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 -74.420083 0) to (42.966455 74.420083 6.7376777) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.339313 5.6933397 6.7376777 Created 1464 atoms using lattice units in orthogonal box = (0 -74.420083 0) to (42.966455 74.420083 6.7376777) create_atoms CPU = 0.001 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.339313 5.6933397 6.7376777 Created 1466 atoms using lattice units in orthogonal box = (0 -74.420083 0) to (42.966455 74.420083 6.7376777) create_atoms CPU = 0.001 seconds 1466 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 = 10 34 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 = 2928 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 = 10 34 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) = 15.18 | 15.18 | 15.18 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9527.5171 0 -9527.5171 123916.05 290 0 -11353.145 0 -11353.145 6153.0372 Loop time of 8.43212 on 1 procs for 290 steps with 2928 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9527.51708031921 -11353.1342361459 -11353.1450312632 Force two-norm initial, final = 1517.2862 0.46260247 Force max component initial, final = 340.3539 0.13113831 Final line search alpha, max atom move = 0.6844989 0.089764027 Iterations, force evaluations = 290 546 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.3058 | 8.3058 | 8.3058 | 0.0 | 98.50 Neigh | 0.074131 | 0.074131 | 0.074131 | 0.0 | 0.88 Comm | 0.029326 | 0.029326 | 0.029326 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02287 | | | 0.27 Nlocal: 2928 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14034 ave 14034 max 14034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291544 ave 291544 max 291544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291544 Ave neighs/atom = 99.571038 Neighbor list builds = 11 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 : 290 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.18 | 15.18 | 15.18 Mbytes Step Temp E_pair E_mol TotEng Press Volume 290 0 -11353.145 0 -11353.145 6153.0372 43088.354 294 0 -11353.492 0 -11353.492 56.744546 43220.429 Loop time of 0.107783 on 1 procs for 4 steps with 2928 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 = -11353.1450312632 -11353.4919160685 -11353.492013615 Force two-norm initial, final = 297.17689 2.9966626 Force max component initial, final = 225.40374 2.3295602 Final line search alpha, max atom move = 0.00030697192 0.00071510958 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10609 | 0.10609 | 0.10609 | 0.0 | 98.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034305 | 0.00034305 | 0.00034305 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001351 | | | 1.25 Nlocal: 2928 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14028 ave 14028 max 14028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291562 ave 291562 max 291562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291562 Ave neighs/atom = 99.577186 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 = 10 34 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) = 14.07 | 14.07 | 14.07 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11353.492 0 -11353.492 56.744546 Loop time of 7.01e-07 on 1 procs for 0 steps with 2928 atoms 142.7% 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 | | 7.01e-07 | | |100.00 Nlocal: 2928 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14028 ave 14028 max 14028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291438 ave 291438 max 291438 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 = 291438 Ave neighs/atom = 99.534836 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) = 14.07 | 14.07 | 14.07 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 -11353.492 -11353.492 42.945198 149.25336 6.7429563 56.744546 56.744546 18.817804 86.596273 64.819561 2.5087973 1308.7394 Loop time of 5.51e-07 on 1 procs for 0 steps with 2928 atoms 363.0% 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 | | 5.51e-07 | | |100.00 Nlocal: 2928 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14028 ave 14028 max 14028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291438 ave 291438 max 291438 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 582876 ave 582876 max 582876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 582876 Ave neighs/atom = 199.06967 Neighbor list builds = 0 Dangerous builds = 0 2928 -11353.492013615 eV 2.50879725433581 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08