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 -40.491195 0.0000000) to (28.629106 40.491195 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3377434 5.5210460 4.9836877 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.491195 0.0000000) to (28.629106 40.491195 4.9836877) create_atoms CPU = 0.001 seconds 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3377434 5.5210460 4.9836877 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.491195 0.0000000) to (28.629106 40.491195 4.9836877) create_atoms CPU = 0.001 seconds 532 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 = 7 19 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 16 atoms, new total = 1048 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 = 7 19 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) = 7.766 | 7.766 | 7.766 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4599.4238 0 -4599.4238 17349.978 39 0 -4632.8745 0 -4632.8745 -2194.5758 Loop time of 1.32065 on 1 procs for 39 steps with 1048 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 = -4599.42384387886 -4632.87043775032 -4632.87446474668 Force two-norm initial, final = 81.725386 0.21545553 Force max component initial, final = 14.762223 0.040028837 Final line search alpha, max atom move = 1.0000000 0.040028837 Iterations, force evaluations = 39 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3037 | 1.3037 | 1.3037 | 0.0 | 98.72 Neigh | 0.0062156 | 0.0062156 | 0.0062156 | 0.0 | 0.47 Comm | 0.0064549 | 0.0064549 | 0.0064549 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004265 | | | 0.32 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8816.00 ave 8816 max 8816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130924.0 ave 130924 max 130924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130924 Ave neighs/atom = 124.92748 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 : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.766 | 7.766 | 7.766 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -4632.8745 0 -4632.8745 -2194.5758 11554.448 42 0 -4632.9048 0 -4632.9048 913.0437 11534.866 Loop time of 0.106778 on 1 procs for 3 steps with 1048 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 = -4632.87446474671 -4632.90469696719 -4632.9048261424 Force two-norm initial, final = 37.118420 0.22465260 Force max component initial, final = 33.769456 0.029290914 Final line search alpha, max atom move = 0.00036041251 1.0556812e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10493 | 0.10493 | 0.10493 | 0.0 | 98.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036798 | 0.00036798 | 0.00036798 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001477 | | | 1.38 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8816.00 ave 8816 max 8816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130912.0 ave 130912 max 130912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130912 Ave neighs/atom = 124.91603 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 = 7 19 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) = 7.397 | 7.397 | 7.397 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4632.9048 0 -4632.9048 913.0437 Loop time of 1.914e-06 on 1 procs for 0 steps with 1048 atoms 156.7% 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 | | 1.914e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8816.00 ave 8816 max 8816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131004.0 ave 131004 max 131004 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 = 131004 Ave neighs/atom = 125.00382 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) = 7.397 | 7.397 | 7.397 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 -4632.9048 -4632.9048 28.575319 80.982389 4.9846063 913.0437 913.0437 -1.939573 2744.4838 -3.4131771 2.2640411 509.83261 Loop time of 1.96e-06 on 1 procs for 0 steps with 1048 atoms 255.1% 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 | | 1.96e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8816.00 ave 8816 max 8816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131004.0 ave 131004 max 131004 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 262008.0 ave 262008 max 262008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262008 Ave neighs/atom = 250.00763 Neighbor list builds = 0 Dangerous builds = 0 1048 -4632.9048261424 eV 2.26404106058274 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01