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 = 3.31169 3.31169 3.31169 Created orthogonal box = (0 -35.3625 0) to (25.0027 35.3625 4.68343) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.70237 5.58302 4.68343 Created 458 atoms create_atoms CPU = 0.000267029 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.70237 5.58302 4.68343 Created 458 atoms create_atoms CPU = 0.0001719 secs 458 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 19 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 910 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.994 | 4.994 | 4.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3347.7873 0 -3347.7873 115428.46 444 0 -3545.723 0 -3545.723 235760.3 Loop time of 4.05277 on 1 procs for 444 steps with 910 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3347.7873427 -3545.71966308 -3545.72298999 Force two-norm initial, final = 239.32 0.284894 Force max component initial, final = 55.1468 0.0336281 Final line search alpha, max atom move = 0.359452 0.0120877 Iterations, force evaluations = 444 878 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9739 | 3.9739 | 3.9739 | 0.0 | 98.05 Neigh | 0.023578 | 0.023578 | 0.023578 | 0.0 | 0.58 Comm | 0.034669 | 0.034669 | 0.034669 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02062 | | | 0.51 Nlocal: 910 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6045 ave 6045 max 6045 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: 174744 ave 174744 max 174744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174744 Ave neighs/atom = 192.026 Neighbor list builds = 5 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 : 444 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.995 | 4.995 | 4.995 Mbytes Step Temp E_pair E_mol TotEng Press Volume 444 0 -3545.723 0 -3545.723 235760.3 8281.7789 994 0 -3652.9589 0 -3652.9589 -19954.133 9890.3786 Loop time of 2.42924 on 1 procs for 550 steps with 910 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3545.72298999 -3652.95597155 -3652.95893958 Force two-norm initial, final = 1679.85 7.5567 Force max component initial, final = 1479.16 5.76245 Final line search alpha, max atom move = 0.000173404 0.000999229 Iterations, force evaluations = 550 585 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3357 | 2.3357 | 2.3357 | 0.0 | 96.15 Neigh | 0.006572 | 0.006572 | 0.006572 | 0.0 | 0.27 Comm | 0.019079 | 0.019079 | 0.019079 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06787 | | | 2.79 Nlocal: 910 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5244 ave 5244 max 5244 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: 152004 ave 152004 max 152004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152004 Ave neighs/atom = 167.037 Neighbor list builds = 2 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.125 | 5.125 | 5.125 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3652.9589 0 -3652.9589 -19954.133 Loop time of 9.53674e-07 on 1 procs for 0 steps with 910 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: 910 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5183 ave 5183 max 5183 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: 151844 ave 151844 max 151844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151844 Ave neighs/atom = 166.862 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) = 5.125 | 5.125 | 5.125 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 -3652.9589 -3652.9589 24.886925 70.72492 5.6191316 -19954.133 -19954.133 -259.81435 -58482.608 -1119.9775 2.2790117 1696.5651 Loop time of 2.14577e-06 on 1 procs for 0 steps with 910 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 | | 2.146e-06 | | |100.00 Nlocal: 910 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5183 ave 5183 max 5183 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75922 ave 75922 max 75922 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 151844 ave 151844 max 151844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151844 Ave neighs/atom = 166.862 Neighbor list builds = 0 Dangerous builds = 0 910 -3652.95893958414 eV 2.2790117397658 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06