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 -45.6279 0) to (26.3413 45.6279 6.09682) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.64456 5.43148 6.09682 Created 676 atoms create_atoms CPU = 0.000292063 secs 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.64456 5.43148 6.09682 Created 676 atoms create_atoms CPU = 0.000213146 secs 676 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 7 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 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1328 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 7 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 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) = 5.905 | 5.905 | 5.905 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5858.3367 0 -5858.3367 298.02112 59 0 -5882.5464 0 -5882.5464 -12594.278 Loop time of 0.680098 on 1 procs for 59 steps with 1328 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 = -5858.33668599 -5882.5410358 -5882.54640204 Force two-norm initial, final = 17.5364 0.237224 Force max component initial, final = 3.6542 0.0191091 Final line search alpha, max atom move = 1 0.0191091 Iterations, force evaluations = 59 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66253 | 0.66253 | 0.66253 | 0.0 | 97.42 Neigh | 0.007875 | 0.007875 | 0.007875 | 0.0 | 1.16 Comm | 0.0059948 | 0.0059948 | 0.0059948 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003693 | | | 0.54 Nlocal: 1328 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8174 ave 8174 max 8174 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: 296504 ave 296504 max 296504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296504 Ave neighs/atom = 223.271 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.905 | 5.905 | 5.905 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -5882.5464 0 -5882.5464 -12594.278 14655.505 63 0 -5882.7148 0 -5882.7148 -5575.1622 14596.571 Loop time of 0.050571 on 1 procs for 4 steps with 1328 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5882.54640204 -5882.71386809 -5882.71479043 Force two-norm initial, final = 109.957 0.279112 Force max component initial, final = 92.4155 0.0280889 Final line search alpha, max atom move = 0.000160233 4.50078e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049069 | 0.049069 | 0.049069 | 0.0 | 97.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035977 | 0.00035977 | 0.00035977 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001142 | | | 2.26 Nlocal: 1328 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8204 ave 8204 max 8204 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: 297600 ave 297600 max 297600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297600 Ave neighs/atom = 224.096 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 7 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 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) = 6.043 | 6.043 | 6.043 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5882.7148 0 -5882.7148 -5575.1622 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1328 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 | | 1.907e-06 | | |100.00 Nlocal: 1328 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8212 ave 8212 max 8212 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: 297760 ave 297760 max 297760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297760 Ave neighs/atom = 224.217 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) = 6.043 | 6.043 | 6.043 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 -5882.7148 -5882.7148 26.264389 91.25587 6.0900765 -5575.1622 -5575.1622 -0.2662023 -16722.141 -3.0797372 2.2408468 768.95073 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1328 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 | | 1.192e-06 | | |100.00 Nlocal: 1328 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8212 ave 8212 max 8212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 148880 ave 148880 max 148880 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 297760 ave 297760 max 297760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297760 Ave neighs/atom = 224.217 Neighbor list builds = 0 Dangerous builds = 0 1328 -5882.71479043225 eV 2.24084682987636 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00