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 -47.958396 0.0000000) to (29.368400 47.958396 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3397091 5.4498178 5.9032705 Created 1054 atoms using lattice units in orthogonal box = (0.0000000 -47.958396 0.0000000) to (29.368400 47.958396 8.8549058) create_atoms CPU = 0.002 seconds 1054 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3397091 5.4498178 5.9032705 Created 1078 atoms using lattice units in orthogonal box = (0.0000000 -47.958396 0.0000000) to (29.368400 47.958396 8.8549058) create_atoms CPU = 0.001 seconds 1078 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 = 8 24 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 20 atoms, new total = 2112 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 = 8 24 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) = 8.496 | 8.496 | 8.496 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7457.3968 0 -7457.3968 3730.1434 13 0 -7466.2715 0 -7466.2715 2317.0116 Loop time of 0.580159 on 1 procs for 13 steps with 2112 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 = -7457.3967958328 -7466.26896871704 -7466.27149205615 Force two-norm initial, final = 18.877268 0.096149967 Force max component initial, final = 1.9497601 0.0057813411 Final line search alpha, max atom move = 1.0000000 0.0057813411 Iterations, force evaluations = 13 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57553 | 0.57553 | 0.57553 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021761 | 0.0021761 | 0.0021761 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002456 | | | 0.42 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8820.00 ave 8820 max 8820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210528.0 ave 210528 max 210528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210528 Ave neighs/atom = 99.681818 Neighbor list builds = 0 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 : 13 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.496 | 8.496 | 8.496 Mbytes Step Temp E_pair E_mol TotEng Press Volume 13 0 -7466.2715 0 -7466.2715 2317.0116 24943.585 18 0 -7466.4698 0 -7466.4698 199.51985 24980.994 Loop time of 0.159612 on 1 procs for 5 steps with 2112 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 = -7466.27149205615 -7466.46828456222 -7466.46978244095 Force two-norm initial, final = 95.484399 5.6709595 Force max component initial, final = 94.918817 4.4909684 Final line search alpha, max atom move = 0.00017704015 0.00079508173 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15641 | 0.15641 | 0.15641 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046487 | 0.00046487 | 0.00046487 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002738 | | | 1.72 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8820.00 ave 8820 max 8820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210288.0 ave 210288 max 210288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210288 Ave neighs/atom = 99.568182 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 = 8 24 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) = 8.128 | 8.128 | 8.128 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7466.4698 0 -7466.4698 199.51985 Loop time of 2.433e-06 on 1 procs for 0 steps with 2112 atoms 164.4% 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 | | 2.433e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8820.00 ave 8820 max 8820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 209952.0 ave 209952 max 209952 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 = 209952 Ave neighs/atom = 99.409091 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) = 8.128 | 8.128 | 8.128 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 -7466.4698 -7466.4698 29.317537 96.321561 8.8462402 199.51985 199.51985 131.16577 289.24743 178.14636 2.4119146 646.68666 Loop time of 2.368e-06 on 1 procs for 0 steps with 2112 atoms 295.6% 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 | | 2.368e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8820.00 ave 8820 max 8820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 209952.0 ave 209952 max 209952 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 419904.0 ave 419904 max 419904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 419904 Ave neighs/atom = 198.81818 Neighbor list builds = 0 Dangerous builds = 0 2112 -7466.46978244095 eV 2.41191462040866 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01