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 # Using KIM Simulator Model : Sim_LAMMPS_ADP_XuWangQian_2022_NiRh__SM_306597220004_000 # For Simulator : LAMMPS 30 Jul 2021 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239998 3.5239998 3.5239998 Created orthogonal box = (0.0000000 -44.853194 0.0000000) to (10.571999 44.853194 4.9836883) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8733329 4.9836883 4.9836883 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -44.853194 0.0000000) to (10.571999 44.853194 4.9836883) create_atoms CPU = 0.001 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8733329 4.9836883 4.9836883 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -44.853194 0.0000000) to (10.571999 44.853194 4.9836883) create_atoms CPU = 0.000 seconds 218 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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, bins = 3 21 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 adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Deleted 2 atoms, new total = 432 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/SM_306597220004_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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 7.177 | 7.177 | 7.177 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1759.6593 0 -1759.6593 116182.96 59 0 -1911.6142 0 -1911.6142 8587.7737 Loop time of 0.94495 on 1 procs for 59 steps with 432 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 = -1759.65934518894 -1911.61275635933 -1911.61415194359 Force two-norm initial, final = 447.24906 0.12288445 Force max component initial, final = 142.39573 0.018920716 Final line search alpha, max atom move = 1.0000000 0.018920716 Iterations, force evaluations = 59 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.93197 | 0.93197 | 0.93197 | 0.0 | 98.63 Neigh | 0.0026754 | 0.0026754 | 0.0026754 | 0.0 | 0.28 Comm | 0.0064229 | 0.0064229 | 0.0064229 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003883 | | | 0.41 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5820.00 ave 5820 max 5820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53896.0 ave 53896 max 53896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53896 Ave neighs/atom = 124.75926 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.180 | 7.180 | 7.180 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -1911.6142 0 -1911.6142 8587.7737 4726.4097 66 0 -1911.7703 0 -1911.7703 -171.89488 4748.7509 Loop time of 0.0807652 on 1 procs for 7 steps with 432 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 = -1911.61415194359 -1911.76843859594 -1911.77033979379 Force two-norm initial, final = 53.696255 0.91780328 Force max component initial, final = 49.710894 0.55566367 Final line search alpha, max atom move = 0.00027511698 0.00015287251 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.078253 | 0.078253 | 0.078253 | 0.0 | 96.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046704 | 0.00046704 | 0.00046704 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002045 | | | 2.53 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6212.00 ave 6212 max 6212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53966.0 ave 53966 max 53966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53966 Ave neighs/atom = 124.92130 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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, bins = 3 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/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, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.811 | 6.811 | 6.811 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1911.7703 0 -1911.7703 -171.89488 Loop time of 2.277e-06 on 1 procs for 0 steps with 432 atoms 175.7% 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 | | 2.277e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6194.00 ave 6194 max 6194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53828.0 ave 53828 max 53828 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53828 Ave neighs/atom = 124.60185 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.811 | 6.811 | 6.811 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 -1911.7703 -1911.7703 10.555273 90.31475 4.9813978 -171.89488 -171.89488 -174.61766 -153.67831 -187.38867 2.3211394 228.90782 Loop time of 3.356e-06 on 1 procs for 0 steps with 432 atoms 178.8% 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 | | 3.356e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6194.00 ave 6194 max 6194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53828.0 ave 53828 max 53828 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107656.0 ave 107656 max 107656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107656 Ave neighs/atom = 249.20370 Neighbor list builds = 0 Dangerous builds = 0 432 -1911.77033979379 eV 2.32113936102322 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01