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_PunDarlingKecskes_2015_CuTa__SM_399364650444_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -42.773258 0.0000000) to (52.386329 42.773258 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9870090 5.4994189 5.9032705 Created 1659 atoms using lattice units in orthogonal box = (0.0000000 -42.773258 0.0000000) to (52.386329 42.773258 8.8549058) create_atoms CPU = 0.003 seconds 1659 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9870090 5.4994189 5.9032705 Created 1683 atoms using lattice units in orthogonal box = (0.0000000 -42.773258 0.0000000) to (52.386329 42.773258 8.8549058) create_atoms CPU = 0.003 seconds 1683 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 = 8.150959 ghost atom cutoff = 8.150959 binsize = 4.0754795, bins = 13 21 3 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 3 atoms, new total = 3339 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_399364650444_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 = 8.150959 ghost atom cutoff = 8.150959 binsize = 4.0754795, bins = 13 21 3 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) = 9.193 | 9.193 | 9.193 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11622.141 0 -11622.141 15449.9 107 0 -11775.847 0 -11775.847 -3100.894 Loop time of 8.27988 on 1 procs for 107 steps with 3339 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 = -11622.1408478565 -11775.8367890536 -11775.8467716565 Force two-norm initial, final = 114.17285 0.32531227 Force max component initial, final = 9.9893090 0.088054715 Final line search alpha, max atom move = 0.87288221 0.076861395 Iterations, force evaluations = 107 200 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.1498 | 8.1498 | 8.1498 | 0.0 | 98.43 Neigh | 0.066525 | 0.066525 | 0.066525 | 0.0 | 0.80 Comm | 0.028209 | 0.028209 | 0.028209 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0353 | | | 0.43 Nlocal: 3339.00 ave 3339 max 3339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11504.0 ave 11504 max 11504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 328263.0 ave 328263 max 328263 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328263 Ave neighs/atom = 98.311770 Neighbor list builds = 4 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 : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 9.194 | 9.194 | 9.194 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -11775.847 0 -11775.847 -3100.894 39682.977 110 0 -11775.967 0 -11775.967 26.812308 39592.903 Loop time of 0.250165 on 1 procs for 3 steps with 3339 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 = -11775.8467716565 -11775.9668773371 -11775.9669456824 Force two-norm initial, final = 140.03235 1.5701847 Force max component initial, final = 96.405008 1.4129315 Final line search alpha, max atom move = 0.00033989378 0.00048024664 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2461 | 0.2461 | 0.2461 | 0.0 | 98.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056345 | 0.00056345 | 0.00056345 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003503 | | | 1.40 Nlocal: 3339.00 ave 3339 max 3339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11505.0 ave 11505 max 11505 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 328240.0 ave 328240 max 328240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328240 Ave neighs/atom = 98.304882 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 = 8.150959 ghost atom cutoff = 8.150959 binsize = 4.0754795, bins = 13 22 3 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) = 8.826 | 8.826 | 8.826 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11775.967 0 -11775.967 26.812308 Loop time of 2.401e-06 on 1 procs for 0 steps with 3339 atoms 166.6% 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 | | 2.401e-06 | | |100.00 Nlocal: 3339.00 ave 3339 max 3339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11537.0 ave 11537 max 11537 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 328471.0 ave 328471 max 328471 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 = 328471 Ave neighs/atom = 98.374064 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) = 8.826 | 8.826 | 8.826 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 -11775.967 -11775.967 52.312641 85.589341 8.8428247 26.812308 26.812308 57.095621 24.043643 -0.70234037 2.2647661 1793.9357 Loop time of 2.63e-06 on 1 procs for 0 steps with 3339 atoms 304.2% 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 | | 2.63e-06 | | |100.00 Nlocal: 3339.00 ave 3339 max 3339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11537.0 ave 11537 max 11537 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 328471.0 ave 328471 max 328471 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 656942.0 ave 656942 max 656942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 656942 Ave neighs/atom = 196.74813 Neighbor list builds = 0 Dangerous builds = 0 3339 -11775.9669456824 eV 2.26476614092174 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09