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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -69.131072 0.0000000) to (34.563513 69.131072 4.0453532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2082006 5.2082006 4.0453532 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -69.131072 0.0000000) to (34.563513 69.131072 4.0453532) create_atoms CPU = 0.001 seconds 586 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2082006 5.2082006 4.0453532 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -69.131072 0.0000000) to (34.563513 69.131072 4.0453532) create_atoms CPU = 0.001 seconds 586 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 = 12 45 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1156 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 = 12 45 2 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) = 4.623 | 4.623 | 4.623 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3862.7378 0 -3862.7378 -606.10687 58 0 -3873.7503 0 -3873.7503 -4305.1973 Loop time of 4.01288 on 1 procs for 58 steps with 1156 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 = -3862.73780155079 -3873.7467341586 -3873.75025701507 Force two-norm initial, final = 13.996131 0.13614705 Force max component initial, final = 3.9544023 0.0081729242 Final line search alpha, max atom move = 1.0000000 0.0081729242 Iterations, force evaluations = 58 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9915 | 3.9915 | 3.9915 | 0.0 | 99.47 Neigh | 0.0051588 | 0.0051588 | 0.0051588 | 0.0 | 0.13 Comm | 0.008297 | 0.008297 | 0.008297 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007952 | | | 0.20 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5759.00 ave 5759 max 5759 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: 62444.0 ave 62444 max 62444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62444 Ave neighs/atom = 54.017301 Neighbor list builds = 1 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 = 12 45 2 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -3873.7503 0 -3873.7503 -4305.1973 19332.037 62 0 -3873.8903 0 -3873.8903 -362.17825 19226.041 Loop time of 0.234432 on 1 procs for 4 steps with 1156 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 = -3873.75025701507 -3873.88804635155 -3873.89031988891 Force two-norm initial, final = 71.925787 4.0603522 Force max component initial, final = 56.886483 3.9166752 Final line search alpha, max atom move = 0.00015963747 0.00062524811 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23241 | 0.23241 | 0.23241 | 0.0 | 99.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034878 | 0.00034878 | 0.00034878 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001674 | | | 0.71 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6522.00 ave 6522 max 6522 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: 62496.0 ave 62496 max 62496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62496 Ave neighs/atom = 54.062284 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 = 12 45 2 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) = 4.771 | 4.771 | 4.771 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3873.8903 0 -3873.8903 -362.17825 Loop time of 2.371e-06 on 1 procs for 0 steps with 1156 atoms 210.9% 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 | | 2.371e-06 | | |100.00 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6535.00 ave 6535 max 6535 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: 62504.0 ave 62504 max 62504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62504 Ave neighs/atom = 54.069204 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 = 12 45 2 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) = 4.771 | 4.771 | 4.771 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 -3873.8903 -3873.8903 34.500696 138.26214 4.0304982 -362.17825 -362.17825 325.7977 -1499.9957 87.663245 2.5378194 578.1579 Loop time of 2.849e-06 on 1 procs for 0 steps with 1156 atoms 210.6% 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 | | 2.849e-06 | | |100.00 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6535.00 ave 6535 max 6535 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31252.0 ave 31252 max 31252 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62504.0 ave 62504 max 62504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62504 Ave neighs/atom = 54.069204 Neighbor list builds = 0 Dangerous builds = 0 1156 -3873.89031988891 eV 2.53781935792321 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04