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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -40.441730 0.0000000) to (28.596621 40.441730 4.9780328) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0659500 5.5147813 4.9780328 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -40.441730 0.0000000) to (28.596621 40.441730 4.9780328) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0659500 5.5147813 4.9780328 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.441730 0.0000000) to (28.596621 40.441730 4.9780328) create_atoms CPU = 0.001 seconds 532 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 21 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1056 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.027 | 5.027 | 5.027 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4086.9296 0 -4086.9296 106264.99 86 0 -4682.4349 0 -4682.4349 3780.8336 Loop time of 1.6851 on 1 procs for 86 steps with 1056 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4086.92955532469 -4682.43068448753 -4682.43487688302 Force two-norm initial, final = 911.03046 0.24096018 Force max component initial, final = 164.75950 0.034209939 Final line search alpha, max atom move = 1.0000000 0.034209939 Iterations, force evaluations = 86 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6402 | 1.6402 | 1.6402 | 0.0 | 97.34 Neigh | 0.023087 | 0.023087 | 0.023087 | 0.0 | 1.37 Comm | 0.011968 | 0.011968 | 0.011968 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009822 | | | 0.58 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6656.00 ave 6656 max 6656 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: 188656.0 ave 188656 max 188656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188656 Ave neighs/atom = 178.65152 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.026 | 5.026 | 5.026 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -4682.4349 0 -4682.4349 3780.8336 11514.158 89 0 -4682.4926 0 -4682.4926 90.336116 11536.452 Loop time of 0.0528559 on 1 procs for 3 steps with 1056 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 = -4682.43487688303 -4682.49116252971 -4682.49259906266 Force two-norm initial, final = 58.299321 1.5631122 Force max component initial, final = 55.210369 1.4971559 Final line search alpha, max atom move = 0.00014275006 0.00021371909 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.051229 | 0.051229 | 0.051229 | 0.0 | 96.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030301 | 0.00030301 | 0.00030301 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001324 | | | 2.50 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6656.00 ave 6656 max 6656 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: 187784.0 ave 187784 max 187784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187784 Ave neighs/atom = 177.82576 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.164 | 5.164 | 5.164 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4682.4926 0 -4682.4926 90.336116 Loop time of 2.543e-06 on 1 procs for 0 steps with 1056 atoms 157.3% 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 | | 2.543e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6656.00 ave 6656 max 6656 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: 187504.0 ave 187504 max 187504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187504 Ave neighs/atom = 177.56061 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.164 | 5.164 | 5.164 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 -4682.4926 -4682.4926 28.655858 80.881135 4.9775039 90.336116 90.336116 208.35494 13.383865 49.269544 2.344958 675.3301 Loop time of 2.282e-06 on 1 procs for 0 steps with 1056 atoms 262.9% 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 | | 2.282e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6656.00 ave 6656 max 6656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93752.0 ave 93752 max 93752 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 187504.0 ave 187504 max 187504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187504 Ave neighs/atom = 177.56061 Neighbor list builds = 0 Dangerous builds = 0 1056 -4682.49259906266 eV 2.34495796868107 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02