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 -42.612816 0) to (8.6983046 42.612816 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2189827 5.6817088 6.3523435 Created 240 atoms using lattice units in orthogonal box = (0 -42.612816 0) to (8.6983046 42.612816 9.5285152) create_atoms CPU = 0.000 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2189827 5.6817088 6.3523435 Created 242 atoms using lattice units in orthogonal box = (0 -42.612816 0) to (8.6983046 42.612816 9.5285152) create_atoms CPU = 0.000 seconds 242 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 = 2 20 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 = 480 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 = 2 20 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) = 7.219 | 7.219 | 7.219 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1579.404 0 -1579.404 144545.75 54 0 -1856.38 0 -1856.38 12095.323 Loop time of 0.275489 on 1 procs for 54 steps with 480 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 = -1579.40398729852 -1856.37828188053 -1856.38002951276 Force two-norm initial, final = 541.40089 0.18610249 Force max component initial, final = 170.41084 0.051772669 Final line search alpha, max atom move = 1 0.051772669 Iterations, force evaluations = 54 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27313 | 0.27313 | 0.27313 | 0.0 | 99.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015929 | 0.0015929 | 0.0015929 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00077 | | | 0.28 Nlocal: 480 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4470 ave 4470 max 4470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48032 ave 48032 max 48032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48032 Ave neighs/atom = 100.06667 Neighbor list builds = 0 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.221 | 7.221 | 7.221 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -1856.38 0 -1856.38 12095.323 7063.6646 64 0 -1856.715 0 -1856.715 188.02771 7104.9734 Loop time of 0.0325821 on 1 procs for 10 steps with 480 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 = -1856.38002951276 -1856.71489817833 -1856.71503034618 Force two-norm initial, final = 101.39424 1.5751534 Force max component initial, final = 86.79703 0.92159601 Final line search alpha, max atom move = 0.0011710546 0.0010792392 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.031702 | 0.031702 | 0.031702 | 0.0 | 97.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019547 | 0.00019547 | 0.00019547 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006844 | | | 2.10 Nlocal: 480 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4725 ave 4725 max 4725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47738 ave 47738 max 47738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47738 Ave neighs/atom = 99.454167 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 = 2 20 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) = 6.853 | 6.853 | 6.853 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1856.715 0 -1856.715 188.02771 Loop time of 5.61e-07 on 1 procs for 0 steps with 480 atoms 178.3% 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 | | 5.61e-07 | | |100.00 Nlocal: 480 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4725 ave 4725 max 4725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47674 ave 47674 max 47674 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 = 47674 Ave neighs/atom = 99.320833 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) = 6.853 | 6.853 | 6.853 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 -1856.715 -1856.715 8.6879701 85.99931 9.5093136 188.02771 188.02771 175.65787 209.70714 178.71812 2.4921506 340.22258 Loop time of 4.91e-07 on 1 procs for 0 steps with 480 atoms 407.3% 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 | | 4.91e-07 | | |100.00 Nlocal: 480 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4725 ave 4725 max 4725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47674 ave 47674 max 47674 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95348 ave 95348 max 95348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95348 Ave neighs/atom = 198.64167 Neighbor list builds = 0 Dangerous builds = 0 480 -1856.71503034618 eV 2.49215056329 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00