LAMMPS (30 Jul 2021) 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 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created orthogonal box = (0.0000000 -35.590649 0.0000000) to (25.166389 35.590649 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4411275 5.5828469 4.9836877 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -35.590649 0.0000000) to (25.166389 35.590649 4.9836877) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4411275 5.5828469 4.9836877 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -35.590649 0.0000000) to (25.166389 35.590649 4.9836877) create_atoms CPU = 0.001 seconds 410 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 = 6 16 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 0 atoms, new total = 818 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:189) 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 = 6 16 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) = 7.659 | 7.659 | 7.659 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3229.8884 0 -3229.8884 177964.6 84 0 -3612.6826 0 -3612.6826 17454.809 Loop time of 2.6698 on 1 procs for 84 steps with 818 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3229.88835534613 -3612.67933586635 -3612.68256294992 Force two-norm initial, final = 645.06230 0.20309413 Force max component initial, final = 188.55761 0.047646799 Final line search alpha, max atom move = 1.0000000 0.047646799 Iterations, force evaluations = 84 159 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6423 | 2.6423 | 2.6423 | 0.0 | 98.97 Neigh | 0.0058193 | 0.0058193 | 0.0058193 | 0.0 | 0.22 Comm | 0.013118 | 0.013118 | 0.013118 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008599 | | | 0.32 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7026.00 ave 7026 max 7026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104752.0 ave 104752 max 104752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104752 Ave neighs/atom = 128.05868 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.659 | 7.659 | 7.659 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -3612.6826 0 -3612.6826 17454.809 8927.66 92 0 -3613.348 0 -3613.348 288.19303 9009.8877 Loop time of 0.166465 on 1 procs for 8 steps with 818 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3612.68256294993 -3613.34541744079 -3613.34795615634 Force two-norm initial, final = 185.89833 3.4012258 Force max component initial, final = 156.97366 2.4914819 Final line search alpha, max atom move = 0.00018727131 0.00046658307 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16288 | 0.16288 | 0.16288 | 0.0 | 97.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059047 | 0.00059047 | 0.00059047 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002995 | | | 1.80 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7030.00 ave 7030 max 7030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104756.0 ave 104756 max 104756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104756 Ave neighs/atom = 128.06357 Neighbor list builds = 0 Dangerous builds = 0 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 = 6 17 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) = 7.290 | 7.290 | 7.290 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3613.348 0 -3613.348 288.19303 Loop time of 2.076e-06 on 1 procs for 0 steps with 818 atoms 144.5% 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 | | 2.076e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7012.00 ave 7012 max 7012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103138.0 ave 103138 max 103138 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103138 Ave neighs/atom = 126.08557 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.290 | 7.290 | 7.290 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 -3613.348 -3613.348 25.218209 71.706736 4.9824756 288.19303 288.19303 14.82878 406.81219 442.93813 2.3336232 634.92267 Loop time of 2.28e-06 on 1 procs for 0 steps with 818 atoms 263.2% 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 | | 2.28e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7012.00 ave 7012 max 7012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103138.0 ave 103138 max 103138 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206276.0 ave 206276 max 206276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206276 Ave neighs/atom = 252.17115 Neighbor list builds = 0 Dangerous builds = 0 818 -3613.34795615634 eV 2.33362315492271 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03