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 -65.5563 0) to (23.1764 65.5563 5.11881) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.21805 5.59596 5.11881 Created 658 atoms create_atoms CPU = 0.000411034 secs 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.21805 5.59596 5.11881 Created 658 atoms create_atoms CPU = 0.000273943 secs 658 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXlfZxwv/CuH.bop.table with DATE: 2015-07-06 Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXlfZxwv/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 = 7 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 12 atoms, new total = 1304 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 = 7 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) = 17.42 | 17.42 | 17.42 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4495.5403 0 -4495.5403 -6004.5585 48 0 -4520.8179 0 -4520.8179 -11785.077 Loop time of 9.84552 on 1 procs for 48 steps with 1304 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 = -4495.54034798 -4520.81360896 -4520.81789549 Force two-norm initial, final = 19.9862 0.20508 Force max component initial, final = 4.60853 0.0138448 Final line search alpha, max atom move = 1 0.0138448 Iterations, force evaluations = 48 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.7759 | 9.7759 | 9.7759 | 0.0 | 99.29 Neigh | 0.058396 | 0.058396 | 0.058396 | 0.0 | 0.59 Comm | 0.0082901 | 0.0082901 | 0.0082901 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002923 | | | 0.03 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15460 ave 15460 max 15460 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: 171924 ave 171924 max 171924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171924 Ave neighs/atom = 131.844 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 : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 17.38 | 17.38 | 17.38 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -4520.8179 0 -4520.8179 -11785.077 15554.61 54 0 -4521.2148 0 -4521.2148 -2262.6263 15449.026 Loop time of 1.08774 on 1 procs for 6 steps with 1304 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4520.81789549 -4521.21340224 -4521.21478509 Force two-norm initial, final = 151.088 0.25496 Force max component initial, final = 128.52 0.0312392 Final line search alpha, max atom move = 0.000133608 4.17379e-06 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0849 | 1.0849 | 1.0849 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077415 | 0.00077415 | 0.00077415 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002094 | | | 0.19 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15449 ave 15449 max 15449 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: 171976 ave 171976 max 171976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171976 Ave neighs/atom = 131.883 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 = 7 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) = 16.02 | 16.02 | 16.02 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4521.2148 0 -4521.2148 -2262.6263 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1304 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: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15482 ave 15482 max 15482 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: 172232 ave 172232 max 172232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172232 Ave neighs/atom = 132.08 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) = 16.02 | 16.02 | 16.02 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 -4521.2148 -4521.2148 23.137258 131.11267 5.0926584 -2262.6263 -2262.6263 -0.99890329 -6787.7801 0.90007223 2.3441665 476.12982 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1304 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: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15482 ave 15482 max 15482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86116 ave 86116 max 86116 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 172232 ave 172232 max 172232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172232 Ave neighs/atom = 132.08 Neighbor list builds = 0 Dangerous builds = 0 1304 -4521.21478509287 eV 2.34416651630856 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11