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 = 3.58787 3.58787 3.58787 Created orthogonal box = (0 -66.5487 0) to (23.5272 66.5487 5.07402) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0186 6.19024 5.07402 Created 690 atoms create_atoms CPU = 0.000678062 secs 690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0186 6.19024 5.07402 Created 690 atoms create_atoms CPU = 0.000513077 secs 690 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 = 8.23106 ghost atom cutoff = 8.23106 binsize = 4.11553, bins = 6 33 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 8.23106 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1368 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 = 8.23106 ghost atom cutoff = 8.23106 binsize = 4.11553, bins = 6 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.23106 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) = 5.544 | 5.544 | 5.544 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4784.0038 0 -4784.0038 5763.4646 80 0 -4809.5092 0 -4809.5092 -5019.3964 Loop time of 2.52014 on 1 procs for 80 steps with 1368 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 = -4784.00377582 -4809.50496418 -4809.50915339 Force two-norm initial, final = 41.7431 0.220604 Force max component initial, final = 13.3794 0.0579331 Final line search alpha, max atom move = 1 0.0579331 Iterations, force evaluations = 80 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5 | 2.5 | 2.5 | 0.0 | 99.20 Neigh | 0.0060999 | 0.0060999 | 0.0060999 | 0.0 | 0.24 Comm | 0.0091052 | 0.0091052 | 0.0091052 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004932 | | | 0.20 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9699 ave 9699 max 9699 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: 272752 ave 272752 max 272752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272752 Ave neighs/atom = 199.38 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 : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.547 | 5.547 | 5.547 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -4809.5092 0 -4809.5092 -5019.3964 15888.853 82 0 -4809.5387 0 -4809.5387 -2348.1755 15858.864 Loop time of 0.095063 on 1 procs for 2 steps with 1368 atoms 105.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4809.50915339 -4809.53862156 -4809.53865021 Force two-norm initial, final = 44.4176 0.872192 Force max component initial, final = 31.8742 0.802358 Final line search alpha, max atom move = 0.0202945 0.0162834 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.093974 | 0.093974 | 0.093974 | 0.0 | 98.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027633 | 0.00027633 | 0.00027633 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000813 | | | 0.86 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9699 ave 9699 max 9699 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: 272864 ave 272864 max 272864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272864 Ave neighs/atom = 199.462 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 = 8.23106 ghost atom cutoff = 8.23106 binsize = 4.11553, bins = 6 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.23106 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) = 5.685 | 5.685 | 5.685 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4809.5387 0 -4809.5387 -2348.1755 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1368 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: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9699 ave 9699 max 9699 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: 272864 ave 272864 max 272864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272864 Ave neighs/atom = 199.462 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) = 5.685 | 5.685 | 5.685 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 -4809.5387 -4809.5387 23.505723 133.09739 5.0690777 -2348.1755 -2348.1755 -26.536409 -7098.9711 80.981025 2.3538666 373.02392 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1368 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: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9699 ave 9699 max 9699 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136432 ave 136432 max 136432 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 272864 ave 272864 max 272864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272864 Ave neighs/atom = 199.462 Neighbor list builds = 0 Dangerous builds = 0 1368 -4809.538650212 eV 2.35386659328272 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02