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 -46.721236 0.0000000) to (26.972437 46.721236 6.2429061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7798079 5.5616228 6.2429061 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -46.721236 0.0000000) to (26.972437 46.721236 6.2429061) create_atoms CPU = 0.001 seconds 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7798079 5.5616228 6.2429061 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -46.721236 0.0000000) to (26.972437 46.721236 6.2429061) create_atoms CPU = 0.001 seconds 676 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 31 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 1324 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.054 | 5.054 | 5.054 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5576.2086 0 -5576.2086 -5883.006 74 0 -5605.7052 0 -5605.7052 -19924.824 Loop time of 5.72679 on 1 procs for 74 steps with 1324 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 = -5576.20858564902 -5605.70058947956 -5605.70522155355 Force two-norm initial, final = 17.626430 0.20446839 Force max component initial, final = 3.8837304 0.020989651 Final line search alpha, max atom move = 1.0000000 0.020989651 Iterations, force evaluations = 74 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6981 | 5.6981 | 5.6981 | 0.0 | 99.50 Neigh | 0.014655 | 0.014655 | 0.014655 | 0.0 | 0.26 Comm | 0.0062601 | 0.0062601 | 0.0062601 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007754 | | | 0.14 Nlocal: 1324.00 ave 1324 max 1324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5173.00 ave 5173 max 5173 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: 102408.0 ave 102408 max 102408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102408 Ave neighs/atom = 77.347432 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.054 | 5.054 | 5.054 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -5605.7052 0 -5605.7052 -19924.824 15734.44 83 0 -5606.5058 0 -5606.5058 -6400.2465 15598.653 Loop time of 0.526461 on 1 procs for 9 steps with 1324 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 = -5605.70522155356 -5606.50571457285 -5606.50583284809 Force two-norm initial, final = 219.79615 0.41429512 Force max component initial, final = 194.47937 0.051314877 Final line search alpha, max atom move = 0.00039508157 2.0273562e-05 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5235 | 0.5235 | 0.5235 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043384 | 0.00043384 | 0.00043384 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002527 | | | 0.48 Nlocal: 1324.00 ave 1324 max 1324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5148.00 ave 5148 max 5148 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: 102384.0 ave 102384 max 102384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102384 Ave neighs/atom = 77.329305 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.192 | 5.192 | 5.192 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5606.5058 0 -5606.5058 -6400.2465 Loop time of 1.735e-06 on 1 procs for 0 steps with 1324 atoms 172.9% 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 | | 1.735e-06 | | |100.00 Nlocal: 1324.00 ave 1324 max 1324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5169.00 ave 5169 max 5169 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: 102472.0 ave 102472 max 102472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102472 Ave neighs/atom = 77.395770 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.192 | 5.192 | 5.192 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 -5606.5058 -5606.5058 26.766371 93.442471 6.2366775 -6400.2465 -6400.2465 4.884393 -19207.768 2.1439274 2.2578465 952.75829 Loop time of 1.578e-06 on 1 procs for 0 steps with 1324 atoms 190.1% 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 | | 1.578e-06 | | |100.00 Nlocal: 1324.00 ave 1324 max 1324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5169.00 ave 5169 max 5169 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51236.0 ave 51236 max 51236 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102472.0 ave 102472 max 102472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102472 Ave neighs/atom = 77.395770 Neighbor list builds = 0 Dangerous builds = 0 1324 -5606.50583284809 eV 2.25784650641984 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06