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 -51.313730 0.0000000) to (25.655103 51.313730 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3565269 4.3565269 3.5239994 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -51.313730 0.0000000) to (25.655103 51.313730 3.5239994) create_atoms CPU = 0.002 seconds 426 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3565269 4.3565269 3.5239994 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -51.313730 0.0000000) to (25.655103 51.313730 3.5239994) create_atoms CPU = 0.001 seconds 426 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 = 6 24 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 12 atoms, new total = 840 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 = 6 24 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) = 7.696 | 7.696 | 7.696 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3702.7682 0 -3702.7682 2758.6346 45 0 -3714.9759 0 -3714.9759 -7045.4972 Loop time of 3.08006 on 1 procs for 45 steps with 840 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 = -3702.76823892475 -3714.97241638516 -3714.97589733106 Force two-norm initial, final = 33.003353 0.19512279 Force max component initial, final = 9.8340888 0.022247985 Final line search alpha, max atom move = 1.0000000 0.022247985 Iterations, force evaluations = 45 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0355 | 3.0355 | 3.0355 | 0.0 | 98.55 Neigh | 0.012625 | 0.012625 | 0.012625 | 0.0 | 0.41 Comm | 0.020353 | 0.020353 | 0.020353 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01158 | | | 0.38 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9990.00 ave 9990 max 9990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104468.0 ave 104468 max 104468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104468 Ave neighs/atom = 124.36667 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 : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.698 | 7.698 | 7.698 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -3714.9759 0 -3714.9759 -7045.4972 9278.4015 48 0 -3715.0411 0 -3715.0411 -846.25256 9247.0893 Loop time of 0.257121 on 1 procs for 3 steps with 840 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3714.97589733106 -3715.04104379838 -3715.04109966353 Force two-norm initial, final = 55.901805 1.5716650 Force max component initial, final = 40.816903 1.1813127 Final line search alpha, max atom move = 0.032033405 0.037841468 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25115 | 0.25115 | 0.25115 | 0.0 | 97.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014411 | 0.0014411 | 0.0014411 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004534 | | | 1.76 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9952.00 ave 9952 max 9952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104426.0 ave 104426 max 104426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104426 Ave neighs/atom = 124.31667 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 = 6 24 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) = 7.329 | 7.329 | 7.329 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3715.0411 0 -3715.0411 -846.25256 Loop time of 7.698e-06 on 1 procs for 0 steps with 840 atoms 181.9% 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 | | 7.698e-06 | | |100.00 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9952.00 ave 9952 max 9952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104556.0 ave 104556 max 104556 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 = 104556 Ave neighs/atom = 124.47143 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) = 7.329 | 7.329 | 7.329 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 -3715.0411 -3715.0411 25.610849 102.62746 3.5181756 -846.25256 -846.25256 175.0959 -2918.1928 204.33928 2.2761665 350.7761 Loop time of 7.538e-06 on 1 procs for 0 steps with 840 atoms 278.6% 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 | | 7.538e-06 | | |100.00 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9952.00 ave 9952 max 9952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104556.0 ave 104556 max 104556 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 209112.0 ave 209112 max 209112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209112 Ave neighs/atom = 248.94286 Neighbor list builds = 0 Dangerous builds = 0 840 -3715.04109966353 eV 2.27616654965243 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03