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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -59.005646 0.0000000) to (41.723293 59.005646 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2273571 5.7244284 5.0973115 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -59.005646 0.0000000) to (41.723293 59.005646 5.0973115) create_atoms CPU = 0.003 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2273571 5.7244284 5.0973115 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.005646 0.0000000) to (41.723293 59.005646 5.0973115) create_atoms CPU = 0.003 seconds 1080 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 ghost atom cutoff = 6 binsize = 3, bins = 14 40 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2128 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_492310898779_001#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 ghost atom cutoff = 6 binsize = 3, bins = 14 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.214 | 5.214 | 5.214 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8971.2241 0 -8971.2241 108.07187 372 0 -9048.6683 0 -9048.6683 -18212.141 Loop time of 56.6662 on 1 procs for 372 steps with 2128 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8971.22412237573 -9048.65980182101 -9048.66825212821 Force two-norm initial, final = 47.113720 0.27973845 Force max component initial, final = 8.4413614 0.054689607 Final line search alpha, max atom move = 1.0000000 0.054689607 Iterations, force evaluations = 372 695 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 56.393 | 56.393 | 56.393 | 0.0 | 99.52 Neigh | 0.11341 | 0.11341 | 0.11341 | 0.0 | 0.20 Comm | 0.079669 | 0.079669 | 0.079669 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08019 | | | 0.14 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7993.00 ave 7993 max 7993 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: 143440.0 ave 143440 max 143440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143440 Ave neighs/atom = 67.406015 Neighbor list builds = 9 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 ghost atom cutoff = 6 binsize = 3, bins = 14 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 372 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.217 | 5.217 | 5.217 Mbytes Step Temp E_pair E_mol TotEng Press Volume 372 0 -9048.6683 0 -9048.6683 -18212.141 25098.242 403 0 -9069.2345 0 -9069.2345 64.241895 24783.049 Loop time of 2.81029 on 1 procs for 31 steps with 2128 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 = -9048.66825212822 -9069.23283439983 -9069.23451177889 Force two-norm initial, final = 1091.3759 10.221205 Force max component initial, final = 871.19226 7.8076379 Final line search alpha, max atom move = 0.0015116808 0.011802656 Iterations, force evaluations = 31 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7511 | 2.7511 | 2.7511 | 0.0 | 97.89 Neigh | 0.039219 | 0.039219 | 0.039219 | 0.0 | 1.40 Comm | 0.0032392 | 0.0032392 | 0.0032392 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01672 | | | 0.59 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8097.00 ave 8097 max 8097 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: 142292.0 ave 142292 max 142292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142292 Ave neighs/atom = 66.866541 Neighbor list builds = 3 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 ghost atom cutoff = 6 binsize = 3, bins = 14 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.356 | 5.356 | 5.356 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9069.2345 0 -9069.2345 64.241895 Loop time of 2.203e-06 on 1 procs for 0 steps with 2128 atoms 227.0% 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 | | 2.203e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8092.00 ave 8092 max 8092 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: 142292.0 ave 142292 max 142292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142292 Ave neighs/atom = 66.866541 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 ghost atom cutoff = 6 binsize = 3, bins = 14 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.356 | 5.356 | 5.356 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 -9069.2345 -9069.2345 41.191578 121.09386 4.9684871 64.241895 64.241895 498.31636 63.11701 -368.70769 2.3696049 5355.353 Loop time of 2.676e-06 on 1 procs for 0 steps with 2128 atoms 261.6% 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 | | 2.676e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8092.00 ave 8092 max 8092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71146.0 ave 71146 max 71146 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 142292.0 ave 142292 max 142292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142292 Ave neighs/atom = 66.866541 Neighbor list builds = 0 Dangerous builds = 0 2128 -9069.23451177889 eV 2.36960490658694 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:00