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 = 3.65836 3.65836 3.65836 Created orthogonal box = (0 -51.4814 0) to (12.1334 51.4814 5.17371) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.51519 6.23973 5.17371 Created 266 atoms create_atoms CPU = 0.000389099 secs 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.51519 6.23973 5.17371 Created 266 atoms create_atoms CPU = 0.000247002 secs 266 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 524 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.532 | 4.532 | 4.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2081.3786 0 -2081.3786 277.37607 978 0 -2119.5933 0 -2119.5933 -65205.221 Loop time of 3.50136 on 1 procs for 978 steps with 524 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2081.37856716 -2119.59124234 -2119.59334491 Force two-norm initial, final = 17.6608 0.149086 Force max component initial, final = 7.4805 0.0355882 Final line search alpha, max atom move = 1 0.0355882 Iterations, force evaluations = 978 1925 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3833 | 3.3833 | 3.3833 | 0.0 | 96.63 Neigh | 0.031871 | 0.031871 | 0.031871 | 0.0 | 0.91 Comm | 0.056917 | 0.056917 | 0.056917 | 0.0 | 1.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02926 | | | 0.84 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4937 ave 4937 max 4937 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: 80300 ave 80300 max 80300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80300 Ave neighs/atom = 153.244 Neighbor list builds = 15 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 : 978 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.536 | 4.536 | 4.536 Mbytes Step Temp E_pair E_mol TotEng Press Volume 978 0 -2119.5933 0 -2119.5933 -65205.221 6463.4715 1020 0 -2130.0646 0 -2130.0646 -217.92201 6166.1253 Loop time of 0.068702 on 1 procs for 42 steps with 524 atoms 101.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2119.59334491 -2130.06312212 -2130.0645821 Force two-norm initial, final = 461.799 1.90966 Force max component initial, final = 413.715 0.893435 Final line search alpha, max atom move = 0.00024583 0.000219633 Iterations, force evaluations = 42 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.062538 | 0.062538 | 0.062538 | 0.0 | 91.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001009 | 0.001009 | 0.001009 | 0.0 | 1.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005155 | | | 7.50 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4939 ave 4939 max 4939 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: 80288 ave 80288 max 80288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80288 Ave neighs/atom = 153.221 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.675 | 4.675 | 4.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2130.0646 0 -2130.0646 -217.92201 Loop time of 2.14577e-06 on 1 procs for 0 steps with 524 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: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5079 ave 5079 max 5079 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: 82896 ave 82896 max 82896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82896 Ave neighs/atom = 158.198 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) = 4.675 | 4.675 | 4.675 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 -2130.0646 -2130.0646 12.072756 102.96283 4.9604998 -217.92201 -217.92201 -230.98514 -238.32519 -184.45571 2.2633292 806.84989 Loop time of 9.53674e-07 on 1 procs for 0 steps with 524 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: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5079 ave 5079 max 5079 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41448 ave 41448 max 41448 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82896 ave 82896 max 82896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82896 Ave neighs/atom = 158.198 Neighbor list builds = 0 Dangerous builds = 0 524 -2130.06458210149 eV 2.26332922815001 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03