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 -32.8427 0) to (23.2211 32.8427 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.16024 4.25698 4.4689 Created 218 atoms create_atoms CPU = 0.000236988 secs 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.16024 4.25698 4.4689 Created 218 atoms create_atoms CPU = 0.000103951 secs 218 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXMIzcj2/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-XXXXXXMIzcj2/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 20 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 10 atoms, new total = 426 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 20 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) = 4.736 | 4.736 | 4.736 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9483.9495 0 -9483.9495 4074.9938 50 0 -9516.2783 0 -9516.2783 -4481.0714 Loop time of 7.20996 on 1 procs for 50 steps with 426 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 = -9483.94946158 -9516.27128499 -9516.27827859 Force two-norm initial, final = 71.415 0.316403 Force max component initial, final = 32.3594 0.0571895 Final line search alpha, max atom move = 1 0.0571895 Iterations, force evaluations = 50 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2053 | 7.2053 | 7.2053 | 0.0 | 99.94 Neigh | 0.0011921 | 0.0011921 | 0.0011921 | 0.0 | 0.02 Comm | 0.0021276 | 0.0021276 | 0.0021276 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001322 | | | 0.02 Nlocal: 426 ave 426 max 426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2774 ave 2774 max 2774 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: 27340 ave 27340 max 27340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27340 Ave neighs/atom = 64.1784 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.742 | 4.742 | 4.742 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -9516.2783 0 -9516.2783 -4481.0714 6816.3507 52 0 -9516.3126 0 -9516.3126 1479.4714 6800.7095 Loop time of 0.290199 on 1 procs for 2 steps with 426 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 = -9516.27827859 -9516.30893926 -9516.31260683 Force two-norm initial, final = 40.8171 4.69223 Force max component initial, final = 34.9033 4.59863 Final line search alpha, max atom move = 8.23444e-05 0.000378672 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28993 | 0.28993 | 0.28993 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.0109e-05 | 8.0109e-05 | 8.0109e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001848 | | | 0.06 Nlocal: 426 ave 426 max 426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2786 ave 2786 max 2786 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: 27348 ave 27348 max 27348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27348 Ave neighs/atom = 64.1972 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 20 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) = 4.374 | 4.374 | 4.374 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9516.3126 0 -9516.3126 1479.4714 Loop time of 9.53674e-07 on 1 procs for 0 steps with 426 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: 426 ave 426 max 426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2786 ave 2786 max 2786 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: 27356 ave 27356 max 27356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27356 Ave neighs/atom = 64.216 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) = 4.374 | 4.374 | 4.374 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 -9516.3126 -9516.3126 23.204488 65.685442 4.4618309 1479.4714 1479.4714 1082.6162 3561.9499 -206.15196 2.388392 492.73645 Loop time of 9.53674e-07 on 1 procs for 0 steps with 426 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: 426 ave 426 max 426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2786 ave 2786 max 2786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13678 ave 13678 max 13678 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27356 ave 27356 max 27356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27356 Ave neighs/atom = 64.216 Neighbor list builds = 0 Dangerous builds = 0 426 -2156.82357882283 eV 2.38839195615426 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07