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 = 3.6149590 3.6149590 3.6149590 Created orthogonal box = (0.0000000 -71.572536 0.0000000) to (43.829048 71.572536 8.8548049) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0686654 5.1123240 5.9032033 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -71.572536 0.0000000) to (43.829048 71.572536 8.8548049) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0686654 5.1123240 5.9032033 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.572536 0.0000000) to (43.829048 71.572536 8.8548049) create_atoms CPU = 0.003 seconds 2358 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 12 38 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 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 4692 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_759493141826_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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 12.29 | 12.29 | 12.29 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16049.288 0 -16049.288 21726.49 51 0 -16569.134 0 -16569.134 3961.7035 Loop time of 3.47233 on 1 procs for 51 steps with 4692 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -16049.2878925614 -16569.1216234939 -16569.1339046864 Force two-norm initial, final = 588.51697 0.35335539 Force max component initial, final = 113.91238 0.041961582 Final line search alpha, max atom move = 1.0000000 0.041961582 Iterations, force evaluations = 51 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3331 | 3.3331 | 3.3331 | 0.0 | 95.99 Neigh | 0.096536 | 0.096536 | 0.096536 | 0.0 | 2.78 Comm | 0.017725 | 0.017725 | 0.017725 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02494 | | | 0.72 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14603.0 ave 14603 max 14603 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: 807864.0 ave 807864 max 807864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 807864 Ave neighs/atom = 172.17903 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.29 | 12.29 | 12.29 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -16569.134 0 -16569.134 3961.7035 55554.269 56 0 -16569.676 0 -16569.676 -361.95667 55726.803 Loop time of 0.26157 on 1 procs for 5 steps with 4692 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 = -16569.1339046864 -16569.67069472 -16569.6758036141 Force two-norm initial, final = 286.83249 25.725631 Force max component initial, final = 263.41065 21.312667 Final line search alpha, max atom move = 3.4372115e-05 0.00073256146 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25472 | 0.25472 | 0.25472 | 0.0 | 97.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094518 | 0.00094518 | 0.00094518 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005908 | | | 2.26 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14609.0 ave 14609 max 14609 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: 812664.0 ave 812664 max 812664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 812664 Ave neighs/atom = 173.20205 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 11.80 | 11.80 | 11.80 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16569.676 0 -16569.676 -361.95667 Loop time of 2.379e-06 on 1 procs for 0 steps with 4692 atoms 210.2% 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 | | 2.379e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14609.0 ave 14609 max 14609 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: 811992.0 ave 811992 max 811992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 811992 Ave neighs/atom = 173.05882 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 11.80 | 11.80 | 11.80 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 -16569.676 -16569.676 43.815632 143.78681 8.8453701 -361.95667 -361.95667 -612.56344 -64.749712 -408.55686 2.2937923 1824.5012 Loop time of 3.027e-06 on 1 procs for 0 steps with 4692 atoms 264.3% 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 | | 3.027e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14609.0 ave 14609 max 14609 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 405996.0 ave 405996 max 405996 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 811992.0 ave 811992 max 811992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 811992 Ave neighs/atom = 173.05882 Neighbor list builds = 0 Dangerous builds = 0 4692 -16569.6758036141 eV 2.29379226811889 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04