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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -53.383945 0.0000000) to (43.587809 53.383945 8.8361734) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3738394 5.1190084 5.8907823 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -53.383945 0.0000000) to (43.587809 53.383945 8.8361734) create_atoms CPU = 0.003 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3738394 5.1190084 5.8907823 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -53.383945 0.0000000) to (43.587809 53.383945 8.8361734) create_atoms CPU = 0.002 seconds 1756 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 8 18 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3504 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_151002396060_004#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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 8 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 17.75 | 17.75 | 17.75 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11985.333 0 -11985.333 24271.876 74 0 -12308.86 0 -12308.86 5922.8326 Loop time of 11.0465 on 1 procs for 74 steps with 3504 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11985.3330928455 -12308.8501836929 -12308.8598646433 Force two-norm initial, final = 211.38040 0.41979687 Force max component initial, final = 35.656232 0.11222971 Final line search alpha, max atom move = 1.0000000 0.11222971 Iterations, force evaluations = 74 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.767 | 10.767 | 10.767 | 0.0 | 97.47 Neigh | 0.20962 | 0.20962 | 0.20962 | 0.0 | 1.90 Comm | 0.041739 | 0.041739 | 0.041739 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02765 | | | 0.25 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21608.0 ave 21608 max 21608 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: 2.20344e+06 ave 2.20344e+06 max 2.20344e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2203442 Ave neighs/atom = 628.83619 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 8 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 17.75 | 17.75 | 17.75 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -12308.86 0 -12308.86 5922.8326 41121.593 79 0 -12309.389 0 -12309.389 -107.91542 41299.519 Loop time of 0.667803 on 1 procs for 5 steps with 3504 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 = -12308.8598646432 -12309.3877000005 -12309.3889436841 Force two-norm initial, final = 295.57351 5.4194915 Force max component initial, final = 258.17263 4.3670894 Final line search alpha, max atom move = 0.00011193033 0.00048880977 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66031 | 0.66031 | 0.66031 | 0.0 | 98.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013726 | 0.0013726 | 0.0013726 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006117 | | | 0.92 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21586.0 ave 21586 max 21586 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: 2.19652e+06 ave 2.19652e+06 max 2.19652e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2196524 Ave neighs/atom = 626.86187 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 8 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 17.27 | 17.27 | 17.27 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12309.389 0 -12309.389 -107.91542 Loop time of 2.412e-06 on 1 procs for 0 steps with 3504 atoms 207.3% 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 | | 2.412e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21578.0 ave 21578 max 21578 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: 2.19321e+06 ave 2.19321e+06 max 2.19321e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2193212 Ave neighs/atom = 625.91667 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 8 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 17.27 | 17.27 | 17.27 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 -12309.389 -12309.389 43.600325 107.19858 8.836214 -107.91542 -107.91542 -169.46583 -117.1261 -37.15432 2.2533562 1515.8907 Loop time of 2.828e-06 on 1 procs for 0 steps with 3504 atoms 282.9% 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 | | 2.828e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21578.0 ave 21578 max 21578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.09661e+06 ave 1.09661e+06 max 1.09661e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.19321e+06 ave 2.19321e+06 max 2.19321e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2193212 Ave neighs/atom = 625.91667 Neighbor list builds = 0 Dangerous builds = 0 3504 -12309.3889436841 eV 2.25335617068028 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13