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 = 4.0816549 4.0816549 4.0816549 Created orthogonal box = (0.0000000 -78.086657 0.0000000) to (45.083352 78.086657 7.0696337) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6516421 5.9738426 7.0696337 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -78.086657 0.0000000) to (45.083352 78.086657 7.0696337) create_atoms CPU = 0.002 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6516421 5.9738426 7.0696337 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -78.086657 0.0000000) to (45.083352 78.086657 7.0696337) create_atoms CPU = 0.002 seconds 1466 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 8 26 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 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2926 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_049243498555_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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 13.74 | 13.74 | 13.74 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10297.968 0 -10297.968 7812.8777 133 0 -10459.653 0 -10459.653 2771.8564 Loop time of 17.0567 on 1 procs for 133 steps with 2926 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 = -10297.9682237884 -10459.6431276705 -10459.6526561235 Force two-norm initial, final = 160.16436 0.19182751 Force max component initial, final = 36.238345 0.039047035 Final line search alpha, max atom move = 0.97474662 0.038060965 Iterations, force evaluations = 133 218 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.481 | 16.481 | 16.481 | 0.0 | 96.63 Neigh | 0.46867 | 0.46867 | 0.46867 | 0.0 | 2.75 Comm | 0.062738 | 0.062738 | 0.062738 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04409 | | | 0.26 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21296.0 ave 21296 max 21296 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: 1.24980e+06 ave 1.2498e+06 max 1.2498e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1249796 Ave neighs/atom = 427.13465 Neighbor list builds = 7 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 133 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.74 | 13.74 | 13.74 Mbytes Step Temp E_pair E_mol TotEng Press Volume 133 0 -10459.653 0 -10459.653 2771.8564 49775.994 137 0 -10459.875 0 -10459.875 -84.190166 49927.484 Loop time of 0.453554 on 1 procs for 4 steps with 2926 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10459.6526561233 -10459.8709950108 -10459.8754277293 Force two-norm initial, final = 161.51237 6.4888680 Force max component initial, final = 136.58657 5.4842932 Final line search alpha, max atom move = 3.8481718e-05 0.00021104503 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44822 | 0.44822 | 0.44822 | 0.0 | 98.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010014 | 0.0010014 | 0.0010014 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004328 | | | 0.95 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21297.0 ave 21297 max 21297 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: 1.24973e+06 ave 1.24973e+06 max 1.24973e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1249728 Ave neighs/atom = 427.11141 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 13.26 | 13.26 | 13.26 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10459.875 0 -10459.875 -84.190166 Loop time of 2.101e-06 on 1 procs for 0 steps with 2926 atoms 190.4% 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 | | 2.101e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21282.0 ave 21282 max 21282 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: 1.24893e+06 ave 1.24893e+06 max 1.24893e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1248932 Ave neighs/atom = 426.83937 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 13.26 | 13.26 | 13.26 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 -10459.875 -10459.875 45.078398 156.70495 7.0678689 -84.190166 -84.190166 -175.97202 30.281431 -106.87991 2.5565536 1176.4149 Loop time of 2.115e-06 on 1 procs for 0 steps with 2926 atoms 283.7% 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 | | 2.115e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21282.0 ave 21282 max 21282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 624466.0 ave 624466 max 624466 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.24893e+06 ave 1.24893e+06 max 1.24893e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1248932 Ave neighs/atom = 426.83937 Neighbor list builds = 0 Dangerous builds = 0 2926 -10459.8754277293 eV 2.55655359651589 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18