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 -59.842467 0) to (36.645877 59.842467 9.3080622) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9106254 5.7912065 6.2053748 Created 1486 atoms using lattice units in orthogonal box = (0 -59.842467 0) to (36.645877 59.842467 9.3080622) create_atoms CPU = 0.001 seconds 1486 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9106254 5.7912065 6.2053748 Created 1492 atoms using lattice units in orthogonal box = (0 -59.842467 0) to (36.645877 59.842467 9.3080622) create_atoms CPU = 0.001 seconds 1492 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 = 9 28 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 2 atoms, new total = 2976 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 = 9 28 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) = 9.152 | 9.152 | 9.152 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13503.152 0 -13503.152 203809.68 67 0 -17056.049 0 -17056.049 9462.1136 Loop time of 1.85737 on 1 procs for 67 steps with 2976 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 = -13503.1519011892 -17056.0326547785 -17056.0486989787 Force two-norm initial, final = 3255.894 0.47114289 Force max component initial, final = 523.55354 0.047516191 Final line search alpha, max atom move = 1 0.047516191 Iterations, force evaluations = 67 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8319 | 1.8319 | 1.8319 | 0.0 | 98.63 Neigh | 0.014143 | 0.014143 | 0.014143 | 0.0 | 0.76 Comm | 0.0056135 | 0.0056135 | 0.0056135 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005726 | | | 0.31 Nlocal: 2976 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11711 ave 11711 max 11711 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 300497 ave 300497 max 300497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300497 Ave neighs/atom = 100.97345 Neighbor list builds = 2 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 9.155 | 9.155 | 9.155 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -17056.049 0 -17056.049 9462.1136 40824.783 72 0 -17056.958 0 -17056.958 -19.119862 40972.683 Loop time of 0.12282 on 1 procs for 5 steps with 2976 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 = -17056.0486989787 -17056.9567838151 -17056.9575627806 Force two-norm initial, final = 499.53317 2.8191477 Force max component initial, final = 451.49487 2.5238743 Final line search alpha, max atom move = 7.1681874e-05 0.00018091604 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12106 | 0.12106 | 0.12106 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032009 | 0.00032009 | 0.00032009 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001442 | | | 1.17 Nlocal: 2976 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11804 ave 11804 max 11804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 299370 ave 299370 max 299370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 299370 Ave neighs/atom = 100.59476 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 = 9 28 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) = 8.787 | 8.787 | 8.787 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -17056.958 0 -17056.958 -19.119862 Loop time of 4.61e-07 on 1 procs for 0 steps with 2976 atoms 216.9% 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 | | 4.61e-07 | | |100.00 Nlocal: 2976 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11804 ave 11804 max 11804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 298933 ave 298933 max 298933 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 = 298933 Ave neighs/atom = 100.44792 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) = 8.787 | 8.787 | 8.787 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 -17056.958 -17056.958 36.666572 120.15586 9.2999181 -19.119862 -19.119862 -98.748125 -0.57129851 41.959837 2.4094442 1137.107 Loop time of 7.32e-07 on 1 procs for 0 steps with 2976 atoms 409.8% 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 | | 7.32e-07 | | |100.00 Nlocal: 2976 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11804 ave 11804 max 11804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 298933 ave 298933 max 298933 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 597866 ave 597866 max 597866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 597866 Ave neighs/atom = 200.89583 Neighbor list builds = 0 Dangerous builds = 0 2976 -17056.9575627806 eV 2.40944419154588 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02