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 = 3.68004 3.68004 3.68004 Created orthogonal box = (0 -43.5466 0) to (53.3289 43.5466 9.01423) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.09473 5.59837 6.00949 Created 1690 atoms create_atoms CPU = 0.000771999 secs 1690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.09473 5.59837 6.00949 Created 1690 atoms create_atoms CPU = 0.000658035 secs 1690 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 19 31 4 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 68 atoms, new total = 3312 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.227 | 5.227 | 5.227 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13877.488 0 -13877.488 3084.905 64 0 -14049.651 0 -14049.651 -24818.141 Loop time of 0.385022 on 1 procs for 64 steps with 3312 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13877.487895 -14049.6402511 -14049.650637 Force two-norm initial, final = 83.136 0.294766 Force max component initial, final = 7.4154 0.0236321 Final line search alpha, max atom move = 1 0.0236321 Iterations, force evaluations = 64 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36719 | 0.36719 | 0.36719 | 0.0 | 95.37 Neigh | 0.0057819 | 0.0057819 | 0.0057819 | 0.0 | 1.50 Comm | 0.0048068 | 0.0048068 | 0.0048068 | 0.0 | 1.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007248 | | | 1.88 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6962 ave 6962 max 6962 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: 182794 ave 182794 max 182794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182794 Ave neighs/atom = 55.1914 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.229 | 5.229 | 5.229 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -14049.651 0 -14049.651 -24818.141 41867.33 74 0 -14053.97 0 -14053.97 -5658.5488 41290.886 Loop time of 0.0410631 on 1 procs for 10 steps with 3312 atoms 121.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14049.650637 -14053.9678073 -14053.9704225 Force two-norm initial, final = 848.084 0.841738 Force max component initial, final = 698.63 0.0536712 Final line search alpha, max atom move = 6.60698e-05 3.54604e-06 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.037917 | 0.037917 | 0.037917 | 0.0 | 92.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050116 | 0.00050116 | 0.00050116 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002645 | | | 6.44 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7276 ave 7276 max 7276 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: 182912 ave 182912 max 182912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182912 Ave neighs/atom = 55.2271 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.367 | 5.367 | 5.367 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14053.97 0 -14053.97 -5658.5488 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3312 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7292 ave 7292 max 7292 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: 183552 ave 183552 max 183552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183552 Ave neighs/atom = 55.4203 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) = 5.367 | 5.367 | 5.367 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 -14053.97 -14053.97 52.844045 87.093112 8.9716916 -5658.5488 -5658.5488 1.1771902 -16974.751 -2.0727305 2.412795 2031.0624 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3312 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7292 ave 7292 max 7292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 91776 ave 91776 max 91776 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 183552 ave 183552 max 183552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183552 Ave neighs/atom = 55.4203 Neighbor list builds = 0 Dangerous builds = 0 3312 -14053.9704225404 eV 2.41279503628783 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00