155 lines
6.3 KiB
Groff
155 lines
6.3 KiB
Groff
LAMMPS (7 Jan 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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units metal
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atom_style full
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processors * * 1
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boundary p p f
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read_data ./bilayer_MoS2_AAprime_stacking.data
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Reading data file ...
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triclinic box = (0 0 -100) to (51.15232 44.299209 100) with tilt (25.57616 0 0)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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1536 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.007 seconds
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mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
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mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
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mass 4 95.94
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# Define potentials
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pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
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pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
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Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
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pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S
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Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
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pair_coeff * * ilp/tmd MoS2.ILP Mo S S Mo S S
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Reading ilp/tmd potential file MoS2.ILP with DATE: 2021-12-02
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# Calculate the pair potential
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compute 0 all pair ilp/tmd
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compute 1 all pair sw/mod 1
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compute 2 all pair sw/mod 2
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variable SW1 equal c_1
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variable SW2 equal c_2
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variable ILP equal c_0
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variable Eatt equal c_0[1]
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variable Erep equal c_0[2]
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thermo_style custom step etotal pe ke v_SW1 v_SW2 v_ILP v_Erep v_Eatt temp
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thermo 100
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thermo_modify lost error
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timestep 1e-3
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velocity all create 300.0 12345
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fix intall all nve
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run 1000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
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@Article{Ouyang2018
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author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
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title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
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journal = {Nano Letters},
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volume = 18,
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pages = {6009}
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year = 2018,
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}
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- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
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@Article{Ouyang2021
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author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
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title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
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journal = {J. Chem. Theory Comput.},
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volume = 17,
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pages = {7237–7245}
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year = 2021,
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 18
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ghost atom cutoff = 18
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binsize = 9, bins = 9 5 23
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4 neighbor lists, perpetual/occasional/extra = 4 0 0
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(1) pair sw/mod, perpetual, skip from (4)
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attributes: full, newton on
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pair build: skip
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stencil: none
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bin: none
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(2) pair sw/mod, perpetual, skip from (4)
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attributes: full, newton on
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pair build: skip
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stencil: none
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bin: none
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(3) pair ilp/tmd, perpetual
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attributes: full, newton on, ghost
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pair build: full/bin/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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(4) neighbor class addition, perpetual, copy from (3)
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attributes: full, newton on
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 30.29 | 30.29 | 30.29 Mbytes
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Step TotEng PotEng KinEng v_SW1 v_SW2 v_ILP v_Erep v_Eatt Temp
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0 -1834.4469 -1893.9712 59.524297 -929.02881 -929.02881 -35.913549 63.00343 -98.916979 300
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100 -1834.4497 -1883.3105 48.860775 -924.84264 -925.08505 -33.382796 56.58255 -89.965346 246.25629
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200 -1834.4381 -1873.7072 39.269085 -922.29961 -922.52535 -28.882252 50.08277 -78.965022 197.91457
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300 -1834.4483 -1881.1263 46.678028 -923.39264 -923.65627 -34.077402 51.011967 -85.089369 235.25534
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400 -1834.431 -1868.0728 33.64182 -916.85743 -916.27044 -34.944916 50.414038 -85.358954 169.55338
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500 -1834.4499 -1881.9059 47.456 -925.22919 -924.29582 -32.380877 44.755168 -77.136045 239.17628
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600 -1834.4343 -1869.8642 35.429976 -920.97805 -919.60784 -29.278358 43.270241 -72.548599 178.56562
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700 -1834.443 -1878.144 43.700934 -921.8051 -921.55671 -34.782141 49.959943 -84.742084 220.2509
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800 -1834.4327 -1869.824 35.391298 -917.19193 -917.91383 -34.718247 55.349728 -90.067976 178.37068
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900 -1834.4465 -1877.6741 43.227638 -923.33877 -922.50874 -31.826599 53.965592 -85.792191 217.86551
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1000 -1834.4412 -1876.1808 41.739587 -923.17282 -923.49367 -29.514347 55.454643 -84.96899 210.3658
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Loop time of 72.8218 on 1 procs for 1000 steps with 1536 atoms
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Performance: 1.186 ns/day, 20.228 hours/ns, 13.732 timesteps/s
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99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 72.781 | 72.781 | 72.781 | 0.0 | 99.94
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Bond | 0.00014503 | 0.00014503 | 0.00014503 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.016691 | 0.016691 | 0.016691 | 0.0 | 0.02
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Output | 0.00057989 | 0.00057989 | 0.00057989 | 0.0 | 0.00
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Modify | 0.013405 | 0.013405 | 0.013405 | 0.0 | 0.02
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Other | | 0.01044 | | | 0.01
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Nlocal: 1536 ave 1536 max 1536 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3510 ave 3510 max 3510 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 992256 ave 992256 max 992256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 992256
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Ave neighs/atom = 646
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:01:12
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