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 = 4.05 4.05 4.05 Created orthogonal box = (0 -59.9386 0) to (48.9364 59.9386 9.92044) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.03325 5.74715 6.61363 Created 1755 atoms create_atoms CPU = 0.000496149 secs 1755 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.03325 5.74715 6.61363 Created 1755 atoms create_atoms CPU = 0.000422001 secs 1755 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 12 29 3 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 38 atoms, new total = 3472 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.621 | 6.621 | 6.621 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11603.152 0 -11603.152 -776.7395 65 0 -11635.692 0 -11635.692 -3793.7736 Loop time of 1.09309 on 1 procs for 65 steps with 3472 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11603.1520927 -11635.6800009 -11635.6915023 Force two-norm initial, final = 23.8477 0.268936 Force max component initial, final = 3.18122 0.0418379 Final line search alpha, max atom move = 1 0.0418379 Iterations, force evaluations = 65 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0472 | 1.0472 | 1.0472 | 0.0 | 95.80 Neigh | 0.02953 | 0.02953 | 0.02953 | 0.0 | 2.70 Comm | 0.0077417 | 0.0077417 | 0.0077417 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008644 | | | 0.79 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10643 ave 10643 max 10643 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: 483698 ave 483698 max 483698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 483698 Ave neighs/atom = 139.314 Neighbor list builds = 2 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.621 | 6.621 | 6.621 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -11635.692 0 -11635.692 -3793.7736 58196.925 68 0 -11636.035 0 -11636.035 -166.51161 57927.62 Loop time of 0.0368431 on 1 procs for 3 steps with 3472 atoms 108.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11635.6915023 -11636.027404 -11636.035135 Force two-norm initial, final = 209.441 0.467467 Force max component initial, final = 150.22 0.265865 Final line search alpha, max atom move = 4.37076e-05 1.16203e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.035615 | 0.035615 | 0.035615 | 0.0 | 96.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026298 | 0.00026298 | 0.00026298 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009654 | | | 2.62 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10652 ave 10652 max 10652 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: 483572 ave 483572 max 483572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 483572 Ave neighs/atom = 139.278 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.756 | 6.756 | 6.756 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11636.035 0 -11636.035 -166.51161 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3472 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: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10707 ave 10707 max 10707 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: 483646 ave 483646 max 483646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 483646 Ave neighs/atom = 139.299 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) = 6.756 | 6.756 | 6.756 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 -11636.035 -11636.035 48.825012 119.87729 9.8970645 -166.51161 -166.51161 7.1666381 -499.36546 -7.3360178 2.5829243 2305.128 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3472 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: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10707 ave 10707 max 10707 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 241823 ave 241823 max 241823 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 483646 ave 483646 max 483646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 483646 Ave neighs/atom = 139.299 Neighbor list builds = 0 Dangerous builds = 0 3472 -11636.0351353936 eV 2.58292426667135 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01