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 = 3.52152 3.52152 3.52152 Created orthogonal box = (0 -67.3742 0) to (38.8965 67.3742 6.09945) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.73882 5.15404 6.09945 Created 1466 atoms create_atoms CPU = 0.000634909 secs 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.73882 5.15404 6.09945 Created 1466 atoms create_atoms CPU = 0.000597 secs 1466 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 45 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2904 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.799 | 5.799 | 5.799 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16703.354 0 -16703.354 -3935.2916 62 0 -16747.966 0 -16747.966 -11915.434 Loop time of 190.217 on 1 procs for 62 steps with 2904 atoms 76.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -16703.3535735 -16747.951114 -16747.9655578 Force two-norm initial, final = 49.8634 0.455863 Force max component initial, final = 8.0532 0.119642 Final line search alpha, max atom move = 0.912714 0.109199 Iterations, force evaluations = 62 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 190.17 | 190.17 | 190.17 | 0.0 | 99.98 Neigh | 0.0083151 | 0.0083151 | 0.0083151 | 0.0 | 0.00 Comm | 0.02769 | 0.02769 | 0.02769 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006658 | | | 0.00 Nlocal: 2904 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9831 ave 9831 max 9831 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: 237112 ave 237112 max 237112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237112 Ave neighs/atom = 81.6501 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) = 5.799 | 5.799 | 5.799 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -16747.966 0 -16747.966 -11915.434 31968.695 65 0 -16748.282 0 -16748.282 -4516.7474 31852.893 Loop time of 8.44927 on 1 procs for 3 steps with 2904 atoms 73.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -16747.9655578 -16748.2797819 -16748.2815171 Force two-norm initial, final = 243.591 1.73103 Force max component initial, final = 186.811 1.38184 Final line search alpha, max atom move = 9.29889e-05 0.000128496 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.448 | 8.448 | 8.448 | 0.0 | 99.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024676 | 0.00024676 | 0.00024676 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001038 | | | 0.01 Nlocal: 2904 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9566 ave 9566 max 9566 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: 237276 ave 237276 max 237276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237276 Ave neighs/atom = 81.7066 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.928 | 5.928 | 5.928 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16748.282 0 -16748.282 -4516.7474 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2904 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: 2904 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9737 ave 9737 max 9737 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: 238680 ave 238680 max 238680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238680 Ave neighs/atom = 82.1901 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) = 5.928 | 5.928 | 5.928 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 -16748.282 -16748.282 38.810201 134.7484 6.0908706 -4516.7474 -4516.7474 46.391831 -13666.042 69.407793 2.2499137 894.91484 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2904 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: 2904 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9737 ave 9737 max 9737 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119340 ave 119340 max 119340 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 238680 ave 238680 max 238680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238680 Ave neighs/atom = 82.1901 Neighbor list builds = 0 Dangerous builds = 0 2904 -8345.37489272387 eV 2.24991367643039 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:03:26