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 -53.211224 0.0000000) to (37.626017 53.211224 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9409501 6.0679466 4.9836877 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -53.211224 0.0000000) to (37.626017 53.211224 4.9836877) create_atoms CPU = 0.003 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9409501 6.0679466 4.9836877 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.211224 0.0000000) to (37.626017 53.211224 4.9836877) create_atoms CPU = 0.002 seconds 916 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 = 9 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 4 atoms, new total = 1824 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 = 9 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) = 8.444 | 8.444 | 8.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6556.8071 0 -6556.8071 142137.58 56 0 -8079.4157 0 -8079.4157 5476.6099 Loop time of 3.54923 on 1 procs for 56 steps with 1824 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6556.80713081199 -8079.40960288565 -8079.41565665739 Force two-norm initial, final = 1846.6004 0.25308410 Force max component initial, final = 430.01963 0.049031589 Final line search alpha, max atom move = 1.0000000 0.049031589 Iterations, force evaluations = 56 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5067 | 3.5067 | 3.5067 | 0.0 | 98.80 Neigh | 0.013164 | 0.013164 | 0.013164 | 0.0 | 0.37 Comm | 0.01736 | 0.01736 | 0.01736 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01199 | | | 0.34 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13026.0 ave 13026 max 13026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231056.0 ave 231056 max 231056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231056 Ave neighs/atom = 126.67544 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.444 | 8.444 | 8.444 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -8079.4157 0 -8079.4157 5476.6099 19955.946 60 0 -8079.5848 0 -8079.5848 -23.482062 20015.124 Loop time of 0.270137 on 1 procs for 4 steps with 1824 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 = -8079.41565665739 -8079.58475549375 -8079.58478688045 Force two-norm initial, final = 135.25929 0.59403445 Force max component initial, final = 121.97533 0.35776800 Final line search alpha, max atom move = 0.00087638788 0.00031354354 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26542 | 0.26542 | 0.26542 | 0.0 | 98.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078471 | 0.00078471 | 0.00078471 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003931 | | | 1.46 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13016.0 ave 13016 max 13016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 229256.0 ave 229256 max 229256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229256 Ave neighs/atom = 125.68860 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 = 9 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) = 8.075 | 8.075 | 8.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8079.5848 0 -8079.5848 -23.482062 Loop time of 2.17e-06 on 1 procs for 0 steps with 1824 atoms 184.3% 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 | | 2.17e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13016.0 ave 13016 max 13016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 228712.0 ave 228712 max 228712 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 = 228712 Ave neighs/atom = 125.39035 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) = 8.075 | 8.075 | 8.075 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 -8079.5848 -8079.5848 37.634161 106.70952 4.9839409 -23.482062 -23.482062 -18.60876 -23.197254 -28.640172 2.3291702 624.69504 Loop time of 2.546e-06 on 1 procs for 0 steps with 1824 atoms 235.7% 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 | | 2.546e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13016.0 ave 13016 max 13016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 228712.0 ave 228712 max 228712 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 457424.0 ave 457424 max 457424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 457424 Ave neighs/atom = 250.78070 Neighbor list builds = 0 Dangerous builds = 0 1824 -8079.58478688045 eV 2.32917015025096 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04