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 -54.6575 0) to (38.6461 54.6575 5.11881) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.10202 6.23246 5.11881 Created 916 atoms create_atoms CPU = 0.000770807 secs 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.10202 6.23246 5.11881 Created 916 atoms create_atoms CPU = 0.000591993 secs 916 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXq2Px10/CuH.bop.table with DATE: 2015-07-06 Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXq2Px10/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 = 12 32 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 = 1816 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 = 12 32 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) = 18.68 | 18.68 | 18.68 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6255.5218 0 -6255.5218 -4283.381 38 0 -6292.4544 0 -6292.4544 -9259.9529 Loop time of 10.7607 on 1 procs for 38 steps with 1816 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 = -6255.52177394 -6292.44837393 -6292.45440194 Force two-norm initial, final = 25.7343 0.254918 Force max component initial, final = 4.85593 0.0212051 Final line search alpha, max atom move = 1 0.0212051 Iterations, force evaluations = 38 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.677 | 10.677 | 10.677 | 0.0 | 99.22 Neigh | 0.072206 | 0.072206 | 0.072206 | 0.0 | 0.67 Comm | 0.0083494 | 0.0083494 | 0.0083494 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003215 | | | 0.03 Nlocal: 1816 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17511 ave 17511 max 17511 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: 239160 ave 239160 max 239160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239160 Ave neighs/atom = 131.696 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 : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 18.68 | 18.68 | 18.68 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -6292.4544 0 -6292.4544 -9259.9529 21624.94 42 0 -6292.6708 0 -6292.6708 -3213.6956 21531.436 Loop time of 0.941506 on 1 procs for 4 steps with 1816 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6292.45440194 -6292.66991086 -6292.67079696 Force two-norm initial, final = 137.85 0.268189 Force max component initial, final = 107.001 0.0223963 Final line search alpha, max atom move = 0.000204171 4.57268e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9392 | 0.9392 | 0.9392 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069571 | 0.00069571 | 0.00069571 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001613 | | | 0.17 Nlocal: 1816 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17478 ave 17478 max 17478 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: 240032 ave 240032 max 240032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240032 Ave neighs/atom = 132.176 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 = 12 32 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) = 17.31 | 17.31 | 17.31 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6292.6708 0 -6292.6708 -3213.6956 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1816 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: 1816 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17478 ave 17478 max 17478 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: 240144 ave 240144 max 240144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240144 Ave neighs/atom = 132.238 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) = 17.31 | 17.31 | 17.31 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 -6292.6708 -6292.6708 38.585884 109.31505 5.1046339 -3213.6956 -3213.6956 -0.72989489 -9639.8895 -0.46737158 2.3353975 685.44231 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1816 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: 1816 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17478 ave 17478 max 17478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120072 ave 120072 max 120072 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 240144 ave 240144 max 240144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240144 Ave neighs/atom = 132.238 Neighbor list builds = 0 Dangerous builds = 0 1816 -6292.67079695592 eV 2.33539754121274 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12