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 = 3.6149590 3.6149590 3.6149590 Created orthogonal box = (0.0000000 -42.772771 0.0000000) to (52.385732 42.772771 8.8548049) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9869408 5.4993563 5.9032033 Created 1667 atoms using lattice units in orthogonal box = (0.0000000 -42.772771 0.0000000) to (52.385732 42.772771 8.8548049) create_atoms CPU = 0.003 seconds 1667 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9869408 5.4993563 5.9032033 Created 1691 atoms using lattice units in orthogonal box = (0.0000000 -42.772771 0.0000000) to (52.385732 42.772771 8.8548049) create_atoms CPU = 0.003 seconds 1691 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, 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 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3358 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_759493141826_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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 6.970 | 6.970 | 6.970 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11134.431 0 -11134.431 52901.331 86 0 -11848.274 0 -11848.274 10626.439 Loop time of 3.64719 on 1 procs for 86 steps with 3358 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11134.43131572 -11848.264085344 -11848.2737663927 Force two-norm initial, final = 460.70056 0.27894318 Force max component initial, final = 48.219841 0.041226096 Final line search alpha, max atom move = 0.52534738 0.021658021 Iterations, force evaluations = 86 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3828 | 3.3828 | 3.3828 | 0.0 | 92.75 Neigh | 0.21892 | 0.21892 | 0.21892 | 0.0 | 6.00 Comm | 0.018649 | 0.018649 | 0.018649 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02679 | | | 0.73 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10431.0 ave 10431 max 10431 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: 577238.0 ave 577238 max 577238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 577238 Ave neighs/atom = 171.89934 Neighbor list builds = 6 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.967 | 6.967 | 6.967 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -11848.274 0 -11848.274 10626.439 39681.621 96 0 -11850.267 0 -11850.267 67.599581 39976.983 Loop time of 0.30184 on 1 procs for 10 steps with 3358 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 = -11848.2737663928 -11850.2638069992 -11850.2668410222 Force two-norm initial, final = 519.41480 2.9691815 Force max component initial, final = 463.88194 1.7968818 Final line search alpha, max atom move = 0.00010417420 0.00018718873 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29428 | 0.29428 | 0.29428 | 0.0 | 97.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010044 | 0.0010044 | 0.0010044 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006553 | | | 2.17 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10434.0 ave 10434 max 10434 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: 577378.0 ave 577378 max 577378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 577378 Ave neighs/atom = 171.94104 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 7.106 | 7.106 | 7.106 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11850.267 0 -11850.267 67.599581 Loop time of 2.362e-06 on 1 procs for 0 steps with 3358 atoms 127.0% 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 | | 2.362e-06 | | |100.00 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10552.0 ave 10552 max 10552 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: 575194.0 ave 575194 max 575194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 575194 Ave neighs/atom = 171.29065 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 7.106 | 7.106 | 7.106 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 -11850.267 -11850.267 52.396112 86.345712 8.8362945 67.599581 67.599581 64.767662 72.688085 65.342995 2.3595898 1699.4935 Loop time of 2.645e-06 on 1 procs for 0 steps with 3358 atoms 340.3% 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 | | 2.645e-06 | | |100.00 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10552.0 ave 10552 max 10552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 287597.0 ave 287597 max 287597 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 575194.0 ave 575194 max 575194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 575194 Ave neighs/atom = 171.29065 Neighbor list builds = 0 Dangerous builds = 0 3358 -11850.2668410222 eV 2.35958979268258 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04