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 -41.351268 0) to (41.351268 41.351268 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4891064 5.4891064 3.8900001 Created 452 atoms using lattice units in orthogonal box = (0 -41.351268 0) to (41.351268 41.351268 3.8900001) create_atoms CPU = 0.000 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4891064 5.4891064 3.8900001 Created 454 atoms using lattice units in orthogonal box = (0 -41.351268 0) to (41.351268 41.351268 3.8900001) create_atoms CPU = 0.000 seconds 454 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 = 10 19 1 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 0 atoms, new total = 906 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 = 10 19 1 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) = 7.266 | 7.266 | 7.266 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2664.3802 0 -2664.3802 241585.66 90 0 -3513.0685 0 -3513.0685 10789.149 Loop time of 0.82023 on 1 procs for 90 steps with 906 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 = -2664.3802483437 -3513.06515182132 -3513.06850676652 Force two-norm initial, final = 875.93207 0.2288574 Force max component initial, final = 138.85193 0.03634736 Final line search alpha, max atom move = 1 0.03634736 Iterations, force evaluations = 90 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.80824 | 0.80824 | 0.80824 | 0.0 | 98.54 Neigh | 0.0040767 | 0.0040767 | 0.0040767 | 0.0 | 0.50 Comm | 0.0051877 | 0.0051877 | 0.0051877 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00273 | | | 0.33 Nlocal: 906 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7956 ave 7956 max 7956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90240 ave 90240 max 90240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90240 Ave neighs/atom = 99.602649 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 : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.272 | 7.272 | 7.272 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -3513.0685 0 -3513.0685 10789.149 13303.235 96 0 -3513.4186 0 -3513.4186 -10.749149 13373.304 Loop time of 0.0452023 on 1 procs for 6 steps with 906 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 = -3513.06850676652 -3513.41815621732 -3513.41864225227 Force two-norm initial, final = 164.85847 0.90172243 Force max component initial, final = 129.37019 0.59373058 Final line search alpha, max atom move = 0.00017124228 0.00010167178 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.044055 | 0.044055 | 0.044055 | 0.0 | 97.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026041 | 0.00026041 | 0.00026041 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008864 | | | 1.96 Nlocal: 906 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8538 ave 8538 max 8538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90262 ave 90262 max 90262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90262 Ave neighs/atom = 99.626932 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 = 10 19 1 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) = 6.904 | 6.904 | 6.904 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3513.4186 0 -3513.4186 -10.749149 Loop time of 6.21e-07 on 1 procs for 0 steps with 906 atoms 161.0% 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 | | 6.21e-07 | | |100.00 Nlocal: 906 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8526 ave 8526 max 8526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90090 ave 90090 max 90090 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 = 90090 Ave neighs/atom = 99.437086 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) = 6.904 | 6.904 | 6.904 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 -3513.4186 -3513.4186 41.298034 83.089885 3.8972761 -10.749149 -10.749149 -43.521527 -59.99032 71.2644 2.5122017 183.69902 Loop time of 6.672e-06 on 1 procs for 0 steps with 906 atoms 119.9% 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 | | 6.672e-06 | | |100.00 Nlocal: 906 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8526 ave 8526 max 8526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90090 ave 90090 max 90090 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180180 ave 180180 max 180180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180180 Ave neighs/atom = 198.87417 Neighbor list builds = 0 Dangerous builds = 0 906 -3513.41864225227 eV 2.5122017014504 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00