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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -39.078066 0.0000000) to (7.9767767 39.078066 8.7381211) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7860660 5.2104087 5.8254141 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.078066 0.0000000) to (7.9767767 39.078066 8.7381211) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7860660 5.2104087 5.8254141 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.078066 0.0000000) to (7.9767767 39.078066 8.7381211) create_atoms CPU = 0.000 seconds 242 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 28 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 482 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_058735400462_001#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 28 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.445 | 4.445 | 4.445 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1858.9116 0 -1858.9116 94404.812 94 0 -2028.0495 0 -2028.0495 54589.965 Loop time of 2.52284 on 1 procs for 94 steps with 482 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 = -1858.91160143735 -2028.04766497464 -2028.04951432141 Force two-norm initial, final = 246.24728 0.20687535 Force max component initial, final = 83.486506 0.055250707 Final line search alpha, max atom move = 1.0000000 0.055250707 Iterations, force evaluations = 94 177 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5079 | 2.5079 | 2.5079 | 0.0 | 99.41 Neigh | 0.005616 | 0.005616 | 0.005616 | 0.0 | 0.22 Comm | 0.0044347 | 0.0044347 | 0.0044347 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004912 | | | 0.19 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2570.00 ave 2570 max 2570 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: 28240.0 ave 28240 max 28240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28240 Ave neighs/atom = 58.589212 Neighbor list builds = 2 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 28 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -2028.0495 0 -2028.0495 54589.965 5447.6418 149 0 -2031.6507 0 -2031.6507 -115.61475 5686.6275 Loop time of 0.697856 on 1 procs for 55 steps with 482 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 = -2028.04951432141 -2031.64885332533 -2031.65071832208 Force two-norm initial, final = 321.63526 4.0044864 Force max component initial, final = 189.86820 3.2632501 Final line search alpha, max atom move = 0.0024363725 0.0079504927 Iterations, force evaluations = 55 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.69021 | 0.69021 | 0.69021 | 0.0 | 98.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012324 | 0.0012324 | 0.0012324 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00641 | | | 0.92 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2587.00 ave 2587 max 2587 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: 28048.0 ave 28048 max 28048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28048 Ave neighs/atom = 58.190871 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 28 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.582 | 4.582 | 4.582 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2031.6507 0 -2031.6507 -115.61475 Loop time of 1.832e-06 on 1 procs for 0 steps with 482 atoms 109.2% 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 | | 1.832e-06 | | |100.00 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2502.00 ave 2502 max 2502 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: 28044.0 ave 28044 max 28044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28044 Ave neighs/atom = 58.182573 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 28 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.582 | 4.582 | 4.582 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 -2031.6507 -2031.6507 8.2358668 77.437106 8.9165398 -115.61475 -115.61475 -949.26576 58.998121 543.42338 2.2286123 347.16877 Loop time of 1.515e-06 on 1 procs for 0 steps with 482 atoms 132.0% 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 | | 1.515e-06 | | |100.00 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2502.00 ave 2502 max 2502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14022.0 ave 14022 max 14022 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28044.0 ave 28044 max 28044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28044 Ave neighs/atom = 58.182573 Neighbor list builds = 0 Dangerous builds = 0 482 -2031.65071832208 eV 2.22861229332724 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04