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 -29.724023 0.0000000) to (21.018058 29.724023 4.0449272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6706796 3.8531141 4.0449272 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -29.724023 0.0000000) to (21.018058 29.724023 4.0449272) create_atoms CPU = 0.001 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6706796 3.8531141 4.0449272 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -29.724023 0.0000000) to (21.018058 29.724023 4.0449272) create_atoms CPU = 0.000 seconds 218 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 23 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 = 434 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 23 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) = 4.816 | 4.816 | 4.816 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1751.5174 0 -1751.5174 60068.73 47 0 -1841.8756 0 -1841.8756 19841.648 Loop time of 2.70231 on 1 procs for 47 steps with 434 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1751.51742017985 -1841.87407198034 -1841.87557968688 Force two-norm initial, final = 116.91352 0.15506245 Force max component initial, final = 32.249510 0.038939077 Final line search alpha, max atom move = 1.0000000 0.038939077 Iterations, force evaluations = 47 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.697 | 2.697 | 2.697 | 0.0 | 99.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0025462 | 0.0025462 | 0.0025462 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002784 | | | 0.10 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2249.00 ave 2249 max 2249 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: 25144.0 ave 25144 max 25144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25144 Ave neighs/atom = 57.935484 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 23 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 : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.815 | 4.815 | 4.815 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1841.8756 0 -1841.8756 19841.648 5054.0657 67 0 -1842.7938 0 -1842.7938 0.48036854 5110.8772 Loop time of 0.753821 on 1 procs for 20 steps with 434 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 = -1841.87557968688 -1842.79368991724 -1842.79383128512 Force two-norm initial, final = 127.73844 1.2002348 Force max component initial, final = 117.71612 0.80646752 Final line search alpha, max atom move = 0.0035041149 0.0028259549 Iterations, force evaluations = 20 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73924 | 0.73924 | 0.73924 | 0.0 | 98.07 Neigh | 0.011077 | 0.011077 | 0.011077 | 0.0 | 1.47 Comm | 0.00059298 | 0.00059298 | 0.00059298 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002907 | | | 0.39 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2228.00 ave 2228 max 2228 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: 24860.0 ave 24860 max 24860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24860 Ave neighs/atom = 57.281106 Neighbor list builds = 1 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 23 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) = 4.953 | 4.953 | 4.953 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1842.7938 0 -1842.7938 0.48036854 Loop time of 2.031e-06 on 1 procs for 0 steps with 434 atoms 147.7% 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 | | 2.031e-06 | | |100.00 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2228.00 ave 2228 max 2228 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: 24860.0 ave 24860 max 24860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24860 Ave neighs/atom = 57.281106 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 23 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) = 4.953 | 4.953 | 4.953 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 -1842.7938 -1842.7938 20.965728 60.499826 4.0293164 0.48036854 0.48036854 -207.16687 -43.230713 251.83869 2.2447541 405.55594 Loop time of 1.975e-06 on 1 procs for 0 steps with 434 atoms 202.5% 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 | | 1.975e-06 | | |100.00 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2228.00 ave 2228 max 2228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12430.0 ave 12430 max 12430 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24860.0 ave 24860 max 24860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24860 Ave neighs/atom = 57.281106 Neighbor list builds = 0 Dangerous builds = 0 434 -1842.79383128512 eV 2.24475410712954 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03