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 -34.6191 0) to (7.06595 34.6191 7.74036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.23957 4.61546 5.16024 Created 122 atoms create_atoms CPU = 0.000168085 secs 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.23957 4.61546 5.16024 Created 122 atoms create_atoms CPU = 4.1008e-05 secs 122 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXA9DOVw/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-XXXXXXA9DOVw/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 = 3 21 3 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 8 atoms, new total = 236 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 = 3 21 3 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) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5268.2384 0 -5268.2384 -8809.5494 29 0 -5274.9319 0 -5274.9319 -15337.598 Loop time of 2.23254 on 1 procs for 29 steps with 236 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5268.23844906 -5274.9288148 -5274.93189394 Force two-norm initial, final = 11.106 0.183139 Force max component initial, final = 3.03493 0.0366564 Final line search alpha, max atom move = 1 0.0366564 Iterations, force evaluations = 29 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2312 | 2.2312 | 2.2312 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078821 | 0.00078821 | 0.00078821 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000519 | | | 0.02 Nlocal: 236 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1930 ave 1930 max 1930 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: 15088 ave 15088 max 15088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15088 Ave neighs/atom = 63.9322 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 : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -5274.9319 0 -5274.9319 -15337.598 3786.8428 32 0 -5275.0095 0 -5275.0095 -3413.6953 3769.0934 Loop time of 0.15779 on 1 procs for 3 steps with 236 atoms 101.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5274.93189394 -5275.00530316 -5275.00953272 Force two-norm initial, final = 46.3123 1.89293 Force max component initial, final = 35.391 1.62772 Final line search alpha, max atom move = 0.000107293 0.000174643 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15755 | 0.15755 | 0.15755 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.6744e-05 | 5.6744e-05 | 5.6744e-05 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001805 | | | 0.11 Nlocal: 236 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1930 ave 1930 max 1930 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: 15144 ave 15144 max 15144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15144 Ave neighs/atom = 64.1695 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 = 3 21 3 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) = 4.242 | 4.242 | 4.242 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5275.0095 0 -5275.0095 -3413.6953 Loop time of 9.53674e-07 on 1 procs for 0 steps with 236 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: 236 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1930 ave 1930 max 1930 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: 15156 ave 15156 max 15156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15156 Ave neighs/atom = 64.2203 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) = 4.242 | 4.242 | 4.242 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 -5275.0095 -5275.0095 7.051764 69.238193 7.7195753 -3413.6953 -3413.6953 690.5246 -10532.402 -399.20851 2.4785191 258.20657 Loop time of 9.53674e-07 on 1 procs for 0 steps with 236 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: 236 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1930 ave 1930 max 1930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7578 ave 7578 max 7578 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15156 ave 15156 max 15156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15156 Ave neighs/atom = 64.2203 Neighbor list builds = 0 Dangerous builds = 0 236 -1197.92171438234 eV 2.47851905841091 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02