LAMMPS (23 Jun 2022) 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_WangXuQian_2021_AuRh__SM_066295357485_000 # For Simulator : LAMMPS 30 Jul 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.0800001 4.0800001 4.0800001 Created orthogonal box = (0 -49.635343 0) to (24.817672 49.635343 4.0800001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6952352 4.6952352 4.0800001 Created 296 atoms using lattice units in orthogonal box = (0 -49.635343 0) to (24.817672 49.635343 4.0800001) create_atoms CPU = 0.000 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6952352 4.6952352 4.0800001 Created 298 atoms using lattice units in orthogonal box = (0 -49.635343 0) to (24.817672 49.635343 4.0800001) create_atoms CPU = 0.000 seconds 298 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 = 9.3498742 ghost atom cutoff = 9.3498742 binsize = 4.6749371, bins = 6 22 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 6 atoms, new total = 588 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_066295357485_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:187) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.3498742 ghost atom cutoff = 9.3498742 binsize = 4.6749371, bins = 6 22 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) = 7.16 | 7.16 | 7.16 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1825.5173 0 -1825.5173 91647.868 60 0 -2232.6843 0 -2232.6843 -4357.1884 Loop time of 0.349108 on 1 procs for 60 steps with 588 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1825.5172679394 -2232.68232075968 -2232.68426116574 Force two-norm initial, final = 728.09892 0.12583699 Force max component initial, final = 246.5326 0.034676544 Final line search alpha, max atom move = 1 0.034676544 Iterations, force evaluations = 60 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34426 | 0.34426 | 0.34426 | 0.0 | 98.61 Neigh | 0.0013585 | 0.0013585 | 0.0013585 | 0.0 | 0.39 Comm | 0.002431 | 0.002431 | 0.002431 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00106 | | | 0.30 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6127 ave 6127 max 6127 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58508 ave 58508 max 58508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58508 Ave neighs/atom = 99.503401 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.16 | 7.16 | 7.16 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -2232.6843 0 -2232.6843 -4357.1884 10051.763 63 0 -2232.7221 0 -2232.7221 -141.56791 10027.969 Loop time of 0.0190779 on 1 procs for 3 steps with 588 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2232.68426116575 -2232.72180211308 -2232.72209106006 Force two-norm initial, final = 47.564609 1.5494205 Force max component initial, final = 30.971773 1.0124199 Final line search alpha, max atom move = 0.0010697556 0.0010830418 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.018569 | 0.018569 | 0.018569 | 0.0 | 97.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012406 | 0.00012406 | 0.00012406 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003846 | | | 2.02 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6125 ave 6125 max 6125 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58508 ave 58508 max 58508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58508 Ave neighs/atom = 99.503401 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.3498742 ghost atom cutoff = 9.3498742 binsize = 4.6749371, bins = 6 22 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) = 6.791 | 6.791 | 6.791 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2232.7221 0 -2232.7221 -141.56791 Loop time of 6.21e-07 on 1 procs for 0 steps with 588 atoms 161.0% 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 | | 6.21e-07 | | |100.00 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6125 ave 6125 max 6125 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58512 ave 58512 max 58512 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58512 Ave neighs/atom = 99.510204 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.791 | 6.791 | 6.791 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 -2232.7221 -2232.7221 24.761205 99.283679 4.0790904 -141.56791 -141.56791 -161.38709 -136.8277 -126.48893 2.653933 283.16549 Loop time of 6.82e-07 on 1 procs for 0 steps with 588 atoms 146.6% 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 | | 6.82e-07 | | |100.00 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6125 ave 6125 max 6125 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58512 ave 58512 max 58512 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117024 ave 117024 max 117024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117024 Ave neighs/atom = 199.02041 Neighbor list builds = 0 Dangerous builds = 0 588 -2232.72209106006 eV 2.65393296799121 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00