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_BOP_ZhouWardFoster_2015_CCu__SM_784926969362_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 7 Aug 2019 # Lattice spacing in x,y,z = 3.60738 3.60738 3.60738 Created orthogonal box = (0 -54.9496 0) to (27.473 54.9496 3.60738) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.73673 4.73673 3.60738 Created 466 atoms create_atoms CPU = 0.000281096 secs 466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.73673 4.73673 3.60738 Created 466 atoms create_atoms CPU = 0.000139952 secs 466 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX4pvslC/CCu_v2.bop.table with DATE: 2015-07-06 Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX4pvslC/CCu_v2.bop.table with DATE: 2015-07-06 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 = 5.736 ghost atom cutoff = 11.5 binsize = 2.868, bins = 10 39 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 bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 16 atoms, new total = 916 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 = 5.736 ghost atom cutoff = 11.5 binsize = 2.868, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 10.02 | 10.02 | 10.02 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7460.829 0 -7460.829 -2378.5706 5 0 -16248.681 0 -16248.681 -1280915.5 Loop time of 5.09135 on 1 procs for 5 steps with 916 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 = -7460.82900035 -16248.6708214 -16248.6814057 Force two-norm initial, final = 66.2527 4744.07 Force max component initial, final = 16.4487 1500.51 Final line search alpha, max atom move = 1.09204e-09 1.63862e-06 Iterations, force evaluations = 5 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0849 | 5.0849 | 5.0849 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0050914 | 0.0050914 | 0.0050914 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001342 | | | 0.03 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13343 ave 13343 max 13343 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: 70176 ave 70176 max 70176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70176 Ave neighs/atom = 76.6114 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 : 5 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.02 | 10.02 | 10.02 Mbytes Step Temp E_pair E_mol TotEng Press Volume 5 0 -16248.681 0 -16248.681 -1280915.5 10891.643 6 0 -16248.682 0 -16248.682 -381002.08 10891.642 Loop time of 0.80537 on 1 procs for 1 steps with 916 atoms 100.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -16248.6814057 -16248.6814057 -16248.6821623 Force two-norm initial, final = 10244.4 3037.11 Force max component initial, final = 8317.26 2455.05 Final line search alpha, max atom move = 4.69656e-10 1.15303e-06 Iterations, force evaluations = 1 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.80287 | 0.80287 | 0.80287 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069928 | 0.00069928 | 0.00069928 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001803 | | | 0.22 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13329 ave 13329 max 13329 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: 70100 ave 70100 max 70100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70100 Ave neighs/atom = 76.5284 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 = 5.736 ghost atom cutoff = 11.5 binsize = 2.868, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/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 attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 9.528 | 9.528 | 9.528 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16248.682 0 -16248.682 -381002.08 Loop time of 9.53674e-07 on 1 procs for 0 steps with 916 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: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13329 ave 13329 max 13329 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: 70100 ave 70100 max 70100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70100 Ave neighs/atom = 76.5284 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) = 9.528 | 9.528 | 9.528 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 -16248.682 -16248.682 27.473012 109.89927 3.6073831 -381002.08 -381002.08 -165505.43 -616359.21 -361141.61 2.3302358 615.60308 Loop time of 1.90735e-06 on 1 procs for 0 steps with 916 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: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13329 ave 13329 max 13329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35050 ave 35050 max 35050 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70100 ave 70100 max 70100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70100 Ave neighs/atom = 76.5284 Neighbor list builds = 0 Dangerous builds = 0 916 -16248.6821623464 eV 2.33023584280138 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06