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