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 -42.580100 0.0000000) to (52.149760 42.580100 8.6318896) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0006619 5.2496014 5.7545931 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -42.580100 0.0000000) to (52.149760 42.580100 8.6318896) create_atoms CPU = 0.002 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0006619 5.2496014 5.7545931 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.580100 0.0000000) to (52.149760 42.580100 8.6318896) 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 14 23 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 3 atoms, new total = 3503 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 = 14 23 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) = 7.419 | 7.419 | 7.419 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14585.764 0 -14585.764 44119.181 88 0 -15472.672 0 -15472.672 8791.3773 Loop time of 4.22358 on 1 procs for 88 steps with 3503 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 = -14585.7635811108 -15472.6582749996 -15472.6721492572 Force two-norm initial, final = 590.48110 0.40602277 Force max component initial, final = 73.605503 0.073196843 Final line search alpha, max atom move = 0.50921932 0.037273247 Iterations, force evaluations = 88 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0748 | 4.0748 | 4.0748 | 0.0 | 96.48 Neigh | 0.10824 | 0.10824 | 0.10824 | 0.0 | 2.56 Comm | 0.017296 | 0.017296 | 0.017296 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02328 | | | 0.55 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11569.0 ave 11569 max 11569 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: 613618.0 ave 613618 max 613618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 613618 Ave neighs/atom = 175.16928 Neighbor list builds = 3 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 = 14 23 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 : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.415 | 7.415 | 7.415 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -15472.672 0 -15472.672 8791.3773 38334.947 95 0 -15473.785 0 -15473.785 -88.669705 38528.827 Loop time of 0.243593 on 1 procs for 7 steps with 3503 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 = -15472.6721492571 -15473.7849235462 -15473.7854514496 Force two-norm initial, final = 423.86542 5.0869950 Force max component initial, final = 386.96931 4.6201092 Final line search alpha, max atom move = 0.00012932579 0.00059749929 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23843 | 0.23843 | 0.23843 | 0.0 | 97.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072263 | 0.00072263 | 0.00072263 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004439 | | | 1.82 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11218.0 ave 11218 max 11218 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: 613916.0 ave 613916 max 613916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 613916 Ave neighs/atom = 175.25435 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 = 14 23 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) = 7.553 | 7.553 | 7.553 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15473.785 0 -15473.785 -88.669705 Loop time of 1.669e-06 on 1 procs for 0 steps with 3503 atoms 179.7% 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 | | 1.669e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11195.0 ave 11195 max 11195 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: 612926.0 ave 612926 max 612926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 612926 Ave neighs/atom = 174.97174 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 = 14 23 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) = 7.553 | 7.553 | 7.553 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 -15473.785 -15473.785 52.116182 85.679387 8.6285306 -88.669705 -88.669705 -191.99817 10.023328 -84.034272 2.1636369 1353.6638 Loop time of 2.36e-06 on 1 procs for 0 steps with 3503 atoms 254.2% 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 | | 2.36e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11195.0 ave 11195 max 11195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306463.0 ave 306463 max 306463 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 612926.0 ave 612926 max 612926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 612926 Ave neighs/atom = 174.97174 Neighbor list builds = 0 Dangerous builds = 0 3503 -15473.7854514496 eV 2.16363694574718 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05