LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.02485 4.02485 4.02485 Created orthogonal box = (0 -41.0496 0) to (20.5228 41.0496 4.02485) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.73602 4.73602 4.02485 Created 209 atoms create_atoms CPU = 0.000161171 secs 209 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.73602 4.73602 4.02485 Created 209 atoms create_atoms CPU = 6.10352e-05 secs 209 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 5 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 409 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 4.474 | 4.474 | 4.474 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1072.6964 0 -1072.6964 -2038.8765 236 0 -1077.2166 0 -1077.2166 -5818.0017 Loop time of 0.593716 on 1 procs for 236 steps with 409 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1072.69639266 -1077.2165746 -1077.2165746 Force two-norm initial, final = 9.42695 9.90381e-06 Force max component initial, final = 3.31292 3.07503e-06 Final line search alpha, max atom move = 1 3.07503e-06 Iterations, force evaluations = 236 465 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57951 | 0.57951 | 0.57951 | 0.0 | 97.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0095468 | 0.0095468 | 0.0095468 | 0.0 | 1.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004663 | | | 0.79 Nlocal: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026 ave 4026 max 4026 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: 56706 ave 56706 max 56706 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56706 Ave neighs/atom = 138.645 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 : 236 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.475 | 4.475 | 4.475 Mbytes Step Temp E_pair E_mol TotEng Press Volume 236 0 -1077.2166 0 -1077.2166 -5818.0017 6781.465 1074 0 -1077.2982 0 -1077.2982 -700.22539 6736.6812 Loop time of 2.57969 on 1 procs for 838 steps with 409 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 = -1077.2165746 -1077.29820927 -1077.29820927 Force two-norm initial, final = 34.1585 0.000322264 Force max component initial, final = 25.6316 0.00026308 Final line search alpha, max atom move = 1 0.00026308 Iterations, force evaluations = 838 1673 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4297 | 2.4297 | 2.4297 | 0.0 | 94.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.035914 | 0.035914 | 0.035914 | 0.0 | 1.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.114 | | | 4.42 Nlocal: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4111 ave 4111 max 4111 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: 57002 ave 57002 max 57002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57002 Ave neighs/atom = 139.369 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 4.613 | 4.613 | 4.613 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1077.2982 0 -1077.2982 -700.22539 Loop time of 9.53674e-07 on 1 procs for 0 steps with 409 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: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4186 ave 4186 max 4186 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: 57046 ave 57046 max 57046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57046 Ave neighs/atom = 139.477 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.613 | 4.613 | 4.613 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 -1077.2982 -1077.2982 20.471456 82.09911 4.008287 -700.22539 -700.22539 0.062411541 -2100.7632 0.024652229 2.5304535 334.17549 Loop time of 9.53674e-07 on 1 procs for 0 steps with 409 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: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4186 ave 4186 max 4186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28523 ave 28523 max 28523 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57046 ave 57046 max 57046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57046 Ave neighs/atom = 139.477 Neighbor list builds = 0 Dangerous builds = 0 409 -1064.72789565838 eV 2.530453487982 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03