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 -58.6122 0) to (20.7214 58.6122 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.30083 5.452 4.4689 Created 345 atoms create_atoms CPU = 0.000448942 secs 345 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.30083 5.452 4.4689 Created 345 atoms create_atoms CPU = 0.000324965 secs 345 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXRr3uRO/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-XXXXXXRr3uRO/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 = 7 36 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 = 7 36 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) = 4.929 | 4.929 | 4.929 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15285.036 0 -15285.036 5436.5897 9 0 -15304.854 0 -15304.854 879.38706 Loop time of 1.64409 on 1 procs for 9 steps with 684 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15285.0357074 -15304.8456451 -15304.8542233 Force two-norm initial, final = 39.5845 0.277714 Force max component initial, final = 11.2372 0.0556331 Final line search alpha, max atom move = 0.739773 0.0411559 Iterations, force evaluations = 9 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6434 | 1.6434 | 1.6434 | 0.0 | 99.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003624 | 0.0003624 | 0.0003624 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002811 | | | 0.02 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3674 ave 3674 max 3674 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: 43920 ave 43920 max 43920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43920 Ave neighs/atom = 64.2105 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 : 9 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.929 | 4.929 | 4.929 Mbytes Step Temp E_pair E_mol TotEng Press Volume 9 0 -15304.854 0 -15304.854 879.38706 10855.21 10 0 -15304.856 0 -15304.856 23.77057 10858.804 Loop time of 0.360022 on 1 procs for 1 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 = -15304.8542233 -15304.8542233 -15304.8560706 Force two-norm initial, final = 9.44052 4.51869 Force max component initial, final = 9.33353 4.45317 Final line search alpha, max atom move = 0.000107141 0.000477116 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35975 | 0.35975 | 0.35975 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.6996e-05 | 6.6996e-05 | 6.6996e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002046 | | | 0.06 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3665 ave 3665 max 3665 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: 43814 ave 43814 max 43814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43814 Ave neighs/atom = 64.0556 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 = 7 36 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) = 4.56 | 4.56 | 4.56 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15304.856 0 -15304.856 23.77057 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: 3665 ave 3665 max 3665 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: 43814 ave 43814 max 43814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43814 Ave neighs/atom = 64.0556 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) = 4.56 | 4.56 | 4.56 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 -15304.856 -15304.856 20.729488 117.22442 4.4686394 23.77057 23.77057 -105.22112 833.54406 -657.01123 2.5080646 413.05687 Loop time of 2.14577e-06 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 | | 2.146e-06 | | |100.00 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3665 ave 3665 max 3665 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21907 ave 21907 max 21907 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43814 ave 43814 max 43814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43814 Ave neighs/atom = 64.0556 Neighbor list builds = 0 Dangerous builds = 0 684 -3488.2117157774 eV 2.50806461205855 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02