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 = 2.85531 2.85531 2.85531 Created orthogonal box = (0 -32.307 0) to (13.9881 32.307 4.94555) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.66271 4.03802 4.94555 Created 204 atoms create_atoms CPU = 0.000226021 secs 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.66271 4.03802 4.94555 Created 204 atoms create_atoms CPU = 9.20296e-05 secs 204 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 16 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 384 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.508 | 4.508 | 4.508 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1537.4389 0 -1537.4389 -340.91572 6 0 -1538.3357 0 -1538.3357 -1050.0845 Loop time of 0.0296199 on 1 procs for 6 steps with 384 atoms 101.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1537.43890499 -1538.33475535 -1538.335742 Force two-norm initial, final = 2.79545 0.0694911 Force max component initial, final = 0.411939 0.00676526 Final line search alpha, max atom move = 1 0.00676526 Iterations, force evaluations = 6 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.029115 | 0.029115 | 0.029115 | 0.0 | 98.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003469 | 0.0003469 | 0.0003469 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001581 | | | 0.53 Nlocal: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4593 ave 4593 max 4593 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: 87168 ave 87168 max 87168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87168 Ave neighs/atom = 227 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 : 6 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.508 | 4.508 | 4.508 Mbytes Step Temp E_pair E_mol TotEng Press Volume 6 0 -1538.3357 0 -1538.3357 -1050.0845 4469.9287 8 0 -1538.3412 0 -1538.3412 341.77791 4466.436 Loop time of 0.00942993 on 1 procs for 2 steps with 384 atoms 106.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1538.335742 -1538.34072192 -1538.3412436 Force two-norm initial, final = 9.72069 0.257088 Force max component initial, final = 9.71564 0.233738 Final line search alpha, max atom move = 0.00036713 8.58123e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0090373 | 0.0090373 | 0.0090373 | 0.0 | 95.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010371 | 0.00010371 | 0.00010371 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000289 | | | 3.06 Nlocal: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4593 ave 4593 max 4593 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: 86912 ave 86912 max 86912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86912 Ave neighs/atom = 226.333 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.646 | 4.646 | 4.646 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1538.3412 0 -1538.3412 341.77791 Loop time of 9.53674e-07 on 1 procs for 0 steps with 384 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: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4593 ave 4593 max 4593 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: 86912 ave 86912 max 86912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86912 Ave neighs/atom = 226.333 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) = 4.646 | 4.646 | 4.646 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 -1538.3412 -1538.3412 13.992823 64.614059 4.9400206 341.77791 341.77791 -29.053312 1138.1386 -83.75157 2.4080103 142.6185 Loop time of 9.53674e-07 on 1 procs for 0 steps with 384 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: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4593 ave 4593 max 4593 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43456 ave 43456 max 43456 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86912 ave 86912 max 86912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86912 Ave neighs/atom = 226.333 Neighbor list builds = 0 Dangerous builds = 0 384 -1538.34124360324 eV 2.40801033287973 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00