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 = 3.52 3.52 3.52 Created orthogonal box = (0 -45.0815 0) to (31.875 45.0815 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.44207 6.04705 4.97803 Created 660 atoms create_atoms CPU = 0.000555038 secs 660 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.44207 6.04705 4.97803 Created 660 atoms create_atoms CPU = 0.000422955 secs 660 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 8 22 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1304 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.508 | 5.508 | 5.508 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5745.4253 0 -5745.4253 10187.236 62 0 -5785.9335 0 -5785.9335 -3812.1165 Loop time of 0.801285 on 1 procs for 62 steps with 1304 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5745.42527065 -5785.92793027 -5785.93348613 Force two-norm initial, final = 58.2893 0.24609 Force max component initial, final = 15.9537 0.0400364 Final line search alpha, max atom move = 1 0.0400364 Iterations, force evaluations = 62 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78102 | 0.78102 | 0.78102 | 0.0 | 97.47 Neigh | 0.008455 | 0.008455 | 0.008455 | 0.0 | 1.06 Comm | 0.0074022 | 0.0074022 | 0.0074022 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004406 | | | 0.55 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9334 ave 9334 max 9334 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: 291720 ave 291720 max 291720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291720 Ave neighs/atom = 223.712 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.509 | 5.509 | 5.509 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -5785.9335 0 -5785.9335 -3812.1165 14306.577 64 0 -5785.9659 0 -5785.9659 -1095.1477 14284.697 Loop time of 0.0197809 on 1 procs for 2 steps with 1304 atoms 101.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5785.93348613 -5785.96053004 -5785.96590018 Force two-norm initial, final = 43.307 2.62036 Force max component initial, final = 41.2394 2.1343 Final line search alpha, max atom move = 9.10627e-05 0.000194355 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.019033 | 0.019033 | 0.019033 | 0.0 | 96.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021577 | 0.00021577 | 0.00021577 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005322 | | | 2.69 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9334 ave 9334 max 9334 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: 291728 ave 291728 max 291728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291728 Ave neighs/atom = 223.718 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.647 | 5.647 | 5.647 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5785.9659 0 -5785.9659 -1095.1477 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1304 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: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9334 ave 9334 max 9334 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: 291760 ave 291760 max 291760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291760 Ave neighs/atom = 223.742 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) = 5.647 | 5.647 | 5.647 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 -5785.9659 -5785.9659 31.821859 90.163029 4.9787118 -1095.1477 -1095.1477 167.80259 -3692.6618 239.41601 2.28955 582.59221 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1304 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: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9334 ave 9334 max 9334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145880 ave 145880 max 145880 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 291760 ave 291760 max 291760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291760 Ave neighs/atom = 223.742 Neighbor list builds = 0 Dangerous builds = 0 1304 -5785.96590018303 eV 2.28954998477072 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00