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 -43.4458 0) to (11.8236 43.4458 7.74036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.06725 4.82696 5.16024 Created 254 atoms create_atoms CPU = 0.000255108 secs 254 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.06725 4.82696 5.16024 Created 254 atoms create_atoms CPU = 0.00012207 secs 254 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXOZBStY/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-XXXXXXOZBStY/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 = 4 27 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 8 atoms, new total = 500 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 = 4 27 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) = 4.816 | 4.816 | 4.816 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11135.433 0 -11135.433 17315.432 43 0 -11179.871 0 -11179.871 985.6907 Loop time of 6.46806 on 1 procs for 43 steps with 500 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 = -11135.4328005 -11179.8632582 -11179.8705388 Force two-norm initial, final = 69.4769 0.293009 Force max component initial, final = 20.2633 0.0423946 Final line search alpha, max atom move = 1 0.0423946 Iterations, force evaluations = 43 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.464 | 6.464 | 6.464 | 0.0 | 99.94 Neigh | 0.0014029 | 0.0014029 | 0.0014029 | 0.0 | 0.02 Comm | 0.0015068 | 0.0015068 | 0.0015068 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00116 | | | 0.02 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2850 ave 2850 max 2850 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: 32172 ave 32172 max 32172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32172 Ave neighs/atom = 64.344 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 : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.818 | 4.818 | 4.818 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -11179.871 0 -11179.871 985.6907 7952.2224 44 0 -11179.873 0 -11179.873 1048.6547 7952.0299 Loop time of 0.179144 on 1 procs for 1 steps with 500 atoms 94.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11179.8705388 -11179.8705388 -11179.8728274 Force two-norm initial, final = 7.11819 0.398967 Force max component initial, final = 5.16013 0.193202 Final line search alpha, max atom move = 0.000193794 3.74413e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17898 | 0.17898 | 0.17898 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 4.6968e-05 | 4.6968e-05 | 4.6968e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000118 | | | 0.07 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2793 ave 2793 max 2793 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: 32136 ave 32136 max 32136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32136 Ave neighs/atom = 64.272 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 = 4 27 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) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11179.873 0 -11179.873 1048.6547 Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 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: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2793 ave 2793 max 2793 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: 32136 ave 32136 max 32136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32136 Ave neighs/atom = 64.272 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) = 4.449 | 4.449 | 4.449 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 -11179.873 -11179.873 11.828821 86.891631 7.7367505 1048.6547 1048.6547 37.512986 3069.543 38.908211 2.4433068 398.5547 Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 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: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2793 ave 2793 max 2793 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16068 ave 16068 max 16068 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32136 ave 32136 max 32136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32136 Ave neighs/atom = 64.272 Neighbor list builds = 0 Dangerous builds = 0 500 -2541.9749072285 eV 2.44330681161243 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06