LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-512-g13c57ab9b5) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # monolayer MoS2 units metal boundary p p f processors * * 1 atom_style atomic read_data single_layer_MoS2.data Reading data file ... triclinic box = (0 0 -100) to (51.15232 44.299209 100) with tilt (25.57616 0 0) WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221) 2 by 2 by 1 MPI processor grid reading atoms ... 768 atoms read_data CPU = 0.003 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 ########################## Define potentials ################################ pair_style sw/mod maxdelcs 0.25 0.35 pair_coeff * * tmd.sw.mod Mo S S Reading sw potential file tmd.sw.mod with DATE: 2018-03-26 ######################################################################### ### Simulation settings #### timestep 0.001 velocity all create 300.0 12345 ############################ # Output thermo 500 thermo_style custom step etotal pe ke temp thermo_modify lost warn ###### Run molecular dynamics ###### fix thermostat all nve run 5000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.158796 ghost atom cutoff = 5.158796 binsize = 2.579398, bins = 30 18 78 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair sw/mod, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.165 | 3.165 | 3.165 Mbytes Step TotEng PotEng KinEng Temp 0 -899.28605 -929.02881 29.742759 300 500 -899.28626 -922.45519 23.168929 233.69313 1000 -899.29247 -925.86547 26.573002 268.02828 1500 -899.27957 -916.95478 17.675214 178.28084 2000 -899.28171 -918.38728 19.105573 192.70814 2500 -899.28732 -922.50423 23.21691 234.17709 3000 -899.28195 -918.74112 19.459174 196.27473 3500 -899.27944 -918.03105 18.751604 189.13784 4000 -899.28397 -920.50737 21.223397 214.06955 4500 -899.28386 -919.79154 20.507685 206.85053 5000 -899.28077 -918.78947 19.508698 196.77425 Loop time of 0.595509 on 4 procs for 5000 steps with 768 atoms Performance: 725.430 ns/day, 0.033 hours/ns, 8396.182 timesteps/s, 6.448 Matom-step/s 99.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4603 | 0.49732 | 0.54269 | 4.2 | 83.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.03293 | 0.078347 | 0.11558 | 10.6 | 13.16 Output | 0.00010079 | 0.00010935 | 0.00012827 | 0.0 | 0.02 Modify | 0.0073413 | 0.0082665 | 0.0091767 | 0.7 | 1.39 Other | | 0.01146 | | | 1.92 Nlocal: 192 ave 194 max 190 min Histogram: 1 0 0 0 0 2 0 0 0 1 Nghost: 194 ave 196 max 192 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: 5120 ave 5170 max 5070 min Histogram: 1 0 0 0 0 2 0 0 0 1 Total # of neighbors = 20480 Ave neighs/atom = 26.666667 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:00