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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -48.411133 0.0000000) to (13.175841 48.411133 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6467892 5.3790147 5.7504086 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -48.411133 0.0000000) to (13.175841 48.411133 8.6256130) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6467892 5.3790147 5.7504086 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -48.411133 0.0000000) to (13.175841 48.411133 8.6256130) create_atoms CPU = 0.001 seconds 507 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1008 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_115454747503_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3717.8987 0 -3717.8987 124401.88 74 0 -4465.8389 0 -4465.8389 10307.426 Loop time of 6.24238 on 1 procs for 74 steps with 1008 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 = -3717.8987241701 -4465.8345701094 -4465.838854052 Force two-norm initial, final = 1033.5538 0.22454467 Force max component initial, final = 219.79686 0.076316137 Final line search alpha, max atom move = 1.0000000 0.076316137 Iterations, force evaluations = 74 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.213 | 6.213 | 6.213 | 0.0 | 99.53 Neigh | 0.014765 | 0.014765 | 0.014765 | 0.0 | 0.24 Comm | 0.0066635 | 0.0066635 | 0.0066635 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007915 | | | 0.13 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4677.00 ave 4677 max 4677 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: 89026.0 ave 89026 max 89026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89026 Ave neighs/atom = 88.319444 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.590 | 4.590 | 4.590 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -4465.8389 0 -4465.8389 10307.426 11003.822 81 0 -4466.2548 0 -4466.2548 -136.51928 11064.963 Loop time of 0.460051 on 1 procs for 7 steps with 1008 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 = -4465.83885405201 -4466.25348706699 -4466.25475894587 Force two-norm initial, final = 146.00828 1.7051969 Force max component initial, final = 133.30680 1.0743920 Final line search alpha, max atom move = 0.00018724361 0.00020117305 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45756 | 0.45756 | 0.45756 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038433 | 0.00038433 | 0.00038433 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002111 | | | 0.46 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4638.00 ave 4638 max 4638 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: 88420.0 ave 88420 max 88420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88420 Ave neighs/atom = 87.718254 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.728 | 4.728 | 4.728 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4466.2548 0 -4466.2548 -136.51928 Loop time of 2.783e-06 on 1 procs for 0 steps with 1008 atoms 179.7% 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 | | 2.783e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4644.00 ave 4644 max 4644 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: 88008.0 ave 88008 max 88008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88008 Ave neighs/atom = 87.309524 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.728 | 4.728 | 4.728 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 -4466.2548 -4466.2548 13.182265 97.440259 8.6143301 -136.51928 -136.51928 -155.64488 -109.11215 -144.8008 2.2649796 384.6033 Loop time of 2.16e-06 on 1 procs for 0 steps with 1008 atoms 231.5% 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 | | 2.16e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4644.00 ave 4644 max 4644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 44004.0 ave 44004 max 44004 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 88008.0 ave 88008 max 88008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88008 Ave neighs/atom = 87.309524 Neighbor list builds = 0 Dangerous builds = 0 1008 -4466.25475894587 eV 2.26497960290163 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07