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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -42.535851 0.0000000) to (52.091254 42.535851 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950518 5.2437120 5.7481372 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -42.535851 0.0000000) to (52.091254 42.535851 8.6222058) create_atoms CPU = 0.002 seconds 1754 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950518 5.2437120 5.7481372 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -42.535851 0.0000000) to (52.091254 42.535851 8.6222058) create_atoms CPU = 0.002 seconds 1754 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 38 atoms, new total = 3470 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.388 | 7.388 | 7.388 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15242.652 0 -15242.652 4167.3322 52 0 -15376.69 0 -15376.69 -11128.91 Loop time of 2.90898 on 1 procs for 52 steps with 3470 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 = -15242.6519960141 -15376.6750828317 -15376.6895008428 Force two-norm initial, final = 65.435664 0.57292457 Force max component initial, final = 7.4110925 0.12199939 Final line search alpha, max atom move = 1.0000000 0.12199939 Iterations, force evaluations = 52 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8429 | 2.8429 | 2.8429 | 0.0 | 97.73 Neigh | 0.039445 | 0.039445 | 0.039445 | 0.0 | 1.36 Comm | 0.011219 | 0.011219 | 0.011219 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01539 | | | 0.53 Nlocal: 3470.00 ave 3470 max 3470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11329.0 ave 11329 max 11329 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: 614828.0 ave 614828 max 614828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614828 Ave neighs/atom = 177.18386 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.391 | 7.391 | 7.391 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -15376.69 0 -15376.69 -11128.91 38209.233 55 0 -15377.159 0 -15377.159 -3085.9183 38046.762 Loop time of 0.138908 on 1 procs for 3 steps with 3470 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 = -15376.6895008429 -15377.1441370846 -15377.1585355875 Force two-norm initial, final = 309.73229 11.614948 Force max component initial, final = 239.76419 10.779218 Final line search alpha, max atom move = 2.0582296e-05 0.00022186106 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13606 | 0.13606 | 0.13606 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042692 | 0.00042692 | 0.00042692 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002422 | | | 1.74 Nlocal: 3470.00 ave 3470 max 3470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11554.0 ave 11554 max 11554 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: 613408.0 ave 613408 max 613408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 613408 Ave neighs/atom = 176.77464 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.529 | 7.529 | 7.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15377.159 0 -15377.159 -3085.9183 Loop time of 1.837e-06 on 1 procs for 0 steps with 3470 atoms 163.3% 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 | | 1.837e-06 | | |100.00 Nlocal: 3470.00 ave 3470 max 3470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11568.0 ave 11568 max 11568 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: 614736.0 ave 614736 max 614736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614736 Ave neighs/atom = 177.15735 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.529 | 7.529 | 7.529 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 -15377.159 -15377.159 51.960314 85.071702 8.6071786 -3085.9183 -3085.9183 -179.26391 -9531.6204 453.12953 2.2454344 1458.7337 Loop time of 2.613e-06 on 1 procs for 0 steps with 3470 atoms 267.9% 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 | | 2.613e-06 | | |100.00 Nlocal: 3470.00 ave 3470 max 3470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11568.0 ave 11568 max 11568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 307368.0 ave 307368 max 307368 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 614736.0 ave 614736 max 614736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614736 Ave neighs/atom = 177.15735 Neighbor list builds = 0 Dangerous builds = 0 3470 -15377.1585355875 eV 2.24543437339149 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03