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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -51.733581 0.0000000) to (18.290583 51.733581 4.9780662) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7420030 5.7481757 4.9780662 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -51.733581 0.0000000) to (18.290583 51.733581 4.9780662) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7420030 5.7481757 4.9780662 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -51.733581 0.0000000) to (18.290583 51.733581 4.9780662) create_atoms CPU = 0.001 seconds 434 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 5 25 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 864 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.031 | 5.031 | 5.031 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3633.6258 0 -3633.6258 67918.985 93 0 -3828.6148 0 -3828.6148 9259.7038 Loop time of 1.87209 on 1 procs for 93 steps with 864 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3633.62584324 -3828.61140531355 -3828.61479521472 Force two-norm initial, final = 556.47354 0.19260414 Force max component initial, final = 162.22773 0.016323623 Final line search alpha, max atom move = 1.0000000 0.016323623 Iterations, force evaluations = 93 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8232 | 1.8232 | 1.8232 | 0.0 | 97.39 Neigh | 0.02426 | 0.02426 | 0.02426 | 0.0 | 1.30 Comm | 0.014448 | 0.014448 | 0.014448 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01022 | | | 0.55 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7360.00 ave 7360 max 7360 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: 192660.0 ave 192660 max 192660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192660 Ave neighs/atom = 222.98611 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.032 | 5.032 | 5.032 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -3828.6148 0 -3828.6148 9259.7038 9420.8644 98 0 -3828.8578 0 -3828.8578 275.25859 9468.4509 Loop time of 0.0757216 on 1 procs for 5 steps with 864 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 = -3828.61479521473 -3828.85406384092 -3828.85784694086 Force two-norm initial, final = 109.08011 2.9182973 Force max component initial, final = 94.577357 2.2033860 Final line search alpha, max atom move = 0.00011616247 0.00025595077 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.073131 | 0.073131 | 0.073131 | 0.0 | 96.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047305 | 0.00047305 | 0.00047305 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002117 | | | 2.80 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7493.00 ave 7493 max 7493 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: 192936.0 ave 192936 max 192936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192936 Ave neighs/atom = 223.30556 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.170 | 5.170 | 5.170 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3828.8578 0 -3828.8578 275.25859 Loop time of 2.077e-06 on 1 procs for 0 steps with 864 atoms 144.4% 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 | | 2.077e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7580.00 ave 7580 max 7580 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: 192744.0 ave 192744 max 192744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192744 Ave neighs/atom = 223.08333 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.170 | 5.170 | 5.170 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 -3828.8578 -3828.8578 18.317509 103.92245 4.9739698 275.25859 275.25859 242.53679 374.4802 208.75878 2.2370073 401.48684 Loop time of 2.72e-06 on 1 procs for 0 steps with 864 atoms 257.4% 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 | | 2.72e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7580.00 ave 7580 max 7580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96372.0 ave 96372 max 96372 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 192744.0 ave 192744 max 192744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192744 Ave neighs/atom = 223.08333 Neighbor list builds = 0 Dangerous builds = 0 864 -3805.30399578566 eV 2.23700730318383 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02