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 -41.9251 0) to (14.8217 41.9251 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.38969 4.76386 4.4689 Created 177 atoms create_atoms CPU = 0.000195026 secs 177 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.38969 4.76386 4.4689 Created 177 atoms create_atoms CPU = 6.81877e-05 secs 177 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXs521RW/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-XXXXXXs521RW/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 = 5 26 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 6 atoms, new total = 348 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 = 5 26 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) = 4.687 | 4.687 | 4.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7766.7269 0 -7766.7269 -42.183203 36 0 -7780.608 0 -7780.608 -7976.9532 Loop time of 3.78388 on 1 procs for 36 steps with 348 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 = -7766.72692103 -7780.60303653 -7780.60801545 Force two-norm initial, final = 30.2233 0.22006 Force max component initial, final = 10.551 0.0316269 Final line search alpha, max atom move = 1 0.0316269 Iterations, force evaluations = 36 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7809 | 3.7809 | 3.7809 | 0.0 | 99.92 Neigh | 0.00094008 | 0.00094008 | 0.00094008 | 0.0 | 0.02 Comm | 0.0012486 | 0.0012486 | 0.0012486 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008116 | | | 0.02 Nlocal: 348 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2648 ave 2648 max 2648 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: 22280 ave 22280 max 22280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22280 Ave neighs/atom = 64.023 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 : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.692 | 4.692 | 4.692 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -7780.608 0 -7780.608 -7976.9532 5553.9477 38 0 -7780.6574 0 -7780.6574 -84.120254 5536.866 Loop time of 0.238809 on 1 procs for 2 steps with 348 atoms 96.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7780.60801545 -7780.65099149 -7780.65735453 Force two-norm initial, final = 45.1079 0.875086 Force max component initial, final = 32.2414 0.598866 Final line search alpha, max atom move = 8.26147e-05 4.94751e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23854 | 0.23854 | 0.23854 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.4611e-05 | 6.4611e-05 | 6.4611e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002077 | | | 0.09 Nlocal: 348 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704 ave 2704 max 2704 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: 22292 ave 22292 max 22292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22292 Ave neighs/atom = 64.0575 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 = 5 26 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) = 4.324 | 4.324 | 4.324 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7780.6574 0 -7780.6574 -84.120254 Loop time of 9.53674e-07 on 1 procs for 0 steps with 348 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: 348 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704 ave 2704 max 2704 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: 22296 ave 22296 max 22296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22296 Ave neighs/atom = 64.069 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) = 4.324 | 4.324 | 4.324 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 -7780.6574 -7780.6574 14.798247 83.850282 4.4622018 -84.120254 -84.120254 -173.0173 -250.46906 171.1256 2.4506836 307.67004 Loop time of 9.53674e-07 on 1 procs for 0 steps with 348 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: 348 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704 ave 2704 max 2704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11148 ave 11148 max 11148 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22296 ave 22296 max 22296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22296 Ave neighs/atom = 64.069 Neighbor list builds = 0 Dangerous builds = 0 348 -1768.68040207338 eV 2.45068361198818 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04