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 = 2.8665000 2.8665000 2.8665000 Created orthogonal box = (0.0000000 -46.575113 0.0000000) to (9.5071051 46.575113 7.0214624) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3214114 4.2341012 4.6809750 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -46.575113 0.0000000) to (9.5071051 46.575113 7.0214624) create_atoms CPU = 0.002 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3214114 4.2341012 4.6809750 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -46.575113 0.0000000) to (9.5071051 46.575113 7.0214624) create_atoms CPU = 0.002 seconds 266 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 3 25 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 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 528 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_960699513424_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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 65207.493 0 65207.493 61867342 73 0 -2249.3412 0 -2249.3412 6855.023 Loop time of 1.31517 on 1 procs for 73 steps with 528 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 = 65207.4930580188 -2249.33980465012 -2249.3412436001 Force two-norm initial, final = 436750.10 0.18717629 Force max component initial, final = 140659.42 0.026097888 Final line search alpha, max atom move = 1.0000000 0.026097888 Iterations, force evaluations = 73 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2738 | 1.2738 | 1.2738 | 0.0 | 96.85 Neigh | 0.012591 | 0.012591 | 0.012591 | 0.0 | 0.96 Comm | 0.016766 | 0.016766 | 0.016766 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01205 | | | 0.92 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4645.00 ave 4645 max 4645 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: 87888.0 ave 87888 max 87888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87888 Ave neighs/atom = 166.45455 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.576 | 4.576 | 4.576 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -2249.3412 0 -2249.3412 6855.023 6218.1298 78 0 -2249.4279 0 -2249.4279 -24.07099 6242.0062 Loop time of 0.0967406 on 1 procs for 5 steps with 528 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 = -2249.3412436001 -2249.42735782937 -2249.42794644821 Force two-norm initial, final = 50.968315 0.73930889 Force max component initial, final = 44.375707 0.47629723 Final line search alpha, max atom move = 0.00021490469 0.00010235851 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.091993 | 0.091993 | 0.091993 | 0.0 | 95.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001067 | 0.001067 | 0.001067 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003681 | | | 3.80 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4518.00 ave 4518 max 4518 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: 87840.0 ave 87840 max 87840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87840 Ave neighs/atom = 166.36364 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.714 | 4.714 | 4.714 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2249.4279 0 -2249.4279 -24.07099 Loop time of 8.349e-06 on 1 procs for 0 steps with 528 atoms 155.7% 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 | | 8.349e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4518.00 ave 4518 max 4518 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: 87800.0 ave 87800 max 87800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87800 Ave neighs/atom = 166.28788 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.714 | 4.714 | 4.714 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 -2249.4279 -2249.4279 9.503368 93.521695 7.0231878 -24.07099 -24.07099 -122.20627 -60.052105 110.0454 2.3312278 413.97553 Loop time of 8.149e-06 on 1 procs for 0 steps with 528 atoms 208.6% 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 | | 8.149e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4518.00 ave 4518 max 4518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43900.0 ave 43900 max 43900 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87800.0 ave 87800 max 87800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87800 Ave neighs/atom = 166.28788 Neighbor list builds = 0 Dangerous builds = 0 528 -2249.42794644821 eV 2.33122778063093 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01