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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -38.988594 0.0000000) to (19.494297 38.988594 3.6200001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7055199 4.7055199 3.6200001 Created 232 atoms using lattice units in orthogonal box = (0.0000000 -38.988594 0.0000000) to (19.494297 38.988594 3.6200001) create_atoms CPU = 0.002 seconds 232 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7055199 4.7055199 3.6200001 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -38.988594 0.0000000) to (19.494297 38.988594 3.6200001) create_atoms CPU = 0.001 seconds 234 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 = 5 20 1 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 2 atoms, new total = 464 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_803527979660_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 = 5 20 1 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) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1610.3727 0 -1610.3727 15626.308 29 0 -1635.1706 0 -1635.1706 9096.3689 Loop time of 0.527851 on 1 procs for 29 steps with 464 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 = -1610.37269830646 -1635.16904198362 -1635.17055218872 Force two-norm initial, final = 67.371773 0.17352985 Force max component initial, final = 23.029532 0.050475050 Final line search alpha, max atom move = 1.0000000 0.050475050 Iterations, force evaluations = 29 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.51751 | 0.51751 | 0.51751 | 0.0 | 98.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0058861 | 0.0058861 | 0.0058861 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004458 | | | 0.84 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4591.00 ave 4591 max 4591 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: 81272.0 ave 81272 max 81272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81272 Ave neighs/atom = 175.15517 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 20 1 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 : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -1635.1706 0 -1635.1706 9096.3689 5502.7999 44 0 -1635.5416 0 -1635.5416 404.99001 5538.1497 Loop time of 0.186337 on 1 procs for 15 steps with 464 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 = -1635.17055218872 -1635.54126697782 -1635.54161191238 Force two-norm initial, final = 67.563640 2.5184655 Force max component initial, final = 64.167162 1.6226858 Final line search alpha, max atom move = 0.0034734747 0.0056363579 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16713 | 0.16713 | 0.16713 | 0.0 | 89.69 Neigh | 0.011479 | 0.011479 | 0.011479 | 0.0 | 6.16 Comm | 0.001966 | 0.001966 | 0.001966 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005758 | | | 3.09 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4551.00 ave 4551 max 4551 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: 80248.0 ave 80248 max 80248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80248 Ave neighs/atom = 172.94828 Neighbor list builds = 1 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 = 5 21 1 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) = 4.632 | 4.632 | 4.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1635.5416 0 -1635.5416 404.99001 Loop time of 6.034e-06 on 1 procs for 0 steps with 464 atoms 182.3% 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 | | 6.034e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4551.00 ave 4551 max 4551 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: 80248.0 ave 80248 max 80248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80248 Ave neighs/atom = 172.94828 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 = 5 21 1 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) = 4.632 | 4.632 | 4.632 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 -1635.5416 -1635.5416 19.474745 79.014069 3.599055 404.99001 404.99001 388.72732 359.51885 466.72385 2.3233108 303.9516 Loop time of 6.846e-06 on 1 procs for 0 steps with 464 atoms 204.5% 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 | | 6.846e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4551.00 ave 4551 max 4551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40124.0 ave 40124 max 40124 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80248.0 ave 80248 max 80248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80248 Ave neighs/atom = 172.94828 Neighbor list builds = 0 Dangerous builds = 0 464 -1635.54161191239 eV 2.32331078557284 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01