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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -57.783247 0.0000000) to (40.856065 57.783247 5.7209934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4087945 5.0981648 5.7209934 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -57.783247 0.0000000) to (40.856065 57.783247 5.7209934) create_atoms CPU = 0.002 seconds 822 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4087945 5.0981648 5.7209934 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -57.783247 0.0000000) to (40.856065 57.783247 5.7209934) create_atoms CPU = 0.001 seconds 822 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 37 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1630 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.727 | 4.727 | 4.727 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5419.256 0 -5419.256 6942.3125 29 0 -5461.2248 0 -5461.2248 1832.3655 Loop time of 2.76491 on 1 procs for 29 steps with 1630 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5419.25597198903 -5461.22120653986 -5461.22478602598 Force two-norm initial, final = 31.325050 0.12411513 Force max component initial, final = 5.1080684 0.019792453 Final line search alpha, max atom move = 1.0000000 0.019792453 Iterations, force evaluations = 29 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7457 | 2.7457 | 2.7457 | 0.0 | 99.30 Neigh | 0.008309 | 0.008309 | 0.008309 | 0.0 | 0.30 Comm | 0.0050109 | 0.0050109 | 0.0050109 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005939 | | | 0.21 Nlocal: 1630.00 ave 1630 max 1630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5994.00 ave 5994 max 5994 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: 88916.0 ave 88916 max 88916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88916 Ave neighs/atom = 54.549693 Neighbor list builds = 1 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.726 | 4.726 | 4.726 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -5461.2248 0 -5461.2248 1832.3655 27012.198 31 0 -5461.2448 0 -5461.2448 760.60195 27051.735 Loop time of 0.214256 on 1 procs for 2 steps with 1630 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 = -5461.22478602597 -5461.24261206965 -5461.24475580441 Force two-norm initial, final = 30.144357 0.16138756 Force max component initial, final = 27.295258 0.067127903 Final line search alpha, max atom move = 0.00021584493 1.4489217e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21287 | 0.21287 | 0.21287 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021118 | 0.00021118 | 0.00021118 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001174 | | | 0.55 Nlocal: 1630.00 ave 1630 max 1630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5994.00 ave 5994 max 5994 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: 88856.0 ave 88856 max 88856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88856 Ave neighs/atom = 54.512883 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.864 | 4.864 | 4.864 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5461.2448 0 -5461.2448 760.60195 Loop time of 2.438e-06 on 1 procs for 0 steps with 1630 atoms 164.1% 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 | | 2.438e-06 | | |100.00 Nlocal: 1630.00 ave 1630 max 1630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5994.00 ave 5994 max 5994 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: 88848.0 ave 88848 max 88848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88848 Ave neighs/atom = 54.507975 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.864 | 4.864 | 4.864 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 -5461.2448 -5461.2448 40.915807 115.56649 5.7210016 760.60195 760.60195 3.9815566 2273.9001 3.9241826 2.5291242 785.42251 Loop time of 2.531e-06 on 1 procs for 0 steps with 1630 atoms 237.1% 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 | | 2.531e-06 | | |100.00 Nlocal: 1630.00 ave 1630 max 1630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5994.00 ave 5994 max 5994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 44424.0 ave 44424 max 44424 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 88848.0 ave 88848 max 88848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88848 Ave neighs/atom = 54.507975 Neighbor list builds = 0 Dangerous builds = 0 1630 -5461.24475580441 eV 2.52912419666985 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03