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 -43.589465 0.0000000) to (20.548271 43.589465 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0436091 5.9828678 4.9836877 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -43.589465 0.0000000) to (20.548271 43.589465 4.9836877) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0436091 5.9828678 4.9836877 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -43.589465 0.0000000) to (20.548271 43.589465 4.9836877) create_atoms CPU = 0.001 seconds 412 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 = 5 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 4 atoms, new total = 816 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 = 5 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) = 7.687 | 7.687 | 7.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2134.7584 0 -2134.7584 241557.4 56 0 -3610.904 0 -3610.904 7530.2455 Loop time of 1.80672 on 1 procs for 56 steps with 816 atoms 90.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2134.75838714271 -3610.90093445137 -3610.90398349494 Force two-norm initial, final = 1932.3440 0.18358529 Force max component initial, final = 455.63487 0.021816398 Final line search alpha, max atom move = 1.0000000 0.021816398 Iterations, force evaluations = 56 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7846 | 1.7846 | 1.7846 | 0.0 | 98.77 Neigh | 0.0062123 | 0.0062123 | 0.0062123 | 0.0 | 0.34 Comm | 0.0092491 | 0.0092491 | 0.0092491 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006703 | | | 0.37 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7847.00 ave 7847 max 7847 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103500.0 ave 103500 max 103500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103500 Ave neighs/atom = 126.83824 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.690 | 7.690 | 7.690 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -3610.904 0 -3610.904 7530.2455 8927.66 60 0 -3611.016 0 -3611.016 3.7285873 8964.0405 Loop time of 0.116067 on 1 procs for 4 steps with 816 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 = -3610.90398349494 -3611.01511230776 -3611.01602615504 Force two-norm initial, final = 77.568870 0.63158086 Force max component initial, final = 63.990988 0.44831531 Final line search alpha, max atom move = 0.00018920938 8.4825462e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11355 | 0.11355 | 0.11355 | 0.0 | 97.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044393 | 0.00044393 | 0.00044393 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002074 | | | 1.79 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7857.00 ave 7857 max 7857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102656.0 ave 102656 max 102656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102656 Ave neighs/atom = 125.80392 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 = 5 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) = 7.322 | 7.322 | 7.322 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3611.016 0 -3611.016 3.7285873 Loop time of 2.383e-06 on 1 procs for 0 steps with 816 atoms 167.9% 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 | | 2.383e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7857.00 ave 7857 max 7857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102456.0 ave 102456 max 102456 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 = 102456 Ave neighs/atom = 125.55882 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) = 7.322 | 7.322 | 7.322 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 -3611.016 -3611.016 20.558355 87.439407 4.9866427 3.7285873 3.7285873 80.168396 0.62980917 -69.612443 2.3772357 500.83827 Loop time of 2.358e-06 on 1 procs for 0 steps with 816 atoms 254.5% 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 | | 2.358e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7857.00 ave 7857 max 7857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102456.0 ave 102456 max 102456 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 204912.0 ave 204912 max 204912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204912 Ave neighs/atom = 251.11765 Neighbor list builds = 0 Dangerous builds = 0 816 -3611.01602615504 eV 2.3772356773976 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02