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 = 3.3901167 3.3901167 3.3901167 Created orthogonal box = (0.0000000 -44.331528 0.0000000) to (20.898083 44.331528 4.7943490) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3995963 5.4442227 4.7943490 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -44.331528 0.0000000) to (20.898083 44.331528 4.7943490) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3995963 5.4442227 4.7943490 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -44.331528 0.0000000) to (20.898083 44.331528 4.7943490) create_atoms CPU = 0.000 seconds 230 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 3 9 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 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 452 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_959249795837_003#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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 3 9 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 11.72 | 11.72 | 11.72 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 33590.708 0 33590.708 36411013 380 0 -16460.937 0 -16460.937 -392549.73 Loop time of 7.45929 on 1 procs for 380 steps with 452 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 = 33590.7078937317 -16460.9215848604 -16460.9373495115 Force two-norm initial, final = 268278.84 1.9160954 Force max component initial, final = 92974.577 0.17282485 Final line search alpha, max atom move = 0.12613949 0.021800038 Iterations, force evaluations = 380 708 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9294 | 6.9294 | 6.9294 | 0.0 | 92.90 Neigh | 0.3585 | 0.3585 | 0.3585 | 0.0 | 4.81 Comm | 0.13258 | 0.13258 | 0.13258 | 0.0 | 1.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03876 | | | 0.52 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19028.0 ave 19028 max 19028 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: 829862.0 ave 829862 max 829862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 829862 Ave neighs/atom = 1835.9779 Neighbor list builds = 11 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 3 9 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 380 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.72 | 11.72 | 11.72 Mbytes Step Temp E_pair E_mol TotEng Press Volume 380 0 -16460.937 0 -16460.937 -392549.73 8883.391 411 0 -16584.023 0 -16584.023 -1053.7396 8697.3314 Loop time of 0.397088 on 1 procs for 31 steps with 452 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -16460.9373495114 -16584.0094981326 -16584.0227808214 Force two-norm initial, final = 6675.4939 48.775340 Force max component initial, final = 5722.8645 25.771049 Final line search alpha, max atom move = 3.9579340e-05 0.0010200011 Iterations, force evaluations = 31 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31464 | 0.31464 | 0.31464 | 0.0 | 79.24 Neigh | 0.060832 | 0.060832 | 0.060832 | 0.0 | 15.32 Comm | 0.0051855 | 0.0051855 | 0.0051855 | 0.0 | 1.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01643 | | | 4.14 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17602.0 ave 17602 max 17602 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: 847612.0 ave 847612 max 847612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 847612 Ave neighs/atom = 1875.2478 Neighbor list builds = 2 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 3 9 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 11.22 | 11.22 | 11.22 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16584.023 0 -16584.023 -1053.7396 Loop time of 1.697e-06 on 1 procs for 0 steps with 452 atoms 176.8% 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 | | 1.697e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17602.0 ave 17602 max 17602 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: 849454.0 ave 849454 max 849454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 849454 Ave neighs/atom = 1879.3230 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 3 9 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 11.22 | 11.22 | 11.22 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 -16584.023 -16584.023 20.74377 85.978585 4.8764978 -1053.7396 -1053.7396 -4712.3516 3545.5841 -1994.4513 2.825367 3233.3769 Loop time of 2.339e-06 on 1 procs for 0 steps with 452 atoms 256.5% 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 | | 2.339e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17602.0 ave 17602 max 17602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 424727.0 ave 424727 max 424727 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 849454.0 ave 849454 max 849454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 849454 Ave neighs/atom = 1879.3230 Neighbor list builds = 0 Dangerous builds = 0 452 -16584.0227808214 eV 2.82536701291916 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08