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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -38.390690 0.0000000) to (38.387079 38.390690 3.6111526) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0956300 5.0956300 3.6111526 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -38.390690 0.0000000) to (38.387079 38.390690 3.6111526) create_atoms CPU = 0.001 seconds 453 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0956300 5.0956300 3.6111526 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -38.390690 0.0000000) to (38.387079 38.390690 3.6111526) create_atoms CPU = 0.001 seconds 453 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 = 15 29 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 4 atoms, new total = 902 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_137964310702_004#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 = 15 29 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) = 5.306 | 5.306 | 5.306 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3750.895 0 -3750.895 24792.113 99 0 -3822.8826 0 -3822.8826 -606.79045 Loop time of 7.26862 on 1 procs for 99 steps with 902 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3750.89495517672 -3822.88015492525 -3822.88262027721 Force two-norm initial, final = 53.359799 0.14684598 Force max component initial, final = 13.892165 0.053019530 Final line search alpha, max atom move = 1.0000000 0.053019530 Iterations, force evaluations = 99 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2377 | 7.2377 | 7.2377 | 0.0 | 99.57 Neigh | 0.017742 | 0.017742 | 0.017742 | 0.0 | 0.24 Comm | 0.0062719 | 0.0062719 | 0.0062719 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006937 | | | 0.10 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4322.00 ave 4322 max 4322 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: 48706.0 ave 48706 max 48706 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48706 Ave neighs/atom = 53.997783 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 15 29 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 : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.305 | 5.305 | 5.305 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -3822.8826 0 -3822.8826 -606.79045 10643.558 105 0 -3823.0124 0 -3823.0124 -1238.0053 10647.825 Loop time of 0.405436 on 1 procs for 6 steps with 902 atoms 92.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3822.88262027721 -3823.01236330087 -3823.01236817966 Force two-norm initial, final = 41.426069 0.35159098 Force max component initial, final = 33.552141 0.19948260 Final line search alpha, max atom move = 0.0047841000 0.00095434472 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40059 | 0.40059 | 0.40059 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029974 | 0.00029974 | 0.00029974 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004544 | | | 1.12 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4326.00 ave 4326 max 4326 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: 48730.0 ave 48730 max 48730 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48730 Ave neighs/atom = 54.024390 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 = 15 29 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) = 5.443 | 5.443 | 5.443 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3823.0124 0 -3823.0124 -1238.0053 Loop time of 1.688e-06 on 1 procs for 0 steps with 902 atoms 177.7% 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 | | 1.688e-06 | | |100.00 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4326.00 ave 4326 max 4326 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: 48728.0 ave 48728 max 48728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48728 Ave neighs/atom = 54.022173 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 = 15 29 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) = 5.443 | 5.443 | 5.443 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 -3823.0124 -3823.0124 38.223359 76.78138 3.628074 -1238.0053 -1238.0053 29.888098 -3765.5763 21.672343 2.2989972 101.03654 Loop time of 1.657e-06 on 1 procs for 0 steps with 902 atoms 181.1% 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 | | 1.657e-06 | | |100.00 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4326.00 ave 4326 max 4326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24364.0 ave 24364 max 24364 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48728.0 ave 48728 max 48728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48728 Ave neighs/atom = 54.022173 Neighbor list builds = 0 Dangerous builds = 0 902 -3823.01236817966 eV 2.29899722655687 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08