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 -46.082272 0.0000000) to (21.723391 46.082272 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5733455 5.6592263 4.9836877 Created 450 atoms using lattice units in orthogonal box = (0.0000000 -46.082272 0.0000000) to (21.723391 46.082272 4.9836877) create_atoms CPU = 0.001 seconds 450 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5733455 5.6592263 4.9836877 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -46.082272 0.0000000) to (21.723391 46.082272 4.9836877) create_atoms CPU = 0.001 seconds 458 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 = 5 21 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 0 atoms, new total = 908 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 = 5 21 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) = 7.735 | 7.735 | 7.735 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3550.1535 0 -3550.1535 155504.75 109 0 -4015.0527 0 -4015.0527 2791.0148 Loop time of 3.77091 on 1 procs for 109 steps with 908 atoms 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3550.15345606331 -4015.04893670872 -4015.05271177414 Force two-norm initial, final = 789.10955 0.22351614 Force max component initial, final = 132.54092 0.041844948 Final line search alpha, max atom move = 1.0000000 0.041844948 Iterations, force evaluations = 109 208 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7267 | 3.7267 | 3.7267 | 0.0 | 98.83 Neigh | 0.012469 | 0.012469 | 0.012469 | 0.0 | 0.33 Comm | 0.019547 | 0.019547 | 0.019547 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01223 | | | 0.32 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8421.00 ave 8421 max 8421 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113850.0 ave 113850 max 113850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113850 Ave neighs/atom = 125.38546 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 : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.735 | 7.735 | 7.735 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -4015.0527 0 -4015.0527 2791.0148 9977.9729 111 0 -4015.0704 0 -4015.0704 -2.5369876 9993.1066 Loop time of 0.08999 on 1 procs for 2 steps with 908 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4015.05271177414 -4015.06913200537 -4015.07039039356 Force two-norm initial, final = 32.391424 0.51499784 Force max component initial, final = 25.418567 0.35833125 Final line search alpha, max atom move = 0.00017791310 6.3751822e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.08818 | 0.08818 | 0.08818 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034103 | 0.00034103 | 0.00034103 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001469 | | | 1.63 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8425.00 ave 8425 max 8425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113854.0 ave 113854 max 113854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113854 Ave neighs/atom = 125.38987 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 = 5 21 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) = 7.365 | 7.365 | 7.365 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4015.0704 0 -4015.0704 -2.5369876 Loop time of 2.408e-06 on 1 procs for 0 steps with 908 atoms 166.1% 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 | | 2.408e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8415.00 ave 8415 max 8415 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113756.0 ave 113756 max 113756 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 = 113756 Ave neighs/atom = 125.28194 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) = 7.365 | 7.365 | 7.365 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 -4015.0704 -4015.0704 21.735709 92.257511 4.9833911 -2.5369876 -2.5369876 57.483169 -37.961117 -27.133015 2.3022865 523.24249 Loop time of 2.647e-06 on 1 procs for 0 steps with 908 atoms 302.2% 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 | | 2.647e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8415.00 ave 8415 max 8415 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113756.0 ave 113756 max 113756 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227512.0 ave 227512 max 227512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227512 Ave neighs/atom = 250.56388 Neighbor list builds = 0 Dangerous builds = 0 908 -4015.07039039356 eV 2.302286522229 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04