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_NiPd__SM_559286646876_000 # For Simulator : LAMMPS 29 Sep 2021 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created orthogonal box = (0.0000000 -53.211224 0.0000000) to (37.626017 53.211224 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9409501 5.1344163 4.9836877 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -53.211224 0.0000000) to (37.626017 53.211224 4.9836877) create_atoms CPU = 0.003 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9409501 5.1344163 4.9836877 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.211224 0.0000000) to (37.626017 53.211224 4.9836877) create_atoms CPU = 0.002 seconds 916 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 9 24 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 4 atoms, new total = 1824 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_559286646876_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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 9 24 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) = 8.438 | 8.438 | 8.438 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6311.6848 0 -6311.6848 180449.02 69 0 -8078.0378 0 -8078.0378 5683.3357 Loop time of 4.67263 on 1 procs for 69 steps with 1824 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 = -6311.68479120418 -8078.0303892148 -8078.03781275954 Force two-norm initial, final = 1926.8641 0.29371203 Force max component initial, final = 274.65788 0.037238104 Final line search alpha, max atom move = 1.0000000 0.037238104 Iterations, force evaluations = 69 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6242 | 4.6242 | 4.6242 | 0.0 | 98.96 Neigh | 0.011235 | 0.011235 | 0.011235 | 0.0 | 0.24 Comm | 0.021341 | 0.021341 | 0.021341 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01587 | | | 0.34 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12288.0 ave 12288 max 12288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231484.0 ave 231484 max 231484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231484 Ave neighs/atom = 126.91009 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 : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.443 | 8.443 | 8.443 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -8078.0378 0 -8078.0378 5683.3357 19955.946 74 0 -8078.3398 0 -8078.3398 -307.79861 20020.687 Loop time of 0.265639 on 1 procs for 5 steps with 1824 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8078.03781275954 -8078.33615464317 -8078.33980898873 Force two-norm initial, final = 152.77513 6.9438655 Force max component initial, final = 144.20909 4.7055286 Final line search alpha, max atom move = 8.0513964e-05 0.00037886076 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26102 | 0.26102 | 0.26102 | 0.0 | 98.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073039 | 0.00073039 | 0.00073039 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003884 | | | 1.46 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13018.0 ave 13018 max 13018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230332.0 ave 230332 max 230332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230332 Ave neighs/atom = 126.27851 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 9 25 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) = 8.075 | 8.075 | 8.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8078.3398 0 -8078.3398 -307.79861 Loop time of 2.367e-06 on 1 procs for 0 steps with 1824 atoms 169.0% 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 | | 2.367e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13018.0 ave 13018 max 13018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 229508.0 ave 229508 max 229508 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 = 229508 Ave neighs/atom = 125.82675 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) = 8.075 | 8.075 | 8.075 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 -8078.3398 -8078.3398 37.595795 106.903 4.9813815 -307.79861 -307.79861 -364.46706 -182.53814 -376.39062 2.311391 695.86408 Loop time of 2.978e-06 on 1 procs for 0 steps with 1824 atoms 268.6% 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 | | 2.978e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13018.0 ave 13018 max 13018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 229508.0 ave 229508 max 229508 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 459016.0 ave 459016 max 459016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459016 Ave neighs/atom = 251.65351 Neighbor list builds = 0 Dangerous builds = 0 1824 -8078.33980898874 eV 2.31139100680696 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05