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 -37.626017 0.0000000) to (26.605612 37.626017 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0679466 5.9409501 4.9836877 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.626017 0.0000000) to (26.605612 37.626017 4.9836877) create_atoms CPU = 0.002 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0679466 5.9409501 4.9836877 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.626017 0.0000000) to (26.605612 37.626017 4.9836877) create_atoms CPU = 0.001 seconds 458 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 = 6 17 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 2 atoms, new total = 912 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 = 6 17 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) = 7.695 | 7.695 | 7.695 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3593.3866 0 -3593.3866 132499.63 99 0 -4032.916 0 -4032.916 7639.9257 Loop time of 3.85256 on 1 procs for 99 steps with 912 atoms 96.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3593.38660423648 -4032.91224567829 -4032.91595984563 Force two-norm initial, final = 838.58950 0.21936817 Force max component initial, final = 268.90376 0.053904027 Final line search alpha, max atom move = 1.0000000 0.053904027 Iterations, force evaluations = 99 191 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8219 | 3.8219 | 3.8219 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018316 | 0.018316 | 0.018316 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01239 | | | 0.32 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7539.00 ave 7539 max 7539 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114214.0 ave 114214 max 114214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114214 Ave neighs/atom = 125.23465 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 : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.705 | 7.705 | 7.705 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -4032.916 0 -4032.916 7639.9257 9977.9729 102 0 -4033.0253 0 -4033.0253 1.8916878 10019.515 Loop time of 0.117416 on 1 procs for 3 steps with 912 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 = -4032.91595984563 -4033.02308875064 -4033.02528900563 Force two-norm initial, final = 84.196356 0.61322113 Force max component initial, final = 61.161162 0.46693694 Final line search alpha, max atom move = 0.00016682219 7.7895443e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11524 | 0.11524 | 0.11524 | 0.0 | 98.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039548 | 0.00039548 | 0.00039548 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001779 | | | 1.52 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8019.00 ave 8019 max 8019 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116092.0 ave 116092 max 116092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116092 Ave neighs/atom = 127.29386 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 = 6 17 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) = 7.336 | 7.336 | 7.336 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4033.0253 0 -4033.0253 1.8916878 Loop time of 2.18e-06 on 1 procs for 0 steps with 912 atoms 183.5% 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 | | 2.18e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7999.00 ave 7999 max 7999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115652.0 ave 115652 max 115652 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 = 115652 Ave neighs/atom = 126.81140 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) = 7.336 | 7.336 | 7.336 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 -4033.0253 -4033.0253 26.637204 75.428904 4.9867808 1.8916878 1.8916878 74.754486 -23.108927 -45.970495 2.3131286 742.73482 Loop time of 2.739e-06 on 1 procs for 0 steps with 912 atoms 255.6% 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 | | 2.739e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7999.00 ave 7999 max 7999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115652.0 ave 115652 max 115652 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 231304.0 ave 231304 max 231304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231304 Ave neighs/atom = 253.62281 Neighbor list builds = 0 Dangerous builds = 0 912 -4033.02528900563 eV 2.31312856891731 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04