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 -35.239994 0.0000000) to (17.619997 35.239994 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9335992 4.9335992 3.5239994 Created 199 atoms using lattice units in orthogonal box = (0.0000000 -35.239994 0.0000000) to (17.619997 35.239994 3.5239994) create_atoms CPU = 0.001 seconds 199 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9335992 4.9335992 3.5239994 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -35.239994 0.0000000) to (17.619997 35.239994 3.5239994) create_atoms CPU = 0.000 seconds 201 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 16 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 0 atoms, new total = 400 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 16 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) = 7.092 | 7.092 | 7.092 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1530.5789 0 -1530.5789 190235.96 66 0 -1768.2703 0 -1768.2703 10222.059 Loop time of 0.986547 on 1 procs for 66 steps with 400 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 = -1530.57886077973 -1768.26863785916 -1768.27030097376 Force two-norm initial, final = 561.73064 0.13239287 Force max component initial, final = 200.70297 0.020543637 Final line search alpha, max atom move = 1.0000000 0.020543637 Iterations, force evaluations = 66 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96907 | 0.96907 | 0.96907 | 0.0 | 98.23 Neigh | 0.0060247 | 0.0060247 | 0.0060247 | 0.0 | 0.61 Comm | 0.0074534 | 0.0074534 | 0.0074534 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003997 | | | 0.41 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5728.00 ave 5728 max 5728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51339.0 ave 51339 max 51339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51339 Ave neighs/atom = 128.34750 Neighbor list builds = 2 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 : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.096 | 7.096 | 7.096 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -1768.2703 0 -1768.2703 10222.059 4376.3039 73 0 -1768.4349 0 -1768.4349 -80.580313 4400.6968 Loop time of 0.0879284 on 1 procs for 7 steps with 400 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1768.27030097376 -1768.43484007356 -1768.4349133285 Force two-norm initial, final = 59.498998 0.67440892 Force max component initial, final = 53.381881 0.61901970 Final line search alpha, max atom move = 0.00097701024 0.00060478858 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.084792 | 0.084792 | 0.084792 | 0.0 | 96.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051501 | 0.00051501 | 0.00051501 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002622 | | | 2.98 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6165.00 ave 6165 max 6165 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50873.0 ave 50873 max 50873 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50873 Ave neighs/atom = 127.18250 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 16 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) = 6.727 | 6.727 | 6.727 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1768.4349 0 -1768.4349 -80.580313 Loop time of 1.785e-06 on 1 procs for 0 steps with 400 atoms 168.1% 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 | | 1.785e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6139.00 ave 6139 max 6139 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50483.0 ave 50483 max 50483 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 = 50483 Ave neighs/atom = 126.20750 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) = 6.727 | 6.727 | 6.727 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 -1768.4349 -1768.4349 17.594001 70.884288 3.5286359 -80.580313 -80.580313 32.500015 -48.575852 -225.6651 2.2492712 147.54217 Loop time of 2.234e-06 on 1 procs for 0 steps with 400 atoms 223.8% 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 | | 2.234e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6139.00 ave 6139 max 6139 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50483.0 ave 50483 max 50483 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 100966.0 ave 100966 max 100966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100966 Ave neighs/atom = 252.41500 Neighbor list builds = 0 Dangerous builds = 0 400 -1768.4349133285 eV 2.24927124942633 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02