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 -53.478659 0) to (14.555047 53.478659 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2378775 5.9420732 6.3523435 Created 503 atoms using lattice units in orthogonal box = (0 -53.478659 0) to (14.555047 53.478659 9.5285152) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2378775 5.9420732 6.3523435 Created 507 atoms using lattice units in orthogonal box = (0 -53.478659 0) to (14.555047 53.478659 9.5285152) create_atoms CPU = 0.000 seconds 507 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 = 4 25 3 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 = 1008 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 = 4 25 3 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) = 7.8 | 7.8 | 7.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2774.5854 0 -2774.5854 177575.08 95 0 -3904.9299 0 -3904.9299 8482.3094 Loop time of 0.988311 on 1 procs for 95 steps with 1008 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 = -2774.5854311276 -3904.92617210666 -3904.92987609711 Force two-norm initial, final = 1320.7993 0.21799581 Force max component initial, final = 222.06327 0.034963197 Final line search alpha, max atom move = 1 0.034963197 Iterations, force evaluations = 95 183 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.97662 | 0.97662 | 0.97662 | 0.0 | 98.82 Neigh | 0.0046921 | 0.0046921 | 0.0046921 | 0.0 | 0.47 Comm | 0.0042089 | 0.0042089 | 0.0042089 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002787 | | | 0.28 Nlocal: 1008 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6406 ave 6406 max 6406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100512 ave 100512 max 100512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100512 Ave neighs/atom = 99.714286 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 : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.801 | 7.801 | 7.801 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -3904.9299 0 -3904.9299 8482.3094 14833.696 101 0 -3905.2112 0 -3905.2112 -75.30827 14896.679 Loop time of 0.048118 on 1 procs for 6 steps with 1008 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 = -3904.92987609711 -3905.20785530819 -3905.21117938043 Force two-norm initial, final = 145.39948 1.5066345 Force max component initial, final = 112.33308 1.3328534 Final line search alpha, max atom move = 6.6992257e-05 8.9290857e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.047162 | 0.047162 | 0.047162 | 0.0 | 98.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019679 | 0.00019679 | 0.00019679 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007594 | | | 1.58 Nlocal: 1008 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6557 ave 6557 max 6557 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100493 ave 100493 max 100493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100493 Ave neighs/atom = 99.695437 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 = 4 25 3 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) = 7.433 | 7.433 | 7.433 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3905.2112 0 -3905.2112 -75.30827 Loop time of 4.21e-07 on 1 procs for 0 steps with 1008 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: 1008 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6557 ave 6557 max 6557 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100403 ave 100403 max 100403 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 = 100403 Ave neighs/atom = 99.606151 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) = 7.433 | 7.433 | 7.433 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 -3905.2112 -3905.2112 14.579338 107.44744 9.5094541 -75.30827 -75.30827 -143.59109 -67.154648 -15.179075 2.5276355 479.31011 Loop time of 6.51e-07 on 1 procs for 0 steps with 1008 atoms 153.6% 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 | | 6.51e-07 | | |100.00 Nlocal: 1008 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6557 ave 6557 max 6557 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100403 ave 100403 max 100403 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 200806 ave 200806 max 200806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200806 Ave neighs/atom = 199.2123 Neighbor list builds = 0 Dangerous builds = 0 1008 -3905.21117938043 eV 2.52763548388487 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01