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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -69.119067 0.0000000) to (34.557511 69.119067 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2072962 5.2072962 4.0446508 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -69.119067 0.0000000) to (34.557511 69.119067 4.0446508) create_atoms CPU = 0.003 seconds 586 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2072962 5.2072962 4.0446508 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -69.119067 0.0000000) to (34.557511 69.119067 4.0446508) create_atoms CPU = 0.002 seconds 586 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 43 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1156 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_616482358807_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.625 | 4.625 | 4.625 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3860.9621 0 -3860.9621 77.276475 60 0 -3873.6063 0 -3873.6063 -4527.7432 Loop time of 11.7467 on 1 procs for 60 steps with 1156 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 = -3860.96207758909 -3873.60292363531 -3873.60633360262 Force two-norm initial, final = 19.389151 0.13941430 Force max component initial, final = 5.5351186 0.029105262 Final line search alpha, max atom move = 1.0000000 0.029105262 Iterations, force evaluations = 60 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.697 | 11.697 | 11.697 | 0.0 | 99.58 Neigh | 0.014631 | 0.014631 | 0.014631 | 0.0 | 0.12 Comm | 0.017684 | 0.017684 | 0.017684 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01739 | | | 0.15 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6018.00 ave 6018 max 6018 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: 88388.0 ave 88388 max 88388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88388 Ave neighs/atom = 76.460208 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.635 | 4.635 | 4.635 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -3873.6063 0 -3873.6063 -4527.7432 19321.968 64 0 -3873.7513 0 -3873.7513 -483.4753 19221.35 Loop time of 0.657614 on 1 procs for 4 steps with 1156 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 = -3873.60633360262 -3873.75052295978 -3873.75134622666 Force two-norm initial, final = 77.169861 0.17788271 Force max component initial, final = 58.278213 0.046916503 Final line search alpha, max atom move = 0.00040188034 1.8854820e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65328 | 0.65328 | 0.65328 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094112 | 0.00094112 | 0.00094112 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003389 | | | 0.52 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6643.00 ave 6643 max 6643 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: 88840.0 ave 88840 max 88840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88840 Ave neighs/atom = 76.851211 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.773 | 4.773 | 4.773 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3873.7513 0 -3873.7513 -483.4753 Loop time of 6.134e-06 on 1 procs for 0 steps with 1156 atoms 195.6% 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 | | 6.134e-06 | | |100.00 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6651.00 ave 6651 max 6651 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: 88908.0 ave 88908 max 88908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88908 Ave neighs/atom = 76.910035 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.773 | 4.773 | 4.773 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 -3873.7513 -3873.7513 34.490471 138.23813 4.0314094 -483.4753 -483.4753 -0.75587663 -1450.4617 0.79162543 2.5488813 600.79536 Loop time of 8.109e-06 on 1 procs for 0 steps with 1156 atoms 0.0% 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 | | 8.109e-06 | | |100.00 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6651.00 ave 6651 max 6651 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 44454.0 ave 44454 max 44454 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 88908.0 ave 88908 max 88908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88908 Ave neighs/atom = 76.910035 Neighbor list builds = 0 Dangerous builds = 0 1156 -3873.75134622666 eV 2.54888127457259 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13