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 -40.4708 0) to (28.6149 40.4708 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.88547 5.42858 4.4689 Created 330 atoms create_atoms CPU = 0.000241995 secs 330 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.88547 5.42858 4.4689 Created 330 atoms create_atoms CPU = 0.000128984 secs 330 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXy71M9e/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-XXXXXXy71M9e/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 = 9 25 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 8 atoms, new total = 652 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 = 9 25 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) = 4.893 | 4.893 | 4.893 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14533.163 0 -14533.163 17592.75 24 0 -14579.564 0 -14579.564 7346.8156 Loop time of 4.31567 on 1 procs for 24 steps with 652 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14533.1634535 -14579.5542356 -14579.5638532 Force two-norm initial, final = 67.7477 0.28506 Force max component initial, final = 19.3133 0.0361534 Final line search alpha, max atom move = 0.495886 0.0179279 Iterations, force evaluations = 24 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3124 | 4.3124 | 4.3124 | 0.0 | 99.92 Neigh | 0.001523 | 0.001523 | 0.001523 | 0.0 | 0.04 Comm | 0.00097919 | 0.00097919 | 0.00097919 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000756 | | | 0.02 Nlocal: 652 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3230 ave 3230 max 3230 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: 41852 ave 41852 max 41852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41852 Ave neighs/atom = 64.1902 Neighbor list builds = 1 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 : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.893 | 4.893 | 4.893 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -14579.564 0 -14579.564 7346.8156 10350.567 27 0 -14579.644 0 -14579.644 2143.8473 10371.292 Loop time of 0.599446 on 1 procs for 3 steps with 652 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14579.5638532 -14579.6375141 -14579.6438516 Force two-norm initial, final = 66.194 2.61188 Force max component initial, final = 64.6035 2.0402 Final line search alpha, max atom move = 8.75109e-05 0.00017854 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59897 | 0.59897 | 0.59897 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012231 | 0.00012231 | 0.00012231 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003562 | | | 0.06 Nlocal: 652 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3226 ave 3226 max 3226 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: 41856 ave 41856 max 41856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41856 Ave neighs/atom = 64.1963 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 = 9 25 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) = 4.525 | 4.525 | 4.525 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14579.644 0 -14579.644 2143.8473 Loop time of 1.90735e-06 on 1 procs for 0 steps with 652 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: 652 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3226 ave 3226 max 3226 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: 41840 ave 41840 max 41840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41840 Ave neighs/atom = 64.1718 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) = 4.525 | 4.525 | 4.525 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 -14579.644 -14579.644 28.599605 80.941508 4.4802428 2143.8473 2143.8473 247.22905 5868.3392 315.97354 2.4441104 533.6757 Loop time of 9.53674e-07 on 1 procs for 0 steps with 652 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: 652 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3226 ave 3226 max 3226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20920 ave 20920 max 20920 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41840 ave 41840 max 41840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41840 Ave neighs/atom = 64.1718 Neighbor list builds = 0 Dangerous builds = 0 652 -3315.824963682 eV 2.44411041421578 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05