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 -62.724366 0) to (31.362183 62.724366 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3424561 4.3424561 3.8900001 Created 520 atoms using lattice units in orthogonal box = (0 -62.724366 0) to (31.362183 62.724366 3.8900001) create_atoms CPU = 0.000 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3424561 4.3424561 3.8900001 Created 522 atoms using lattice units in orthogonal box = (0 -62.724366 0) to (31.362183 62.724366 3.8900001) create_atoms CPU = 0.000 seconds 522 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 = 8 29 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 = 1036 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 = 8 29 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) = 7.728 | 7.728 | 7.728 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2812.8452 0 -2812.8452 128406.53 74 0 -4016.1898 0 -4016.1898 -363.12759 Loop time of 0.75528 on 1 procs for 74 steps with 1036 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2812.84517567562 -4016.18674252116 -4016.18976433904 Force two-norm initial, final = 1502.8641 0.21197545 Force max component initial, final = 472.74357 0.041400922 Final line search alpha, max atom move = 0.91250407 0.03777851 Iterations, force evaluations = 74 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74495 | 0.74495 | 0.74495 | 0.0 | 98.63 Neigh | 0.0024382 | 0.0024382 | 0.0024382 | 0.0 | 0.32 Comm | 0.0053007 | 0.0053007 | 0.0053007 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002595 | | | 0.34 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9172 ave 9172 max 9172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102990 ave 102990 max 102990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102990 Ave neighs/atom = 99.411197 Neighbor list builds = 1 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 : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.728 | 7.728 | 7.728 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -4016.1898 0 -4016.1898 -363.12759 15304.607 75 0 -4016.1911 0 -4016.1911 338.89094 15299.171 Loop time of 0.0165461 on 1 procs for 1 steps with 1036 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 = -4016.18976433904 -4016.18976433904 -4016.19111756288 Force two-norm initial, final = 8.8809957 7.6525517 Force max component initial, final = 6.4226093 7.4811013 Final line search alpha, max atom move = 0.00015569996 0.0011648072 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.016182 | 0.016182 | 0.016182 | 0.0 | 97.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.5549e-05 | 9.5549e-05 | 9.5549e-05 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002689 | | | 1.62 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9149 ave 9149 max 9149 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103048 ave 103048 max 103048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103048 Ave neighs/atom = 99.467181 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 = 8 29 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) = 7.359 | 7.359 | 7.359 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4016.1911 0 -4016.1911 338.89094 Loop time of 6.71e-07 on 1 procs for 0 steps with 1036 atoms 149.0% 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 | | 6.71e-07 | | |100.00 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9149 ave 9149 max 9149 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103056 ave 103056 max 103056 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 = 103056 Ave neighs/atom = 99.474903 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) = 7.359 | 7.359 | 7.359 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 -4016.1911 -4016.1911 31.355309 125.42372 3.8902467 338.89094 338.89094 97.107567 136.07152 783.49373 2.5604999 247.80044 Loop time of 7.91e-07 on 1 procs for 0 steps with 1036 atoms 252.8% 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 | | 7.91e-07 | | |100.00 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9149 ave 9149 max 9149 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103056 ave 103056 max 103056 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206112 ave 206112 max 206112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206112 Ave neighs/atom = 198.94981 Neighbor list builds = 0 Dangerous builds = 0 1036 -4016.19111756288 eV 2.56049994496177 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00