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 = 3.6406460 3.6406460 3.6406460 Created orthogonal box = (0.0000000 -54.972549 0.0000000) to (38.871462 54.972549 5.1486510) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1375993 6.2687995 5.1486510 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.972549 0.0000000) to (38.871462 54.972549 5.1486510) create_atoms CPU = 0.003 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1375993 6.2687995 5.1486510 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.972549 0.0000000) to (38.871462 54.972549 5.1486510) create_atoms CPU = 0.002 seconds 916 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 23 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1824 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_945018740343_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.808 | 6.808 | 6.808 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4614.3088 0 -4614.3088 145720.76 52 0 -5960.9837 0 -5960.9837 4658.7434 Loop time of 6.173 on 1 procs for 52 steps with 1824 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 = -4614.30879376209 -5960.97808625594 -5960.98374607079 Force two-norm initial, final = 2499.7481 0.19713812 Force max component initial, final = 613.35118 0.011626983 Final line search alpha, max atom move = 1.0000000 0.011626983 Iterations, force evaluations = 52 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0905 | 6.0905 | 6.0905 | 0.0 | 98.66 Neigh | 0.057974 | 0.057974 | 0.057974 | 0.0 | 0.94 Comm | 0.013789 | 0.013789 | 0.013789 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0107 | | | 0.17 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13402.0 ave 13402 max 13402 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: 580304.0 ave 580304 max 580304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 580304 Ave neighs/atom = 318.14912 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.808 | 6.808 | 6.808 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -5960.9837 0 -5960.9837 4658.7434 22003.927 57 0 -5961.2023 0 -5961.2023 -9.2781892 22075.25 Loop time of 0.559788 on 1 procs for 5 steps with 1824 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 = -5960.98374607077 -5961.20152624646 -5961.20231435652 Force two-norm initial, final = 131.99514 1.1299870 Force max component initial, final = 122.21922 0.76858917 Final line search alpha, max atom move = 0.00011288990 8.6765952e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5556 | 0.5556 | 0.5556 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076378 | 0.00076378 | 0.00076378 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003421 | | | 0.61 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13357.0 ave 13357 max 13357 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: 579744.0 ave 579744 max 579744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 579744 Ave neighs/atom = 317.84211 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.946 | 6.946 | 6.946 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5961.2023 0 -5961.2023 -9.2781892 Loop time of 2.146e-06 on 1 procs for 0 steps with 1824 atoms 186.4% 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 | | 2.146e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13357.0 ave 13357 max 13357 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: 579344.0 ave 579344 max 579344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 579344 Ave neighs/atom = 317.62281 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.946 | 6.946 | 6.946 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 -5961.2023 -5961.2023 38.876879 110.3517 5.1455906 -9.2781892 -9.2781892 52.056759 -24.141854 -55.749473 2.3682517 642.96323 Loop time of 2.599e-06 on 1 procs for 0 steps with 1824 atoms 230.9% 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 | | 2.599e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13357.0 ave 13357 max 13357 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 289672.0 ave 289672 max 289672 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 579344.0 ave 579344 max 579344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 579344 Ave neighs/atom = 317.62281 Neighbor list builds = 0 Dangerous builds = 0 1824 -5961.20231435652 eV 2.36825169925385 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07