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 -59.250716 0) to (29.625358 59.250716 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1078203 5.1078203 3.8900001 Created 464 atoms using lattice units in orthogonal box = (0 -59.250716 0) to (29.625358 59.250716 3.8900001) create_atoms CPU = 0.000 seconds 464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1078203 5.1078203 3.8900001 Created 466 atoms using lattice units in orthogonal box = (0 -59.250716 0) to (29.625358 59.250716 3.8900001) create_atoms CPU = 0.000 seconds 466 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 27 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 = 930 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 27 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) = 7.304 | 7.304 | 7.304 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2889.0631 0 -2889.0631 135322.6 38 0 -3600.6897 0 -3600.6897 15024.657 Loop time of 0.336171 on 1 procs for 38 steps with 930 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 = -2889.06307644569 -3600.68649714946 -3600.6897268721 Force two-norm initial, final = 1032.6922 0.21462318 Force max component initial, final = 400.89718 0.049310873 Final line search alpha, max atom move = 1 0.049310873 Iterations, force evaluations = 38 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33308 | 0.33308 | 0.33308 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020314 | 0.0020314 | 0.0020314 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001056 | | | 0.31 Nlocal: 930 ave 930 max 930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8494 ave 8494 max 8494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93230 ave 93230 max 93230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93230 Ave neighs/atom = 100.24731 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 : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.304 | 7.304 | 7.304 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -3600.6897 0 -3600.6897 15024.657 13656.418 49 0 -3601.5154 0 -3601.5154 31.836395 13757.422 Loop time of 0.0730942 on 1 procs for 11 steps with 930 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 = -3600.6897268721 -3601.51454233378 -3601.51541376513 Force two-norm initial, final = 236.33795 2.1662913 Force max component initial, final = 193.29373 1.8827324 Final line search alpha, max atom move = 9.8064149e-05 0.00018462855 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.068884 | 0.068884 | 0.068884 | 0.0 | 94.24 Neigh | 0.0022571 | 0.0022571 | 0.0022571 | 0.0 | 3.09 Comm | 0.00048629 | 0.00048629 | 0.00048629 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001467 | | | 2.01 Nlocal: 930 ave 930 max 930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8494 ave 8494 max 8494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92400 ave 92400 max 92400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92400 Ave neighs/atom = 99.354839 Neighbor list builds = 1 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 27 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) = 6.935 | 6.935 | 6.935 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3601.5154 0 -3601.5154 31.836395 Loop time of 6.51e-07 on 1 procs for 0 steps with 930 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: 930 ave 930 max 930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8476 ave 8476 max 8476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92390 ave 92390 max 92390 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 = 92390 Ave neighs/atom = 99.344086 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) = 6.935 | 6.935 | 6.935 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 -3601.5154 -3601.5154 29.576989 119.67663 3.8866348 31.836395 31.836395 218.90328 -41.583684 -81.810417 2.493163 466.82074 Loop time of 1.062e-06 on 1 procs for 0 steps with 930 atoms 188.3% 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 | | 1.062e-06 | | |100.00 Nlocal: 930 ave 930 max 930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8476 ave 8476 max 8476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92390 ave 92390 max 92390 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 184780 ave 184780 max 184780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184780 Ave neighs/atom = 198.68817 Neighbor list builds = 0 Dangerous builds = 0 930 -3601.51541376513 eV 2.49316295532967 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00