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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -40.853015 0.0000000) to (28.884584 40.853015 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0972795 6.4076816 5.7200000 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.853015 0.0000000) to (28.884584 40.853015 5.7200000) create_atoms CPU = 0.001 seconds 410 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0972795 6.4076816 5.7200000 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.853015 0.0000000) to (28.884584 40.853015 5.7200000) create_atoms CPU = 0.001 seconds 410 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 806 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_353977746962_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.537 | 4.537 | 4.537 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2685.1072 0 -2685.1072 1557.9181 28 0 -2697.3262 0 -2697.3262 -3705.9549 Loop time of 1.23399 on 1 procs for 28 steps with 806 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2685.10715453687 -2697.3235365189 -2697.32615832966 Force two-norm initial, final = 23.296635 0.12491921 Force max component initial, final = 6.6082239 0.011063949 Final line search alpha, max atom move = 1.0000000 0.011063949 Iterations, force evaluations = 28 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2301 | 1.2301 | 1.2301 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016877 | 0.0016877 | 0.0016877 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002189 | | | 0.18 Nlocal: 806.000 ave 806 max 806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3586.00 ave 3586 max 3586 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: 61544.0 ave 61544 max 61544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61544 Ave neighs/atom = 76.357320 Neighbor list builds = 0 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.537 | 4.537 | 4.537 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -2697.3262 0 -2697.3262 -3705.9549 13499.456 31 0 -2697.3816 0 -2697.3816 -684.87778 13447.087 Loop time of 0.127173 on 1 procs for 3 steps with 806 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 = -2697.32615832966 -2697.38065949501 -2697.38157131758 Force two-norm initial, final = 40.184606 1.9875585 Force max component initial, final = 31.880791 1.9667946 Final line search alpha, max atom move = 0.00022176537 0.00043616694 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12641 | 0.12641 | 0.12641 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013517 | 0.00013517 | 0.00013517 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006319 | | | 0.50 Nlocal: 806.000 ave 806 max 806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3586.00 ave 3586 max 3586 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: 61264.0 ave 61264 max 61264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61264 Ave neighs/atom = 76.009926 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.675 | 4.675 | 4.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2697.3816 0 -2697.3816 -684.87778 Loop time of 1.58e-06 on 1 procs for 0 steps with 806 atoms 189.9% 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 | | 1.58e-06 | | |100.00 Nlocal: 806.000 ave 806 max 806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3586.00 ave 3586 max 3586 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: 61352.0 ave 61352 max 61352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61352 Ave neighs/atom = 76.119107 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.675 | 4.675 | 4.675 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 -2697.3816 -2697.3816 28.841664 81.70603 5.7062896 -684.87778 -684.87778 233.98894 -2259.5877 -29.034551 2.5698381 591.02625 Loop time of 1.532e-06 on 1 procs for 0 steps with 806 atoms 130.5% 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 | | 1.532e-06 | | |100.00 Nlocal: 806.000 ave 806 max 806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3586.00 ave 3586 max 3586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30676.0 ave 30676 max 30676 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61352.0 ave 61352 max 61352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61352 Ave neighs/atom = 76.119107 Neighbor list builds = 0 Dangerous builds = 0 806 -2697.38157131758 eV 2.5698380875803 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01