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 -55.012908 0) to (27.506454 55.012908 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4010327 4.4010327 3.8900001 Created 400 atoms using lattice units in orthogonal box = (0 -55.012908 0) to (27.506454 55.012908 3.8900001) create_atoms CPU = 0.000 seconds 400 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4010327 4.4010327 3.8900001 Created 402 atoms using lattice units in orthogonal box = (0 -55.012908 0) to (27.506454 55.012908 3.8900001) create_atoms CPU = 0.000 seconds 402 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 25 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 6 atoms, new total = 796 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 25 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) = 7.241 | 7.241 | 7.241 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2294.0637 0 -2294.0637 125054.55 69 0 -3083.7649 0 -3083.7649 -1111.2655 Loop time of 0.540587 on 1 procs for 69 steps with 796 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 = -2294.06374298904 -3083.76306066115 -3083.76494542795 Force two-norm initial, final = 1159.2444 0.16740238 Force max component initial, final = 379.03544 0.037754256 Final line search alpha, max atom move = 1 0.037754256 Iterations, force evaluations = 69 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53357 | 0.53357 | 0.53357 | 0.0 | 98.70 Neigh | 0.0018865 | 0.0018865 | 0.0018865 | 0.0 | 0.35 Comm | 0.0034668 | 0.0034668 | 0.0034668 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00166 | | | 0.31 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7597 ave 7597 max 7597 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79012 ave 79012 max 79012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79012 Ave neighs/atom = 99.261307 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 : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.241 | 7.241 | 7.241 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -3083.7649 0 -3083.7649 -1111.2655 11772.774 70 0 -3083.7679 0 -3083.7679 137.50801 11765.318 Loop time of 0.0127801 on 1 procs for 1 steps with 796 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 = -3083.76494542794 -3083.76494542794 -3083.76792146415 Force two-norm initial, final = 15.140435 5.0429827 Force max component initial, final = 11.327273 4.7366717 Final line search alpha, max atom move = 8.8282505e-05 0.00041816525 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.012491 | 0.012491 | 0.012491 | 0.0 | 97.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.7675e-05 | 7.7675e-05 | 7.7675e-05 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002111 | | | 1.65 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7599 ave 7599 max 7599 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79118 ave 79118 max 79118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79118 Ave neighs/atom = 99.394472 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 25 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) = 6.873 | 6.873 | 6.873 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3083.7679 0 -3083.7679 137.50801 Loop time of 5.71e-07 on 1 procs for 0 steps with 796 atoms 175.1% 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 | | 5.71e-07 | | |100.00 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7599 ave 7599 max 7599 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79120 ave 79120 max 79120 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 = 79120 Ave neighs/atom = 99.396985 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) = 6.873 | 6.873 | 6.873 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 -3083.7679 -3083.7679 27.498397 109.99951 3.8896055 137.50801 137.50801 -234.50386 2.0632394 644.96466 2.5597138 245.7078 Loop time of 4.51e-07 on 1 procs for 0 steps with 796 atoms 221.7% 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 | | 4.51e-07 | | |100.00 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7599 ave 7599 max 7599 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79120 ave 79120 max 79120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 158240 ave 158240 max 158240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158240 Ave neighs/atom = 198.79397 Neighbor list builds = 0 Dangerous builds = 0 796 -3083.76792146415 eV 2.55971378398298 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00