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 -36.5827 0) to (25.8656 36.5827 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0187 5.45963 4.4689 Created 269 atoms create_atoms CPU = 0.000231028 secs 269 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0187 5.45963 4.4689 Created 269 atoms create_atoms CPU = 0.000108957 secs 269 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXkNKh4Z/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-XXXXXXkNKh4Z/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 23 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 6 atoms, new total = 532 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 23 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) = 4.807 | 4.807 | 4.807 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11855.117 0 -11855.117 20286.369 38 0 -11893.538 0 -11893.538 5755.3432 Loop time of 5.74191 on 1 procs for 38 steps with 532 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11855.1174226 -11893.5268834 -11893.5380469 Force two-norm initial, final = 52.4926 0.409435 Force max component initial, final = 14.2013 0.103335 Final line search alpha, max atom move = 0.257622 0.0266214 Iterations, force evaluations = 38 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7393 | 5.7393 | 5.7393 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015631 | 0.0015631 | 0.0015631 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001084 | | | 0.02 Nlocal: 532 ave 532 max 532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3276 ave 3276 max 3276 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: 34292 ave 34292 max 34292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34292 Ave neighs/atom = 64.4586 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 : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.807 | 4.807 | 4.807 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -11893.538 0 -11893.538 5755.3432 8457.2408 40 0 -11893.574 0 -11893.574 808.92227 8473.3522 Loop time of 0.367175 on 1 procs for 2 steps with 532 atoms 100.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11893.5380469 -11893.5664422 -11893.5737976 Force two-norm initial, final = 41.2915 6.9433 Force max component initial, final = 39.8526 6.65327 Final line search alpha, max atom move = 6.55443e-05 0.000436084 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36684 | 0.36684 | 0.36684 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.4639e-05 | 8.4639e-05 | 8.4639e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002553 | | | 0.07 Nlocal: 532 ave 532 max 532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3252 ave 3252 max 3252 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: 34112 ave 34112 max 34112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34112 Ave neighs/atom = 64.1203 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 23 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) = 4.438 | 4.438 | 4.438 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11893.574 0 -11893.574 808.92227 Loop time of 9.53674e-07 on 1 procs for 0 steps with 532 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: 532 ave 532 max 532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3252 ave 3252 max 3252 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: 34104 ave 34104 max 34104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34104 Ave neighs/atom = 64.1053 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) = 4.438 | 4.438 | 4.438 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 -11893.574 -11893.574 25.865977 73.165336 4.4773495 808.92227 808.92227 -1258.0457 4052.1651 -367.35251 2.4545624 497.99554 Loop time of 9.53674e-07 on 1 procs for 0 steps with 532 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: 532 ave 532 max 532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3252 ave 3252 max 3252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17052 ave 17052 max 17052 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34104 ave 34104 max 34104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34104 Ave neighs/atom = 64.1053 Neighbor list builds = 0 Dangerous builds = 0 532 -2702.8504104614 eV 2.45456235500804 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06