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_NiRh__SM_306597220004_000 # For Simulator : LAMMPS 30 Jul 2021 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239998 3.5239998 3.5239998 Created orthogonal box = (0.0000000 -42.584175 0.0000000) to (52.150434 42.584175 8.6320013) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0007266 5.2496693 5.7546675 Created 1753 atoms using lattice units in orthogonal box = (0.0000000 -42.584175 0.0000000) to (52.150434 42.584175 8.6320013) create_atoms CPU = 0.002 seconds 1753 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0007266 5.2496693 5.7546675 Created 1753 atoms using lattice units in orthogonal box = (0.0000000 -42.584175 0.0000000) to (52.150434 42.584175 8.6320013) create_atoms CPU = 0.002 seconds 1753 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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, 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 50 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_306597220004_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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, 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 -15213.116 0 -15213.116 1727.4565 50 0 -15288.61 0 -15288.61 -16546.737 Loop time of 4.99857 on 1 procs for 50 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 = -15213.1161814829 -15288.5947749852 -15288.6100029958 Force two-norm initial, final = 100.10313 0.41551663 Force max component initial, final = 19.499730 0.043879025 Final line search alpha, max atom move = 1.0000000 0.043879025 Iterations, force evaluations = 50 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9527 | 4.9527 | 4.9527 | 0.0 | 99.08 Neigh | 0.01968 | 0.01968 | 0.01968 | 0.0 | 0.39 Comm | 0.012442 | 0.012442 | 0.012442 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01375 | | | 0.28 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13792.0 ave 13792 max 13792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 429637.0 ave 429637 max 429637 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 429637 Ave neighs/atom = 124.31626 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) = 16.20 | 16.20 | 16.20 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -15288.61 0 -15288.61 -16546.737 38339.607 55 0 -15290.001 0 -15290.001 -3141.2879 38054.407 Loop time of 0.399559 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 = -15288.6100029958 -15289.9940749736 -15290.0011023432 Force two-norm initial, final = 523.20346 10.590725 Force max component initial, final = 401.61240 10.526629 Final line search alpha, max atom move = 3.0046762e-05 0.00031629111 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39507 | 0.39507 | 0.39507 | 0.0 | 98.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068273 | 0.00068273 | 0.00068273 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003809 | | | 0.95 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13780.0 ave 13780 max 13780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 429529.0 ave 429529 max 429529 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 429529 Ave neighs/atom = 124.28501 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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, 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 -15290.001 0 -15290.001 -3141.2879 Loop time of 1.992e-06 on 1 procs for 0 steps with 3456 atoms 200.8% 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 | | 1.992e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13804.0 ave 13804 max 13804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 430614.0 ave 430614 max 430614 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 = 430614 Ave neighs/atom = 124.59896 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 -15290.001 -15290.001 51.920049 85.16835 8.6058075 -3141.2879 -3141.2879 -41.511972 -9824.2017 441.84998 2.2360492 1481.5594 Loop time of 2.034e-06 on 1 procs for 0 steps with 3456 atoms 245.8% 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 | | 2.034e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13804.0 ave 13804 max 13804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 430614.0 ave 430614 max 430614 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 861228.0 ave 861228 max 861228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 861228 Ave neighs/atom = 249.19792 Neighbor list builds = 0 Dangerous builds = 0 3456 -15290.0011023432 eV 2.23604918886726 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06