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 -50.868351 0) to (23.979571 50.868351 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0483307 6.2469905 5.5012908 Created 452 atoms using lattice units in orthogonal box = (0 -50.868351 0) to (23.979571 50.868351 5.5012908) create_atoms CPU = 0.001 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0483307 6.2469905 5.5012908 Created 460 atoms using lattice units in orthogonal box = (0 -50.868351 0) to (23.979571 50.868351 5.5012908) create_atoms CPU = 0.000 seconds 460 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 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 0 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 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) = 7.303 | 7.303 | 7.303 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1525.3855 0 -1525.3855 249990.84 111 0 -3532.4846 0 -3532.4846 9465.0377 Loop time of 0.991024 on 1 procs for 111 steps with 912 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 = -1525.38545708154 -3532.48206008339 -3532.48463064507 Force two-norm initial, final = 1912.7262 0.18203166 Force max component initial, final = 304.60948 0.026347767 Final line search alpha, max atom move = 1 0.026347767 Iterations, force evaluations = 111 206 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9785 | 0.9785 | 0.9785 | 0.0 | 98.74 Neigh | 0.0043183 | 0.0043183 | 0.0043183 | 0.0 | 0.44 Comm | 0.0051494 | 0.0051494 | 0.0051494 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003052 | | | 0.31 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6947 ave 6947 max 6947 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90796 ave 90796 max 90796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90796 Ave neighs/atom = 99.557018 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 : 111 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.303 | 7.303 | 7.303 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -3532.4846 0 -3532.4846 9465.0377 13420.963 116 0 -3532.7432 0 -3532.7432 -114.71084 13485.477 Loop time of 0.0335337 on 1 procs for 5 steps with 912 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 = -3532.48463064507 -3532.74023127896 -3532.74322569927 Force two-norm initial, final = 143.6494 2.3038095 Force max component initial, final = 111.23452 2.0387298 Final line search alpha, max atom move = 6.0715451e-05 0.0001237824 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.032786 | 0.032786 | 0.032786 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016332 | 0.00016332 | 0.00016332 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005845 | | | 1.74 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6939 ave 6939 max 6939 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90806 ave 90806 max 90806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90806 Ave neighs/atom = 99.567982 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 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) = 6.935 | 6.935 | 6.935 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3532.7432 0 -3532.7432 -114.71084 Loop time of 7.22e-07 on 1 procs for 0 steps with 912 atoms 138.5% 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 | | 7.22e-07 | | |100.00 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6939 ave 6939 max 6939 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90740 ave 90740 max 90740 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 = 90740 Ave neighs/atom = 99.495614 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) = 6.935 | 6.935 | 6.935 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 -3532.7432 -3532.7432 24.006639 102.16122 5.4985589 -114.71084 -114.71084 -242.48991 19.350195 -120.9928 2.5849895 670.44231 Loop time of 5.21e-07 on 1 procs for 0 steps with 912 atoms 383.9% 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 | | 5.21e-07 | | |100.00 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6939 ave 6939 max 6939 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90740 ave 90740 max 90740 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 181480 ave 181480 max 181480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181480 Ave neighs/atom = 198.99123 Neighbor list builds = 0 Dangerous builds = 0 912 -3532.74322569927 eV 2.58498949152902 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01