LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_SNAP_ChenDengTran_2017_Mo__SM_003882782678_000 # For Simulator : LAMMPS 12 Dec 2018 # Running on : LAMMPS 7 Aug 2019 # Lattice spacing in x,y,z = 3.15999 3.15999 3.15999 Created orthogonal box = (0 -47.7179 0) to (33.7394 47.7179 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.32728 5.44116 4.4689 Created 458 atoms create_atoms CPU = 0.000431061 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.32728 5.44116 4.4689 Created 458 atoms create_atoms CPU = 0.00031805 secs 458 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXTXXC8f/Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18 SNAP Element = Mo, Radius 0.5, Weight 1 Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXTXXC8f/Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18 SNAP keyword rcutfac 4.615858 SNAP keyword twojmax 6 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 11 29 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 908 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.07 | 5.07 | 5.07 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20252.284 0 -20252.284 15729.372 14 0 -20309.64 0 -20309.64 8478.7812 Loop time of 3.78314 on 1 procs for 14 steps with 908 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20252.2838356 -20309.6289014 -20309.639717 Force two-norm initial, final = 85.7414 0.352333 Force max component initial, final = 23.6878 0.0675414 Final line search alpha, max atom move = 1 0.0675414 Iterations, force evaluations = 14 23 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7817 | 3.7817 | 3.7817 | 0.0 | 99.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077391 | 0.00077391 | 0.00077391 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006154 | | | 0.02 Nlocal: 908 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4848 ave 4848 max 4848 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: 58428 ave 58428 max 58428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58428 Ave neighs/atom = 64.348 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 14 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.07 | 5.07 | 5.07 Mbytes Step Temp E_pair E_mol TotEng Press Volume 14 0 -20309.64 0 -20309.64 8478.7812 14389.642 16 0 -20309.707 0 -20309.707 2583.2203 14422.266 Loop time of 0.681378 on 1 procs for 2 steps with 908 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20309.639717 -20309.7007086 -20309.7066923 Force two-norm initial, final = 82.1057 8.16855 Force max component initial, final = 69.0823 8.04287 Final line search alpha, max atom move = 4.53908e-05 0.000365072 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68088 | 0.68088 | 0.68088 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011826 | 0.00011826 | 0.00011826 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003757 | | | 0.06 Nlocal: 908 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4848 ave 4848 max 4848 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: 58236 ave 58236 max 58236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58236 Ave neighs/atom = 64.1366 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (3) compute pair/local, occasional, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.701 | 4.701 | 4.701 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20309.707 0 -20309.707 2583.2203 Loop time of 9.53674e-07 on 1 procs for 0 steps with 908 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 908 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4848 ave 4848 max 4848 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: 58228 ave 58228 max 58228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58228 Ave neighs/atom = 64.1278 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.701 | 4.701 | 4.701 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -20309.707 -20309.707 33.791003 95.435871 4.4721956 2583.2203 2583.2203 152.86966 8490.9367 -894.14557 2.4722027 671.63573 Loop time of 1.90735e-06 on 1 procs for 0 steps with 908 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.907e-06 | | |100.00 Nlocal: 908 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4848 ave 4848 max 4848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29114 ave 29114 max 29114 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 58228 ave 58228 max 58228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58228 Ave neighs/atom = 64.1278 Neighbor list builds = 0 Dangerous builds = 0 908 -4623.2840691897 eV 2.47220269376593 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05