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 -52.882845 0) to (30.531925 52.882845 7.0667674) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5425553 6.2955768 7.0667674 Created 672 atoms using lattice units in orthogonal box = (0 -52.882845 0) to (30.531925 52.882845 7.0667674) create_atoms CPU = 0.001 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5425553 6.2955768 7.0667674 Created 676 atoms using lattice units in orthogonal box = (0 -52.882845 0) to (30.531925 52.882845 7.0667674) create_atoms CPU = 0.000 seconds 676 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 = 7 23 2 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 4 atoms, new total = 1344 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 = 7 23 2 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) = 7.854 | 7.854 | 7.854 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3934.4379 0 -3934.4379 124456.06 75 0 -5105.197 0 -5105.197 7259.9241 Loop time of 0.994563 on 1 procs for 75 steps with 1344 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3934.43792681622 -5105.19199392872 -5105.19700923753 Force two-norm initial, final = 1257.595 0.21609363 Force max component initial, final = 225.1505 0.037813808 Final line search alpha, max atom move = 1 0.037813808 Iterations, force evaluations = 75 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.98456 | 0.98456 | 0.98456 | 0.0 | 98.99 Neigh | 0.0029708 | 0.0029708 | 0.0029708 | 0.0 | 0.30 Comm | 0.0039249 | 0.0039249 | 0.0039249 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003112 | | | 0.31 Nlocal: 1344 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7233 ave 7233 max 7233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133724 ave 133724 max 133724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133724 Ave neighs/atom = 99.497024 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 : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.86 | 7.86 | 7.86 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -5105.197 0 -5105.197 7259.9241 22820.218 81 0 -5105.5316 0 -5105.5316 -100.8997 22912.314 Loop time of 0.0634459 on 1 procs for 6 steps with 1344 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5105.19700923753 -5105.52892739423 -5105.53159156786 Force two-norm initial, final = 188.06274 3.1790109 Force max component initial, final = 146.99867 2.7496424 Final line search alpha, max atom move = 7.4273884e-05 0.00020422662 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.062258 | 0.062258 | 0.062258 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024461 | 0.00024461 | 0.00024461 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009436 | | | 1.49 Nlocal: 1344 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7886 ave 7886 max 7886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133748 ave 133748 max 133748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133748 Ave neighs/atom = 99.514881 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 = 7 23 2 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) = 7.492 | 7.492 | 7.492 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5105.5316 0 -5105.5316 -100.8997 Loop time of 6.21e-07 on 1 procs for 0 steps with 1344 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: 1344 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7912 ave 7912 max 7912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133612 ave 133612 max 133612 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 = 133612 Ave neighs/atom = 99.41369 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) = 7.492 | 7.492 | 7.492 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 -5105.5316 -5105.5316 30.547154 106.29324 7.0565518 -100.8997 -100.8997 -192.36861 -110.00408 -0.32640741 2.6773804 1047.2699 Loop time of 6.91e-07 on 1 procs for 0 steps with 1344 atoms 289.4% 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 | | 6.91e-07 | | |100.00 Nlocal: 1344 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7912 ave 7912 max 7912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133612 ave 133612 max 133612 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267224 ave 267224 max 267224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267224 Ave neighs/atom = 198.82738 Neighbor list builds = 0 Dangerous builds = 0 1344 -5105.53159156786 eV 2.67738042637254 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01