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 -60.218128 0.0000000) to (30.109064 60.218128 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5369822 4.5369822 3.5239994 Created 584 atoms using lattice units in orthogonal box = (0.0000000 -60.218128 0.0000000) to (30.109064 60.218128 3.5239994) create_atoms CPU = 0.001 seconds 584 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5369822 4.5369822 3.5239994 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -60.218128 0.0000000) to (30.109064 60.218128 3.5239994) create_atoms CPU = 0.001 seconds 586 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 2 atoms, new total = 1168 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) = 7.812 | 7.812 | 7.812 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4864.2944 0 -4864.2944 76408.018 24 0 -5167.7429 0 -5167.7429 9428.0258 Loop time of 0.944845 on 1 procs for 24 steps with 1168 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4864.2943916716 -5167.73832114217 -5167.74288888758 Force two-norm initial, final = 685.42136 0.25815518 Force max component initial, final = 234.44715 0.066569163 Final line search alpha, max atom move = 1.0000000 0.066569163 Iterations, force evaluations = 24 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.93472 | 0.93472 | 0.93472 | 0.0 | 98.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0063291 | 0.0063291 | 0.0063291 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003793 | | | 0.40 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11624.0 ave 11624 max 11624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145656.0 ave 145656 max 145656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 145656 Ave neighs/atom = 124.70548 Neighbor list builds = 0 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 : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.812 | 7.812 | 7.812 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -5167.7429 0 -5167.7429 9428.0258 12778.807 31 0 -5168.1759 0 -5168.1759 -268.67517 12845.344 Loop time of 0.215072 on 1 procs for 7 steps with 1168 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 = -5167.74288888757 -5168.17088873644 -5168.17590791005 Force two-norm initial, final = 152.98619 4.4693508 Force max component initial, final = 139.47436 3.7957604 Final line search alpha, max atom move = 0.00010743474 0.00040779654 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20995 | 0.20995 | 0.20995 | 0.0 | 97.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092925 | 0.00092925 | 0.00092925 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004197 | | | 1.95 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11588.0 ave 11588 max 11588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146024.0 ave 146024 max 146024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146024 Ave neighs/atom = 125.02055 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) = 7.443 | 7.443 | 7.443 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5168.1759 0 -5168.1759 -268.67517 Loop time of 2.157e-06 on 1 procs for 0 steps with 1168 atoms 185.4% 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 | | 2.157e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11588.0 ave 11588 max 11588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145478.0 ave 145478 max 145478 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 = 145478 Ave neighs/atom = 124.55308 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) = 7.443 | 7.443 | 7.443 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 -5168.1759 -5168.1759 30.077257 121.25492 3.5221524 -268.67517 -268.67517 -48.167295 -284.66801 -473.1902 2.2292065 456.83097 Loop time of 2.25e-06 on 1 procs for 0 steps with 1168 atoms 311.1% 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 | | 2.25e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11588.0 ave 11588 max 11588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145478.0 ave 145478 max 145478 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 290956.0 ave 290956 max 290956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290956 Ave neighs/atom = 249.10616 Neighbor list builds = 0 Dangerous builds = 0 1168 -5168.17590791005 eV 2.22920646872086 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01