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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -39.949508 0.0000000) to (34.597289 39.949508 6.7850866) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2097698 6.1460782 6.7850866 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -39.949508 0.0000000) to (34.597289 39.949508 6.7850866) create_atoms CPU = 0.001 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2097698 6.1460782 6.7850866 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -39.949508 0.0000000) to (34.597289 39.949508 6.7850866) create_atoms CPU = 0.001 seconds 629 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 1247 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.635 | 4.635 | 4.635 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6631.2863 0 -6631.2863 76545.08 67 0 -7136.3962 0 -7136.3962 17173.921 Loop time of 2.37702 on 1 procs for 67 steps with 1247 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 = -6631.28627243012 -7136.39019198199 -7136.39624948545 Force two-norm initial, final = 553.82301 0.34755923 Force max component initial, final = 133.23862 0.10105187 Final line search alpha, max atom move = 1.0000000 0.10105187 Iterations, force evaluations = 67 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3565 | 2.3565 | 2.3565 | 0.0 | 99.14 Neigh | 0.0069183 | 0.0069183 | 0.0069183 | 0.0 | 0.29 Comm | 0.0057257 | 0.0057257 | 0.0057257 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007867 | | | 0.33 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4717.00 ave 4717 max 4717 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: 96168.0 ave 96168 max 96168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96168 Ave neighs/atom = 77.119487 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.635 | 4.635 | 4.635 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -7136.3962 0 -7136.3962 17173.921 18755.943 77 0 -7138.1878 0 -7138.1878 64.468391 18937.333 Loop time of 0.234539 on 1 procs for 10 steps with 1247 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 = -7136.39624948544 -7138.18575179703 -7138.18784681783 Force two-norm initial, final = 410.58630 1.8056781 Force max component initial, final = 365.04859 1.3964119 Final line search alpha, max atom move = 0.00012977821 0.00018122383 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23145 | 0.23145 | 0.23145 | 0.0 | 98.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044115 | 0.00044115 | 0.00044115 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002646 | | | 1.13 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4714.00 ave 4714 max 4714 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: 96088.0 ave 96088 max 96088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96088 Ave neighs/atom = 77.055333 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.773 | 4.773 | 4.773 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7138.1878 0 -7138.1878 64.468391 Loop time of 1.953e-06 on 1 procs for 0 steps with 1247 atoms 204.8% 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 | | 1.953e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4714.00 ave 4714 max 4714 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: 95934.0 ave 95934 max 95934 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95934 Ave neighs/atom = 76.931836 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.773 | 4.773 | 4.773 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 -7138.1878 -7138.1878 34.65944 80.643264 6.77531 64.468391 64.468391 18.246108 57.187085 117.97198 2.4358809 1023.8326 Loop time of 1.97e-06 on 1 procs for 0 steps with 1247 atoms 203.0% 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 | | 1.97e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4714.00 ave 4714 max 4714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47967.0 ave 47967 max 47967 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95934.0 ave 95934 max 95934 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95934 Ave neighs/atom = 76.931836 Neighbor list builds = 0 Dangerous builds = 0 1247 -7138.18784681783 eV 2.43588092889446 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03