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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -55.454933 0.0000000) to (33.959072 55.454933 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4772697 5.3666064 5.7504086 Created 1488 atoms using lattice units in orthogonal box = (0.0000000 -55.454933 0.0000000) to (33.959072 55.454933 8.6256130) create_atoms CPU = 0.003 seconds 1488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4772697 5.3666064 5.7504086 Created 1494 atoms using lattice units in orthogonal box = (0.0000000 -55.454933 0.0000000) to (33.959072 55.454933 8.6256130) create_atoms CPU = 0.002 seconds 1494 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 11 36 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2976 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 11 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.646 | 5.646 | 5.646 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9370.4153 0 -9370.4153 277383.75 85 0 -13202.952 0 -13202.952 7451.6569 Loop time of 17.5527 on 1 procs for 85 steps with 2976 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9370.41531872812 -13202.9397808815 -13202.9522920338 Force two-norm initial, final = 5213.8342 0.42354361 Force max component initial, final = 871.30766 0.049523495 Final line search alpha, max atom move = 1.0000000 0.049523495 Iterations, force evaluations = 85 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.463 | 17.463 | 17.463 | 0.0 | 99.49 Neigh | 0.044834 | 0.044834 | 0.044834 | 0.0 | 0.26 Comm | 0.01787 | 0.01787 | 0.01787 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02717 | | | 0.15 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8152.00 ave 8152 max 8152 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: 256176.0 ave 256176 max 256176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 256176 Ave neighs/atom = 86.080645 Neighbor list builds = 2 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 11 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.643 | 5.643 | 5.643 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -13202.952 0 -13202.952 7451.6569 32487.475 91 0 -13203.654 0 -13203.654 -9.9458475 32617.024 Loop time of 0.979825 on 1 procs for 6 steps with 2976 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13202.9522920338 -13203.6537821873 -13203.6543850034 Force two-norm initial, final = 317.09809 1.5077960 Force max component initial, final = 293.93411 1.2242242 Final line search alpha, max atom move = 0.00010440913 0.00012782019 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.97448 | 0.97448 | 0.97448 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064974 | 0.00064974 | 0.00064974 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004691 | | | 0.48 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7955.00 ave 7955 max 7955 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: 255456.0 ave 255456 max 255456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255456 Ave neighs/atom = 85.838710 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 11 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.781 | 5.781 | 5.781 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13203.654 0 -13203.654 -9.9458475 Loop time of 1.0161e-05 on 1 procs for 0 steps with 2976 atoms 137.8% 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 | | 1.016e-05 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7955.00 ave 7955 max 7955 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: 255288.0 ave 255288 max 255288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255288 Ave neighs/atom = 85.782258 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 11 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.781 | 5.781 | 5.781 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 -13203.654 -13203.654 33.959698 111.4632 8.6168595 -9.9458475 -9.9458475 -60.13606 -5.2914399 35.589958 2.2354868 1021.534 Loop time of 2.232e-06 on 1 procs for 0 steps with 2976 atoms 179.2% 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 | | 2.232e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7955.00 ave 7955 max 7955 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 127644.0 ave 127644 max 127644 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 255288.0 ave 255288 max 255288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255288 Ave neighs/atom = 85.782258 Neighbor list builds = 0 Dangerous builds = 0 2976 -13203.6543850034 eV 2.23548676674135 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19