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 = 2.8665000 2.8665000 2.8665000 Created orthogonal box = (0.0000000 -30.471313 0.0000000) to (30.471313 30.471313 2.8665000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0448645 4.0448645 2.8665000 Created 226 atoms using lattice units in orthogonal box = (0.0000000 -30.471313 0.0000000) to (30.471313 30.471313 2.8665000) create_atoms CPU = 0.002 seconds 226 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0448645 4.0448645 2.8665000 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -30.471313 0.0000000) to (30.471313 30.471313 2.8665000) create_atoms CPU = 0.001 seconds 227 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 11 22 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 453 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_142799717516_005#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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 11 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.440 | 4.440 | 4.440 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1875.9434 0 -1875.9434 32318.859 45 0 -1946.0396 0 -1946.0396 10578.187 Loop time of 0.260431 on 1 procs for 45 steps with 453 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 = -1875.94337967774 -1946.03768250642 -1946.03956323282 Force two-norm initial, final = 77.550868 0.15885874 Force max component initial, final = 21.981928 0.036677157 Final line search alpha, max atom move = 1.0000000 0.036677157 Iterations, force evaluations = 45 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2414 | 0.2414 | 0.2414 | 0.0 | 92.69 Neigh | 0.0054376 | 0.0054376 | 0.0054376 | 0.0 | 2.09 Comm | 0.0071535 | 0.0071535 | 0.0071535 | 0.0 | 2.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006441 | | | 2.47 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3272.00 ave 3272 max 3272 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: 27274.0 ave 27274 max 27274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27274 Ave neighs/atom = 60.207506 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 11 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.440 | 4.440 | 4.440 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -1946.0396 0 -1946.0396 10578.187 5323.0955 56 0 -1946.3732 0 -1946.3732 -6.3347357 5352.986 Loop time of 0.03783 on 1 procs for 11 steps with 453 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1946.03956323282 -1946.37240063858 -1946.37316343075 Force two-norm initial, final = 76.951842 0.24780835 Force max component initial, final = 72.329960 0.051680727 Final line search alpha, max atom move = 0.00055116153 2.8484428e-05 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.033737 | 0.033737 | 0.033737 | 0.0 | 89.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084407 | 0.00084407 | 0.00084407 | 0.0 | 2.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003249 | | | 8.59 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3272.00 ave 3272 max 3272 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: 27244.0 ave 27244 max 27244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27244 Ave neighs/atom = 60.141280 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 11 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.590 | 4.590 | 4.590 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1946.3732 0 -1946.3732 -6.3347357 Loop time of 6.315e-06 on 1 procs for 0 steps with 453 atoms 174.2% 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 | | 6.315e-06 | | |100.00 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3266.00 ave 3266 max 3266 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: 27944.0 ave 27944 max 27944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27944 Ave neighs/atom = 61.686534 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 11 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.590 | 4.590 | 4.590 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 -1946.3732 -1946.3732 30.568346 61.482915 2.848195 -6.3347357 -6.3347357 -14.497562 -3.3631759 -1.1434692 2.3072587 134.06119 Loop time of 6.695e-06 on 1 procs for 0 steps with 453 atoms 179.2% 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 | | 6.695e-06 | | |100.00 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3266.00 ave 3266 max 3266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13972.0 ave 13972 max 13972 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27944.0 ave 27944 max 27944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27944 Ave neighs/atom = 61.686534 Neighbor list builds = 0 Dangerous builds = 0 453 -1946.37316343075 eV 2.30725871967304 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00