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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -42.552660 0.0000000) to (52.111839 42.552660 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9970257 5.2457842 5.7504086 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.552660 0.0000000) to (52.111839 42.552660 8.6256130) create_atoms CPU = 0.002 seconds 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9970257 5.2457842 5.7504086 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.552660 0.0000000) to (52.111839 42.552660 8.6256130) create_atoms CPU = 0.002 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 ghost atom cutoff = 6 binsize = 3, 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 56 atoms, new total = 3456 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_000553624872_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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.681 | 5.681 | 5.681 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15231.097 0 -15231.097 1290.5541 64 0 -15315.538 0 -15315.538 -15770.48 Loop time of 12.6665 on 1 procs for 64 steps with 3456 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15231.0970183929 -15315.522955368 -15315.5380364641 Force two-norm initial, final = 70.430099 0.40749201 Force max component initial, final = 11.517359 0.048818121 Final line search alpha, max atom move = 1.0000000 0.048818121 Iterations, force evaluations = 64 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.594 | 12.594 | 12.594 | 0.0 | 99.42 Neigh | 0.04028 | 0.04028 | 0.04028 | 0.0 | 0.32 Comm | 0.012318 | 0.012318 | 0.012318 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02037 | | | 0.16 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8242.00 ave 8242 max 8242 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: 268606.0 ave 268606 max 268606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 268606 Ave neighs/atom = 77.721644 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.682 | 5.682 | 5.682 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -15315.538 0 -15315.538 -15770.48 38254.548 68 0 -15316.588 0 -15316.588 -4099.5114 38009.014 Loop time of 0.590987 on 1 procs for 4 steps with 3456 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 = -15315.5380364642 -15316.5814319754 -15316.5875060817 Force two-norm initial, final = 459.66659 3.1866083 Force max component initial, final = 327.10244 2.4436756 Final line search alpha, max atom move = 3.5670816e-05 8.7167902e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58805 | 0.58805 | 0.58805 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038227 | 0.00038227 | 0.00038227 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002556 | | | 0.43 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8219.00 ave 8219 max 8219 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: 268584.0 ave 268584 max 268584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 268584 Ave neighs/atom = 77.715278 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.820 | 5.820 | 5.820 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15316.588 0 -15316.588 -4099.5114 Loop time of 2.214e-06 on 1 procs for 0 steps with 3456 atoms 180.7% 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 | | 2.214e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8219.00 ave 8219 max 8219 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: 268816.0 ave 268816 max 268816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 268816 Ave neighs/atom = 77.782407 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.820 | 5.820 | 5.820 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 -15316.588 -15316.588 51.941757 85.10532 8.5983131 -4099.5114 -4099.5114 -82.332294 -12318.883 102.68112 2.2180038 1441.3534 Loop time of 2.205e-06 on 1 procs for 0 steps with 3456 atoms 226.8% 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 | | 2.205e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8219.00 ave 8219 max 8219 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134408.0 ave 134408 max 134408 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 268816.0 ave 268816 max 268816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 268816 Ave neighs/atom = 77.782407 Neighbor list builds = 0 Dangerous builds = 0 3456 -15316.5875060817 eV 2.21800378112372 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13