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 -46.875632 0) to (33.146077 46.875632 5.7699915) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 7.0309861 6.3921317 5.7699915 Created 528 atoms using lattice units in orthogonal box = (0 -46.875632 0) to (33.146077 46.875632 5.7699915) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 7.0309861 6.3921317 5.7699915 Created 532 atoms using lattice units in orthogonal box = (0 -46.875632 0) to (33.146077 46.875632 5.7699915) create_atoms CPU = 0.000 seconds 532 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 21 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 = 1056 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 21 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) = 7.721 | 7.721 | 7.721 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1991.0556 0 -1991.0556 190866.96 137 0 -4014.7493 0 -4014.7493 4896.7332 Loop time of 1.44914 on 1 procs for 137 steps with 1056 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1991.05563023205 -4014.74611918445 -4014.74931857926 Force two-norm initial, final = 1804.8717 0.1453474 Force max component initial, final = 306.74919 0.022972812 Final line search alpha, max atom move = 1 0.022972812 Iterations, force evaluations = 137 253 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4314 | 1.4314 | 1.4314 | 0.0 | 98.78 Neigh | 0.0067767 | 0.0067767 | 0.0067767 | 0.0 | 0.47 Comm | 0.0066724 | 0.0066724 | 0.0066724 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004295 | | | 0.30 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7305 ave 7305 max 7305 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105148 ave 105148 max 105148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105148 Ave neighs/atom = 99.57197 Neighbor list builds = 3 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 : 137 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.721 | 7.721 | 7.721 Mbytes Step Temp E_pair E_mol TotEng Press Volume 137 0 -4014.7493 0 -4014.7493 4896.7332 17930.172 142 0 -4014.8995 0 -4014.8995 2.638241 17978.135 Loop time of 0.0463938 on 1 procs for 5 steps with 1056 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 = -4014.74931857926 -4014.89645248853 -4014.89950571625 Force two-norm initial, final = 102.85463 1.7523744 Force max component initial, final = 81.546646 1.397042 Final line search alpha, max atom move = 4.6688312e-05 6.5225534e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.045501 | 0.045501 | 0.045501 | 0.0 | 98.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019399 | 0.00019399 | 0.00019399 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006989 | | | 1.51 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6824 ave 6824 max 6824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105344 ave 105344 max 105344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105344 Ave neighs/atom = 99.757576 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 21 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) = 7.35 | 7.35 | 7.35 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4014.8995 0 -4014.8995 2.638241 Loop time of 6.81e-07 on 1 procs for 0 steps with 1056 atoms 146.8% 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 | | 6.81e-07 | | |100.00 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6987 ave 6987 max 6987 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105264 ave 105264 max 105264 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 = 105264 Ave neighs/atom = 99.681818 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) = 7.35 | 7.35 | 7.35 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 -4014.8995 -4014.8995 33.257769 93.884195 5.7578327 2.638241 2.638241 -89.029958 124.6782 -27.733524 2.7055428 1048.8907 Loop time of 4.81e-07 on 1 procs for 0 steps with 1056 atoms 415.8% 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: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6987 ave 6987 max 6987 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105264 ave 105264 max 105264 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 210528 ave 210528 max 210528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210528 Ave neighs/atom = 199.36364 Neighbor list builds = 0 Dangerous builds = 0 1056 -4014.89950571625 eV 2.70554280379457 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01