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 (24.908154 49.816307 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4676435 5.4676435 3.8900001 Created 328 atoms using lattice units in orthogonal box = (0 -49.816307 0) to (24.908154 49.816307 3.8900001) create_atoms CPU = 0.001 seconds 328 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4676435 5.4676435 3.8900001 Created 330 atoms using lattice units in orthogonal box = (0 -49.816307 0) to (24.908154 49.816307 3.8900001) create_atoms CPU = 0.000 seconds 330 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 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 0 atoms, new total = 658 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 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) = 7.185 | 7.185 | 7.185 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1947.5496 0 -1947.5496 214505.01 79 0 -2550.5081 0 -2550.5081 13346.706 Loop time of 0.52178 on 1 procs for 79 steps with 658 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 = -1947.54960946626 -2550.50583507394 -2550.50806014339 Force two-norm initial, final = 815.87073 0.19227132 Force max component initial, final = 188.48299 0.048892877 Final line search alpha, max atom move = 1 0.048892877 Iterations, force evaluations = 79 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.51511 | 0.51511 | 0.51511 | 0.0 | 98.72 Neigh | 0.0014759 | 0.0014759 | 0.0014759 | 0.0 | 0.28 Comm | 0.0036111 | 0.0036111 | 0.0036111 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001586 | | | 0.30 Nlocal: 658 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6742 ave 6742 max 6742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65478 ave 65478 max 65478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65478 Ave neighs/atom = 99.510638 Neighbor list builds = 1 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 : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.19 | 7.19 | 7.19 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -2550.5081 0 -2550.5081 13346.706 9653.675 86 0 -2550.8965 0 -2550.8965 -6.64766 9716.6366 Loop time of 0.036246 on 1 procs for 7 steps with 658 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 = -2550.50806014339 -2550.89642146511 -2550.89645023654 Force two-norm initial, final = 147.86205 0.29604115 Force max component initial, final = 116.81724 0.075333012 Final line search alpha, max atom move = 0.0010474279 7.8905896e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.035181 | 0.035181 | 0.035181 | 0.0 | 97.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024682 | 0.00024682 | 0.00024682 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008182 | | | 2.26 Nlocal: 658 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7298 ave 7298 max 7298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65524 ave 65524 max 65524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65524 Ave neighs/atom = 99.580547 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 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) = 6.821 | 6.821 | 6.821 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2550.8965 0 -2550.8965 -6.64766 Loop time of 6.81e-07 on 1 procs for 0 steps with 658 atoms 146.8% 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 | | 6.81e-07 | | |100.00 Nlocal: 658 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7304 ave 7304 max 7304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65418 ave 65418 max 65418 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 = 65418 Ave neighs/atom = 99.419453 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) = 6.821 | 6.821 | 6.821 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 -2550.8965 -2550.8965 24.872381 100.23024 3.8976232 -6.64766 -6.64766 -3.8293798 -5.6223976 -10.491203 2.5108382 183.11484 Loop time of 4.81e-07 on 1 procs for 0 steps with 658 atoms 415.8% 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 | | 4.81e-07 | | |100.00 Nlocal: 658 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7304 ave 7304 max 7304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65418 ave 65418 max 65418 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 130836 ave 130836 max 130836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130836 Ave neighs/atom = 198.83891 Neighbor list builds = 0 Dangerous builds = 0 658 -2550.89645023654 eV 2.51083816087758 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00