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 = 3.6284422 3.6284422 3.6284422 Created orthogonal box = (0.0000000 -64.091067 0.0000000) to (37.002995 64.091067 6.2846462) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6927684 5.7517624 6.2846462 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -64.091067 0.0000000) to (37.002995 64.091067 6.2846462) create_atoms CPU = 0.003 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6927684 5.7517624 6.2846462 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -64.091067 0.0000000) to (37.002995 64.091067 6.2846462) create_atoms CPU = 0.003 seconds 1249 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 10 34 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 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2494 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_681088298208_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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 6.131 | 6.131 | 6.131 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9748.4949 0 -9748.4949 68097.162 644 0 -10554.155 0 -10554.155 -12985.62 Loop time of 23.0268 on 1 procs for 644 steps with 2494 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 = -9748.49494787746 -10554.1449384185 -10554.1554586524 Force two-norm initial, final = 1061.0339 0.40965472 Force max component initial, final = 198.25118 0.14023421 Final line search alpha, max atom move = 0.37555681 0.052665911 Iterations, force evaluations = 644 1185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.155 | 22.155 | 22.155 | 0.0 | 96.21 Neigh | 0.56325 | 0.56325 | 0.56325 | 0.0 | 2.45 Comm | 0.15609 | 0.15609 | 0.15609 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1523 | | | 0.66 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10873.0 ave 10873 max 10873 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: 387622.0 ave 387622 max 387622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 387622 Ave neighs/atom = 155.42181 Neighbor list builds = 21 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 644 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.133 | 6.133 | 6.133 Mbytes Step Temp E_pair E_mol TotEng Press Volume 644 0 -10554.155 0 -10554.155 -12985.62 29808.849 659 0 -10560.014 0 -10560.014 -0.44393715 29559.637 Loop time of 0.36465 on 1 procs for 15 steps with 2494 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 = -10554.1554586523 -10560.0081718532 -10560.0143796094 Force two-norm initial, final = 674.48676 2.3229841 Force max component initial, final = 529.08553 0.73539952 Final line search alpha, max atom move = 6.3357320e-05 4.6592943e-05 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32601 | 0.32601 | 0.32601 | 0.0 | 89.40 Neigh | 0.026597 | 0.026597 | 0.026597 | 0.0 | 7.29 Comm | 0.0019672 | 0.0019672 | 0.0019672 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01008 | | | 2.76 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10833.0 ave 10833 max 10833 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: 391854.0 ave 391854 max 391854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391854 Ave neighs/atom = 157.11868 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 6.271 | 6.271 | 6.271 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10560.014 0 -10560.014 -0.44393715 Loop time of 2.427e-06 on 1 procs for 0 steps with 2494 atoms 164.8% 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 | | 2.427e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10822.0 ave 10822 max 10822 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: 391984.0 ave 391984 max 391984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391984 Ave neighs/atom = 157.17081 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 6.271 | 6.271 | 6.271 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 -10560.014 -10560.014 36.558803 127.15208 6.3589246 -0.44393715 -0.44393715 39.381267 -28.723592 -11.989487 2.1979694 5062.573 Loop time of 2.758e-06 on 1 procs for 0 steps with 2494 atoms 253.8% 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 | | 2.758e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10822.0 ave 10822 max 10822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 195992.0 ave 195992 max 195992 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 391984.0 ave 391984 max 391984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391984 Ave neighs/atom = 157.17081 Neighbor list builds = 0 Dangerous builds = 0 2494 -10560.0143796094 eV 2.19796943811922 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23