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 (7.74036 32.8427 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.16024 5.47326 4.4689 Created 74 atoms create_atoms CPU = 0.000215054 secs 74 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.16024 5.47326 4.4689 Created 74 atoms create_atoms CPU = 6.69956e-05 secs 74 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXZvJIrH/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-XXXXXXZvJIrH/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 = 3 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 4 atoms, new total = 144 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 = 3 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) = 4.549 | 4.549 | 4.549 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3198.2569 0 -3198.2569 42295.563 12 0 -3218.6273 0 -3218.6273 26602.533 Loop time of 0.505538 on 1 procs for 12 steps with 144 atoms 100.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3198.25691148 -3218.62473317 -3218.62726413 Force two-norm initial, final = 53.7114 0.149742 Force max component initial, final = 19.9322 0.0469641 Final line search alpha, max atom move = 1 0.0469641 Iterations, force evaluations = 12 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50511 | 0.50511 | 0.50511 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025439 | 0.00025439 | 0.00025439 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000174 | | | 0.03 Nlocal: 144 ave 144 max 144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1596 ave 1596 max 1596 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: 9360 ave 9360 max 9360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9360 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 : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.549 | 4.549 | 4.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -3218.6273 0 -3218.6273 26602.533 2272.1169 17 0 -3218.7393 0 -3218.7393 7402.9773 2288.7642 Loop time of 0.190435 on 1 procs for 5 steps with 144 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3218.62726413 -3218.7378983 -3218.73929202 Force two-norm initial, final = 43.583 0.132116 Force max component initial, final = 30.8177 0.0657163 Final line search alpha, max atom move = 1 0.0657163 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19009 | 0.19009 | 0.19009 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.1062e-05 | 8.1062e-05 | 8.1062e-05 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002618 | | | 0.14 Nlocal: 144 ave 144 max 144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1596 ave 1596 max 1596 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: 9264 ave 9264 max 9264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9264 Ave neighs/atom = 64.3333 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 = 3 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) = 4.18 | 4.18 | 4.18 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3218.7393 0 -3218.7393 7402.9773 Loop time of 9.53674e-07 on 1 procs for 0 steps with 144 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: 144 ave 144 max 144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1596 ave 1596 max 1596 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: 9264 ave 9264 max 9264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9264 Ave neighs/atom = 64.3333 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) = 4.18 | 4.18 | 4.18 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 -3218.7393 -3218.7393 7.768663 65.685442 4.4852397 7402.9773 7402.9773 -46.170799 22301.274 -46.170799 2.4738412 143.14274 Loop time of 9.53674e-07 on 1 procs for 0 steps with 144 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: 144 ave 144 max 144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1596 ave 1596 max 1596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4632 ave 4632 max 4632 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 9264 ave 9264 max 9264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9264 Ave neighs/atom = 64.3333 Neighbor list builds = 0 Dangerous builds = 0 144 -731.02469099856 eV 2.47384115422117 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00