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 -67.1361 0) to (23.7349 67.1361 5.11881) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.07173 6.24489 5.11881 Created 690 atoms create_atoms CPU = 0.000484943 secs 690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.07173 6.24489 5.11881 Created 690 atoms create_atoms CPU = 0.000355005 secs 690 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX2uXMoP/CuH.bop.table with DATE: 2015-07-06 Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX2uXMoP/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 = 1368 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) = 17.39 | 17.39 | 17.39 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4719.974 0 -4719.974 -5429.8964 92 0 -4742.5718 0 -4742.5718 -11797.148 Loop time of 20.1143 on 1 procs for 92 steps with 1368 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4719.97404535 -4742.56731148 -4742.57178325 Force two-norm initial, final = 17.0835 0.211556 Force max component initial, final = 4.66301 0.0285389 Final line search alpha, max atom move = 1 0.0285389 Iterations, force evaluations = 92 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.03 | 20.03 | 20.03 | 0.0 | 99.58 Neigh | 0.060526 | 0.060526 | 0.060526 | 0.0 | 0.30 Comm | 0.017344 | 0.017344 | 0.017344 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006179 | | | 0.03 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15146 ave 15146 max 15146 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: 180416 ave 180416 max 180416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180416 Ave neighs/atom = 131.883 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 : 92 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 17.37 | 17.37 | 17.37 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -4742.5718 0 -4742.5718 -11797.148 16313.35 96 0 -4742.8164 0 -4742.8164 -4404.4258 16226.899 Loop time of 0.740185 on 1 procs for 4 steps with 1368 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 = -4742.57178325 -4742.81553021 -4742.81638141 Force two-norm initial, final = 127.839 0.495473 Force max component initial, final = 97.215 0.329716 Final line search alpha, max atom move = 0.000272936 8.99914e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73837 | 0.73837 | 0.73837 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053358 | 0.00053358 | 0.00053358 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00128 | | | 0.17 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15252 ave 15252 max 15252 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: 181016 ave 181016 max 181016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181016 Ave neighs/atom = 132.322 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) = 16.8 | 16.8 | 16.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4742.8164 0 -4742.8164 -4404.4258 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1368 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 | | 2.146e-06 | | |100.00 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16838 ave 16838 max 16838 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: 181056 ave 181056 max 181056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181056 Ave neighs/atom = 132.351 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) = 16.8 | 16.8 | 16.8 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 -4742.8164 -4742.8164 23.685659 134.27229 5.1022727 -4404.4258 -4404.4258 -28.942317 -13151.886 -32.449597 2.321182 388.94249 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1368 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 | | 2.146e-06 | | |100.00 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16838 ave 16838 max 16838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90528 ave 90528 max 90528 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 181056 ave 181056 max 181056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181056 Ave neighs/atom = 132.351 Neighbor list builds = 0 Dangerous builds = 0 1368 -4742.81638141465 eV 2.32118195740402 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21