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 -63.853633 0.0000000) to (36.865912 63.853633 6.2613639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6716788 5.7304543 6.2613639 Created 1247 atoms using lattice units in orthogonal box = (0.0000000 -63.853633 0.0000000) to (36.865912 63.853633 6.2613639) create_atoms CPU = 0.012 seconds 1247 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6716788 5.7304543 6.2613639 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -63.853633 0.0000000) to (36.865912 63.853633 6.2613639) create_atoms CPU = 0.012 seconds 1251 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 = 10 32 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 3 atoms, new total = 2495 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 = 10 32 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) = 8.640 | 8.640 | 8.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8291.709 0 -8291.709 58300.365 117 0 -8806.0894 0 -8806.0894 4040.8904 Loop time of 14.1304 on 1 procs for 117 steps with 2495 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 = -8291.70898823471 -8806.08078127581 -8806.08944127789 Force two-norm initial, final = 969.54822 0.31394366 Force max component initial, final = 263.91300 0.045863079 Final line search alpha, max atom move = 1.0000000 0.045863079 Iterations, force evaluations = 117 213 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.943 | 13.943 | 13.943 | 0.0 | 98.67 Neigh | 0.07151 | 0.07151 | 0.07151 | 0.0 | 0.51 Comm | 0.059536 | 0.059536 | 0.059536 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05667 | | | 0.40 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11078.0 ave 11078 max 11078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 246164.0 ave 246164 max 246164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 246164 Ave neighs/atom = 98.662926 Neighbor list builds = 3 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 : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.650 | 8.650 | 8.650 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -8806.0894 0 -8806.0894 4040.8904 29478.783 122 0 -8806.3294 0 -8806.3294 -9.3983869 29564.533 Loop time of 0.532134 on 1 procs for 5 steps with 2495 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 = -8806.08944127786 -8806.3285099565 -8806.32936599492 Force two-norm initial, final = 151.29601 1.4880405 Force max component initial, final = 138.33850 1.0985653 Final line search alpha, max atom move = 8.9973052e-05 9.8841276e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52239 | 0.52239 | 0.52239 | 0.0 | 98.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002186 | 0.002186 | 0.002186 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007557 | | | 1.42 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11856.0 ave 11856 max 11856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 246837.0 ave 246837 max 246837 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 246837 Ave neighs/atom = 98.932665 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 = 10 32 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) = 8.282 | 8.282 | 8.282 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8806.3294 0 -8806.3294 -9.3983869 Loop time of 6.956e-06 on 1 procs for 0 steps with 2495 atoms 215.6% 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 | | 6.956e-06 | | |100.00 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11880.0 ave 11880 max 11880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 246659.0 ave 246659 max 246659 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 = 246659 Ave neighs/atom = 98.861323 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) = 8.282 | 8.282 | 8.282 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 -8806.3294 -8806.3294 36.856164 128.18281 6.2579359 -9.3983869 -9.3983869 -59.518279 -16.302031 47.62515 2.3050853 982.45538 Loop time of 7.738e-06 on 1 procs for 0 steps with 2495 atoms 258.5% 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 | | 7.738e-06 | | |100.00 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11880.0 ave 11880 max 11880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 246659.0 ave 246659 max 246659 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 493318.0 ave 493318 max 493318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 493318 Ave neighs/atom = 197.72265 Neighbor list builds = 0 Dangerous builds = 0 2495 -8806.32936599492 eV 2.30508534466328 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16