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 = 2.8638485 2.8638485 2.8638485 Created orthogonal box = (0.0000000 -30.577535 0.0000000) to (21.621582 30.577535 4.0500934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1725860 4.8280318 4.0500934 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -30.577535 0.0000000) to (21.621582 30.577535 4.0500934) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1725860 4.8280318 4.0500934 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.577535 0.0000000) to (21.621582 30.577535 4.0500934) create_atoms CPU = 0.001 seconds 230 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 11 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 452 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 11 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.335 | 5.335 | 5.335 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1656.1816 0 -1656.1816 68351.359 77 0 -1873.3635 0 -1873.3635 -5285.6882 Loop time of 1.79675 on 1 procs for 77 steps with 452 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 = -1656.18161885162 -1873.36205344165 -1873.36351797963 Force two-norm initial, final = 400.32047 0.17715167 Force max component initial, final = 137.90234 0.034083633 Final line search alpha, max atom move = 1.0000000 0.034083633 Iterations, force evaluations = 77 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7531 | 1.7531 | 1.7531 | 0.0 | 97.57 Neigh | 0.027328 | 0.027328 | 0.027328 | 0.0 | 1.52 Comm | 0.01092 | 0.01092 | 0.01092 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005372 | | | 0.30 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8129.00 ave 8129 max 8129 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: 271980.0 ave 271980 max 271980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271980 Ave neighs/atom = 601.72566 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 11 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.336 | 5.336 | 5.336 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -1873.3635 0 -1873.3635 -5285.6882 5355.3144 87 0 -1873.6779 0 -1873.6779 -91.905834 5338.269 Loop time of 0.159172 on 1 procs for 10 steps with 452 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 = -1873.36351797963 -1873.67772838099 -1873.67789062244 Force two-norm initial, final = 63.316728 1.2576690 Force max component initial, final = 52.711886 1.0566121 Final line search alpha, max atom move = 0.0057797070 0.0061069084 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15499 | 0.15499 | 0.15499 | 0.0 | 97.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078322 | 0.00078322 | 0.00078322 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003395 | | | 2.13 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8129.00 ave 8129 max 8129 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: 272528.0 ave 272528 max 272528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272528 Ave neighs/atom = 602.93805 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 11 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.475 | 5.475 | 5.475 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1873.6779 0 -1873.6779 -91.905834 Loop time of 2.027e-06 on 1 procs for 0 steps with 452 atoms 148.0% 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 | | 2.027e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8162.00 ave 8162 max 8162 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: 272776.0 ave 272776 max 272776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272776 Ave neighs/atom = 603.48673 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 11 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.475 | 5.475 | 5.475 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 -1873.6779 -1873.6779 21.423244 61.160994 4.0741845 -91.905834 -91.905834 113.39 -70.099817 -319.00768 2.2592152 497.06758 Loop time of 1.926e-06 on 1 procs for 0 steps with 452 atoms 207.7% 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 | | 1.926e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8162.00 ave 8162 max 8162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136388.0 ave 136388 max 136388 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 272776.0 ave 272776 max 272776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272776 Ave neighs/atom = 603.48673 Neighbor list builds = 0 Dangerous builds = 0 452 -1873.67789062244 eV 2.25921520009676 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02