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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -42.476759 0.0000000) to (52.023193 42.476759 9.9204336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6211336 6.1784377 6.6136224 Created 1320 atoms using lattice units in orthogonal box = (0.0000000 -42.476759 0.0000000) to (52.023193 42.476759 9.9204336) create_atoms CPU = 0.006 seconds 1320 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6211336 6.1784377 6.6136224 Created 1326 atoms using lattice units in orthogonal box = (0.0000000 -42.476759 0.0000000) to (52.023193 42.476759 9.9204336) create_atoms CPU = 0.005 seconds 1326 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2640 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_418978237058_005#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.988 | 5.988 | 5.988 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8238.9109 0 -8238.9109 23240.903 58 0 -8852.1886 0 -8852.1886 7339.791 Loop time of 2.95183 on 1 procs for 58 steps with 2640 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 = -8238.91090509419 -8852.17988150621 -8852.18861904958 Force two-norm initial, final = 211.01156 0.19831467 Force max component initial, final = 19.314940 0.027341082 Final line search alpha, max atom move = 1.0000000 0.027341082 Iterations, force evaluations = 58 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8072 | 2.8072 | 2.8072 | 0.0 | 95.10 Neigh | 0.098785 | 0.098785 | 0.098785 | 0.0 | 3.35 Comm | 0.018245 | 0.018245 | 0.018245 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02758 | | | 0.93 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7653.00 ave 7653 max 7653 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: 341988.0 ave 341988 max 341988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341988 Ave neighs/atom = 129.54091 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.988 | 5.988 | 5.988 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -8852.1886 0 -8852.1886 7339.791 43843.885 70 0 -8853.9289 0 -8853.9289 18.739607 44252.107 Loop time of 0.476564 on 1 procs for 12 steps with 2640 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 = -8852.18861904959 -8853.92523835507 -8853.92885901985 Force two-norm initial, final = 383.34544 0.99460686 Force max component initial, final = 331.66661 0.55602867 Final line search alpha, max atom move = 0.00011938829 6.6383310e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41233 | 0.41233 | 0.41233 | 0.0 | 86.52 Neigh | 0.048508 | 0.048508 | 0.048508 | 0.0 | 10.18 Comm | 0.0029698 | 0.0029698 | 0.0029698 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01276 | | | 2.68 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7735.00 ave 7735 max 7735 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: 340416.0 ave 340416 max 340416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340416 Ave neighs/atom = 128.94545 Neighbor list builds = 1 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.126 | 6.126 | 6.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8853.9289 0 -8853.9289 18.739607 Loop time of 6.294e-06 on 1 procs for 0 steps with 2640 atoms 174.8% 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 | | 6.294e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7735.00 ave 7735 max 7735 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: 340392.0 ave 340392 max 340392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340392 Ave neighs/atom = 128.93636 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.126 | 6.126 | 6.126 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 -8853.9289 -8853.9289 52.004175 85.936338 9.9019084 18.739607 18.739607 20.124022 17.805052 18.289747 2.6018958 2046.8442 Loop time of 7.046e-06 on 1 procs for 0 steps with 2640 atoms 255.5% 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 | | 7.046e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7735.00 ave 7735 max 7735 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 170196.0 ave 170196 max 170196 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 340392.0 ave 340392 max 340392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340392 Ave neighs/atom = 128.93636 Neighbor list builds = 0 Dangerous builds = 0 2640 -8853.92885901985 eV 2.60189576537033 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04