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 -51.3469 0) to (10.4805 51.3469 7.74036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.76386 4.66761 5.16024 Created 266 atoms create_atoms CPU = 0.000191927 secs 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.76386 4.66761 5.16024 Created 266 atoms create_atoms CPU = 0.00011301 secs 266 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX6K3mxb/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-XXXXXX6K3mxb/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 = 4 32 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 = 524 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 = 4 32 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) = 4.82 | 4.82 | 4.82 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11704.137 0 -11704.137 4044.0912 22 0 -11719.352 0 -11719.352 -1086.3987 Loop time of 3.78026 on 1 procs for 22 steps with 524 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11704.1368202 -11719.3416582 -11719.3518723 Force two-norm initial, final = 35.8607 0.436586 Force max component initial, final = 12.2435 0.114392 Final line search alpha, max atom move = 1 0.114392 Iterations, force evaluations = 22 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7787 | 3.7787 | 3.7787 | 0.0 | 99.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086093 | 0.00086093 | 0.00086093 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006576 | | | 0.02 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3066 ave 3066 max 3066 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: 33624 ave 33624 max 33624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33624 Ave neighs/atom = 64.1679 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 : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.826 | 4.826 | 4.826 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -11719.352 0 -11719.352 -1086.3987 8330.8064 23 0 -11719.356 0 -11719.356 660.0146 8325.1712 Loop time of 0.324844 on 1 procs for 1 steps with 524 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11719.3518723 -11719.3518723 -11719.3562439 Force two-norm initial, final = 14.919 5.00105 Force max component initial, final = 14.6832 4.90035 Final line search alpha, max atom move = 6.81049e-05 0.000333738 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32462 | 0.32462 | 0.32462 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.7936e-05 | 5.7936e-05 | 5.7936e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001674 | | | 0.05 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3032 ave 3032 max 3032 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: 33644 ave 33644 max 33644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33644 Ave neighs/atom = 64.2061 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 = 4 32 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) = 4.458 | 4.458 | 4.458 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11719.356 0 -11719.356 660.0146 Loop time of 9.53674e-07 on 1 procs for 0 steps with 524 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: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3032 ave 3032 max 3032 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: 33648 ave 33648 max 33648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33648 Ave neighs/atom = 64.2137 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) = 4.458 | 4.458 | 4.458 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 -11719.356 -11719.356 10.474474 102.69378 7.7395696 660.0146 660.0146 -172.60814 1209.6769 942.975 2.388686 311.27143 Loop time of 9.53674e-07 on 1 procs for 0 steps with 524 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: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3032 ave 3032 max 3032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16824 ave 16824 max 16824 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33648 ave 33648 max 33648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33648 Ave neighs/atom = 64.2137 Neighbor list builds = 0 Dangerous builds = 0 524 -2666.8392235567 eV 2.38868598165002 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04