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 = 3.61503 3.61503 3.61503 Created orthogonal box = (0 -58.741 0) to (20.7668 58.741 5.11243) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.66367 6.22972 5.11243 Created 530 atoms create_atoms CPU = 0.000601053 secs 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.66367 6.22972 5.11243 Created 530 atoms create_atoms CPU = 0.000446081 secs 530 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 = 7.77721 ghost atom cutoff = 7.77721 binsize = 3.8886, bins = 6 31 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 7.77721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1052 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 = 7.77721 ghost atom cutoff = 7.77721 binsize = 3.8886, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.77721 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) = 5.061 | 5.061 | 5.061 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3695.6249 0 -3695.6249 7117.1612 44 0 -3717.5576 0 -3717.5576 -2633.9464 Loop time of 0.350069 on 1 procs for 44 steps with 1052 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 = -3695.62492138 -3717.55418172 -3717.55758558 Force two-norm initial, final = 35.9451 0.173587 Force max component initial, final = 12.4713 0.0295599 Final line search alpha, max atom move = 1 0.0295599 Iterations, force evaluations = 44 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33838 | 0.33838 | 0.33838 | 0.0 | 96.66 Neigh | 0.0055189 | 0.0055189 | 0.0055189 | 0.0 | 1.58 Comm | 0.0039403 | 0.0039403 | 0.0039403 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002227 | | | 0.64 Nlocal: 1052 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7762 ave 7762 max 7762 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: 182460 ave 182460 max 182460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182460 Ave neighs/atom = 173.441 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 : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.062 | 5.062 | 5.062 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -3717.5576 0 -3717.5576 -2633.9464 12472.914 48 0 -3717.6074 0 -3717.6074 626.92059 12443.395 Loop time of 0.0332901 on 1 procs for 4 steps with 1052 atoms 90.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3717.55758558 -3717.60721179 -3717.6073577 Force two-norm initial, final = 44.1544 0.188661 Force max component initial, final = 40.1244 0.046231 Final line search alpha, max atom move = 0.000354797 1.64026e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.031991 | 0.031991 | 0.031991 | 0.0 | 96.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031185 | 0.00031185 | 0.00031185 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009873 | | | 2.97 Nlocal: 1052 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7760 ave 7760 max 7760 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: 182132 ave 182132 max 182132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182132 Ave neighs/atom = 173.129 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 = 7.77721 ghost atom cutoff = 7.77721 binsize = 3.8886, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.77721 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) = 5.2 | 5.2 | 5.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3717.6074 0 -3717.6074 626.92059 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1052 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 | | 1.192e-06 | | |100.00 Nlocal: 1052 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7778 ave 7778 max 7778 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: 182328 ave 182328 max 182328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182328 Ave neighs/atom = 173.316 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) = 5.2 | 5.2 | 5.2 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 -3717.6074 -3717.6074 20.713536 117.48194 5.1134444 626.92059 626.92059 1.1121695 1885.6034 -5.9537597 2.3512732 420.37605 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1052 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: 1052 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7778 ave 7778 max 7778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 91164 ave 91164 max 91164 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 182328 ave 182328 max 182328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182328 Ave neighs/atom = 173.316 Neighbor list builds = 0 Dangerous builds = 0 1052 -3717.60735770126 eV 2.35127322376436 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00