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 -33.7426 0) to (23.8574 33.7426 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.60406 5.32728 4.4689 Created 230 atoms create_atoms CPU = 0.000256777 secs 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.60406 5.32728 4.4689 Created 230 atoms create_atoms CPU = 0.000120163 secs 230 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX9WVspY/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-XXXXXX9WVspY/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 = 8 21 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 = 452 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 = 8 21 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) = 4.749 | 4.749 | 4.749 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10064.345 0 -10064.345 17363.979 18 0 -10100.791 0 -10100.791 5367.3911 Loop time of 2.13164 on 1 procs for 18 steps with 452 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 = -10064.3450002 -10100.7833449 -10100.7905742 Force two-norm initial, final = 61.0946 0.238142 Force max component initial, final = 17.077 0.0344473 Final line search alpha, max atom move = 0.659689 0.0227245 Iterations, force evaluations = 18 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1294 | 2.1294 | 2.1294 | 0.0 | 99.90 Neigh | 0.0011392 | 0.0011392 | 0.0011392 | 0.0 | 0.05 Comm | 0.00063896 | 0.00063896 | 0.00063896 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004439 | | | 0.02 Nlocal: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2908 ave 2908 max 2908 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: 29108 ave 29108 max 29108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29108 Ave neighs/atom = 64.3982 Neighbor list builds = 1 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 : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.751 | 4.751 | 4.751 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -10100.791 0 -10100.791 5367.3911 7195.0184 20 0 -10100.821 0 -10100.821 745.32367 7207.8838 Loop time of 0.273259 on 1 procs for 2 steps with 452 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10100.7905742 -10100.8139196 -10100.8213185 Force two-norm initial, final = 33.8145 5.47234 Force max component initial, final = 33.2659 5.11031 Final line search alpha, max atom move = 7.53147e-05 0.000384882 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27298 | 0.27298 | 0.27298 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.3181e-05 | 6.3181e-05 | 6.3181e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002146 | | | 0.08 Nlocal: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2908 ave 2908 max 2908 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: 29092 ave 29092 max 29092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29092 Ave neighs/atom = 64.3628 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 = 8 21 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) = 4.383 | 4.383 | 4.383 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10100.821 0 -10100.821 745.32367 Loop time of 1.90735e-06 on 1 procs for 0 steps with 452 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: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2908 ave 2908 max 2908 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: 29084 ave 29084 max 29084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29084 Ave neighs/atom = 64.3451 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) = 4.383 | 4.383 | 4.383 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 -10100.821 -10100.821 23.852921 67.485203 4.4777274 745.32367 745.32367 -1135.7137 3803.9479 -432.26324 2.452563 521.76566 Loop time of 9.53674e-07 on 1 procs for 0 steps with 452 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: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2908 ave 2908 max 2908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14542 ave 14542 max 14542 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29084 ave 29084 max 29084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29084 Ave neighs/atom = 64.3451 Neighbor list builds = 0 Dangerous builds = 0 452 -2292.1615986296 eV 2.45256297117552 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02