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 -46.7667 0) to (38.1823 46.7667 7.74036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7074 4.48418 5.16024 Created 877 atoms create_atoms CPU = 0.000305891 secs 877 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7074 4.48418 5.16024 Created 877 atoms create_atoms CPU = 0.000211954 secs 877 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXCtghcB/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-XXXXXXCtghcB/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 = 12 29 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 15 atoms, new total = 1739 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 = 12 29 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) = 5.953 | 5.953 | 5.953 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -38754.572 0 -38754.572 15439.054 101 0 -38882.015 0 -38882.015 4110.2254 Loop time of 50.9076 on 1 procs for 101 steps with 1739 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -38754.5715704 -38881.9823861 -38882.0148805 Force two-norm initial, final = 115.125 0.655133 Force max component initial, final = 21.737 0.163329 Final line search alpha, max atom move = 0.582877 0.0952006 Iterations, force evaluations = 101 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 50.878 | 50.878 | 50.878 | 0.0 | 99.94 Neigh | 0.015713 | 0.015713 | 0.015713 | 0.0 | 0.03 Comm | 0.006588 | 0.006588 | 0.006588 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007009 | | | 0.01 Nlocal: 1739 ave 1739 max 1739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5382 ave 5382 max 5382 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: 111662 ave 111662 max 111662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111662 Ave neighs/atom = 64.2105 Neighbor list builds = 4 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 : 101 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.967 | 5.967 | 5.967 Mbytes Step Temp E_pair E_mol TotEng Press Volume 101 0 -38882.015 0 -38882.015 4110.2254 27643.297 102 0 -38882.028 0 -38882.028 2329.6976 27662.244 Loop time of 0.822698 on 1 procs for 1 steps with 1739 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 = -38882.0148805 -38882.0148805 -38882.0275136 Force two-norm initial, final = 49.0302 11.2978 Force max component initial, final = 44.6494 10.3478 Final line search alpha, max atom move = 2.23967e-05 0.000231757 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8223 | 0.8223 | 0.8223 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011206 | 0.00011206 | 0.00011206 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002847 | | | 0.03 Nlocal: 1739 ave 1739 max 1739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5802 ave 5802 max 5802 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: 111452 ave 111452 max 111452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111452 Ave neighs/atom = 64.0897 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 = 12 29 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) = 5.599 | 5.599 | 5.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -38882.028 0 -38882.028 2329.6976 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1739 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: 1739 ave 1739 max 1739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5802 ave 5802 max 5802 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: 111444 ave 111444 max 111444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111444 Ave neighs/atom = 64.0851 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) = 5.599 | 5.599 | 5.599 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 -38882.028 -38882.028 38.190447 93.53343 7.7440083 2329.6976 2329.6976 -599.46551 7328.5689 259.98951 2.39796 1295.6425 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1739 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 | | 1.907e-06 | | |100.00 Nlocal: 1739 ave 1739 max 1739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5802 ave 5802 max 5802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55722 ave 55722 max 55722 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 111444 ave 111444 max 111444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111444 Ave neighs/atom = 64.0851 Neighbor list builds = 0 Dangerous builds = 0 1739 -8839.4185471229 eV 2.39795997621812 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:52