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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -42.832419 0.0000000) to (52.458786 42.832419 8.8671532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9952898 5.5070253 5.9114354 Created 1669 atoms using lattice units in orthogonal box = (0.0000000 -42.832419 0.0000000) to (52.458786 42.832419 8.8671532) create_atoms CPU = 0.003 seconds 1669 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9952898 5.5070253 5.9114354 Created 1693 atoms using lattice units in orthogonal box = (0.0000000 -42.832419 0.0000000) to (52.458786 42.832419 8.8671532) create_atoms CPU = 0.002 seconds 1693 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3362 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.970 | 6.970 | 6.970 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11508.789 0 -11508.789 28044.2 80 0 -11860.581 0 -11860.581 8063.3516 Loop time of 3.67682 on 1 procs for 80 steps with 3362 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 = -11508.788997499 -11860.5696088219 -11860.5805535725 Force two-norm initial, final = 332.07515 0.35345449 Force max component initial, final = 82.027630 0.081379386 Final line search alpha, max atom move = 0.42502137 0.034587978 Iterations, force evaluations = 80 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4673 | 3.4673 | 3.4673 | 0.0 | 94.30 Neigh | 0.17435 | 0.17435 | 0.17435 | 0.0 | 4.74 Comm | 0.014208 | 0.014208 | 0.014208 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02098 | | | 0.57 Nlocal: 3362.00 ave 3362 max 3362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10774.0 ave 10774 max 10774 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: 584726.0 ave 584726 max 584726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 584726 Ave neighs/atom = 173.92207 Neighbor list builds = 5 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.971 | 6.971 | 6.971 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -11860.581 0 -11860.581 8063.3516 39847.864 89 0 -11862.088 0 -11862.088 -35.76091 40092.495 Loop time of 0.289147 on 1 procs for 9 steps with 3362 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 = -11860.5805535725 -11862.0832192501 -11862.088090452 Force two-norm initial, final = 414.44818 1.7544916 Force max component initial, final = 383.63437 1.0181128 Final line search alpha, max atom move = 7.3955261e-05 7.5294800e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28253 | 0.28253 | 0.28253 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089763 | 0.00089763 | 0.00089763 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005714 | | | 1.98 Nlocal: 3362.00 ave 3362 max 3362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10773.0 ave 10773 max 10773 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: 584788.0 ave 584788 max 584788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 584788 Ave neighs/atom = 173.94051 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.109 | 7.109 | 7.109 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11862.088 0 -11862.088 -35.76091 Loop time of 1.813e-06 on 1 procs for 0 steps with 3362 atoms 165.5% 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 | | 1.813e-06 | | |100.00 Nlocal: 3362.00 ave 3362 max 3362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10773.0 ave 10773 max 10773 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: 583954.0 ave 583954 max 583954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 583954 Ave neighs/atom = 173.69244 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.109 | 7.109 | 7.109 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 -11862.088 -11862.088 52.441224 86.391829 8.849477 -35.76091 -35.76091 -29.604302 -37.073704 -40.604725 2.3131785 1525.4331 Loop time of 2.32e-06 on 1 procs for 0 steps with 3362 atoms 258.6% 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 | | 2.32e-06 | | |100.00 Nlocal: 3362.00 ave 3362 max 3362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10773.0 ave 10773 max 10773 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291977.0 ave 291977 max 291977 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 583954.0 ave 583954 max 583954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 583954 Ave neighs/atom = 173.69244 Neighbor list builds = 0 Dangerous builds = 0 3362 -11862.088090452 eV 2.31317847768433 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04