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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -43.261180 0.0000000) to (11.773346 43.261180 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0457195 4.8064482 5.1383093 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -43.261180 0.0000000) to (11.773346 43.261180 7.7074639) create_atoms CPU = 0.002 seconds 254 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0457195 4.8064482 5.1383093 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -43.261180 0.0000000) to (11.773346 43.261180 7.7074639) create_atoms CPU = 0.002 seconds 254 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 30 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 500 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.436 | 4.436 | 4.436 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3373.3618 0 -3373.3618 -2664.744 17 0 -3385.8903 0 -3385.8903 -9564.0135 Loop time of 0.923656 on 1 procs for 17 steps with 500 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 = -3373.36177855291 -3385.88718491746 -3385.89027048209 Force two-norm initial, final = 18.139805 0.16439552 Force max component initial, final = 4.9128922 0.026038369 Final line search alpha, max atom move = 1.0000000 0.026038369 Iterations, force evaluations = 17 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91948 | 0.91948 | 0.91948 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018913 | 0.0018913 | 0.0018913 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002286 | | | 0.25 Nlocal: 500.000 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2217.00 ave 2217 max 2217 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: 28648.0 ave 28648 max 28648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28648 Ave neighs/atom = 57.296000 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.436 | 4.436 | 4.436 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -3385.8903 0 -3385.8903 -9564.0135 7851.2671 20 0 -3385.956 0 -3385.956 -1799.6983 7827.8483 Loop time of 0.169168 on 1 procs for 3 steps with 500 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3385.89027048209 -3385.955923437 -3385.95595899382 Force two-norm initial, final = 61.951165 0.18077316 Force max component initial, final = 45.165533 0.041921188 Final line search alpha, max atom move = 0.0016399665 6.8749343e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16764 | 0.16764 | 0.16764 | 0.0 | 99.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030309 | 0.00030309 | 0.00030309 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001226 | | | 0.72 Nlocal: 500.000 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2227.00 ave 2227 max 2227 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: 28712.0 ave 28712 max 28712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28712 Ave neighs/atom = 57.424000 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.574 | 4.574 | 4.574 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3385.956 0 -3385.956 -1799.6983 Loop time of 6.495e-06 on 1 procs for 0 steps with 500 atoms 154.0% 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 | | 6.495e-06 | | |100.00 Nlocal: 500.000 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2227.00 ave 2227 max 2227 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: 28724.0 ave 28724 max 28724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28724 Ave neighs/atom = 57.448000 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.574 | 4.574 | 4.574 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 -3385.956 -3385.956 11.754344 86.522361 7.6968967 -1799.6983 -1799.6983 1.9041492 -5392.4306 -8.5685176 2.2911762 382.47511 Loop time of 7.337e-06 on 1 procs for 0 steps with 500 atoms 231.7% 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 | | 7.337e-06 | | |100.00 Nlocal: 500.000 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2227.00 ave 2227 max 2227 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14362.0 ave 14362 max 14362 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28724.0 ave 28724 max 28724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28724 Ave neighs/atom = 57.448000 Neighbor list builds = 0 Dangerous builds = 0 500 -3385.95595899382 eV 2.29117624371691 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01