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 -37.914441 0.0000000) to (46.435518 37.914441 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9099750 5.5148278 5.9032705 Created 1317 atoms using lattice units in orthogonal box = (0.0000000 -37.914441 0.0000000) to (46.435518 37.914441 8.8549058) create_atoms CPU = 0.003 seconds 1317 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9099750 5.5148278 5.9032705 Created 1323 atoms using lattice units in orthogonal box = (0.0000000 -37.914441 0.0000000) to (46.435518 37.914441 8.8549058) create_atoms CPU = 0.002 seconds 1323 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 = 12 19 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 0 atoms, new total = 2640 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 = 12 19 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) = 8.600 | 8.600 | 8.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8894.6246 0 -8894.6246 53917.862 72 0 -9303.0742 0 -9303.0742 7075.917 Loop time of 3.61944 on 1 procs for 72 steps with 2640 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 = -8894.62462174944 -9303.06620628636 -9303.07424186054 Force two-norm initial, final = 354.01877 0.31817036 Force max component initial, final = 56.851514 0.062422685 Final line search alpha, max atom move = 1.0000000 0.062422685 Iterations, force evaluations = 72 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5538 | 3.5538 | 3.5538 | 0.0 | 98.19 Neigh | 0.035737 | 0.035737 | 0.035737 | 0.0 | 0.99 Comm | 0.013575 | 0.013575 | 0.013575 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01636 | | | 0.45 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9793.00 ave 9793 max 9793 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 259767.0 ave 259767 max 259767 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259767 Ave neighs/atom = 98.396591 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 : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.601 | 8.601 | 8.601 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -9303.0742 0 -9303.0742 7075.917 31179.482 79 0 -9303.7922 0 -9303.7922 60.322472 31335.881 Loop time of 0.267735 on 1 procs for 7 steps with 2640 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 = -9303.07424186052 -9303.79191618924 -9303.79217555799 Force two-norm initial, final = 271.29623 2.1478658 Force max component initial, final = 234.81576 1.5489787 Final line search alpha, max atom move = 0.00043448513 0.00067300822 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2631 | 0.2631 | 0.2631 | 0.0 | 98.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066571 | 0.00066571 | 0.00066571 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003968 | | | 1.48 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9810.00 ave 9810 max 9810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 259797.0 ave 259797 max 259797 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259797 Ave neighs/atom = 98.407955 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 = 12 19 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) = 8.233 | 8.233 | 8.233 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9303.7922 0 -9303.7922 60.322472 Loop time of 2.473e-06 on 1 procs for 0 steps with 2640 atoms 161.7% 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 | | 2.473e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9866.00 ave 9866 max 9866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 259241.0 ave 259241 max 259241 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 = 259241 Ave neighs/atom = 98.197348 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) = 8.233 | 8.233 | 8.233 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 -9303.7922 -9303.7922 46.478189 76.290833 8.8373152 60.322472 60.322472 54.775078 79.680417 46.511921 2.3160475 1479.8935 Loop time of 2.216e-06 on 1 procs for 0 steps with 2640 atoms 361.0% 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 | | 2.216e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9866.00 ave 9866 max 9866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 259241.0 ave 259241 max 259241 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 518482.0 ave 518482 max 518482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518482 Ave neighs/atom = 196.39470 Neighbor list builds = 0 Dangerous builds = 0 2640 -9303.79217555799 eV 2.31604746629439 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04