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 -63.183509 0.0000000) to (31.589732 63.183509 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6965091 5.6965091 4.0446508 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -63.183509 0.0000000) to (31.589732 63.183509 4.0446508) create_atoms CPU = 0.002 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6965091 5.6965091 4.0446508 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -63.183509 0.0000000) to (31.589732 63.183509 4.0446508) create_atoms CPU = 0.002 seconds 490 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 = 10 39 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 8 atoms, new total = 972 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_616482358807_001#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 = 10 39 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) = 4.583 | 4.583 | 4.583 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3235.9532 0 -3235.9532 6220.4632 76 0 -3260.3418 0 -3260.3418 -1402.1627 Loop time of 10.3184 on 1 procs for 76 steps with 972 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 = -3235.95316909959 -3260.33909748294 -3260.34181056042 Force two-norm initial, final = 19.488364 0.12990756 Force max component initial, final = 5.1123847 0.013559085 Final line search alpha, max atom move = 1.0000000 0.013559085 Iterations, force evaluations = 76 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.26 | 10.26 | 10.26 | 0.0 | 99.43 Neigh | 0.023681 | 0.023681 | 0.023681 | 0.0 | 0.23 Comm | 0.018 | 0.018 | 0.018 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01708 | | | 0.17 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5844.00 ave 5844 max 5844 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: 74048.0 ave 74048 max 74048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74048 Ave neighs/atom = 76.181070 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 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 : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.583 | 4.583 | 4.583 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -3260.3418 0 -3260.3418 -1402.1627 16145.843 78 0 -3260.3562 0 -3260.3562 -81.27113 16118.724 Loop time of 0.326809 on 1 procs for 2 steps with 972 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 = -3260.34181056043 -3260.35485898611 -3260.35619421133 Force two-norm initial, final = 21.107844 0.51262189 Force max component initial, final = 18.075464 0.37338372 Final line search alpha, max atom move = 0.00034159159 0.00012754474 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32471 | 0.32471 | 0.32471 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051747 | 0.00051747 | 0.00051747 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001579 | | | 0.48 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5843.00 ave 5843 max 5843 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: 74352.0 ave 74352 max 74352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74352 Ave neighs/atom = 76.493827 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 = 10 39 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) = 4.721 | 4.721 | 4.721 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3260.3562 0 -3260.3562 -81.27113 Loop time of 6.224e-06 on 1 procs for 0 steps with 972 atoms 176.7% 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 | | 6.224e-06 | | |100.00 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5843.00 ave 5843 max 5843 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: 74376.0 ave 74376 max 74376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74376 Ave neighs/atom = 76.518519 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 = 10 39 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) = 4.721 | 4.721 | 4.721 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 -3260.3562 -3260.3562 31.584905 126.36702 4.0384745 -81.27113 -81.27113 37.108099 -313.32012 32.398631 2.5576266 173.83359 Loop time of 7.478e-06 on 1 procs for 0 steps with 972 atoms 280.8% 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 | | 7.478e-06 | | |100.00 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5843.00 ave 5843 max 5843 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37188.0 ave 37188 max 37188 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74376.0 ave 74376 max 74376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74376 Ave neighs/atom = 76.518519 Neighbor list builds = 0 Dangerous builds = 0 972 -3260.35619421133 eV 2.55762655612603 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11