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Interlayer Potential for TMDs and Metal Surfaces

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This commit is contained in:
Wengen Ouyang
2022-02-12 06:05:11 +02:00
parent 81587527fe
commit 922b240678
23 changed files with 42196 additions and 14 deletions
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examples/PACKAGES/interlayer/ilp_tmds/MoS2.ILP Normal file
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# DATE: 2021-12-02 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com
# CITATION: W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021).
# Interlayer Potential (ILP) for bilayer and bulk Molybdenum Disulfide.
# The parameters below are fitted against the HSE + MBD-NL DFT reference data.
#
# --------------- Repulsion Potential ----------------++++++++++++++ Vdw Potential ++++++++++++++++*****
# beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut
Mo Mo 5.5794503728 9.3776624643 2.0272224617 144.1517754265 97.9785701736 89.4375967588 2.0590305447 5.1220549022 491850.3161946840 1.0000 4.0
S S 3.1614021873 8.0932627454 1.9531402037 4.5867641760 118.0654664611 58.8094158385 0.2153665787 4.2996001250 148811.2434089213 1.0000 4.0
Mo S 3.6271521213 19.9713750996 7.5850312329 76.1019310047 3.3174955929 45.7203284638 0.9474703731 4.4104250318 150597.8577162951 1.0000 4.0
# symmetric part
S Mo 3.6271521213 19.9713750996 7.5850312329 76.1019310047 3.3174955929 45.7203284638 0.9474703731 4.4104250318 150597.8577162951 1.0000 4.0

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examples/PACKAGES/interlayer/ilp_tmds/bilayer_MoS2_AAprime_stacking.data Normal file
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units metal
atom_style full
processors * * 1
boundary p p f
read_data ./bilayer_MoS2_AAprime_stacking.data
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
mass 4 95.94
# Define potentials
pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S
pair_coeff * * ilp/tmd MoS2.ILP Mo S S Mo S S
# Calculate the pair potential
compute 0 all pair ilp/tmd
compute 1 all pair sw/mod 1
compute 2 all pair sw/mod 2
variable SW1 equal c_1
variable SW2 equal c_2
variable ILP equal c_0
variable Eatt equal c_0[1]
variable Erep equal c_0[2]
thermo_style custom step etotal pe ke v_SW1 v_SW2 v_ILP v_Erep v_Eatt temp
thermo 100
thermo_modify lost error
timestep 1e-3
velocity all create 300.0 12345
fix intall all nve
run 1000

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examples/PACKAGES/interlayer/ilp_tmds/log.7Jan22.mos2.g++.1 Normal file
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LAMMPS (7 Jan 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style full
processors * * 1
boundary p p f
read_data ./bilayer_MoS2_AAprime_stacking.data
Reading data file ...
triclinic box = (0 0 -100) to (51.15232 44.299209 100) with tilt (25.57616 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
1536 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.007 seconds
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
mass 4 95.94
# Define potentials
pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
pair_coeff * * ilp/tmd MoS2.ILP Mo S S Mo S S
Reading ilp/tmd potential file MoS2.ILP with DATE: 2021-12-02
# Calculate the pair potential
compute 0 all pair ilp/tmd
compute 1 all pair sw/mod 1
compute 2 all pair sw/mod 2
variable SW1 equal c_1
variable SW2 equal c_2
variable ILP equal c_0
variable Eatt equal c_0[1]
variable Erep equal c_0[2]
thermo_style custom step etotal pe ke v_SW1 v_SW2 v_ILP v_Erep v_Eatt temp
thermo 100
thermo_modify lost error
timestep 1e-3
velocity all create 300.0 12345
fix intall all nve
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
year = 2018,
}
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
@Article{Ouyang2021
author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
journal = {J. Chem. Theory Comput.},
volume = 17,
pages = {7237–7245}
year = 2021,
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 9 5 23
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair sw/mod, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair sw/mod, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/tmd, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 30.29 | 30.29 | 30.29 Mbytes
Step TotEng PotEng KinEng v_SW1 v_SW2 v_ILP v_Erep v_Eatt Temp
0 -1834.4469 -1893.9712 59.524297 -929.02881 -929.02881 -35.913549 63.00343 -98.916979 300
100 -1834.4497 -1883.3105 48.860775 -924.84264 -925.08505 -33.382796 56.58255 -89.965346 246.25629
200 -1834.4381 -1873.7072 39.269085 -922.29961 -922.52535 -28.882252 50.08277 -78.965022 197.91457
300 -1834.4483 -1881.1263 46.678028 -923.39264 -923.65627 -34.077402 51.011967 -85.089369 235.25534
400 -1834.431 -1868.0728 33.64182 -916.85743 -916.27044 -34.944916 50.414038 -85.358954 169.55338
500 -1834.4499 -1881.9059 47.456 -925.22919 -924.29582 -32.380877 44.755168 -77.136045 239.17628
600 -1834.4343 -1869.8642 35.429976 -920.97805 -919.60784 -29.278358 43.270241 -72.548599 178.56562
700 -1834.443 -1878.144 43.700934 -921.8051 -921.55671 -34.782141 49.959943 -84.742084 220.2509
800 -1834.4327 -1869.824 35.391298 -917.19193 -917.91383 -34.718247 55.349728 -90.067976 178.37068
900 -1834.4465 -1877.6741 43.227638 -923.33877 -922.50874 -31.826599 53.965592 -85.792191 217.86551
1000 -1834.4412 -1876.1808 41.739587 -923.17282 -923.49367 -29.514347 55.454643 -84.96899 210.3658
Loop time of 72.8218 on 1 procs for 1000 steps with 1536 atoms
Performance: 1.186 ns/day, 20.228 hours/ns, 13.732 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 | 72.781 | 72.781 | 72.781 | 0.0 | 99.94
Bond | 0.00014503 | 0.00014503 | 0.00014503 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.016691 | 0.016691 | 0.016691 | 0.0 | 0.02
Output | 0.00057989 | 0.00057989 | 0.00057989 | 0.0 | 0.00
Modify | 0.013405 | 0.013405 | 0.013405 | 0.0 | 0.02
Other | | 0.01044 | | | 0.01
Nlocal: 1536 ave 1536 max 1536 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3510 ave 3510 max 3510 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 992256 ave 992256 max 992256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 992256
Ave neighs/atom = 646
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:12

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examples/PACKAGES/interlayer/ilp_tmds/log.7Jan22.mos2.g++.4 Normal file
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LAMMPS (7 Jan 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style full
processors * * 1
boundary p p f
read_data ./bilayer_MoS2_AAprime_stacking.data
Reading data file ...
triclinic box = (0 0 -100) to (51.15232 44.299209 100) with tilt (25.57616 0 0)
2 by 2 by 1 MPI processor grid
reading atoms ...
1536 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
mass 4 95.94
# Define potentials
pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
pair_coeff * * ilp/tmd MoS2.ILP Mo S S Mo S S
Reading ilp/tmd potential file MoS2.ILP with DATE: 2021-12-02
# Calculate the pair potential
compute 0 all pair ilp/tmd
compute 1 all pair sw/mod 1
compute 2 all pair sw/mod 2
variable SW1 equal c_1
variable SW2 equal c_2
variable ILP equal c_0
variable Eatt equal c_0[1]
variable Erep equal c_0[2]
thermo_style custom step etotal pe ke v_SW1 v_SW2 v_ILP v_Erep v_Eatt temp
thermo 100
thermo_modify lost error
timestep 1e-3
velocity all create 300.0 12345
fix intall all nve
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
year = 2018,
}
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
@Article{Ouyang2021
author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
journal = {J. Chem. Theory Comput.},
volume = 17,
pages = {7237–7245}
year = 2021,
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 9 5 23
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair sw/mod, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair sw/mod, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/tmd, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.98 | 17.98 | 17.98 Mbytes
Step TotEng PotEng KinEng v_SW1 v_SW2 v_ILP v_Erep v_Eatt Temp
0 -1834.4469 -1893.9712 59.524297 -929.02881 -929.02881 -35.913549 63.00343 -98.916979 300
100 -1834.4497 -1883.3105 48.860775 -924.84264 -925.08505 -33.382796 56.58255 -89.965346 246.25629
200 -1834.4381 -1873.7072 39.269085 -922.29961 -922.52535 -28.882252 50.08277 -78.965022 197.91457
300 -1834.4483 -1881.1263 46.678028 -923.39264 -923.65627 -34.077402 51.011967 -85.089369 235.25534
400 -1834.431 -1868.0728 33.64182 -916.85743 -916.27044 -34.944916 50.414038 -85.358954 169.55338
500 -1834.4499 -1881.9059 47.456 -925.22919 -924.29582 -32.380877 44.755168 -77.136045 239.17628
600 -1834.4343 -1869.8642 35.429976 -920.97805 -919.60784 -29.278358 43.270241 -72.548599 178.56562
700 -1834.443 -1878.144 43.700934 -921.8051 -921.55671 -34.782141 49.959943 -84.742084 220.2509
800 -1834.4327 -1869.824 35.391298 -917.19193 -917.91383 -34.718247 55.349728 -90.067976 178.37068
900 -1834.4465 -1877.6741 43.227638 -923.33877 -922.50874 -31.826599 53.965592 -85.792191 217.86551
1000 -1834.4412 -1876.1808 41.739587 -923.17282 -923.49367 -29.514347 55.454643 -84.96899 210.3658
Loop time of 24.6309 on 4 procs for 1000 steps with 1536 atoms
Performance: 3.508 ns/day, 6.842 hours/ns, 40.599 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 22.906 | 23.627 | 24.36 | 14.0 | 95.92
Bond | 0.00010889 | 0.00011572 | 0.00012719 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.25886 | 0.992 | 1.7126 | 68.3 | 4.03
Output | 0.00050901 | 0.00054202 | 0.00062029 | 0.0 | 0.00
Modify | 0.0030735 | 0.0033236 | 0.0035581 | 0.3 | 0.01
Other | | 0.008194 | | | 0.03
Nlocal: 384 ave 387 max 381 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 2262 ave 2265 max 2259 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 248064 ave 250002 max 246126 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 992256
Ave neighs/atom = 646
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:24

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# DATE: 2018-03-26 UNITS: metal CONTRIBUTOR: Jin-Wu Jiang jwjiang5918@hotmail.com
# CITATION: J.-W. Jiang, Acta Mech. Solida. Sin 32, 17 (2019).
# The Stillinger-Weber parameters, for transition-metal dichalcogenide (TMD) lateral heterostructures.
# M = Mo, W; X = S, Se, Te
# these entries are in LAMMPS "metal" units:
# epsilon = eV; sigma = Angstroms
# other quantities are unitless
# format of a single entry (one or more lines):
# element 1, element 2, element 3,
# epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
# M-X-X terms
Mo S S 1.000 1.252 2.523 67.883 1.000 0.143 6.918 7.223 4 0 0.0
Mo Se Se 1.000 0.913 3.672 32.526 1.000 0.143 5.737 27.084 4 0 0.0
Mo Te Te 1.000 0.880 4.097 23.705 1.000 0.143 5.086 40.810 4 0 0.0
W S S 1.000 0.889 3.558 37.687 1.000 0.143 5.664 24.525 4 0 0.0
W Se Se 1.000 0.706 4.689 25.607 1.000 0.143 5.476 65.662 4 0 0.0
W Te Te 1.000 0.778 4.632 21.313 1.000 0.143 4.326 62.148 4 0 0.0
# X-M-M terms
S Mo Mo 1.000 1.252 2.523 62.449 1.000 0.143 6.918 7.223 4 0 0.0
S W W 1.000 0.889 3.558 33.553 1.000 0.143 5.664 24.525 4 0 0.0
Se Mo Mo 1.000 0.913 3.672 27.079 1.000 0.143 5.737 27.084 4 0 0.0
Se W W 1.000 0.706 4.689 23.218 1.000 0.143 5.476 65.662 4 0 0.0
Te Mo Mo 1.000 0.880 4.097 20.029 1.000 0.143 5.086 40.810 4 0 0.0
Te W W 1.000 0.778 4.632 17.370 1.000 0.143 4.326 62.148 4 0 0.0
# M-X1-X2 terms
Mo S Se 1.000 0.000 0.000 46.989 1.000 0.143 0.000 0.000 4 0 0.0
Mo S Te 1.000 0.000 0.000 40.114 1.000 0.143 0.000 0.000 4 0 0.0
Mo Se S 1.000 0.000 0.000 46.989 1.000 0.143 0.000 0.000 4 0 0.0
Mo Se Te 1.000 0.000 0.000 27.767 1.000 0.143 0.000 0.000 4 0 0.0
Mo Te S 1.000 0.000 0.000 40.114 1.000 0.143 0.000 0.000 4 0 0.0
Mo Te Se 1.000 0.000 0.000 27.767 1.000 0.143 0.000 0.000 4 0 0.0
W S Se 1.000 0.000 0.000 31.065 1.000 0.143 0.000 0.000 4 0 0.0
W S Te 1.000 0.000 0.000 28.341 1.000 0.143 0.000 0.000 4 0 0.0
W Se S 1.000 0.000 0.000 31.065 1.000 0.143 0.000 0.000 4 0 0.0
W Se Te 1.000 0.000 0.000 23.362 1.000 0.143 0.000 0.000 4 0 0.0
W Te S 1.000 0.000 0.000 28.341 1.000 0.143 0.000 0.000 4 0 0.0
W Te Se 1.000 0.000 0.000 23.362 1.000 0.143 0.000 0.000 4 0 0.0
# X-M1-M2 terms
S Mo W 1.000 0.000 0.000 45.775 1.000 0.143 0.000 0.000 4 0 0.0
S W Mo 1.000 0.000 0.000 45.775 1.000 0.143 0.000 0.000 4 0 0.0
Se Mo W 1.000 0.000 0.000 25.074 1.000 0.143 0.000 0.000 4 0 0.0
Se W Mo 1.000 0.000 0.000 25.074 1.000 0.143 0.000 0.000 4 0 0.0
Te Mo W 1.000 0.000 0.000 18.652 1.000 0.143 0.000 0.000 4 0 0.0
Te W Mo 1.000 0.000 0.000 18.652 1.000 0.143 0.000 0.000 4 0 0.0
# zero terms
Mo Mo Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Mo W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0

218
examples/PACKAGES/interlayer/saip_metal/3Lgold_1Lgr_atop_sliding.data Normal file
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@ -0,0 +1,218 @@
Gold/graphene heterjunction atop2
206 atoms
2 atom types
0 17.216640 xlo xhi
0 14.910048 ylo yhi
-30 30.000000 zlo zhi
8.60832 0 0 xy xz yz
Atoms
1 1 1 0 -8.60832 -4.97002 3.5
2 1 1 0 -7.1736 -4.14166 5.85461
3 1 1 0 -5.73888 -3.31334 8.20922
4 1 1 0 -7.1736 -2.48501 3.5
5 1 1 0 -5.73888 -1.65666 5.85461
6 1 1 0 -4.30416 -0.828336 8.20922
7 1 1 0 -5.73888 0 3.5
8 1 1 0 -4.30416 0.828352 5.85461
9 1 1 0 -2.86944 1.65667 8.20922
10 1 1 0 -4.30416 2.48501 3.5
11 1 1 0 -2.86944 3.31336 5.85461
12 1 1 0 -1.43472 4.14168 8.20922
13 1 1 0 -2.86944 4.97002 3.5
14 1 1 0 -1.43472 5.79837 5.85461
15 1 1 0 0 6.62669 8.20922
16 1 1 0 -1.43472 7.45502 3.5
17 1 1 0 0 8.28337 5.85461
18 1 1 0 1.43472 9.11167 8.20922
19 1 1 0 -5.73888 -4.97002 3.5
20 1 1 0 -4.30416 -4.14166 5.85461
21 1 1 0 -2.86944 -3.31334 8.20922
22 1 1 0 -4.30416 -2.48501 3.5
23 1 1 0 -2.86944 -1.65666 5.85461
24 1 1 0 -1.43472 -0.828336 8.20922
25 1 1 0 -2.86944 0 3.5
26 1 1 0 -1.43472 0.828352 5.85461
27 1 1 0 0 1.65667 8.20922
28 1 1 0 -1.43472 2.48501 3.5
29 1 1 0 0 3.31336 5.85461
30 1 1 0 1.43472 4.14168 8.20922
31 1 1 0 0 4.97002 3.5
32 1 1 0 1.43472 5.79837 5.85461
33 1 1 0 2.86944 6.62669 8.20922
34 1 1 0 1.43472 7.45502 3.5
35 1 1 0 2.86944 8.28337 5.85461
36 1 1 0 4.30416 9.11167 8.20922
37 1 1 0 -2.86944 -4.97002 3.5
38 1 1 0 -1.43472 -4.14166 5.85461
39 1 1 0 0 -3.31334 8.20922
40 1 1 0 -1.43472 -2.48501 3.5
41 1 1 0 0 -1.65666 5.85461
42 1 1 0 1.43472 -0.828336 8.20922
43 1 1 0 0 0 3.5
44 1 1 0 1.43472 0.828352 5.85461
45 1 1 0 2.86944 1.65667 8.20922
46 1 1 0 1.43472 2.48501 3.5
47 1 1 0 2.86944 3.31336 5.85461
48 1 1 0 4.30416 4.14168 8.20922
49 1 1 0 2.86944 4.97002 3.5
50 1 1 0 4.30416 5.79837 5.85461
51 1 1 0 5.73888 6.62669 8.20922
52 1 1 0 4.30416 7.45502 3.5
53 1 1 0 5.73888 8.28337 5.85461
54 1 1 0 7.1736 9.11167 8.20922
55 1 1 0 0 -4.97002 3.5
56 1 1 0 1.43472 -4.14166 5.85461
57 1 1 0 2.86944 -3.31334 8.20922
58 1 1 0 1.43472 -2.48501 3.5
59 1 1 0 2.86944 -1.65666 5.85461
60 1 1 0 4.30416 -0.828336 8.20922
61 1 1 0 2.86944 0 3.5
62 1 1 0 4.30416 0.828352 5.85461
63 1 1 0 5.73888 1.65667 8.20922
64 1 1 0 4.30416 2.48501 3.5
65 1 1 0 5.73888 3.31336 5.85461
66 1 1 0 7.1736 4.14168 8.20922
67 1 1 0 5.73888 4.97002 3.5
68 1 1 0 7.1736 5.79837 5.85461
69 1 1 0 8.60832 6.62669 8.20922
70 1 1 0 7.1736 7.45502 3.5
71 1 1 0 8.60832 8.28337 5.85461
72 1 1 0 10.0431 9.11167 8.20922
73 1 1 0 2.86944 -4.97002 3.5
74 1 1 0 4.30416 -4.14166 5.85461
75 1 1 0 5.73888 -3.31334 8.20922
76 1 1 0 4.30416 -2.48501 3.5
77 1 1 0 5.73888 -1.65666 5.85461
78 1 1 0 7.1736 -0.828336 8.20922
79 1 1 0 5.73888 0 3.5
80 1 1 0 7.1736 0.828352 5.85461
81 1 1 0 8.60832 1.65667 8.20922
82 1 1 0 7.1736 2.48501 3.5
83 1 1 0 8.60832 3.31336 5.85461
84 1 1 0 10.0431 4.14168 8.20922
85 1 1 0 8.60832 4.97002 3.5
86 1 1 0 10.0431 5.79837 5.85461
87 1 1 0 11.4777 6.62669 8.20922
88 1 1 0 10.0431 7.45502 3.5
89 1 1 0 11.4777 8.28337 5.85461
90 1 1 0 12.9124 9.11167 8.20922
91 1 1 0 5.73888 -4.97002 3.5
92 1 1 0 7.1736 -4.14166 5.85461
93 1 1 0 8.60832 -3.31334 8.20922
94 1 1 0 7.1736 -2.48501 3.5
95 1 1 0 8.60832 -1.65666 5.85461
96 1 1 0 10.0431 -0.828336 8.20922
97 1 1 0 8.60832 0 3.5
98 1 1 0 10.0431 0.828352 5.85461
99 1 1 0 11.4777 1.65667 8.20922
100 1 1 0 10.0431 2.48501 3.5
101 1 1 0 11.4777 3.31336 5.85461
102 1 1 0 12.9124 4.14168 8.20922
103 1 1 0 11.4777 4.97002 3.5
104 1 1 0 12.9124 5.79837 5.85461
105 1 1 0 14.3472 6.62669 8.20922
106 1 1 0 12.9124 7.45502 3.5
107 1 1 0 14.3472 8.28337 5.85461
108 1 1 0 15.7819 9.11167 8.20922
109 2 2 0 -11.0678 -6.39002 0
110 2 2 0 -9.83808 -5.68001 0
111 2 2 0 -9.83808 -4.26001 0
112 2 2 0 -8.60832 -3.55001 0
113 2 2 0 -8.60832 -2.13001 0
114 2 2 0 -7.37856 -1.42 0
115 2 2 0 -7.37856 0 0
116 2 2 0 -6.1488 0.710007 0
117 2 2 0 -6.1488 2.13001 0
118 2 2 0 -4.91904 2.84001 0
119 2 2 0 -4.91904 4.26001 0
120 2 2 0 -3.68928 4.97002 0
121 2 2 0 -3.68928 6.39002 0
122 2 2 0 -2.45952 7.10003 0
123 2 2 0 -8.60832 -6.39002 0
124 2 2 0 -7.37856 -5.68001 0
125 2 2 0 -7.37856 -4.26001 0
126 2 2 0 -6.1488 -3.55001 0
127 2 2 0 -6.1488 -2.13001 0
128 2 2 0 -4.91904 -1.42 0
129 2 2 0 -4.91904 0 0
130 2 2 0 -3.68928 0.710007 0
131 2 2 0 -3.68928 2.13001 0
132 2 2 0 -2.45952 2.84001 0
133 2 2 0 -2.45952 4.26001 0
134 2 2 0 -1.22976 4.97002 0
135 2 2 0 -1.22976 6.39002 0
136 2 2 0 0 7.10003 0
137 2 2 0 -6.1488 -6.39002 0
138 2 2 0 -4.91904 -5.68001 0
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140 2 2 0 -3.68928 -3.55001 0
141 2 2 0 -3.68928 -2.13001 0
142 2 2 0 -2.45952 -1.42 0
143 2 2 0 -2.45952 0 0
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145 2 2 0 -1.22976 2.13001 0
146 2 2 0 0 2.84001 0
147 2 2 0 0 4.26001 0
148 2 2 0 1.22976 4.97002 0
149 2 2 0 1.22976 6.39002 0
150 2 2 0 2.45952 7.10003 0
151 2 2 0 -3.68928 -6.39002 0
152 2 2 0 -2.45952 -5.68001 0
153 2 2 0 -2.45952 -4.26001 0
154 2 2 0 -1.22976 -3.55001 0
155 2 2 0 -1.22976 -2.13001 0
156 2 2 0 0 -1.42 0
157 2 2 0 0 0 0
158 2 2 0 1.22976 0.710007 0
159 2 2 0 1.22976 2.13001 0
160 2 2 0 2.45952 2.84001 0
161 2 2 0 2.45952 4.26001 0
162 2 2 0 3.68928 4.97002 0
163 2 2 0 3.68928 6.39002 0
164 2 2 0 4.91904 7.10003 0
165 2 2 0 -1.22976 -6.39002 0
166 2 2 0 0 -5.68001 0
167 2 2 0 0 -4.26001 0
168 2 2 0 1.22976 -3.55001 0
169 2 2 0 1.22976 -2.13001 0
170 2 2 0 2.45952 -1.42 0
171 2 2 0 2.45952 0 0
172 2 2 0 3.68928 0.710007 0
173 2 2 0 3.68928 2.13001 0
174 2 2 0 4.91904 2.84001 0
175 2 2 0 4.91904 4.26001 0
176 2 2 0 6.1488 4.97002 0
177 2 2 0 6.1488 6.39002 0
178 2 2 0 7.37856 7.10003 0
179 2 2 0 1.22976 -6.39002 0
180 2 2 0 2.45952 -5.68001 0
181 2 2 0 2.45952 -4.26001 0
182 2 2 0 3.68928 -3.55001 0
183 2 2 0 3.68928 -2.13001 0
184 2 2 0 4.91904 -1.42 0
185 2 2 0 4.91904 0 0
186 2 2 0 6.1488 0.710007 0
187 2 2 0 6.1488 2.13001 0
188 2 2 0 7.37856 2.84001 0
189 2 2 0 7.37856 4.26001 0
190 2 2 0 8.60832 4.97002 0
191 2 2 0 8.60832 6.39002 0
192 2 2 0 9.83808 7.10003 0
193 2 2 0 3.68928 -6.39002 0
194 2 2 0 4.91904 -5.68001 0
195 2 2 0 4.91904 -4.26001 0
196 2 2 0 6.1488 -3.55001 0
197 2 2 0 6.1488 -2.13001 0
198 2 2 0 7.37856 -1.42 0
199 2 2 0 7.37856 0 0
200 2 2 0 8.60832 0.710007 0
201 2 2 0 8.60832 2.13001 0
202 2 2 0 9.83808 2.84001 0
203 2 2 0 9.83808 4.26001 0
204 2 2 0 11.0678 4.97002 0
205 2 2 0 11.0678 6.39002 0
206 2 2 0 12.2976 7.10003 0

304
examples/PACKAGES/interlayer/saip_metal/Au_u3.eam Normal file
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@ -0,0 +1,304 @@
DATE: 2007-06-11 CONTRIBUTOR: Stephen Foiles, foiles@sandia.gov CITATION: Foiles et al, Phys Rev B, 33, 7983 (1986) COMMENT: Au functions (universal 3)
79 196.97 4.0800 FCC
500 5.0100200400801306e-04 500 1.1212121212121229e-02 5.5500000000000114e+00
0. -4.8957152905617285e-01 -7.9715640025473178e-01 -1.0578883960846852e+00 -1.2926127947875230e+00
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6.9222751882549137e-06 6.6292831950053900e-06 6.3457618686353938e-06 6.0714202854210658e-06 5.8059758758126974e-06
5.5491542064604101e-06 5.3006887671412965e-06 5.0603207624608454e-06 4.8277989082726527e-06 4.6028792327467837e-06
4.3853248819745191e-06 4.1749059300766062e-06 3.9713991936930954e-06 3.7745880508142688e-06 3.5842622638456757e-06
3.4002178068596534e-06 3.2222566969260485e-06 3.0501868294746811e-06 2.8838218176012410e-06 2.7229808352391242e-06
2.5674884641312622e-06 2.4171745445294654e-06 2.2718740295380683e-06 2.1314268430473412e-06 1.9956777411659336e-06
1.8644761770997796e-06 1.7376761694013680e-06 1.6151361735109885e-06 1.4967189565443510e-06 1.3822914752352456e-06
1.2717247569860561e-06 1.1648937839490780e-06 1.0616773800793238e-06 9.6195810109658104e-07 8.6562212728696897e-07
7.7255915909348342e-07 6.8266231542009619e-07 5.9582803460662395e-07 5.1195597799675132e-07 4.3094893605718154e-07
3.5271273698142622e-07 2.7715615772249259e-07 2.0419083740348351e-07 1.3373119304687232e-07 6.5694337570851248e-08
0. 0. 0. 0. 0.

37595
examples/PACKAGES/interlayer/saip_metal/CH.rebo Normal file
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examples/PACKAGES/interlayer/saip_metal/CHAu.ILP Normal file
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# DATE: 2021-12-02 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com
# CITATION: W. Ouyang, O. Hod, and R. Guerra, J. Chem. Theory Comput. 17, 7215 (2021).
# Semi-anisotropic interlayer Potential (SAIP) for graphene/gold, benzene/gold heterojunctions
# The parameters below are fitted against the PBE + D3 DFT reference data.
# The parameters for C-C, C-H and H-H are taken from Nano Letters 18, 6009-6016 (2018).
#
# --------------- Repulsion Potential ----------------++++++++++++++ Vdw Potential ++++++++++++++++*****
# beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut
C C 3.205843 7.511126 1.235334 1.528338E-5 37.530428 15.499947 0.7954443 3.681440 25.714535E3 1.0 2.0
H H 3.974540 6.53799 1.080633 0.6700556 0.8333833 15.022371 0.7490632 2.767223 1.6159581E3 1.0 1.2
C H 2.642950 12.91410 1.020257 0.9750012 25.340996 15.222927 0.8115998 3.887324 5.6874617E3 1.0 1.5
Au C 3.6913278482 13.5655648421 1.0175514400 0.0070964784 -0.0010368264 11.0586486772 1.0635582839 3.7552608806 81.5847131142 1000.0 1.0
Au H 3.7899616131 4.3065009639 10.6811825156 0.2250887843 -0.1116891520 18.6149213872 0.9833194192 3.3507558896 70.6865381780 1000.0 1.0
Au Au 3.6671967387 12.8109735143 1.0353581041 0.0000000000 0.0000000000 10.1628585345 1.0642897301 3.7372959779 0.0000000000 1000.0 1.0
# Symmetric part
C Au 3.6913278482 13.5655648421 1.0175514400 0.0070964784 -0.0010368264 11.0586486772 1.0635582839 3.7552608806 81.5847131142 1000.0 2.0
H Au 3.7899616131 4.3065009639 10.6811825156 0.2250887843 -0.1116891520 18.6149213872 0.9833194192 3.3507558896 70.6865381780 1000.0 1.5
H C 2.642950 12.91410 1.020257 0.9750012 25.340996 15.222927 0.8115998 3.887324 5.6874617E3 1.0 1.5

44
examples/PACKAGES/interlayer/saip_metal/in.gold_gr Normal file
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units metal
atom_style full
processors * * 1
boundary p p f
read_data ./3Lgold_1Lgr_atop_sliding.data
# global group definition
group gold type 1
group gra type 2
# Define mass
mass * 12.0107 # mass of carbon atom , uint: a.u.=1.66X10^(-27)kg
mass 1 196.96657 # mass of gold atom , uint: a.u.=1.66X10^(-27)kg
# Define potentials
pair_style hybrid/overlay eam rebo saip/metal 16.0
pair_coeff 1 1 eam ./Au_u3.eam
pair_coeff * * rebo ./CH.rebo NULL C
pair_coeff * * saip/metal ./CHAu.ILP Au C
# compute energy
compute 0 all pair rebo
compute 1 all pair eam
compute 2 all pair saip/metal
variable REBO equal c_0
variable EAM equal c_1
variable ILP equal c_2
thermo_style custom step etotal pe ke v_REBO v_ILP temp
thermo 100
thermo_modify lost error
# Creat initial velocity
velocity all set 0.0 0.0 0.0
velocity gra create 300.0 4928459 mom yes rot yes dist gaussian
velocity gold create 300.0 4928459 mom yes rot yes dist gaussian
# Integration
fix intsub gold nve
fix intrib gra nve
timestep 1e-3
run 1000

164
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LAMMPS (7 Jan 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style full
processors * * 1
boundary p p f
read_data ./3Lgold_1Lgr_atop_sliding.data
Reading data file ...
triclinic box = (0 0 -30) to (17.21664 14.910048 30) with tilt (8.60832 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
206 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.003 seconds
# global group definition
group gold type 1
108 atoms in group gold
group gra type 2
98 atoms in group gra
# Define mass
mass * 12.0107 # mass of carbon atom , uint: a.u.=1.66X10^(-27)kg
mass 1 196.96657 # mass of gold atom , uint: a.u.=1.66X10^(-27)kg
# Define potentials
pair_style hybrid/overlay eam rebo saip/metal 16.0
pair_coeff 1 1 eam ./Au_u3.eam
Reading eam potential file ./Au_u3.eam with DATE: 2007-06-11
pair_coeff * * rebo ./CH.rebo NULL C
Reading rebo potential file ./CH.rebo with DATE: 2018-7-3
pair_coeff * * saip/metal ./CHAu.ILP Au C
Reading saip/metal potential file ./CHAu.ILP with DATE: 2021-12-02
# compute energy
compute 0 all pair rebo
compute 1 all pair eam
compute 2 all pair saip/metal
variable REBO equal c_0
variable EAM equal c_1
variable ILP equal c_2
thermo_style custom step etotal pe ke v_REBO v_ILP temp
thermo 100
thermo_modify lost error
# Creat initial velocity
velocity all set 0.0 0.0 0.0
velocity gra create 300.0 4928459 mom yes rot yes dist gaussian
velocity gold create 300.0 4928459 mom yes rot yes dist gaussian
# Integration
fix intsub gold nve
fix intrib gra nve
timestep 1e-3
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
year = 2018,
}
- saip/metal potential doi.org/10.1021/acs.jctc.1c00622
@Article{Ouyang2021
author = {W. Ouyang, O. Hod, and R. Guerra},
title = {Registry-Dependent Potential for Interfaces of Gold with Graphitic Systems},
journal = {J. Chem. Theory Comput.},
volume = 17,
pages = {7215-7223}
year = 2021,
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 3 2 7
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair eam, perpetual, skip from (4)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(3) pair saip/metal, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.747 | 9.747 | 9.747 Mbytes
Step TotEng PotEng KinEng v_REBO v_ILP Temp
0 -1121.4621 -1129.3728 7.9107209 -724.70925 -6.0302289 298.53659
100 -1121.4483 -1124.9731 3.5248501 -723.03272 -5.9765533 133.02159
200 -1121.4403 -1125.2912 3.8509646 -722.66784 -6.0468507 145.32858
300 -1121.4424 -1126.4665 5.0240531 -722.72787 -6.0350568 189.59886
400 -1121.4419 -1125.1443 3.7023978 -722.59976 -5.8294548 139.72193
500 -1121.4413 -1125.2711 3.8297939 -722.5342 -6.0189944 144.52963
600 -1121.4449 -1125.8808 4.4359049 -722.77707 -5.8685221 167.40319
700 -1121.4489 -1126.1966 4.747709 -723.13681 -5.8666379 179.17012
800 -1121.4443 -1125.8469 4.402607 -722.94487 -6.0094567 166.14658
900 -1121.4424 -1125.8437 4.4013317 -722.94918 -5.8699702 166.09846
1000 -1121.4467 -1125.7453 4.2986881 -722.66682 -6.0651168 162.22487
Loop time of 6.43246 on 1 procs for 1000 steps with 206 atoms
Performance: 13.432 ns/day, 1.787 hours/ns, 155.462 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.4201 | 6.4201 | 6.4201 | 0.0 | 99.81
Bond | 8.9059e-05 | 8.9059e-05 | 8.9059e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0071852 | 0.0071852 | 0.0071852 | 0.0 | 0.11
Output | 0.00026031 | 0.00026031 | 0.00026031 | 0.0 | 0.00
Modify | 0.0019433 | 0.0019433 | 0.0019433 | 0.0 | 0.03
Other | | 0.002875 | | | 0.04
Nlocal: 206 ave 206 max 206 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2187 ave 2187 max 2187 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 158548 ave 158548 max 158548 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 158548
Ave neighs/atom = 769.65049
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:06

164
examples/PACKAGES/interlayer/saip_metal/log.7Jan22.gold_gr.g++.4 Normal file
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@ -0,0 +1,164 @@
LAMMPS (7 Jan 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style full
processors * * 1
boundary p p f
read_data ./3Lgold_1Lgr_atop_sliding.data
Reading data file ...
triclinic box = (0 0 -30) to (17.21664 14.910048 30) with tilt (8.60832 0 0)
2 by 2 by 1 MPI processor grid
reading atoms ...
206 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
# global group definition
group gold type 1
108 atoms in group gold
group gra type 2
98 atoms in group gra
# Define mass
mass * 12.0107 # mass of carbon atom , uint: a.u.=1.66X10^(-27)kg
mass 1 196.96657 # mass of gold atom , uint: a.u.=1.66X10^(-27)kg
# Define potentials
pair_style hybrid/overlay eam rebo saip/metal 16.0
pair_coeff 1 1 eam ./Au_u3.eam
Reading eam potential file ./Au_u3.eam with DATE: 2007-06-11
pair_coeff * * rebo ./CH.rebo NULL C
Reading rebo potential file ./CH.rebo with DATE: 2018-7-3
pair_coeff * * saip/metal ./CHAu.ILP Au C
Reading saip/metal potential file ./CHAu.ILP with DATE: 2021-12-02
# compute energy
compute 0 all pair rebo
compute 1 all pair eam
compute 2 all pair saip/metal
variable REBO equal c_0
variable EAM equal c_1
variable ILP equal c_2
thermo_style custom step etotal pe ke v_REBO v_ILP temp
thermo 100
thermo_modify lost error
# Creat initial velocity
velocity all set 0.0 0.0 0.0
velocity gra create 300.0 4928459 mom yes rot yes dist gaussian
velocity gold create 300.0 4928459 mom yes rot yes dist gaussian
# Integration
fix intsub gold nve
fix intrib gra nve
timestep 1e-3
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
year = 2018,
}
- saip/metal potential doi.org/10.1021/acs.jctc.1c00622
@Article{Ouyang2021
author = {W. Ouyang, O. Hod, and R. Guerra},
title = {Registry-Dependent Potential for Interfaces of Gold with Graphitic Systems},
journal = {J. Chem. Theory Comput.},
volume = 17,
pages = {7215-7223}
year = 2021,
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 3 2 7
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair eam, perpetual, skip from (4)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(3) pair saip/metal, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.299 | 9.299 | 9.3 Mbytes
Step TotEng PotEng KinEng v_REBO v_ILP Temp
0 -1121.4621 -1129.3728 7.9107209 -724.70925 -6.0302289 298.53659
100 -1121.4483 -1124.9731 3.5248501 -723.03272 -5.9765533 133.02159
200 -1121.4403 -1125.2912 3.8509646 -722.66784 -6.0468507 145.32858
300 -1121.4424 -1126.4665 5.0240531 -722.72787 -6.0350568 189.59886
400 -1121.4419 -1125.1443 3.7023978 -722.59976 -5.8294548 139.72193
500 -1121.4413 -1125.2711 3.8297939 -722.5342 -6.0189944 144.52963
600 -1121.4449 -1125.8808 4.4359049 -722.77707 -5.8685221 167.40319
700 -1121.4489 -1126.1966 4.747709 -723.13681 -5.8666379 179.17012
800 -1121.4443 -1125.8469 4.402607 -722.94487 -6.0094567 166.14658
900 -1121.4424 -1125.8437 4.4013317 -722.94918 -5.8699702 166.09846
1000 -1121.4467 -1125.7453 4.2986881 -722.66682 -6.0651168 162.22487
Loop time of 2.44776 on 4 procs for 1000 steps with 206 atoms
Performance: 35.298 ns/day, 0.680 hours/ns, 408.537 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6906 | 2.0172 | 2.3939 | 19.2 | 82.41
Bond | 5.4278e-05 | 6.3818e-05 | 7.3153e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.049363 | 0.42514 | 0.75161 | 41.7 | 17.37
Output | 0.00018596 | 0.00020656 | 0.00024754 | 0.0 | 0.01
Modify | 0.00063656 | 0.00074701 | 0.00089514 | 0.0 | 0.03
Other | | 0.004362 | | | 0.18
Nlocal: 51.5 ave 61 max 44 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 1670.75 ave 1699 max 1641 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 39637 ave 47080 max 33737 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 158548
Ave neighs/atom = 769.65049
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02