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 -42.584171 0.0000000) to (52.150429 42.584171 8.6320004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0007260 5.2496688 5.7546669 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.584171 0.0000000) to (52.150429 42.584171 8.6320004) create_atoms CPU = 0.002 seconds 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0007260 5.2496688 5.7546669 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.584171 0.0000000) to (52.150429 42.584171 8.6320004) create_atoms CPU = 0.002 seconds 1756 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 = 12 20 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 56 atoms, new total = 3456 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 = 12 20 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) = 16.20 | 16.20 | 16.20 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15212.969 0 -15212.969 1912.7509 68 0 -15288.611 0 -15288.611 -16514.914 Loop time of 7.62161 on 1 procs for 68 steps with 3456 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15212.9686710574 -15288.597389809 -15288.6114415569 Force two-norm initial, final = 100.28103 0.44794998 Force max component initial, final = 19.556318 0.10766357 Final line search alpha, max atom move = 1.0000000 0.10766357 Iterations, force evaluations = 68 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.5457 | 7.5457 | 7.5457 | 0.0 | 99.00 Neigh | 0.039508 | 0.039508 | 0.039508 | 0.0 | 0.52 Comm | 0.017713 | 0.017713 | 0.017713 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01864 | | | 0.24 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13790.0 ave 13790 max 13790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 433120.0 ave 433120 max 433120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 433120 Ave neighs/atom = 125.32407 Neighbor list builds = 2 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 : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 16.20 | 16.20 | 16.20 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -15288.611 0 -15288.611 -16514.914 38339.595 73 0 -15289.978 0 -15289.978 -3221.2483 38056.823 Loop time of 0.419331 on 1 procs for 5 steps with 3456 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 = -15288.6114415569 -15289.9722522212 -15289.9777837572 Force two-norm initial, final = 518.70640 9.6950620 Force max component initial, final = 397.56543 9.6710114 Final line search alpha, max atom move = 3.4685110e-05 0.00033544009 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41487 | 0.41487 | 0.41487 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006813 | 0.0006813 | 0.0006813 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003778 | | | 0.90 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13802.0 ave 13802 max 13802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 432956.0 ave 432956 max 432956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432956 Ave neighs/atom = 125.27662 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 = 12 20 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) = 15.08 | 15.08 | 15.08 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15289.978 0 -15289.978 -3221.2483 Loop time of 1.923e-06 on 1 procs for 0 steps with 3456 atoms 208.0% 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 | | 1.923e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13802.0 ave 13802 max 13802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 435814.0 ave 435814 max 435814 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 = 435814 Ave neighs/atom = 126.10359 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) = 15.08 | 15.08 | 15.08 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 -15289.978 -15289.978 51.921889 85.168341 8.6060498 -3221.2483 -3221.2483 -3.5256615 -10066.141 405.92157 2.2359454 1488.9449 Loop time of 2.008e-06 on 1 procs for 0 steps with 3456 atoms 249.0% 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 | | 2.008e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13802.0 ave 13802 max 13802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 435814.0 ave 435814 max 435814 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 871628.0 ave 871628 max 871628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 871628 Ave neighs/atom = 252.20718 Neighbor list builds = 0 Dangerous builds = 0 3456 -15289.9777837572 eV 2.23594538875124 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08