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 -45.1368 0) to (31.9143 45.1368 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.00617 3.98238 4.4689 Created 409 atoms create_atoms CPU = 0.000305176 secs 409 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.00617 3.98238 4.4689 Created 409 atoms create_atoms CPU = 0.00019908 secs 409 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXt9ke0S/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-XXXXXXt9ke0S/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 28 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 10 atoms, new total = 808 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 28 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) = 5.006 | 5.006 | 5.006 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18002.418 0 -18002.418 7184.3762 50 0 -18065.913 0 -18065.913 -3666.7584 Loop time of 11.1128 on 1 procs for 50 steps with 808 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 = -18002.4176921 -18065.8981623 -18065.9130948 Force two-norm initial, final = 98.118 0.4965 Force max component initial, final = 25.4711 0.200417 Final line search alpha, max atom move = 0.708858 0.142067 Iterations, force evaluations = 50 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.104 | 11.104 | 11.104 | 0.0 | 99.92 Neigh | 0.0042169 | 0.0042169 | 0.0042169 | 0.0 | 0.04 Comm | 0.0025864 | 0.0025864 | 0.0025864 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00181 | | | 0.02 Nlocal: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4432 ave 4432 max 4432 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: 51752 ave 51752 max 51752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51752 Ave neighs/atom = 64.0495 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.008 | 5.008 | 5.008 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -18065.913 0 -18065.913 -3666.7584 12874.992 52 0 -18065.946 0 -18065.946 451.88509 12854.481 Loop time of 0.705351 on 1 procs for 2 steps with 808 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -18065.9130948 -18065.9451635 -18065.945599 Force two-norm initial, final = 55.9637 0.526232 Force max component initial, final = 43.6218 0.212609 Final line search alpha, max atom move = 0.000356901 7.58802e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70484 | 0.70484 | 0.70484 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012589 | 0.00012589 | 0.00012589 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003815 | | | 0.05 Nlocal: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4432 ave 4432 max 4432 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: 51740 ave 51740 max 51740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51740 Ave neighs/atom = 64.0347 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 28 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) = 4.64 | 4.64 | 4.64 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18065.946 0 -18065.946 451.88509 Loop time of 9.53674e-07 on 1 procs for 0 steps with 808 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: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4432 ave 4432 max 4432 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: 51748 ave 51748 max 51748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51748 Ave neighs/atom = 64.0446 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) = 4.64 | 4.64 | 4.64 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 -18065.946 -18065.946 31.896762 90.273639 4.4642345 451.88509 451.88509 -10.149822 1362.8971 2.9079878 2.4102989 546.78284 Loop time of 9.53674e-07 on 1 procs for 0 steps with 808 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: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4432 ave 4432 max 4432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25874 ave 25874 max 25874 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 51748 ave 51748 max 51748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51748 Ave neighs/atom = 64.0446 Neighbor list builds = 0 Dangerous builds = 0 808 -4107.1025599286 eV 2.41029894156086 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12