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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -37.620143 0.0000000) to (26.601458 37.620143 5.1194531) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9114352 4.8766852 5.1194531 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -37.620143 0.0000000) to (26.601458 37.620143 5.1194531) create_atoms CPU = 0.002 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9114352 4.8766852 5.1194531 Created 440 atoms using lattice units in orthogonal box = (0.0000000 -37.620143 0.0000000) to (26.601458 37.620143 5.1194531) create_atoms CPU = 0.002 seconds 440 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 ghost atom cutoff = 6 binsize = 3, bins = 9 26 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 864 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_227887284491_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 ghost atom cutoff = 6 binsize = 3, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.550 | 4.550 | 4.550 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2866.8744 0 -2866.8744 82135.082 71 0 -3045.7235 0 -3045.7235 7242.2075 Loop time of 4.29134 on 1 procs for 71 steps with 864 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 = -2866.87439471754 -3045.72151538685 -3045.72350359436 Force two-norm initial, final = 371.11869 0.10321316 Force max component initial, final = 58.762250 0.0095793916 Final line search alpha, max atom move = 1.0000000 0.0095793916 Iterations, force evaluations = 71 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2722 | 4.2722 | 4.2722 | 0.0 | 99.55 Neigh | 0.0051985 | 0.0051985 | 0.0051985 | 0.0 | 0.12 Comm | 0.0066199 | 0.0066199 | 0.0066199 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00731 | | | 0.17 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3869.00 ave 3869 max 3869 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: 66512.0 ave 66512 max 66512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66512 Ave neighs/atom = 76.981481 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 ghost atom cutoff = 6 binsize = 3, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.550 | 4.550 | 4.550 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -3045.7235 0 -3045.7235 7242.2075 10246.592 83 0 -3046.2509 0 -3046.2509 -4.2518741 10297.514 Loop time of 0.457855 on 1 procs for 12 steps with 864 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 = -3045.72350359436 -3046.2484588477 -3046.25090250643 Force two-norm initial, final = 105.28905 0.58823628 Force max component initial, final = 97.755797 0.077807406 Final line search alpha, max atom move = 0.00025335810 1.9713137e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45447 | 0.45447 | 0.45447 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050379 | 0.00050379 | 0.00050379 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002885 | | | 0.63 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3853.00 ave 3853 max 3853 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: 66560.0 ave 66560 max 66560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66560 Ave neighs/atom = 77.037037 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 ghost atom cutoff = 6 binsize = 3, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.688 | 4.688 | 4.688 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3046.2509 0 -3046.2509 -4.2518741 Loop time of 2.402e-06 on 1 procs for 0 steps with 864 atoms 166.5% 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 | | 2.402e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3853.00 ave 3853 max 3853 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: 66496.0 ave 66496 max 66496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66496 Ave neighs/atom = 76.962963 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 ghost atom cutoff = 6 binsize = 3, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.688 | 4.688 | 4.688 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 -3046.2509 -3046.2509 26.469642 76.13018 5.1100773 -4.2518741 -4.2518741 -9.9089743 -12.249132 9.4024839 2.4145079 744.7247 Loop time of 2.336e-06 on 1 procs for 0 steps with 864 atoms 256.8% 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 | | 2.336e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3853.00 ave 3853 max 3853 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33248.0 ave 33248 max 33248 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 66496.0 ave 66496 max 66496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66496 Ave neighs/atom = 76.962963 Neighbor list builds = 0 Dangerous builds = 0 864 -3046.25090250643 eV 2.41450794183967 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05