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 -65.788025 0) to (32.894012 65.788025 4.0800001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5545556 4.5545556 4.0800001 Created 520 atoms using lattice units in orthogonal box = (0 -65.788025 0) to (32.894012 65.788025 4.0800001) create_atoms CPU = 0.000 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5545556 4.5545556 4.0800001 Created 522 atoms using lattice units in orthogonal box = (0 -65.788025 0) to (32.894012 65.788025 4.0800001) create_atoms CPU = 0.000 seconds 522 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 29 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 = 1036 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 29 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) = 7.728 | 7.728 | 7.728 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2824.4066 0 -2824.4066 101425.51 76 0 -3937.9379 0 -3937.9379 -1541.9382 Loop time of 0.758504 on 1 procs for 76 steps with 1036 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2824.40661443264 -3937.93433540696 -3937.93789946272 Force two-norm initial, final = 1339.3424 0.18420075 Force max component initial, final = 419.69672 0.043419856 Final line search alpha, max atom move = 1 0.043419856 Iterations, force evaluations = 76 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74903 | 0.74903 | 0.74903 | 0.0 | 98.75 Neigh | 0.0023986 | 0.0023986 | 0.0023986 | 0.0 | 0.32 Comm | 0.0046489 | 0.0046489 | 0.0046489 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00243 | | | 0.32 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9182 ave 9182 max 9182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103220 ave 103220 max 103220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103220 Ave neighs/atom = 99.633205 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 : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.728 | 7.728 | 7.728 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -3937.9379 0 -3937.9379 -1541.9382 17658.502 78 0 -3937.9494 0 -3937.9494 0.62586115 17643.29 Loop time of 0.021741 on 1 procs for 2 steps with 1036 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 = -3937.93789946272 -3937.94575768474 -3937.94940870954 Force two-norm initial, final = 29.987879 0.5585741 Force max component initial, final = 21.663147 0.41363824 Final line search alpha, max atom move = 0.00022312833 9.229441e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.021244 | 0.021244 | 0.021244 | 0.0 | 97.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012411 | 0.00012411 | 0.00012411 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003727 | | | 1.71 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9179 ave 9179 max 9179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103086 ave 103086 max 103086 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103086 Ave neighs/atom = 99.503861 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 29 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) = 7.36 | 7.36 | 7.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3937.9494 0 -3937.9494 0.62586115 Loop time of 6.82e-07 on 1 procs for 0 steps with 1036 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: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9179 ave 9179 max 9179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103096 ave 103096 max 103096 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 = 103096 Ave neighs/atom = 99.513514 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) = 7.36 | 7.36 | 7.36 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 -3937.9494 -3937.9494 32.848722 131.61558 4.0808798 0.62586115 0.62586115 -37.510521 13.989722 25.398383 2.6648882 293.59583 Loop time of 4.81e-07 on 1 procs for 0 steps with 1036 atoms 207.9% 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 | | 4.81e-07 | | |100.00 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9179 ave 9179 max 9179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103096 ave 103096 max 103096 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206192 ave 206192 max 206192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206192 Ave neighs/atom = 199.02703 Neighbor list builds = 0 Dangerous builds = 0 1036 -3937.94940870954 eV 2.6648882343073 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00