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 -36.622476 0.0000000) to (25.896001 36.622476 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7546669 4.7473580 4.9836877 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -36.622476 0.0000000) to (25.896001 36.622476 4.9836877) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7546669 4.7473580 4.9836877 Created 440 atoms using lattice units in orthogonal box = (0.0000000 -36.622476 0.0000000) to (25.896001 36.622476 4.9836877) create_atoms CPU = 0.001 seconds 440 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 17 2 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 8 atoms, new total = 864 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 17 2 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) = 7.691 | 7.691 | 7.691 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3779.8884 0 -3779.8884 27470.838 16 0 -3819.6658 0 -3819.6658 10589.243 Loop time of 0.546715 on 1 procs for 16 steps with 864 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 = -3779.88839426435 -3819.66300181681 -3819.66582979482 Force two-norm initial, final = 53.607086 0.17226417 Force max component initial, final = 8.1676874 0.020956282 Final line search alpha, max atom move = 1.0000000 0.020956282 Iterations, force evaluations = 16 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54193 | 0.54193 | 0.54193 | 0.0 | 99.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028326 | 0.0028326 | 0.0028326 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001949 | | | 0.36 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7831.00 ave 7831 max 7831 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108176.0 ave 108176 max 108176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108176 Ave neighs/atom = 125.20370 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 : 16 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.694 | 7.694 | 7.694 Mbytes Step Temp E_pair E_mol TotEng Press Volume 16 0 -3819.6658 0 -3819.6658 10589.243 9452.8165 22 0 -3819.9181 0 -3819.9181 -122.1998 9507.9149 Loop time of 0.139787 on 1 procs for 6 steps with 864 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 = -3819.66582979482 -3819.91686412772 -3819.91809156912 Force two-norm initial, final = 113.43629 1.9832678 Force max component initial, final = 90.238631 1.3831888 Final line search alpha, max atom move = 0.00012245321 0.00016937590 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13676 | 0.13676 | 0.13676 | 0.0 | 97.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052735 | 0.00052735 | 0.00052735 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002501 | | | 1.79 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7831.00 ave 7831 max 7831 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108672.0 ave 108672 max 108672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108672 Ave neighs/atom = 125.77778 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 17 2 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) = 7.325 | 7.325 | 7.325 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3819.9181 0 -3819.9181 -122.1998 Loop time of 2.423e-06 on 1 procs for 0 steps with 864 atoms 165.1% 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 | | 2.423e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7697.00 ave 7697 max 7697 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108048.0 ave 108048 max 108048 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 = 108048 Ave neighs/atom = 125.05556 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) = 7.325 | 7.325 | 7.325 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 -3819.9181 -3819.9181 25.906687 73.634546 4.9841579 -122.1998 -122.1998 -217.70538 84.208781 -233.1028 2.3575977 423.79418 Loop time of 3.877e-06 on 1 procs for 0 steps with 864 atoms 232.1% 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 | | 3.877e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7697.00 ave 7697 max 7697 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108048.0 ave 108048 max 108048 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 216096.0 ave 216096 max 216096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216096 Ave neighs/atom = 250.11111 Neighbor list builds = 0 Dangerous builds = 0 864 -3819.91809156912 eV 2.35759767679883 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01