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 -44.575458 0.0000000) to (11.143865 44.575458 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4575458 4.4575458 3.5239994 Created 160 atoms using lattice units in orthogonal box = (0.0000000 -44.575458 0.0000000) to (11.143865 44.575458 3.5239994) create_atoms CPU = 0.001 seconds 160 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4575458 4.4575458 3.5239994 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -44.575458 0.0000000) to (11.143865 44.575458 3.5239994) create_atoms CPU = 0.000 seconds 162 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 21 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 2 atoms, new total = 320 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 21 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) = 7.088 | 7.088 | 7.088 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1386.3993 0 -1386.3993 53459.963 42 0 -1414.5672 0 -1414.5672 11951.077 Loop time of 0.51535 on 1 procs for 42 steps with 320 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1386.39930370046 -1414.56593950445 -1414.56722380536 Force two-norm initial, final = 111.83167 0.12178262 Force max component initial, final = 39.473097 0.017338902 Final line search alpha, max atom move = 1.0000000 0.017338902 Iterations, force evaluations = 42 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50897 | 0.50897 | 0.50897 | 0.0 | 98.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043316 | 0.0043316 | 0.0043316 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002049 | | | 0.40 Nlocal: 320.000 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5638.00 ave 5638 max 5638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39982.0 ave 39982 max 39982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39982 Ave neighs/atom = 124.94375 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.088 | 7.088 | 7.088 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -1414.5672 0 -1414.5672 11951.077 3501.0431 51 0 -1414.7496 0 -1414.7496 8.4028605 3523.5777 Loop time of 0.0664123 on 1 procs for 9 steps with 320 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 = -1414.56722380536 -1414.74835945814 -1414.74958174157 Force two-norm initial, final = 51.839758 0.60017898 Force max component initial, final = 46.647253 0.42560145 Final line search alpha, max atom move = 0.00053949334 0.00022960915 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.064244 | 0.064244 | 0.064244 | 0.0 | 96.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044791 | 0.00044791 | 0.00044791 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001721 | | | 2.59 Nlocal: 320.000 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5638.00 ave 5638 max 5638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40020.0 ave 40020 max 40020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40020 Ave neighs/atom = 125.06250 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 21 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) = 6.720 | 6.720 | 6.720 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1414.7496 0 -1414.7496 8.4028605 Loop time of 1.791e-06 on 1 procs for 0 steps with 320 atoms 167.5% 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 | | 1.791e-06 | | |100.00 Nlocal: 320.000 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5638.00 ave 5638 max 5638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39828.0 ave 39828 max 39828 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 = 39828 Ave neighs/atom = 124.46250 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) = 6.720 | 6.720 | 6.720 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 -1414.7496 -1414.7496 11.134075 89.927619 3.5191405 8.4028605 8.4028605 193.35167 -86.815089 -81.327999 2.285769 165.90287 Loop time of 2.163e-06 on 1 procs for 0 steps with 320 atoms 138.7% 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 | | 2.163e-06 | | |100.00 Nlocal: 320.000 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5638.00 ave 5638 max 5638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39828.0 ave 39828 max 39828 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 79656.0 ave 79656 max 79656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79656 Ave neighs/atom = 248.92500 Neighbor list builds = 0 Dangerous builds = 0 320 -1414.74958174157 eV 2.28576898854494 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00