LAMMPS (23 Jun 2022) 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 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -47.00305 0) to (57.566744 47.00305 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5200987 5.7948965 6.3523435 Created 1751 atoms using lattice units in orthogonal box = (0 -47.00305 0) to (57.566744 47.00305 9.5285152) create_atoms CPU = 0.001 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5200987 5.7948965 6.3523435 Created 1757 atoms using lattice units in orthogonal box = (0 -47.00305 0) to (57.566744 47.00305 9.5285152) create_atoms CPU = 0.001 seconds 1757 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 = 13 22 3 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 28 atoms, new total = 3480 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:187) 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 = 13 22 3 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) = 9.242 | 9.242 | 9.242 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10111.948 0 -10111.948 133423.91 83 0 -13483.401 0 -13483.401 -5985.664 Loop time of 2.61811 on 1 procs for 83 steps with 3480 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 = -10111.9475928855 -13483.3907000136 -13483.4013892501 Force two-norm initial, final = 2315.2919 0.36338924 Force max component initial, final = 339.44465 0.085776893 Final line search alpha, max atom move = 1 0.085776893 Iterations, force evaluations = 83 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5883 | 2.5883 | 2.5883 | 0.0 | 98.86 Neigh | 0.016559 | 0.016559 | 0.016559 | 0.0 | 0.63 Comm | 0.0060847 | 0.0060847 | 0.0060847 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0072 | | | 0.28 Nlocal: 3480 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11850 ave 11850 max 11850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 345485 ave 345485 max 345485 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 345485 Ave neighs/atom = 99.277299 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 9.242 | 9.242 | 9.242 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -13483.401 0 -13483.401 -5985.664 51564.752 87 0 -13483.793 0 -13483.793 -137.54341 51410.337 Loop time of 0.129465 on 1 procs for 4 steps with 3480 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 = -13483.4013892502 -13483.7925308516 -13483.7931016419 Force two-norm initial, final = 343.83566 8.6843525 Force max component initial, final = 249.41482 7.5142535 Final line search alpha, max atom move = 0.00013496228 0.0010141408 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12783 | 0.12783 | 0.12783 | 0.0 | 98.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028443 | 0.00028443 | 0.00028443 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001346 | | | 1.04 Nlocal: 3480 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11874 ave 11874 max 11874 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 345737 ave 345737 max 345737 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 345737 Ave neighs/atom = 99.349713 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) 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 = 13 22 3 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) = 8.873 | 8.873 | 8.873 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13483.793 0 -13483.793 -137.54341 Loop time of 7.11e-07 on 1 procs for 0 steps with 3480 atoms 281.3% 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 | | 7.11e-07 | | |100.00 Nlocal: 3480 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11872 ave 11872 max 11872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 346099 ave 346099 max 346099 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346099 Ave neighs/atom = 99.453736 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 8.873 | 8.873 | 8.873 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 -13483.793 -13483.793 57.511933 93.762251 9.5337654 -137.54341 -137.54341 -56.396188 -233.57037 -122.66367 2.5691705 1723.6852 Loop time of 6.51e-07 on 1 procs for 0 steps with 3480 atoms 307.2% 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 | | 6.51e-07 | | |100.00 Nlocal: 3480 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11872 ave 11872 max 11872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 346099 ave 346099 max 346099 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 692198 ave 692198 max 692198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 692198 Ave neighs/atom = 198.90747 Neighbor list builds = 0 Dangerous builds = 0 3480 -13483.7931016419 eV 2.56917045446701 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02