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 -60.763743 0) to (30.381872 60.763743 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4786982 5.4786982 3.8900001 Created 488 atoms using lattice units in orthogonal box = (0 -60.763743 0) to (30.381872 60.763743 3.8900001) create_atoms CPU = 0.000 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4786982 5.4786982 3.8900001 Created 490 atoms using lattice units in orthogonal box = (0 -60.763743 0) to (30.381872 60.763743 3.8900001) create_atoms CPU = 0.000 seconds 490 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 = 7 28 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 = 978 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 = 7 28 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) = 7.32 | 7.32 | 7.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3183.9598 0 -3183.9598 179196.63 110 0 -3794.5691 0 -3794.5691 9267.2373 Loop time of 1.0719 on 1 procs for 110 steps with 978 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3183.9598210849 -3794.56637200785 -3794.56912526593 Force two-norm initial, final = 657.44633 0.21957022 Force max component initial, final = 124.70721 0.050902576 Final line search alpha, max atom move = 1 0.050902576 Iterations, force evaluations = 110 205 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0596 | 1.0596 | 1.0596 | 0.0 | 98.85 Neigh | 0.0022253 | 0.0022253 | 0.0022253 | 0.0 | 0.21 Comm | 0.0066316 | 0.0066316 | 0.0066316 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00345 | | | 0.32 Nlocal: 978 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8794 ave 8794 max 8794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 97454 ave 97454 max 97454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97454 Ave neighs/atom = 99.646217 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 : 110 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.321 | 7.321 | 7.321 Mbytes Step Temp E_pair E_mol TotEng Press Volume 110 0 -3794.5691 0 -3794.5691 9267.2373 14362.785 116 0 -3794.8515 0 -3794.8515 -38.014182 14428.779 Loop time of 0.04767 on 1 procs for 6 steps with 978 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3794.56912526593 -3794.8507459489 -3794.85150391691 Force two-norm initial, final = 152.63266 0.68297785 Force max component initial, final = 119.95265 0.51635233 Final line search alpha, max atom move = 0.00015438568 7.9717407e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.046476 | 0.046476 | 0.046476 | 0.0 | 97.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027239 | 0.00027239 | 0.00027239 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009217 | | | 1.93 Nlocal: 978 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8788 ave 8788 max 8788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 97422 ave 97422 max 97422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97422 Ave neighs/atom = 99.613497 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 = 7 28 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) = 6.952 | 6.952 | 6.952 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3794.8515 0 -3794.8515 -38.014182 Loop time of 5.51e-07 on 1 procs for 0 steps with 978 atoms 181.5% 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 | | 5.51e-07 | | |100.00 Nlocal: 978 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8788 ave 8788 max 8788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 97350 ave 97350 max 97350 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 = 97350 Ave neighs/atom = 99.539877 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) = 6.952 | 6.952 | 6.952 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 -3794.8515 -3794.8515 30.349512 122.0373 3.8956981 -38.014182 -38.014182 -31.337912 -57.576463 -25.12817 2.5103141 183.13865 Loop time of 4.1e-07 on 1 procs for 0 steps with 978 atoms 487.8% 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 | | 4.1e-07 | | |100.00 Nlocal: 978 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8788 ave 8788 max 8788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 97350 ave 97350 max 97350 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 194700 ave 194700 max 194700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194700 Ave neighs/atom = 199.07975 Neighbor list builds = 0 Dangerous builds = 0 978 -3794.85150391691 eV 2.51031407967159 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01