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 -57.233 0) to (20.2338 57.233 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.42858 4.88547 4.4689 Created 330 atoms create_atoms CPU = 0.000346184 secs 330 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.42858 4.88547 4.4689 Created 330 atoms create_atoms CPU = 0.000221968 secs 330 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXgdPL06/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-XXXXXXgdPL06/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 = 7 35 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 = 7 35 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) = 4.904 | 4.904 | 4.904 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14553.402 0 -14553.402 4648.183 40 0 -14587.307 0 -14587.307 -915.6276 Loop time of 7.78793 on 1 procs for 40 steps with 652 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 = -14553.4015796 -14587.2952874 -14587.3072881 Force two-norm initial, final = 65.7591 0.362748 Force max component initial, final = 23.0755 0.0584096 Final line search alpha, max atom move = 0.920734 0.0537797 Iterations, force evaluations = 40 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.7849 | 7.7849 | 7.7849 | 0.0 | 99.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001797 | 0.001797 | 0.001797 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001243 | | | 0.02 Nlocal: 652 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3545 ave 3545 max 3545 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: 41836 ave 41836 max 41836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41836 Ave neighs/atom = 64.1656 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.909 | 4.909 | 4.909 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -14587.307 0 -14587.307 -915.6276 10350.33 41 0 -14587.316 0 -14587.316 1571.8952 10340.345 Loop time of 0.308345 on 1 procs for 1 steps with 652 atoms 100.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14587.3072881 -14587.3072881 -14587.3163786 Force two-norm initial, final = 26.4894 0.799979 Force max component initial, final = 19.007 0.567054 Final line search alpha, max atom move = 5.26123e-05 2.98341e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30812 | 0.30812 | 0.30812 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.9843e-05 | 5.9843e-05 | 5.9843e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001662 | | | 0.05 Nlocal: 652 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3552 ave 3552 max 3552 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: 41792 ave 41792 max 41792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41792 Ave neighs/atom = 64.0982 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 = 7 35 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) = 4.54 | 4.54 | 4.54 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14587.316 0 -14587.316 1571.8952 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: 3552 ave 3552 max 3552 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: 41792 ave 41792 max 41792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41792 Ave neighs/atom = 64.0982 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) = 4.54 | 4.54 | 4.54 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 -14587.316 -14587.316 20.223889 114.46596 4.4667742 1571.8952 1571.8952 -87.818756 4737.1475 66.356858 2.4305195 406.42531 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: 3552 ave 3552 max 3552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20896 ave 20896 max 20896 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41792 ave 41792 max 41792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41792 Ave neighs/atom = 64.0982 Neighbor list builds = 0 Dangerous builds = 0 652 -3323.4974906497 eV 2.43051946989554 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08