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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -41.649362 0.0000000) to (51.009842 41.649362 8.6222370) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8296962 5.3549179 5.7481580 Created 1666 atoms using lattice units in orthogonal box = (0.0000000 -41.649362 0.0000000) to (51.009842 41.649362 8.6222370) create_atoms CPU = 0.003 seconds 1666 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8296962 5.3549179 5.7481580 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -41.649362 0.0000000) to (51.009842 41.649362 8.6222370) create_atoms CPU = 0.002 seconds 1690 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 20 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3356 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.892 | 7.892 | 7.892 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14716.735 0 -14716.735 13666.414 113 0 -14863.389 0 -14863.389 5689.6383 Loop time of 6.8615 on 1 procs for 113 steps with 3356 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14716.7345630224 -14863.3771723304 -14863.3893119216 Force two-norm initial, final = 208.22704 0.36965420 Force max component initial, final = 31.998187 0.043523263 Final line search alpha, max atom move = 0.56906610 0.024767614 Iterations, force evaluations = 113 176 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.4685 | 6.4685 | 6.4685 | 0.0 | 94.27 Neigh | 0.316 | 0.316 | 0.316 | 0.0 | 4.61 Comm | 0.033991 | 0.033991 | 0.033991 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04302 | | | 0.63 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12853.0 ave 12853 max 12853 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: 752934.0 ave 752934 max 752934 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 752934 Ave neighs/atom = 224.35459 Neighbor list builds = 7 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 113 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.892 | 7.892 | 7.892 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -14863.389 0 -14863.389 5689.6383 36636.357 118 0 -14863.919 0 -14863.919 -152.61263 36758.042 Loop time of 0.251508 on 1 procs for 5 steps with 3356 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 = -14863.3893119216 -14863.9178437589 -14863.9191786351 Force two-norm initial, final = 279.94567 6.8535024 Force max component initial, final = 265.55377 5.2570509 Final line search alpha, max atom move = 8.2216351e-05 0.00043221555 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24614 | 0.24614 | 0.24614 | 0.0 | 97.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072869 | 0.00072869 | 0.00072869 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004637 | | | 1.84 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12853.0 ave 12853 max 12853 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: 752786.0 ave 752786 max 752786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 752786 Ave neighs/atom = 224.31049 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.029 | 8.029 | 8.029 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14863.919 0 -14863.919 -152.61263 Loop time of 2.08e-06 on 1 procs for 0 steps with 3356 atoms 192.3% 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 | | 2.08e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12853.0 ave 12853 max 12853 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: 752082.0 ave 752082 max 752082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 752082 Ave neighs/atom = 224.10072 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.029 | 8.029 | 8.029 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 -14863.919 -14863.919 50.998631 83.649247 8.6165184 -152.61263 -152.61263 -184.94908 -43.901164 -228.98764 2.2406566 1643.1138 Loop time of 2.794e-06 on 1 procs for 0 steps with 3356 atoms 250.5% 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 | | 2.794e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12853.0 ave 12853 max 12853 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 376041.0 ave 376041 max 376041 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 752082.0 ave 752082 max 752082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 752082 Ave neighs/atom = 224.10072 Neighbor list builds = 0 Dangerous builds = 0 3356 -14772.4299143555 eV 2.24065655232654 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07