LAMMPS (30 Jul 2021) 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 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created orthogonal box = (0.0000000 -63.431989 0.0000000) to (44.853190 63.431989 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0911739 5.8733323 4.9836877 Created 1295 atoms using lattice units in orthogonal box = (0.0000000 -63.431989 0.0000000) to (44.853190 63.431989 4.9836877) create_atoms CPU = 0.004 seconds 1295 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0911739 5.8733323 4.9836877 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -63.431989 0.0000000) to (44.853190 63.431989 4.9836877) create_atoms CPU = 0.004 seconds 1299 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 = 11 29 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 10 atoms, new total = 2584 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:189) 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 = 11 29 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) = 15.48 | 15.48 | 15.48 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9522.3658 0 -9522.3658 123207.62 46 0 -11445.173 0 -11445.173 -467.8216 Loop time of 3.70239 on 1 procs for 46 steps with 2584 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9522.36582675434 -11445.1628221234 -11445.1729543627 Force two-norm initial, final = 2081.3104 0.38231756 Force max component initial, final = 400.96847 0.059859473 Final line search alpha, max atom move = 1.0000000 0.059859473 Iterations, force evaluations = 46 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6337 | 3.6337 | 3.6337 | 0.0 | 98.14 Neigh | 0.036632 | 0.036632 | 0.036632 | 0.0 | 0.99 Comm | 0.018349 | 0.018349 | 0.018349 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01372 | | | 0.37 Nlocal: 2584.00 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16965.0 ave 16965 max 16965 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 324126.0 ave 324126 max 324126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 324126 Ave neighs/atom = 125.43576 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.49 | 15.49 | 15.49 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -11445.173 0 -11445.173 -467.8216 28358.449 48 0 -11445.189 0 -11445.189 -4.4691253 28351.303 Loop time of 0.24978 on 1 procs for 2 steps with 2584 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11445.1729543627 -11445.187486399 -11445.1885471733 Force two-norm initial, final = 39.005846 0.42265405 Force max component initial, final = 26.751007 0.14810284 Final line search alpha, max atom move = 7.3584091e-05 1.0898013e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24628 | 0.24628 | 0.24628 | 0.0 | 98.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067973 | 0.00067973 | 0.00067973 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002821 | | | 1.13 Nlocal: 2584.00 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16945.0 ave 16945 max 16945 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 323900.0 ave 323900 max 323900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 323900 Ave neighs/atom = 125.34830 Neighbor list builds = 0 Dangerous builds = 0 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 = 11 29 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) = 14.37 | 14.37 | 14.37 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11445.189 0 -11445.189 -4.4691253 Loop time of 2.237e-06 on 1 procs for 0 steps with 2584 atoms 178.8% 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 | | 2.237e-06 | | |100.00 Nlocal: 2584.00 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16925.0 ave 16925 max 16925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 323956.0 ave 323956 max 323956 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 323956 Ave neighs/atom = 125.36997 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.37 | 14.37 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 -11445.189 -11445.189 44.878352 126.80156 4.9820896 -4.4691253 -4.4691253 -1.2481416 -8.3654053 -3.793829 2.3411291 1230.0712 Loop time of 1.993e-06 on 1 procs for 0 steps with 2584 atoms 301.1% 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 | | 1.993e-06 | | |100.00 Nlocal: 2584.00 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16925.0 ave 16925 max 16925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 323956.0 ave 323956 max 323956 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 647912.0 ave 647912 max 647912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 647912 Ave neighs/atom = 250.73994 Neighbor list builds = 0 Dangerous builds = 0 2584 -11445.1885471733 eV 2.34112906093323 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04