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 = 2.8667458 2.8667458 2.8667458 Created orthogonal box = (0.0000000 -29.794963 0.0000000) to (21.066193 29.794963 4.0541907) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6813762 3.8619383 4.0541907 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -29.794963 0.0000000) to (21.066193 29.794963 4.0541907) create_atoms CPU = 0.001 seconds 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6813762 3.8619383 4.0541907 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -29.794963 0.0000000) to (21.066193 29.794963 4.0541907) create_atoms CPU = 0.000 seconds 218 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 16 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 428 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.468 | 4.468 | 4.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1730.6352 0 -1730.6352 49459.23 134 0 -1813.0422 0 -1813.0422 684.18384 Loop time of 0.86528 on 1 procs for 134 steps with 428 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 = -1730.63521934 -1813.04085293828 -1813.04223632962 Force two-norm initial, final = 196.02743 0.11567408 Force max component initial, final = 66.419085 0.015723398 Final line search alpha, max atom move = 0.86252632 0.013561844 Iterations, force evaluations = 134 260 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84465 | 0.84465 | 0.84465 | 0.0 | 97.62 Neigh | 0.0076072 | 0.0076072 | 0.0076072 | 0.0 | 0.88 Comm | 0.0075594 | 0.0075594 | 0.0075594 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005468 | | | 0.63 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3723.00 ave 3723 max 3723 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: 70764.0 ave 70764 max 70764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70764 Ave neighs/atom = 165.33645 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 134 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.468 | 4.468 | 4.468 Mbytes Step Temp E_pair E_mol TotEng Press Volume 134 0 -1813.0422 0 -1813.0422 684.18384 5089.3588 135 0 -1813.0431 0 -1813.0431 1489.5922 5087.4904 Loop time of 0.0108514 on 1 procs for 1 steps with 428 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 = -1813.04223632963 -1813.04223632963 -1813.04312432378 Force two-norm initial, final = 4.9130952 0.99891102 Force max component initial, final = 4.9108483 0.99178306 Final line search alpha, max atom move = 0.00020363081 0.00020195758 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.010418 | 0.010418 | 0.010418 | 0.0 | 96.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.6605e-05 | 9.6605e-05 | 9.6605e-05 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003363 | | | 3.10 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3766.00 ave 3766 max 3766 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: 70824.0 ave 70824 max 70824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70824 Ave neighs/atom = 165.47664 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1813.0431 0 -1813.0431 1489.5922 Loop time of 1.895e-06 on 1 procs for 0 steps with 428 atoms 158.3% 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 | | 1.895e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3766.00 ave 3766 max 3766 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: 70830.0 ave 70830 max 70830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70830 Ave neighs/atom = 165.49065 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.606 | 4.606 | 4.606 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 -1813.0431 -1813.0431 21.058603 59.589925 4.054163 1489.5922 1489.5922 -8.8077408 4165.2496 312.33487 2.3523901 357.86069 Loop time of 1.97e-06 on 1 procs for 0 steps with 428 atoms 152.3% 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 | | 1.97e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3766.00 ave 3766 max 3766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35415.0 ave 35415 max 35415 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70830.0 ave 70830 max 70830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70830 Ave neighs/atom = 165.49065 Neighbor list builds = 0 Dangerous builds = 0 428 -1813.04312432378 eV 2.35239005024403 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01