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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -69.159025 0.0000000) to (39.928982 69.159025 6.2613639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8911613 5.2908544 6.2613639 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -69.159025 0.0000000) to (39.928982 69.159025 6.2613639) create_atoms CPU = 0.008 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8911613 5.2908544 6.2613639 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.159025 0.0000000) to (39.928982 69.159025 6.2613639) create_atoms CPU = 0.007 seconds 1466 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 36 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, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2924 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.991 | 6.991 | 6.991 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10184.937 0 -10184.937 8020.734 87 0 -10325.007 0 -10325.007 1782.9866 Loop time of 7.63337 on 1 procs for 87 steps with 2924 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 = -10184.9371432078 -10324.9967774557 -10325.0069463513 Force two-norm initial, final = 78.772719 0.30057049 Force max component initial, final = 10.988292 0.034566675 Final line search alpha, max atom move = 1.0000000 0.034566675 Iterations, force evaluations = 87 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3936 | 7.3936 | 7.3936 | 0.0 | 96.86 Neigh | 0.13602 | 0.13602 | 0.13602 | 0.0 | 1.78 Comm | 0.05413 | 0.05413 | 0.05413 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04966 | | | 0.65 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12070.0 ave 12070 max 12070 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: 496204.0 ave 496204 max 496204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496204 Ave neighs/atom = 169.70041 Neighbor list builds = 2 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.991 | 6.991 | 6.991 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -10325.007 0 -10325.007 1782.9866 34580.88 89 0 -10325.034 0 -10325.034 -3.7915672 34625.676 Loop time of 0.221717 on 1 procs for 2 steps with 2924 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 = -10325.006946351 -10325.0330527251 -10325.0342063719 Force two-norm initial, final = 67.642885 1.0962563 Force max component initial, final = 43.999570 0.81227907 Final line search alpha, max atom move = 0.00014701919 0.00011942061 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21594 | 0.21594 | 0.21594 | 0.0 | 97.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013699 | 0.0013699 | 0.0013699 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004412 | | | 1.99 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12050.0 ave 12050 max 12050 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: 492268.0 ave 492268 max 492268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 492268 Ave neighs/atom = 168.35431 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.748 | 6.748 | 6.748 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10325.034 0 -10325.034 -3.7915672 Loop time of 6.475e-06 on 1 procs for 0 steps with 2924 atoms 200.8% 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 | | 6.475e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12050.0 ave 12050 max 12050 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: 489728.0 ave 489728 max 489728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489728 Ave neighs/atom = 167.48564 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.748 | 6.748 | 6.748 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 -10325.034 -10325.034 39.932479 138.39934 6.2652438 -3.7915672 -3.7915672 -4.5476831 30.781515 -37.608533 2.3248428 985.41065 Loop time of 7.337e-06 on 1 procs for 0 steps with 2924 atoms 245.3% 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 | | 7.337e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12050.0 ave 12050 max 12050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 244864.0 ave 244864 max 244864 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 489728.0 ave 489728 max 489728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489728 Ave neighs/atom = 167.48564 Neighbor list builds = 0 Dangerous builds = 0 2924 -10325.0342063719 eV 2.32484277890839 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08