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