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 -41.096542 0.0000000) to (20.548271 41.096542 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8348873 4.8348873 3.5239994 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -41.096542 0.0000000) to (20.548271 41.096542 3.5239994) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8348873 4.8348873 3.5239994 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.096542 0.0000000) to (20.548271 41.096542 3.5239994) create_atoms CPU = 0.000 seconds 274 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 = 5 19 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 2 atoms, new total = 544 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 = 5 19 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) = 7.163 | 7.163 | 7.163 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1865.3847 0 -1865.3847 201720.06 58 0 -2404.212 0 -2404.212 11419.726 Loop time of 1.14716 on 1 procs for 58 steps with 544 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 = -1865.38471216313 -2404.20965348714 -2404.21202830358 Force two-norm initial, final = 1028.8013 0.16367224 Force max component initial, final = 286.95863 0.018923721 Final line search alpha, max atom move = 1.0000000 0.018923721 Iterations, force evaluations = 58 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1315 | 1.1315 | 1.1315 | 0.0 | 98.64 Neigh | 0.0037835 | 0.0037835 | 0.0037835 | 0.0 | 0.33 Comm | 0.0075446 | 0.0075446 | 0.0075446 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004299 | | | 0.37 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6830.00 ave 6830 max 6830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70316.0 ave 70316 max 70316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70316 Ave neighs/atom = 129.25735 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.163 | 7.163 | 7.163 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -2404.212 0 -2404.212 11419.726 5951.7733 65 0 -2404.4601 0 -2404.4601 -43.975535 5988.5969 Loop time of 0.0944913 on 1 procs for 7 steps with 544 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 = -2404.21202830358 -2404.45924346187 -2404.46005983531 Force two-norm initial, final = 85.852244 1.1994250 Force max component initial, final = 76.152668 0.74294372 Final line search alpha, max atom move = 0.00041084991 0.00030523836 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.091934 | 0.091934 | 0.091934 | 0.0 | 97.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049693 | 0.00049693 | 0.00049693 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00206 | | | 2.18 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6866.00 ave 6866 max 6866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68424.0 ave 68424 max 68424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68424 Ave neighs/atom = 125.77941 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 = 5 19 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) = 6.794 | 6.794 | 6.794 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2404.4601 0 -2404.4601 -43.975535 Loop time of 1.951e-06 on 1 procs for 0 steps with 544 atoms 153.8% 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 | | 1.951e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6830.00 ave 6830 max 6830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68028.0 ave 68028 max 68028 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 = 68028 Ave neighs/atom = 125.05147 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) = 6.794 | 6.794 | 6.794 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 -2404.4601 -2404.4601 20.526214 82.72116 3.5269525 -43.975535 -43.975535 198.55223 -131.92341 -198.55543 2.2624967 246.0579 Loop time of 2.63e-06 on 1 procs for 0 steps with 544 atoms 190.1% 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 | | 2.63e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6830.00 ave 6830 max 6830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68028.0 ave 68028 max 68028 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 136056.0 ave 136056 max 136056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136056 Ave neighs/atom = 250.10294 Neighbor list builds = 0 Dangerous builds = 0 544 -2404.46005983531 eV 2.26249670778837 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01