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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -65.646719 0.0000000) to (32.821579 65.646719 3.5600001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0197710 5.0197710 3.5600001 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -65.646719 0.0000000) to (32.821579 65.646719 3.5600001) create_atoms CPU = 0.001 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0197710 5.0197710 3.5600001 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -65.646719 0.0000000) to (32.821579 65.646719 3.5600001) create_atoms CPU = 0.001 seconds 682 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 34 1 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1348 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 34 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.503 | 5.503 | 5.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5892.3086 0 -5892.3086 -3164.1096 35 0 -5921.3073 0 -5921.3073 -3367.2297 Loop time of 0.740943 on 1 procs for 35 steps with 1348 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 = -5892.30859023345 -5921.30291766148 -5921.30733794334 Force two-norm initial, final = 26.347265 0.37916537 Force max component initial, final = 7.1094516 0.11601765 Final line search alpha, max atom move = 1.0000000 0.11601765 Iterations, force evaluations = 35 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73209 | 0.73209 | 0.73209 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0049413 | 0.0049413 | 0.0049413 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003908 | | | 0.53 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9752.00 ave 9752 max 9752 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: 235220.0 ave 235220 max 235220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235220 Ave neighs/atom = 174.49555 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 34 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.503 | 5.503 | 5.503 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -5921.3073 0 -5921.3073 -3367.2297 15340.959 43 0 -5921.6815 0 -5921.6815 -141.90155 15322.898 Loop time of 0.126518 on 1 procs for 8 steps with 1348 atoms 97.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5921.30733794334 -5921.67793088034 -5921.68147504938 Force two-norm initial, final = 74.159411 0.63635285 Force max component initial, final = 67.471653 0.15818602 Final line search alpha, max atom move = 0.00017534357 2.7736902e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.122 | 0.122 | 0.122 | 0.0 | 96.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078211 | 0.00078211 | 0.00078211 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003741 | | | 2.96 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9767.00 ave 9767 max 9767 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: 236012.0 ave 236012 max 236012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236012 Ave neighs/atom = 175.08309 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 34 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.641 | 5.641 | 5.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5921.6815 0 -5921.6815 -141.90155 Loop time of 1.773e-06 on 1 procs for 0 steps with 1348 atoms 112.8% 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 | | 1.773e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9722.00 ave 9722 max 9722 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: 235796.0 ave 235796 max 235796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235796 Ave neighs/atom = 174.92285 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 34 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.641 | 5.641 | 5.641 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 -5921.6815 -5921.6815 33.029532 131.29344 3.5334217 -141.90155 -141.90155 -4.4864227 -423.94878 2.7305461 2.3148505 161.82479 Loop time of 2.105e-06 on 1 procs for 0 steps with 1348 atoms 190.0% 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 | | 2.105e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9722.00 ave 9722 max 9722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117898.0 ave 117898 max 117898 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235796.0 ave 235796 max 235796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235796 Ave neighs/atom = 174.92285 Neighbor list builds = 0 Dangerous builds = 0 1348 -5921.68147504938 eV 2.31485053244749 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01