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 = 3.4986963 3.4986963 3.4986963 Created orthogonal box = (0.0000000 -41.400632 0.0000000) to (50.700927 41.400632 8.5700208) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7943916 5.3224886 5.7133472 Created 1683 atoms using lattice units in orthogonal box = (0.0000000 -41.400632 0.0000000) to (50.700927 41.400632 8.5700208) create_atoms CPU = 0.003 seconds 1683 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7943916 5.3224886 5.7133472 Created 1683 atoms using lattice units in orthogonal box = (0.0000000 -41.400632 0.0000000) to (50.700927 41.400632 8.5700208) create_atoms CPU = 0.002 seconds 1683 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 54 atoms, new total = 3312 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.994 | 6.994 | 6.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13469.324 0 -13469.324 1603.3128 63 0 -13580.437 0 -13580.437 -11451.532 Loop time of 3.10652 on 1 procs for 63 steps with 3312 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13469.3243048249 -13580.4285789364 -13580.4370604723 Force two-norm initial, final = 54.033059 0.27958658 Force max component initial, final = 4.6860477 0.062320006 Final line search alpha, max atom move = 1.0000000 0.062320006 Iterations, force evaluations = 63 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0461 | 3.0461 | 3.0461 | 0.0 | 98.05 Neigh | 0.032847 | 0.032847 | 0.032847 | 0.0 | 1.06 Comm | 0.011478 | 0.011478 | 0.011478 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01611 | | | 0.52 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10725.0 ave 10725 max 10725 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: 575482.0 ave 575482 max 575482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 575482 Ave neighs/atom = 173.75664 Neighbor list builds = 1 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.998 | 6.998 | 6.998 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -13580.437 0 -13580.437 -11451.532 35977.811 68 0 -13581.255 0 -13581.255 -3353.7687 35716.002 Loop time of 0.203775 on 1 procs for 5 steps with 3312 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 = -13580.4370604722 -13581.2541884583 -13581.2545034433 Force two-norm initial, final = 314.31679 0.78830960 Force max component initial, final = 222.98082 0.14233629 Final line search alpha, max atom move = 0.00026295532 3.7428085e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19946 | 0.19946 | 0.19946 | 0.0 | 97.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065415 | 0.00065415 | 0.00065415 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003656 | | | 1.79 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11169.0 ave 11169 max 11169 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: 576070.0 ave 576070 max 576070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576070 Ave neighs/atom = 173.93418 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.136 | 7.136 | 7.136 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13581.255 0 -13581.255 -3353.7687 Loop time of 1.673e-06 on 1 procs for 0 steps with 3312 atoms 179.3% 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 | | 1.673e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11179.0 ave 11179 max 11179 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: 576352.0 ave 576352 max 576352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576352 Ave neighs/atom = 174.01932 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.136 | 7.136 | 7.136 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 -13581.255 -13581.255 50.527256 82.801264 8.5368993 -3353.7687 -3353.7687 -6.3631619 -10055.506 0.563012 2.326265 1541.0462 Loop time of 2.539e-06 on 1 procs for 0 steps with 3312 atoms 236.3% 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 | | 2.539e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11179.0 ave 11179 max 11179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 288176.0 ave 288176 max 288176 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 576352.0 ave 576352 max 576352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576352 Ave neighs/atom = 174.01932 Neighbor list builds = 0 Dangerous builds = 0 3312 -13581.2545034433 eV 2.32626503731182 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03