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 -54.7358 0) to (22.3445 54.7358 7.74036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.36268 4.74349 5.16024 Created 602 atoms create_atoms CPU = 0.000362158 secs 602 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.36268 4.74349 5.16024 Created 602 atoms create_atoms CPU = 0.000248909 secs 602 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXtMvFsI/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-XXXXXXtMvFsI/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 = 7 34 3 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 12 atoms, new total = 1192 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 = 7 34 3 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) = 5.247 | 5.247 | 5.247 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -26560.143 0 -26560.143 19186.731 70 0 -26661.759 0 -26661.759 -460.69388 Loop time of 19.1499 on 1 procs for 70 steps with 1192 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 = -26560.142642 -26661.7364689 -26661.7586126 Force two-norm initial, final = 97.4419 0.549884 Force max component initial, final = 28.2141 0.075711 Final line search alpha, max atom move = 0.417101 0.0315791 Iterations, force evaluations = 70 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.131 | 19.131 | 19.131 | 0.0 | 99.90 Neigh | 0.012867 | 0.012867 | 0.012867 | 0.0 | 0.07 Comm | 0.0031538 | 0.0031538 | 0.0031538 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003038 | | | 0.02 Nlocal: 1192 ave 1192 max 1192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4484 ave 4484 max 4484 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: 76560 ave 76560 max 76560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76560 Ave neighs/atom = 64.2282 Neighbor list builds = 4 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 : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.256 | 5.256 | 5.256 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -26661.759 0 -26661.759 -460.69388 18933.579 71 0 -26661.759 0 -26661.759 -742.61024 18935.667 Loop time of 0.499254 on 1 procs for 1 steps with 1192 atoms 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -26661.7586126 -26661.7586126 -26661.7588759 Force two-norm initial, final = 5.09612 2.36397 Force max component initial, final = 5.05436 2.29811 Final line search alpha, max atom move = 0.000197849 0.000454679 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49897 | 0.49897 | 0.49897 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.9155e-05 | 7.9155e-05 | 7.9155e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002007 | | | 0.04 Nlocal: 1192 ave 1192 max 1192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4481 ave 4481 max 4481 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: 76548 ave 76548 max 76548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76548 Ave neighs/atom = 64.2181 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 = 7 34 3 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) = 4.887 | 4.887 | 4.887 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -26661.759 0 -26661.759 -742.61024 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1192 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: 1192 ave 1192 max 1192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4481 ave 4481 max 4481 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: 76544 ave 76544 max 76544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76544 Ave neighs/atom = 64.2148 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) = 4.887 | 4.887 | 4.887 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 -26661.759 -26661.759 22.346796 109.47152 7.7404138 -742.61024 -742.61024 5.6087971 -2038.9914 -194.44813 2.4521862 696.78793 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1192 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: 1192 ave 1192 max 1192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4481 ave 4481 max 4481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38272 ave 38272 max 38272 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 76544 ave 76544 max 76544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76544 Ave neighs/atom = 64.2148 Neighbor list builds = 0 Dangerous builds = 0 1192 -6069.0102341689 eV 2.45218624331967 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20