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 -41.446 0) to (29.3045 41.446 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.452 5.30083 4.4689 Created 345 atoms create_atoms CPU = 0.000360012 secs 345 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.452 5.30083 4.4689 Created 345 atoms create_atoms CPU = 0.000218153 secs 345 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXH77B4w/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-XXXXXXH77B4w/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 = 9 26 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 6 atoms, new total = 684 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 = 9 26 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) = 4.913 | 4.913 | 4.913 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15248.109 0 -15248.109 17814.857 17 0 -15298.649 0 -15298.649 4087.3408 Loop time of 2.48012 on 1 procs for 17 steps with 684 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15248.1093377 -15298.633444 -15298.6485093 Force two-norm initial, final = 69.7423 0.438937 Force max component initial, final = 18.8369 0.1508 Final line search alpha, max atom move = 0.544938 0.0821768 Iterations, force evaluations = 17 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4774 | 2.4774 | 2.4774 | 0.0 | 99.89 Neigh | 0.0016189 | 0.0016189 | 0.0016189 | 0.0 | 0.07 Comm | 0.00058389 | 0.00058389 | 0.00058389 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004745 | | | 0.02 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3338 ave 3338 max 3338 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: 43896 ave 43896 max 43896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43896 Ave neighs/atom = 64.1754 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 : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.913 | 4.913 | 4.913 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -15298.649 0 -15298.649 4087.3408 10855.453 18 0 -15298.663 0 -15298.663 1043.9385 10868.356 Loop time of 0.372887 on 1 procs for 1 steps with 684 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15298.6485093 -15298.6485093 -15298.6629556 Force two-norm initial, final = 32.6746 7.25422 Force max component initial, final = 29.2932 6.51611 Final line search alpha, max atom move = 3.41377e-05 0.000222445 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37265 | 0.37265 | 0.37265 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.3896e-05 | 6.3896e-05 | 6.3896e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001702 | | | 0.05 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3338 ave 3338 max 3338 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: 43904 ave 43904 max 43904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43904 Ave neighs/atom = 64.1871 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 = 9 26 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) = 4.545 | 4.545 | 4.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15298.663 0 -15298.663 1043.9385 Loop time of 9.53674e-07 on 1 procs for 0 steps with 684 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: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3338 ave 3338 max 3338 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: 43902 ave 43902 max 43902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43902 Ave neighs/atom = 64.1842 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) = 4.545 | 4.545 | 4.545 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 -15298.663 -15298.663 29.327836 82.892034 4.470654 1043.9385 1043.9385 465.90766 3626.8686 -960.96084 2.5011765 442.77003 Loop time of 9.53674e-07 on 1 procs for 0 steps with 684 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: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3338 ave 3338 max 3338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21951 ave 21951 max 21951 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43902 ave 43902 max 43902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43902 Ave neighs/atom = 64.1842 Neighbor list builds = 0 Dangerous builds = 0 684 -3482.0186007983 eV 2.50117645383381 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03