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update log files in the examples

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oywg11
2023-06-04 10:17:21 +08:00
parent 196641927f
commit bf8a4402ce
4 changed files with 174 additions and 154 deletions
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83
examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (23 Jun 2022)
LAMMPS (23 Jun 2022 - Update 4)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Initialization
@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 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
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 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)
@ -41,14 +41,14 @@ 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_style hybrid/overlay aip/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 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
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
@ -62,7 +62,7 @@ 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 2 all pair aip/water/2dm
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
@ -72,18 +72,18 @@ 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
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
find clusters CPU = 0.000 seconds
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
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
@ -91,22 +91,24 @@ 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},
author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
pages = 6009,
year = 2018,
}
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
- 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,
author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
A. Tkatchenko and L. Kronik and 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
@ -132,6 +134,8 @@ PPPM initialization ...
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)
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 100000, page size: 1000000
@ -139,7 +143,7 @@ Neighbor list info ...
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
(1) pair aip/water/2dm, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
@ -154,10 +158,11 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
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
Per MPI rank memory allocation (min/avg/max) = 32.9 | 32.9 | 32.9 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
@ -200,22 +205,22 @@ 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
Loop time of 20.3334 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
Performance: 4.249 ns/day, 5.648 hours/ns, 49.180 timesteps/s
99.5% 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
Pair | 16.179 | 16.179 | 16.179 | 0.0 | 79.57
Bond | 0.00021103 | 0.00021103 | 0.00021103 | 0.0 | 0.00
Kspace | 3.3118 | 3.3118 | 3.3118 | 0.0 | 16.29
Neigh | 0.79017 | 0.79017 | 0.79017 | 0.0 | 3.89
Comm | 0.026379 | 0.026379 | 0.026379 | 0.0 | 0.13
Output | 0.00046496 | 0.00046496 | 0.00046496 | 0.0 | 0.00
Modify | 0.017013 | 0.017013 | 0.017013 | 0.0 | 0.08
Other | | 0.008835 | | | 0.04
Nlocal: 936 ave 936 max 936 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -231,4 +236,4 @@ Ave neighs/atom = 460.87821
Ave special neighs/atom = 0.30769231
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:00:21
Total wall time: 0:00:20

81
examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (23 Jun 2022)
LAMMPS (23 Jun 2022 - Update 4)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Initialization
@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 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
special bonds CPU = 0.001 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)
@ -41,14 +41,14 @@ 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_style hybrid/overlay aip/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 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
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
@ -62,7 +62,7 @@ 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 2 all pair aip/water/2dm
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
@ -72,18 +72,18 @@ 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
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
find clusters CPU = 0.000 seconds
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
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
@ -91,22 +91,24 @@ 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},
author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
pages = 6009,
year = 2018,
}
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
- 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,
author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
A. Tkatchenko and L. Kronik and 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
@ -132,6 +134,8 @@ PPPM initialization ...
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)
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 100000, page size: 1000000
@ -139,7 +143,7 @@ Neighbor list info ...
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
(1) pair aip/water/2dm, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
@ -154,10 +158,11 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
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
Per MPI rank memory allocation (min/avg/max) = 25.22 | 25.25 | 25.29 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
@ -200,22 +205,22 @@ 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
Loop time of 9.05361 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
Performance: 9.543 ns/day, 2.515 hours/ns, 110.453 timesteps/s
99.6% 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
Pair | 2.462 | 4.2266 | 7.1075 | 89.3 | 46.68
Bond | 0.00018424 | 0.00019878 | 0.00022125 | 0.0 | 0.00
Kspace | 1.4698 | 4.338 | 6.1001 | 87.8 | 47.91
Neigh | 0.39462 | 0.39489 | 0.39518 | 0.0 | 4.36
Comm | 0.043753 | 0.055826 | 0.062746 | 3.1 | 0.62
Output | 0.00048755 | 0.00053971 | 0.00062785 | 0.0 | 0.01
Modify | 0.027255 | 0.028664 | 0.030278 | 0.7 | 0.32
Other | | 0.008904 | | | 0.10
Nlocal: 234 ave 302 max 198 min
Histogram: 2 0 0 1 0 0 0 0 0 1

83
examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (23 Jun 2022)
LAMMPS (23 Jun 2022 - Update 4)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Initialization
@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 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
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 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)
@ -41,14 +41,14 @@ 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_style hybrid/overlay aip/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 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
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
@ -62,7 +62,7 @@ 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 2 all pair aip/water/2dm/opt
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
@ -72,18 +72,18 @@ 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
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
find clusters CPU = 0.000 seconds
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
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
@ -91,22 +91,24 @@ 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},
author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
pages = 6009,
year = 2018,
}
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
- 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,
author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
A. Tkatchenko and L. Kronik and 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
@ -149,6 +151,8 @@ PPPM initialization ...
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)
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 100000, page size: 1000000
@ -156,7 +160,7 @@ Neighbor list info ...
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
(1) pair aip/water/2dm/opt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
@ -171,10 +175,11 @@ Neighbor list info ...
pair build: halffull/newton
stencil: none
bin: none
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
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
Per MPI rank memory allocation (min/avg/max) = 25.27 | 25.27 | 25.27 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
@ -217,22 +222,22 @@ 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
Loop time of 8.11929 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
Performance: 10.641 ns/day, 2.255 hours/ns, 123.163 timesteps/s
99.7% 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
Pair | 4.6849 | 4.6849 | 4.6849 | 0.0 | 57.70
Bond | 0.00017678 | 0.00017678 | 0.00017678 | 0.0 | 0.00
Kspace | 3.2098 | 3.2098 | 3.2098 | 0.0 | 39.53
Neigh | 0.17546 | 0.17546 | 0.17546 | 0.0 | 2.16
Comm | 0.024693 | 0.024693 | 0.024693 | 0.0 | 0.30
Output | 0.00037798 | 0.00037798 | 0.00037798 | 0.0 | 0.00
Modify | 0.015853 | 0.015853 | 0.015853 | 0.0 | 0.20
Other | | 0.007983 | | | 0.10
Nlocal: 936 ave 936 max 936 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -248,4 +253,4 @@ Ave neighs/atom = 460.87821
Ave special neighs/atom = 0.30769231
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:00:09
Total wall time: 0:00:08

81
examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (23 Jun 2022)
LAMMPS (23 Jun 2022 - Update 4)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Initialization
@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 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
special bonds CPU = 0.001 seconds
read_data CPU = 0.014 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)
@ -41,14 +41,14 @@ 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_style hybrid/overlay aip/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 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
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
@ -62,7 +62,7 @@ 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 2 all pair aip/water/2dm/opt
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
@ -72,18 +72,18 @@ 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
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
find clusters CPU = 0.000 seconds
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
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
@ -91,22 +91,24 @@ 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},
author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
pages = 6009,
year = 2018,
}
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
- 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,
author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
A. Tkatchenko and L. Kronik and 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
@ -149,6 +151,8 @@ PPPM initialization ...
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)
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 100000, page size: 1000000
@ -156,7 +160,7 @@ Neighbor list info ...
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
(1) pair aip/water/2dm/opt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
@ -171,10 +175,11 @@ Neighbor list info ...
pair build: halffull/newton
stencil: none
bin: none
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
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
Per MPI rank memory allocation (min/avg/max) = 21.4 | 21.44 | 21.48 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
@ -217,22 +222,22 @@ 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
Loop time of 4.24862 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
Performance: 20.336 ns/day, 1.180 hours/ns, 235.370 timesteps/s
99.6% 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
Pair | 0.25749 | 1.1806 | 2.6872 | 89.0 | 27.79
Bond | 0.00018656 | 0.00020786 | 0.00025377 | 0.0 | 0.00
Kspace | 1.4259 | 2.9204 | 3.8414 | 56.3 | 68.74
Neigh | 0.057504 | 0.057852 | 0.05818 | 0.1 | 1.36
Comm | 0.041952 | 0.053593 | 0.05876 | 3.0 | 1.26
Output | 0.0004296 | 0.00046809 | 0.00055317 | 0.0 | 0.01
Modify | 0.026204 | 0.027251 | 0.028382 | 0.6 | 0.64
Other | | 0.008209 | | | 0.19
Nlocal: 234 ave 302 max 198 min
Histogram: 2 0 0 1 0 0 0 0 0 1