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 -46.754664 0.0000000) to (28.629109 46.754664 8.6320013) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2052926 5.3126295 5.7546675 Created 1074 atoms using lattice units in orthogonal box = (0.0000000 -46.754664 0.0000000) to (28.629109 46.754664 8.6320013) create_atoms CPU = 0.002 seconds 1074 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2052926 5.3126295 5.7546675 Created 1074 atoms using lattice units in orthogonal box = (0.0000000 -46.754664 0.0000000) to (28.629109 46.754664 8.6320013) create_atoms CPU = 0.001 seconds 1074 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 = 7 22 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 36 atoms, new total = 2112 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 = 7 22 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) = 8.650 | 8.650 | 8.650 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9352.4451 0 -9352.4451 4073.7171 12 0 -9363.2121 0 -9363.2121 3404.6956 Loop time of 0.858654 on 1 procs for 12 steps with 2112 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 = -9352.44512195864 -9363.20555136719 -9363.21211570726 Force two-norm initial, final = 22.473656 0.16009418 Force max component initial, final = 2.3328804 0.0077410716 Final line search alpha, max atom move = 1.0000000 0.0077410716 Iterations, force evaluations = 12 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85414 | 0.85414 | 0.85414 | 0.0 | 99.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023377 | 0.0023377 | 0.0023377 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002181 | | | 0.25 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10419.0 ave 10419 max 10419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 262896.0 ave 262896 max 262896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262896 Ave neighs/atom = 124.47727 Neighbor list builds = 0 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 : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.650 | 8.650 | 8.650 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -9363.2121 0 -9363.2121 3404.6956 23108.634 13 0 -9363.2128 0 -9363.2128 3084.18 23112.598 Loop time of 0.104685 on 1 procs for 1 steps with 2112 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 = -9363.21211570724 -9363.21211570724 -9363.21282853163 Force two-norm initial, final = 8.3088330 2.6492222 Force max component initial, final = 8.3072570 2.6442525 Final line search alpha, max atom move = 0.00012037668 0.00031830634 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1036 | 0.1036 | 0.1036 | 0.0 | 98.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021908 | 0.00021908 | 0.00021908 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008655 | | | 0.83 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10419.0 ave 10419 max 10419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 262896.0 ave 262896 max 262896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262896 Ave neighs/atom = 124.47727 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 = 7 22 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) = 8.281 | 8.281 | 8.281 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9363.2128 0 -9363.2128 3084.18 Loop time of 1.996e-06 on 1 procs for 0 steps with 2112 atoms 150.3% 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 | | 1.996e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10419.0 ave 10419 max 10419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 262896.0 ave 262896 max 262896 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 = 262896 Ave neighs/atom = 124.47727 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) = 8.281 | 8.281 | 8.281 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 -9363.2128 -9363.2128 28.629095 93.509328 8.6334863 3084.18 3084.18 -183.30078 9438.0462 -2.2055088 2.3512281 636.07089 Loop time of 2.304e-06 on 1 procs for 0 steps with 2112 atoms 260.4% 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 | | 2.304e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10419.0 ave 10419 max 10419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 262896.0 ave 262896 max 262896 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 525792.0 ave 525792 max 525792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 525792 Ave neighs/atom = 248.95455 Neighbor list builds = 0 Dangerous builds = 0 2112 -9363.21282853163 eV 2.351228143783 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01