoms
reading velocities ...
936 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
96 bonds
reading angles ...
48 angles
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
2 = max # of special neighbors
special bonds CPU = 0.005 seconds
read_data CPU = 0.020 seconds
mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
792 atoms in group gr
group water molecule 2
144 atoms in group water
######################## Potential defition ##############################
# Interlayer potential
pair_style hybrid/overlay ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * ilp/water/2dm COH.ILP C Ow Hw # C-water
Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
# define kspace calculation
kspace_style pppm/tip4p 1E-5
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair ilp/water/2dm
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt
############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100
thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
48 = # of frozen angles
find clusters CPU = 0.001 seconds
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
year = 2018,
}
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
@Article{Ouyang2021
author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
journal = {J. Chem. Theory Comput.},
volume = 17,
pages = {7237–7245}
year = 2021,
}
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@Article{Feng2023
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
journal = {J. Phys. Chem. C},
volume = 127,
pages = {8704-8713}
year = 2023,
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.28684806
grid = 25 24 80
stencil order = 5
estimated absolute RMS force accuracy = 0.0001640931
estimated relative force accuracy = 1.1395635e-05
using single precision MKL FFT
3d grid and FFT values/proc = 84320 48000
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 100000, page size: 1000000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 5 23
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair ilp/water/2dm, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
Bond: 1 0.957201 2.19705e-06 96
Angle: 1 104.52 0.000203056 48
Per MPI rank memory allocation (min/avg/max) = 33.53 | 33.53 | 33.53 Mbytes
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
SHAKE stats (type/ave/delta/count) on step 100
Bond: 1 0.9572 9.54949e-07 96
Angle: 1 104.52 6.01522e-05 48
100 -17.494868 -20.796993 3.3021253 188.4955 -1.8981262 268.90898
SHAKE stats (type/ave/delta/count) on step 200
Bond: 1 0.9572 9.63922e-07 96
Angle: 1 104.52 7.7021e-05 48
200 -17.486271 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
SHAKE stats (type/ave/delta/count) on step 300
Bond: 1 0.9572 1.4264e-06 96
Angle: 1 104.52 6.48393e-05 48
300 -17.502844 -20.993704 3.49086 188.23268 -1.8457229 284.27861
SHAKE stats (type/ave/delta/count) on step 400
Bond: 1 0.9572 1.33728e-06 96
Angle: 1 104.52 7.6239e-05 48
400 -17.495287 -20.828353 3.3330658 188.48002 -1.8429075 271.42862
SHAKE stats (type/ave/delta/count) on step 500
Bond: 1 0.9572 1.14685e-06 96
Angle: 1 104.52 8.58621e-05 48
500 -17.491435 -20.443044 2.9516084 188.7589 -1.8566335 240.36459
SHAKE stats (type/ave/delta/count) on step 600
Bond: 1 0.9572 9.17601e-07 96
Angle: 1 104.52 8.24516e-05 48
600 -17.505684 -20.608457 3.1027731 188.72078 -1.9560796 252.67471
SHAKE stats (type/ave/delta/count) on step 700
Bond: 1 0.9572 9.50422e-07 96
Angle: 1 104.52 5.62423e-05 48
700 -17.496703 -21.072663 3.5759596 188.2777 -1.9833956 291.20871
SHAKE stats (type/ave/delta/count) on step 800
Bond: 1 0.9572 1.15262e-06 96
Angle: 1 104.52 7.02157e-05 48
800 -17.478623 -20.819504 3.3408809 188.37868 -1.9112996 272.06505
SHAKE stats (type/ave/delta/count) on step 900
Bond: 1 0.9572 9.14138e-07 96
Angle: 1 104.52 6.98742e-05 48
900 -17.48086 -20.728495 3.2476349 188.59022 -1.8922102 264.47155
SHAKE stats (type/ave/delta/count) on step 1000
Bond: 1 0.9572 1.00586e-06 96
Angle: 1 104.52 0.000111712 48
1000 -17.498465 -20.331545 2.8330804 188.87473 -1.812177 230.71225
Loop time of 20.801 on 1 procs for 1000 steps with 936 atoms
Performance: 4.154 ns/day, 5.778 hours/ns, 48.075 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.429 | 16.429 | 16.429 | 0.0 | 78.98
Bond | 0.0010991 | 0.0010991 | 0.0010991 | 0.0 | 0.01
Kspace | 3.4769 | 3.4769 | 3.4769 | 0.0 | 16.72
Neigh | 0.83359 | 0.83359 | 0.83359 | 0.0 | 4.01
Comm | 0.028825 | 0.028825 | 0.028825 | 0.0 | 0.14
Output | 0.00046349 | 0.00046349 | 0.00046349 | 0.0 | 0.00
Modify | 0.01943 | 0.01943 | 0.01943 | 0.0 | 0.09
Other | | 0.01154 | | | 0.06
Nlocal: 936 ave 936 max 936 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5242 ave 5242 max 5242 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 431382 ave 431382 max 431382 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 431382
Ave neighs/atom = 460.87821
Ave special neighs/atom = 0.30769231
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:00:21

234
examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.4 Normal file
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LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data
Reading data file ...
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
2 by 2 by 1 MPI processor grid
reading atoms ...
936 atoms
reading velocities ...
936 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
96 bonds
reading angles ...
48 angles
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
2 = max # of special neighbors
special bonds CPU = 0.003 seconds
read_data CPU = 0.018 seconds
mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
792 atoms in group gr
group water molecule 2
144 atoms in group water
######################## Potential defition ##############################
# Interlayer potential
pair_style hybrid/overlay ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * ilp/water/2dm COH.ILP C Ow Hw # C-water
Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
# define kspace calculation
kspace_style pppm/tip4p 1E-5
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair ilp/water/2dm
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt
############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100
thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
48 = # of frozen angles
find clusters CPU = 0.001 seconds
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
year = 2018,
}
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
@Article{Ouyang2021
author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
journal = {J. Chem. Theory Comput.},
volume = 17,
pages = {7237–7245}
year = 2021,
}
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@Article{Feng2023
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
journal = {J. Phys. Chem. C},
volume = 127,
pages = {8704-8713}
year = 2023,
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.28684806
grid = 25 24 80
stencil order = 5
estimated absolute RMS force accuracy = 0.0001640931
estimated relative force accuracy = 1.1395635e-05
using single precision MKL FFT
3d grid and FFT values/proc = 30685 12480
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 100000, page size: 1000000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 5 23
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair ilp/water/2dm, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
Bond: 1 0.957201 2.19705e-06 96
Angle: 1 104.52 0.000203056 48
Per MPI rank memory allocation (min/avg/max) = 25.84 | 25.88 | 25.92 Mbytes
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
SHAKE stats (type/ave/delta/count) on step 100
Bond: 1 0.9572 9.54949e-07 96
Angle: 1 104.52 6.01522e-05 48
100 -17.494869 -20.796995 3.3021253 188.4955 -1.8981262 268.90898
SHAKE stats (type/ave/delta/count) on step 200
Bond: 1 0.9572 9.63922e-07 96
Angle: 1 104.52 7.7021e-05 48
200 -17.48627 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
SHAKE stats (type/ave/delta/count) on step 300
Bond: 1 0.9572 1.4264e-06 96
Angle: 1 104.52 6.48393e-05 48
300 -17.502843 -20.993703 3.4908599 188.23268 -1.8457229 284.27861
SHAKE stats (type/ave/delta/count) on step 400
Bond: 1 0.9572 1.33728e-06 96
Angle: 1 104.52 7.6239e-05 48
400 -17.495285 -20.82835 3.333065 188.48003 -1.8429074 271.42856
SHAKE stats (type/ave/delta/count) on step 500
Bond: 1 0.9572 1.14685e-06 96
Angle: 1 104.52 8.58621e-05 48
500 -17.491436 -20.443043 2.9516075 188.7589 -1.8566335 240.36452
SHAKE stats (type/ave/delta/count) on step 600
Bond: 1 0.9572 9.17601e-07 96
Angle: 1 104.52 8.24517e-05 48
600 -17.505683 -20.608456 3.1027734 188.72078 -1.9560795 252.67474
SHAKE stats (type/ave/delta/count) on step 700
Bond: 1 0.9572 9.50425e-07 96
Angle: 1 104.52 5.62422e-05 48
700 -17.496706 -21.072664 3.575958 188.2777 -1.9833951 291.20858
SHAKE stats (type/ave/delta/count) on step 800
Bond: 1 0.9572 1.15256e-06 96
Angle: 1 104.52 7.02177e-05 48
800 -17.478628 -20.819507 3.340879 188.37868 -1.9113009 272.06489
SHAKE stats (type/ave/delta/count) on step 900
Bond: 1 0.9572 9.14163e-07 96
Angle: 1 104.52 6.98849e-05 48
900 -17.480865 -20.728504 3.2476386 188.5902 -1.8922108 264.47185
SHAKE stats (type/ave/delta/count) on step 1000
Bond: 1 0.9572 1.00568e-06 96
Angle: 1 104.52 0.000111707 48
1000 -17.498474 -20.331607 2.833133 188.87466 -1.8121689 230.71654
Loop time of 9.42273 on 4 procs for 1000 steps with 936 atoms
Performance: 9.169 ns/day, 2.617 hours/ns, 106.126 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2328 | 4.3228 | 7.5931 | 103.1 | 45.88
Bond | 0.00084131 | 0.00088983 | 0.00095229 | 0.0 | 0.01
Kspace | 1.3979 | 4.6476 | 6.7252 | 98.8 | 49.32
Neigh | 0.34367 | 0.34371 | 0.34376 | 0.0 | 3.65
Comm | 0.042806 | 0.062908 | 0.075887 | 5.4 | 0.67
Output | 0.00037677 | 0.00041431 | 0.0004619 | 0.0 | 0.00
Modify | 0.028432 | 0.031138 | 0.034528 | 1.3 | 0.33
Other | | 0.01321 | | | 0.14
Nlocal: 234 ave 302 max 198 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 2876.5 ave 3122 max 2632 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 107846 ave 150684 max 82181 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 431382
Ave neighs/atom = 460.87821
Ave special neighs/atom = 0.30769231
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:00:09

251
examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.1 Normal file
View File

@ -0,0 +1,251 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data
Reading data file ...
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
1 by 1 by 1 MPI processor grid
reading atoms ...
936 atoms
reading velocities ...
936 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
96 bonds
reading angles ...
48 angles
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
2 = max # of special neighbors
special bonds CPU = 0.005 seconds
read_data CPU = 0.020 seconds
mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
792 atoms in group gr
group water molecule 2
144 atoms in group water
######################## Potential defition ##############################
# Interlayer potential
pair_style hybrid/overlay ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * ilp/water/2dm/opt COH.ILP C Ow Hw # C-water
Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
# define kspace calculation
kspace_style pppm/tip4p 1E-5
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair ilp/water/2dm/opt
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt
############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100
thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
48 = # of frozen angles
find clusters CPU = 0.001 seconds
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
year = 2018,
}
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
@Article{Ouyang2021
author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
journal = {J. Chem. Theory Comput.},
volume = 17,
pages = {7237–7245}
year = 2021,
}
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@Article{Feng2023
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
journal = {J. Phys. Chem. C},
volume = 127,
pages = {8704-8713}
year = 2023,
}
- ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137
@inproceedings{gao2021lmff
author = {Gao, Ping and Duan, Xiaohui and Others},
title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors},
year = {2021},
isbn = {9781450384421},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {https://doi.org/10.1145/3458817.3476137},
doi = {10.1145/3458817.3476137},
booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
articleno = {42},
numpages = {14},
location = {St. Louis, Missouri},
series = {SC'21},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.28684806
grid = 25 24 80
stencil order = 5
estimated absolute RMS force accuracy = 0.0001640931
estimated relative force accuracy = 1.1395635e-05
using single precision MKL FFT
3d grid and FFT values/proc = 84320 48000
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 100000, page size: 1000000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 5 23
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair ilp/water/2dm/opt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
SHAKE stats (type/ave/delta/count) on step 0
Bond: 1 0.957201 2.19705e-06 96
Angle: 1 104.52 0.000203056 48
Per MPI rank memory allocation (min/avg/max) = 25.89 | 25.89 | 25.89 Mbytes
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
SHAKE stats (type/ave/delta/count) on step 100
Bond: 1 0.9572 9.54949e-07 96
Angle: 1 104.52 6.01522e-05 48
100 -17.494868 -20.796993 3.3021253 188.4955 -1.8981262 268.90898
SHAKE stats (type/ave/delta/count) on step 200
Bond: 1 0.9572 9.63922e-07 96
Angle: 1 104.52 7.7021e-05 48
200 -17.486271 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
SHAKE stats (type/ave/delta/count) on step 300
Bond: 1 0.9572 1.4264e-06 96
Angle: 1 104.52 6.48393e-05 48
300 -17.502844 -20.993704 3.49086 188.23268 -1.8457229 284.27861
SHAKE stats (type/ave/delta/count) on step 400
Bond: 1 0.9572 1.33728e-06 96
Angle: 1 104.52 7.6239e-05 48
400 -17.495287 -20.828353 3.3330658 188.48002 -1.8429075 271.42862
SHAKE stats (type/ave/delta/count) on step 500
Bond: 1 0.9572 1.14685e-06 96
Angle: 1 104.52 8.58621e-05 48
500 -17.491436 -20.443044 2.9516084 188.7589 -1.8566335 240.36459
SHAKE stats (type/ave/delta/count) on step 600
Bond: 1 0.9572 9.17601e-07 96
Angle: 1 104.52 8.24516e-05 48
600 -17.505684 -20.608457 3.1027731 188.72078 -1.9560796 252.67471
SHAKE stats (type/ave/delta/count) on step 700
Bond: 1 0.9572 9.50422e-07 96
Angle: 1 104.52 5.62423e-05 48
700 -17.496701 -21.07266 3.5759595 188.2777 -1.9833956 291.20871
SHAKE stats (type/ave/delta/count) on step 800
Bond: 1 0.9572 1.15262e-06 96
Angle: 1 104.52 7.02158e-05 48
800 -17.478623 -20.819504 3.340881 188.37868 -1.9112996 272.06506
SHAKE stats (type/ave/delta/count) on step 900
Bond: 1 0.9572 9.14138e-07 96
Angle: 1 104.52 6.98742e-05 48
900 -17.480864 -20.728498 3.2476343 188.59022 -1.8922102 264.4715
SHAKE stats (type/ave/delta/count) on step 1000
Bond: 1 0.9572 1.00586e-06 96
Angle: 1 104.52 0.000111711 48
1000 -17.498466 -20.331547 2.8330808 188.87473 -1.8121768 230.71228
Loop time of 8.95265 on 1 procs for 1000 steps with 936 atoms
Performance: 9.651 ns/day, 2.487 hours/ns, 111.699 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.2127 | 5.2127 | 5.2127 | 0.0 | 58.23
Bond | 0.00083377 | 0.00083377 | 0.00083377 | 0.0 | 0.01
Kspace | 3.5005 | 3.5005 | 3.5005 | 0.0 | 39.10
Neigh | 0.17946 | 0.17946 | 0.17946 | 0.0 | 2.00
Comm | 0.028553 | 0.028553 | 0.028553 | 0.0 | 0.32
Output | 0.00035446 | 0.00035446 | 0.00035446 | 0.0 | 0.00
Modify | 0.01889 | 0.01889 | 0.01889 | 0.0 | 0.21
Other | | 0.01135 | | | 0.13
Nlocal: 936 ave 936 max 936 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5242 ave 5242 max 5242 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 431382 ave 431382 max 431382 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 431382
Ave neighs/atom = 460.87821
Ave special neighs/atom = 0.30769231
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:00:09

251
examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.4 Normal file
View File

@ -0,0 +1,251 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data
Reading data file ...
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
2 by 2 by 1 MPI processor grid
reading atoms ...
936 atoms
reading velocities ...
936 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
96 bonds
reading angles ...
48 angles
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
2 = max # of special neighbors
special bonds CPU = 0.003 seconds
read_data CPU = 0.017 seconds
mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
792 atoms in group gr
group water molecule 2
144 atoms in group water
######################## Potential defition ##############################
# Interlayer potential
pair_style hybrid/overlay ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * ilp/water/2dm/opt COH.ILP C Ow Hw # C-water
Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
# define kspace calculation
kspace_style pppm/tip4p 1E-5
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair ilp/water/2dm/opt
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt
############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100
thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
48 = # of frozen angles
find clusters CPU = 0.001 seconds
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
year = 2018,
}
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
@Article{Ouyang2021
author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
journal = {J. Chem. Theory Comput.},
volume = 17,
pages = {7237–7245}
year = 2021,
}
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@Article{Feng2023
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
journal = {J. Phys. Chem. C},
volume = 127,
pages = {8704-8713}
year = 2023,
}
- ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137
@inproceedings{gao2021lmff
author = {Gao, Ping and Duan, Xiaohui and Others},
title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors},
year = {2021},
isbn = {9781450384421},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {https://doi.org/10.1145/3458817.3476137},
doi = {10.1145/3458817.3476137},
booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
articleno = {42},
numpages = {14},
location = {St. Louis, Missouri},
series = {SC'21},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.28684806
grid = 25 24 80
stencil order = 5
estimated absolute RMS force accuracy = 0.0001640931
estimated relative force accuracy = 1.1395635e-05
using single precision MKL FFT
3d grid and FFT values/proc = 30685 12480
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 100000, page size: 1000000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 5 23
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair ilp/water/2dm/opt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
SHAKE stats (type/ave/delta/count) on step 0
Bond: 1 0.957201 2.19705e-06 96
Angle: 1 104.52 0.000203056 48
Per MPI rank memory allocation (min/avg/max) = 22.03 | 22.06 | 22.1 Mbytes
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
SHAKE stats (type/ave/delta/count) on step 100
Bond: 1 0.9572 9.54949e-07 96
Angle: 1 104.52 6.01522e-05 48
100 -17.494869 -20.796995 3.3021253 188.4955 -1.8981262 268.90898
SHAKE stats (type/ave/delta/count) on step 200
Bond: 1 0.9572 9.63922e-07 96
Angle: 1 104.52 7.7021e-05 48
200 -17.48627 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
SHAKE stats (type/ave/delta/count) on step 300
Bond: 1 0.9572 1.4264e-06 96
Angle: 1 104.52 6.48393e-05 48
300 -17.502843 -20.993703 3.4908599 188.23268 -1.8457229 284.27861
SHAKE stats (type/ave/delta/count) on step 400
Bond: 1 0.9572 1.33728e-06 96
Angle: 1 104.52 7.6239e-05 48
400 -17.495285 -20.82835 3.333065 188.48003 -1.8429074 271.42856
SHAKE stats (type/ave/delta/count) on step 500
Bond: 1 0.9572 1.14685e-06 96
Angle: 1 104.52 8.58621e-05 48
500 -17.491436 -20.443043 2.9516075 188.7589 -1.8566335 240.36452
SHAKE stats (type/ave/delta/count) on step 600
Bond: 1 0.9572 9.17601e-07 96
Angle: 1 104.52 8.24517e-05 48
600 -17.505682 -20.608456 3.1027734 188.72078 -1.9560795 252.67474
SHAKE stats (type/ave/delta/count) on step 700
Bond: 1 0.9572 9.50425e-07 96
Angle: 1 104.52 5.62423e-05 48
700 -17.496706 -21.072664 3.575958 188.2777 -1.9833951 291.20858
SHAKE stats (type/ave/delta/count) on step 800
Bond: 1 0.9572 1.15256e-06 96
Angle: 1 104.52 7.02177e-05 48
800 -17.478628 -20.819507 3.340879 188.37868 -1.9113009 272.0649
SHAKE stats (type/ave/delta/count) on step 900
Bond: 1 0.9572 9.14163e-07 96
Angle: 1 104.52 6.98849e-05 48
900 -17.480868 -20.728506 3.2476383 188.5902 -1.8922108 264.47182
SHAKE stats (type/ave/delta/count) on step 1000
Bond: 1 0.9572 1.00568e-06 96
Angle: 1 104.52 0.000111707 48
1000 -17.498472 -20.331605 2.8331335 188.87466 -1.8121689 230.71657
Loop time of 4.7828 on 4 procs for 1000 steps with 936 atoms
Performance: 18.065 ns/day, 1.329 hours/ns, 209.082 timesteps/s
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.26735 | 1.3839 | 3.2059 | 99.7 | 28.93
Bond | 0.00079377 | 0.00086039 | 0.00093529 | 0.0 | 0.02
Kspace | 1.4248 | 3.2254 | 4.3332 | 64.6 | 67.44
Neigh | 0.061885 | 0.061916 | 0.061951 | 0.0 | 1.29
Comm | 0.044281 | 0.065185 | 0.078628 | 5.1 | 1.36
Output | 0.0003482 | 0.0003787 | 0.00040746 | 0.0 | 0.01
Modify | 0.028727 | 0.031529 | 0.034914 | 1.3 | 0.66
Other | | 0.01367 | | | 0.29
Nlocal: 234 ave 302 max 198 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 2876.5 ave 3122 max 2632 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 107846 ave 150684 max 82181 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 431382
Ave neighs/atom = 460.87821
Ave special neighs/atom = 0.30769231
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:00:04