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 = 3.61115 3.61115 3.61115 Created orthogonal box = (0 -41.4926 0) to (29.3371 41.4926 5.10694) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.22303 5.65759 5.10694 Created 532 atoms create_atoms CPU = 0.000308037 secs 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.22303 5.65759 5.10694 Created 532 atoms create_atoms CPU = 0.000179052 secs 532 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 32 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.355 | 5.355 | 5.355 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4399.4013 0 -4399.4013 4705.8775 41 0 -4437.8628 0 -4437.8628 -8143.8485 Loop time of 1.912 on 1 procs for 41 steps with 1048 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 = -4399.40133007 -4437.85922015 -4437.86281257 Force two-norm initial, final = 38.1048 0.196549 Force max component initial, final = 7.43776 0.0216864 Final line search alpha, max atom move = 1 0.0216864 Iterations, force evaluations = 41 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8992 | 1.8992 | 1.8992 | 0.0 | 99.33 Neigh | 0.0080199 | 0.0080199 | 0.0080199 | 0.0 | 0.42 Comm | 0.0027232 | 0.0027232 | 0.0027232 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002023 | | | 0.11 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4213 ave 4213 max 4213 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: 56432 ave 56432 max 56432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56432 Ave neighs/atom = 53.8473 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.355 | 5.355 | 5.355 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -4437.8628 0 -4437.8628 -8143.8485 12433.095 44 0 -4437.9462 0 -4437.9462 -2878.5368 12392.543 Loop time of 0.114192 on 1 procs for 3 steps with 1048 atoms 105.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4437.86281257 -4437.94337711 -4437.94624216 Force two-norm initial, final = 66.0854 2.95109 Force max component initial, final = 58.233 2.80128 Final line search alpha, max atom move = 0.000105119 0.000294467 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11359 | 0.11359 | 0.11359 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013185 | 0.00013185 | 0.00013185 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004661 | | | 0.41 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4227 ave 4227 max 4227 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: 56472 ave 56472 max 56472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56472 Ave neighs/atom = 53.8855 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.493 | 5.493 | 5.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4437.9462 0 -4437.9462 -2878.5368 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4227 ave 4227 max 4227 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: 56480 ave 56480 max 56480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56480 Ave neighs/atom = 53.8931 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) = 5.493 | 5.493 | 5.493 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 -4437.9462 -4437.9462 29.315971 82.985192 5.0939603 -2878.5368 -2878.5368 361.90313 -9113.78 116.26644 2.384363 346.42958 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4227 ave 4227 max 4227 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28240 ave 28240 max 28240 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56480 ave 56480 max 56480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56480 Ave neighs/atom = 53.8931 Neighbor list builds = 0 Dangerous builds = 0 1048 -4437.9462421605 eV 2.38436299848839 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02