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 -37.421634 0.0000000) to (37.418114 37.421634 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9670062 4.9670062 3.5200000 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -37.421634 0.0000000) to (37.418114 37.421634 3.5200000) create_atoms CPU = 0.002 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9670062 4.9670062 3.5200000 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -37.421634 0.0000000) to (37.418114 37.421634 3.5200000) create_atoms CPU = 0.002 seconds 454 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 = 9 18 1 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 6 atoms, new total = 902 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 = 9 18 1 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) = 5.398 | 5.398 | 5.398 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3935.5572 0 -3935.5572 31545.783 57 0 -4002.9018 0 -4002.9018 105.91483 Loop time of 2.29826 on 1 procs for 57 steps with 902 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3935.55722463823 -4002.89835028755 -4002.90181072981 Force two-norm initial, final = 53.714234 0.19572870 Force max component initial, final = 13.541982 0.022602537 Final line search alpha, max atom move = 1.0000000 0.022602537 Iterations, force evaluations = 57 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2374 | 2.2374 | 2.2374 | 0.0 | 97.35 Neigh | 0.028072 | 0.028072 | 0.028072 | 0.0 | 1.22 Comm | 0.019544 | 0.019544 | 0.019544 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01328 | | | 0.58 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8812.00 ave 8812 max 8812 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: 204024.0 ave 204024 max 204024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204024 Ave neighs/atom = 226.19069 Neighbor list builds = 1 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 = 9 18 1 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 : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.398 | 5.398 | 5.398 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -4002.9018 0 -4002.9018 105.91483 9857.7385 61 0 -4002.9461 0 -4002.9461 -41.540843 9858.4916 Loop time of 0.165546 on 1 procs for 4 steps with 902 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4002.90181072981 -4002.94599813178 -4002.946143141 Force two-norm initial, final = 27.326440 0.21094987 Force max component initial, final = 23.426633 0.025593294 Final line search alpha, max atom move = 0.00039127839 1.0014103e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16058 | 0.16058 | 0.16058 | 0.0 | 97.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012251 | 0.0012251 | 0.0012251 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003737 | | | 2.26 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8758.00 ave 8758 max 8758 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: 203032.0 ave 203032 max 203032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203032 Ave neighs/atom = 225.09091 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 = 9 18 1 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) = 5.536 | 5.536 | 5.536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4002.9461 0 -4002.9461 -41.540843 Loop time of 6.756e-06 on 1 procs for 0 steps with 902 atoms 177.6% 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 | | 6.756e-06 | | |100.00 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8782.00 ave 8782 max 8782 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: 202992.0 ave 202992 max 202992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202992 Ave neighs/atom = 225.04656 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 = 9 18 1 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) = 5.536 | 5.536 | 5.536 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 -4002.9461 -4002.9461 37.33116 74.843267 3.5284686 -41.540843 -41.540843 -3.6352922 -118.7881 -2.1991385 2.2297396 134.3698 Loop time of 6.706e-06 on 1 procs for 0 steps with 902 atoms 268.4% 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 | | 6.706e-06 | | |100.00 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8782.00 ave 8782 max 8782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101496.0 ave 101496 max 101496 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 202992.0 ave 202992 max 202992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202992 Ave neighs/atom = 225.04656 Neighbor list builds = 0 Dangerous builds = 0 902 -3978.3834957482 eV 2.22973963772616 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03