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_NiPd__SM_559286646876_000 # For Simulator : LAMMPS 29 Sep 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -61.259782 0) to (37.513802 61.259782 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0506132 5.928366 6.3523435 Created 1487 atoms using lattice units in orthogonal box = (0 -61.259782 0) to (37.513802 61.259782 9.5285152) create_atoms CPU = 0.001 seconds 1487 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0506132 5.928366 6.3523435 Created 1493 atoms using lattice units in orthogonal box = (0 -61.259782 0) to (37.513802 61.259782 9.5285152) create_atoms CPU = 0.001 seconds 1493 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 28 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 4 atoms, new total = 2976 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:187) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 9 28 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) = 9.152 | 9.152 | 9.152 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7238.7071 0 -7238.7071 179922.32 83 0 -11539.078 0 -11539.078 5963.1563 Loop time of 2.36593 on 1 procs for 83 steps with 2976 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 = -7238.70713706846 -11539.0678627813 -11539.0775584275 Force two-norm initial, final = 2782.8635 0.38314016 Force max component initial, final = 417.67501 0.058151053 Final line search alpha, max atom move = 1 0.058151053 Iterations, force evaluations = 83 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3389 | 2.3389 | 2.3389 | 0.0 | 98.86 Neigh | 0.01397 | 0.01397 | 0.01397 | 0.0 | 0.59 Comm | 0.0064212 | 0.0064212 | 0.0064212 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006642 | | | 0.28 Nlocal: 2976 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11375 ave 11375 max 11375 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296498 ave 296498 max 296498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296498 Ave neighs/atom = 99.629704 Neighbor list builds = 2 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 9.154 | 9.154 | 9.154 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -11539.078 0 -11539.078 5963.1563 43794.721 87 0 -11539.449 0 -11539.449 123.21918 43922.184 Loop time of 0.108752 on 1 procs for 4 steps with 2976 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11539.0775584275 -11539.4476855986 -11539.4489450885 Force two-norm initial, final = 298.23911 9.4505958 Force max component initial, final = 207.78541 7.7067503 Final line search alpha, max atom move = 6.307089e-05 0.0004860716 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10725 | 0.10725 | 0.10725 | 0.0 | 98.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027353 | 0.00027353 | 0.00027353 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001224 | | | 1.13 Nlocal: 2976 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11646 ave 11646 max 11646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296674 ave 296674 max 296674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296674 Ave neighs/atom = 99.688844 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 9 28 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) = 8.785 | 8.785 | 8.785 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11539.449 0 -11539.449 123.21918 Loop time of 7.01e-07 on 1 procs for 0 steps with 2976 atoms 285.3% 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 | | 7.01e-07 | | |100.00 Nlocal: 2976 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11646 ave 11646 max 11646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296497 ave 296497 max 296497 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 = 296497 Ave neighs/atom = 99.629368 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) = 8.785 | 8.785 | 8.785 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 -11539.449 -11539.449 37.592677 122.75292 9.5180692 123.21918 123.21918 177.8206 281.6593 -89.822351 2.5260473 1084.4766 Loop time of 6.91e-07 on 1 procs for 0 steps with 2976 atoms 434.2% 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 | | 6.91e-07 | | |100.00 Nlocal: 2976 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11646 ave 11646 max 11646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296497 ave 296497 max 296497 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 592994 ave 592994 max 592994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 592994 Ave neighs/atom = 199.25874 Neighbor list builds = 0 Dangerous builds = 0 2976 -11539.4489450885 eV 2.5260472646176 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02