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 -42.871303 0.0000000) to (21.435651 42.871303 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0553935 4.0553935 3.5239994 Created 296 atoms using lattice units in orthogonal box = (0.0000000 -42.871303 0.0000000) to (21.435651 42.871303 3.5239994) create_atoms CPU = 0.001 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0553935 4.0553935 3.5239994 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -42.871303 0.0000000) to (21.435651 42.871303 3.5239994) create_atoms CPU = 0.000 seconds 298 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 20 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 = 588 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 20 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) = 7.191 | 7.191 | 7.191 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2288.5291 0 -2288.5291 116342.9 51 0 -2599.5499 0 -2599.5499 -2104.9976 Loop time of 1.18311 on 1 procs for 51 steps with 588 atoms 96.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2288.52914985775 -2599.5483113686 -2599.54990206322 Force two-norm initial, final = 740.99148 0.14606485 Force max component initial, final = 252.79149 0.029202103 Final line search alpha, max atom move = 1.0000000 0.029202103 Iterations, force evaluations = 51 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1655 | 1.1655 | 1.1655 | 0.0 | 98.51 Neigh | 0.0045839 | 0.0045839 | 0.0045839 | 0.0 | 0.39 Comm | 0.0086231 | 0.0086231 | 0.0086231 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004442 | | | 0.38 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7824.00 ave 7824 max 7824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74662.0 ave 74662 max 74662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74662 Ave neighs/atom = 126.97619 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 : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.191 | 7.191 | 7.191 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -2599.5499 0 -2599.5499 -2104.9976 6476.9298 54 0 -2599.5597 0 -2599.5597 9.9507546 6469.3244 Loop time of 0.0777109 on 1 procs for 3 steps with 588 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 = -2599.54990206322 -2599.55972466121 -2599.55973510081 Force two-norm initial, final = 16.100010 0.19055604 Force max component initial, final = 13.134143 0.11939166 Final line search alpha, max atom move = 0.0054194998 0.00064704307 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.075687 | 0.075687 | 0.075687 | 0.0 | 97.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040899 | 0.00040899 | 0.00040899 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001615 | | | 2.08 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7889.00 ave 7889 max 7889 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73788.0 ave 73788 max 73788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73788 Ave neighs/atom = 125.48980 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 20 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) = 6.823 | 6.823 | 6.823 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2599.5597 0 -2599.5597 9.9507546 Loop time of 1.994e-06 on 1 procs for 0 steps with 588 atoms 200.6% 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 | | 1.994e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7889.00 ave 7889 max 7889 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73882.0 ave 73882 max 73882 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 = 73882 Ave neighs/atom = 125.64966 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) = 6.823 | 6.823 | 6.823 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 -2599.5597 -2599.5597 21.426389 85.620026 3.5264246 9.9507546 9.9507546 29.555459 2.1038807 -1.8070757 2.3066516 193.36812 Loop time of 2.39e-06 on 1 procs for 0 steps with 588 atoms 209.2% 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 | | 2.39e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7889.00 ave 7889 max 7889 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73882.0 ave 73882 max 73882 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 147764.0 ave 147764 max 147764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147764 Ave neighs/atom = 251.29932 Neighbor list builds = 0 Dangerous builds = 0 588 -2599.55973510081 eV 2.30665164651223 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01