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 -69.723521 0.0000000) to (42.694606 69.723521 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9374714 4.9800000 5.7504086 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -69.723521 0.0000000) to (42.694606 69.723521 8.6256130) create_atoms CPU = 0.003 seconds 2358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9374714 4.9800000 5.7504086 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -69.723521 0.0000000) to (42.694606 69.723521 8.6256130) create_atoms CPU = 0.003 seconds 2358 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 = 14 45 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 48 atoms, new total = 4668 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 = 14 45 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) = 6.661 | 6.661 | 6.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20606.049 0 -20606.049 5195.6325 63 0 -20710.6 0 -20710.6 -5988.7685 Loop time of 31.6231 on 1 procs for 63 steps with 4668 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20606.0493202036 -20710.5795782134 -20710.599756507 Force two-norm initial, final = 101.40498 0.55589243 Force max component initial, final = 11.221171 0.054161717 Final line search alpha, max atom move = 1.0000000 0.054161717 Iterations, force evaluations = 63 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 31.551 | 31.551 | 31.551 | 0.0 | 99.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.026679 | 0.026679 | 0.026679 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04531 | | | 0.14 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11181.0 ave 11181 max 11181 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: 399660.0 ave 399660 max 399660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 399660 Ave neighs/atom = 85.616967 Neighbor list builds = 0 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 = 14 45 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.17 | 10.17 | 10.17 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -20710.6 0 -20710.6 -5988.7685 51353.764 66 0 -20710.861 0 -20710.861 -911.41909 51212.381 Loop time of 1.75293 on 1 procs for 3 steps with 4668 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 = -20710.5997565071 -20710.8607430198 -20710.8607539847 Force two-norm initial, final = 267.45169 0.75238438 Force max component initial, final = 200.40838 0.47750173 Final line search alpha, max atom move = 0.0014072098 0.00067194511 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7451 | 1.7451 | 1.7451 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011241 | 0.0011241 | 0.0011241 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006743 | | | 0.38 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11757.0 ave 11757 max 11757 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: 400428.0 ave 400428 max 400428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400428 Ave neighs/atom = 85.781491 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 = 14 45 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) = 9.928 | 9.928 | 9.928 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20710.861 0 -20710.861 -911.41909 Loop time of 3.612e-06 on 1 procs for 0 steps with 4668 atoms 166.1% 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 | | 3.612e-06 | | |100.00 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11777.0 ave 11777 max 11777 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: 400452.0 ave 400452 max 400452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400452 Ave neighs/atom = 85.786632 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 = 14 45 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) = 9.928 | 9.928 | 9.928 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 -20710.861 -20710.861 42.638726 139.44704 8.6131387 -911.41909 -911.41909 14.919063 -2749.5665 0.39013704 2.1809565 1706.8696 Loop time of 3.861e-06 on 1 procs for 0 steps with 4668 atoms 207.2% 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 | | 3.861e-06 | | |100.00 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11777.0 ave 11777 max 11777 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 200226.0 ave 200226 max 200226 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 400452.0 ave 400452 max 400452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400452 Ave neighs/atom = 85.786632 Neighbor list builds = 0 Dangerous builds = 0 4668 -20710.8607539847 eV 2.18095645128974 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:35