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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -44.446906 0.0000000) to (54.436121 44.446906 9.0103308) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2199020 5.4797556 6.0068872 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -44.446906 0.0000000) to (54.436121 44.446906 9.0103308) create_atoms CPU = 0.006 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2199020 5.4797556 6.0068872 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -44.446906 0.0000000) to (54.436121 44.446906 9.0103308) create_atoms CPU = 0.006 seconds 1756 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 18 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.630 | 5.630 | 5.630 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14058.696 0 -14058.696 40772.581 114 0 -14771.312 0 -14771.312 -2412.24 Loop time of 4.64185 on 1 procs for 114 steps with 3506 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14058.6964177961 -14771.2986316595 -14771.3123756039 Force two-norm initial, final = 268.60320 0.49971671 Force max component initial, final = 33.569238 0.11653504 Final line search alpha, max atom move = 0.72200383 0.084138749 Iterations, force evaluations = 114 201 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3912 | 4.3912 | 4.3912 | 0.0 | 94.60 Neigh | 0.13765 | 0.13765 | 0.13765 | 0.0 | 2.97 Comm | 0.04149 | 0.04149 | 0.04149 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07148 | | | 1.54 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8226.00 ave 8226 max 8226 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: 272026.0 ave 272026 max 272026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272026 Ave neighs/atom = 77.588705 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 114 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.633 | 5.633 | 5.633 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -14771.312 0 -14771.312 -2412.24 43601.3 120 0 -14771.964 0 -14771.964 27.361897 43504.704 Loop time of 0.200264 on 1 procs for 6 steps with 3506 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 = -14771.3123756039 -14771.9633742144 -14771.9642874419 Force two-norm initial, final = 226.38450 1.4729480 Force max component initial, final = 187.59139 0.76557637 Final line search alpha, max atom move = 0.00017040872 0.00013046089 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19009 | 0.19009 | 0.19009 | 0.0 | 94.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001686 | 0.001686 | 0.001686 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008486 | | | 4.24 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8243.00 ave 8243 max 8243 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: 271940.0 ave 271940 max 271940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271940 Ave neighs/atom = 77.564176 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.771 | 5.771 | 5.771 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14771.964 0 -14771.964 27.361897 Loop time of 6.515e-06 on 1 procs for 0 steps with 3506 atoms 184.2% 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 | | 6.515e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8232.00 ave 8232 max 8232 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: 272168.0 ave 272168 max 272168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272168 Ave neighs/atom = 77.629207 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.771 | 5.771 | 5.771 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 -14771.964 -14771.964 54.399657 88.447084 9.041834 27.361897 27.361897 28.175502 27.750505 26.159684 2.25526 1798.1495 Loop time of 6.505e-06 on 1 procs for 0 steps with 3506 atoms 307.5% 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 | | 6.505e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8232.00 ave 8232 max 8232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136084.0 ave 136084 max 136084 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 272168.0 ave 272168 max 272168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272168 Ave neighs/atom = 77.629207 Neighbor list builds = 0 Dangerous builds = 0 3506 -14771.9639368419 eV 2.2552599523842 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05