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 -51.310206 0.0000000) to (25.655103 51.310206 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3565269 4.3565269 3.5239994 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -51.310206 0.0000000) to (25.655103 51.310206 3.5239994) create_atoms CPU = 0.001 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3565269 4.3565269 3.5239994 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -51.310206 0.0000000) to (25.655103 51.310206 3.5239994) create_atoms CPU = 0.001 seconds 426 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 = 6 24 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 2 atoms, new total = 848 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 = 6 24 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) = 7.692 | 7.692 | 7.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2979.1913 0 -2979.1913 179914.19 50 0 -3750.226 0 -3750.226 10355.236 Loop time of 1.41889 on 1 procs for 50 steps with 848 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 = -2979.19127281419 -3750.22273968025 -3750.22600335271 Force two-norm initial, final = 1255.1023 0.19583454 Force max component initial, final = 346.74391 0.037387932 Final line search alpha, max atom move = 1.0000000 0.037387932 Iterations, force evaluations = 50 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3978 | 1.3978 | 1.3978 | 0.0 | 98.52 Neigh | 0.0063688 | 0.0063688 | 0.0063688 | 0.0 | 0.45 Comm | 0.009242 | 0.009242 | 0.009242 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00544 | | | 0.38 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10080.0 ave 10080 max 10080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107332.0 ave 107332 max 107332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107332 Ave neighs/atom = 126.57075 Neighbor list builds = 1 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.695 | 7.695 | 7.695 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -3750.226 0 -3750.226 10355.236 9277.7643 58 0 -3750.5402 0 -3750.5402 32.040813 9329.3228 Loop time of 0.169658 on 1 procs for 8 steps with 848 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 = -3750.22600335271 -3750.5399675593 -3750.54022988087 Force two-norm initial, final = 114.85735 1.0661344 Force max component initial, final = 99.649319 0.93976684 Final line search alpha, max atom move = 0.00026083617 0.00024512518 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16549 | 0.16549 | 0.16549 | 0.0 | 97.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082336 | 0.00082336 | 0.00082336 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003345 | | | 1.97 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10114.0 ave 10114 max 10114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106050.0 ave 106050 max 106050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106050 Ave neighs/atom = 125.05896 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 = 6 24 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) = 7.326 | 7.326 | 7.326 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3750.5402 0 -3750.5402 32.040813 Loop time of 2.295e-06 on 1 procs for 0 steps with 848 atoms 174.3% 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 | | 2.295e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10114.0 ave 10114 max 10114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105644.0 ave 105644 max 105644 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 = 105644 Ave neighs/atom = 124.58019 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) = 7.326 | 7.326 | 7.326 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 -3750.5402 -3750.5402 25.636777 103.32554 3.5219161 32.040813 32.040813 161.2761 -2.8484542 -62.305209 2.2718303 352.5729 Loop time of 2.726e-06 on 1 procs for 0 steps with 848 atoms 220.1% 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 | | 2.726e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10114.0 ave 10114 max 10114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105644.0 ave 105644 max 105644 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 211288.0 ave 211288 max 211288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211288 Ave neighs/atom = 249.16038 Neighbor list builds = 0 Dangerous builds = 0 848 -3750.54022988087 eV 2.27183030653677 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01