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 = 3.52753 3.52753 3.15999 Created 261 atoms create_atoms CPU = 0.000154018 secs 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.52753 3.52753 3.15999 Created 261 atoms create_atoms CPU = 4.31538e-05 secs 261 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXVuBDOu/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-XXXXXXVuBDOu/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) = 4.818 | 4.818 | 4.818 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11523.961 0 -11523.961 5213.9295 14 0 -11545.029 0 -11545.029 -4575.7689 Loop time of 1.82326 on 1 procs for 14 steps with 516 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11523.9614942 -11545.0208797 -11545.028976 Force two-norm initial, final = 30.3527 0.311286 Force max component initial, final = 12.2074 0.0730136 Final line search alpha, max atom move = 0.811214 0.0592297 Iterations, force evaluations = 14 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8222 | 1.8222 | 1.8222 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061655 | 0.00061655 | 0.00061655 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004184 | | | 0.02 Nlocal: 516 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4345 ave 4345 max 4345 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: 33112 ave 33112 max 33112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33112 Ave neighs/atom = 64.1705 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 : 14 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.818 | 4.818 | 4.818 Mbytes Step Temp E_pair E_mol TotEng Press Volume 14 0 -11545.029 0 -11545.029 -4575.7689 8204.5859 16 0 -11545.047 0 -11545.047 -686.89781 8192.1653 Loop time of 0.456226 on 1 procs for 2 steps with 516 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11545.028976 -11545.0469299 -11545.0469453 Force two-norm initial, final = 33.5634 0.382854 Force max component initial, final = 23.871 0.20113 Final line search alpha, max atom move = 0.00257894 0.000518703 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45576 | 0.45576 | 0.45576 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014472 | 0.00014472 | 0.00014472 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003252 | | | 0.07 Nlocal: 516 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4339 ave 4339 max 4339 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: 33054 ave 33054 max 33054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33054 Ave neighs/atom = 64.0581 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) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11545.047 0 -11545.047 -686.89781 Loop time of 2.14577e-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 | | 2.146e-06 | | |100.00 Nlocal: 516 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4339 ave 4339 max 4339 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: 33054 ave 33054 max 33054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33054 Ave neighs/atom = 64.0581 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) = 4.449 | 4.449 | 4.449 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 -11545.047 -11545.047 25.456447 101.91288 3.1577072 -686.89781 -686.89781 39.304637 -2085.7271 -14.270936 2.5401438 149.82141 Loop time of 1.90735e-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 | | 1.907e-06 | | |100.00 Nlocal: 516 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4339 ave 4339 max 4339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16527 ave 16527 max 16527 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33054 ave 33054 max 33054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33054 Ave neighs/atom = 64.0581 Neighbor list builds = 0 Dangerous builds = 0 516 -2630.7362916915 eV 2.54014384948975 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02