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 -36.5592 0) to (25.8487 36.5592 5.11881) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.56154 5.73421 5.11881 Created 410 atoms create_atoms CPU = 0.000349045 secs 410 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.56154 5.73421 5.11881 Created 410 atoms create_atoms CPU = 0.00022006 secs 410 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXk6pKS4/CuH.bop.table with DATE: 2015-07-06 Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXk6pKS4/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 = 8 22 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 14 atoms, new total = 806 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 = 8 22 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) = 10.65 | 10.65 | 10.65 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2766.0315 0 -2766.0315 -8983.9303 32 0 -2783.3041 0 -2783.3041 -14755.681 Loop time of 4.09776 on 1 procs for 32 steps with 806 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2766.03151599 -2783.30145971 -2783.30411635 Force two-norm initial, final = 17.1182 0.175066 Force max component initial, final = 3.42766 0.016118 Final line search alpha, max atom move = 1 0.016118 Iterations, force evaluations = 32 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0927 | 4.0927 | 4.0927 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0036526 | 0.0036526 | 0.0036526 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001394 | | | 0.03 Nlocal: 806 ave 806 max 806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9674 ave 9674 max 9674 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: 105528 ave 105528 max 105528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105528 Ave neighs/atom = 130.928 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 : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.65 | 10.65 | 10.65 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -2783.3041 0 -2783.3041 -14755.681 9674.6324 41 0 -2783.744 0 -2783.744 -1966.9799 9585.4413 Loop time of 0.775839 on 1 procs for 9 steps with 806 atoms 100.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2783.30411635 -2783.74362211 -2783.74398584 Force two-norm initial, final = 121.33 1.67147 Force max component initial, final = 97.7619 1.61439 Final line search alpha, max atom move = 0.000322483 0.000520613 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77352 | 0.77352 | 0.77352 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061154 | 0.00061154 | 0.00061154 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001707 | | | 0.22 Nlocal: 806 ave 806 max 806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9674 ave 9674 max 9674 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: 105264 ave 105264 max 105264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105264 Ave neighs/atom = 130.6 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 = 8 22 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) = 10.16 | 10.16 | 10.16 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2783.744 0 -2783.744 -1966.9799 Loop time of 9.53674e-07 on 1 procs for 0 steps with 806 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: 806 ave 806 max 806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9747 ave 9747 max 9747 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: 105464 ave 105464 max 105464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105464 Ave neighs/atom = 130.849 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) = 10.16 | 10.16 | 10.16 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 -2783.744 -2783.744 25.638629 73.118429 5.1131728 -1966.9799 -1966.9799 -46.141522 -6124.3412 269.54299 2.2335109 493.10497 Loop time of 9.53674e-07 on 1 procs for 0 steps with 806 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: 806 ave 806 max 806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9747 ave 9747 max 9747 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52732 ave 52732 max 52732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105464 ave 105464 max 105464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105464 Ave neighs/atom = 130.849 Neighbor list builds = 0 Dangerous builds = 0 806 -2783.74398584072 eV 2.23351091773601 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05