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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -30.542956 0.0000000) to (21.595108 30.542956 4.0451344) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1674771 4.8221203 4.0451344 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.542956 0.0000000) to (21.595108 30.542956 4.0451344) create_atoms CPU = 0.001 seconds 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1674771 4.8221203 4.0451344 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.542956 0.0000000) to (21.595108 30.542956 4.0451344) create_atoms CPU = 0.000 seconds 230 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 16 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 455 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.475 | 4.475 | 4.475 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1876.1295 0 -1876.1295 42165.99 183 0 -1976.9513 0 -1976.9513 11991.064 Loop time of 1.26812 on 1 procs for 183 steps with 455 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 = -1876.12953674934 -1976.94940563846 -1976.95130153444 Force two-norm initial, final = 109.72669 0.21405855 Force max component initial, final = 33.406125 0.065844743 Final line search alpha, max atom move = 1.0000000 0.065844743 Iterations, force evaluations = 183 335 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2283 | 1.2283 | 1.2283 | 0.0 | 96.86 Neigh | 0.022183 | 0.022183 | 0.022183 | 0.0 | 1.75 Comm | 0.010299 | 0.010299 | 0.010299 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007326 | | | 0.58 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3999.00 ave 3999 max 3999 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: 74138.0 ave 74138 max 74138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74138 Ave neighs/atom = 162.94066 Neighbor list builds = 5 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 183 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.476 | 4.476 | 4.476 Mbytes Step Temp E_pair E_mol TotEng Press Volume 183 0 -1976.9513 0 -1976.9513 11991.064 5336.1669 186 0 -1977.0213 0 -1977.0213 2171.4656 5355.878 Loop time of 0.0223419 on 1 procs for 3 steps with 455 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 = -1976.95130153443 -1977.02108555437 -1977.02127056882 Force two-norm initial, final = 54.109159 0.29839561 Force max component initial, final = 40.632050 0.050425010 Final line search alpha, max atom move = 0.00079053168 3.9862568e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02151 | 0.02151 | 0.02151 | 0.0 | 96.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017569 | 0.00017569 | 0.00017569 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006565 | | | 2.94 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4015.00 ave 4015 max 4015 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: 74086.0 ave 74086 max 74086 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74086 Ave neighs/atom = 162.82637 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.614 | 4.614 | 4.614 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1977.0213 0 -1977.0213 2171.4656 Loop time of 1.594e-06 on 1 procs for 0 steps with 455 atoms 188.2% 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 | | 1.594e-06 | | |100.00 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4015.00 ave 4015 max 4015 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: 73840.0 ave 73840 max 73840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73840 Ave neighs/atom = 162.28571 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.614 | 4.614 | 4.614 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 -1977.0213 -1977.0213 21.636529 61.085911 4.052304 2171.4656 2171.4656 -15.11325 6520.654 8.8559684 2.2875676 2756.2505 Loop time of 1.474e-06 on 1 procs for 0 steps with 455 atoms 135.7% 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 | | 1.474e-06 | | |100.00 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4015.00 ave 4015 max 4015 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36920.0 ave 36920 max 36920 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73840.0 ave 73840 max 73840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73840 Ave neighs/atom = 162.28571 Neighbor list builds = 0 Dangerous builds = 0 455 -1977.02127056882 eV 2.28756760792592 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01