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 = 3.5878716 3.5878716 3.5878716 Created orthogonal box = (0.0000000 -63.374448 0.0000000) to (36.589255 63.374448 6.2143759) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6291161 5.6874505 6.2143759 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -63.374448 0.0000000) to (36.589255 63.374448 6.2143759) create_atoms CPU = 0.004 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6291161 5.6874505 6.2143759 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.374448 0.0000000) to (36.589255 63.374448 6.2143759) create_atoms CPU = 0.003 seconds 1249 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 9 31 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 8.231060792441781 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2494 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_228059236215_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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 6.931 | 6.931 | 6.931 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8212.7033 0 -8212.7033 46513.036 82 0 -8756.2783 0 -8756.2783 4803.8804 Loop time of 7.07662 on 1 procs for 82 steps with 2494 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8212.70334731399 -8756.2699805419 -8756.27825087916 Force two-norm initial, final = 696.15487 0.31977587 Force max component initial, final = 169.24858 0.12584168 Final line search alpha, max atom move = 0.48132987 0.060571358 Iterations, force evaluations = 82 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.8457 | 6.8457 | 6.8457 | 0.0 | 96.74 Neigh | 0.1857 | 0.1857 | 0.1857 | 0.0 | 2.62 Comm | 0.024043 | 0.024043 | 0.024043 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02121 | | | 0.30 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12473.0 ave 12473 max 12473 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: 496904.0 ave 496904 max 496904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496904 Ave neighs/atom = 199.23978 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.931 | 6.931 | 6.931 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -8756.2783 0 -8756.2783 4803.8804 28820.086 87 0 -8756.5504 0 -8756.5504 -11.073684 28917.307 Loop time of 0.405003 on 1 procs for 5 steps with 2494 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 = -8756.27825087916 -8756.54860003988 -8756.55041136829 Force two-norm initial, final = 169.57036 1.7579844 Force max component initial, final = 150.69314 1.3303758 Final line search alpha, max atom move = 6.0245167e-05 8.0148714e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40018 | 0.40018 | 0.40018 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083612 | 0.00083612 | 0.00083612 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003988 | | | 0.98 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12473.0 ave 12473 max 12473 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: 496926.0 ave 496926 max 496926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496926 Ave neighs/atom = 199.24860 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 9 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 7.068 | 7.068 | 7.068 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8756.5504 0 -8756.5504 -11.073684 Loop time of 1.969e-06 on 1 procs for 0 steps with 2494 atoms 152.4% 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 | | 1.969e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12425.0 ave 12425 max 12425 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: 496642.0 ave 496642 max 496642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496642 Ave neighs/atom = 199.13472 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 9 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 7.068 | 7.068 | 7.068 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 -8756.5504 -8756.5504 36.58658 127.22719 6.2123525 -11.073684 -11.073684 -73.704688 -17.035985 57.519619 2.3047834 1003.8052 Loop time of 2.392e-06 on 1 procs for 0 steps with 2494 atoms 250.8% 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 | | 2.392e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12425.0 ave 12425 max 12425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 248321.0 ave 248321 max 248321 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 496642.0 ave 496642 max 496642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496642 Ave neighs/atom = 199.13472 Neighbor list builds = 0 Dangerous builds = 0 2494 -8756.55041136829 eV 2.30478343527644 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08