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 -46.220343 0.0000000) to (32.680226 46.220343 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0800420 5.9114536 4.9836877 Created 693 atoms using lattice units in orthogonal box = (0.0000000 -46.220343 0.0000000) to (32.680226 46.220343 4.9836877) create_atoms CPU = 0.002 seconds 693 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0800420 5.9114536 4.9836877 Created 693 atoms using lattice units in orthogonal box = (0.0000000 -46.220343 0.0000000) to (32.680226 46.220343 4.9836877) create_atoms CPU = 0.002 seconds 693 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 = 8 21 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 18 atoms, new total = 1368 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 = 8 21 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) = 7.889 | 7.889 | 7.889 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5985.5529 0 -5985.5529 28330.553 62 0 -6054.269 0 -6054.269 -4020.3214 Loop time of 2.57847 on 1 procs for 62 steps with 1368 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 = -5985.55286784512 -6054.2635082811 -6054.26897610262 Force two-norm initial, final = 136.45185 0.27395386 Force max component initial, final = 26.058248 0.046728606 Final line search alpha, max atom move = 1.0000000 0.046728606 Iterations, force evaluations = 62 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5381 | 2.5381 | 2.5381 | 0.0 | 98.43 Neigh | 0.018162 | 0.018162 | 0.018162 | 0.0 | 0.70 Comm | 0.012328 | 0.012328 | 0.012328 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009904 | | | 0.38 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9954.00 ave 9954 max 9954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 171429.0 ave 171429 max 171429 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171429 Ave neighs/atom = 125.31360 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.889 | 7.889 | 7.889 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -6054.269 0 -6054.269 -4020.3214 15055.633 64 0 -6054.2803 0 -6054.2803 -2599.449 15044.005 Loop time of 0.119518 on 1 procs for 2 steps with 1368 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 = -6054.26897610264 -6054.27932187813 -6054.2802986123 Force two-norm initial, final = 27.025105 0.27149629 Force max component initial, final = 26.492585 0.043412535 Final line search alpha, max atom move = 0.00014983222 6.5045965e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11772 | 0.11772 | 0.11772 | 0.0 | 98.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035642 | 0.00035642 | 0.00035642 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001442 | | | 1.21 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9963.00 ave 9963 max 9963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 171640.0 ave 171640 max 171640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171640 Ave neighs/atom = 125.46784 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 = 8 21 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) = 7.521 | 7.521 | 7.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6054.2803 0 -6054.2803 -2599.449 Loop time of 2.184e-06 on 1 procs for 0 steps with 1368 atoms 137.4% 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 | | 2.184e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9963.00 ave 9963 max 9963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 171640.0 ave 171640 max 171640 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 = 171640 Ave neighs/atom = 125.46784 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) = 7.521 | 7.521 | 7.521 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 -6054.2803 -6054.2803 32.68352 92.440686 4.9793367 -2599.449 -2599.449 -2.3156585 -7794.7339 -1.297439 2.3328191 926.81368 Loop time of 4.507e-06 on 1 procs for 0 steps with 1368 atoms 221.9% 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 | | 4.507e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9963.00 ave 9963 max 9963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 171640.0 ave 171640 max 171640 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 343280.0 ave 343280 max 343280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 343280 Ave neighs/atom = 250.93567 Neighbor list builds = 0 Dangerous builds = 0 1368 -6054.2802986123 eV 2.33281911133389 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03