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 -49.511618 0) to (11.67 49.511618 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4833334 5.5012908 5.5012908 Created 216 atoms using lattice units in orthogonal box = (0 -49.511618 0) to (11.67 49.511618 5.5012908) create_atoms CPU = 0.000 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4833334 5.5012908 5.5012908 Created 218 atoms using lattice units in orthogonal box = (0 -49.511618 0) to (11.67 49.511618 5.5012908) create_atoms CPU = 0.000 seconds 218 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 = 3 23 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 = 432 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 = 3 23 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) = 7.142 | 7.142 | 7.142 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1427.1502 0 -1427.1502 127315.21 85 0 -1674.5026 0 -1674.5026 5905.8511 Loop time of 0.383351 on 1 procs for 85 steps with 432 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1427.15016925082 -1674.50095927106 -1674.50256407363 Force two-norm initial, final = 525.17535 0.12752615 Force max component initial, final = 165.04886 0.017108117 Final line search alpha, max atom move = 1 0.017108117 Iterations, force evaluations = 85 161 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37811 | 0.37811 | 0.37811 | 0.0 | 98.63 Neigh | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.29 Comm | 0.0028746 | 0.0028746 | 0.0028746 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001255 | | | 0.33 Nlocal: 432 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5010 ave 5010 max 5010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42962 ave 42962 max 42962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42962 Ave neighs/atom = 99.449074 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 : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.142 | 7.142 | 7.142 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -1674.5026 0 -1674.5026 5905.8511 6357.2981 89 0 -1674.5469 0 -1674.5469 155.53539 6375.6222 Loop time of 0.0167527 on 1 procs for 4 steps with 432 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1674.50256407363 -1674.54668601587 -1674.54689381462 Force two-norm initial, final = 41.613913 1.1411277 Force max component initial, final = 28.703493 0.90964848 Final line search alpha, max atom move = 0.00078597452 0.00071496053 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.01626 | 0.01626 | 0.01626 | 0.0 | 97.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011742 | 0.00011742 | 0.00011742 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003757 | | | 2.24 Nlocal: 432 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4994 ave 4994 max 4994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42926 ave 42926 max 42926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42926 Ave neighs/atom = 99.365741 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 = 3 23 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) = 6.774 | 6.774 | 6.774 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1674.5469 0 -1674.5469 155.53539 Loop time of 6.51e-07 on 1 procs for 0 steps with 432 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: 432 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4994 ave 4994 max 4994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42912 ave 42912 max 42912 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 = 42912 Ave neighs/atom = 99.333333 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) = 6.774 | 6.774 | 6.774 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 -1674.5469 -1674.5469 11.682462 99.259469 5.4981458 155.53539 155.53539 136.07824 229.13752 101.39041 2.6340668 332.09437 Loop time of 3.61e-07 on 1 procs for 0 steps with 432 atoms 277.0% 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 | | 3.61e-07 | | |100.00 Nlocal: 432 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4994 ave 4994 max 4994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42912 ave 42912 max 42912 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 85824 ave 85824 max 85824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85824 Ave neighs/atom = 198.66667 Neighbor list builds = 0 Dangerous builds = 0 432 -1674.54689381462 eV 2.6340667570601 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00