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_CuH__SM_404135993060_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 7 Aug 2019 # Lattice spacing in x,y,z = 3.61954 3.61954 3.61954 Created orthogonal box = (0 -42.2144 0) to (14.9238 42.2144 5.11881) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.14508 6.20747 5.11881 Created 274 atoms create_atoms CPU = 0.000240088 secs 274 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.14508 6.20747 5.11881 Created 274 atoms create_atoms CPU = 0.000124931 secs 274 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXfGSx0I/CuH.bop.table with DATE: 2015-07-06 Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXfGSx0I/CuH.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 = 6.9 ghost atom cutoff = 11.5 binsize = 3.45, bins = 5 25 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 8 atoms, new total = 540 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 = 6.9 ghost atom cutoff = 11.5 binsize = 3.45, bins = 5 25 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) = 10.22 | 10.22 | 10.22 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1855.199 0 -1855.199 -5217.8177 60 0 -1869.1586 0 -1869.1586 -12289.451 Loop time of 6.01007 on 1 procs for 60 steps with 540 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 = -1855.19897809 -1869.15686505 -1869.15855306 Force two-norm initial, final = 14.629 0.125779 Force max component initial, final = 4.84734 0.0149936 Final line search alpha, max atom move = 1 0.0149936 Iterations, force evaluations = 60 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9668 | 5.9668 | 5.9668 | 0.0 | 99.28 Neigh | 0.034358 | 0.034358 | 0.034358 | 0.0 | 0.57 Comm | 0.0067942 | 0.0067942 | 0.0067942 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00215 | | | 0.04 Nlocal: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8658 ave 8658 max 8658 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: 70756 ave 70756 max 70756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70756 Ave neighs/atom = 131.03 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.22 | 10.22 | 10.22 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1869.1586 0 -1869.1586 -12289.451 6449.6694 64 0 -1869.261 0 -1869.261 -4542.0267 6413.7066 Loop time of 0.332466 on 1 procs for 4 steps with 540 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1869.15855306 -1869.25946573 -1869.26103081 Force two-norm initial, final = 51.3206 2.23267 Force max component initial, final = 40.9977 2.2265 Final line search alpha, max atom move = 0.000182679 0.000406734 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33132 | 0.33132 | 0.33132 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030804 | 0.00030804 | 0.00030804 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000839 | | | 0.25 Nlocal: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8581 ave 8581 max 8581 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: 71048 ave 71048 max 71048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71048 Ave neighs/atom = 131.57 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 = 6.9 ghost atom cutoff = 11.5 binsize = 3.45, bins = 5 25 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) = 9.745 | 9.745 | 9.745 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1869.261 0 -1869.261 -4542.0267 Loop time of 9.53674e-07 on 1 procs for 0 steps with 540 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: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9457 ave 9457 max 9457 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: 71136 ave 71136 max 71136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71136 Ave neighs/atom = 131.733 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) = 9.745 | 9.745 | 9.745 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 -1869.261 -1869.261 14.893715 84.428769 5.1005334 -4542.0267 -4542.0267 555.07169 -14162.203 -18.948464 2.3634268 297.98079 Loop time of 1.90735e-06 on 1 procs for 0 steps with 540 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: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9457 ave 9457 max 9457 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35568 ave 35568 max 35568 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71136 ave 71136 max 71136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71136 Ave neighs/atom = 131.733 Neighbor list builds = 0 Dangerous builds = 0 540 -1869.26103081106 eV 2.36342679633888 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06