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 = 3.5239542 3.5239542 3.5239542 Created orthogonal box = (0.0000000 -52.149760 0.0000000) to (42.580100 52.149760 8.6318896) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2496014 5.0006619 5.7545931 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -52.149760 0.0000000) to (42.580100 52.149760 8.6318896) create_atoms CPU = 0.002 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2496014 5.0006619 5.7545931 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -52.149760 0.0000000) to (42.580100 52.149760 8.6318896) create_atoms CPU = 0.002 seconds 1758 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 3504 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 7.439 | 7.439 | 7.439 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14759.658 0 -14759.658 34628.164 53 0 -15474.343 0 -15474.343 9139.1545 Loop time of 2.51695 on 1 procs for 53 steps with 3504 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14759.6584330831 -15474.3309112782 -15474.3426328567 Force two-norm initial, final = 546.83286 0.34612763 Force max component initial, final = 75.170697 0.035314229 Final line search alpha, max atom move = 1.0000000 0.035314229 Iterations, force evaluations = 53 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4581 | 2.4581 | 2.4581 | 0.0 | 97.66 Neigh | 0.034846 | 0.034846 | 0.034846 | 0.0 | 1.38 Comm | 0.0099408 | 0.0099408 | 0.0099408 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01402 | | | 0.56 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11987.0 ave 11987 max 11987 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: 614540.0 ave 614540 max 614540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614540 Ave neighs/atom = 175.38242 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.439 | 7.439 | 7.439 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -15474.343 0 -15474.343 9139.1545 38334.947 59 0 -15475.365 0 -15475.365 -61.904403 38532.312 Loop time of 0.218452 on 1 procs for 6 steps with 3504 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 = -15474.3426328567 -15475.3562336777 -15475.3653685659 Force two-norm initial, final = 429.20824 3.5524646 Force max component initial, final = 382.92304 2.8047460 Final line search alpha, max atom move = 4.5869681e-05 0.00012865281 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21333 | 0.21333 | 0.21333 | 0.0 | 97.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074802 | 0.00074802 | 0.00074802 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004377 | | | 2.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12001.0 ave 12001 max 12001 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: 613598.0 ave 613598 max 613598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 613598 Ave neighs/atom = 175.11358 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 7.576 | 7.576 | 7.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15475.365 0 -15475.365 -61.904403 Loop time of 1.865e-06 on 1 procs for 0 steps with 3504 atoms 160.9% 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 | | 1.865e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11968.0 ave 11968 max 11968 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: 613182.0 ave 613182 max 613182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 613182 Ave neighs/atom = 174.99486 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 7.576 | 7.576 | 7.576 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 -15475.365 -15475.365 42.565929 104.87729 8.6314049 -61.904403 -61.904403 -116.58274 -85.444107 16.31364 2.1857633 1344.6926 Loop time of 1.998e-06 on 1 procs for 0 steps with 3504 atoms 250.3% 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 | | 1.998e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11968.0 ave 11968 max 11968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306591.0 ave 306591 max 306591 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 613182.0 ave 613182 max 613182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 613182 Ave neighs/atom = 174.99486 Neighbor list builds = 0 Dangerous builds = 0 3504 -15475.3653685659 eV 2.18576326169083 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03