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 -37.464151 0.0000000) to (37.460627 37.464151 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9726497 4.9726497 3.5239994 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -37.464151 0.0000000) to (37.460627 37.464151 3.5239994) create_atoms CPU = 0.002 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9726497 4.9726497 3.5239994 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -37.464151 0.0000000) to (37.460627 37.464151 3.5239994) create_atoms CPU = 0.002 seconds 454 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 = 9 17 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 8 atoms, new total = 900 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 = 9 17 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) = 7.684 | 7.684 | 7.684 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3919.0822 0 -3919.0822 39258.088 63 0 -3985.0223 0 -3985.0223 -2226.9875 Loop time of 4.09588 on 1 procs for 63 steps with 900 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 = -3919.08223925606 -3985.01871182309 -3985.02231790109 Force two-norm initial, final = 76.289330 0.18564991 Force max component initial, final = 22.084346 0.024589199 Final line search alpha, max atom move = 1.0000000 0.024589199 Iterations, force evaluations = 63 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0418 | 4.0418 | 4.0418 | 0.0 | 98.68 Neigh | 0.014181 | 0.014181 | 0.014181 | 0.0 | 0.35 Comm | 0.024492 | 0.024492 | 0.024492 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01539 | | | 0.38 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9787.00 ave 9787 max 9787 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115458.0 ave 115458 max 115458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115458 Ave neighs/atom = 128.28667 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.686 | 7.686 | 7.686 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -3985.0223 0 -3985.0223 -2226.9875 9891.3773 65 0 -3985.0329 0 -3985.0329 -1024.8008 9884.7752 Loop time of 0.187232 on 1 procs for 2 steps with 900 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3985.02231790109 -3985.03050784145 -3985.03289871239 Force two-norm initial, final = 19.223065 0.19351735 Force max component initial, final = 19.036993 0.023900271 Final line search alpha, max atom move = 0.00015013555 3.5882804e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18352 | 0.18352 | 0.18352 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010431 | 0.0010431 | 0.0010431 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002665 | | | 1.42 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9743.00 ave 9743 max 9743 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114756.0 ave 114756 max 114756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114756 Ave neighs/atom = 127.50667 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 = 9 17 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) = 7.317 | 7.317 | 7.317 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3985.0329 0 -3985.0329 -1024.8008 Loop time of 7.106e-06 on 1 procs for 0 steps with 900 atoms 182.9% 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 | | 7.106e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9743.00 ave 9743 max 9743 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114972.0 ave 114972 max 114972 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 = 114972 Ave neighs/atom = 127.74667 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) = 7.317 | 7.317 | 7.317 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 -3985.0329 -3985.0329 37.416384 74.928303 3.5258114 -1024.8008 -1024.8008 3.7746482 -3079.9946 1.8175677 2.2565455 136.34169 Loop time of 7.908e-06 on 1 procs for 0 steps with 900 atoms 215.0% 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 | | 7.908e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9743.00 ave 9743 max 9743 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114972.0 ave 114972 max 114972 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 229944.0 ave 229944 max 229944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229944 Ave neighs/atom = 255.49333 Neighbor list builds = 0 Dangerous builds = 0 900 -3985.03289871239 eV 2.25654552025425 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04