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 -51.795526 0.0000000) to (18.311238 51.795526 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7473580 5.7546669 4.9836877 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -51.795526 0.0000000) to (18.311238 51.795526 4.9836877) create_atoms CPU = 0.002 seconds 434 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7473580 5.7546669 4.9836877 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -51.795526 0.0000000) to (18.311238 51.795526 4.9836877) create_atoms CPU = 0.001 seconds 434 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 24 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 12 atoms, new total = 856 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 24 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) = 7.727 | 7.727 | 7.727 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3766.0377 0 -3766.0377 8504.1948 76 0 -3786.5309 0 -3786.5309 -6928.8624 Loop time of 2.12765 on 1 procs for 76 steps with 856 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3766.0377162545 -3786.52747587759 -3786.53087343283 Force two-norm initial, final = 60.286466 0.19716512 Force max component initial, final = 21.705191 0.045557590 Final line search alpha, max atom move = 1.0000000 0.045557590 Iterations, force evaluations = 76 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1063 | 2.1063 | 2.1063 | 0.0 | 98.99 Neigh | 0.0046325 | 0.0046325 | 0.0046325 | 0.0 | 0.22 Comm | 0.010228 | 0.010228 | 0.010228 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006528 | | | 0.31 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7991.00 ave 7991 max 7991 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106866.0 ave 106866 max 106866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106866 Ave neighs/atom = 124.84346 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 : 76 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 76 0 -3786.5309 0 -3786.5309 -6928.8624 9453.4597 79 0 -3786.565 0 -3786.565 -3132.408 9433.8198 Loop time of 0.0885024 on 1 procs for 3 steps with 856 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 = -3786.53087343283 -3786.56367138512 -3786.56498439583 Force two-norm initial, final = 37.973931 0.21171735 Force max component initial, final = 33.328496 0.043206516 Final line search alpha, max atom move = 0.00014761710 6.3780206e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.086826 | 0.086826 | 0.086826 | 0.0 | 98.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034724 | 0.00034724 | 0.00034724 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001329 | | | 1.50 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8162.00 ave 8162 max 8162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106564.0 ave 106564 max 106564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106564 Ave neighs/atom = 124.49065 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 24 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) = 7.360 | 7.360 | 7.360 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3786.565 0 -3786.565 -3132.408 Loop time of 1.587e-06 on 1 procs for 0 steps with 856 atoms 189.0% 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 | | 1.587e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8162.00 ave 8162 max 8162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106636.0 ave 106636 max 106636 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 = 106636 Ave neighs/atom = 124.57477 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) = 7.360 | 7.360 | 7.360 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 -3786.565 -3786.565 18.274669 103.59105 4.9832861 -3132.408 -3132.408 -2.2970299 -9387.5897 -7.3373126 2.306614 457.60268 Loop time of 2.211e-06 on 1 procs for 0 steps with 856 atoms 180.9% 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 | | 2.211e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8162.00 ave 8162 max 8162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106636.0 ave 106636 max 106636 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 213272.0 ave 213272 max 213272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213272 Ave neighs/atom = 249.14953 Neighbor list builds = 0 Dangerous builds = 0 856 -3786.56498439583 eV 2.30661396674292 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02