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 -56.468107 0.0000000) to (28.234054 56.468107 3.6150001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0913867 5.0913867 3.6150001 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -56.468107 0.0000000) to (28.234054 56.468107 3.6150001) create_atoms CPU = 0.001 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0913867 5.0913867 3.6150001 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.468107 0.0000000) to (28.234054 56.468107 3.6150001) create_atoms CPU = 0.001 seconds 490 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 = 7 28 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 0 atoms, new total = 978 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 = 7 28 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) = 7.320 | 7.320 | 7.320 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3262.2379 0 -3262.2379 60908.632 91 0 -3455.1649 0 -3455.1649 5614.5767 Loop time of 2.0389 on 1 procs for 91 steps with 978 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3262.23792610579 -3455.16191780258 -3455.16488209055 Force two-norm initial, final = 323.57893 0.16366062 Force max component initial, final = 67.139436 0.033990829 Final line search alpha, max atom move = 1.0000000 0.033990829 Iterations, force evaluations = 91 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2 | 2 | 2 | 0.0 | 98.09 Neigh | 0.010353 | 0.010353 | 0.010353 | 0.0 | 0.51 Comm | 0.017227 | 0.017227 | 0.017227 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01131 | | | 0.55 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8813.00 ave 8813 max 8813 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96264.0 ave 96264 max 96264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96264 Ave neighs/atom = 98.429448 Neighbor list builds = 2 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 : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.325 | 7.325 | 7.325 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -3455.1649 0 -3455.1649 5614.5767 11526.96 96 0 -3455.321 0 -3455.321 -70.13351 11573.682 Loop time of 0.0892748 on 1 procs for 5 steps with 978 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 = -3455.16488209055 -3455.32065455104 -3455.3209956573 Force two-norm initial, final = 80.920944 1.6278970 Force max component initial, final = 68.716601 1.6081545 Final line search alpha, max atom move = 0.00033797490 0.00054351584 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.086365 | 0.086365 | 0.086365 | 0.0 | 96.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005307 | 0.0005307 | 0.0005307 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002379 | | | 2.66 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9378.00 ave 9378 max 9378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96434.0 ave 96434 max 96434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96434 Ave neighs/atom = 98.603272 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 = 7 28 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) = 6.952 | 6.952 | 6.952 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3455.321 0 -3455.321 -70.13351 Loop time of 2.011e-06 on 1 procs for 0 steps with 978 atoms 198.9% 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 | | 2.011e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8837.00 ave 8837 max 8837 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96268.0 ave 96268 max 96268 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 = 96268 Ave neighs/atom = 98.433538 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) = 6.952 | 6.952 | 6.952 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 -3455.321 -3455.321 28.197319 113.36858 3.6205204 -70.13351 -70.13351 -222.33158 -9.9301267 21.86118 2.3108021 156.53496 Loop time of 2.182e-06 on 1 procs for 0 steps with 978 atoms 229.1% 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 | | 2.182e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8837.00 ave 8837 max 8837 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96268.0 ave 96268 max 96268 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 192536.0 ave 192536 max 192536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192536 Ave neighs/atom = 196.86708 Neighbor list builds = 0 Dangerous builds = 0 978 -3455.3209956573 eV 2.3108021129822 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02