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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -49.540038 0.0000000) to (20.224636 49.540038 7.0060194) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8539126 4.2934700 4.6706796 Created 599 atoms using lattice units in orthogonal box = (0.0000000 -49.540038 0.0000000) to (20.224636 49.540038 7.0060194) create_atoms CPU = 0.001 seconds 599 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8539126 4.2934700 4.6706796 Created 601 atoms using lattice units in orthogonal box = (0.0000000 -49.540038 0.0000000) to (20.224636 49.540038 7.0060194) create_atoms CPU = 0.001 seconds 601 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 = 8 38 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 1200 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 = 8 38 3 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) = 5.322 | 5.322 | 5.322 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5026.3129 0 -5026.3129 21045.573 32 0 -5112.1499 0 -5112.1499 5266.9249 Loop time of 4.60824 on 1 procs for 32 steps with 1200 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 = -5026.31289681394 -5112.14705704186 -5112.14990404605 Force two-norm initial, final = 126.73556 0.21258951 Force max component initial, final = 54.978542 0.047359243 Final line search alpha, max atom move = 1.0000000 0.047359243 Iterations, force evaluations = 32 56 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.601 | 4.601 | 4.601 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028411 | 0.0028411 | 0.0028411 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00445 | | | 0.10 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3854.00 ave 3854 max 3854 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: 69362.0 ave 69362 max 69362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69362 Ave neighs/atom = 57.801667 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 = 8 38 3 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 : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.322 | 5.322 | 5.322 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -5112.1499 0 -5112.1499 5266.9249 14039.071 37 0 -5112.382 0 -5112.382 126.48939 14079.211 Loop time of 0.58645 on 1 procs for 5 steps with 1200 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 = -5112.14990404605 -5112.37904205485 -5112.38198552609 Force two-norm initial, final = 111.58649 2.0310044 Force max component initial, final = 109.70352 1.3561114 Final line search alpha, max atom move = 0.00013515921 0.00018329095 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58456 | 0.58456 | 0.58456 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026067 | 0.00026067 | 0.00026067 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001633 | | | 0.28 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3849.00 ave 3849 max 3849 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: 69202.0 ave 69202 max 69202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69202 Ave neighs/atom = 57.668333 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 = 8 38 3 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) = 5.460 | 5.460 | 5.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5112.382 0 -5112.382 126.48939 Loop time of 2.367e-06 on 1 procs for 0 steps with 1200 atoms 211.2% 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 | | 2.367e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3849.00 ave 3849 max 3849 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: 69186.0 ave 69186 max 69186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69186 Ave neighs/atom = 57.655000 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 = 8 38 3 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) = 5.460 | 5.460 | 5.460 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 -5112.382 -5112.382 20.214183 99.516683 6.9988424 126.48939 126.48939 154.24209 139.79414 85.431932 2.2412388 580.26581 Loop time of 2.395e-06 on 1 procs for 0 steps with 1200 atoms 208.8% 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 | | 2.395e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3849.00 ave 3849 max 3849 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34593.0 ave 34593 max 34593 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69186.0 ave 69186 max 69186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69186 Ave neighs/atom = 57.655000 Neighbor list builds = 0 Dangerous builds = 0 1200 -5112.38198552609 eV 2.24123881234438 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05