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 -38.316 0) to (31.2823 38.316 7.74036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4689 4.43073 5.16024 Created 590 atoms create_atoms CPU = 0.00030899 secs 590 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4689 4.43073 5.16024 Created 590 atoms create_atoms CPU = 0.000178099 secs 590 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXTDM1B0/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-XXXXXXTDM1B0/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 = 10 24 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 20 atoms, new total = 1160 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 = 10 24 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) = 5.2 | 5.2 | 5.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -25844.33 0 -25844.33 2541.2649 58 0 -25924.683 0 -25924.683 -7136.0863 Loop time of 21.503 on 1 procs for 58 steps with 1160 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 = -25844.3299173 -25924.6665989 -25924.6832322 Force two-norm initial, final = 98.2933 0.403436 Force max component initial, final = 28.7234 0.0572989 Final line search alpha, max atom move = 1 0.0572989 Iterations, force evaluations = 58 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.493 | 21.493 | 21.493 | 0.0 | 99.95 Neigh | 0.004442 | 0.004442 | 0.004442 | 0.0 | 0.02 Comm | 0.0030868 | 0.0030868 | 0.0030868 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002947 | | | 0.01 Nlocal: 1160 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4004 ave 4004 max 4004 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: 74332 ave 74332 max 74332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74332 Ave neighs/atom = 64.0793 Neighbor list builds = 2 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.209 | 5.209 | 5.209 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -25924.683 0 -25924.683 -7136.0863 18555.366 60 0 -25924.778 0 -25924.778 -1145.7254 18512.194 Loop time of 0.666015 on 1 procs for 2 steps with 1160 atoms 100.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -25924.6832322 -25924.7758769 -25924.7778244 Force two-norm initial, final = 114.591 1.41537 Force max component initial, final = 81.1432 0.987066 Final line search alpha, max atom move = 7.82598e-05 7.72476e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66564 | 0.66564 | 0.66564 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.203e-05 | 9.203e-05 | 9.203e-05 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002849 | | | 0.04 Nlocal: 1160 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4288 ave 4288 max 4288 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: 74300 ave 74300 max 74300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74300 Ave neighs/atom = 64.0517 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 = 10 24 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) = 4.84 | 4.84 | 4.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -25924.778 0 -25924.778 -1145.7254 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1160 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: 1160 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4288 ave 4288 max 4288 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: 74300 ave 74300 max 74300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74300 Ave neighs/atom = 64.0517 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) = 4.84 | 4.84 | 4.84 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 -25924.778 -25924.778 31.246376 76.631962 7.7312248 -1145.7254 -1145.7254 85.329609 -3443.5983 -78.907655 2.4314367 1090.8884 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1160 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: 1160 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4288 ave 4288 max 4288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37150 ave 37150 max 37150 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74300 ave 74300 max 74300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74300 Ave neighs/atom = 64.0517 Neighbor list builds = 0 Dangerous builds = 0 1160 -5884.8546495856 eV 2.43143668887185 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22