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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -41.652722 0.0000000) to (51.009647 41.652722 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8296739 5.3548974 5.7481360 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -41.652722 0.0000000) to (51.009647 41.652722 8.6222040) create_atoms CPU = 0.002 seconds 1688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8296739 5.3548974 5.7481360 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -41.652722 0.0000000) to (51.009647 41.652722 8.6222040) create_atoms CPU = 0.002 seconds 1688 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 20 3 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 64 atoms, new total = 3312 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_103383163946_000#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.880 | 7.880 | 7.880 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14576.878 0 -14576.878 7501.8649 48 0 -14672.116 0 -14672.116 -17617.56 Loop time of 2.72746 on 1 procs for 48 steps with 3312 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14576.877941958 -14672.1054901749 -14672.1162003207 Force two-norm initial, final = 84.786903 0.33197426 Force max component initial, final = 7.1925569 0.024371438 Final line search alpha, max atom move = 1.0000000 0.024371438 Iterations, force evaluations = 48 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6681 | 2.6681 | 2.6681 | 0.0 | 97.82 Neigh | 0.037709 | 0.037709 | 0.037709 | 0.0 | 1.38 Comm | 0.009383 | 0.009383 | 0.009383 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01227 | | | 0.45 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12383.0 ave 12383 max 12383 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: 739318.0 ave 739318 max 739318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 739318 Ave neighs/atom = 223.22403 Neighbor list builds = 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.893 | 7.893 | 7.893 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -14672.116 0 -14672.116 -17617.56 36639.032 53 0 -14673.229 0 -14673.229 -5720.7675 36388.302 Loop time of 0.250714 on 1 procs for 5 steps with 3312 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 = -14672.1162003207 -14673.2284913244 -14673.2285327725 Force two-norm initial, final = 456.74333 0.43025722 Force max component initial, final = 323.57190 0.072650006 Final line search alpha, max atom move = 0.00070391436 5.1139382e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24606 | 0.24606 | 0.24606 | 0.0 | 98.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069364 | 0.00069364 | 0.00069364 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003959 | | | 1.58 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12624.0 ave 12624 max 12624 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: 740226.0 ave 740226 max 740226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 740226 Ave neighs/atom = 223.49819 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.031 | 8.031 | 8.031 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14673.229 0 -14673.229 -5720.7675 Loop time of 1.802e-06 on 1 procs for 0 steps with 3312 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 | | 1.802e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12636.0 ave 12636 max 12636 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: 740980.0 ave 740980 max 740980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 740980 Ave neighs/atom = 223.72585 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.031 | 8.031 | 8.031 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 -14673.229 -14673.229 50.838498 83.305444 8.5920283 -5720.7675 -5720.7675 -3.1880463 -17161.451 2.3368998 2.3267358 1595.6617 Loop time of 1.93e-06 on 1 procs for 0 steps with 3312 atoms 259.1% 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 | | 1.93e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12636.0 ave 12636 max 12636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 370490.0 ave 370490 max 370490 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 740980.0 ave 740980 max 740980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 740980 Ave neighs/atom = 223.72585 Neighbor list builds = 0 Dangerous builds = 0 3312 -14583.0384128557 eV 2.32673576582624 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03