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 = 3.5200004 3.5200004 3.5200004 Created orthogonal box = (0.0000000 -69.692452 0.0000000) to (42.677736 69.692452 8.6222048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9355205 4.9780323 5.7481365 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -69.692452 0.0000000) to (42.677736 69.692452 8.6222048) create_atoms CPU = 0.003 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9355205 4.9780323 5.7481365 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -69.692452 0.0000000) to (42.677736 69.692452 8.6222048) create_atoms CPU = 0.003 seconds 2357 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 37 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 4692 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_418978237058_005#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 12.29 | 12.29 | 12.29 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20573.302 0 -20573.302 6240.7389 99 0 -20824.519 0 -20824.519 5021.6479 Loop time of 6.92105 on 1 procs for 99 steps with 4692 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 = -20573.3024350497 -20824.5004777654 -20824.5189853597 Force two-norm initial, final = 81.940857 0.48187355 Force max component initial, final = 10.193309 0.12436607 Final line search alpha, max atom move = 1.0000000 0.12436607 Iterations, force evaluations = 99 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.7574 | 6.7574 | 6.7574 | 0.0 | 97.64 Neigh | 0.095042 | 0.095042 | 0.095042 | 0.0 | 1.37 Comm | 0.028225 | 0.028225 | 0.028225 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04034 | | | 0.58 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14972.0 ave 14972 max 14972 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: 819914.0 ave 819914 max 819914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 819914 Ave neighs/atom = 174.74723 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.29 | 12.29 | 12.29 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -20824.519 0 -20824.519 5021.6479 51290.325 104 0 -20825.055 0 -20825.055 -22.341756 51435.484 Loop time of 0.32257 on 1 procs for 5 steps with 4692 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 = -20824.5189853599 -20825.0535870399 -20825.0553564302 Force two-norm initial, final = 333.11975 4.3056553 Force max component initial, final = 307.43937 3.2491149 Final line search alpha, max atom move = 4.4860804e-05 0.00014575791 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31525 | 0.31525 | 0.31525 | 0.0 | 97.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001023 | 0.001023 | 0.001023 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006298 | | | 1.95 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14761.0 ave 14761 max 14761 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: 819778.0 ave 819778 max 819778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 819778 Ave neighs/atom = 174.71824 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 11.81 | 11.81 | 11.81 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20825.055 0 -20825.055 -22.341756 Loop time of 2.373e-06 on 1 procs for 0 steps with 4692 atoms 0.0% 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 | | 2.373e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14761.0 ave 14761 max 14761 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: 819522.0 ave 819522 max 819522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 819522 Ave neighs/atom = 174.66368 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 11.81 | 11.81 | 11.81 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 -20825.055 -20825.055 42.661859 139.91188 8.6172457 -22.341756 -22.341756 -101.16982 -41.258421 75.402974 2.2126505 1758.5771 Loop time of 2.639e-06 on 1 procs for 0 steps with 4692 atoms 341.0% 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 | | 2.639e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14761.0 ave 14761 max 14761 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 409761.0 ave 409761 max 409761 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 819522.0 ave 819522 max 819522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 819522 Ave neighs/atom = 174.66368 Neighbor list builds = 0 Dangerous builds = 0 4692 -20825.0553564302 eV 2.2126504641697 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08