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 -49.836877 0.0000000) to (24.918439 49.836877 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9869502 3.9869502 3.5239994 Created 400 atoms using lattice units in orthogonal box = (0.0000000 -49.836877 0.0000000) to (24.918439 49.836877 3.5239994) create_atoms CPU = 0.001 seconds 400 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9869502 3.9869502 3.5239994 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -49.836877 0.0000000) to (24.918439 49.836877 3.5239994) create_atoms CPU = 0.000 seconds 402 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 = 6 23 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 6 atoms, new total = 796 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 = 6 23 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) = 7.675 | 7.675 | 7.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2936.8614 0 -2936.8614 131186.23 56 0 -3521.7668 0 -3521.7668 -892.34235 Loop time of 1.67257 on 1 procs for 56 steps with 796 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 = -2936.86137936361 -3521.76398961916 -3521.76677155099 Force two-norm initial, final = 1106.1941 0.18892115 Force max component initial, final = 367.57320 0.033342123 Final line search alpha, max atom move = 1.0000000 0.033342123 Iterations, force evaluations = 56 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6473 | 1.6473 | 1.6473 | 0.0 | 98.49 Neigh | 0.0056351 | 0.0056351 | 0.0056351 | 0.0 | 0.34 Comm | 0.012868 | 0.012868 | 0.012868 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006759 | | | 0.40 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9647.00 ave 9647 max 9647 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101438.0 ave 101438 max 101438 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101438 Ave neighs/atom = 127.43467 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.677 | 7.677 | 7.677 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -3521.7668 0 -3521.7668 -892.34235 8752.6078 58 0 -3521.7739 0 -3521.7739 -3.0551373 8748.2072 Loop time of 0.0734889 on 1 procs for 2 steps with 796 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3521.76677155099 -3521.77070883892 -3521.77393891703 Force two-norm initial, final = 11.880263 0.25616307 Force max component initial, final = 10.844935 0.14644775 Final line search alpha, max atom move = 0.00012970369 1.8994814e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071692 | 0.071692 | 0.071692 | 0.0 | 97.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003673 | 0.0003673 | 0.0003673 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001429 | | | 1.95 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9609.00 ave 9609 max 9609 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100192.0 ave 100192 max 100192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100192 Ave neighs/atom = 125.86935 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 = 6 23 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) = 7.308 | 7.308 | 7.308 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3521.7739 0 -3521.7739 -3.0551373 Loop time of 2.017e-06 on 1 procs for 0 steps with 796 atoms 148.7% 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 | | 2.017e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9609.00 ave 9609 max 9609 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100224.0 ave 100224 max 100224 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 = 100224 Ave neighs/atom = 125.90955 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) = 7.308 | 7.308 | 7.308 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 -3521.7739 -3521.7739 24.914666 99.556305 3.5269169 -3.0551373 -3.0551373 -26.816879 8.8430398 8.8084275 2.3084338 195.47423 Loop time of 2.4e-06 on 1 procs for 0 steps with 796 atoms 250.0% 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 | | 2.4e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9609.00 ave 9609 max 9609 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100224.0 ave 100224 max 100224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 200448.0 ave 200448 max 200448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200448 Ave neighs/atom = 251.81910 Neighbor list builds = 0 Dangerous builds = 0 796 -3521.77393891703 eV 2.30843380979908 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02