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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -50.033612 0.0000000) to (23.584164 50.033612 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9365188 6.8668033 5.7200000 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -50.033612 0.0000000) to (23.584164 50.033612 5.7200000) create_atoms CPU = 0.001 seconds 412 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9365188 6.8668033 5.7200000 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -50.033612 0.0000000) to (23.584164 50.033612 5.7200000) create_atoms CPU = 0.001 seconds 412 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 31 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 808 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_353977746962_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2696.5089 0 -2696.5089 1469.8775 57 0 -2707.3952 0 -2707.3952 -4201.1215 Loop time of 2.56582 on 1 procs for 57 steps with 808 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 = -2696.50894683168 -2707.39252356742 -2707.39515140796 Force two-norm initial, final = 14.889321 0.11742789 Force max component initial, final = 4.7956105 0.011934807 Final line search alpha, max atom move = 1.0000000 0.011934807 Iterations, force evaluations = 57 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5536 | 2.5536 | 2.5536 | 0.0 | 99.52 Neigh | 0.0039427 | 0.0039427 | 0.0039427 | 0.0 | 0.15 Comm | 0.0042171 | 0.0042171 | 0.0042171 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004057 | | | 0.16 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4162.00 ave 4162 max 4162 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: 61464.0 ave 61464 max 61464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61464 Ave neighs/atom = 76.069307 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -2707.3952 0 -2707.3952 -4201.1215 13499.21 60 0 -2707.4573 0 -2707.4573 -1012.1482 13444.056 Loop time of 0.125708 on 1 procs for 3 steps with 808 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 = -2707.39515140796 -2707.45680697676 -2707.45730563708 Force two-norm initial, final = 42.938472 0.97202012 Force max component initial, final = 31.957066 0.89052410 Final line search alpha, max atom move = 0.00029359069 0.00026144958 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12485 | 0.12485 | 0.12485 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016018 | 0.00016018 | 0.00016018 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000698 | | | 0.56 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4169.00 ave 4169 max 4169 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: 61664.0 ave 61664 max 61664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61664 Ave neighs/atom = 76.316832 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.691 | 4.691 | 4.691 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2707.4573 0 -2707.4573 -1012.1482 Loop time of 1.452e-06 on 1 procs for 0 steps with 808 atoms 137.7% 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 | | 1.452e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4169.00 ave 4169 max 4169 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: 61688.0 ave 61688 max 61688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61688 Ave neighs/atom = 76.346535 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.691 | 4.691 | 4.691 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 -2707.4573 -2707.4573 23.540778 100.06722 5.7071286 -1012.1482 -1012.1482 105.93172 -3098.4197 -43.95675 2.7012683 562.44046 Loop time of 1.554e-06 on 1 procs for 0 steps with 808 atoms 193.1% 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 | | 1.554e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4169.00 ave 4169 max 4169 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30844.0 ave 30844 max 30844 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61688.0 ave 61688 max 61688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61688 Ave neighs/atom = 76.346535 Neighbor list builds = 0 Dangerous builds = 0 808 -2707.45730563708 eV 2.70126827512651 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02