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 -39.9742 0) to (9.99276 39.9742 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9971 3.9971 3.15999 Created 82 atoms create_atoms CPU = 0.000181913 secs 82 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9971 3.9971 3.15999 Created 82 atoms create_atoms CPU = 3.8147e-05 secs 82 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXhQCBrB/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-XXXXXXhQCBrB/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 25 1 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 4 atoms, new total = 160 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 25 1 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) = 4.56 | 4.56 | 4.56 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3570.8086 0 -3570.8086 29742.664 11 0 -3577.3704 0 -3577.3704 21625.205 Loop time of 0.65184 on 1 procs for 11 steps with 160 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3570.8085697 -3577.36806127 -3577.3703783 Force two-norm initial, final = 19.1667 0.136675 Force max component initial, final = 5.72831 0.0207863 Final line search alpha, max atom move = 1 0.0207863 Iterations, force evaluations = 11 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65136 | 0.65136 | 0.65136 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030112 | 0.00030112 | 0.00030112 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001774 | | | 0.03 Nlocal: 160 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1975 ave 1975 max 1975 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: 10400 ave 10400 max 10400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10400 Ave neighs/atom = 65 Neighbor list builds = 0 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 : 11 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.56 | 4.56 | 4.56 Mbytes Step Temp E_pair E_mol TotEng Press Volume 11 0 -3577.3704 0 -3577.3704 21625.205 2524.531 14 0 -3577.4014 0 -3577.4014 12057.751 2533.6099 Loop time of 0.168021 on 1 procs for 3 steps with 160 atoms 101.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3577.3703783 -3577.40105581 -3577.40142079 Force two-norm initial, final = 24.2663 0.714267 Force max component initial, final = 19.4939 0.663363 Final line search alpha, max atom move = 0.000515843 0.000342191 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16777 | 0.16777 | 0.16777 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.9141e-05 | 6.9141e-05 | 6.9141e-05 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001845 | | | 0.11 Nlocal: 160 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1981 ave 1981 max 1981 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: 10256 ave 10256 max 10256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10256 Ave neighs/atom = 64.1 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 25 1 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) = 4.192 | 4.192 | 4.192 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3577.4014 0 -3577.4014 12057.751 Loop time of 9.53674e-07 on 1 procs for 0 steps with 160 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: 160 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1981 ave 1981 max 1981 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: 10256 ave 10256 max 10256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10256 Ave neighs/atom = 64.1 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) = 4.192 | 4.192 | 4.192 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 -3577.4014 -3577.4014 10.016194 79.948401 3.1639326 12057.751 12057.751 -137.88106 36731.148 -420.01378 2.5006853 120.47181 Loop time of 9.53674e-07 on 1 procs for 0 steps with 160 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: 160 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1981 ave 1981 max 1981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5128 ave 5128 max 5128 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 10256 ave 10256 max 10256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10256 Ave neighs/atom = 64.1 Neighbor list builds = 0 Dangerous builds = 0 160 -813.27408632205 eV 2.50068528053017 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00