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 -41.533835 0) to (23.979571 41.533835 6.7376777) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3104134 5.8293102 6.7376777 Created 456 atoms using lattice units in orthogonal box = (0 -41.533835 0) to (23.979571 41.533835 6.7376777) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3104134 5.8293102 6.7376777 Created 458 atoms using lattice units in orthogonal box = (0 -41.533835 0) to (23.979571 41.533835 6.7376777) create_atoms CPU = 0.000 seconds 458 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 = 6 19 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 2 atoms, new total = 912 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 = 6 19 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) = 7.314 | 7.314 | 7.314 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2699.6639 0 -2699.6639 183017.8 103 0 -3527.434 0 -3527.434 10725.823 Loop time of 0.966371 on 1 procs for 103 steps with 912 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2699.66394143705 -3527.43044885094 -3527.43395292248 Force two-norm initial, final = 1047.6863 0.22261072 Force max component initial, final = 285.30855 0.040359841 Final line search alpha, max atom move = 1 0.040359841 Iterations, force evaluations = 103 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94984 | 0.94984 | 0.94984 | 0.0 | 98.29 Neigh | 0.0088715 | 0.0088715 | 0.0088715 | 0.0 | 0.92 Comm | 0.0048246 | 0.0048246 | 0.0048246 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002832 | | | 0.29 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6178 ave 6178 max 6178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90562 ave 90562 max 90562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90562 Ave neighs/atom = 99.300439 Neighbor list builds = 4 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 : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.314 | 7.314 | 7.314 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -3527.434 0 -3527.434 10725.823 13420.963 108 0 -3527.7062 0 -3527.7062 -16.581294 13492.789 Loop time of 0.0443362 on 1 procs for 5 steps with 912 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 = -3527.43395292248 -3527.70619064496 -3527.70623768828 Force two-norm initial, final = 158.25534 0.37174766 Force max component initial, final = 108.27121 0.21051451 Final line search alpha, max atom move = 0.0014519881 0.00030566456 Iterations, force evaluations = 5 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.043451 | 0.043451 | 0.043451 | 0.0 | 98.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019078 | 0.00019078 | 0.00019078 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006941 | | | 1.57 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6183 ave 6183 max 6183 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90580 ave 90580 max 90580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90580 Ave neighs/atom = 99.320175 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 = 6 19 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) = 6.945 | 6.945 | 6.945 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3527.7062 0 -3527.7062 -16.581294 Loop time of 4.71e-07 on 1 procs for 0 steps with 912 atoms 212.3% 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 | | 4.71e-07 | | |100.00 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6179 ave 6179 max 6179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90466 ave 90466 max 90466 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 = 90466 Ave neighs/atom = 99.195175 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) = 6.945 | 6.945 | 6.945 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 -3527.7062 -3527.7062 24.025489 83.350784 6.7378262 -16.581294 -16.581294 -11.64965 -25.082355 -13.011876 2.5476577 750.28583 Loop time of 6.31e-07 on 1 procs for 0 steps with 912 atoms 317.0% 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 | | 6.31e-07 | | |100.00 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6179 ave 6179 max 6179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90466 ave 90466 max 90466 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180932 ave 180932 max 180932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180932 Ave neighs/atom = 198.39035 Neighbor list builds = 0 Dangerous builds = 0 912 -3527.70623768828 eV 2.54765770272205 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01