LAMMPS (23 Jun 2022) 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 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -49.816307 0) to (35.225449 49.816307 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.014101 6.6826754 5.5012908 Created 656 atoms using lattice units in orthogonal box = (0 -49.816307 0) to (35.225449 49.816307 5.5012908) create_atoms CPU = 0.001 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.014101 6.6826754 5.5012908 Created 660 atoms using lattice units in orthogonal box = (0 -49.816307 0) to (35.225449 49.816307 5.5012908) create_atoms CPU = 0.001 seconds 660 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 = 8 23 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 4 atoms, new total = 1312 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:187) 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 = 8 23 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) = 7.826 | 7.826 | 7.826 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3918.1212 0 -3918.1212 141146.94 96 0 -5086.5459 0 -5086.5459 6506.491 Loop time of 1.23852 on 1 procs for 96 steps with 1312 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3918.12123710519 -5086.54197368309 -5086.54588852645 Force two-norm initial, final = 1342.7039 0.23702652 Force max component initial, final = 320.40672 0.037067892 Final line search alpha, max atom move = 1 0.037067892 Iterations, force evaluations = 96 180 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.223 | 1.223 | 1.223 | 0.0 | 98.74 Neigh | 0.0061446 | 0.0061446 | 0.0061446 | 0.0 | 0.50 Comm | 0.0056332 | 0.0056332 | 0.0056332 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003774 | | | 0.30 Nlocal: 1312 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8567 ave 8567 max 8567 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130600 ave 130600 max 130600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130600 Ave neighs/atom = 99.542683 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.826 | 7.826 | 7.826 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -5086.5459 0 -5086.5459 6506.491 19307.35 102 0 -5086.8564 0 -5086.8564 2.6059195 19368.942 Loop time of 0.0616952 on 1 procs for 6 steps with 1312 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5086.54588852646 -5086.85409014062 -5086.85642067818 Force two-norm initial, final = 157.74585 1.7852993 Force max component initial, final = 143.86645 1.4200041 Final line search alpha, max atom move = 6.474065e-05 9.1931987e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060444 | 0.060444 | 0.060444 | 0.0 | 97.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026431 | 0.00026431 | 0.00026431 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009872 | | | 1.60 Nlocal: 1312 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8571 ave 8571 max 8571 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130728 ave 130728 max 130728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130728 Ave neighs/atom = 99.640244 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) 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 = 8 23 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) = 7.457 | 7.457 | 7.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5086.8564 0 -5086.8564 2.6059195 Loop time of 4.21e-07 on 1 procs for 0 steps with 1312 atoms 237.5% 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 | | 4.21e-07 | | |100.00 Nlocal: 1312 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8547 ave 8547 max 8547 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130592 ave 130592 max 130592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130592 Ave neighs/atom = 99.536585 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.457 | 7.457 | 7.457 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 -5086.8564 -5086.8564 35.181302 100.11703 5.4990297 2.6059195 2.6059195 -77.319834 -32.275223 117.41282 2.5591964 722.7998 Loop time of 8.81e-07 on 1 procs for 0 steps with 1312 atoms 340.5% 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 | | 8.81e-07 | | |100.00 Nlocal: 1312 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8547 ave 8547 max 8547 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130592 ave 130592 max 130592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 261184 ave 261184 max 261184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261184 Ave neighs/atom = 199.07317 Neighbor list builds = 0 Dangerous builds = 0 1312 -5086.85642067818 eV 2.55919639620311 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01