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 -32.2288 0) to (27.9083 32.2288 5.47326) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.00917 4.9578 5.47326 Created 318 atoms create_atoms CPU = 0.000305891 secs 318 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.00917 4.9578 5.47326 Created 316 atoms create_atoms CPU = 0.000149965 secs 316 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXPWx792/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-XXXXXXPWx792/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 20 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 = 624 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 20 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) = 4.882 | 4.882 | 4.882 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13874.154 0 -13874.154 46365.816 19 0 -13942.336 0 -13942.336 27594.884 Loop time of 3.09309 on 1 procs for 19 steps with 624 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13874.1535979 -13942.323587 -13942.3359348 Force two-norm initial, final = 77.5543 0.374312 Force max component initial, final = 16.2218 0.064008 Final line search alpha, max atom move = 0.598921 0.0383357 Iterations, force evaluations = 19 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.09 | 3.09 | 3.09 | 0.0 | 99.90 Neigh | 0.0017102 | 0.0017102 | 0.0017102 | 0.0 | 0.06 Comm | 0.00078845 | 0.00078845 | 0.00078845 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005944 | | | 0.02 Nlocal: 624 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3232 ave 3232 max 3232 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: 40276 ave 40276 max 40276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40276 Ave neighs/atom = 64.5449 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 : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.882 | 4.882 | 4.882 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -13942.336 0 -13942.336 27594.884 9845.8579 24 0 -13942.823 0 -13942.823 8346.215 9917.8665 Loop time of 0.950931 on 1 procs for 5 steps with 624 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13942.3359348 -13942.8223797 -13942.8226882 Force two-norm initial, final = 189.294 0.500834 Force max component initial, final = 142.76 0.0722789 Final line search alpha, max atom move = 0.000487926 3.52668e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95016 | 0.95016 | 0.95016 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016809 | 0.00016809 | 0.00016809 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006058 | | | 0.06 Nlocal: 624 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3234 ave 3234 max 3234 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: 40286 ave 40286 max 40286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40286 Ave neighs/atom = 64.5609 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 20 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) = 4.514 | 4.514 | 4.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13942.823 0 -13942.823 8346.215 Loop time of 9.53674e-07 on 1 procs for 0 steps with 624 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: 624 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3228 ave 3228 max 3228 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: 40248 ave 40248 max 40248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40248 Ave neighs/atom = 64.5 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) = 4.514 | 4.514 | 4.514 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 -13942.823 -13942.823 28.023809 64.457686 5.4905566 8346.215 8346.215 -8.3472434 25036.669 10.323605 2.5073596 538.04324 Loop time of 2.14577e-06 on 1 procs for 0 steps with 624 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 | | 2.146e-06 | | |100.00 Nlocal: 624 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3228 ave 3228 max 3228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20124 ave 20124 max 20124 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40248 ave 40248 max 40248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40248 Ave neighs/atom = 64.5 Neighbor list builds = 0 Dangerous builds = 0 624 -3162.7260838116 eV 2.50735956898812 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04