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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -41.258113 0.0000000) to (29.173891 41.258113 4.0851619) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5762967 3.6404217 4.0851619 Created 407 atoms using lattice units in orthogonal box = (0.0000000 -41.258113 0.0000000) to (29.173891 41.258113 4.0851619) create_atoms CPU = 0.001 seconds 407 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5762967 3.6404217 4.0851619 Created 409 atoms using lattice units in orthogonal box = (0.0000000 -41.258113 0.0000000) to (29.173891 41.258113 4.0851619) create_atoms CPU = 0.001 seconds 409 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 31 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 816 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.287 | 5.287 | 5.287 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3255.3229 0 -3255.3229 46270.425 125 0 -3389.5867 0 -3389.5867 6077.679 Loop time of 20.41 on 1 procs for 125 steps with 816 atoms 97.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3255.32290293664 -3389.58415011802 -3389.58666726859 Force two-norm initial, final = 140.61590 0.21439175 Force max component initial, final = 41.309281 0.061013128 Final line search alpha, max atom move = 1.0000000 0.061013128 Iterations, force evaluations = 125 238 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.379 | 20.379 | 20.379 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014757 | 0.014757 | 0.014757 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01618 | | | 0.08 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3582.00 ave 3582 max 3582 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: 46982.0 ave 46982 max 46982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46982 Ave neighs/atom = 57.575980 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.291 | 5.291 | 5.291 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -3389.5867 0 -3389.5867 6077.679 9834.2895 133 0 -3389.8776 0 -3389.8776 76.14479 9866.7406 Loop time of 0.627919 on 1 procs for 8 steps with 816 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3389.58666726859 -3389.87587056367 -3389.87758424447 Force two-norm initial, final = 86.958438 1.1941139 Force max component initial, final = 84.284384 0.53502938 Final line search alpha, max atom move = 0.00026206249 0.00014021113 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62557 | 0.62557 | 0.62557 | 0.0 | 99.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035543 | 0.00035543 | 0.00035543 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001993 | | | 0.32 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4212.00 ave 4212 max 4212 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: 46914.0 ave 46914 max 46914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46914 Ave neighs/atom = 57.492647 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.430 | 5.430 | 5.430 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3389.8776 0 -3389.8776 76.14479 Loop time of 2.045e-06 on 1 procs for 0 steps with 816 atoms 195.6% 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 | | 2.045e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4212.00 ave 4212 max 4212 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: 46880.0 ave 46880 max 46880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46880 Ave neighs/atom = 57.450980 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.430 | 5.430 | 5.430 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 -3389.8776 -3389.8776 29.12678 83.138803 4.0745295 76.14479 76.14479 86.738598 61.481165 80.214608 2.2783384 461.62417 Loop time of 2.382e-06 on 1 procs for 0 steps with 816 atoms 209.9% 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 | | 2.382e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4212.00 ave 4212 max 4212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23440.0 ave 23440 max 23440 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46880.0 ave 46880 max 46880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46880 Ave neighs/atom = 57.450980 Neighbor list builds = 0 Dangerous builds = 0 816 -3389.87758424447 eV 2.27833841251273 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21