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 = 3.14096 3.14096 3.14096 Created orthogonal box = (0 -37.6947 0) to (13.326 37.6947 4.44199) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.44199 5.23494 4.44199 Created 146 atoms create_atoms CPU = 0.000255108 secs 146 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.44199 5.23494 4.44199 Created 146 atoms create_atoms CPU = 0.000114202 secs 146 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 3 14 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 11.5437 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 291 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 3 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 4.893 | 4.893 | 4.893 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1622.0344 0 -1622.0344 242751 207 0 -1954.028 0 -1954.028 43743.017 Loop time of 1.30566 on 1 procs for 207 steps with 291 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1622.0343676 -1954.02634766 -1954.02803835 Force two-norm initial, final = 546.609 0.249934 Force max component initial, final = 109.453 0.039393 Final line search alpha, max atom move = 1 0.039393 Iterations, force evaluations = 207 394 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2739 | 1.2739 | 1.2739 | 0.0 | 97.57 Neigh | 0.012514 | 0.012514 | 0.012514 | 0.0 | 0.96 Comm | 0.014534 | 0.014534 | 0.014534 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004717 | | | 0.36 Nlocal: 291 ave 291 max 291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6058 ave 6058 max 6058 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: 120474 ave 120474 max 120474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120474 Ave neighs/atom = 414 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 : 207 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.894 | 4.894 | 4.894 Mbytes Step Temp E_pair E_mol TotEng Press Volume 207 0 -1954.028 0 -1954.028 43743.017 4462.5908 215 0 -1954.7633 0 -1954.7633 6703.7427 4518.2348 Loop time of 0.0396481 on 1 procs for 8 steps with 291 atoms 100.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1954.02803835 -1954.76315371 -1954.76331644 Force two-norm initial, final = 169.44 0.76507 Force max component initial, final = 129.13 0.226511 Final line search alpha, max atom move = 0.000841918 0.000190704 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.038203 | 0.038203 | 0.038203 | 0.0 | 96.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038695 | 0.00038695 | 0.00038695 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001059 | | | 2.67 Nlocal: 291 ave 291 max 291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6055 ave 6055 max 6055 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: 120418 ave 120418 max 120418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120418 Ave neighs/atom = 413.808 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 3 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 5.031 | 5.031 | 5.031 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1954.7633 0 -1954.7633 6703.7427 Loop time of 9.53674e-07 on 1 procs for 0 steps with 291 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: 291 ave 291 max 291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6022 ave 6022 max 6022 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: 119138 ave 119138 max 119138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119138 Ave neighs/atom = 409.409 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) = 5.031 | 5.031 | 5.031 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 -1954.7633 -1954.7633 13.407539 75.389389 4.4700203 6703.7427 6703.7427 -80.812827 20119.135 72.905822 2.5594504 410.65175 Loop time of 9.53674e-07 on 1 procs for 0 steps with 291 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: 291 ave 291 max 291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6022 ave 6022 max 6022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59569 ave 59569 max 59569 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119138 ave 119138 max 119138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119138 Ave neighs/atom = 409.409 Neighbor list builds = 0 Dangerous builds = 0 291 -1954.76331643786 eV 2.55945035130689 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01