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 -38.117882 0.0000000) to (12.705961 38.117882 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8869079 4.8869079 3.5239994 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -38.117882 0.0000000) to (12.705961 38.117882 3.5239994) create_atoms CPU = 0.001 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8869079 4.8869079 3.5239994 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -38.117882 0.0000000) to (12.705961 38.117882 3.5239994) create_atoms CPU = 0.000 seconds 158 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 = 3 18 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 = 312 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 = 3 18 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) = 7.072 | 7.072 | 7.072 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1282.147 0 -1282.147 115859.95 17 0 -1378.8819 0 -1378.8819 11183.731 Loop time of 0.179694 on 1 procs for 17 steps with 312 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1282.14700213244 -1378.88067775422 -1378.88188864959 Force two-norm initial, final = 332.10945 0.12098304 Force max component initial, final = 117.42828 0.029568137 Final line search alpha, max atom move = 1.0000000 0.029568137 Iterations, force evaluations = 17 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17758 | 0.17758 | 0.17758 | 0.0 | 98.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013494 | 0.0013494 | 0.0013494 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007599 | | | 0.42 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5298.00 ave 5298 max 5298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39068.0 ave 39068 max 39068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39068 Ave neighs/atom = 125.21795 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 : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.072 | 7.072 | 7.072 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -1378.8819 0 -1378.8819 11183.731 3413.5171 24 0 -1379.0373 0 -1379.0373 188.203 3433.7986 Loop time of 0.0538662 on 1 procs for 7 steps with 312 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1378.88188864959 -1379.03603758531 -1379.03729976105 Force two-norm initial, final = 50.548091 1.1101852 Force max component initial, final = 45.859416 0.94589948 Final line search alpha, max atom move = 0.00039690731 0.00037543441 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.052182 | 0.052182 | 0.052182 | 0.0 | 96.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003663 | 0.0003663 | 0.0003663 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001318 | | | 2.45 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5298.00 ave 5298 max 5298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39382.0 ave 39382 max 39382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39382 Ave neighs/atom = 126.22436 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 = 3 18 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) = 6.703 | 6.703 | 6.703 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1379.0373 0 -1379.0373 188.203 Loop time of 2.23e-06 on 1 procs for 0 steps with 312 atoms 134.5% 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 | | 2.23e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5238.00 ave 5238 max 5238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39140.0 ave 39140 max 39140 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 = 39140 Ave neighs/atom = 125.44872 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) = 6.703 | 6.703 | 6.703 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 -1379.0373 -1379.0373 12.686371 76.735502 3.5272892 188.203 188.203 440.6669 223.85124 -99.909152 2.2488513 146.8709 Loop time of 2.316e-06 on 1 procs for 0 steps with 312 atoms 129.5% 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 | | 2.316e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5238.00 ave 5238 max 5238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39140.0 ave 39140 max 39140 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78280.0 ave 78280 max 78280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78280 Ave neighs/atom = 250.89744 Neighbor list builds = 0 Dangerous builds = 0 312 -1379.03729976105 eV 2.24885132554007 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00