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 -42.291517 0.0000000) to (14.951063 42.291517 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9836877 5.8733323 4.9836877 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -42.291517 0.0000000) to (14.951063 42.291517 4.9836877) create_atoms CPU = 0.001 seconds 292 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9836877 5.8733323 4.9836877 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -42.291517 0.0000000) to (14.951063 42.291517 4.9836877) create_atoms CPU = 0.001 seconds 292 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 = 4 20 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 = 576 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 = 4 20 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) = 7.223 | 7.223 | 7.223 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2426.3132 0 -2426.3132 134377.22 45 0 -2546.5538 0 -2546.5538 11500.45 Loop time of 0.789117 on 1 procs for 45 steps with 576 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 = -2426.31316276669 -2546.55196086921 -2546.55384302371 Force two-norm initial, final = 226.59032 0.14093281 Force max component initial, final = 46.905479 0.014076189 Final line search alpha, max atom move = 1.0000000 0.014076189 Iterations, force evaluations = 45 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77946 | 0.77946 | 0.77946 | 0.0 | 98.78 Neigh | 0.0032607 | 0.0032607 | 0.0032607 | 0.0 | 0.41 Comm | 0.0040007 | 0.0040007 | 0.0040007 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002397 | | | 0.30 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6237.00 ave 6237 max 6237 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73692.0 ave 73692 max 73692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73692 Ave neighs/atom = 127.93750 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 : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.223 | 7.223 | 7.223 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -2546.5538 0 -2546.5538 11500.45 6302.4028 50 0 -2546.6319 0 -2546.6319 4822.9836 6324.7972 Loop time of 0.0848038 on 1 procs for 5 steps with 576 atoms 96.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2546.55384302371 -2546.63181831384 -2546.63192588258 Force two-norm initial, final = 45.751166 0.19118520 Force max component initial, final = 42.251284 0.025442707 Final line search alpha, max atom move = 0.00057460131 1.4619413e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.082651 | 0.082651 | 0.082651 | 0.0 | 97.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037456 | 0.00037456 | 0.00037456 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001779 | | | 2.10 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6246.00 ave 6246 max 6246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71992.0 ave 71992 max 71992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71992 Ave neighs/atom = 124.98611 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 = 4 20 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) = 6.854 | 6.854 | 6.854 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2546.6319 0 -2546.6319 4822.9836 Loop time of 1.87e-06 on 1 procs for 0 steps with 576 atoms 213.9% 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 | | 1.87e-06 | | |100.00 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6210.00 ave 6210 max 6210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71936.0 ave 71936 max 71936 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 = 71936 Ave neighs/atom = 124.88889 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) = 6.854 | 6.854 | 6.854 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 -2546.6319 -2546.6319 15.008247 84.583033 4.9823403 4822.9836 4822.9836 -4.2454958 14479.509 -6.3126902 2.312729 344.10746 Loop time of 1.991e-06 on 1 procs for 0 steps with 576 atoms 200.9% 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 | | 1.991e-06 | | |100.00 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6210.00 ave 6210 max 6210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71936.0 ave 71936 max 71936 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 143872.0 ave 143872 max 143872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143872 Ave neighs/atom = 249.77778 Neighbor list builds = 0 Dangerous builds = 0 576 -2546.63192588258 eV 2.31272900057374 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01