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 = 3.39012 3.39012 3.39012 Created orthogonal box = (0 -44.3349 0) to (20.8981 44.3349 4.79435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3996 5.44422 4.79435 Created 230 atoms create_atoms CPU = 0.000277996 secs 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3996 5.44422 4.79435 Created 230 atoms create_atoms CPU = 0.000128031 secs 230 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.2653, bins = 3 9 1 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 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 458 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.2653, bins = 3 9 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 11.72 | 11.72 | 11.72 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 21379.637 0 21379.637 28323933 244 0 -16667.691 0 -16667.691 -24640.76 Loop time of 2.34615 on 1 procs for 244 steps with 458 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 21379.6365822 -16667.6763242 -16667.6911213 Force two-norm initial, final = 133526 2.4504 Force max component initial, final = 38755.5 0.738832 Final line search alpha, max atom move = 0.101658 0.0751084 Iterations, force evaluations = 244 429 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1473 | 2.1473 | 2.1473 | 0.0 | 91.52 Neigh | 0.13547 | 0.13547 | 0.13547 | 0.0 | 5.77 Comm | 0.053028 | 0.053028 | 0.053028 | 0.0 | 2.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01039 | | | 0.44 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19712 ave 19712 max 19712 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: 849514 ave 849514 max 849514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 849514 Ave neighs/atom = 1854.83 Neighbor list builds = 9 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 : 244 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.72 | 11.72 | 11.72 Mbytes Step Temp E_pair E_mol TotEng Press Volume 244 0 -16667.691 0 -16667.691 -24640.76 8884.0703 258 0 -16690.257 0 -16690.257 -207233.54 8944.0792 Loop time of 0.0896702 on 1 procs for 14 steps with 458 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -16667.6911213 -16690.2529271 -16690.2567594 Force two-norm initial, final = 3315.64 47.4703 Force max component initial, final = 3247.9 34.3373 Final line search alpha, max atom move = 0.00026156 0.00898128 Iterations, force evaluations = 14 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.08295 | 0.08295 | 0.08295 | 0.0 | 92.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018604 | 0.0018604 | 0.0018604 | 0.0 | 2.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00486 | | | 5.42 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19722 ave 19722 max 19722 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: 849584 ave 849584 max 849584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 849584 Ave neighs/atom = 1854.99 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.2653, bins = 3 9 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 11.22 | 11.22 | 11.22 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16690.257 0 -16690.257 -207233.54 Loop time of 1.90735e-06 on 1 procs for 0 steps with 458 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: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17731 ave 17731 max 17731 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: 847816 ave 847816 max 847816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 847816 Ave neighs/atom = 1851.13 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) = 11.22 | 11.22 | 11.22 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 -16690.257 -16690.257 20.773516 88.669836 4.8556762 -207233.54 -207233.54 6114.2697 -633106.15 5291.265 2.7993254 4038.9237 Loop time of 9.53674e-07 on 1 procs for 0 steps with 458 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: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17731 ave 17731 max 17731 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 423908 ave 423908 max 423908 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 847816 ave 847816 max 847816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 847816 Ave neighs/atom = 1851.13 Neighbor list builds = 0 Dangerous builds = 0 458 -16690.2567593521 eV 2.79932541570758 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02