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 -55.560314 0) to (39.287075 55.560314 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1626784 4.9023807 5.5012908 Created 816 atoms using lattice units in orthogonal box = (0 -55.560314 0) to (39.287075 55.560314 5.5012908) create_atoms CPU = 0.001 seconds 816 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1626784 4.9023807 5.5012908 Created 824 atoms using lattice units in orthogonal box = (0 -55.560314 0) to (39.287075 55.560314 5.5012908) create_atoms CPU = 0.001 seconds 824 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 = 9 25 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 8 atoms, new total = 1632 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 = 9 25 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) = 7.941 | 7.941 | 7.941 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4469.4186 0 -4469.4186 157472.22 93 0 -6324.5591 0 -6324.5591 8177.5712 Loop time of 1.53083 on 1 procs for 93 steps with 1632 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 = -4469.41856908117 -6324.55368134484 -6324.55913473584 Force two-norm initial, final = 1718.6164 0.26791404 Force max component initial, final = 261.28393 0.033344035 Final line search alpha, max atom move = 1 0.033344035 Iterations, force evaluations = 93 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5158 | 1.5158 | 1.5158 | 0.0 | 99.02 Neigh | 0.0037234 | 0.0037234 | 0.0037234 | 0.0 | 0.24 Comm | 0.0065441 | 0.0065441 | 0.0065441 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004777 | | | 0.31 Nlocal: 1632 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10025 ave 10025 max 10025 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162408 ave 162408 max 162408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162408 Ave neighs/atom = 99.514706 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 : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.941 | 7.941 | 7.941 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -6324.5591 0 -6324.5591 8177.5712 24016.46 98 0 -6324.8912 0 -6324.8912 285.51396 24112.111 Loop time of 0.0589047 on 1 procs for 5 steps with 1632 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 = -6324.55913473587 -6324.89004946415 -6324.89116159487 Force two-norm initial, final = 216.52172 9.0282343 Force max component initial, final = 155.74325 8.4726907 Final line search alpha, max atom move = 0.00016373057 0.0013872385 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.057783 | 0.057783 | 0.057783 | 0.0 | 98.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022172 | 0.00022172 | 0.00022172 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009001 | | | 1.53 Nlocal: 1632 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9376 ave 9376 max 9376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162632 ave 162632 max 162632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162632 Ave neighs/atom = 99.651961 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 = 9 26 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) = 7.567 | 7.567 | 7.567 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6324.8912 0 -6324.8912 285.51396 Loop time of 1.192e-06 on 1 procs for 0 steps with 1632 atoms 167.8% 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 | | 1.192e-06 | | |100.00 Nlocal: 1632 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9376 ave 9376 max 9376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162496 ave 162496 max 162496 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 = 162496 Ave neighs/atom = 99.568627 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) = 7.567 | 7.567 | 7.567 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 -6324.8912 -6324.8912 39.301396 111.5747 5.498719 285.51396 285.51396 141.4925 565.28508 149.76428 2.6071146 936.21216 Loop time of 8.21e-07 on 1 procs for 0 steps with 1632 atoms 487.2% 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 | | 8.21e-07 | | |100.00 Nlocal: 1632 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9376 ave 9376 max 9376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162496 ave 162496 max 162496 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 324992 ave 324992 max 324992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 324992 Ave neighs/atom = 199.13725 Neighbor list builds = 0 Dangerous builds = 0 1632 -6324.89116159487 eV 2.60711457632556 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01