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 = 3.6336621 3.6336621 3.6336621 Created orthogonal box = (0.0000000 -67.001418 0.0000000) to (33.500709 67.001418 3.6336621) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1236379 5.1236379 3.6336621 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -67.001418 0.0000000) to (33.500709 67.001418 3.6336621) create_atoms CPU = 0.001 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1236379 5.1236379 3.6336621 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -67.001418 0.0000000) to (33.500709 67.001418 3.6336621) create_atoms CPU = 0.001 seconds 682 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 48 2 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1362 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_529419924683_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 48 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.665 | 4.665 | 4.665 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5479.3182 0 -5479.3182 13219.902 95 0 -5578.6715 0 -5578.6715 5505.9812 Loop time of 77.5419 on 1 procs for 95 steps with 1362 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 = -5479.31818444224 -5578.66632833342 -5578.67154902402 Force two-norm initial, final = 59.021886 0.21521961 Force max component initial, final = 7.9532849 0.053044113 Final line search alpha, max atom move = 1.0000000 0.053044113 Iterations, force evaluations = 95 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 77.495 | 77.495 | 77.495 | 0.0 | 99.94 Neigh | 0.014705 | 0.014705 | 0.014705 | 0.0 | 0.02 Comm | 0.017226 | 0.017226 | 0.017226 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01497 | | | 0.02 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6554.00 ave 6554 max 6554 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: 78128.0 ave 78128 max 78128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78128 Ave neighs/atom = 57.362702 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 48 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -5578.6715 0 -5578.6715 5505.9812 16312.2 100 0 -5578.8862 0 -5578.8862 -124.26633 16374.986 Loop time of 2.80524 on 1 procs for 5 steps with 1362 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 = -5578.67154902402 -5578.88315745481 -5578.88617454347 Force two-norm initial, final = 114.10384 6.4744355 Force max component initial, final = 93.760156 6.0719244 Final line search alpha, max atom move = 8.6371002e-05 0.00052443820 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8028 | 2.8028 | 2.8028 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042002 | 0.00042002 | 0.00042002 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002066 | | | 0.07 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6546.00 ave 6546 max 6546 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: 77756.0 ave 77756 max 77756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77756 Ave neighs/atom = 57.089574 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 48 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.802 | 4.802 | 4.802 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5578.8862 0 -5578.8862 -124.26633 Loop time of 1.64e-06 on 1 procs for 0 steps with 1362 atoms 122.0% 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 | | 1.64e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6546.00 ave 6546 max 6546 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: 77444.0 ave 77444 max 77444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77444 Ave neighs/atom = 56.860499 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 48 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.802 | 4.802 | 4.802 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 -5578.8862 -5578.8862 33.437079 134.43655 3.6427992 -124.26633 -124.26633 4.0719294 -596.0177 219.14677 2.3436638 161.26854 Loop time of 1.733e-06 on 1 procs for 0 steps with 1362 atoms 173.1% 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 | | 1.733e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6546.00 ave 6546 max 6546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38722.0 ave 38722 max 38722 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77444.0 ave 77444 max 77444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77444 Ave neighs/atom = 56.860499 Neighbor list builds = 0 Dangerous builds = 0 1362 -3487.89607780989 eV 2.34366383464784 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:22