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 -42.287993 0.0000000) to (14.951063 42.287993 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9836877 5.8733323 4.9836877 Created 288 atoms using lattice units in orthogonal box = (0.0000000 -42.287993 0.0000000) to (14.951063 42.287993 4.9836877) create_atoms CPU = 0.001 seconds 288 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9836877 5.8733323 4.9836877 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -42.287993 0.0000000) to (14.951063 42.287993 4.9836877) create_atoms CPU = 0.001 seconds 292 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 = 4 20 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 = 576 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 = 4 20 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) = 7.228 | 7.228 | 7.228 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2330.1173 0 -2330.1173 146076.61 48 0 -2546.5436 0 -2546.5436 11723.283 Loop time of 1.12677 on 1 procs for 48 steps with 576 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2330.11731989894 -2546.54115723032 -2546.5436425074 Force two-norm initial, final = 483.71600 0.17231340 Force max component initial, final = 109.91903 0.025053446 Final line search alpha, max atom move = 1.0000000 0.025053446 Iterations, force evaluations = 48 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1112 | 1.1112 | 1.1112 | 0.0 | 98.62 Neigh | 0.0040947 | 0.0040947 | 0.0040947 | 0.0 | 0.36 Comm | 0.0072331 | 0.0072331 | 0.0072331 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004238 | | | 0.38 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6693.00 ave 6693 max 6693 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 72492.0 ave 72492 max 72492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72492 Ave neighs/atom = 125.85417 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 : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.228 | 7.228 | 7.228 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -2546.5436 0 -2546.5436 11723.283 6301.8776 54 0 -2546.7745 0 -2546.7745 191.6427 6340.8145 Loop time of 0.0999384 on 1 procs for 6 steps with 576 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 = -2546.5436425074 -2546.77394083622 -2546.77453112247 Force two-norm initial, final = 90.379178 1.6246020 Force max component initial, final = 77.593175 1.4556205 Final line search alpha, max atom move = 0.00028607658 0.00041641895 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.097212 | 0.097212 | 0.097212 | 0.0 | 97.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048987 | 0.00048987 | 0.00048987 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002237 | | | 2.24 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6713.00 ave 6713 max 6713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71972.0 ave 71972 max 71972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71972 Ave neighs/atom = 124.95139 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 = 4 20 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) = 6.859 | 6.859 | 6.859 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2546.7745 0 -2546.7745 191.6427 Loop time of 2.126e-06 on 1 procs for 0 steps with 576 atoms 188.1% 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 | | 2.126e-06 | | |100.00 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6632.00 ave 6632 max 6632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71736.0 ave 71736 max 71736 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 = 71736 Ave neighs/atom = 124.54167 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) = 6.859 | 6.859 | 6.859 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 -2546.7745 -2546.7745 14.976723 85.005817 4.9805765 191.6427 191.6427 157.15692 369.67072 48.10047 2.3132937 344.45565 Loop time of 2.323e-06 on 1 procs for 0 steps with 576 atoms 258.3% 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 | | 2.323e-06 | | |100.00 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6632.00 ave 6632 max 6632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71736.0 ave 71736 max 71736 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 143472.0 ave 143472 max 143472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143472 Ave neighs/atom = 249.08333 Neighbor list builds = 0 Dangerous builds = 0 576 -2546.77453112247 eV 2.31329366952492 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01