LAMMPS (23 Jun 2022) 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 23 Jun 2022 # Lattice spacing in x,y,z = 3.8000005 3.8000005 3.8000005 Created orthogonal box = (0 -45.91558 0) to (56.234872 45.91558 9.3080622) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.392385 5.660825 6.2053748 Created 1750 atoms using lattice units in orthogonal box = (0 -45.91558 0) to (56.234872 45.91558 9.3080622) create_atoms CPU = 0.001 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.392385 5.660825 6.2053748 Created 1756 atoms using lattice units in orthogonal box = (0 -45.91558 0) to (56.234872 45.91558 9.3080622) create_atoms CPU = 0.001 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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, bins = 13 21 3 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 = 3502 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:187) 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 = 13 21 3 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) = 9.348 | 9.348 | 9.348 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15849.142 0 -15849.142 229640.8 100 0 -20056.054 0 -20056.054 10074.545 Loop time of 2.95921 on 1 procs for 100 steps with 3502 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 = -15849.1419293983 -20056.0344205624 -20056.0537902969 Force two-norm initial, final = 3357.7215 0.56673425 Force max component initial, final = 419.0078 0.14760413 Final line search alpha, max atom move = 1 0.14760413 Iterations, force evaluations = 100 156 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8994 | 2.8994 | 2.8994 | 0.0 | 97.98 Neigh | 0.043054 | 0.043054 | 0.043054 | 0.0 | 1.45 Comm | 0.0077891 | 0.0077891 | 0.0077891 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008943 | | | 0.30 Nlocal: 3502 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12453 ave 12453 max 12453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 353953 ave 353953 max 353953 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 353953 Ave neighs/atom = 101.07167 Neighbor list builds = 5 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : metal Current step : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 9.358 | 9.358 | 9.358 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -20056.054 0 -20056.054 10074.545 48067.89 105 0 -20057.333 0 -20057.333 321.38746 48249.108 Loop time of 0.12947 on 1 procs for 5 steps with 3502 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 = -20056.0537902969 -20057.3131280612 -20057.3328680246 Force two-norm initial, final = 629.33398 17.282258 Force max component initial, final = 580.72642 11.716722 Final line search alpha, max atom move = 2.329767e-05 0.00027297233 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12777 | 0.12777 | 0.12777 | 0.0 | 98.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028585 | 0.00028585 | 0.00028585 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001409 | | | 1.09 Nlocal: 3502 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12110 ave 12110 max 12110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 353570 ave 353570 max 353570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 353570 Ave neighs/atom = 100.96231 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) 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 = 13 21 3 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) = 8.986 | 8.986 | 8.986 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20057.333 0 -20057.333 321.38746 Loop time of 6.92e-07 on 1 procs for 0 steps with 3502 atoms 289.0% 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 | | 6.92e-07 | | |100.00 Nlocal: 3502 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12106 ave 12106 max 12106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 352747 ave 352747 max 352747 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 352747 Ave neighs/atom = 100.7273 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 8.986 | 8.986 | 8.986 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 -20057.333 -20057.333 56.236643 92.242147 9.3012323 321.38746 321.38746 207.42621 390.81078 365.92539 2.3808184 1702.5637 Loop time of 9.42e-07 on 1 procs for 0 steps with 3502 atoms 318.5% 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 | | 9.42e-07 | | |100.00 Nlocal: 3502 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12106 ave 12106 max 12106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 352747 ave 352747 max 352747 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 705494 ave 705494 max 705494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 705494 Ave neighs/atom = 201.4546 Neighbor list builds = 0 Dangerous builds = 0 3502 -20057.3328680246 eV 2.38081842282666 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03