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 -39.873026 0.0000000) to (17.264001 39.873026 6.1037460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7546669 4.9836877 6.1037460 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -39.873026 0.0000000) to (17.264001 39.873026 6.1037460) create_atoms CPU = 0.003 seconds 396 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7546669 4.9836877 6.1037460 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -39.873026 0.0000000) to (17.264001 39.873026 6.1037460) create_atoms CPU = 0.002 seconds 396 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 = 4 18 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 28 atoms, new total = 764 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 = 4 18 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) = 7.333 | 7.333 | 7.333 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3238.8431 0 -3238.8431 108039.81 90 0 -3377.4515 0 -3377.4515 612.77616 Loop time of 5.10653 on 1 procs for 90 steps with 764 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3238.84306203772 -3377.44831705626 -3377.45146697418 Force two-norm initial, final = 225.13086 0.19357336 Force max component initial, final = 39.665461 0.034199993 Final line search alpha, max atom move = 1.0000000 0.034199993 Iterations, force evaluations = 90 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.038 | 5.038 | 5.038 | 0.0 | 98.66 Neigh | 0.022593 | 0.022593 | 0.022593 | 0.0 | 0.44 Comm | 0.026697 | 0.026697 | 0.026697 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0192 | | | 0.38 Nlocal: 764.000 ave 764 max 764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6788.00 ave 6788 max 6788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96079.0 ave 96079 max 96079 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96079 Ave neighs/atom = 125.75785 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 : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.333 | 7.333 | 7.333 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -3377.4515 0 -3377.4515 612.77616 8403.2462 92 0 -3377.4783 0 -3377.4783 691.07425 8402.8437 Loop time of 0.124572 on 1 procs for 2 steps with 764 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3377.45146697418 -3377.4752734646 -3377.47834914932 Force two-norm initial, final = 26.253141 0.51562522 Force max component initial, final = 19.311340 0.37964226 Final line search alpha, max atom move = 0.00014216357 5.3971298e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12241 | 0.12241 | 0.12241 | 0.0 | 98.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054698 | 0.00054698 | 0.00054698 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001612 | | | 1.29 Nlocal: 764.000 ave 764 max 764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6728.00 ave 6728 max 6728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96140.0 ave 96140 max 96140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96140 Ave neighs/atom = 125.83770 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 = 4 18 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) = 6.962 | 6.962 | 6.962 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3377.4783 0 -3377.4783 691.07425 Loop time of 6.565e-06 on 1 procs for 0 steps with 764 atoms 182.8% 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 | | 6.565e-06 | | |100.00 Nlocal: 764.000 ave 764 max 764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6732.00 ave 6732 max 6732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96145.0 ave 96145 max 96145 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 = 96145 Ave neighs/atom = 125.84424 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) = 6.962 | 6.962 | 6.962 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 -3377.4783 -3377.4783 17.238663 79.746052 6.1124244 691.07425 691.07425 53.603452 1947.1297 72.489594 2.3542792 459.76133 Loop time of 8.099e-06 on 1 procs for 0 steps with 764 atoms 580.3% 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 | | 8.099e-06 | | |100.00 Nlocal: 764.000 ave 764 max 764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6732.00 ave 6732 max 6732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96145.0 ave 96145 max 96145 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 192290.0 ave 192290 max 192290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192290 Ave neighs/atom = 251.68848 Neighbor list builds = 0 Dangerous builds = 0 764 -3377.47834914932 eV 2.35427924137189 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05