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 Lattice spacing in x,y,z = 3.61115 3.61115 3.61115 Created orthogonal box = (0 -42.7313 0) to (52.3306 42.7313 8.84548) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.98064 5.49357 5.89699 Created 1689 atoms create_atoms CPU = 0.00075984 secs 1689 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.98064 5.49357 5.89699 Created 1689 atoms create_atoms CPU = 0.000661135 secs 1689 atoms in group lower Displacing atoms ... 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 20 32 4 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 66 atoms, new total = 3312 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 20 32 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 6.358 | 6.358 | 6.358 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13886.906 0 -13886.906 580.72948 70 0 -14014.167 0 -14014.167 -18975.786 Loop time of 8.30261 on 1 procs for 70 steps with 3312 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 = -13886.9055704 -14014.154177 -14014.1672977 Force two-norm initial, final = 55.3752 0.511863 Force max component initial, final = 5.14423 0.168494 Final line search alpha, max atom move = 0.873707 0.147214 Iterations, force evaluations = 70 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2735 | 8.2735 | 8.2735 | 0.0 | 99.65 Neigh | 0.015042 | 0.015042 | 0.015042 | 0.0 | 0.18 Comm | 0.0056436 | 0.0056436 | 0.0056436 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00846 | | | 0.10 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6670 ave 6670 max 6670 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: 177740 ave 177740 max 177740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177740 Ave neighs/atom = 53.6655 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 : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.358 | 6.358 | 6.358 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -14014.167 0 -14014.167 -18975.786 39559.749 75 0 -14015.806 0 -14015.806 -5434.5593 39228.468 Loop time of 0.590884 on 1 procs for 5 steps with 3312 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 = -14014.1672977 -14015.7962365 -14015.8059854 Force two-norm initial, final = 548.736 1.56813 Force max component initial, final = 401.738 0.947986 Final line search alpha, max atom move = 3.28512e-05 3.11424e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58914 | 0.58914 | 0.58914 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029588 | 0.00029588 | 0.00029588 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001446 | | | 0.24 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6416 ave 6416 max 6416 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: 178264 ave 178264 max 178264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178264 Ave neighs/atom = 53.8237 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 20 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (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) = 6.494 | 6.494 | 6.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14015.806 0 -14015.806 -5434.5593 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3312 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6422 ave 6422 max 6422 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: 178300 ave 178300 max 178300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178300 Ave neighs/atom = 53.8345 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) = 6.494 | 6.494 | 6.494 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 -14015.806 -14015.806 52.104558 85.46269 8.8094556 -5434.5593 -5434.5593 32.876425 -16297.994 -38.560134 2.3340077 1178.7122 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3312 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6422 ave 6422 max 6422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89150 ave 89150 max 89150 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 178300 ave 178300 max 178300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178300 Ave neighs/atom = 53.8345 Neighbor list builds = 0 Dangerous builds = 0 3312 -14015.8059854086 eV 2.3340077029474 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09