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 -60.632702 0.0000000) to (30.314589 60.632702 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9158793 4.9158793 3.5239994 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -60.632702 0.0000000) to (30.314589 60.632702 3.5239994) create_atoms CPU = 0.003 seconds 594 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9158793 4.9158793 3.5239994 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -60.632702 0.0000000) to (30.314589 60.632702 3.5239994) create_atoms CPU = 0.002 seconds 594 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 28 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 8 atoms, new total = 1180 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 = 7 28 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) = 7.831 | 7.831 | 7.831 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5171.4515 0 -5171.4515 25360.1 61 0 -5225.1381 0 -5225.1381 318.61407 Loop time of 4.90884 on 1 procs for 61 steps with 1180 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5171.45149942582 -5225.13358073125 -5225.13807738489 Force two-norm initial, final = 73.291575 0.27528515 Force max component initial, final = 23.281780 0.059614940 Final line search alpha, max atom move = 1.0000000 0.059614940 Iterations, force evaluations = 61 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8435 | 4.8435 | 4.8435 | 0.0 | 98.67 Neigh | 0.017976 | 0.017976 | 0.017976 | 0.0 | 0.37 Comm | 0.030016 | 0.030016 | 0.030016 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01738 | | | 0.35 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12759.0 ave 12759 max 12759 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 148188.0 ave 148188 max 148188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148188 Ave neighs/atom = 125.58305 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 : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.831 | 7.831 | 7.831 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -5225.1381 0 -5225.1381 318.61407 12954.613 63 0 -5225.1462 0 -5225.1462 386.62513 12954.027 Loop time of 0.236064 on 1 procs for 2 steps with 1180 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5225.13807738491 -5225.14488310832 -5225.14622917279 Force two-norm initial, final = 14.260430 0.28291064 Force max component initial, final = 12.594409 0.063689661 Final line search alpha, max atom move = 0.00010130023 6.4517773e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23124 | 0.23124 | 0.23124 | 0.0 | 97.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013444 | 0.0013444 | 0.0013444 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003482 | | | 1.47 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12755.0 ave 12755 max 12755 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 147694.0 ave 147694 max 147694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147694 Ave neighs/atom = 125.16441 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 = 7 28 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) = 7.462 | 7.462 | 7.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5225.1462 0 -5225.1462 386.62513 Loop time of 6.695e-06 on 1 procs for 0 steps with 1180 atoms 179.2% 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 | | 6.695e-06 | | |100.00 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12782.0 ave 12782 max 12782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 147696.0 ave 147696 max 147696 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 = 147696 Ave neighs/atom = 125.16610 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) = 7.462 | 7.462 | 7.462 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 -5225.1462 -5225.1462 30.28856 121.2654 3.5268685 386.62513 386.62513 -2.1528099 1164.4404 -2.4122351 2.2487418 293.58576 Loop time of 7.076e-06 on 1 procs for 0 steps with 1180 atoms 282.6% 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 | | 7.076e-06 | | |100.00 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12782.0 ave 12782 max 12782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 147696.0 ave 147696 max 147696 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 295392.0 ave 295392 max 295392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295392 Ave neighs/atom = 250.33220 Neighbor list builds = 0 Dangerous builds = 0 1180 -5225.14622917279 eV 2.248741808851 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05