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 -38.121410 0.0000000) to (12.705962 38.121410 3.5239998) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8869084 4.8869084 3.5239998 Created 157 atoms using lattice units in orthogonal box = (0.0000000 -38.121410 0.0000000) to (12.705962 38.121410 3.5239998) create_atoms CPU = 0.002 seconds 157 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8869084 4.8869084 3.5239998 Created 157 atoms using lattice units in orthogonal box = (0.0000000 -38.121410 0.0000000) to (12.705962 38.121410 3.5239998) create_atoms CPU = 0.001 seconds 157 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 = 3 18 1 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 = 310 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 = 3 18 1 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) = 7.073 | 7.073 | 7.073 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1348.7711 0 -1348.7711 36460.649 39 0 -1370.1264 0 -1370.1264 -431.15621 Loop time of 0.855638 on 1 procs for 39 steps with 310 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1348.77107995207 -1370.12527336619 -1370.12643934739 Force two-norm initial, final = 62.686005 0.13320241 Force max component initial, final = 28.544049 0.051862302 Final line search alpha, max atom move = 1.0000000 0.051862302 Iterations, force evaluations = 39 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83801 | 0.83801 | 0.83801 | 0.0 | 97.94 Neigh | 0.0047352 | 0.0047352 | 0.0047352 | 0.0 | 0.55 Comm | 0.0080443 | 0.0080443 | 0.0080443 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004844 | | | 0.57 Nlocal: 310.000 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5192.00 ave 5192 max 5192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38635.0 ave 38635 max 38635 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38635 Ave neighs/atom = 124.62903 Neighbor list builds = 1 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 : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.073 | 7.073 | 7.073 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -1370.1264 0 -1370.1264 -431.15621 3413.8337 41 0 -1370.1302 0 -1370.1302 537.13694 3411.9938 Loop time of 0.065055 on 1 procs for 2 steps with 310 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 = -1370.12643934739 -1370.12917209937 -1370.13018659305 Force two-norm initial, final = 6.1127066 0.13903959 Force max component initial, final = 6.1104903 0.051045092 Final line search alpha, max atom move = 0.00035644107 1.8194567e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.063119 | 0.063119 | 0.063119 | 0.0 | 97.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052871 | 0.00052871 | 0.00052871 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001407 | | | 2.16 Nlocal: 310.000 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5186.00 ave 5186 max 5186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38581.0 ave 38581 max 38581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38581 Ave neighs/atom = 124.45484 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 = 3 18 1 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) = 6.704 | 6.704 | 6.704 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1370.1302 0 -1370.1302 537.13694 Loop time of 6.094e-06 on 1 procs for 0 steps with 310 atoms 180.5% 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 | | 6.094e-06 | | |100.00 Nlocal: 310.000 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5186.00 ave 5186 max 5186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38584.0 ave 38584 max 38584 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 = 38584 Ave neighs/atom = 124.46452 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) = 6.704 | 6.704 | 6.704 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 -1370.1302 -1370.1302 12.690281 76.242819 3.5264525 537.13694 537.13694 6.0307268 1605.7539 -0.37382008 2.2453392 147.83004 Loop time of 6.986e-06 on 1 procs for 0 steps with 310 atoms 257.7% 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 | | 6.986e-06 | | |100.00 Nlocal: 310.000 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5186.00 ave 5186 max 5186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38584.0 ave 38584 max 38584 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77168.0 ave 77168 max 77168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77168 Ave neighs/atom = 248.92903 Neighbor list builds = 0 Dangerous builds = 0 310 -1370.13018659305 eV 2.245339202087 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01