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 = 6.6981602 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 = 6.6981602 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 2 atoms, new total = 912 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 -2433.6754 0 -2433.6754 197958.26 81 0 -3532.0405 0 -3532.0405 7623.72 Loop time of 0.743789 on 1 procs for 81 steps with 912 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 = -2433.67544491341 -3532.03767353094 -3532.04049399978 Force two-norm initial, final = 1294.2627 0.19132855 Force max component initial, final = 318.86957 0.037727496 Final line search alpha, max atom move = 1 0.037727496 Iterations, force evaluations = 81 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73584 | 0.73584 | 0.73584 | 0.0 | 98.93 Neigh | 0.0021382 | 0.0021382 | 0.0021382 | 0.0 | 0.29 Comm | 0.0037343 | 0.0037343 | 0.0037343 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002079 | | | 0.28 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6641 ave 6641 max 6641 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90712 ave 90712 max 90712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90712 Ave neighs/atom = 99.464912 Neighbor list builds = 1 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 : 81 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 81 0 -3532.0405 0 -3532.0405 7623.72 13420.963 85 0 -3532.1847 0 -3532.1847 -7.7434344 13471.68 Loop time of 0.0397721 on 1 procs for 4 steps with 912 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 = -3532.04049399978 -3532.18468413639 -3532.18474598531 Force two-norm initial, final = 113.11337 0.25967922 Force max component initial, final = 81.55241 0.092170396 Final line search alpha, max atom move = 0.0010105586 9.3143583e-05 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.03896 | 0.03896 | 0.03896 | 0.0 | 97.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017996 | 0.00017996 | 0.00017996 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006325 | | | 1.59 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6613 ave 6613 max 6613 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90746 ave 90746 max 90746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90746 Ave neighs/atom = 99.502193 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) = 6.917 | 6.917 | 6.917 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3532.1847 0 -3532.1847 -7.7434344 Loop time of 5.71e-07 on 1 procs for 0 steps with 912 atoms 175.1% 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 | | 5.71e-07 | | |100.00 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6613 ave 6613 max 6613 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90672 ave 90672 max 90672 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 = 90672 Ave neighs/atom = 99.421053 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) = 6.917 | 6.917 | 6.917 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 -3532.1847 -3532.1847 29.40547 83.294747 5.5001686 -7.7434344 -7.7434344 -10.97542 -7.7915116 -4.4633712 2.588409 949.52591 Loop time of 4.41e-07 on 1 procs for 0 steps with 912 atoms 453.5% 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 | | 4.41e-07 | | |100.00 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6613 ave 6613 max 6613 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90672 ave 90672 max 90672 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 181344 ave 181344 max 181344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181344 Ave neighs/atom = 198.84211 Neighbor list builds = 0 Dangerous builds = 0 912 -3532.18474598531 eV 2.58840903998423 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00