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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -44.204674 0.0000000) to (54.139447 44.204674 8.9612251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1914539 5.4498913 5.9741501 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -44.204674 0.0000000) to (54.139447 44.204674 8.9612251) create_atoms CPU = 0.002 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1914539 5.4498913 5.9741501 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -44.204674 0.0000000) to (54.139447 44.204674 8.9612251) create_atoms CPU = 0.002 seconds 1756 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 25 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 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_249706810527_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.533 | 6.533 | 6.533 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12870.314 0 -12870.314 70818.815 1022 0 -13794.069 0 -13794.069 -54496.027 Loop time of 45.4963 on 1 procs for 1022 steps with 3506 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 = -12870.313713241 -13794.0556361195 -13794.0689892665 Force two-norm initial, final = 545.92981 0.35103880 Force max component initial, final = 105.03149 0.034429567 Final line search alpha, max atom move = 1.0000000 0.034429567 Iterations, force evaluations = 1022 1962 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 44.237 | 44.237 | 44.237 | 0.0 | 97.23 Neigh | 0.73822 | 0.73822 | 0.73822 | 0.0 | 1.62 Comm | 0.20586 | 0.20586 | 0.20586 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3153 | | | 0.69 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10077.0 ave 10077 max 10077 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: 485956.0 ave 485956 max 485956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 485956 Ave neighs/atom = 138.60696 Neighbor list builds = 23 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1022 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.535 | 6.535 | 6.535 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1022 0 -13794.069 0 -13794.069 -54496.027 42892.305 1065 0 -13858.666 0 -13858.666 515.39891 41430.41 Loop time of 1.08363 on 1 procs for 43 steps with 3506 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13794.0689892666 -13858.6586049669 -13858.6659458522 Force two-norm initial, final = 3025.2731 24.410989 Force max component initial, final = 2193.7422 15.313186 Final line search alpha, max atom move = 8.3829925e-05 0.0012837033 Iterations, force evaluations = 43 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96136 | 0.96136 | 0.96136 | 0.0 | 88.72 Neigh | 0.093593 | 0.093593 | 0.093593 | 0.0 | 8.64 Comm | 0.0042119 | 0.0042119 | 0.0042119 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02446 | | | 2.26 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9950.00 ave 9950 max 9950 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: 496100.0 ave 496100 max 496100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496100 Ave neighs/atom = 141.50029 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 7.053 | 7.053 | 7.053 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13858.666 0 -13858.666 515.39891 Loop time of 1.606e-06 on 1 procs for 0 steps with 3506 atoms 186.8% 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 | | 1.606e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9952.00 ave 9952 max 9952 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: 496232.0 ave 496232 max 496232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496232 Ave neighs/atom = 141.53793 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 7.053 | 7.053 | 7.053 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 -13858.666 -13858.666 52.644282 85.588703 9.1949966 515.39891 515.39891 515.94698 573.29079 456.95897 2.2339347 7951.6385 Loop time of 2.337e-06 on 1 procs for 0 steps with 3506 atoms 256.7% 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 | | 2.337e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9952.00 ave 9952 max 9952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 248116.0 ave 248116 max 248116 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 496232.0 ave 496232 max 496232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496232 Ave neighs/atom = 141.53793 Neighbor list builds = 0 Dangerous builds = 0 3506 -13858.6659458522 eV 2.2339347134822 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:47