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 = 3.6584 3.6584 3.6584 Created orthogonal box = (0 -59.4457 0) to (21.0159 59.4457 5.17376) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.73162 6.30446 5.17376 Created 530 atoms create_atoms CPU = 0.000394821 secs 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.73162 6.30446 5.17376 Created 530 atoms create_atoms CPU = 0.000245094 secs 530 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 28 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1044 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.466 | 5.466 | 5.466 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4038.2547 0 -4038.2547 -2159.9918 834 0 -4145.7845 0 -4145.7845 -85599.504 Loop time of 8.05855 on 1 procs for 834 steps with 1044 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4038.2547428 -4145.78035384 -4145.78449273 Force two-norm initial, final = 10.0497 0.191248 Force max component initial, final = 1.99627 0.0213426 Final line search alpha, max atom move = 1 0.0213426 Iterations, force evaluations = 834 1526 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.8254 | 7.8254 | 7.8254 | 0.0 | 97.11 Neigh | 0.11282 | 0.11282 | 0.11282 | 0.0 | 1.40 Comm | 0.078507 | 0.078507 | 0.078507 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04181 | | | 0.52 Nlocal: 1044 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8036 ave 8036 max 8036 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: 198376 ave 198376 max 198376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198376 Ave neighs/atom = 190.015 Neighbor list builds = 20 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 : 834 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.467 | 5.467 | 5.467 Mbytes Step Temp E_pair E_mol TotEng Press Volume 834 0 -4145.7845 0 -4145.7845 -85599.504 12927.225 882 0 -4173.614 0 -4173.614 -10404.078 12254.243 Loop time of 0.325134 on 1 procs for 48 steps with 1044 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4145.78449273 -4173.61319894 -4173.61401265 Force two-norm initial, final = 1086.78 2.7894 Force max component initial, final = 980.912 1.34765 Final line search alpha, max atom move = 0.000216805 0.000292177 Iterations, force evaluations = 48 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31424 | 0.31424 | 0.31424 | 0.0 | 96.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002331 | 0.002331 | 0.002331 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008564 | | | 2.63 Nlocal: 1044 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8022 ave 8022 max 8022 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: 198320 ave 198320 max 198320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198320 Ave neighs/atom = 189.962 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.603 | 5.603 | 5.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4173.614 0 -4173.614 -10404.078 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1044 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: 1044 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8460 ave 8460 max 8460 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: 226764 ave 226764 max 226764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226764 Ave neighs/atom = 217.207 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) = 5.603 | 5.603 | 5.603 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 -4173.614 -4173.614 20.904584 118.89134 4.9305429 -10404.078 -10404.078 -167.7239 -30876.596 -167.91452 2.4036499 2046.5347 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1044 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: 1044 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8460 ave 8460 max 8460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113382 ave 113382 max 113382 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 226764 ave 226764 max 226764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226764 Ave neighs/atom = 217.207 Neighbor list builds = 0 Dangerous builds = 0 1044 -4173.61401265297 eV 2.40364985342873 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08