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 = 3.5483741 3.5483741 3.5483741 Created orthogonal box = (0.0000000 -57.654255 0.0000000) to (20.383857 57.654255 5.0181587) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5592338 4.3677466 5.0181587 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.654255 0.0000000) to (20.383857 57.654255 5.0181587) create_atoms CPU = 0.003 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5592338 4.3677466 5.0181587 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.654255 0.0000000) to (20.383857 57.654255 5.0181587) create_atoms CPU = 0.002 seconds 530 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 ghost atom cutoff = 8 binsize = 4, bins = 6 29 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1058 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_922363340570_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 ghost atom cutoff = 8 binsize = 4, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.448 | 5.448 | 5.448 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4032.5641 0 -4032.5641 80296.552 80 0 -4269.3301 0 -4269.3301 18778.117 Loop time of 3.4706 on 1 procs for 80 steps with 1058 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 = -4032.56409019232 -4269.32600881024 -4269.33013678927 Force two-norm initial, final = 333.16535 0.25462665 Force max component initial, final = 91.349380 0.068268338 Final line search alpha, max atom move = 1.0000000 0.068268338 Iterations, force evaluations = 80 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3669 | 3.3669 | 3.3669 | 0.0 | 97.01 Neigh | 0.053759 | 0.053759 | 0.053759 | 0.0 | 1.55 Comm | 0.028816 | 0.028816 | 0.028816 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02117 | | | 0.61 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8100.00 ave 8100 max 8100 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: 208708.0 ave 208708 max 208708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208708 Ave neighs/atom = 197.26654 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.448 | 5.448 | 5.448 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -4269.3301 0 -4269.3301 18778.117 11794.842 89 0 -4270.1123 0 -4270.1123 -68.111003 11883.612 Loop time of 0.282684 on 1 procs for 9 steps with 1058 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4269.33013678926 -4270.11190537794 -4270.11232255825 Force two-norm initial, final = 252.39432 1.7959255 Force max component initial, final = 199.02596 1.2228323 Final line search alpha, max atom move = 0.00017680246 0.00021619976 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24732 | 0.24732 | 0.24732 | 0.0 | 87.49 Neigh | 0.026633 | 0.026633 | 0.026633 | 0.0 | 9.42 Comm | 0.0023696 | 0.0023696 | 0.0023696 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006365 | | | 2.25 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8068.00 ave 8068 max 8068 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: 208196.0 ave 208196 max 208196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208196 Ave neighs/atom = 196.78261 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.586 | 5.586 | 5.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4270.1123 0 -4270.1123 -68.111003 Loop time of 6.264e-06 on 1 procs for 0 steps with 1058 atoms 191.6% 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 | | 6.264e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8068.00 ave 8068 max 8068 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: 208324.0 ave 208324 max 208324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208324 Ave neighs/atom = 196.90359 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 ghost atom cutoff = 8 binsize = 4, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.586 | 5.586 | 5.586 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 -4270.1123 -4270.1123 20.401271 116.24532 5.0109002 -68.111003 -68.111003 -165.00597 87.573598 -126.90064 2.3318728 478.09304 Loop time of 6.405e-06 on 1 procs for 0 steps with 1058 atoms 296.6% 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 | | 6.405e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8068.00 ave 8068 max 8068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104162.0 ave 104162 max 104162 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 208324.0 ave 208324 max 208324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208324 Ave neighs/atom = 196.90359 Neighbor list builds = 0 Dangerous builds = 0 1058 -4270.11232255825 eV 2.33187279337187 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04