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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -42.549139 0.0000000) to (52.111839 42.549139 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9970257 5.2457842 5.7504087 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -42.549139 0.0000000) to (52.111839 42.549139 8.6256130) create_atoms CPU = 0.003 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9970257 5.2457842 5.7504087 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -42.549139 0.0000000) to (52.111839 42.549139 8.6256130) create_atoms CPU = 0.002 seconds 1754 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 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, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3502 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_700541006254_001#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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.678 | 5.678 | 5.678 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14832.044 0 -14832.044 69796.223 47 0 -15527.961 0 -15527.961 7855.6598 Loop time of 9.96246 on 1 procs for 47 steps with 3502 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14832.0444319903 -15527.9478917802 -15527.9613924632 Force two-norm initial, final = 1029.0201 0.44203943 Force max component initial, final = 229.80132 0.10601840 Final line search alpha, max atom move = 1.0000000 0.10601840 Iterations, force evaluations = 47 84 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.9342 | 9.9342 | 9.9342 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0107 | 0.0107 | 0.0107 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0176 | | | 0.18 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8374.00 ave 8374 max 8374 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: 274244.0 ave 274244 max 274244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274244 Ave neighs/atom = 78.310680 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.678 | 5.678 | 5.678 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -15527.961 0 -15527.961 7855.6598 38251.383 53 0 -15528.887 0 -15528.887 -256.38892 38417.446 Loop time of 0.971288 on 1 procs for 6 steps with 3502 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15527.9613924632 -15528.8831103722 -15528.8866578264 Force two-norm initial, final = 392.47426 11.461566 Force max component initial, final = 361.15601 8.7786539 Final line search alpha, max atom move = 5.4512351e-05 0.00047854506 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96624 | 0.96624 | 0.96624 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058429 | 0.00058429 | 0.00058429 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004462 | | | 0.46 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8358.00 ave 8358 max 8358 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: 273274.0 ave 273274 max 273274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273274 Ave neighs/atom = 78.033695 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.816 | 5.816 | 5.816 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15528.887 0 -15528.887 -256.38892 Loop time of 2.368e-06 on 1 procs for 0 steps with 3502 atoms 168.9% 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 | | 2.368e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8339.00 ave 8339 max 8339 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: 272922.0 ave 272922 max 272922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272922 Ave neighs/atom = 77.933181 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.816 | 5.816 | 5.816 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 -15528.887 -15528.887 52.113036 85.553149 8.616802 -256.38892 -256.38892 -366.11689 -122.23904 -280.81083 2.1941113 1516.4993 Loop time of 2.665e-06 on 1 procs for 0 steps with 3502 atoms 300.2% 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 | | 2.665e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8339.00 ave 8339 max 8339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136461.0 ave 136461 max 136461 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 272922.0 ave 272922 max 272922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272922 Ave neighs/atom = 77.933181 Neighbor list builds = 0 Dangerous builds = 0 3502 -15528.8866578264 eV 2.1941112766263 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11