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 -46.754659 0.0000000) to (28.629106 46.754659 8.6320004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2052921 5.3126290 5.7546669 Created 1075 atoms using lattice units in orthogonal box = (0.0000000 -46.754659 0.0000000) to (28.629106 46.754659 8.6320004) create_atoms CPU = 0.001 seconds 1075 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2052921 5.3126290 5.7546669 Created 1075 atoms using lattice units in orthogonal box = (0.0000000 -46.754659 0.0000000) to (28.629106 46.754659 8.6320004) create_atoms CPU = 0.001 seconds 1075 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 = 7 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 adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Deleted 38 atoms, new total = 2112 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 = 7 22 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) = 8.662 | 8.662 | 8.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9258.7436 0 -9258.7436 26482.857 37 0 -9363.2138 0 -9363.2138 3405.4418 Loop time of 2.54194 on 1 procs for 37 steps with 2112 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 = -9258.74359141559 -9363.20721130194 -9363.21378829687 Force two-norm initial, final = 130.56146 0.23549150 Force max component initial, final = 12.863570 0.014527831 Final line search alpha, max atom move = 1.0000000 0.014527831 Iterations, force evaluations = 37 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5284 | 2.5284 | 2.5284 | 0.0 | 99.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0068272 | 0.0068272 | 0.0068272 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006716 | | | 0.26 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10549.0 ave 10549 max 10549 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 263620.0 ave 263620 max 263620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263620 Ave neighs/atom = 124.82008 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 : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.662 | 8.662 | 8.662 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -9363.2138 0 -9363.2138 3405.4418 23108.626 38 0 -9363.2148 0 -9363.2148 2960.4332 23114.128 Loop time of 0.105587 on 1 procs for 1 steps with 2112 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 = -9363.21378829686 -9363.21378829686 -9363.2148013884 Force two-norm initial, final = 10.790888 2.1980771 Force max component initial, final = 10.235382 2.0831636 Final line search alpha, max atom move = 9.7700307e-05 0.00020352572 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10451 | 0.10451 | 0.10451 | 0.0 | 98.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020711 | 0.00020711 | 0.00020711 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000865 | | | 0.82 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10152.0 ave 10152 max 10152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 262896.0 ave 262896 max 262896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262896 Ave neighs/atom = 124.47727 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 = 7 22 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) = 8.290 | 8.290 | 8.290 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9363.2148 0 -9363.2148 2960.4332 Loop time of 1.604e-06 on 1 procs for 0 steps with 2112 atoms 187.0% 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 | | 1.604e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10152.0 ave 10152 max 10152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 262896.0 ave 262896 max 262896 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 = 262896 Ave neighs/atom = 124.47727 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) = 8.290 | 8.290 | 8.290 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 -9363.2148 -9363.2148 28.630809 93.509318 8.6335418 2960.4332 2960.4332 -144.40494 8979.8665 45.837926 2.3501587 636.07867 Loop time of 3.875e-06 on 1 procs for 0 steps with 2112 atoms 206.5% 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 | | 3.875e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10152.0 ave 10152 max 10152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 262896.0 ave 262896 max 262896 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 525792.0 ave 525792 max 525792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 525792 Ave neighs/atom = 248.95455 Neighbor list builds = 0 Dangerous builds = 0 2112 -9363.2148013884 eV 2.35015865124114 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03