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 -53.571109 0.0000000) to (43.740627 53.571109 8.8671530) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3926800 5.1369556 5.9114353 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -53.571109 0.0000000) to (43.740627 53.571109 8.8671530) create_atoms CPU = 0.003 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3926800 5.1369556 5.9114353 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -53.571109 0.0000000) to (43.740627 53.571109 8.8671530) create_atoms CPU = 0.002 seconds 1756 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 = 12 28 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 2 atoms, new total = 3502 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_803527979660_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 = 12 28 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) = 7.395 | 7.395 | 7.395 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11625.823 0 -11625.823 34564.378 174 0 -12356.801 0 -12356.801 5768.2444 Loop time of 9.92362 on 1 procs for 174 steps with 3502 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11625.8228788612 -12356.7900200491 -12356.8011666938 Force two-norm initial, final = 731.13467 0.42498374 Force max component initial, final = 89.210964 0.11581111 Final line search alpha, max atom move = 1.0000000 0.11581111 Iterations, force evaluations = 174 322 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.6647 | 9.6647 | 9.6647 | 0.0 | 97.39 Neigh | 0.15402 | 0.15402 | 0.15402 | 0.0 | 1.55 Comm | 0.045025 | 0.045025 | 0.045025 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0599 | | | 0.60 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11453.0 ave 11453 max 11453 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: 609928.0 ave 609928 max 609928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609928 Ave neighs/atom = 174.16562 Neighbor list builds = 4 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 = 12 28 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 : 174 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.395 | 7.395 | 7.395 Mbytes Step Temp E_pair E_mol TotEng Press Volume 174 0 -12356.801 0 -12356.801 5768.2444 41555.627 181 0 -12357.666 0 -12357.666 -34.821002 41735.479 Loop time of 0.283026 on 1 procs for 7 steps with 3502 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 = -12356.8011666938 -12357.6571740771 -12357.6656306328 Force two-norm initial, final = 309.22209 2.1491420 Force max component initial, final = 286.32703 1.4365597 Final line search alpha, max atom move = 7.0360081e-05 0.00010107646 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27587 | 0.27587 | 0.27587 | 0.0 | 97.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009308 | 0.0009308 | 0.0009308 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00623 | | | 2.20 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11457.0 ave 11457 max 11457 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: 609968.0 ave 609968 max 609968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609968 Ave neighs/atom = 174.17704 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 = 12 28 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) = 7.533 | 7.533 | 7.533 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12357.666 0 -12357.666 -34.821002 Loop time of 1.954e-06 on 1 procs for 0 steps with 3502 atoms 204.7% 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 | | 1.954e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11459.0 ave 11459 max 11459 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: 609364.0 ave 609364 max 609364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609364 Ave neighs/atom = 174.00457 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 = 12 28 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) = 7.533 | 7.533 | 7.533 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 -12357.666 -12357.666 43.639745 107.84942 8.8675852 -34.821002 -34.821002 -52.408152 -55.511868 3.4570132 2.3145672 1489.7898 Loop time of 2.249e-06 on 1 procs for 0 steps with 3502 atoms 311.2% 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 | | 2.249e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11459.0 ave 11459 max 11459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 304682.0 ave 304682 max 304682 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 609364.0 ave 609364 max 609364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609364 Ave neighs/atom = 174.00457 Neighbor list builds = 0 Dangerous builds = 0 3502 -12357.6656306328 eV 2.31456719939423 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10