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 -44.856714 0.0000000) to (31.715995 44.856714 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8733323 6.0911739 4.9836877 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -44.856714 0.0000000) to (31.715995 44.856714 4.9836877) create_atoms CPU = 0.002 seconds 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8733323 6.0911739 4.9836877 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -44.856714 0.0000000) to (31.715995 44.856714 4.9836877) create_atoms CPU = 0.001 seconds 650 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 12 atoms, new total = 1288 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) = 7.868 | 7.868 | 7.868 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5652.837 0 -5652.837 19055.833 58 0 -5705.7253 0 -5705.7253 -6528.2485 Loop time of 2.36567 on 1 procs for 58 steps with 1288 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 = -5652.83700786612 -5705.72011731824 -5705.7252940701 Force two-norm initial, final = 108.07482 0.24070495 Force max component initial, final = 34.364481 0.041650657 Final line search alpha, max atom move = 1.0000000 0.041650657 Iterations, force evaluations = 58 105 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3408 | 2.3408 | 2.3408 | 0.0 | 98.95 Neigh | 0.0075297 | 0.0075297 | 0.0075297 | 0.0 | 0.32 Comm | 0.010179 | 0.010179 | 0.010179 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007134 | | | 0.30 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10186.0 ave 10186 max 10186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162840.0 ave 162840 max 162840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162840 Ave neighs/atom = 126.42857 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) = 7.868 | 7.868 | 7.868 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -5705.7253 0 -5705.7253 -6528.2485 14180.339 60 0 -5705.7486 0 -5705.7486 -3744.9422 14158.837 Loop time of 0.111937 on 1 procs for 2 steps with 1288 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 = -5705.72529407011 -5705.74854664537 -5705.74855762191 Force two-norm initial, final = 43.302268 0.27444858 Force max component initial, final = 31.578531 0.11483468 Final line search alpha, max atom move = 0.0024825131 0.00028507859 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11019 | 0.11019 | 0.11019 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035568 | 0.00035568 | 0.00035568 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001388 | | | 1.24 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10169.0 ave 10169 max 10169 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162382.0 ave 162382 max 162382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162382 Ave neighs/atom = 126.07298 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) = 7.499 | 7.499 | 7.499 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5705.7486 0 -5705.7486 -3744.9422 Loop time of 1.983e-06 on 1 procs for 0 steps with 1288 atoms 151.3% 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 | | 1.983e-06 | | |100.00 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10169.0 ave 10169 max 10169 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162552.0 ave 162552 max 162552 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 = 162552 Ave neighs/atom = 126.20497 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) = 7.499 | 7.499 | 7.499 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 -5705.7486 -5705.7486 31.690419 89.713427 4.980147 -3744.9422 -3744.9422 12.983909 -11242.999 -4.8118095 2.3136178 451.79953 Loop time of 1.915e-06 on 1 procs for 0 steps with 1288 atoms 261.1% 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 | | 1.915e-06 | | |100.00 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10169.0 ave 10169 max 10169 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162552.0 ave 162552 max 162552 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 325104.0 ave 325104 max 325104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 325104 Ave neighs/atom = 252.40994 Neighbor list builds = 0 Dangerous builds = 0 1288 -5705.74855762191 eV 2.31361775792664 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02