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 -39.403035 0.0000000) to (7.8799022 39.403035 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7279413 4.7279413 3.5239994 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -39.403035 0.0000000) to (7.8799022 39.403035 3.5239994) create_atoms CPU = 0.002 seconds 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7279413 4.7279413 3.5239994 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -39.403035 0.0000000) to (7.8799022 39.403035 3.5239994) create_atoms CPU = 0.001 seconds 102 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 = 2 18 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 6 atoms, new total = 198 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 = 2 18 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) = 7.051 | 7.051 | 7.051 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -868.95285 0 -868.95285 9208.2968 43 0 -874.61979 0 -874.61979 -4622.5192 Loop time of 0.700496 on 1 procs for 43 steps with 198 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 = -868.952848496438 -874.618933918097 -874.619789105266 Force two-norm initial, final = 15.665265 0.10478895 Force max component initial, final = 8.2344666 0.024869763 Final line search alpha, max atom move = 1.0000000 0.024869763 Iterations, force evaluations = 43 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68221 | 0.68221 | 0.68221 | 0.0 | 97.39 Neigh | 0.0032962 | 0.0032962 | 0.0032962 | 0.0 | 0.47 Comm | 0.0097699 | 0.0097699 | 0.0097699 | 0.0 | 1.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005218 | | | 0.74 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5027.00 ave 5027 max 5027 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24698.0 ave 24698 max 24698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24698 Ave neighs/atom = 124.73737 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 : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.051 | 7.051 | 7.051 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -874.61979 0 -874.61979 -4622.5192 2188.3477 45 0 -874.62898 0 -874.62898 25.914947 2182.7984 Loop time of 0.0343719 on 1 procs for 2 steps with 198 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 = -874.619789105266 -874.628504008555 -874.628978960439 Force two-norm initial, final = 10.307357 0.54810869 Force max component initial, final = 7.4071019 0.46142922 Final line search alpha, max atom move = 0.00051090080 0.00023574456 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.032881 | 0.032881 | 0.032881 | 0.0 | 95.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041128 | 0.00041128 | 0.00041128 | 0.0 | 1.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00108 | | | 3.14 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5021.00 ave 5021 max 5021 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24628.0 ave 24628 max 24628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24628 Ave neighs/atom = 124.38384 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 = 2 18 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) = 6.683 | 6.683 | 6.683 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -874.62898 0 -874.62898 25.914947 Loop time of 6.595e-06 on 1 procs for 0 steps with 198 atoms 151.6% 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 | | 6.595e-06 | | |100.00 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5021.00 ave 5021 max 5021 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24658.0 ave 24658 max 24658 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 = 24658 Ave neighs/atom = 124.53535 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) = 6.683 | 6.683 | 6.683 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 -874.62898 -874.62898 7.8706196 78.80607 3.5192087 25.914947 25.914947 338.2906 -62.743243 -197.80251 2.2553013 119.83292 Loop time of 6.856e-06 on 1 procs for 0 steps with 198 atoms 189.6% 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 | | 6.856e-06 | | |100.00 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5021.00 ave 5021 max 5021 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24658.0 ave 24658 max 24658 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49316.0 ave 49316 max 49316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49316 Ave neighs/atom = 249.07071 Neighbor list builds = 0 Dangerous builds = 0 198 -874.628978960439 eV 2.25530134332829 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01