LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.86385 2.86385 2.86385 Created orthogonal box = (0 -34.6069 0) to (42.3811 34.6069 7.01497) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.06394 4.26625 4.67665 Created 879 atoms create_atoms CPU = 0.000765085 secs 879 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.06394 4.26625 4.67665 Created 879 atoms create_atoms CPU = 0.00068593 secs 879 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 8 12 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 11.9775 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1740 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 8 12 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 12.68 | 12.68 | 12.68 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6970.9137 0 -6970.9137 28371.19 54 0 -7216.3837 0 -7216.3837 -3038.0139 Loop time of 3.48897 on 1 procs for 54 steps with 1740 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 = -6970.91367774 -7216.37664461 -7216.3837386 Force two-norm initial, final = 201.613 0.3729 Force max component initial, final = 24.7263 0.0418182 Final line search alpha, max atom move = 1 0.0418182 Iterations, force evaluations = 54 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4144 | 3.4144 | 3.4144 | 0.0 | 97.86 Neigh | 0.0558 | 0.0558 | 0.0558 | 0.0 | 1.60 Comm | 0.012606 | 0.012606 | 0.012606 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006136 | | | 0.18 Nlocal: 1740 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14707 ave 14707 max 14707 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: 1.04909e+06 ave 1.04909e+06 max 1.04909e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1049092 Ave neighs/atom = 602.926 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.68 | 12.68 | 12.68 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -7216.3837 0 -7216.3837 -3038.0139 20577.385 57 0 -7216.4494 0 -7216.4494 143.36241 20538.551 Loop time of 0.207566 on 1 procs for 3 steps with 1740 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 = -7216.3837386 -7216.44874167 -7216.44936303 Force two-norm initial, final = 78.3081 0.419204 Force max component initial, final = 74.2837 0.0536473 Final line search alpha, max atom move = 0.000158188 8.48635e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20517 | 0.20517 | 0.20517 | 0.0 | 98.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065494 | 0.00065494 | 0.00065494 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00174 | | | 0.84 Nlocal: 1740 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14745 ave 14745 max 14745 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: 1.05078e+06 ave 1.05078e+06 max 1.05078e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1050782 Ave neighs/atom = 603.898 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 8 12 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 12.19 | 12.19 | 12.19 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7216.4494 0 -7216.4494 143.36241 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1740 atoms 251.7% 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 | | 1.192e-06 | | |100.00 Nlocal: 1740 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14745 ave 14745 max 14745 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: 1.05154e+06 ave 1.05154e+06 max 1.05154e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1051538 Ave neighs/atom = 604.332 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) = 12.19 | 12.19 | 12.19 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 -7216.4494 -7216.4494 42.373099 69.213754 7.0030488 143.36241 143.36241 -4.1841453 436.74584 -2.4744709 2.31823 1790.4134 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1740 atoms 186.4% 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: 1740 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14745 ave 14745 max 14745 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 525769 ave 525769 max 525769 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.05154e+06 ave 1.05154e+06 max 1.05154e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1051538 Ave neighs/atom = 604.332 Neighbor list builds = 0 Dangerous builds = 0 1740 -7216.44936303338 eV 2.31822996318034 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04