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 -66.490688 0.0000000) to (33.245344 66.490688 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8560615 4.8560615 3.5239994 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -66.490688 0.0000000) to (33.245344 66.490688 3.5239994) create_atoms CPU = 0.001 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8560615 4.8560615 3.5239994 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -66.490688 0.0000000) to (33.245344 66.490688 3.5239994) create_atoms CPU = 0.001 seconds 714 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 30 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 0 atoms, new total = 1426 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 = 8 30 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) = 7.926 | 7.926 | 7.926 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5967.7067 0 -5967.7067 106237.63 57 0 -6313.5238 0 -6313.5238 9653.1425 Loop time of 2.99591 on 1 procs for 57 steps with 1426 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 = -5967.70669447963 -6313.5182058368 -6313.52383921602 Force two-norm initial, final = 531.80105 0.26959239 Force max component initial, final = 103.97036 0.063009590 Final line search alpha, max atom move = 1.0000000 0.063009590 Iterations, force evaluations = 57 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9698 | 2.9698 | 2.9698 | 0.0 | 99.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01666 | 0.01666 | 0.01666 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00949 | | | 0.32 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13442.0 ave 13442 max 13442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 178088.0 ave 178088 max 178088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178088 Ave neighs/atom = 124.88640 Neighbor list builds = 0 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 : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.941 | 7.941 | 7.941 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -6313.5238 0 -6313.5238 9653.1425 15579.642 63 0 -6313.9882 0 -6313.9882 170.97772 15658.679 Loop time of 0.203691 on 1 procs for 6 steps with 1426 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 = -6313.52383921602 -6313.98573381041 -6313.98815730511 Force two-norm initial, final = 190.75063 4.3016779 Force max component initial, final = 170.44335 4.1101655 Final line search alpha, max atom move = 0.00015943603 0.00065530845 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19957 | 0.19957 | 0.19957 | 0.0 | 97.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081656 | 0.00081656 | 0.00081656 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0033 | | | 1.62 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14687.0 ave 14687 max 14687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 178506.0 ave 178506 max 178506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178506 Ave neighs/atom = 125.17952 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 = 8 31 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) = 7.573 | 7.573 | 7.573 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6313.9882 0 -6313.9882 170.97772 Loop time of 1.739e-06 on 1 procs for 0 steps with 1426 atoms 172.5% 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 | | 1.739e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14667.0 ave 14667 max 14667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 178036.0 ave 178036 max 178036 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 = 178036 Ave neighs/atom = 124.84993 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) = 7.573 | 7.573 | 7.573 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 -6313.9882 -6313.9882 33.216987 133.69613 3.5259493 170.97772 170.97772 420.1883 121.3636 -28.618734 2.2337848 398.99729 Loop time of 1.974e-06 on 1 procs for 0 steps with 1426 atoms 202.6% 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 | | 1.974e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14667.0 ave 14667 max 14667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 178036.0 ave 178036 max 178036 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 356072.0 ave 356072 max 356072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 356072 Ave neighs/atom = 249.69986 Neighbor list builds = 0 Dangerous builds = 0 1426 -6313.98815730511 eV 2.23378484354271 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03