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 -75.236171 0) to (46.072557 75.236171 9.3080622) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3281189 5.3740122 6.2053748 Created 2352 atoms using lattice units in orthogonal box = (0 -75.236171 0) to (46.072557 75.236171 9.3080622) create_atoms CPU = 0.001 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3281189 5.3740122 6.2053748 Created 2358 atoms using lattice units in orthogonal box = (0 -75.236171 0) to (46.072557 75.236171 9.3080622) create_atoms CPU = 0.001 seconds 2358 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 = 11 35 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 18 atoms, new total = 4692 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 = 11 35 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) = 16.52 | 16.52 | 16.52 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -23363.297 0 -23363.297 123279.2 95 0 -26896.363 0 -26896.363 4859.6337 Loop time of 4.09511 on 1 procs for 95 steps with 4692 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 = -23363.2973755792 -26896.3411226589 -26896.3632171733 Force two-norm initial, final = 3254.3028 0.56188738 Force max component initial, final = 477.4853 0.075978673 Final line search alpha, max atom move = 1 0.075978673 Iterations, force evaluations = 95 168 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0383 | 4.0383 | 4.0383 | 0.0 | 98.61 Neigh | 0.033956 | 0.033956 | 0.033956 | 0.0 | 0.83 Comm | 0.010883 | 0.010883 | 0.010883 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01192 | | | 0.29 Nlocal: 4692 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16482 ave 16482 max 16482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 469842 ave 469842 max 469842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 469842 Ave neighs/atom = 100.13683 Neighbor list builds = 3 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 : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 16.52 | 16.52 | 16.52 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -26896.363 0 -26896.363 4859.6337 64529.496 99 0 -26896.992 0 -26896.992 -34.218352 64650.748 Loop time of 0.165254 on 1 procs for 4 steps with 4692 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 = -26896.3632171732 -26896.9884071034 -26896.9915643513 Force two-norm initial, final = 471.02048 7.8585409 Force max component initial, final = 457.9261 6.6118253 Final line search alpha, max atom move = 2.5741316e-05 0.00017019708 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16305 | 0.16305 | 0.16305 | 0.0 | 98.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038856 | 0.00038856 | 0.00038856 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001816 | | | 1.10 Nlocal: 4692 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16393 ave 16393 max 16393 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 469410 ave 469410 max 469410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 469410 Ave neighs/atom = 100.04476 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 = 11 35 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) = 15.4 | 15.4 | 15.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -26896.992 0 -26896.992 -34.218352 Loop time of 5.31e-07 on 1 procs for 0 steps with 4692 atoms 188.3% 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 | | 5.31e-07 | | |100.00 Nlocal: 4692 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16393 ave 16393 max 16393 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 469200 ave 469200 max 469200 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 = 469200 Ave neighs/atom = 100 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) = 15.4 | 15.4 | 15.4 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 -26896.992 -26896.992 46.059191 150.90315 9.3016276 -34.218352 -34.218352 -163.80689 -35.861267 97.013099 2.3764679 1911.6834 Loop time of 7.71e-07 on 1 procs for 0 steps with 4692 atoms 389.1% 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 | | 7.71e-07 | | |100.00 Nlocal: 4692 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16393 ave 16393 max 16393 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 469200 ave 469200 max 469200 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 938400 ave 938400 max 938400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 938400 Ave neighs/atom = 200 Neighbor list builds = 0 Dangerous builds = 0 4692 -26896.9915643513 eV 2.37646793951723 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04