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 -50.9564 0) to (25.4766 50.9564 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.31143 4.31143 3.15999 Created 261 atoms create_atoms CPU = 0.000163078 secs 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.31143 4.31143 3.15999 Created 261 atoms create_atoms CPU = 5.60284e-05 secs 261 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXgKUpve/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-XXXXXXgKUpve/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 = 8 31 1 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 = 516 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 = 8 31 1 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) = 4.813 | 4.813 | 4.813 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11514.625 0 -11514.625 9083.9132 26 0 -11540.398 0 -11540.398 -422.43555 Loop time of 3.92465 on 1 procs for 26 steps with 516 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 = -11514.6251717 -11540.388139 -11540.3980836 Force two-norm initial, final = 47.6126 0.33465 Force max component initial, final = 17.8557 0.0832544 Final line search alpha, max atom move = 0.499014 0.0415451 Iterations, force evaluations = 26 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9214 | 3.9214 | 3.9214 | 0.0 | 99.92 Neigh | 0.001333 | 0.001333 | 0.001333 | 0.0 | 0.03 Comm | 0.0012274 | 0.0012274 | 0.0012274 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007169 | | | 0.02 Nlocal: 516 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3926 ave 3926 max 3926 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: 33156 ave 33156 max 33156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33156 Ave neighs/atom = 64.2558 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 : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.813 | 4.813 | 4.813 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -11540.398 0 -11540.398 -422.43555 8204.5859 27 0 -11540.409 0 -11540.409 1517.5448 8198.4745 Loop time of 0.218126 on 1 procs for 1 steps with 516 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 = -11540.3980836 -11540.3980836 -11540.4092345 Force two-norm initial, final = 21.0442 7.69583 Force max component initial, final = 20.3873 7.56021 Final line search alpha, max atom move = 4.90502e-05 0.00037083 Iterations, force evaluations = 1 1 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21796 | 0.21796 | 0.21796 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 4.7684e-05 | 4.7684e-05 | 4.7684e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001173 | | | 0.05 Nlocal: 516 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3922 ave 3922 max 3922 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: 33156 ave 33156 max 33156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33156 Ave neighs/atom = 64.2558 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 = 8 31 1 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) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11540.409 0 -11540.409 1517.5448 Loop time of 9.53674e-07 on 1 procs for 0 steps with 516 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: 516 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3926 ave 3926 max 3926 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: 33158 ave 33158 max 33158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33158 Ave neighs/atom = 64.2597 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) = 4.444 | 4.444 | 4.444 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 -11540.409 -11540.409 25.483146 101.91288 3.1568282 1517.5448 1517.5448 1477.8212 2801.8754 272.9377 2.4479643 287.52189 Loop time of 1.19209e-06 on 1 procs for 0 steps with 516 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 | | 1.192e-06 | | |100.00 Nlocal: 516 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3926 ave 3926 max 3926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16579 ave 16579 max 16579 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33158 ave 33158 max 33158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33158 Ave neighs/atom = 64.2597 Neighbor list builds = 0 Dangerous builds = 0 516 -2626.0985808866 eV 2.44796427208775 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04