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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -36.506982 0.0000000) to (25.814335 36.506982 5.1120000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5554708 5.7265854 5.1120000 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -36.506982 0.0000000) to (25.814335 36.506982 5.1120000) create_atoms CPU = 0.003 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5554708 5.7265854 5.1120000 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -36.506982 0.0000000) to (25.814335 36.506982 5.1120000) create_atoms CPU = 0.002 seconds 410 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 10 27 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 808 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_887933271505_002#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.530 | 4.530 | 4.530 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2654.458 0 -2654.458 43465.296 58 0 -2848.0787 0 -2848.0787 93.650924 Loop time of 1.47898 on 1 procs for 58 steps with 808 atoms 43.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2654.45799407491 -2848.075838239 -2848.07866917926 Force two-norm initial, final = 388.08913 0.18478625 Force max component initial, final = 130.16524 0.021730986 Final line search alpha, max atom move = 1.0000000 0.021730986 Iterations, force evaluations = 58 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4551 | 1.4551 | 1.4551 | 0.0 | 98.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012258 | 0.012258 | 0.012258 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01164 | | | 0.79 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3455.00 ave 3455 max 3455 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: 43464.0 ave 43464 max 43464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43464 Ave neighs/atom = 53.792079 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.530 | 4.530 | 4.530 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -2848.0787 0 -2848.0787 93.650924 9635.1329 62 0 -2848.1246 0 -2848.1246 94.733526 9635.233 Loop time of 0.092157 on 1 procs for 4 steps with 808 atoms 47.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2848.07866917925 -2848.12450262757 -2848.12461472352 Force two-norm initial, final = 27.011069 1.0522528 Force max component initial, final = 21.513990 0.77640627 Final line search alpha, max atom move = 0.00088711381 0.00068876073 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.089063 | 0.089063 | 0.089063 | 0.0 | 96.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064384 | 0.00064384 | 0.00064384 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002451 | | | 2.66 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3425.00 ave 3425 max 3425 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: 43680.0 ave 43680 max 43680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43680 Ave neighs/atom = 54.059406 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.668 | 4.668 | 4.668 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 2853.791 0 2853.791 94.733526 Loop time of 6.445e-06 on 1 procs for 0 steps with 808 atoms 93.1% 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 | | 6.445e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3425.00 ave 3425 max 3425 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: 43664.0 ave 43664 max 43664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43664 Ave neighs/atom = 54.039604 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.668 | 4.668 | 4.668 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 2853.791 -2848.1246 25.791154 73.21562 5.1025551 94.733526 94.733526 61.70762 93.628239 128.86472 2.3113309 552.73536 Loop time of 6.986e-06 on 1 procs for 0 steps with 808 atoms 229.0% 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 | | 6.986e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3425.00 ave 3425 max 3425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21832.0 ave 21832 max 21832 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43664.0 ave 43664 max 43664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43664 Ave neighs/atom = 54.039604 Neighbor list builds = 0 Dangerous builds = 0 808 2853.79099444316 eV 2.31133088466084 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01