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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -44.143524 0.0000000) to (54.064555 44.143524 8.9488288) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1842724 5.4423523 5.9658858 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -44.143524 0.0000000) to (54.064555 44.143524 8.9488288) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1842724 5.4423523 5.9658858 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -44.143524 0.0000000) to (54.064555 44.143524 8.9488288) create_atoms CPU = 0.002 seconds 1756 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 13 21 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 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_673777079812_004#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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 8.276 | 8.276 | 8.276 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10772.293 0 -10772.293 35284.83 114 0 -11420.824 0 -11420.824 1174.855 Loop time of 5.39525 on 1 procs for 114 steps with 3506 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10772.2929468185 -11420.8141409176 -11420.8242477807 Force two-norm initial, final = 448.19289 0.51635157 Force max component initial, final = 75.090598 0.17681525 Final line search alpha, max atom move = 0.74662523 0.13201472 Iterations, force evaluations = 114 214 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.185 | 5.185 | 5.185 | 0.0 | 96.10 Neigh | 0.14163 | 0.14163 | 0.14163 | 0.0 | 2.63 Comm | 0.028577 | 0.028577 | 0.028577 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04008 | | | 0.74 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12753.0 ave 12753 max 12753 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: 787030.0 ave 787030 max 787030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 787030 Ave neighs/atom = 224.48089 Neighbor list builds = 3 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 114 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.276 | 8.276 | 8.276 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -11420.824 0 -11420.824 1174.855 42714.549 118 0 -11421.12 0 -11421.12 -107.8645 42760.183 Loop time of 0.138807 on 1 procs for 4 steps with 3506 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 = -11420.8242477806 -11421.1187905387 -11421.1198139823 Force two-norm initial, final = 145.26086 5.9460414 Force max component initial, final = 114.73075 4.7375232 Final line search alpha, max atom move = 0.00010196450 0.00048305917 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13484 | 0.13484 | 0.13484 | 0.0 | 97.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058648 | 0.00058648 | 0.00058648 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003385 | | | 2.44 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12753.0 ave 12753 max 12753 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: 787120.0 ave 787120 max 787120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 787120 Ave neighs/atom = 224.50656 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 8.414 | 8.414 | 8.414 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11421.12 0 -11421.12 -107.8645 Loop time of 2.04e-06 on 1 procs for 0 steps with 3506 atoms 196.1% 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 | | 2.04e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12749.0 ave 12749 max 12749 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: 786806.0 ave 786806 max 786806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 786806 Ave neighs/atom = 224.41700 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 8.414 | 8.414 | 8.414 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 -11421.12 -11421.12 53.920887 88.562914 8.9542793 -107.8645 -107.8645 -177.03802 -15.361845 -131.19364 2.2313482 1557.8586 Loop time of 2.607e-06 on 1 procs for 0 steps with 3506 atoms 345.2% 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 | | 2.607e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12749.0 ave 12749 max 12749 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 393403.0 ave 393403 max 393403 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 786806.0 ave 786806 max 786806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 786806 Ave neighs/atom = 224.41700 Neighbor list builds = 0 Dangerous builds = 0 3506 -11421.1198139823 eV 2.23134815865161 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06