LAMMPS (23 Jun 2022) 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 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -41.533835 0) to (29.368856 41.533835 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.667674 6.557974 5.5012908 Created 456 atoms using lattice units in orthogonal box = (0 -41.533835 0) to (29.368856 41.533835 5.5012908) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.667674 6.557974 5.5012908 Created 458 atoms using lattice units in orthogonal box = (0 -41.533835 0) to (29.368856 41.533835 5.5012908) create_atoms CPU = 0.000 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 = 7 19 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 4 atoms, new total = 910 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:187) 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 19 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) = 7.285 | 7.285 | 7.285 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2511.4729 0 -2511.4729 176041.82 87 0 -3520.9188 0 -3520.9188 7653.7181 Loop time of 0.791012 on 1 procs for 87 steps with 910 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2511.47294680142 -3520.9156318869 -3520.91883458 Force two-norm initial, final = 1245.3753 0.23071969 Force max component initial, final = 295.46531 0.064563922 Final line search alpha, max atom move = 1 0.064563922 Iterations, force evaluations = 87 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7806 | 0.7806 | 0.7806 | 0.0 | 98.68 Neigh | 0.00419 | 0.00419 | 0.00419 | 0.0 | 0.53 Comm | 0.0039241 | 0.0039241 | 0.0039241 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002296 | | | 0.29 Nlocal: 910 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6593 ave 6593 max 6593 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90386 ave 90386 max 90386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90386 Ave neighs/atom = 99.325275 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.285 | 7.285 | 7.285 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -3520.9188 0 -3520.9188 7653.7181 13420.963 92 0 -3521.1163 0 -3521.1163 -3.4366074 13472.158 Loop time of 0.0385844 on 1 procs for 5 steps with 910 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3520.91883458 -3521.11371993935 -3521.1163291632 Force two-norm initial, final = 119.38037 0.4783445 Force max component initial, final = 96.549466 0.24880269 Final line search alpha, max atom move = 6.8403781e-05 1.7019045e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.037762 | 0.037762 | 0.037762 | 0.0 | 97.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016993 | 0.00016993 | 0.00016993 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000652 | | | 1.69 Nlocal: 910 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6163 ave 6163 max 6163 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90470 ave 90470 max 90470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90470 Ave neighs/atom = 99.417582 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) 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 19 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) = 6.913 | 6.913 | 6.913 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3521.1163 0 -3521.1163 -3.4366074 Loop time of 4.91e-07 on 1 procs for 0 steps with 910 atoms 203.7% 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 | | 4.91e-07 | | |100.00 Nlocal: 910 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6256 ave 6256 max 6256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90396 ave 90396 max 90396 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90396 Ave neighs/atom = 99.336264 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.913 | 6.913 | 6.913 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 -3521.1163 -3521.1163 29.400439 83.385863 5.4952938 -3.4366074 -3.4366074 29.620681 -19.624955 -20.305549 2.5551745 781.51503 Loop time of 7.02e-07 on 1 procs for 0 steps with 910 atoms 142.5% 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 | | 7.02e-07 | | |100.00 Nlocal: 910 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6256 ave 6256 max 6256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90396 ave 90396 max 90396 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180792 ave 180792 max 180792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180792 Ave neighs/atom = 198.67253 Neighbor list builds = 0 Dangerous builds = 0 910 -3521.1163291632 eV 2.55517451649781 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00