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 = 3.5240105 3.5240105 3.5240105 Created orthogonal box = (0.0000000 -66.490897 0.0000000) to (33.245449 66.490897 3.5240105) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8560768 4.8560768 3.5240105 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -66.490897 0.0000000) to (33.245449 66.490897 3.5240105) create_atoms CPU = 0.001 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8560768 4.8560768 3.5240105 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -66.490897 0.0000000) to (33.245449 66.490897 3.5240105) create_atoms CPU = 0.001 seconds 714 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 35 1 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1426 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_535504325462_003#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.543 | 5.543 | 5.543 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6345.4578 0 -6345.4578 16352.201 54 0 -6439.0267 0 -6439.0267 10825.45 Loop time of 1.391 on 1 procs for 54 steps with 1426 atoms 93.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6345.45779884267 -6439.0212156902 -6439.02670097834 Force two-norm initial, final = 68.443636 0.25919009 Force max component initial, final = 9.1603469 0.045875291 Final line search alpha, max atom move = 1.0000000 0.045875291 Iterations, force evaluations = 54 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3607 | 1.3607 | 1.3607 | 0.0 | 97.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0094567 | 0.0094567 | 0.0094567 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02081 | | | 1.50 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11333.0 ave 11333 max 11333 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: 250888.0 ave 250888 max 250888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250888 Ave neighs/atom = 175.93829 Neighbor list builds = 0 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.543 | 5.543 | 5.543 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -6439.0267 0 -6439.0267 10825.45 15579.789 61 0 -6439.6226 0 -6439.6226 -359.00579 15675.034 Loop time of 0.119571 on 1 procs for 7 steps with 1426 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 = -6439.02670097834 -6439.61953411199 -6439.62258254636 Force two-norm initial, final = 213.02623 6.3667211 Force max component initial, final = 191.41397 4.7617474 Final line search alpha, max atom move = 0.00017625803 0.00083929624 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11562 | 0.11562 | 0.11562 | 0.0 | 96.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073525 | 0.00073525 | 0.00073525 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003218 | | | 2.69 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11338.0 ave 11338 max 11338 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: 249432.0 ave 249432 max 249432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249432 Ave neighs/atom = 174.91725 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.681 | 5.681 | 5.681 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6439.6226 0 -6439.6226 -359.00579 Loop time of 1.758e-06 on 1 procs for 0 steps with 1426 atoms 113.8% 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 | | 1.758e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11338.0 ave 11338 max 11338 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: 249256.0 ave 249256 max 249256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249256 Ave neighs/atom = 174.79383 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.681 | 5.681 | 5.681 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 -6439.6226 -6439.6226 33.231005 133.84082 3.5243289 -359.00579 -359.00579 -215.58767 -374.67804 -486.75166 2.2150257 424.61079 Loop time of 1.761e-06 on 1 procs for 0 steps with 1426 atoms 170.4% 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 | | 1.761e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11338.0 ave 11338 max 11338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124628.0 ave 124628 max 124628 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 249256.0 ave 249256 max 249256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249256 Ave neighs/atom = 174.79383 Neighbor list builds = 0 Dangerous builds = 0 1426 -6439.62258254636 eV 2.21502565025598 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01