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 = 3.7999997 3.7999997 3.7999997 Created orthogonal box = (0 -38.752545 0) to (33.560688 38.752545 6.5817925) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0237133 5.96193 6.5817925 Created 622 atoms using lattice units in orthogonal box = (0 -38.752545 0) to (33.560688 38.752545 6.5817925) create_atoms CPU = 0.001 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0237133 5.96193 6.5817925 Created 629 atoms using lattice units in orthogonal box = (0 -38.752545 0) to (33.560688 38.752545 6.5817925) create_atoms CPU = 0.001 seconds 629 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 = 8 17 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 1 atoms, new total = 1250 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 = 8 17 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) = 7.826 | 7.826 | 7.826 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4923.4651 0 -4923.4651 256734.99 110 0 -7139.7519 0 -7139.7519 29991.103 Loop time of 1.87065 on 1 procs for 110 steps with 1250 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 = -4923.46511663654 -7139.74543913857 -7139.75191242197 Force two-norm initial, final = 1865.8058 0.44252947 Force max component initial, final = 387.8825 0.16318707 Final line search alpha, max atom move = 0.47717386 0.077868603 Iterations, force evaluations = 110 190 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.847 | 1.847 | 1.847 | 0.0 | 98.74 Neigh | 0.013898 | 0.013898 | 0.013898 | 0.0 | 0.74 Comm | 0.0057719 | 0.0057719 | 0.0057719 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003969 | | | 0.21 Nlocal: 1250 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7569 ave 7569 max 7569 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 153417 ave 153417 max 153417 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153417 Ave neighs/atom = 122.7336 Neighbor list builds = 4 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 : 110 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.826 | 7.826 | 7.826 Mbytes Step Temp E_pair E_mol TotEng Press Volume 110 0 -7139.7519 0 -7139.7519 29991.103 17120.059 123 0 -7143.4271 0 -7143.4271 -105.14737 17313.054 Loop time of 0.155443 on 1 procs for 13 steps with 1250 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 = -7139.75191242197 -7143.42694828977 -7143.42713746465 Force two-norm initial, final = 676.60401 2.6688026 Force max component initial, final = 628.6787 1.2159171 Final line search alpha, max atom move = 0.00032661317 0.00039713455 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15333 | 0.15333 | 0.15333 | 0.0 | 98.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042091 | 0.00042091 | 0.00042091 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001692 | | | 1.09 Nlocal: 1250 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7565 ave 7565 max 7565 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 153448 ave 153448 max 153448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153448 Ave neighs/atom = 122.7584 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 = 8 17 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) = 7.457 | 7.457 | 7.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7143.4271 0 -7143.4271 -105.14737 Loop time of 5.81e-07 on 1 procs for 0 steps with 1250 atoms 172.1% 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 | | 5.81e-07 | | |100.00 Nlocal: 1250 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7557 ave 7557 max 7557 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 152731 ave 152731 max 152731 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 = 152731 Ave neighs/atom = 122.1848 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) = 7.457 | 7.457 | 7.457 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 -7143.4271 -7143.4271 33.579891 78.430871 6.5736621 -105.14737 -105.14737 -110.25268 -113.86689 -91.322553 2.4307247 992.98483 Loop time of 4.51e-07 on 1 procs for 0 steps with 1250 atoms 221.7% 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 | | 4.51e-07 | | |100.00 Nlocal: 1250 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7557 ave 7557 max 7557 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 152731 ave 152731 max 152731 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 305462 ave 305462 max 305462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305462 Ave neighs/atom = 244.3696 Neighbor list builds = 0 Dangerous builds = 0 1250 -7143.42713746465 eV 2.43072465459997 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02