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 = 3.63909 3.63909 3.63909 Created orthogonal box = (0 -55.4325 0) to (27.7144 55.4325 3.63909) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.77835 4.77835 3.63909 Created 466 atoms create_atoms CPU = 0.000206947 secs 466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.77835 4.77835 3.63909 Created 466 atoms create_atoms CPU = 9.29832e-05 secs 466 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 24 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 920 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.452 | 5.452 | 5.452 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3000.2756 0 -3000.2756 -1908.9152 52 0 -3007.1325 0 -3007.1325 -6611.6328 Loop time of 0.632503 on 1 procs for 52 steps with 920 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3000.27556171 -3007.13005509 -3007.13251069 Force two-norm initial, final = 10.0607 0.124571 Force max component initial, final = 2.52977 0.0113609 Final line search alpha, max atom move = 1 0.0113609 Iterations, force evaluations = 52 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62428 | 0.62428 | 0.62428 | 0.0 | 98.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0058067 | 0.0058067 | 0.0058067 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002416 | | | 0.38 Nlocal: 920 ave 920 max 920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10986 ave 10986 max 10986 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: 290956 ave 290956 max 290956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290956 Ave neighs/atom = 316.257 Neighbor list builds = 0 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 : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.452 | 5.452 | 5.452 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -3007.1325 0 -3007.1325 -6611.6328 11181.321 55 0 -3007.2264 0 -3007.2264 -634.5162 11135.456 Loop time of 0.0379379 on 1 procs for 3 steps with 920 atoms 79.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3007.13251069 -3007.22620673 -3007.22640751 Force two-norm initial, final = 65.1511 1.20872 Force max component initial, final = 47.4858 1.1443 Final line search alpha, max atom move = 0.000391524 0.00044802 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.036829 | 0.036829 | 0.036829 | 0.0 | 97.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002985 | 0.0002985 | 0.0002985 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008109 | | | 2.14 Nlocal: 920 ave 920 max 920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10934 ave 10934 max 10934 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: 291832 ave 291832 max 291832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291832 Ave neighs/atom = 317.209 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.59 | 5.59 | 5.59 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3007.2264 0 -3007.2264 -634.5162 Loop time of 2.14577e-06 on 1 procs for 0 steps with 920 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: 920 ave 920 max 920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10946 ave 10946 max 10946 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: 291876 ave 291876 max 291876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291876 Ave neighs/atom = 317.257 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) = 5.59 | 5.59 | 5.59 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 -3007.2264 -3007.2264 27.657779 110.86506 3.6315829 -634.5162 -634.5162 164.30563 -2016.047 -51.807176 2.2457959 385.90577 Loop time of 9.53674e-07 on 1 procs for 0 steps with 920 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: 920 ave 920 max 920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10946 ave 10946 max 10946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145938 ave 145938 max 145938 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 291876 ave 291876 max 291876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291876 Ave neighs/atom = 317.257 Neighbor list builds = 0 Dangerous builds = 0 920 -3007.22640751303 eV 2.2457959170606 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00