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Moved hBN_shift example to ./examples/tersoff and removed ./examples/USER/misc/tersoff_shift

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This commit is contained in:
Aidan Thompson
2021-01-13 19:28:13 -07:00
parent 7bff94910f
commit 84ca5b53e3
24 changed files with 1022 additions and 2099 deletions
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1
examples/USER/misc/tersoff_shift/BNC.tersoff
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../../../../potentials/BNC.tersoff

1
examples/USER/misc/tersoff_shift/Si.tersoff
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../../../../potentials/Si.tersoff

98
examples/USER/misc/tersoff_shift/after_change.lmp
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LAMMPS (30 Nov 2020)
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.007 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
#velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
Step TotEng PotEng KinEng Temp
0 -6604.6119 -6604.6119 0 0
100 -6604.6147 -6604.831 0.21628592 1.9035958
200 -6604.6142 -6604.812 0.19784607 1.7413013
300 -6604.6146 -6604.8412 0.22652026 1.9936713
400 -6604.6143 -6604.7986 0.18429458 1.6220306
500 -6604.614 -6604.7824 0.16835542 1.4817454
600 -6604.6145 -6604.8173 0.20279935 1.7848965
700 -6604.6148 -6604.8472 0.23241961 2.0455932
800 -6604.6141 -6604.8086 0.19442247 1.7111692
900 -6604.6146 -6604.8192 0.20463626 1.8010637
1000 -6604.6139 -6604.7789 0.16495493 1.4518167
Loop time of 2.01396 on 1 procs for 1000 steps with 880 atoms
Performance: 42.901 ns/day, 0.559 hours/ns, 496.535 timesteps/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9741 | 1.9741 | 1.9741 | 0.0 | 98.02
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013615 | 0.013615 | 0.013615 | 0.0 | 0.68
Output | 0.00099606 | 0.00099606 | 0.00099606 | 0.0 | 0.05
Modify | 0.014839 | 0.014839 | 0.014839 | 0.0 | 0.74
Other | | 0.01045 | | | 0.52
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1518.00 ave 1518 max 1518 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15840.0 ave 15840 max 15840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15840
Ave neighs/atom = 18.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

98
examples/USER/misc/tersoff_shift/before_change.lmp
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LAMMPS (30 Nov 2020)
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.014 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
#velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
Step TotEng PotEng KinEng Temp
0 -6604.6119 -6604.6119 0 0
100 -6604.6148 -6604.831 0.21618057 1.9026686
200 -6604.6142 -6604.812 0.19780992 1.7409831
300 -6604.6147 -6604.8411 0.22645852 1.9931278
400 -6604.6143 -6604.7988 0.1844863 1.623718
500 -6604.6141 -6604.7823 0.16817044 1.4801174
600 -6604.6145 -6604.8172 0.20269951 1.7840178
700 -6604.6149 -6604.8489 0.23401257 2.0596132
800 -6604.6142 -6604.8089 0.19466676 1.7133192
900 -6604.6146 -6604.8186 0.20395195 1.7950409
1000 -6604.614 -6604.778 0.1640674 1.4440053
Loop time of 1.62583 on 1 procs for 1000 steps with 880 atoms
Performance: 53.142 ns/day, 0.452 hours/ns, 615.069 timesteps/s
99.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5875 | 1.5875 | 1.5875 | 0.0 | 97.64
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013392 | 0.013392 | 0.013392 | 0.0 | 0.82
Output | 0.00091558 | 0.00091558 | 0.00091558 | 0.0 | 0.06
Modify | 0.014704 | 0.014704 | 0.014704 | 0.0 | 0.90
Other | | 0.009355 | | | 0.58
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1518.00 ave 1518 max 1518 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15840.0 ave 15840 max 15840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15840
Ave neighs/atom = 18.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

36
examples/USER/misc/tersoff_shift/in.Si_shift
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# Generate tip
units metal
dimension 3
boundary p p p
atom_style atomic
variable xm equal 10
variable ym equal 10
variable zm equal 5
lattice diamond 5.481 # Si-Si
region recbox block 0.0 ${xm} 0.0 ${ym} 0.0 ${zm}
create_box 1 recbox
create_atoms 1 region recbox units box
mass * 28.0855
pair_style tersoff shift 0.05
pair_coeff * * Si.tersoff Si
thermo_style custom step cpu etotal pe ke temp
thermo 100
thermo_modify flush yes norm no lost warn
thermo_modify line one format float %20.15g
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000

103
examples/USER/misc/tersoff_shift/log.31Dec20.Si_shift.g++.1
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@ -1,103 +0,0 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Generate tip
units metal
dimension 3
boundary p p p
atom_style atomic
variable xm equal 10
variable ym equal 10
variable zm equal 5
lattice diamond 5.481 # Si-Si
Lattice spacing in x,y,z = 5.4810000 5.4810000 5.4810000
region recbox block 0.0 ${xm} 0.0 ${ym} 0.0 ${zm}
region recbox block 0.0 10 0.0 ${ym} 0.0 ${zm}
region recbox block 0.0 10 0.0 10 0.0 ${zm}
region recbox block 0.0 10 0.0 10 0.0 5
create_box 1 recbox
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (54.810000 54.810000 27.405000)
1 by 1 by 1 MPI processor grid
create_atoms 1 region recbox units box
Created 4000 atoms
create_atoms CPU = 0.001 seconds
mass * 28.0855
pair_style tersoff shift 0.05
pair_coeff * * Si.tersoff Si
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
thermo_style custom step cpu etotal pe ke temp
thermo 100
thermo_modify flush yes norm no lost warn
thermo_modify line one format float %20.15g
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:693)
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.2
ghost atom cutoff = 5.2
binsize = 2.6, bins = 22 22 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.677 | 3.677 | 3.677 Mbytes
Step TotEng PotEng KinEng Temp
0 -18183.755 -18338.829 155.0734 300
100 -18183.651 -18249.335 65.684288 127.07071
200 -18183.643 -18241.96 58.317656 112.81946
300 -18183.675 -18265.042 81.367616 157.41117
400 -18183.661 -18257.198 73.536882 142.26208
500 -18183.669 -18261.964 78.295204 151.46738
600 -18183.665 -18258.552 74.886287 144.8726
700 -18183.662 -18256.924 73.261529 141.7294
800 -18183.67 -18263.155 79.484227 153.76763
900 -18183.663 -18259.152 75.488804 146.03821
1000 -18183.667 -18261.116 77.448767 149.82989
Loop time of 9.3615 on 1 procs for 1000 steps with 4000 atoms
Performance: 9.229 ns/day, 2.600 hours/ns, 106.820 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.3018 | 9.3018 | 9.3018 | 0.0 | 99.36
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015455 | 0.015455 | 0.015455 | 0.0 | 0.17
Output | 0.000312 | 0.000312 | 0.000312 | 0.0 | 0.00
Modify | 0.030194 | 0.030194 | 0.030194 | 0.0 | 0.32
Other | | 0.01378 | | | 0.15
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3470.00 ave 3470 max 3470 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 112000.0 ave 112000 max 112000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 112000
Ave neighs/atom = 28.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:09

103
examples/USER/misc/tersoff_shift/log.31Dec20.Si_shift.g++.4
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@ -1,103 +0,0 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Generate tip
units metal
dimension 3
boundary p p p
atom_style atomic
variable xm equal 10
variable ym equal 10
variable zm equal 5
lattice diamond 5.481 # Si-Si
Lattice spacing in x,y,z = 5.4810000 5.4810000 5.4810000
region recbox block 0.0 ${xm} 0.0 ${ym} 0.0 ${zm}
region recbox block 0.0 10 0.0 ${ym} 0.0 ${zm}
region recbox block 0.0 10 0.0 10 0.0 ${zm}
region recbox block 0.0 10 0.0 10 0.0 5
create_box 1 recbox
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (54.810000 54.810000 27.405000)
2 by 2 by 1 MPI processor grid
create_atoms 1 region recbox units box
Created 4000 atoms
create_atoms CPU = 0.001 seconds
mass * 28.0855
pair_style tersoff shift 0.05
pair_coeff * * Si.tersoff Si
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
thermo_style custom step cpu etotal pe ke temp
thermo 100
thermo_modify flush yes norm no lost warn
thermo_modify line one format float %20.15g
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:693)
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.2
ghost atom cutoff = 5.2
binsize = 2.6, bins = 22 22 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.127 | 3.127 | 3.127 Mbytes
Step TotEng PotEng KinEng Temp
0 -18183.755 -18338.829 155.0734 300
100 -18183.651 -18249.335 65.684288 127.07071
200 -18183.643 -18241.96 58.317656 112.81946
300 -18183.675 -18265.042 81.367616 157.41117
400 -18183.661 -18257.198 73.536882 142.26208
500 -18183.669 -18261.964 78.295204 151.46738
600 -18183.665 -18258.552 74.886287 144.8726
700 -18183.662 -18256.924 73.261529 141.7294
800 -18183.67 -18263.155 79.484227 153.76763
900 -18183.663 -18259.152 75.488804 146.03821
1000 -18183.667 -18261.116 77.448767 149.82989
Loop time of 2.63101 on 4 procs for 1000 steps with 4000 atoms
Performance: 32.839 ns/day, 0.731 hours/ns, 380.082 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 | 2.4651 | 2.5025 | 2.5216 | 1.4 | 95.11
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.093127 | 0.11216 | 0.14937 | 6.5 | 4.26
Output | 0.000129 | 0.00016075 | 0.000253 | 0.0 | 0.01
Modify | 0.008488 | 0.0086423 | 0.008735 | 0.1 | 0.33
Other | | 0.007586 | | | 0.29
Nlocal: 1000.00 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1470.00 ave 1470 max 1470 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 28000.0 ave 28000 max 28000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 112000
Ave neighs/atom = 28.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

100
examples/USER/misc/tersoff_shift/log.31Dec20.hBN_no_shift.g++.1
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@ -1,100 +0,0 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.005 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.545 | 3.545 | 3.545 Mbytes
Step TotEng PotEng KinEng Temp
0 -6517.7517 -6551.8376 34.0859 300
100 -6517.5918 -6540.7795 23.187734 204.08204
200 -6517.5423 -6546.3342 28.791974 253.4066
300 -6517.547 -6552.0178 34.47074 303.38708
400 -6517.5499 -6554.1682 36.618359 322.28891
500 -6517.5482 -6553.3948 35.846598 315.49641
600 -6517.5438 -6557.8044 40.260609 354.34542
700 -6517.5489 -6554.8963 37.3474 328.70542
800 -6517.5426 -6557.376 39.833345 350.58494
900 -6517.5508 -6557.1115 39.560726 348.18554
1000 -6517.5427 -6559.2989 41.756142 367.50804
Loop time of 1.03247 on 1 procs for 1000 steps with 880 atoms
Performance: 83.682 ns/day, 0.287 hours/ns, 968.547 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0048 | 1.0048 | 1.0048 | 0.0 | 97.32
Neigh | 0.010752 | 0.010752 | 0.010752 | 0.0 | 1.04
Comm | 0.006344 | 0.006344 | 0.006344 | 0.0 | 0.61
Output | 0.000193 | 0.000193 | 0.000193 | 0.0 | 0.02
Modify | 0.00687 | 0.00687 | 0.00687 | 0.0 | 0.67
Other | | 0.003494 | | | 0.34
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1538.00 ave 1538 max 1538 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15860.0 ave 15860 max 15860 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15860
Ave neighs/atom = 18.022727
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:01

100
examples/USER/misc/tersoff_shift/log.31Dec20.hBN_no_shift.g++.4
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@ -1,100 +0,0 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
2 by 2 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.006 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.297 | 3.297 | 3.297 Mbytes
Step TotEng PotEng KinEng Temp
0 -6517.7517 -6551.8376 34.0859 300
100 -6517.5918 -6540.7795 23.187734 204.08204
200 -6517.5423 -6546.3342 28.791974 253.4066
300 -6517.547 -6552.0178 34.47074 303.38708
400 -6517.5499 -6554.1682 36.618359 322.28891
500 -6517.5482 -6553.3948 35.846598 315.49641
600 -6517.5438 -6557.8044 40.260609 354.34542
700 -6517.5489 -6554.8963 37.3474 328.70542
800 -6517.5426 -6557.376 39.833345 350.58494
900 -6517.5508 -6557.1115 39.560726 348.18554
1000 -6517.5427 -6559.2989 41.756142 367.50804
Loop time of 0.305524 on 4 procs for 1000 steps with 880 atoms
Performance: 282.792 ns/day, 0.085 hours/ns, 3273.060 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.25887 | 0.26645 | 0.2696 | 0.9 | 87.21
Neigh | 0.002987 | 0.0031222 | 0.003244 | 0.2 | 1.02
Comm | 0.026999 | 0.030267 | 0.037861 | 2.6 | 9.91
Output | 0.000102 | 0.0001325 | 0.000211 | 0.0 | 0.04
Modify | 0.002206 | 0.002269 | 0.002366 | 0.1 | 0.74
Other | | 0.003286 | | | 1.08
Nlocal: 220.000 ave 231 max 210 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 578.500 ave 590 max 572 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3965.00 ave 4169 max 3784 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 15860
Ave neighs/atom = 18.022727
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

100
examples/USER/misc/tersoff_shift/log.31Dec20.hBN_shift.g++.1
View File

@ -1,100 +0,0 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.003 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.0
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.545 | 3.545 | 3.545 Mbytes
Step TotEng PotEng KinEng Temp
0 -6517.7517 -6551.8376 34.0859 300
100 -6517.5918 -6540.7795 23.187734 204.08204
200 -6517.5423 -6546.3342 28.791974 253.4066
300 -6517.547 -6552.0178 34.47074 303.38708
400 -6517.5499 -6554.1682 36.618359 322.28891
500 -6517.5482 -6553.3948 35.846598 315.49641
600 -6517.5438 -6557.8044 40.260609 354.34542
700 -6517.5489 -6554.8963 37.3474 328.70542
800 -6517.5426 -6557.376 39.833345 350.58494
900 -6517.5508 -6557.1115 39.560726 348.18554
1000 -6517.5427 -6559.2989 41.756142 367.50804
Loop time of 1.18721 on 1 procs for 1000 steps with 880 atoms
Performance: 72.776 ns/day, 0.330 hours/ns, 842.310 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 | 1.1609 | 1.1609 | 1.1609 | 0.0 | 97.78
Neigh | 0.010489 | 0.010489 | 0.010489 | 0.0 | 0.88
Comm | 0.006158 | 0.006158 | 0.006158 | 0.0 | 0.52
Output | 0.000196 | 0.000196 | 0.000196 | 0.0 | 0.02
Modify | 0.00643 | 0.00643 | 0.00643 | 0.0 | 0.54
Other | | 0.003079 | | | 0.26
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1538.00 ave 1538 max 1538 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15860.0 ave 15860 max 15860 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15860
Ave neighs/atom = 18.022727
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:01

100
examples/USER/misc/tersoff_shift/log.31Dec20.hBN_shift.g++.4
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@ -1,100 +0,0 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
2 by 2 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.007 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.0
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.297 | 3.297 | 3.297 Mbytes
Step TotEng PotEng KinEng Temp
0 -6517.7517 -6551.8376 34.0859 300
100 -6517.5918 -6540.7795 23.187734 204.08204
200 -6517.5423 -6546.3342 28.791974 253.4066
300 -6517.547 -6552.0178 34.47074 303.38708
400 -6517.5499 -6554.1682 36.618359 322.28891
500 -6517.5482 -6553.3948 35.846598 315.49641
600 -6517.5438 -6557.8044 40.260609 354.34542
700 -6517.5489 -6554.8963 37.3474 328.70542
800 -6517.5426 -6557.376 39.833345 350.58494
900 -6517.5508 -6557.1115 39.560726 348.18554
1000 -6517.5427 -6559.2989 41.756142 367.50804
Loop time of 0.398907 on 4 procs for 1000 steps with 880 atoms
Performance: 216.592 ns/day, 0.111 hours/ns, 2506.850 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.32415 | 0.32873 | 0.33831 | 1.0 | 82.41
Neigh | 0.003216 | 0.0032905 | 0.003397 | 0.1 | 0.82
Comm | 0.050126 | 0.059974 | 0.064634 | 2.4 | 15.03
Output | 0.0001 | 0.000131 | 0.000221 | 0.0 | 0.03
Modify | 0.002423 | 0.0024955 | 0.002658 | 0.2 | 0.63
Other | | 0.004282 | | | 1.07
Nlocal: 220.000 ave 231 max 210 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 578.500 ave 590 max 572 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3965.00 ave 4169 max 3784 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 15860
Ave neighs/atom = 18.022727
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

99
examples/USER/misc/tersoff_shift/shift0.05_300K_after_change_corrected2.lmp
View File

@ -1,99 +0,0 @@
LAMMPS (30 Nov 2020)
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.008 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 4928459 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
Step TotEng PotEng KinEng Temp
0 -6570.525999324201 -6604.6118995607 34.0859002365 300
100 -6570.310828576854 -6584.788128201215 14.47729962436111 127.4189579026445
200 -6570.372315728006 -6587.981402302972 17.60908657496559 154.9827329140865
300 -6570.341402414298 -6587.005611017617 16.66420860331855 146.6665849019365
400 -6570.373381655082 -6587.812074340176 17.43869268509345 153.4830463396682
500 -6570.357279692746 -6587.139105628338 16.78182593559257 147.7017695218933
600 -6570.364533408488 -6588.19904338089 17.83450997240154 156.9667503160493
700 -6570.362000654085 -6587.514376495219 17.15237584113411 150.9630878644091
800 -6570.358394689029 -6587.200486866495 16.842092177466 148.232190383205
900 -6570.372035122417 -6588.096861613295 17.72482649087753 156.0013938422904
1000 -6570.355748883552 -6587.399428461644 17.04367957809142 150.0064201898998
Loop time of 1.44364 on 1 procs for 1000 steps with 880 atoms
Performance: 59.849 ns/day, 0.401 hours/ns, 692.693 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4138 | 1.4138 | 1.4138 | 0.0 | 97.93
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.010364 | 0.010364 | 0.010364 | 0.0 | 0.72
Output | 0.00061329 | 0.00061329 | 0.00061329 | 0.0 | 0.04
Modify | 0.011744 | 0.011744 | 0.011744 | 0.0 | 0.81
Other | | 0.007168 | | | 0.50
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1518.00 ave 1518 max 1518 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15840.0 ave 15840 max 15840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15840
Ave neighs/atom = 18.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

189
examples/USER/misc/tersoff_shift/shift0.05_300K_after_change_optimized.lmp
View File

@ -1,189 +0,0 @@
LAMMPS (30 Nov 2020)
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.005 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 4928459 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
Step TotEng PotEng KinEng Temp
0 -6570.525999324201 -6604.6118995607 34.0859002365 300
100 -6570.310828576854 -6584.788128201215 14.47729962436111 127.4189579026445
200 -6570.372315728006 -6587.981402302972 17.60908657496559 154.9827329140865
300 -6570.341402414298 -6587.005611017617 16.66420860331855 146.6665849019365
400 -6570.373381655082 -6587.812074340176 17.43869268509345 153.4830463396682
500 -6570.357279692746 -6587.139105628338 16.78182593559257 147.7017695218933
600 -6570.364533408488 -6588.19904338089 17.83450997240154 156.9667503160493
700 -6570.362000654085 -6587.514376495219 17.15237584113411 150.9630878644091
800 -6570.358394689029 -6587.200486866495 16.842092177466 148.232190383205
900 -6570.372035122417 -6588.096861613295 17.72482649087753 156.0013938422904
1000 -6570.355748883552 -6587.399428461644 17.04367957809142 150.0064201898998
1100 -6570.361365644219 -6587.907834467077 17.54646882285796 154.4316157218765
1200 -6570.361813996117 -6587.798045021229 17.43623102511208 153.4613805485555
1300 -6570.361628085057 -6588.170864228915 17.80923614385793 156.7443079422092
1400 -6570.356471561069 -6587.351733222872 16.99526166180266 149.580279915304
1500 -6570.36141372807 -6587.835844910846 17.47443118277596 153.7975913342367
1600 -6570.357696225688 -6587.619683012595 17.26198678690715 151.9278059297604
1700 -6570.34881238022 -6586.878985906404 16.53017352618356 145.4869028967231
1800 -6570.357028448558 -6587.381031274739 17.02400282618144 149.8332393282522
1900 -6570.359005417783 -6587.467319652452 17.1083142346686 150.5752887495863
2000 -6570.36091037262 -6586.982995798013 16.62208542539215 146.2958464649218
2100 -6570.354665996011 -6587.699965418245 17.34529942223466 152.6610648557338
2200 -6570.35819624477 -6587.5992298846 17.24103363983104 151.7433911400902
2300 -6570.360299283439 -6587.831629030664 17.47132974722501 153.7702946907909
2400 -6570.355286249777 -6587.431449500739 17.07616325096244 150.2923185171757
2500 -6570.356642607305 -6587.443603945456 17.08696133815104 150.3873556478985
2600 -6570.35526016161 -6587.016518357713 16.66125819610273 146.640617503141
2700 -6570.351798519564 -6587.688868062773 17.33706954320849 152.5886312778989
2800 -6570.374860360643 -6588.520382930915 18.14552257027169 159.704063360847
2900 -6570.35205092338 -6587.510378979472 17.15832805609137 151.0154750530938
3000 -6570.354046732308 -6587.046608472696 16.69256174038792 146.9161291727873
3100 -6570.358411403415 -6587.593087111401 17.23467570798547 151.6874331181386
3200 -6570.357587199112 -6587.115184729086 16.75759752997459 147.4885282216794
3300 -6570.358116221894 -6587.521832809624 17.16371658772983 151.0629010996503
3400 -6570.356540455745 -6587.758047495112 17.4015070393674 153.1557645709482
3500 -6570.360225765387 -6587.911628398988 17.55140263360139 154.475039636538
3600 -6570.356181541004 -6587.363918007856 17.00773646685256 149.690074331441
3700 -6570.35967466597 -6587.622428237049 17.26275357107865 151.9345546220306
3800 -6570.360685222803 -6587.537826596812 17.17714137400863 151.1810565790626
3900 -6570.35057732402 -6587.745007371039 17.39443004701849 153.0934778867197
4000 -6570.359488130042 -6587.443613189241 17.08412505919851 150.362392725404
4100 -6570.354004742672 -6587.017177531804 16.66317278913197 146.6574683976394
4200 -6570.353423800386 -6587.869177111406 17.51575331102021 154.1612794981773
4300 -6570.358994609919 -6588.112477475875 17.75348286595655 156.2536069997561
4400 -6570.357303158688 -6587.508847453375 17.15154429468683 150.9557691803652
4500 -6570.362938219268 -6588.385259101808 18.02232088253876 158.6197291914857
4600 -6570.359102404123 -6587.085078141023 16.72597573689907 147.2102155511371
4700 -6570.356110179577 -6587.183410342242 16.82730016266573 148.1020015247828
4800 -6570.35562680495 -6587.837727166148 17.48210036119904 153.8650900216986
4900 -6570.352338656291 -6587.386834120213 17.03449546392231 149.9255881088453
5000 -6570.367121347556 -6588.444950818433 18.0778294708762 159.1082765493577
5100 -6570.361382611042 -6587.534012491176 17.17262988013372 151.1413495989598
5200 -6570.359268581228 -6587.745372149951 17.38610356872261 153.0201941103948
5300 -6570.354331404702 -6587.217635519133 16.86330411443108 148.4188828585502
5400 -6570.356619490695 -6586.554472402563 16.19785291186736 142.5620517529032
5500 -6570.355672766053 -6587.041991570509 16.68631880445584 146.8611832635806
5600 -6570.353935359069 -6587.486943124099 17.13300776502998 150.7926237490146
5700 -6570.351180482215 -6587.00816576186 16.65698527964516 146.6030103128254
5800 -6570.355843895516 -6587.836380591459 17.4805366959429 153.851327745403
5900 -6570.364359099949 -6588.030179035721 17.66581993577153 155.4820598534864
6000 -6570.350300217592 -6586.7779334263 16.4276332087071 144.5844155037102
6100 -6570.353901655363 -6587.425845813611 17.07194415824805 150.2551850454018
6200 -6570.349898250398 -6587.021967423165 16.67206917276712 146.7357680779187
6300 -6570.362282461761 -6588.083887323363 17.72160486160278 155.9730393386477
6400 -6570.357979747159 -6587.813502869913 17.4555231227541 153.6311759552324
6500 -6570.352185004057 -6587.457490320936 17.10530531687892 150.5488063820783
6600 -6570.361772138931 -6588.330633729713 17.96886159078122 158.1492182935488
6700 -6570.357238585532 -6587.383530855699 17.02629227016666 149.8533893958989
6800 -6570.354156250069 -6587.400928228129 17.04677197806131 150.033637308548
6900 -6570.359839482358 -6587.644337698784 17.28449821642625 152.1259356200098
7000 -6570.355344713296 -6587.331255619772 16.97591090647551 149.4099682451452
7100 -6570.349282345109 -6587.312061369505 16.96277902439674 149.2943907014601
7200 -6570.365957425844 -6587.802519493792 17.43656206794697 153.464294153588
7300 -6570.356682488402 -6587.144183584986 16.78750109658476 147.7517182774152
7400 -6570.357774145175 -6587.338925099133 16.98115095395788 149.456087439117
7500 -6570.356850022339 -6587.714803897848 17.35795387550852 152.7724404085523
7600 -6570.357518819829 -6587.544880858974 17.18736203914436 151.2710116490312
7700 -6570.353015479423 -6587.491407643446 17.13839216402376 150.8400134229539
7800 -6570.357010766867 -6587.375086387927 17.01807562106018 149.7810722584655
7900 -6570.35737518473 -6587.456724581177 17.09934939644683 150.4963865804233
8000 -6570.355805415603 -6587.993548800505 17.63774338490175 155.2349498988573
8100 -6570.356028475375 -6587.745343882384 17.38931540700939 153.0484624406824
8200 -6570.362873461094 -6587.9246872152 17.56181375410575 154.5666709600364
8300 -6570.355161254283 -6587.524505801784 17.16934454750149 151.1124344233937
8400 -6570.354472314787 -6586.775210847252 16.42073853246494 144.5237334369818
8500 -6570.352373901433 -6587.234412112469 16.88203821103649 148.5837671345303
8600 -6570.356411536388 -6587.481263722403 17.12485218601496 150.7208441073584
8700 -6570.35677367573 -6587.511633765302 17.15486008957125 150.9849524631427
8800 -6570.361987596463 -6588.144322118942 17.78233452247868 156.5075388864478
8900 -6570.354866384156 -6587.404845623377 17.04997923922069 150.0618653541956
9000 -6570.359490031804 -6587.582952771737 17.22346273993308 151.5887444993146
9100 -6570.353390031263 -6587.183793899719 16.83040386845556 148.1293181492665
9200 -6570.360998438286 -6588.066914239206 17.70591580092016 155.8349553164529
9300 -6570.350073905195 -6587.350322038781 17.00024813358561 149.6241673152115
9400 -6570.365217495622 -6588.102982567933 17.7377650723109 156.1152700903308
9500 -6570.3484371035 -6587.046777075795 16.69833997229527 146.966985085648
9600 -6570.362189735035 -6587.552791505401 17.19060177036567 151.2995254732122
9700 -6570.363365059221 -6587.585852508567 17.22248744934615 151.5801606809601
9800 -6570.363766480248 -6588.408240091656 18.04447361140759 158.8147018521618
9900 -6570.352510004204 -6587.557869126676 17.20535912247233 151.4294092551067
10000 -6570.354530295501 -6587.569684149578 17.21515385407785 151.5156155592169
Loop time of 13.6615 on 1 procs for 10000 steps with 880 atoms
Performance: 63.244 ns/day, 0.379 hours/ns, 731.986 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.345 | 13.345 | 13.345 | 0.0 | 97.69
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.10801 | 0.10801 | 0.10801 | 0.0 | 0.79
Output | 0.0089688 | 0.0089688 | 0.0089688 | 0.0 | 0.07
Modify | 0.12259 | 0.12259 | 0.12259 | 0.0 | 0.90
Other | | 0.07648 | | | 0.56
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1518.00 ave 1518 max 1518 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15840.0 ave 15840 max 15840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15840
Ave neighs/atom = 18.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:13

189
examples/USER/misc/tersoff_shift/shift0.05_300K_before_change_long.lmp
View File

@ -1,189 +0,0 @@
LAMMPS (30 Nov 2020)
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.004 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 4928459 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
Step TotEng PotEng KinEng Temp
0 -6570.525999324201 -6604.6118995607 34.0859002365 300
100 -6570.310828576859 -6584.788128201219 14.47729962436133 127.4189579026464
200 -6570.372315728009 -6587.981402302975 17.60908657496529 154.9827329140839
300 -6570.341402414291 -6587.005611017611 16.66420860331987 146.6665849019482
400 -6570.373381655075 -6587.812074340168 17.43869268509273 153.4830463396618
500 -6570.357279692751 -6587.139105628346 16.78182593559452 147.7017695219105
600 -6570.364533408485 -6588.199043380885 17.83450997240024 156.9667503160379
700 -6570.36200065409 -6587.514376495224 17.15237584113493 150.9630878644163
800 -6570.358394688987 -6587.200486866453 16.8420921774656 148.2321903832015
900 -6570.372035122419 -6588.096861613297 17.72482649087754 156.0013938422906
1000 -6570.355748883598 -6587.399428461688 17.04367957809044 150.0064201898913
1100 -6570.361365644249 -6587.907834467105 17.54646882285712 154.4316157218691
1200 -6570.361813996135 -6587.798045021246 17.43623102511173 153.4613805485525
1300 -6570.361628085057 -6588.170864228916 17.80923614385877 156.7443079422166
1400 -6570.356471561063 -6587.351733222865 16.99526166180189 149.5802799152973
1500 -6570.361413728087 -6587.835844910863 17.47443118277618 153.7975913342386
1600 -6570.357696225701 -6587.619683012607 17.26198678690646 151.9278059297543
1700 -6570.348812380212 -6586.878985906395 16.53017352618314 145.4869028967195
1800 -6570.357028448588 -6587.38103127477 17.02400282618253 149.8332393282618
1900 -6570.359005417781 -6587.467319652451 17.1083142346694 150.5752887495933
2000 -6570.360910372626 -6586.982995798019 16.62208542539338 146.2958464649326
2100 -6570.354665996016 -6587.699965418249 17.34529942223363 152.6610648557247
2200 -6570.358196244768 -6587.599229884595 17.24103363982704 151.7433911400549
2300 -6570.360299283449 -6587.831629030676 17.47132974722745 153.7702946908123
2400 -6570.3552862498 -6587.431449500761 17.07616325096092 150.2923185171623
2500 -6570.356642607308 -6587.443603945459 17.08696133815061 150.3873556478947
2600 -6570.355260161621 -6587.016518357724 16.66125819610244 146.6406175031385
2700 -6570.351798519555 -6587.688868062763 17.33706954320784 152.5886312778933
2800 -6570.374860360645 -6588.520382930916 18.14552257027101 159.704063360841
2900 -6570.35205092336 -6587.510378979452 17.15832805609189 151.0154750530984
3000 -6570.354046732288 -6587.046608472678 16.69256174038983 146.9161291728041
3100 -6570.358411403405 -6587.59308711139 17.23467570798513 151.6874331181356
3200 -6570.357587199138 -6587.115184729113 16.75759752997486 147.4885282216817
3300 -6570.358116221875 -6587.521832809604 17.16371658772937 151.0629010996463
3400 -6570.356540455725 -6587.758047495098 17.40150703937349 153.1557645710017
3500 -6570.360225765383 -6587.911628398982 17.5514026335995 154.4750396365213
3600 -6570.356181541018 -6587.363918007874 17.00773646685577 149.6900743314693
3700 -6570.359674665961 -6587.622428237041 17.26275357108029 151.934554622045
3800 -6570.36068522278 -6587.537826596795 17.17714137401455 151.1810565791147
3900 -6570.35057732405 -6587.74500737107 17.39443004701957 153.0934778867292
4000 -6570.359488130031 -6587.443613189231 17.08412505920063 150.3623927254226
4100 -6570.354004742664 -6587.017177531799 16.66317278913412 146.6574683976584
4200 -6570.353423800372 -6587.869177111396 17.51575331102369 154.1612794982078
4300 -6570.358994609902 -6588.112477475862 17.75348286596034 156.2536069997894
4400 -6570.357303158663 -6587.508847453352 17.15154429468956 150.9557691803892
4500 -6570.362938219255 -6588.385259101793 18.02232088253793 158.6197291914784
4600 -6570.359102404124 -6587.085078141023 16.72597573689809 147.2102155511285
4700 -6570.356110179548 -6587.183410342215 16.82730016266803 148.1020015248031
4800 -6570.355626804948 -6587.837727166151 17.48210036120291 153.8650900217327
4900 -6570.352338656287 -6587.386834120214 17.03449546392803 149.9255881088957
5000 -6570.367121347545 -6588.444950818423 18.0778294708777 159.1082765493709
5100 -6570.361382611043 -6587.534012491175 17.17262988013209 151.1413495989456
5200 -6570.35926858121 -6587.745372149933 17.38610356872295 153.0201941103978
5300 -6570.354331404706 -6587.217635519139 16.86330411443332 148.41888285857
5400 -6570.356619490692 -6586.554472402558 16.19785291186641 142.5620517528948
5500 -6570.355672766049 -6587.041991570508 16.68631880445905 146.8611832636088
5600 -6570.353935359065 -6587.486943124098 17.13300776503303 150.7926237490415
5700 -6570.351180482223 -6587.008165761865 16.65698527964211 146.6030103127985
5800 -6570.355843895504 -6587.836380591454 17.48053669594962 153.8513277454621
5900 -6570.364359099945 -6588.030179035712 17.66581993576601 155.4820598534378
6000 -6570.350300217616 -6586.777933426324 16.4276332087085 144.5844155037225
6100 -6570.353901655382 -6587.425845813632 17.07194415824931 150.255185045413
6200 -6570.34989825042 -6587.021967423186 16.67206917276628 146.7357680779112
6300 -6570.362282461717 -6588.083887323323 17.72160486160671 155.9730393386823
6400 -6570.357979747161 -6587.813502869915 17.45552312275401 153.6311759552316
6500 -6570.352185004061 -6587.457490320935 17.10530531687417 150.5488063820365
6600 -6570.361772138939 -6588.330633729718 17.9688615907788 158.1492182935275
6700 -6570.35723858555 -6587.38353085572 17.02629227016985 149.853389395927
6800 -6570.354156250063 -6587.400928228118 17.04677197805407 150.0336373084843
6900 -6570.359839482354 -6587.644337698783 17.28449821642918 152.1259356200355
7000 -6570.355344713283 -6587.331255619759 16.97591090647605 149.40996824515
7100 -6570.349282345091 -6587.312061369486 16.96277902439603 149.2943907014538
7200 -6570.365957425851 -6587.802519493803 17.43656206795228 153.4642941536347
7300 -6570.356682488394 -6587.144183584973 16.78750109657942 147.7517182773682
7400 -6570.35777414521 -6587.338925099166 16.98115095395578 149.4560874390986
7500 -6570.356850022354 -6587.714803897856 17.3579538755024 152.7724404084984
7600 -6570.357518819848 -6587.544880858988 17.1873620391397 151.2710116489902
7700 -6570.353015479428 -6587.491407643447 17.1383921640193 150.8400134229147
7800 -6570.357010766854 -6587.375086387916 17.01807562106238 149.7810722584849
7900 -6570.357375184736 -6587.45672458118 17.09934939644311 150.4963865803907
8000 -6570.355805415644 -6587.993548800539 17.63774338489607 155.2349498988073
8100 -6570.356028475385 -6587.745343882396 17.38931540701103 153.0484624406968
8200 -6570.362873461087 -6587.92468721519 17.56181375410316 154.5666709600137
8300 -6570.355161254256 -6587.524505801754 17.16934454749879 151.1124344233699
8400 -6570.35447231479 -6586.775210847256 16.42073853246659 144.5237334369963
8500 -6570.352373901428 -6587.234412112466 16.88203821103806 148.5837671345441
8600 -6570.356411536407 -6587.481263722421 17.12485218601428 150.7208441073525
8700 -6570.356773675732 -6587.511633765302 17.15486008956931 150.9849524631256
8800 -6570.36198759649 -6588.144322118963 17.78233452247365 156.5075388864036
8900 -6570.354866384184 -6587.404845623407 17.0499792392233 150.0618653542186
9000 -6570.359490031817 -6587.58295277175 17.22346273993254 151.5887444993098
9100 -6570.353390031278 -6587.183793899733 16.83040386845595 148.1293181492699
9200 -6570.360998438297 -6588.066914239224 17.70591580092663 155.8349553165098
9300 -6570.350073905222 -6587.350322038807 17.00024813358495 149.6241673152057
9400 -6570.36521749562 -6588.102982567922 17.7377650723023 156.1152700902552
9500 -6570.348437103487 -6587.046777075785 16.69833997229794 146.9669850856715
9600 -6570.36218973505 -6587.552791505413 17.19060177036189 151.2995254731789
9700 -6570.363365059218 -6587.585852508567 17.22248744934841 151.58016068098
9800 -6570.363766480239 -6588.408240091641 18.04447361140224 158.8147018521146
9900 -6570.35251000423 -6587.557869126701 17.20535912247133 151.429409255098
10000 -6570.354530295514 -6587.569684149594 17.21515385407888 151.515615559226
Loop time of 13.7354 on 1 procs for 10000 steps with 880 atoms
Performance: 62.903 ns/day, 0.382 hours/ns, 728.045 timesteps/s
99.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.419 | 13.419 | 13.419 | 0.0 | 97.70
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.10876 | 0.10876 | 0.10876 | 0.0 | 0.79
Output | 0.0090306 | 0.0090306 | 0.0090306 | 0.0 | 0.07
Modify | 0.12319 | 0.12319 | 0.12319 | 0.0 | 0.90
Other | | 0.07528 | | | 0.55
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1518.00 ave 1518 max 1518 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15840.0 ave 15840 max 15840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15840
Ave neighs/atom = 18.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:13

189
examples/USER/misc/tersoff_shift/shift0_0K_after_change.lmp
View File

@ -1,189 +0,0 @@
LAMMPS (30 Nov 2020)
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.005 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.00
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
#velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
Step TotEng PotEng KinEng Temp
0 -6551.83758440293 -6551.83758440293 0 0
100 -6551.840380657681 -6552.044977305669 0.2045966479884039 1.800715074874129
200 -6551.841530763759 -6552.090075168948 0.2485444051890892 2.187512168943174
300 -6551.841665139357 -6552.078462099445 0.2367969600872313 2.084119460928863
400 -6551.841676603799 -6552.08034358658 0.2386669827813768 2.100578078842757
500 -6551.841509448263 -6552.056119528737 0.214610080474919 1.888846229548393
600 -6551.84142207987 -6552.093343113157 0.2519210332867522 2.217230862663171
700 -6551.841781375172 -6552.084992531813 0.2432111566407525 2.140572685068615
800 -6551.842091951669 -6552.081838526557 0.2397465748869133 2.110079885437677
900 -6551.841666912234 -6552.080304400616 0.2386374883815078 2.100318489983454
1000 -6551.840715616244 -6552.05728371738 0.2165681011355425 1.906079343361184
1100 -6551.842074126828 -6552.106004260123 0.2639301332949162 2.322926472209997
1200 -6551.842188603395 -6552.098297277812 0.2561086744172286 2.254087519827168
1300 -6551.841260308251 -6552.048152704549 0.2068923962986277 1.820920628733306
1400 -6551.842388324547 -6552.124269628291 0.2818813037440244 2.480919985579661
1500 -6551.841440278005 -6552.064748455734 0.2233081777285259 1.965400733257461
1600 -6551.8417543223 -6552.076279064868 0.2345247425673758 2.064121008453587
1700 -6551.841597438737 -6552.076569576668 0.2349721379309549 2.068058666198944
1800 -6551.842162898317 -6552.070358112199 0.2281952138816812 2.008412971038309
1900 -6551.84187033836 -6552.097949414831 0.2560790764696407 2.253827019614037
2000 -6551.84242954704 -6552.100561654162 0.2581321071230393 2.271896344224688
2100 -6551.842712691072 -6552.109703914991 0.2669912239185734 2.349868028123894
2200 -6551.842406987503 -6552.121813176925 0.2794061894218752 2.459135778869765
2300 -6551.841269625166 -6552.048494026282 0.2072244011164852 1.823842700459919
2400 -6551.842117146576 -6552.084812413302 0.2426952667257221 2.136032186697286
2500 -6551.841419956284 -6552.050012185658 0.208592229374837 1.83588135792997
2600 -6551.842346075463 -6552.105596047079 0.263249971615804 2.316940169887984
2700 -6551.842399232389 -6552.124147695869 0.281748463480716 2.479750819481185
2800 -6551.842119881001 -6552.085857478666 0.2437375976646823 2.145206046842344
2900 -6551.842771389507 -6552.134521205791 0.291749816284512 2.567775657326773
3000 -6551.842975253373 -6552.140179022041 0.2972037686681092 2.615777491038857
3100 -6551.843221488605 -6552.150979194405 0.3077577057997783 2.708665785539887
3200 -6551.841490626381 -6552.051081317435 0.2095906910548411 1.84466911186702
3300 -6551.840943019135 -6552.052447647754 0.2115046286187543 1.861514237423045
3400 -6551.841023714494 -6552.077249795139 0.2362260806460777 2.079094983618369
3500 -6551.841577153114 -6552.077968261821 0.236391108706599 2.080547443955719
3600 -6551.842252635392 -6552.086062007893 0.2438093725005731 2.145837758213258
3700 -6551.842253480576 -6552.103458348384 0.2612048678080091 2.298940611769186
3800 -6551.841299048828 -6552.058453975489 0.21715492666169 1.911244166840182
3900 -6551.842314033157 -6552.097157445554 0.2548434123970678 2.242951577885938
4000 -6551.841574891869 -6552.082093672056 0.2405187801868552 2.116876290648488
4100 -6551.842382579084 -6552.079615297427 0.2372327183428749 2.087954697075952
4200 -6551.841658347794 -6552.086081658687 0.2444233108932888 2.15124120997885
4300 -6551.841497991208 -6552.04942232197 0.2079243307627577 1.830002986455737
4400 -6551.842107941061 -6552.10024928027 0.2581413392090596 2.271977598520067
4500 -6551.8422545168 -6552.111086664895 0.2688321480959159 2.366070541461399
4600 -6551.841904346708 -6552.101873923228 0.2599695765197279 2.288068451024916
4700 -6551.841053059403 -6552.066907635815 0.2258545764122718 1.987812334530229
4800 -6551.841371115727 -6552.053505472334 0.2121343566070521 1.867056658047954
4900 -6551.841937984535 -6552.109592091871 0.2676541073373525 2.355702259411726
5000 -6551.840851981332 -6552.044390859077 0.2035388777453223 1.791405328887585
5100 -6551.841070214648 -6552.067367827813 0.2262976131654189 1.991711630867481
5200 -6551.841571466906 -6552.093712758334 0.2521412914275312 2.21916941912714
5300 -6551.841486906651 -6552.072873466473 0.2313865598219879 2.036500942177379
5400 -6551.843256267483 -6552.145005653151 0.3017493856685349 2.655784798772142
5500 -6551.84270158117 -6552.134517274862 0.2918156936907907 2.568355463690886
5600 -6551.84163985875 -6552.056711349013 0.2150714902632286 1.892907232354023
5700 -6551.840381085197 -6552.022179207645 0.1817981224477595 1.600058568379124
5800 -6551.84149868601 -6552.080251188141 0.2387525021317378 2.101330759714621
5900 -6551.841216854843 -6552.0591162927 0.2178994378571792 1.917796828119392
6000 -6551.84110540275 -6552.060295375414 0.219189972664102 1.929155203265438
6100 -6551.841467351862 -6552.058791306032 0.2173239541699279 1.912731827489293
6200 -6551.841806857639 -6552.096852253635 0.255045395995332 2.244729294744194
6300 -6551.841325410201 -6552.081736713376 0.2404113031749354 2.115930353960526
6400 -6551.842446147665 -6552.103937221988 0.2614910743220556 2.30145959919854
6500 -6551.841597832866 -6552.080016016779 0.238418183913426 2.098388327072454
6600 -6551.840665386509 -6552.039901358558 0.1992359720502438 1.753534194501607
6700 -6551.841124220146 -6552.070638049088 0.2295138289419996 2.020018488725998
6800 -6551.841838744499 -6552.088979374696 0.2471406301962878 2.175157133725724
6900 -6551.841772926266 -6552.088344114766 0.2465711885006183 2.1701453104347
7000 -6551.84156512443 -6552.098852551235 0.2572874268055971 2.264462065139365
7100 -6551.842478978843 -6552.107722805476 0.265243826633506 2.334488672381989
7200 -6551.841537901573 -6552.094268243856 0.2527303422832519 2.22435382838405
7300 -6551.841978201499 -6552.098139567791 0.2561613662916175 2.254551276459881
7400 -6551.842490520111 -6552.108093934785 0.2656034146743838 2.337653512140213
7500 -6551.841813216483 -6552.0731438128 0.2313305963161162 2.036008390956932
7600 -6551.841416054815 -6552.07249289806 0.2310768432453098 2.03377503579501
7700 -6551.84270195916 -6552.135183767966 0.2924818088062866 2.574218138088869
7800 -6551.842416886451 -6552.114877572559 0.2724606861074197 2.398006368178555
7900 -6551.842013616702 -6552.083631656249 0.2416180395465499 2.126551194512558
8000 -6551.841352982264 -6552.048052020459 0.2066990381952127 1.819218827383714
8100 -6551.842271877219 -6552.119901127442 0.277629250222883 2.443496416083425
8200 -6551.841218957631 -6552.054157401546 0.2129384439153412 1.874133666160194
8300 -6551.841581833686 -6552.076372929738 0.2347910960514888 2.066465263546733
8400 -6551.841448567779 -6552.06355122901 0.2221026612302909 1.954790629168639
8500 -6551.840423567605 -6552.04780826226 0.2073846946551181 1.825253490882241
8600 -6551.841747604018 -6552.097807093885 0.2560594898680117 2.25365463219144
8700 -6551.843382701345 -6552.16148330718 0.3181006058349412 2.799696680690669
8800 -6551.843079858301 -6552.134975688002 0.2918958297006768 2.569060764205146
8900 -6551.842041173826 -6552.090533622544 0.2484924487182639 2.187054884812802
9000 -6551.841666657881 -6552.124145601612 0.2824789437309745 2.486179990298357
9100 -6551.841718135492 -6552.069395244891 0.2276771093996659 2.003852981613762
9200 -6551.842077607607 -6552.082979717109 0.2409021095014363 2.120250084316146
9300 -6551.842138891938 -6552.099457878667 0.257318986728701 2.264739833274149
9400 -6551.842439500782 -6552.134922812212 0.2924833114297478 2.574231363118433
9500 -6551.841065245899 -6552.07399886701 0.2329336211114915 2.050117082095376
9600 -6551.842249869504 -6552.08790605379 0.2456561842850767 2.162092090107294
9700 -6551.842315222852 -6552.104235020752 0.2619197978998719 2.305232921083908
9800 -6551.842195410218 -6552.108615477006 0.2664200667886112 2.344841106792793
9900 -6551.841488257895 -6552.075829625207 0.234341367311278 2.062507069069629
10000 -6551.841363981865 -6552.056912781978 0.2155488001135793 1.897108176266659
Loop time of 15.4494 on 1 procs for 10000 steps with 880 atoms
Performance: 55.924 ns/day, 0.429 hours/ns, 647.273 timesteps/s
99.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.071 | 15.071 | 15.071 | 0.0 | 97.55
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.11306 | 0.11306 | 0.11306 | 0.0 | 0.73
Output | 0.057197 | 0.057197 | 0.057197 | 0.0 | 0.37
Modify | 0.12765 | 0.12765 | 0.12765 | 0.0 | 0.83
Other | | 0.08016 | | | 0.52
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1518.00 ave 1518 max 1518 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15840.0 ave 15840 max 15840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15840
Ave neighs/atom = 18.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:15

189
examples/USER/misc/tersoff_shift/shift0_0K_before_change.lmp
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@ -1,189 +0,0 @@
LAMMPS (30 Nov 2020)
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.010 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.00
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
#velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
Step TotEng PotEng KinEng Temp
0 -6551.83758440293 -6551.83758440293 0 0
100 -6551.840380657675 -6552.044977305663 0.2045966479885492 1.800715074875407
200 -6551.841530763754 -6552.090075168943 0.248544405189058 2.187512168942899
300 -6551.841665139352 -6552.078462099439 0.2367969600871777 2.084119460928391
400 -6551.841676603811 -6552.080343586593 0.2386669827815819 2.100578078844562
500 -6551.841509448283 -6552.056119528758 0.2146100804749217 1.888846229548417
600 -6551.841422079857 -6552.093343113143 0.2519210332866499 2.21723086266227
700 -6551.841781375156 -6552.084992531796 0.2432111566407268 2.140572685068389
800 -6551.842091951654 -6552.081838526541 0.239746574886935 2.110079885437867
900 -6551.84166691225 -6552.080304400632 0.238637488381806 2.100318489986079
1000 -6551.840715616278 -6552.057283717414 0.2165681011355479 1.906079343361231
1100 -6551.842074126798 -6552.106004260093 0.2639301332949472 2.322926472210271
1200 -6551.842188603373 -6552.09829727779 0.2561086744169245 2.254087519824492
1300 -6551.841260308244 -6552.048152704542 0.2068923962981048 1.820920628728703
1400 -6551.842388324547 -6552.124269628291 0.281881303743822 2.480919985577879
1500 -6551.841440278005 -6552.064748455734 0.223308177728463 1.965400733256908
1600 -6551.841754322276 -6552.076279064843 0.2345247425674623 2.064121008454348
1700 -6551.841597438728 -6552.076569576659 0.234972137931356 2.068058666202475
1800 -6551.842162898327 -6552.070358112208 0.2281952138814133 2.008412971035951
1900 -6551.841870338358 -6552.097949414828 0.256079076469683 2.25382701961441
2000 -6551.842429547002 -6552.100561654125 0.2581321071226317 2.271896344221101
2100 -6551.842712691104 -6552.109703915022 0.2669912239183665 2.349868028122073
2200 -6551.842406987498 -6552.12181317692 0.2794061894219664 2.459135778870568
2300 -6551.84126962517 -6552.048494026286 0.2072244011164842 1.82384270045991
2400 -6551.842117146578 -6552.084812413304 0.2426952667259989 2.136032186699723
2500 -6551.841419956272 -6552.050012185648 0.2085922293750494 1.835881357931839
2600 -6551.842346075456 -6552.105596047072 0.2632499716163478 2.316940169892771
2700 -6551.842399232399 -6552.12414769588 0.2817484634815423 2.479750819488458
2800 -6551.842119881037 -6552.085857478702 0.2437375976644999 2.145206046840739
2900 -6551.842771389523 -6552.134521205808 0.2917498162843085 2.567775657324982
3000 -6551.842975253355 -6552.140179022022 0.2972037686674449 2.615777491033011
3100 -6551.843221488635 -6552.150979194435 0.3077577057991795 2.708665785534617
3200 -6551.841490626377 -6552.051081317432 0.2095906910551273 1.844669111869539
3300 -6551.840943019134 -6552.052447647752 0.2115046286183096 1.861514237419131
3400 -6551.841023714474 -6552.077249795121 0.2362260806464103 2.079094983621296
3500 -6551.841577153113 -6552.077968261819 0.2363911087072423 2.080547443961381
3600 -6551.842252635407 -6552.086062007908 0.243809372501 2.145837758217015
3700 -6551.842253480545 -6552.103458348352 0.2612048678077153 2.2989406117666
3800 -6551.841299048841 -6552.058453975504 0.217154926662102 1.911244166843808
3900 -6551.842314033152 -6552.09715744555 0.2548434123974149 2.242951577888993
4000 -6551.841574891866 -6552.082093672053 0.240518780186816 2.116876290648143
4100 -6551.842382579098 -6552.07961529744 0.2372327183423541 2.087954697071368
4200 -6551.841658347791 -6552.086081658685 0.2444233108935672 2.151241209981301
4300 -6551.841497991205 -6552.049422321968 0.2079243307627966 1.830002986456079
4400 -6551.842107941071 -6552.100249280281 0.258141339210149 2.271977598529656
4500 -6551.842254516814 -6552.111086664911 0.2688321480965075 2.366070541466605
4600 -6551.841904346704 -6552.101873923224 0.2599695765198525 2.288068451026013
4700 -6551.841053059394 -6552.066907635806 0.2258545764124127 1.987812334531469
4800 -6551.841371115715 -6552.053505472321 0.2121343566071444 1.867056658048765
4900 -6551.841937984542 -6552.10959209188 0.2676541073377136 2.355702259414904
5000 -6551.840851981356 -6552.044390859101 0.2035388777453816 1.791405328888107
5100 -6551.84107021463 -6552.067367827796 0.2262976131661503 1.991711630873918
5200 -6551.841571466929 -6552.093712758357 0.2521412914275926 2.219169419127681
5300 -6551.841486906684 -6552.072873466504 0.2313865598208315 2.0365009421672
5400 -6551.843256267489 -6552.145005653157 0.301749385667876 2.655784798766343
5500 -6551.842701581178 -6552.134517274868 0.2918156936899855 2.568355463683798
5600 -6551.841639858768 -6552.05671134903 0.2150714902622646 1.89290723234554
5700 -6551.840381085204 -6552.022179207651 0.1817981224471618 1.600058568373864
5800 -6551.84149868602 -6552.080251188151 0.2387525021313672 2.10133075971136
5900 -6551.841216854823 -6552.059116292681 0.2178994378578295 1.917796828125116
6000 -6551.841105402759 -6552.060295375423 0.2191899726639463 1.929155203264068
6100 -6551.841467351845 -6552.058791306014 0.2173239541699141 1.912731827489171
6200 -6551.84180685766 -6552.096852253655 0.2550453959949585 2.244729294740907
6300 -6551.841325410204 -6552.081736713378 0.2404113031737515 2.115930353950106
6400 -6551.842446147646 -6552.103937221967 0.2614910743216328 2.301459599194818
6500 -6551.841597832877 -6552.08001601679 0.2384181839130139 2.098388327068827
6600 -6551.840665386511 -6552.03990135856 0.1992359720486526 1.753534194487602
6700 -6551.841124220147 -6552.070638049088 0.2295138289412654 2.020018488719537
6800 -6551.84183874451 -6552.088979374706 0.2471406301954893 2.175157133718697
6900 -6551.841772926283 -6552.088344114783 0.2465711885001868 2.170145310430902
7000 -6551.841565124399 -6552.098852551203 0.2572874268047295 2.264462065131728
7100 -6551.842478978844 -6552.107722805476 0.2652438266325029 2.33448867237316
7200 -6551.841537901552 -6552.094268243835 0.2527303422828399 2.224353828380424
7300 -6551.841978201506 -6552.098139567796 0.2561613662905221 2.254551276450241
7400 -6551.842490520123 -6552.108093934797 0.2656034146740798 2.337653512137538
7500 -6551.841813216477 -6552.073143812793 0.2313305963159736 2.036008390955676
7600 -6551.841416054795 -6552.072492898041 0.2310768432451864 2.033775035793925
7700 -6551.842701959146 -6552.135183767952 0.2924818088060412 2.57421813808671
7800 -6551.842416886457 -6552.114877572564 0.2724606861073949 2.398006368178336
7900 -6551.842013616739 -6552.083631656285 0.2416180395461416 2.126551194508965
8000 -6551.841352982271 -6552.048052020466 0.2066990381941355 1.819218827374234
8100 -6551.842271877225 -6552.119901127448 0.277629250222223 2.443496416077616
8200 -6551.841218957637 -6552.054157401552 0.21293844391568 1.874133666163176
8300 -6551.841581833704 -6552.076372929756 0.2347910960513656 2.066465263545649
8400 -6551.841448567787 -6552.063551229018 0.2221026612311725 1.954790629176398
8500 -6551.840423567618 -6552.047808262273 0.207384694655468 1.825253490885321
8600 -6551.841747604003 -6552.097807093872 0.2560594898684815 2.253654632195575
8700 -6551.84338270136 -6552.161483307194 0.3181006058341286 2.799696680683518
8800 -6551.84307985832 -6552.13497568802 0.2918958296999429 2.569060764198686
8900 -6551.842041173815 -6552.090533622533 0.248492448717636 2.187054884807275
9000 -6551.841666657886 -6552.124145601616 0.2824789437295646 2.486179990285949
9100 -6551.841718135503 -6552.069395244903 0.2276771093994469 2.003852981611835
9200 -6551.842077607612 -6552.082979717114 0.2409021095020737 2.120250084321757
9300 -6551.842138891918 -6552.099457878646 0.2573189867283065 2.264739833270677
9400 -6551.84243950078 -6552.134922812209 0.2924833114292827 2.574231363114341
9500 -6551.84106524592 -6552.07399886703 0.2329336211107529 2.050117082088875
9600 -6551.84224986949 -6552.087906053775 0.2456561842848073 2.162092090104924
9700 -6551.842315222883 -6552.104235020783 0.2619197978994303 2.305232921080021
9800 -6551.842195410193 -6552.108615476982 0.2664200667882263 2.344841106789405
9900 -6551.841488257887 -6552.075829625198 0.2343413673108504 2.062507069065866
10000 -6551.84136398189 -6552.056912782002 0.2155488001116745 1.897108176249894
Loop time of 14.1489 on 1 procs for 10000 steps with 880 atoms
Performance: 61.065 ns/day, 0.393 hours/ns, 706.767 timesteps/s
99.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.799 | 13.799 | 13.799 | 0.0 | 97.53
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.12306 | 0.12306 | 0.12306 | 0.0 | 0.87
Output | 0.0091433 | 0.0091433 | 0.0091433 | 0.0 | 0.06
Modify | 0.13304 | 0.13304 | 0.13304 | 0.0 | 0.94
Other | | 0.08424 | | | 0.60
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1518.00 ave 1518 max 1518 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15840.0 ave 15840 max 15840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15840
Ave neighs/atom = 18.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:14

189
examples/USER/misc/tersoff_shift/shift0_300K_after_change.lmp
View File

@ -1,189 +0,0 @@
LAMMPS (30 Nov 2020)
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.008 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.00
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
Step TotEng PotEng KinEng Temp
0 -6517.75168416643 -6551.83758440293 34.08590023649997 299.9999999999998
100 -6517.591757868635 -6540.779491471579 23.18773360294392 204.0820407446414
200 -6517.542257518233 -6546.334231680467 28.79197416223492 253.4066047468253
300 -6517.547026665019 -6552.017766231997 34.47073956697721 303.3870837602092
400 -6517.549880169609 -6554.168239147238 36.61835897762826 322.2889117514031
500 -6517.548226470739 -6553.394824124983 35.84659765424357 315.4964141084193
600 -6517.543822188257 -6557.804430840637 40.26060865238051 354.3454188362772
700 -6517.548850551941 -6554.896250559415 37.34740000747415 328.7054155678276
800 -6517.542638411757 -6557.375983041433 39.83334462967532 350.5849429232983
900 -6517.55075885843 -6557.111484488137 39.56072562970743 348.1855431884253
1000 -6517.54273795102 -6559.298879744795 41.75614179377518 367.5080444176888
1100 -6517.549343783575 -6560.886093997487 43.33675021391144 381.4194424664666
1200 -6517.542423332176 -6558.676768888114 41.13434555593687 362.0354334537062
1300 -6517.545344075701 -6561.204696269845 43.65935219414447 384.258757062778
1400 -6517.550486308486 -6559.652130027128 42.10164371864144 370.5489081396594
1500 -6517.547348144133 -6560.675578342398 43.12823019826496 379.5841966827288
1600 -6517.543563176833 -6558.851478162317 41.30791498548372 363.5630688836865
1700 -6517.542623115538 -6561.609360337041 44.06673722150263 387.8442721103335
1800 -6517.554833588377 -6561.212435833928 43.65760224555111 384.2433552522239
1900 -6517.549071422489 -6560.38241286512 42.83334144263117 376.9887943000331
2000 -6517.545980266263 -6557.338387626354 39.79240736009128 350.2246420132446
2100 -6517.554095104669 -6559.87721259204 42.32311748737136 372.4981637015772
2200 -6517.541910494127 -6557.900141553543 40.35823105941543 355.2046222578467
2300 -6517.543741229654 -6555.791430728012 38.24768949835712 336.629127290004
2400 -6517.555255788205 -6560.723935042218 43.16867925401336 379.940200679699
2500 -6517.555074792246 -6557.544526593844 39.98945180159846 351.9588879050065
2600 -6517.549903118179 -6557.918564784741 40.3686616665621 355.2964250889964
2700 -6517.539742897031 -6557.945682615683 40.40593971865226 355.6245201532153
2800 -6517.547251676093 -6556.865915617517 39.31866394142421 346.0550873113292
2900 -6517.545299736506 -6559.862692054109 42.31739231760382 372.4477748041638
3000 -6517.55560248467 -6560.792536373287 43.23693388861683 380.5409297271634
3100 -6517.552205940511 -6558.067955972071 40.51575003156001 356.590992907162
3200 -6517.552750237322 -6559.663276613887 42.11052637656611 370.627087015937
3300 -6517.556463580721 -6559.886913646993 42.33045006627206 372.5626998779712
3400 -6517.553240930869 -6559.759847990668 42.20660705979942 371.4727212743841
3500 -6517.548452643367 -6558.30850296424 40.76005032087284 358.7411513681483
3600 -6517.554196218421 -6559.440190093303 41.88599387488308 368.6509106486549
3700 -6517.55327428666 -6559.20140683827 41.64813255160946 366.5574234153127
3800 -6517.553265790113 -6559.320999047847 41.76773325773447 367.6100642899428
3900 -6517.557526995435 -6558.935061683234 41.37753468779878 364.1758122922397
4000 -6517.555340791266 -6559.073176508879 41.51783571761353 365.4106427838033
4100 -6517.553854213419 -6558.263385298808 40.70953108538969 358.2965167673373
4200 -6517.553680788039 -6558.14054442872 40.58686364068086 357.2168846274402
4300 -6517.558042018571 -6556.578721922002 39.02067990343117 343.4324424412317
4400 -6517.563739283292 -6558.500306214708 40.93656693141579 360.2947258020188
4500 -6517.547020963956 -6555.377454255585 37.83043329162872 332.9567330991509
4600 -6517.548172986324 -6558.772744519205 41.22457153288104 362.8295387258405
4700 -6517.558584079818 -6557.969788651196 40.41120457137863 355.6708576654109
4800 -6517.559372552759 -6557.310265979464 39.75089342670537 349.8592657160261
4900 -6517.55923597315 -6558.176827172919 40.61759119976872 357.4873268825193
5000 -6517.56212653515 -6557.374748952199 39.81262241704939 350.4025606554209
5100 -6517.555552632631 -6557.497202980329 39.94165034769875 351.5381732966079
5200 -6517.561569541295 -6558.157238110723 40.59566856942829 357.2943793864433
5300 -6517.564502194116 -6558.421999422868 40.85749722875147 359.5988101701971
5400 -6517.556534594537 -6557.267621790594 39.71108719605641 349.5089194111953
5500 -6517.563877256539 -6557.142752156087 39.57887489954838 348.345280232614
5600 -6517.56686938866 -6557.809180900105 40.24231151144559 354.1843803352434
5700 -6517.558039039658 -6559.133111388302 41.57507234864435 365.9143991519822
5800 -6517.555738279771 -6557.908663173967 40.35292489419648 355.1579211422933
5900 -6517.561084510689 -6557.042738405876 39.4816538951864 347.4896096736371
6000 -6517.55801940098 -6557.892645435926 40.33462603494598 354.9968675178603
6100 -6517.564254724593 -6558.224594979722 40.66034025512962 357.8635738503061
6200 -6517.560641752437 -6558.21020654546 40.64956479302306 357.7687358495627
6300 -6517.566017136221 -6559.578738119577 42.01272098335624 369.7662730794008
6400 -6517.556093448701 -6556.104820300268 38.54872685156678 339.2786452823787
6500 -6517.560982934479 -6557.084136152714 39.52315321823437 347.8548573809885
6600 -6517.564245932257 -6558.046609845879 40.48236391362233 356.2971518963097
6700 -6517.566290721775 -6557.727671715245 40.16138099347028 353.472087122386
6800 -6517.570284071772 -6557.990328296512 40.42004422474062 355.748658045926
6900 -6517.565184634684 -6556.035668256965 38.47048362228119 338.5900036850376
7000 -6517.559098587035 -6555.986507687455 38.42740910041999 338.2108921911735
7100 -6517.558005558503 -6556.912239013785 39.35423345528209 346.3681450297208
7200 -6517.571145809251 -6556.350273356944 38.77912754769311 341.3064693491723
7300 -6517.561021218117 -6556.99807608988 39.43705487176288 347.0970805946272
7400 -6517.564526723936 -6556.561549105003 38.99702238106649 343.22422565188
7500 -6517.573591127068 -6559.064299272126 41.49070814505833 365.1718850655065
7600 -6517.560285401078 -6556.032090011901 38.47180461082385 338.6016300924391
7700 -6517.560367395816 -6556.511797795351 38.95143039953437 342.8229572574783
7800 -6517.573020066369 -6556.924913541821 39.35189347545233 346.347550181292
7900 -6517.566299833051 -6556.577995911533 39.01169607848268 343.3533731643211
8000 -6517.570136763681 -6557.582657078253 40.01252031457137 352.1619206500376
8100 -6517.575674117457 -6558.320029386858 40.74435526940069 358.6030146192588
8200 -6517.571493793849 -6558.305152064342 40.73365827049295 358.5088671961291
8300 -6517.5784508572 -6559.057530922976 41.47908006577681 365.0695429310681
8400 -6517.571529794804 -6556.983706108324 39.41217631352003 346.8781171105746
8500 -6517.573679430778 -6558.010837981697 40.4371585509185 355.8992862475501
8600 -6517.569221385932 -6557.925020755149 40.35579936921761 355.1832202395844
8700 -6517.577852436772 -6557.081904802895 39.50405236612336 347.6867451822922
8800 -6517.580643488045 -6557.09464429535 39.514000807305 347.7743043294406
8900 -6517.578100930365 -6556.390740011451 38.81263908108628 341.601414178213
9000 -6517.580194960002 -6559.786353631432 42.20615867143003 371.4687748769035
9100 -6517.564119644257 -6558.263714946205 40.69959530194826 358.209069024671
9200 -6517.569716055186 -6557.301587884572 39.73187182938527 349.6918510619774
9300 -6517.57904099131 -6558.208366761209 40.62932576989919 357.5906062741362
9400 -6517.579849744588 -6556.949796893357 39.3699471487698 346.5064458524541
9500 -6517.573257994172 -6556.659853832866 39.0865958386938 344.0125879102258
9600 -6517.571031994579 -6556.369911317095 38.79887932251565 341.4803105094658
9700 -6517.574140115361 -6556.924661161591 39.35052104622968 346.3354710293865
9800 -6517.580185525737 -6557.018312552581 39.43812702684369 347.1065169457875
9900 -6517.573201214946 -6558.960816834054 41.3876156191084 364.2645375238429
10000 -6517.575226749958 -6558.46352748641 40.88830073645191 359.8699208712792
Loop time of 15.95 on 1 procs for 10000 steps with 880 atoms
Performance: 54.169 ns/day, 0.443 hours/ns, 626.959 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.508 | 15.508 | 15.508 | 0.0 | 97.23
Neigh | 0.12432 | 0.12432 | 0.12432 | 0.0 | 0.78
Comm | 0.11079 | 0.11079 | 0.11079 | 0.0 | 0.69
Output | 0.0090941 | 0.0090941 | 0.0090941 | 0.0 | 0.06
Modify | 0.12027 | 0.12027 | 0.12027 | 0.0 | 0.75
Other | | 0.07801 | | | 0.49
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1569.00 ave 1569 max 1569 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15844.0 ave 15844 max 15844 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15844
Ave neighs/atom = 18.004545
Neighbor list builds = 140
Dangerous builds = 0
Total wall time: 0:00:15

189
examples/USER/misc/tersoff_shift/shift0_300K_before_change.lmp
View File

@ -1,189 +0,0 @@
LAMMPS (30 Nov 2020)
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.006 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.00
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
Step TotEng PotEng KinEng Temp
0 -6517.75168416643 -6551.83758440293 34.08590023649997 299.9999999999998
100 -6517.591757868622 -6540.779491471567 23.18773360294435 204.0820407446452
200 -6517.542257518257 -6546.334231680492 28.79197416223515 253.4066047468274
300 -6517.547026665021 -6552.017766231997 34.47073956697689 303.3870837602065
400 -6517.549880169579 -6554.168239147207 36.61835897762799 322.2889117514007
500 -6517.548226470746 -6553.39482412499 35.84659765424382 315.4964141084214
600 -6517.543822188248 -6557.804430840627 40.26060865237962 354.3454188362694
700 -6517.548850551941 -6554.896250559414 37.3474000074727 328.7054155678148
800 -6517.542638411725 -6557.375983041402 39.83334462967638 350.5849429233077
900 -6517.550758858447 -6557.111484488154 39.56072562970709 348.1855431884223
1000 -6517.542737951017 -6559.298879744794 41.75614179377674 367.5080444177026
1100 -6517.549343783598 -6560.886093997509 43.33675021391137 381.4194424664659
1200 -6517.542423332162 -6558.6767688881 41.13434555593789 362.0354334537151
1300 -6517.545344075698 -6561.204696269845 43.65935219414683 384.2587570627988
1400 -6517.550486308489 -6559.652130027135 42.10164371864627 370.5489081397019
1500 -6517.547348144104 -6560.675578342373 43.1282301982695 379.5841966827687
1600 -6517.543563176821 -6558.851478162307 41.30791498548552 363.5630688837024
1700 -6517.542623115535 -6561.609360337039 44.06673722150416 387.844272110347
1800 -6517.554833588375 -6561.212435833932 43.65760224555682 384.2433552522742
1900 -6517.549071422476 -6560.382412865106 42.8333414426301 376.9887943000238
2000 -6517.545980266264 -6557.338387626362 39.79240736009847 350.224642013308
2100 -6517.55409510466 -6559.877212592028 42.32311748736821 372.4981637015495
2200 -6517.54191049412 -6557.900141553538 40.35823105941725 355.2046222578627
2300 -6517.543741229661 -6555.791430728022 38.24768949835975 336.6291272900272
2400 -6517.555255788197 -6560.72393504221 43.16867925401299 379.9402006796957
2500 -6517.555074792231 -6557.544526593826 39.98945180159508 351.9588879049767
2600 -6517.549903118182 -6557.918564784744 40.36866166656313 355.2964250890056
2700 -6517.539742897041 -6557.945682615691 40.40593971865029 355.6245201531979
2800 -6517.547251676129 -6556.865915617547 39.31866394141809 346.0550873112753
2900 -6517.545299736508 -6559.862692054113 42.31739231760414 372.4477748041666
3000 -6517.555602484665 -6560.792536373278 43.23693388861345 380.5409297271336
3100 -6517.552205940496 -6558.067955972054 40.5157500315583 356.5909929071469
3200 -6517.552750237331 -6559.663276613898 42.11052637656773 370.6270870159512
3300 -6517.556463580696 -6559.886913646974 42.33045006627805 372.562699878024
3400 -6517.553240930844 -6559.759847990644 42.20660705979918 371.472721274382
3500 -6517.548452643353 -6558.308502964229 40.76005032087603 358.7411513681764
3600 -6517.554196218422 -6559.440190093313 41.8859938748904 368.6509106487193
3700 -6517.553274286671 -6559.20140683828 41.64813255160929 366.5574234153112
3800 -6517.553265790101 -6559.320999047843 41.76773325774131 367.6100642900029
3900 -6517.557526995423 -6558.935061683234 41.37753468781062 364.1758122923439
4000 -6517.555340791244 -6559.073176508857 41.51783571761244 365.4106427837937
4100 -6517.553854213401 -6558.263385298786 40.70953108538485 358.2965167672946
4200 -6517.553680788023 -6558.140544428711 40.58686364068885 357.2168846275105
4300 -6517.558042018573 -6556.578721921986 39.02067990341268 343.432442441069
4400 -6517.56373928329 -6558.500306214699 40.93656693140823 360.2947258019523
4500 -6517.547020963972 -6555.377454255587 37.83043329161494 332.9567330990297
4600 -6517.548172986329 -6558.772744519233 41.22457153290485 362.8295387260501
4700 -6517.558584079801 -6557.969788651188 40.4112045713863 355.6708576654784
4800 -6517.559372552775 -6557.310265979471 39.75089342669602 349.8592657159439
4900 -6517.559235973134 -6558.176827172923 40.61759119978924 357.4873268826998
5000 -6517.562126535125 -6557.374748952165 39.81262241704019 350.4025606553399
5100 -6517.555552632606 -6557.497202980321 39.94165034771533 351.5381732967538
5200 -6517.561569541294 -6558.157238110736 40.59566856944173 357.2943793865616
5300 -6517.564502194113 -6558.421999422829 40.85749722871626 359.5988101698873
5400 -6517.556534594508 -6557.267621790531 39.71108719602345 349.5089194109053
5500 -6517.563877256513 -6557.142752156086 39.57887489957356 348.3452802328355
5600 -6517.56686938865 -6557.809180900078 40.24231151142835 354.1843803350916
5700 -6517.558039039658 -6559.13311138836 41.57507234870165 365.9143991524865
5800 -6517.55573827974 -6557.908663173943 40.35292489420301 355.1579211423508
5900 -6517.561084510683 -6557.04273840589 39.4816538952069 347.4896096738175
6000 -6517.558019400977 -6557.89264543582 40.33462603484248 354.9968675169494
6100 -6517.564254724565 -6558.224594979706 40.66034025514109 357.8635738504071
6200 -6517.56064175244 -6558.210206545396 40.64956479295609 357.7687358489734
6300 -6517.566017136228 -6559.57873811963 42.01272098340136 369.7662730797979
6400 -6517.556093448677 -6556.104820300296 38.54872685161884 339.2786452828369
6500 -6517.560982934513 -6557.084136152808 39.52315321829535 347.8548573815252
6600 -6517.564245932242 -6558.046609846089 40.48236391384803 356.2971518982962
6700 -6517.566290721787 -6557.727671715357 40.1613809935705 353.472087123268
6800 -6517.570284071749 -6557.99032829645 40.42004422470009 355.7486580455693
6900 -6517.565184634689 -6556.035668256894 38.47048362220527 338.5900036843694
7000 -6517.559098587045 -6555.986507687628 38.42740910058283 338.2108921926067
7100 -6517.558005558484 -6556.912239013699 39.35423345521462 346.368145029127
7200 -6517.571145809221 -6556.350273356967 38.77912754774589 341.3064693496369
7300 -6517.561021218085 -6556.998076089849 39.43705487176427 347.0970805946395
7400 -6517.56452672392 -6556.56154910515 38.99702238123108 343.2242256533286
7500 -6517.573591127047 -6559.064299271949 41.49070814490229 365.1718850641332
7600 -6517.56028540102 -6556.032090011716 38.47180461069512 338.601630091306
7700 -6517.560367395793 -6556.511797795006 38.95143039921296 342.8229572546495
7800 -6517.573020066361 -6556.924913541797 39.35189347543547 346.3475501811437
7900 -6517.566299833007 -6556.577995911759 39.01169607875183 343.3533731666899
8000 -6517.570136763665 -6557.582657078126 40.01252031446108 352.1619206490669
8100 -6517.57567411743 -6558.320029386947 40.74435526951675 358.6030146202803
8200 -6517.57149379382 -6558.305152063933 40.73365827011303 358.5088671927853
8300 -6517.578450857186 -6559.05753092226 41.47908006507382 365.0695429248809
8400 -6517.571529794769 -6556.983706107691 39.41217631292108 346.8781171053031
8500 -6517.573679430764 -6558.010837981783 40.43715855101924 355.8992862484367
8600 -6517.569221385906 -6557.925020754935 40.35579936902884 355.183220237923
8700 -6517.577852436718 -6557.081904801994 39.50405236527634 347.6867451748373
8800 -6517.580643488081 -6557.094644295135 39.51400080705436 347.7743043272346
8900 -6517.578100930351 -6556.390740010627 38.81263908027599 341.6014141710814
9000 -6517.58019495998 -6559.786353631089 42.20615867110849 371.4687748740735
9100 -6517.56411964425 -6558.263714947622 40.69959530337233 358.2090690372046
9200 -6517.569716055122 -6557.30158788063 39.73187182550808 349.6918510278532
9300 -6517.579040991249 -6558.208366760658 40.62932576940932 357.5906062698247
9400 -6517.579849744571 -6556.949796896767 39.36994715219554 346.506445882605
9500 -6517.573257994159 -6556.659853833394 39.08659583923544 344.0125879149929
9600 -6517.571031994539 -6556.369911317792 38.79887932325279 341.4803105159536
9700 -6517.574140115354 -6556.924661165745 39.35052105039076 346.3354710660093
9800 -6517.580185525681 -6557.018312550151 39.438127024469 347.106516924887
9900 -6517.573201214911 -6558.96081683168 41.3876156167692 364.2645375032549
10000 -6517.575226749922 -6558.463527484078 40.88830073415524 359.8699208510655
Loop time of 14.9058 on 1 procs for 10000 steps with 880 atoms
Performance: 57.964 ns/day, 0.414 hours/ns, 670.880 timesteps/s
99.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.454 | 14.454 | 14.454 | 0.0 | 96.97
Neigh | 0.12711 | 0.12711 | 0.12711 | 0.0 | 0.85
Comm | 0.11357 | 0.11357 | 0.11357 | 0.0 | 0.76
Output | 0.0095983 | 0.0095983 | 0.0095983 | 0.0 | 0.06
Modify | 0.12205 | 0.12205 | 0.12205 | 0.0 | 0.82
Other | | 0.07956 | | | 0.53
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1569.00 ave 1569 max 1569 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15844.0 ave 15844 max 15844 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15844
Ave neighs/atom = 18.004545
Neighbor list builds = 140
Dangerous builds = 0
Total wall time: 0:00:14

0
examples/USER/misc/tersoff_shift/hBN-momolayer-5nm.data → examples/hBN-momolayer-5nm.data
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0
examples/USER/misc/tersoff_shift/in.hBN_shift → examples/in.hBN_shift
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892
examples/tersoff/hBN-monolayer-5nm.data Normal file
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@ -0,0 +1,892 @@
Makeup graphene nanoribbon on hBN
880 atoms
2 atom types
0.000000000000000 46.152979739999999 xlo xhi
0.000000000000000 48.443364211584992 ylo yhi
0.000000000000000 100.000000000000000 zlo zhi
Atoms
1 1 0.420 0.000000000000000 0.000000000000000 0.000000000000000
2 2 -0.420 0.698900000000000 1.210530287683010 0.000000000000000
3 1 0.420 2.096700000000000 1.210530287683010 0.000000000000000
4 2 -0.420 2.795600000000000 0.000000000000000 0.000000000000000
5 1 0.420 4.193400000000000 0.000000000000000 0.000000000000000
6 2 -0.420 4.892300000000000 1.210530287683010 0.000000000000000
7 1 0.420 6.290100000000000 1.210530287683010 0.000000000000000
8 2 -0.420 6.989000000000000 0.000000000000000 0.000000000000000
9 1 0.420 8.386799999999999 0.000000000000000 0.000000000000000
10 2 -0.420 9.085699999999999 1.210530287683010 0.000000000000000
11 1 0.420 10.483499999999999 1.210530287683010 0.000000000000000
12 2 -0.420 11.182399999999999 0.000000000000000 0.000000000000000
13 1 0.420 12.580200000000000 0.000000000000000 0.000000000000000
14 2 -0.420 13.279100000000000 1.210530287683010 0.000000000000000
15 1 0.420 14.676900000000000 1.210530287683010 0.000000000000000
16 2 -0.420 15.375800000000000 0.000000000000000 0.000000000000000
17 1 0.420 16.773599999999998 0.000000000000000 0.000000000000000
18 2 -0.420 17.472500000000000 1.210530287683010 0.000000000000000
19 1 0.420 18.870300000000000 1.210530287683010 0.000000000000000
20 2 -0.420 19.569199999999999 0.000000000000000 0.000000000000000
21 1 0.420 20.966999999999999 0.000000000000000 0.000000000000000
22 2 -0.420 21.665900000000001 1.210530287683010 0.000000000000000
23 1 0.420 23.063699999999997 1.210530287683010 0.000000000000000
24 2 -0.420 23.762599999999999 0.000000000000000 0.000000000000000
25 1 0.420 25.160399999999999 0.000000000000000 0.000000000000000
26 2 -0.420 25.859299999999998 1.210530287683010 0.000000000000000
27 1 0.420 27.257099999999998 1.210530287683010 0.000000000000000
28 2 -0.420 27.956000000000000 0.000000000000000 0.000000000000000
29 1 0.420 29.353800000000000 0.000000000000000 0.000000000000000
30 2 -0.420 30.052699999999998 1.210530287683010 0.000000000000000
31 1 0.420 31.450499999999998 1.210530287683010 0.000000000000000
32 2 -0.420 32.149400000000000 0.000000000000000 0.000000000000000
33 1 0.420 33.547199999999997 0.000000000000000 0.000000000000000
34 2 -0.420 34.246099999999998 1.210530287683010 0.000000000000000
35 1 0.420 35.643899999999995 1.210530287683010 0.000000000000000
36 2 -0.420 36.342799999999997 0.000000000000000 0.000000000000000
37 1 0.420 37.740600000000001 0.000000000000000 0.000000000000000
38 2 -0.420 38.439499999999995 1.210530287683010 0.000000000000000
39 1 0.420 39.837299999999999 1.210530287683010 0.000000000000000
40 2 -0.420 40.536200000000001 0.000000000000000 0.000000000000000
41 1 0.420 41.933999999999997 0.000000000000000 0.000000000000000
42 2 -0.420 42.632899999999999 1.210530287683010 0.000000000000000
43 1 0.420 44.030699999999996 1.210530287683010 0.000000000000000
44 2 -0.420 44.729599999999998 0.000000000000000 0.000000000000000
45 1 0.420 0.000000000000000 2.421060575366020 0.000000000000000
46 2 -0.420 0.698900000000000 3.631590863049030 0.000000000000000
47 1 0.420 2.096700000000000 3.631590863049030 0.000000000000000
48 2 -0.420 2.795600000000000 2.421060575366020 0.000000000000000
49 1 0.420 4.193400000000000 2.421060575366020 0.000000000000000
50 2 -0.420 4.892300000000000 3.631590863049030 0.000000000000000
51 1 0.420 6.290100000000000 3.631590863049030 0.000000000000000
52 2 -0.420 6.989000000000000 2.421060575366020 0.000000000000000
53 1 0.420 8.386799999999999 2.421060575366020 0.000000000000000
54 2 -0.420 9.085699999999999 3.631590863049030 0.000000000000000
55 1 0.420 10.483499999999999 3.631590863049030 0.000000000000000
56 2 -0.420 11.182399999999999 2.421060575366020 0.000000000000000
57 1 0.420 12.580200000000000 2.421060575366020 0.000000000000000
58 2 -0.420 13.279100000000000 3.631590863049030 0.000000000000000
59 1 0.420 14.676900000000000 3.631590863049030 0.000000000000000
60 2 -0.420 15.375800000000000 2.421060575366020 0.000000000000000
61 1 0.420 16.773599999999998 2.421060575366020 0.000000000000000
62 2 -0.420 17.472500000000000 3.631590863049030 0.000000000000000
63 1 0.420 18.870300000000000 3.631590863049030 0.000000000000000
64 2 -0.420 19.569199999999999 2.421060575366020 0.000000000000000
65 1 0.420 20.966999999999999 2.421060575366020 0.000000000000000
66 2 -0.420 21.665900000000001 3.631590863049030 0.000000000000000
67 1 0.420 23.063699999999997 3.631590863049030 0.000000000000000
68 2 -0.420 23.762599999999999 2.421060575366020 0.000000000000000
69 1 0.420 25.160399999999999 2.421060575366020 0.000000000000000
70 2 -0.420 25.859299999999998 3.631590863049030 0.000000000000000
71 1 0.420 27.257099999999998 3.631590863049030 0.000000000000000
72 2 -0.420 27.956000000000000 2.421060575366020 0.000000000000000
73 1 0.420 29.353800000000000 2.421060575366020 0.000000000000000
74 2 -0.420 30.052699999999998 3.631590863049030 0.000000000000000
75 1 0.420 31.450499999999998 3.631590863049030 0.000000000000000
76 2 -0.420 32.149400000000000 2.421060575366020 0.000000000000000
77 1 0.420 33.547199999999997 2.421060575366020 0.000000000000000
78 2 -0.420 34.246099999999998 3.631590863049030 0.000000000000000
79 1 0.420 35.643899999999995 3.631590863049030 0.000000000000000
80 2 -0.420 36.342799999999997 2.421060575366020 0.000000000000000
81 1 0.420 37.740600000000001 2.421060575366020 0.000000000000000
82 2 -0.420 38.439499999999995 3.631590863049030 0.000000000000000
83 1 0.420 39.837299999999999 3.631590863049030 0.000000000000000
84 2 -0.420 40.536200000000001 2.421060575366020 0.000000000000000
85 1 0.420 41.933999999999997 2.421060575366020 0.000000000000000
86 2 -0.420 42.632899999999999 3.631590863049030 0.000000000000000
87 1 0.420 44.030699999999996 3.631590863049030 0.000000000000000
88 2 -0.420 44.729599999999998 2.421060575366020 0.000000000000000
89 1 0.420 0.000000000000000 4.842121150732040 0.000000000000000
90 2 -0.420 0.698900000000000 6.052651438415050 0.000000000000000
91 1 0.420 2.096700000000000 6.052651438415050 0.000000000000000
92 2 -0.420 2.795600000000000 4.842121150732040 0.000000000000000
93 1 0.420 4.193400000000000 4.842121150732040 0.000000000000000
94 2 -0.420 4.892300000000000 6.052651438415050 0.000000000000000
95 1 0.420 6.290100000000000 6.052651438415050 0.000000000000000
96 2 -0.420 6.989000000000000 4.842121150732040 0.000000000000000
97 1 0.420 8.386799999999999 4.842121150732040 0.000000000000000
98 2 -0.420 9.085699999999999 6.052651438415050 0.000000000000000
99 1 0.420 10.483499999999999 6.052651438415050 0.000000000000000
100 2 -0.420 11.182399999999999 4.842121150732040 0.000000000000000
101 1 0.420 12.580200000000000 4.842121150732040 0.000000000000000
102 2 -0.420 13.279100000000000 6.052651438415050 0.000000000000000
103 1 0.420 14.676900000000000 6.052651438415050 0.000000000000000
104 2 -0.420 15.375800000000000 4.842121150732040 0.000000000000000
105 1 0.420 16.773599999999998 4.842121150732040 0.000000000000000
106 2 -0.420 17.472500000000000 6.052651438415050 0.000000000000000
107 1 0.420 18.870300000000000 6.052651438415050 0.000000000000000
108 2 -0.420 19.569199999999999 4.842121150732040 0.000000000000000
109 1 0.420 20.966999999999999 4.842121150732040 0.000000000000000
110 2 -0.420 21.665900000000001 6.052651438415050 0.000000000000000
111 1 0.420 23.063699999999997 6.052651438415050 0.000000000000000
112 2 -0.420 23.762599999999999 4.842121150732040 0.000000000000000
113 1 0.420 25.160399999999999 4.842121150732040 0.000000000000000
114 2 -0.420 25.859299999999998 6.052651438415050 0.000000000000000
115 1 0.420 27.257099999999998 6.052651438415050 0.000000000000000
116 2 -0.420 27.956000000000000 4.842121150732040 0.000000000000000
117 1 0.420 29.353800000000000 4.842121150732040 0.000000000000000
118 2 -0.420 30.052699999999998 6.052651438415050 0.000000000000000
119 1 0.420 31.450499999999998 6.052651438415050 0.000000000000000
120 2 -0.420 32.149400000000000 4.842121150732040 0.000000000000000
121 1 0.420 33.547199999999997 4.842121150732040 0.000000000000000
122 2 -0.420 34.246099999999998 6.052651438415050 0.000000000000000
123 1 0.420 35.643899999999995 6.052651438415050 0.000000000000000
124 2 -0.420 36.342799999999997 4.842121150732040 0.000000000000000
125 1 0.420 37.740600000000001 4.842121150732040 0.000000000000000
126 2 -0.420 38.439499999999995 6.052651438415050 0.000000000000000
127 1 0.420 39.837299999999999 6.052651438415050 0.000000000000000
128 2 -0.420 40.536200000000001 4.842121150732040 0.000000000000000
129 1 0.420 41.933999999999997 4.842121150732040 0.000000000000000
130 2 -0.420 42.632899999999999 6.052651438415050 0.000000000000000
131 1 0.420 44.030699999999996 6.052651438415050 0.000000000000000
132 2 -0.420 44.729599999999998 4.842121150732040 0.000000000000000
133 1 0.420 0.000000000000000 7.263181726098059 0.000000000000000
134 2 -0.420 0.698900000000000 8.473712013781070 0.000000000000000
135 1 0.420 2.096700000000000 8.473712013781070 0.000000000000000
136 2 -0.420 2.795600000000000 7.263181726098059 0.000000000000000
137 1 0.420 4.193400000000000 7.263181726098059 0.000000000000000
138 2 -0.420 4.892300000000000 8.473712013781070 0.000000000000000
139 1 0.420 6.290100000000000 8.473712013781070 0.000000000000000
140 2 -0.420 6.989000000000000 7.263181726098059 0.000000000000000
141 1 0.420 8.386799999999999 7.263181726098059 0.000000000000000
142 2 -0.420 9.085699999999999 8.473712013781070 0.000000000000000
143 1 0.420 10.483499999999999 8.473712013781070 0.000000000000000
144 2 -0.420 11.182399999999999 7.263181726098059 0.000000000000000
145 1 0.420 12.580200000000000 7.263181726098059 0.000000000000000
146 2 -0.420 13.279100000000000 8.473712013781070 0.000000000000000
147 1 0.420 14.676900000000000 8.473712013781070 0.000000000000000
148 2 -0.420 15.375800000000000 7.263181726098059 0.000000000000000
149 1 0.420 16.773599999999998 7.263181726098059 0.000000000000000
150 2 -0.420 17.472500000000000 8.473712013781070 0.000000000000000
151 1 0.420 18.870300000000000 8.473712013781070 0.000000000000000
152 2 -0.420 19.569199999999999 7.263181726098059 0.000000000000000
153 1 0.420 20.966999999999999 7.263181726098059 0.000000000000000
154 2 -0.420 21.665900000000001 8.473712013781070 0.000000000000000
155 1 0.420 23.063699999999997 8.473712013781070 0.000000000000000
156 2 -0.420 23.762599999999999 7.263181726098059 0.000000000000000
157 1 0.420 25.160399999999999 7.263181726098059 0.000000000000000
158 2 -0.420 25.859299999999998 8.473712013781070 0.000000000000000
159 1 0.420 27.257099999999998 8.473712013781070 0.000000000000000
160 2 -0.420 27.956000000000000 7.263181726098059 0.000000000000000
161 1 0.420 29.353800000000000 7.263181726098059 0.000000000000000
162 2 -0.420 30.052699999999998 8.473712013781070 0.000000000000000
163 1 0.420 31.450499999999998 8.473712013781070 0.000000000000000
164 2 -0.420 32.149400000000000 7.263181726098059 0.000000000000000
165 1 0.420 33.547199999999997 7.263181726098059 0.000000000000000
166 2 -0.420 34.246099999999998 8.473712013781070 0.000000000000000
167 1 0.420 35.643899999999995 8.473712013781070 0.000000000000000
168 2 -0.420 36.342799999999997 7.263181726098059 0.000000000000000
169 1 0.420 37.740600000000001 7.263181726098059 0.000000000000000
170 2 -0.420 38.439499999999995 8.473712013781070 0.000000000000000
171 1 0.420 39.837299999999999 8.473712013781070 0.000000000000000
172 2 -0.420 40.536200000000001 7.263181726098059 0.000000000000000
173 1 0.420 41.933999999999997 7.263181726098059 0.000000000000000
174 2 -0.420 42.632899999999999 8.473712013781070 0.000000000000000
175 1 0.420 44.030699999999996 8.473712013781070 0.000000000000000
176 2 -0.420 44.729599999999998 7.263181726098059 0.000000000000000
177 1 0.420 0.000000000000000 9.684242301464080 0.000000000000000
178 2 -0.420 0.698900000000000 10.894772589147090 0.000000000000000
179 1 0.420 2.096700000000000 10.894772589147090 0.000000000000000
180 2 -0.420 2.795600000000000 9.684242301464080 0.000000000000000
181 1 0.420 4.193400000000000 9.684242301464080 0.000000000000000
182 2 -0.420 4.892300000000000 10.894772589147090 0.000000000000000
183 1 0.420 6.290100000000000 10.894772589147090 0.000000000000000
184 2 -0.420 6.989000000000000 9.684242301464080 0.000000000000000
185 1 0.420 8.386799999999999 9.684242301464080 0.000000000000000
186 2 -0.420 9.085699999999999 10.894772589147090 0.000000000000000
187 1 0.420 10.483499999999999 10.894772589147090 0.000000000000000
188 2 -0.420 11.182399999999999 9.684242301464080 0.000000000000000
189 1 0.420 12.580200000000000 9.684242301464080 0.000000000000000
190 2 -0.420 13.279100000000000 10.894772589147090 0.000000000000000
191 1 0.420 14.676900000000000 10.894772589147090 0.000000000000000
192 2 -0.420 15.375800000000000 9.684242301464080 0.000000000000000
193 1 0.420 16.773599999999998 9.684242301464080 0.000000000000000
194 2 -0.420 17.472500000000000 10.894772589147090 0.000000000000000
195 1 0.420 18.870300000000000 10.894772589147090 0.000000000000000
196 2 -0.420 19.569199999999999 9.684242301464080 0.000000000000000
197 1 0.420 20.966999999999999 9.684242301464080 0.000000000000000
198 2 -0.420 21.665900000000001 10.894772589147090 0.000000000000000
199 1 0.420 23.063699999999997 10.894772589147090 0.000000000000000
200 2 -0.420 23.762599999999999 9.684242301464080 0.000000000000000
201 1 0.420 25.160399999999999 9.684242301464080 0.000000000000000
202 2 -0.420 25.859299999999998 10.894772589147090 0.000000000000000
203 1 0.420 27.257099999999998 10.894772589147090 0.000000000000000
204 2 -0.420 27.956000000000000 9.684242301464080 0.000000000000000
205 1 0.420 29.353800000000000 9.684242301464080 0.000000000000000
206 2 -0.420 30.052699999999998 10.894772589147090 0.000000000000000
207 1 0.420 31.450499999999998 10.894772589147090 0.000000000000000
208 2 -0.420 32.149400000000000 9.684242301464080 0.000000000000000
209 1 0.420 33.547199999999997 9.684242301464080 0.000000000000000
210 2 -0.420 34.246099999999998 10.894772589147090 0.000000000000000
211 1 0.420 35.643899999999995 10.894772589147090 0.000000000000000
212 2 -0.420 36.342799999999997 9.684242301464080 0.000000000000000
213 1 0.420 37.740600000000001 9.684242301464080 0.000000000000000
214 2 -0.420 38.439499999999995 10.894772589147090 0.000000000000000
215 1 0.420 39.837299999999999 10.894772589147090 0.000000000000000
216 2 -0.420 40.536200000000001 9.684242301464080 0.000000000000000
217 1 0.420 41.933999999999997 9.684242301464080 0.000000000000000
218 2 -0.420 42.632899999999999 10.894772589147090 0.000000000000000
219 1 0.420 44.030699999999996 10.894772589147090 0.000000000000000
220 2 -0.420 44.729599999999998 9.684242301464080 0.000000000000000
221 1 0.420 0.000000000000000 12.105302876830100 0.000000000000000
222 2 -0.420 0.698900000000000 13.315833164513110 0.000000000000000
223 1 0.420 2.096700000000000 13.315833164513110 0.000000000000000
224 2 -0.420 2.795600000000000 12.105302876830100 0.000000000000000
225 1 0.420 4.193400000000000 12.105302876830100 0.000000000000000
226 2 -0.420 4.892300000000000 13.315833164513110 0.000000000000000
227 1 0.420 6.290100000000000 13.315833164513110 0.000000000000000
228 2 -0.420 6.989000000000000 12.105302876830100 0.000000000000000
229 1 0.420 8.386799999999999 12.105302876830100 0.000000000000000
230 2 -0.420 9.085699999999999 13.315833164513110 0.000000000000000
231 1 0.420 10.483499999999999 13.315833164513110 0.000000000000000
232 2 -0.420 11.182399999999999 12.105302876830100 0.000000000000000
233 1 0.420 12.580200000000000 12.105302876830100 0.000000000000000
234 2 -0.420 13.279100000000000 13.315833164513110 0.000000000000000
235 1 0.420 14.676900000000000 13.315833164513110 0.000000000000000
236 2 -0.420 15.375800000000000 12.105302876830100 0.000000000000000
237 1 0.420 16.773599999999998 12.105302876830100 0.000000000000000
238 2 -0.420 17.472500000000000 13.315833164513110 0.000000000000000
239 1 0.420 18.870300000000000 13.315833164513110 0.000000000000000
240 2 -0.420 19.569199999999999 12.105302876830100 0.000000000000000
241 1 0.420 20.966999999999999 12.105302876830100 0.000000000000000
242 2 -0.420 21.665900000000001 13.315833164513110 0.000000000000000
243 1 0.420 23.063699999999997 13.315833164513110 0.000000000000000
244 2 -0.420 23.762599999999999 12.105302876830100 0.000000000000000
245 1 0.420 25.160399999999999 12.105302876830100 0.000000000000000
246 2 -0.420 25.859299999999998 13.315833164513110 0.000000000000000
247 1 0.420 27.257099999999998 13.315833164513110 0.000000000000000
248 2 -0.420 27.956000000000000 12.105302876830100 0.000000000000000
249 1 0.420 29.353800000000000 12.105302876830100 0.000000000000000
250 2 -0.420 30.052699999999998 13.315833164513110 0.000000000000000
251 1 0.420 31.450499999999998 13.315833164513110 0.000000000000000
252 2 -0.420 32.149400000000000 12.105302876830100 0.000000000000000
253 1 0.420 33.547199999999997 12.105302876830100 0.000000000000000
254 2 -0.420 34.246099999999998 13.315833164513110 0.000000000000000
255 1 0.420 35.643899999999995 13.315833164513110 0.000000000000000
256 2 -0.420 36.342799999999997 12.105302876830100 0.000000000000000
257 1 0.420 37.740600000000001 12.105302876830100 0.000000000000000
258 2 -0.420 38.439499999999995 13.315833164513110 0.000000000000000
259 1 0.420 39.837299999999999 13.315833164513110 0.000000000000000
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9
examples/USER/misc/tersoff_shift/in.hBN_no_shift → examples/tersoff/in.hBN_shift
View File

@ -8,12 +8,12 @@ processors * * 1 # domain decomposition over x and y
# we use different molecule ids for each layer of hBN # we use different molecule ids for each layer of hBN
# so that inter- and intra-layer # so that inter- and intra-layer
# interactions can be specified separately # interactions can be specified separately
read_data hBN-momolayer-5nm.data read_data hBN-monolayer-5nm.data
mass 1 10.8110 # boron mass (g/mole) | membrane mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ######################## ######################## Potential defition ########################
pair_style tersoff pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N pair_coeff * * BNC.tersoff B N
#################################################################### ####################################################################
# Neighbor update settings # Neighbor update settings
@ -24,13 +24,14 @@ neigh_modify check yes
#### Simulation settings #### #### Simulation settings ####
timestep 0.001 timestep 0.001
velocity all create 300.0 12345 loop geom velocity all create 300.0 4928459 loop geom
fix thermostat all nve fix thermostat all nve
############# Output ############### ############# Output ###############
thermo 100 thermo 100
thermo_style custom step etotal pe ke temp thermo_style custom step etotal pe ke temp
thermo_modify lost warn #thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ###### ###### Run molecular dynamics ######
run 1000 run 1000

46
examples/USER/misc/tersoff_shift/shift0.05_300K_before_change.lmp → examples/tersoff/log.13Jan21.hBN_shift.g++.1
View File

@ -1,4 +1,6 @@
LAMMPS (30 Nov 2020) LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Initialization # Initialization
units metal units metal
boundary p p p boundary p p p
@ -9,13 +11,13 @@ processors * * 1 # domain decomposition over x and y
# we use different molecule ids for each layer of hBN # we use different molecule ids for each layer of hBN
# so that inter- and intra-layer # so that inter- and intra-layer
# interactions can be specified separately # interactions can be specified separately
read_data hBN-momolayer-5nm.data read_data hBN-monolayer-5nm.data
Reading data file ... Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000) orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
reading atoms ... reading atoms ...
880 atoms 880 atoms
read_data CPU = 0.026 seconds read_data CPU = 0.003 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
@ -55,33 +57,33 @@ Neighbor list info ...
pair build: full/bin/atomonly pair build: full/bin/atomonly
stencil: full/bin/3d stencil: full/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.545 | 3.545 | 3.545 Mbytes
Step TotEng PotEng KinEng Temp Step TotEng PotEng KinEng Temp
0 -6570.525999324201 -6604.6118995607 34.0859002365 300 0 -6570.525999324201 -6604.6118995607 34.0859002365 300
100 -6570.310828576859 -6584.788128201219 14.47729962436133 127.4189579026464 100 -6570.310828576855 -6584.788128201216 14.47729962436115 127.4189579026448
200 -6570.372315728009 -6587.981402302975 17.60908657496529 154.9827329140839 200 -6570.372315727984 -6587.98140230295 17.60908657496611 154.9827329140911
300 -6570.341402414291 -6587.005611017611 16.66420860331987 146.6665849019482 300 -6570.341402414283 -6587.005611017601 16.66420860331832 146.6665849019345
400 -6570.373381655075 -6587.812074340168 17.43869268509273 153.4830463396618 400 -6570.373381655075 -6587.812074340169 17.43869268509366 153.48304633967
500 -6570.357279692751 -6587.139105628346 16.78182593559452 147.7017695219105 500 -6570.357279692746 -6587.139105628337 16.78182593559217 147.7017695218898
600 -6570.364533408485 -6588.199043380885 17.83450997240024 156.9667503160379 600 -6570.364533408486 -6588.199043380888 17.83450997240158 156.9667503160497
700 -6570.36200065409 -6587.514376495224 17.15237584113493 150.9630878644163 700 -6570.362000654088 -6587.514376495223 17.15237584113499 150.9630878644169
800 -6570.358394688987 -6587.200486866453 16.8420921774656 148.2321903832015 800 -6570.358394689025 -6587.200486866491 16.84209217746576 148.2321903832028
900 -6570.372035122419 -6588.096861613297 17.72482649087754 156.0013938422906 900 -6570.372035122432 -6588.096861613308 17.72482649087559 156.0013938422734
1000 -6570.355748883598 -6587.399428461688 17.04367957809044 150.0064201898913 1000 -6570.355748883583 -6587.399428461676 17.04367957809225 150.0064201899072
Loop time of 1.34199 on 1 procs for 1000 steps with 880 atoms Loop time of 0.998048 on 1 procs for 1000 steps with 880 atoms
Performance: 64.382 ns/day, 0.373 hours/ns, 745.161 timesteps/s Performance: 86.569 ns/day, 0.277 hours/ns, 1001.956 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 1.313 | 1.313 | 1.313 | 0.0 | 97.84 Pair | 0.98001 | 0.98001 | 0.98001 | 0.0 | 98.19
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0098526 | 0.0098526 | 0.0098526 | 0.0 | 0.73 Comm | 0.006538 | 0.006538 | 0.006538 | 0.0 | 0.66
Output | 0.00069011 | 0.00069011 | 0.00069011 | 0.0 | 0.05 Output | 0.000224 | 0.000224 | 0.000224 | 0.0 | 0.02
Modify | 0.011561 | 0.011561 | 0.011561 | 0.0 | 0.86 Modify | 0.00781 | 0.00781 | 0.00781 | 0.0 | 0.78
Other | | 0.006894 | | | 0.51 Other | | 0.003467 | | | 0.35
Nlocal: 880.000 ave 880 max 880 min Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

101
examples/tersoff/log.13Jan21.hBN_shift.g++.4 Normal file
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@ -0,0 +1,101 @@
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-monolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
2 by 2 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.010 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 4928459 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.297 | 3.297 | 3.297 Mbytes
Step TotEng PotEng KinEng Temp
0 -6570.525999324095 -6604.611899560595 34.08590023650001 300.0000000000001
100 -6570.310828576847 -6584.788128201208 14.47729962436078 127.4189579026416
200 -6570.372315727983 -6587.981402302948 17.60908657496569 154.9827329140874
300 -6570.341402414288 -6587.005611017607 16.66420860331862 146.6665849019371
400 -6570.373381655087 -6587.81207434018 17.43869268509319 153.4830463396659
500 -6570.357279692746 -6587.139105628339 16.78182593559348 147.7017695219013
600 -6570.364533408483 -6588.199043380885 17.83450997240217 156.9667503160549
700 -6570.362000654081 -6587.514376495217 17.15237584113621 150.9630878644276
800 -6570.358394689017 -6587.200486866481 16.84209217746396 148.2321903831871
900 -6570.372035122433 -6588.096861613309 17.72482649087623 156.001393842279
1000 -6570.355748883587 -6587.399428461678 17.0436795780913 150.0064201898988
Loop time of 0.32051 on 4 procs for 1000 steps with 880 atoms
Performance: 269.571 ns/day, 0.089 hours/ns, 3120.030 timesteps/s
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24483 | 0.26461 | 0.28741 | 2.9 | 82.56
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.026425 | 0.049039 | 0.068616 | 6.8 | 15.30
Output | 0.000126 | 0.00016475 | 0.000248 | 0.0 | 0.05
Modify | 0.002472 | 0.002794 | 0.002933 | 0.4 | 0.87
Other | | 0.003905 | | | 1.22
Nlocal: 220.000 ave 241 max 199 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 563.000 ave 583 max 543 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3960.00 ave 4338 max 3582 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 15840
Ave neighs/atom = 18.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00