LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -41.253826 0.0000000) to (35.726861 41.253826 7.0066140) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4125136 6.3467425 7.0066140 Created 621 atoms using lattice units in orthogonal box = (0.0000000 -41.253826 0.0000000) to (35.726861 41.253826 7.0066140) create_atoms CPU = 0.001 seconds 621 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4125136 6.3467425 7.0066140 Created 626 atoms using lattice units in orthogonal box = (0.0000000 -41.253826 0.0000000) to (35.726861 41.253826 7.0066140) create_atoms CPU = 0.001 seconds 626 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 18 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1247 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_658278549784_005#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.475 | 5.475 | 5.475 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4014.1413 0 -4014.1413 31674.143 146 0 -4234.8231 0 -4234.8231 6632.5979 Loop time of 3.71151 on 1 procs for 146 steps with 1247 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4014.14132082415 -4234.81894706407 -4234.82310323862 Force two-norm initial, final = 392.49416 0.13293366 Force max component initial, final = 115.13222 0.032242634 Final line search alpha, max atom move = 1.0000000 0.032242634 Iterations, force evaluations = 146 257 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.594 | 3.594 | 3.594 | 0.0 | 96.84 Neigh | 0.078816 | 0.078816 | 0.078816 | 0.0 | 2.12 Comm | 0.021661 | 0.021661 | 0.021661 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01699 | | | 0.46 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7339.00 ave 7339 max 7339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 273356.0 ave 273356 max 273356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273356 Ave neighs/atom = 219.21091 Neighbor list builds = 5 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 146 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.475 | 5.475 | 5.475 Mbytes Step Temp E_pair E_mol TotEng Press Volume 146 0 -4234.8231 0 -4234.8231 6632.5979 20653.673 156 0 -4235.4814 0 -4235.4814 -25.852193 20819.247 Loop time of 0.164673 on 1 procs for 10 steps with 1247 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 = -4234.82310323862 -4235.47769974868 -4235.48138438536 Force two-norm initial, final = 166.64501 0.74081101 Force max component initial, final = 147.54594 0.56135216 Final line search alpha, max atom move = 0.00015586262 8.7493820e-05 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16021 | 0.16021 | 0.16021 | 0.0 | 97.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073348 | 0.00073348 | 0.00073348 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003725 | | | 2.26 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7336.00 ave 7336 max 7336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 273410.0 ave 273410 max 273410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273410 Ave neighs/atom = 219.25421 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.613 | 5.613 | 5.613 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4235.4814 0 -4235.4814 -25.852193 Loop time of 1.917e-06 on 1 procs for 0 steps with 1247 atoms 156.5% 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 | | 1.917e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7340.00 ave 7340 max 7340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 269490.0 ave 269490 max 269490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269490 Ave neighs/atom = 216.11067 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.613 | 5.613 | 5.613 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 -4235.4814 -4235.4814 35.711659 83.316529 6.9971925 -25.852193 -25.852193 -43.181318 -26.229028 -8.1462325 2.4309851 1048.7726 Loop time of 2.232e-06 on 1 procs for 0 steps with 1247 atoms 179.2% 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 | | 2.232e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7340.00 ave 7340 max 7340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134745.0 ave 134745 max 134745 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 269490.0 ave 269490 max 269490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269490 Ave neighs/atom = 216.11067 Neighbor list builds = 0 Dangerous builds = 0 1247 -4235.48138438536 eV 2.43098505883106 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04