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 -63.822350 0.0000000) to (22.564608 63.822350 4.9836883) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0539193 5.4482494 4.9836883 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -63.822350 0.0000000) to (22.564608 63.822350 4.9836883) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0539193 5.4482494 4.9836883 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.822350 0.0000000) to (22.564608 63.822350 4.9836883) create_atoms CPU = 0.002 seconds 658 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 = 6 29 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 2 atoms, new total = 1312 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 = 6 29 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) = 7.919 | 7.919 | 7.919 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5340.5874 0 -5340.5874 95131.334 74 0 -5814.9701 0 -5814.9701 3519.8197 Loop time of 3.52878 on 1 procs for 74 steps with 1312 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 = -5340.58741478022 -5814.9650646413 -5814.97006360657 Force two-norm initial, final = 881.25099 0.23744836 Force max component initial, final = 246.15234 0.039308287 Final line search alpha, max atom move = 1.0000000 0.039308287 Iterations, force evaluations = 74 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.481 | 3.481 | 3.481 | 0.0 | 98.65 Neigh | 0.01772 | 0.01772 | 0.01772 | 0.0 | 0.50 Comm | 0.017876 | 0.017876 | 0.017876 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01218 | | | 0.35 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10640.0 ave 10640 max 10640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164014.0 ave 164014 max 164014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164014 Ave neighs/atom = 125.01067 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 : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.919 | 7.919 | 7.919 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -5814.9701 0 -5814.9701 3519.8197 14354.281 77 0 -5815.0209 0 -5815.0209 -59.396452 14382.008 Loop time of 0.14869 on 1 procs for 3 steps with 1312 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 = -5814.97006360657 -5815.02071444813 -5815.02086418013 Force two-norm initial, final = 62.330184 0.97910541 Force max component initial, final = 49.576456 0.66838198 Final line search alpha, max atom move = 0.00043441850 0.00029035749 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14605 | 0.14605 | 0.14605 | 0.0 | 98.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052883 | 0.00052883 | 0.00052883 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002112 | | | 1.42 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10631.0 ave 10631 max 10631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164154.0 ave 164154 max 164154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164154 Ave neighs/atom = 125.11738 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 = 6 29 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) = 7.551 | 7.551 | 7.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5815.0209 0 -5815.0209 -59.396452 Loop time of 2.525e-06 on 1 procs for 0 steps with 1312 atoms 158.4% 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 | | 2.525e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10631.0 ave 10631 max 10631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164050.0 ave 164050 max 164050 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 = 164050 Ave neighs/atom = 125.03811 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) = 7.551 | 7.551 | 7.551 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 -5815.0209 -5815.0209 22.595501 127.77927 4.9812363 -59.396452 -59.396452 -74.560662 -40.368907 -63.259787 2.3237664 490.94364 Loop time of 2.667e-06 on 1 procs for 0 steps with 1312 atoms 300.0% 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 | | 2.667e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10631.0 ave 10631 max 10631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164050.0 ave 164050 max 164050 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 328100.0 ave 328100 max 328100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328100 Ave neighs/atom = 250.07622 Neighbor list builds = 0 Dangerous builds = 0 1312 -5815.02086418013 eV 2.32376640666041 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04