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 -70.5793 0) to (40.7469 70.5793 6.09682) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.47347 5.61797 6.09682 Created 1610 atoms create_atoms CPU = 0.00109506 secs 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.47347 5.61797 6.09682 Created 1610 atoms create_atoms CPU = 0.000983 secs 1610 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 10 35 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 3192 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 10 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 11.74 | 11.74 | 11.74 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14132.593 0 -14132.593 -200.42833 28 0 -14161.663 0 -14161.663 -6522.9136 Loop time of 0.726055 on 1 procs for 28 steps with 3192 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14132.5934159 -14161.6514305 -14161.6628545 Force two-norm initial, final = 23.2094 0.333625 Force max component initial, final = 3.6125 0.0364626 Final line search alpha, max atom move = 0.716727 0.0261337 Iterations, force evaluations = 28 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.69739 | 0.69739 | 0.69739 | 0.0 | 96.05 Neigh | 0.019703 | 0.019703 | 0.019703 | 0.0 | 2.71 Comm | 0.0054519 | 0.0054519 | 0.0054519 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003507 | | | 0.48 Nlocal: 3192 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15178 ave 15178 max 15178 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: 705068 ave 705068 max 705068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 705068 Ave neighs/atom = 220.886 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 : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.74 | 11.74 | 11.74 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -14161.663 0 -14161.663 -6522.9136 35067.574 30 0 -14161.797 0 -14161.797 -2310.1816 34984.449 Loop time of 0.065285 on 1 procs for 2 steps with 3192 atoms 107.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14161.6628545 -14161.7884506 -14161.7968785 Force two-norm initial, final = 158.057 2.01474 Force max component initial, final = 124.456 1.58287 Final line search alpha, max atom move = 3.05396e-05 4.83403e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.063728 | 0.063728 | 0.063728 | 0.0 | 97.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038695 | 0.00038695 | 0.00038695 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00117 | | | 1.79 Nlocal: 3192 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15178 ave 15178 max 15178 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: 706840 ave 706840 max 706840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 706840 Ave neighs/atom = 221.441 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 11.25 | 11.25 | 11.25 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14161.797 0 -14161.797 -2310.1816 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3192 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: 3192 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15178 ave 15178 max 15178 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: 707428 ave 707428 max 707428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 707428 Ave neighs/atom = 221.625 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) = 11.25 | 11.25 | 11.25 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 -14161.797 -14161.797 40.705307 141.1586 6.0885889 -2310.1816 -2310.1816 72.416446 -6948.2009 -54.760354 2.2080842 1020.9697 Loop time of 2.14577e-06 on 1 procs for 0 steps with 3192 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: 3192 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15178 ave 15178 max 15178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 353714 ave 353714 max 353714 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 707428 ave 707428 max 707428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 707428 Ave neighs/atom = 221.625 Neighbor list builds = 0 Dangerous builds = 0 3192 -14089.8286526933 eV 2.20808423347906 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01