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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -41.973727 0.0000000) to (29.679907 41.973727 5.1666087) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2957379 5.7236901 5.1666087 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.973727 0.0000000) to (29.679907 41.973727 5.1666087) create_atoms CPU = 0.006 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2957379 5.7236901 5.1666087 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.973727 0.0000000) to (29.679907 41.973727 5.1666087) create_atoms CPU = 0.005 seconds 532 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 20 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1060 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_673777079812_004#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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.432 | 5.432 | 5.432 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2890.6869 0 -2890.6869 83148.125 179 0 -3457.4463 0 -3457.4463 2380.1857 Loop time of 7.76607 on 1 procs for 179 steps with 1060 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 = -2890.68689958847 -3457.44327101171 -3457.44626321613 Force two-norm initial, final = 539.12441 0.22349935 Force max component initial, final = 138.00618 0.014978905 Final line search alpha, max atom move = 1.0000000 0.014978905 Iterations, force evaluations = 179 322 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.5295 | 7.5295 | 7.5295 | 0.0 | 96.95 Neigh | 0.13085 | 0.13085 | 0.13085 | 0.0 | 1.68 Comm | 0.060191 | 0.060191 | 0.060191 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04555 | | | 0.59 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7979.00 ave 7979 max 7979 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: 238960.0 ave 238960 max 238960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238960 Ave neighs/atom = 225.43396 Neighbor list builds = 4 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 179 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.432 | 5.432 | 5.432 Mbytes Step Temp E_pair E_mol TotEng Press Volume 179 0 -3457.4463 0 -3457.4463 2380.1857 12872.878 184 0 -3457.6145 0 -3457.6145 -46.93878 12901.413 Loop time of 0.19193 on 1 procs for 5 steps with 1060 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 = -3457.44626321614 -3457.61433288952 -3457.6145110682 Force two-norm initial, final = 77.664671 0.73726222 Force max component initial, final = 68.787072 0.42614245 Final line search alpha, max atom move = 0.00049983696 0.00021300174 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18617 | 0.18617 | 0.18617 | 0.0 | 97.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013139 | 0.0013139 | 0.0013139 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004443 | | | 2.31 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8012.00 ave 8012 max 8012 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: 239088.0 ave 239088 max 239088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239088 Ave neighs/atom = 225.55472 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.570 | 5.570 | 5.570 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3457.6145 0 -3457.6145 -46.93878 Loop time of 6.144e-06 on 1 procs for 0 steps with 1060 atoms 195.3% 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 | | 6.144e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8015.00 ave 8015 max 8015 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: 238880.0 ave 238880 max 238880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238880 Ave neighs/atom = 225.35849 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.570 | 5.570 | 5.570 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 -3457.6145 -3457.6145 29.785673 84.044683 5.1537059 -46.93878 -46.93878 -45.881259 -42.146264 -52.788817 2.4381836 771.31131 Loop time of 7.006e-06 on 1 procs for 0 steps with 1060 atoms 271.2% 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 | | 7.006e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8015.00 ave 8015 max 8015 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119440.0 ave 119440 max 119440 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 238880.0 ave 238880 max 238880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238880 Ave neighs/atom = 225.35849 Neighbor list builds = 0 Dangerous builds = 0 1060 -3457.6145110682 eV 2.43818361767101 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08