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 -52.153953 0.0000000) to (42.580647 52.153953 8.6320004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2496688 5.0007260 5.7546669 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -52.153953 0.0000000) to (42.580647 52.153953 8.6320004) create_atoms CPU = 0.002 seconds 1755 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2496688 5.0007260 5.7546669 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -52.153953 0.0000000) to (42.580647 52.153953 8.6320004) create_atoms CPU = 0.002 seconds 1755 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 = 10 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 38 atoms, new total = 3472 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 = 10 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) = 16.24 | 16.24 | 16.24 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15299.197 0 -15299.197 3705.8152 55 0 -15356.548 0 -15356.548 -6838.2001 Loop time of 5.47995 on 1 procs for 55 steps with 3472 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 = -15299.1966041573 -15356.5346610178 -15356.5477522754 Force two-norm initial, final = 72.951970 0.43767975 Force max component initial, final = 18.197158 0.066726646 Final line search alpha, max atom move = 0.62367087 0.041615465 Iterations, force evaluations = 55 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4108 | 5.4108 | 5.4108 | 0.0 | 98.74 Neigh | 0.039602 | 0.039602 | 0.039602 | 0.0 | 0.72 Comm | 0.01425 | 0.01425 | 0.01425 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01529 | | | 0.28 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14265.0 ave 14265 max 14265 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 432436.0 ave 432436 max 432436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432436 Ave neighs/atom = 124.54954 Neighbor list builds = 2 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 16.24 | 16.24 | 16.24 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -15356.548 0 -15356.548 -6838.2001 38339.013 58 0 -15356.76 0 -15356.76 -1647.1932 38230.48 Loop time of 0.352765 on 1 procs for 3 steps with 3472 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 = -15356.5477522753 -15356.7578454203 -15356.7596901231 Force two-norm initial, final = 205.29375 0.47753996 Force max component initial, final = 160.23300 0.059383866 Final line search alpha, max atom move = 9.3295216e-05 5.5402307e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3491 | 0.3491 | 0.3491 | 0.0 | 98.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059776 | 0.00059776 | 0.00059776 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003067 | | | 0.87 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14271.0 ave 14271 max 14271 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 432321.0 ave 432321 max 432321 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432321 Ave neighs/atom = 124.51642 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 = 10 24 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) = 15.12 | 15.12 | 15.12 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15356.76 0 -15356.76 -1647.1932 Loop time of 2.257e-06 on 1 procs for 0 steps with 3472 atoms 132.9% 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 | | 2.257e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14277.0 ave 14277 max 14277 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 432747.0 ave 432747 max 432747 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 = 432747 Ave neighs/atom = 124.63911 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) = 15.12 | 15.12 | 15.12 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 -15356.76 -15356.76 42.50159 104.30791 8.6235752 -1647.1932 -1647.1932 -2.1328403 -4937.1776 -2.2691726 2.2437833 1529.2688 Loop time of 2.088e-06 on 1 procs for 0 steps with 3472 atoms 287.4% 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 | | 2.088e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14277.0 ave 14277 max 14277 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 432747.0 ave 432747 max 432747 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 865494.0 ave 865494 max 865494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 865494 Ave neighs/atom = 249.27823 Neighbor list builds = 0 Dangerous builds = 0 3472 -15356.7596901231 eV 2.24378325331046 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06