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_NiPd__SM_559286646876_000 # For Simulator : LAMMPS 29 Sep 2021 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created orthogonal box = (0.0000000 -46.085796 0.0000000) to (21.723391 46.085796 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5733455 5.6592263 4.9836877 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -46.085796 0.0000000) to (21.723391 46.085796 4.9836877) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5733455 5.6592263 4.9836877 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -46.085796 0.0000000) to (21.723391 46.085796 4.9836877) create_atoms CPU = 0.001 seconds 458 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 5 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 12 atoms, new total = 904 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_559286646876_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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 5 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) = 7.738 | 7.738 | 7.738 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3975.8704 0 -3975.8704 6824.6423 52 0 -3997.8101 0 -3997.8101 -5134.4822 Loop time of 1.54759 on 1 procs for 52 steps with 904 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 = -3975.87037286468 -3997.80719233149 -3997.81012792639 Force two-norm initial, final = 31.907559 0.17226900 Force max component initial, final = 5.1972703 0.021063750 Final line search alpha, max atom move = 1.0000000 0.021063750 Iterations, force evaluations = 52 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5353 | 1.5353 | 1.5353 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0075136 | 0.0075136 | 0.0075136 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00482 | | | 0.31 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8550.00 ave 8550 max 8550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 111844.0 ave 111844 max 111844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111844 Ave neighs/atom = 123.72124 Neighbor list builds = 0 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 : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.741 | 7.741 | 7.741 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -3997.8101 0 -3997.8101 -5134.4822 9978.736 54 0 -3997.8246 0 -3997.8246 -2572.1988 9964.791 Loop time of 0.0778956 on 1 procs for 2 steps with 904 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 = -3997.81012792639 -3997.82346919956 -3997.82457935754 Force two-norm initial, final = 26.564602 0.18565148 Force max component initial, final = 21.770167 0.036540270 Final line search alpha, max atom move = 0.00028967351 1.0584748e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076505 | 0.076505 | 0.076505 | 0.0 | 98.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029262 | 0.00029262 | 0.00029262 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001098 | | | 1.41 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8366.00 ave 8366 max 8366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112656.0 ave 112656 max 112656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112656 Ave neighs/atom = 124.61947 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 5 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) = 7.371 | 7.371 | 7.371 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3997.8246 0 -3997.8246 -2572.1988 Loop time of 1.878e-06 on 1 procs for 0 steps with 904 atoms 159.7% 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 | | 1.878e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8366.00 ave 8366 max 8366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112672.0 ave 112672 max 112672 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 = 112672 Ave neighs/atom = 124.63717 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) = 7.371 | 7.371 | 7.371 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 -3997.8246 -3997.8246 21.698265 92.171591 4.9824863 -2572.1988 -2572.1988 0.99459826 -7711.7172 -5.8736653 2.3553131 531.02464 Loop time of 1.64e-06 on 1 procs for 0 steps with 904 atoms 182.9% 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 | | 1.64e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8366.00 ave 8366 max 8366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112672.0 ave 112672 max 112672 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225344.0 ave 225344 max 225344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225344 Ave neighs/atom = 249.27434 Neighbor list builds = 0 Dangerous builds = 0 904 -3997.82457935754 eV 2.35531308982758 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01