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 = 4.12887 4.12887 4.12887 Created orthogonal box = (0 -44.6647 0) to (14.8869 44.6647 4.12887) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.72571 5.72571 4.12887 Created 158 atoms create_atoms CPU = 0.000142813 secs 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.72571 5.72571 4.12887 Created 158 atoms create_atoms CPU = 6.50883e-05 secs 158 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 4 20 1 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 310 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 4 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 4.468 | 4.468 | 4.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1136.7844 0 -1136.7844 3115.6415 53 0 -1148.171 0 -1148.171 -3736.8864 Loop time of 0.20352 on 1 procs for 53 steps with 310 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1136.78439321 -1148.17012305 -1148.17099365 Force two-norm initial, final = 12.6758 0.065509 Force max component initial, final = 4.74541 0.0153136 Final line search alpha, max atom move = 1 0.0153136 Iterations, force evaluations = 53 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19715 | 0.19715 | 0.19715 | 0.0 | 96.87 Neigh | 0.0029929 | 0.0029929 | 0.0029929 | 0.0 | 1.47 Comm | 0.0022981 | 0.0022981 | 0.0022981 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001075 | | | 0.53 Nlocal: 310 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4261 ave 4261 max 4261 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: 55324 ave 55324 max 55324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55324 Ave neighs/atom = 178.465 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 : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.468 | 4.468 | 4.468 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1148.171 0 -1148.171 -3736.8864 5490.7142 58 0 -1148.2059 0 -1148.2059 216.20649 5469.3185 Loop time of 0.0117218 on 1 procs for 5 steps with 310 atoms 85.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1148.17099365 -1148.2056665 -1148.20590736 Force two-norm initial, final = 20.9217 0.888331 Force max component initial, final = 17.9378 0.785173 Final line search alpha, max atom move = 0.00110003 0.000863715 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.011251 | 0.011251 | 0.011251 | 0.0 | 95.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013256 | 0.00013256 | 0.00013256 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003386 | | | 2.89 Nlocal: 310 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4261 ave 4261 max 4261 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: 55272 ave 55272 max 55272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55272 Ave neighs/atom = 178.297 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 4 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 4.605 | 4.605 | 4.605 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1148.2059 0 -1148.2059 216.20649 Loop time of 9.53674e-07 on 1 procs for 0 steps with 310 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: 310 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4266 ave 4266 max 4266 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: 55860 ave 55860 max 55860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55860 Ave neighs/atom = 180.194 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) = 4.605 | 4.605 | 4.605 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 -1148.2059 -1148.2059 14.826883 89.329404 4.1294188 216.20649 216.20649 118.53848 300.04264 230.03835 2.6124704 205.67367 Loop time of 9.53674e-07 on 1 procs for 0 steps with 310 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: 310 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4266 ave 4266 max 4266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27930 ave 27930 max 27930 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55860 ave 55860 max 55860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55860 Ave neighs/atom = 180.194 Neighbor list builds = 0 Dangerous builds = 0 310 -1148.20590735649 eV 2.61247038812747 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00