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 -43.829547 0.0000000) to (35.786676 43.829547 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1123822 5.0687232 5.9032705 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -43.829547 0.0000000) to (35.786676 43.829547 8.8549058) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1123822 5.0687232 5.9032705 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -43.829547 0.0000000) to (35.786676 43.829547 8.8549058) create_atoms CPU = 0.002 seconds 1184 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 = 9 22 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 24 atoms, new total = 2336 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 = 9 22 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) = 8.538 | 8.538 | 8.538 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7787.553 0 -7787.553 48898.515 80 0 -8231.3819 0 -8231.3819 -1528.7049 Loop time of 4.18305 on 1 procs for 80 steps with 2336 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 = -7787.55302652169 -8231.37437685249 -8231.38190243388 Force two-norm initial, final = 655.96259 0.27243491 Force max component initial, final = 106.22308 0.042522195 Final line search alpha, max atom move = 1.0000000 0.042522195 Iterations, force evaluations = 80 155 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.128 | 4.128 | 4.128 | 0.0 | 98.68 Neigh | 0.023012 | 0.023012 | 0.023012 | 0.0 | 0.55 Comm | 0.01502 | 0.01502 | 0.01502 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01703 | | | 0.41 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9110.00 ave 9110 max 9110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 229824.0 ave 229824 max 229824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229824 Ave neighs/atom = 98.383562 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 : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.539 | 8.539 | 8.539 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -8231.3819 0 -8231.3819 -1528.7049 27778.084 83 0 -8231.4604 0 -8231.4604 297.75388 27741.033 Loop time of 0.140403 on 1 procs for 3 steps with 2336 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 = -8231.38190243387 -8231.45653384047 -8231.46036142679 Force two-norm initial, final = 67.932780 11.803994 Force max component initial, final = 60.328502 11.445660 Final line search alpha, max atom move = 7.7959149e-05 0.00089229393 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13792 | 0.13792 | 0.13792 | 0.0 | 98.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036652 | 0.00036652 | 0.00036652 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002119 | | | 1.51 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9065.00 ave 9065 max 9065 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230336.0 ave 230336 max 230336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230336 Ave neighs/atom = 98.602740 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 = 9 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) = 8.170 | 8.170 | 8.170 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8231.4604 0 -8231.4604 297.75388 Loop time of 2.142e-06 on 1 procs for 0 steps with 2336 atoms 186.7% 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 | | 2.142e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9065.00 ave 9065 max 9065 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230344.0 ave 230344 max 230344 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 = 230344 Ave neighs/atom = 98.606164 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) = 8.170 | 8.170 | 8.170 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 -8231.4604 -8231.4604 35.760127 87.771083 8.8383687 297.75388 297.75388 98.036353 661.88579 133.3395 2.2983225 1335.1746 Loop time of 2.615e-06 on 1 procs for 0 steps with 2336 atoms 267.7% 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 | | 2.615e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9065.00 ave 9065 max 9065 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230344.0 ave 230344 max 230344 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 460688.0 ave 460688 max 460688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 460688 Ave neighs/atom = 197.21233 Neighbor list builds = 0 Dangerous builds = 0 2336 -8231.46036142679 eV 2.29832248757612 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04