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 = 2.85532 2.85532 2.85532 Created orthogonal box = (0 -37.4501 0) to (26.4792 37.4501 4.03804) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.92636 4.78976 4.03804 Created 345 atoms create_atoms CPU = 0.000231028 secs 345 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.92636 4.78976 4.03804 Created 345 atoms create_atoms CPU = 0.000133991 secs 345 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 2 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, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 687 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.533 | 4.533 | 4.533 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2769.4171 0 -2769.4171 28391.868 26 0 -2819.5777 0 -2819.5777 692.70481 Loop time of 0.0788758 on 1 procs for 26 steps with 687 atoms 101.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2769.41708707 -2819.57525995 -2819.57772124 Force two-norm initial, final = 96.6429 0.161394 Force max component initial, final = 24.3259 0.0258997 Final line search alpha, max atom move = 1 0.0258997 Iterations, force evaluations = 26 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076887 | 0.076887 | 0.076887 | 0.0 | 97.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011957 | 0.0011957 | 0.0011957 | 0.0 | 1.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007932 | | | 1.01 Nlocal: 687 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5029 ave 5029 max 5029 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: 93534 ave 93534 max 93534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93534 Ave neighs/atom = 136.148 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 : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.533 | 4.533 | 4.533 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -2819.5777 0 -2819.5777 692.70481 8008.6265 28 0 -2819.5835 0 -2819.5835 148.12021 8011.1453 Loop time of 0.0130391 on 1 procs for 2 steps with 687 atoms 153.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2819.57772124 -2819.58302827 -2819.58349601 Force two-norm initial, final = 11.6615 0.163825 Force max component initial, final = 11.0234 0.027604 Final line search alpha, max atom move = 0.000238162 6.57422e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.012425 | 0.012425 | 0.012425 | 0.0 | 95.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014734 | 0.00014734 | 0.00014734 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004671 | | | 3.58 Nlocal: 687 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5039 ave 5039 max 5039 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: 94600 ave 94600 max 94600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94600 Ave neighs/atom = 137.7 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/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) = 4.671 | 4.671 | 4.671 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2819.5835 0 -2819.5835 148.12021 Loop time of 9.53674e-07 on 1 procs for 0 steps with 687 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: 687 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5039 ave 5039 max 5039 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: 94570 ave 94570 max 94570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94570 Ave neighs/atom = 137.656 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) = 4.671 | 4.671 | 4.671 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 -2819.5835 -2819.5835 26.501963 74.900174 4.0358381 148.12021 148.12021 -0.84181511 444.24002 0.96243295 2.2428992 401.59841 Loop time of 1.90735e-06 on 1 procs for 0 steps with 687 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: 687 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5039 ave 5039 max 5039 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47285 ave 47285 max 47285 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94570 ave 94570 max 94570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94570 Ave neighs/atom = 137.656 Neighbor list builds = 0 Dangerous builds = 0 687 -2819.58349600977 eV 2.24289921860522 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00