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 -55.050154 0.0000000) to (27.523315 55.050154 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9632208 4.9632208 3.5239994 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.050154 0.0000000) to (27.523315 55.050154 3.5239994) create_atoms CPU = 0.003 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9632208 4.9632208 3.5239994 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.050154 0.0000000) to (27.523315 55.050154 3.5239994) create_atoms CPU = 0.002 seconds 490 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 = 7 25 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 = 972 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 = 7 25 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) = 7.748 | 7.748 | 7.748 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4267.036 0 -4267.036 19776.588 69 0 -4306.0967 0 -4306.0967 -2544.126 Loop time of 4.92782 on 1 procs for 69 steps with 972 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 = -4267.03602917186 -4306.09350048399 -4306.0967491439 Force two-norm initial, final = 53.971448 0.22992862 Force max component initial, final = 17.798341 0.054290524 Final line search alpha, max atom move = 1.0000000 0.054290524 Iterations, force evaluations = 69 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8637 | 4.8637 | 4.8637 | 0.0 | 98.70 Neigh | 0.01447 | 0.01447 | 0.01447 | 0.0 | 0.29 Comm | 0.031655 | 0.031655 | 0.031655 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01802 | | | 0.37 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11101.0 ave 11101 max 11101 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122956.0 ave 122956 max 122956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122956 Ave neighs/atom = 126.49794 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 : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.750 | 7.750 | 7.750 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -4306.0967 0 -4306.0967 -2544.126 10678.865 71 0 -4306.1047 0 -4306.1047 -979.12883 10669.771 Loop time of 0.19898 on 1 procs for 2 steps with 972 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 = -4306.0967491439 -4306.10406128923 -4306.10466572831 Force two-norm initial, final = 20.445507 0.23229486 Force max component initial, final = 18.575669 0.055680868 Final line search alpha, max atom move = 0.00034949848 1.9460379e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19489 | 0.19489 | 0.19489 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011537 | 0.0011537 | 0.0011537 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002935 | | | 1.47 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11078.0 ave 11078 max 11078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122492.0 ave 122492 max 122492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122492 Ave neighs/atom = 126.02058 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 = 7 25 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) = 7.381 | 7.381 | 7.381 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4306.1047 0 -4306.1047 -979.12883 Loop time of 6.375e-06 on 1 procs for 0 steps with 972 atoms 203.9% 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 | | 6.375e-06 | | |100.00 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11092.0 ave 11092 max 11092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122564.0 ave 122564 max 122564 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 = 122564 Ave neighs/atom = 126.09465 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) = 7.381 | 7.381 | 7.381 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 -4306.1047 -4306.1047 27.499968 110.10031 3.5239878 -979.12883 -979.12883 -1.9001844 -2932.7382 -2.7481269 2.2564913 148.26346 Loop time of 6.826e-06 on 1 procs for 0 steps with 972 atoms 322.3% 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 | | 6.826e-06 | | |100.00 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11092.0 ave 11092 max 11092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122564.0 ave 122564 max 122564 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 245128.0 ave 245128 max 245128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245128 Ave neighs/atom = 252.18930 Neighbor list builds = 0 Dangerous builds = 0 972 -4306.10466572831 eV 2.25649127848303 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05