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 -46.4453 0) to (16.4198 46.4453 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.25698 5.16024 4.4689 Created 218 atoms create_atoms CPU = 0.00029707 secs 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.25698 5.16024 4.4689 Created 218 atoms create_atoms CPU = 0.000142097 secs 218 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXrguoUj/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-XXXXXXrguoUj/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 = 5 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 = 428 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 = 5 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) = 4.744 | 4.744 | 4.744 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9559.1537 0 -9559.1537 2788.5797 22 0 -9571.8741 0 -9571.8741 -1189.9815 Loop time of 2.60812 on 1 procs for 22 steps with 428 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9559.15373483 -9571.8698284 -9571.87411027 Force two-norm initial, final = 23.2334 0.265113 Force max component initial, final = 6.65121 0.0641403 Final line search alpha, max atom move = 0.850484 0.0545503 Iterations, force evaluations = 22 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.606 | 2.606 | 2.606 | 0.0 | 99.92 Neigh | 0.00076008 | 0.00076008 | 0.00076008 | 0.0 | 0.03 Comm | 0.00083566 | 0.00083566 | 0.00083566 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000519 | | | 0.02 Nlocal: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3088 ave 3088 max 3088 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: 27436 ave 27436 max 27436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27436 Ave neighs/atom = 64.1028 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 : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.746 | 4.746 | 4.746 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -9571.8741 0 -9571.8741 -1189.9815 6816.1586 23 0 -9571.8779 0 -9571.8779 784.3172 6810.9411 Loop time of 0.182063 on 1 procs for 1 steps with 428 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9571.87411027 -9571.87411027 -9571.87792361 Force two-norm initial, final = 13.7599 1.09276 Force max component initial, final = 11.3949 0.848189 Final line search alpha, max atom move = 8.77588e-05 7.44361e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18188 | 0.18188 | 0.18188 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.2929e-05 | 5.2929e-05 | 5.2929e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001252 | | | 0.07 Nlocal: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3088 ave 3088 max 3088 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: 27468 ave 27468 max 27468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27468 Ave neighs/atom = 64.1776 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 = 5 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) = 4.377 | 4.377 | 4.377 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9571.8779 0 -9571.8779 784.3172 Loop time of 1.90735e-06 on 1 procs for 0 steps with 428 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: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3092 ave 3092 max 3092 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: 27468 ave 27468 max 27468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27468 Ave neighs/atom = 64.1776 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) = 4.377 | 4.377 | 4.377 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 -9571.8779 -9571.8779 16.412282 92.890624 4.4675176 784.3172 784.3172 -149.05436 2302.5432 199.46281 2.470637 310.1206 Loop time of 9.53674e-07 on 1 procs for 0 steps with 428 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: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3092 ave 3092 max 3092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13734 ave 13734 max 13734 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27468 ave 27468 max 27468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27468 Ave neighs/atom = 64.1776 Neighbor list builds = 0 Dangerous builds = 0 428 -2177.83730391547 eV 2.47063699370687 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03