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 -63.3607 0) to (36.5795 63.3607 5.47326) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.91367 5.04339 5.47326 Created 806 atoms create_atoms CPU = 0.000409126 secs 806 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.91367 5.04339 5.47326 Created 805 atoms create_atoms CPU = 0.000279188 secs 805 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX8rCKqz/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-XXXXXX8rCKqz/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 = 12 39 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 5 atoms, new total = 1606 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 = 12 39 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) = 5.954 | 5.954 | 5.954 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -35827.739 0 -35827.739 20417.203 20 0 -35931.5 0 -35931.5 10413.381 Loop time of 8.83228 on 1 procs for 20 steps with 1606 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 = -35827.7392997 -35931.4681885 -35931.4996918 Force two-norm initial, final = 110.216 0.617084 Force max component initial, final = 27.3582 0.127091 Final line search alpha, max atom move = 0.497853 0.0632725 Iterations, force evaluations = 20 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.8294 | 8.8294 | 8.8294 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015666 | 0.0015666 | 0.0015666 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001296 | | | 0.01 Nlocal: 1606 ave 1606 max 1606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6829 ave 6829 max 6829 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: 103602 ave 103602 max 103602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103602 Ave neighs/atom = 64.5093 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 : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.954 | 5.954 | 5.954 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -35931.5 0 -35931.5 10413.381 25370.796 22 0 -35931.711 0 -35931.711 2620.5494 25447.016 Loop time of 1.13099 on 1 procs for 2 steps with 1606 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 = -35931.4996918 -35931.6809064 -35931.711446 Force two-norm initial, final = 199.919 4.54252 Force max component initial, final = 151.613 3.68175 Final line search alpha, max atom move = 1.68204e-05 6.19286e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1303 | 1.1303 | 1.1303 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016284 | 0.00016284 | 0.00016284 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005751 | | | 0.05 Nlocal: 1606 ave 1606 max 1606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6812 ave 6812 max 6812 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: 103240 ave 103240 max 103240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103240 Ave neighs/atom = 64.2839 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 = 12 39 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) = 5.586 | 5.586 | 5.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -35931.711 0 -35931.711 2620.5494 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1606 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: 1606 ave 1606 max 1606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6812 ave 6812 max 6812 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: 103232 ave 103232 max 103232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103232 Ave neighs/atom = 64.279 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) = 5.586 | 5.586 | 5.586 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 -35931.711 -35931.711 36.639577 126.72145 5.480703 2620.5494 2620.5494 163.20778 7930.5631 -232.12258 2.4678414 670.99558 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1606 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: 1606 ave 1606 max 1606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6812 ave 6812 max 6812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51616 ave 51616 max 51616 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103232 ave 103232 max 103232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103232 Ave neighs/atom = 64.279 Neighbor list builds = 0 Dangerous builds = 0 1606 -8186.7833263279 eV 2.46784140289202 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11