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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -57.628404 0.0000000) to (40.746946 57.628404 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0816338 5.5904738 4.9780318 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -57.628404 0.0000000) to (40.746946 57.628404 4.9780318) create_atoms CPU = 0.008 seconds 1079 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0816338 5.5904738 4.9780318 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -57.628404 0.0000000) to (40.746946 57.628404 4.9780318) create_atoms CPU = 0.007 seconds 1079 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 28 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 2128 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.477 | 6.477 | 6.477 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9355.2619 0 -9355.2619 14837.606 113 0 -9445.6399 0 -9445.6399 -8349.8226 Loop time of 10.0589 on 1 procs for 113 steps with 2128 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 = -9355.26190790535 -9445.63110377859 -9445.63994092949 Force two-norm initial, final = 98.696812 0.30812828 Force max component initial, final = 18.215296 0.024510715 Final line search alpha, max atom move = 1.0000000 0.024510715 Iterations, force evaluations = 113 195 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.7697 | 9.7697 | 9.7697 | 0.0 | 97.12 Neigh | 0.18461 | 0.18461 | 0.18461 | 0.0 | 1.84 Comm | 0.057588 | 0.057588 | 0.057588 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04705 | | | 0.47 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12581.0 ave 12581 max 12581 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: 478810.0 ave 478810 max 478810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478810 Ave neighs/atom = 225.00470 Neighbor list builds = 3 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 113 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.477 | 6.477 | 6.477 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -9445.6399 0 -9445.6399 -8349.8226 23378.644 116 0 -9445.7181 0 -9445.7181 -5053.9931 23334.883 Loop time of 0.349289 on 1 procs for 3 steps with 2128 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 = -9445.63994092944 -9445.71714433514 -9445.71814987228 Force two-norm initial, final = 89.253135 0.32653836 Force max component initial, final = 85.218463 0.045069916 Final line search alpha, max atom move = 0.00010095679 4.5501139e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34038 | 0.34038 | 0.34038 | 0.0 | 97.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019454 | 0.0019454 | 0.0019454 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006964 | | | 1.99 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12560.0 ave 12560 max 12560 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: 477878.0 ave 477878 max 477878 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 477878 Ave neighs/atom = 224.56673 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.615 | 6.615 | 6.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9445.7181 0 -9445.7181 -5053.9931 Loop time of 8.078e-06 on 1 procs for 0 steps with 2128 atoms 173.3% 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 | | 8.078e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12560.0 ave 12560 max 12560 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: 478016.0 ave 478016 max 478016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478016 Ave neighs/atom = 224.63158 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.615 | 6.615 | 6.615 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 -9445.7181 -9445.7181 40.744486 115.25681 4.9690138 -5053.9931 -5053.9931 -3.0943202 -15157.005 -1.8803345 2.3371569 857.76206 Loop time of 6.826e-06 on 1 procs for 0 steps with 2128 atoms 278.3% 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 | | 6.826e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12560.0 ave 12560 max 12560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 239008.0 ave 239008 max 239008 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 478016.0 ave 478016 max 478016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478016 Ave neighs/atom = 224.63158 Neighbor list builds = 0 Dangerous builds = 0 2128 -9387.76990857308 eV 2.33715692548442 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11