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 = 3.6148132 3.6148132 3.6148132 Created orthogonal box = (0.0000000 -42.155604 0.0000000) to (21.077802 42.155604 3.6148132) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9594828 4.9594828 3.6148132 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.155604 0.0000000) to (21.077802 42.155604 3.6148132) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9594828 4.9594828 3.6148132 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.155604 0.0000000) to (21.077802 42.155604 3.6148132) create_atoms CPU = 0.000 seconds 274 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 4 16 1 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 11.037500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_380822813353_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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 5.367 | 5.367 | 5.367 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1811.1844 0 -1811.1844 39509.824 54 0 -1918.0234 0 -1918.0234 4129.0917 Loop time of 1.58405 on 1 procs for 54 steps with 544 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1811.18442247497 -1918.0217087633 -1918.02341387454 Force two-norm initial, final = 209.87881 0.10861667 Force max component initial, final = 59.390727 0.016333103 Final line search alpha, max atom move = 1.0000000 0.016333103 Iterations, force evaluations = 54 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5578 | 1.5578 | 1.5578 | 0.0 | 98.34 Neigh | 0.012971 | 0.012971 | 0.012971 | 0.0 | 0.82 Comm | 0.0087115 | 0.0087115 | 0.0087115 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004621 | | | 0.29 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9298.00 ave 9298 max 9298 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: 251760.0 ave 251760 max 251760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251760 Ave neighs/atom = 462.79412 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.367 | 5.367 | 5.367 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -1918.0234 0 -1918.0234 4129.0917 6423.8664 59 0 -1918.0875 0 -1918.0875 -29.835275 6443.6065 Loop time of 0.126843 on 1 procs for 5 steps with 544 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 = -1918.02341387455 -1918.08734363779 -1918.08749719394 Force two-norm initial, final = 34.566731 0.62249178 Force max component initial, final = 29.037624 0.47124008 Final line search alpha, max atom move = 0.00055821232 0.00026305202 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12423 | 0.12423 | 0.12423 | 0.0 | 97.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052917 | 0.00052917 | 0.00052917 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002079 | | | 1.64 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9277.00 ave 9277 max 9277 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: 250560.0 ave 250560 max 250560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250560 Ave neighs/atom = 460.58824 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 5.505 | 5.505 | 5.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1918.0875 0 -1918.0875 -29.835275 Loop time of 1.589e-06 on 1 procs for 0 steps with 544 atoms 188.8% 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 | | 1.589e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9277.00 ave 9277 max 9277 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: 250024.0 ave 250024 max 250024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250024 Ave neighs/atom = 459.60294 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 5.505 | 5.505 | 5.505 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 -1918.0875 -1918.0875 21.03337 84.607639 3.6208504 -29.835275 -29.835275 -50.256707 -117.58389 78.334777 2.2715606 245.71144 Loop time of 1.976e-06 on 1 procs for 0 steps with 544 atoms 202.4% 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 | | 1.976e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9277.00 ave 9277 max 9277 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 125012.0 ave 125012 max 125012 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 250024.0 ave 250024 max 250024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250024 Ave neighs/atom = 459.60294 Neighbor list builds = 0 Dangerous builds = 0 544 -1918.08749719394 eV 2.27156062339667 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02