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 -49.038785 0.0000000) to (40.040000 49.038785 9.9073307) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7200000 5.6711520 6.6048871 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -49.038785 0.0000000) to (40.040000 49.038785 9.9073307) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7200000 5.6711520 6.6048871 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -49.038785 0.0000000) to (40.040000 49.038785 9.9073307) create_atoms CPU = 0.002 seconds 1184 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 29 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2336 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_344724145339_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.128 | 5.128 | 5.128 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7605.9776 0 -7605.9776 14290.262 60 0 -7819.9238 0 -7819.9238 -266.91392 Loop time of 10.9668 on 1 procs for 60 steps with 2336 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 = -7605.97762265284 -7819.91835035113 -7819.92377995567 Force two-norm initial, final = 229.57961 0.15749039 Force max component initial, final = 35.769640 0.015112524 Final line search alpha, max atom move = 1.0000000 0.015112524 Iterations, force evaluations = 60 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.913 | 10.913 | 10.913 | 0.0 | 99.51 Neigh | 0.03042 | 0.03042 | 0.03042 | 0.0 | 0.28 Comm | 0.0090498 | 0.0090498 | 0.0090498 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01465 | | | 0.13 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6327.00 ave 6327 max 6327 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: 189024.0 ave 189024 max 189024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189024 Ave neighs/atom = 80.917808 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.128 | 5.128 | 5.128 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -7819.9238 0 -7819.9238 -266.91392 38906.345 65 0 -7820.1273 0 -7820.1273 12.455456 38891.823 Loop time of 0.774435 on 1 procs for 5 steps with 2336 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7819.92377995568 -7820.12638114139 -7820.12728595589 Force two-norm initial, final = 76.161321 0.61836533 Force max component initial, final = 55.016758 0.37827851 Final line search alpha, max atom move = 0.00025306515 9.5729107e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77116 | 0.77116 | 0.77116 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041573 | 0.00041573 | 0.00041573 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00286 | | | 0.37 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6335.00 ave 6335 max 6335 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: 187264.0 ave 187264 max 187264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187264 Ave neighs/atom = 80.164384 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.266 | 5.266 | 5.266 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7820.1273 0 -7820.1273 12.455456 Loop time of 2.304e-06 on 1 procs for 0 steps with 2336 atoms 173.6% 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 | | 2.304e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6340.00 ave 6340 max 6340 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: 190800.0 ave 190800 max 190800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190800 Ave neighs/atom = 81.678082 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.266 | 5.266 | 5.266 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 -7820.1273 -7820.1273 39.945419 98.498238 9.8846855 12.455456 12.455456 10.154391 11.664141 15.547835 2.5540479 1842.4058 Loop time of 2.58e-06 on 1 procs for 0 steps with 2336 atoms 232.6% 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 | | 2.58e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6340.00 ave 6340 max 6340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95400.0 ave 95400 max 95400 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 190800.0 ave 190800 max 190800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190800 Ave neighs/atom = 81.678082 Neighbor list builds = 0 Dangerous builds = 0 2336 -7820.12728595589 eV 2.55404791113739 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12