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 -57.261737 0.0000000) to (11.687784 57.261737 8.6320004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3126290 5.2052921 5.7546669 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.261737 0.0000000) to (11.687784 57.261737 8.6320004) create_atoms CPU = 0.001 seconds 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3126290 5.2052921 5.7546669 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.261737 0.0000000) to (11.687784 57.261737 8.6320004) create_atoms CPU = 0.001 seconds 530 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 = 3 26 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 = 1048 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 = 3 26 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) = 7.992 | 7.992 | 7.992 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4611.2224 0 -4611.2224 10207.239 51 0 -4637.8056 0 -4637.8056 -5651.2129 Loop time of 1.74542 on 1 procs for 51 steps with 1048 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4611.22243285795 -4637.8015693798 -4637.8056434468 Force two-norm initial, final = 70.201812 0.23634112 Force max component initial, final = 22.923932 0.036983081 Final line search alpha, max atom move = 1.0000000 0.036983081 Iterations, force evaluations = 51 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7327 | 1.7327 | 1.7327 | 0.0 | 99.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0073853 | 0.0073853 | 0.0073853 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005309 | | | 0.30 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8446.00 ave 8446 max 8446 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129800.0 ave 129800 max 129800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129800 Ave neighs/atom = 123.85496 Neighbor list builds = 0 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 : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.992 | 7.992 | 7.992 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -4637.8056 0 -4637.8056 -5651.2129 11554.153 53 0 -4637.8531 0 -4637.8531 -1092.3464 11525.491 Loop time of 0.0724785 on 1 procs for 2 steps with 1048 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 = -4637.80564344681 -4637.84953664174 -4637.85307106774 Force two-norm initial, final = 53.851042 3.0335960 Force max component initial, final = 41.567324 2.7183198 Final line search alpha, max atom move = 7.7645879e-05 0.00021106633 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071378 | 0.071378 | 0.071378 | 0.0 | 98.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023026 | 0.00023026 | 0.00023026 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008701 | | | 1.20 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8113.00 ave 8113 max 8113 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130740.0 ave 130740 max 130740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130740 Ave neighs/atom = 124.75191 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 = 3 26 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) = 7.621 | 7.621 | 7.621 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4637.8531 0 -4637.8531 -1092.3464 Loop time of 2.283e-06 on 1 procs for 0 steps with 1048 atoms 175.2% 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 | | 2.283e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8113.00 ave 8113 max 8113 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130856.0 ave 130856 max 130856 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 = 130856 Ave neighs/atom = 124.86260 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) = 7.621 | 7.621 | 7.621 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 -4637.8531 -4637.8531 11.670891 114.52347 8.6230506 -1092.3464 -1092.3464 -183.97551 -3470.5497 377.48608 2.2261094 405.00656 Loop time of 2.231e-06 on 1 procs for 0 steps with 1048 atoms 224.1% 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 | | 2.231e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8113.00 ave 8113 max 8113 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130856.0 ave 130856 max 130856 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 261712.0 ave 261712 max 261712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261712 Ave neighs/atom = 249.72519 Neighbor list builds = 0 Dangerous builds = 0 1048 -4637.85307106774 eV 2.22610939761108 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02