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 -77.018072 0) to (47.163744 77.018072 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4543106 5.5012908 6.3523435 Created 2352 atoms using lattice units in orthogonal box = (0 -77.018072 0) to (47.163744 77.018072 9.5285152) create_atoms CPU = 0.001 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4543106 5.5012908 6.3523435 Created 2358 atoms using lattice units in orthogonal box = (0 -77.018072 0) to (47.163744 77.018072 9.5285152) create_atoms CPU = 0.001 seconds 2358 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 35 3 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 18 atoms, new total = 4692 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 = 11 35 3 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) = 16.43 | 16.43 | 16.43 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15849.524 0 -15849.524 86761.408 102 0 -18189.745 0 -18189.745 2576.4146 Loop time of 4.65896 on 1 procs for 102 steps with 4692 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15849.523851144 -18189.7323622603 -18189.7450751421 Force two-norm initial, final = 1780.6409 0.57478637 Force max component initial, final = 267.30166 0.088131764 Final line search alpha, max atom move = 1 0.088131764 Iterations, force evaluations = 102 191 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6126 | 4.6126 | 4.6126 | 0.0 | 99.00 Neigh | 0.022338 | 0.022338 | 0.022338 | 0.0 | 0.48 Comm | 0.011261 | 0.011261 | 0.011261 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01281 | | | 0.27 Nlocal: 4692 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15674 ave 15674 max 15674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 467076 ave 467076 max 467076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 467076 Ave neighs/atom = 99.547315 Neighbor list builds = 2 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 : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 16.43 | 16.43 | 16.43 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -18189.745 0 -18189.745 2576.4146 69223.913 106 0 -18190.068 0 -18190.068 4.4799468 69313.136 Loop time of 0.166384 on 1 procs for 4 steps with 4692 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 = -18189.745075142 -18190.0499296037 -18190.0677001134 Force two-norm initial, final = 244.84648 6.8337449 Force max component initial, final = 231.87075 5.0562998 Final line search alpha, max atom move = 1.8289303e-05 9.24762e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16422 | 0.16422 | 0.16422 | 0.0 | 98.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037316 | 0.00037316 | 0.00037316 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001791 | | | 1.08 Nlocal: 4692 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15797 ave 15797 max 15797 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 467076 ave 467076 max 467076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 467076 Ave neighs/atom = 99.547315 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 = 11 35 3 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) = 15.32 | 15.32 | 15.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18190.068 0 -18190.068 4.4799468 Loop time of 5.81e-07 on 1 procs for 0 steps with 4692 atoms 344.2% 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 | | 5.81e-07 | | |100.00 Nlocal: 4692 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15848 ave 15848 max 15848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 467016 ave 467016 max 467016 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 = 467016 Ave neighs/atom = 99.534527 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) = 15.32 | 15.32 | 15.32 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 -18190.068 -18190.068 47.130338 154.5263 9.5172746 4.4799468 4.4799468 -104.63937 1.3404701 116.73874 2.487528 2052.3733 Loop time of 1.012e-06 on 1 procs for 0 steps with 4692 atoms 395.3% 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 | | 1.012e-06 | | |100.00 Nlocal: 4692 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15848 ave 15848 max 15848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 467016 ave 467016 max 467016 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 934032 ave 934032 max 934032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 934032 Ave neighs/atom = 199.06905 Neighbor list builds = 0 Dangerous builds = 0 4692 -18190.0677001134 eV 2.48752795530664 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05