LAMMPS (30 Jul 2021) 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_StarikovGordeevLysogorskiy_2020_SiAuAl__SM_113843830602_000 # For Simulator : LAMMPS 3 Mar 2020 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 4.0254352 4.0254352 4.0254352 Created orthogonal box = (0.0000000 -65.899215 0.0000000) to (46.597781 65.899215 5.6928251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9548928 6.3932074 5.6928251 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -65.899215 0.0000000) to (46.597781 65.899215 5.6928251) create_atoms CPU = 0.003 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9548928 6.3932074 5.6928251 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -65.899215 0.0000000) to (46.597781 65.899215 5.6928251) create_atoms CPU = 0.003 seconds 1080 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 = 8.1961461 ghost atom cutoff = 8.1961461 binsize = 4.0980731, bins = 12 33 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 8 atoms, new total = 2144 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_113843830602_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:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1961461 ghost atom cutoff = 8.1961461 binsize = 4.0980731, bins = 12 33 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) = 8.060 | 8.060 | 8.060 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6645.5655 0 -6645.5655 28872.498 125 0 -7237.5348 0 -7237.5348 2783.1336 Loop time of 4.26103 on 1 procs for 125 steps with 2144 atoms 97.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6645.5655216661 -7237.5278363691 -7237.53481609746 Force two-norm initial, final = 551.65091 0.19605702 Force max component initial, final = 94.608984 0.017922187 Final line search alpha, max atom move = 1.0000000 0.017922187 Iterations, force evaluations = 125 232 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1712 | 4.1712 | 4.1712 | 0.0 | 97.89 Neigh | 0.027438 | 0.027438 | 0.027438 | 0.0 | 0.64 Comm | 0.033178 | 0.033178 | 0.033178 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02921 | | | 0.69 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10845.0 ave 10845 max 10845 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 149576.0 ave 149576 max 149576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149576 Ave neighs/atom = 69.764925 Neighbor list builds = 3 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.072 | 8.072 | 8.072 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -7237.5348 0 -7237.5348 2783.1336 34962.567 129 0 -7237.6802 0 -7237.6802 4.4590699 35089.621 Loop time of 0.127688 on 1 procs for 4 steps with 2144 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7237.53481609746 -7237.67988809073 -7237.68016758288 Force two-norm initial, final = 110.28935 0.46408421 Force max component initial, final = 82.710712 0.28873520 Final line search alpha, max atom move = 0.00020844288 6.0184798e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12377 | 0.12377 | 0.12377 | 0.0 | 96.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063096 | 0.00063096 | 0.00063096 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003286 | | | 2.57 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10091.0 ave 10091 max 10091 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 149744.0 ave 149744 max 149744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149744 Ave neighs/atom = 69.843284 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1961461 ghost atom cutoff = 8.1961461 binsize = 4.0980731, bins = 12 33 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) = 7.697 | 7.697 | 7.697 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7237.6802 0 -7237.6802 4.4590699 Loop time of 2.44e-06 on 1 procs for 0 steps with 2144 atoms 163.9% 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 | | 2.44e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10091.0 ave 10091 max 10091 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 149680.0 ave 149680 max 149680 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149680 Ave neighs/atom = 69.813433 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.697 | 7.697 | 7.697 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 -7237.6802 -7237.6802 46.660497 132.15235 5.6905525 4.4590699 4.4590699 -9.6979799 13.218923 9.8562666 2.6640947 1105.5845 Loop time of 2.434e-06 on 1 procs for 0 steps with 2144 atoms 205.4% 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 | | 2.434e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10091.0 ave 10091 max 10091 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 149680.0 ave 149680 max 149680 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 299360.0 ave 299360 max 299360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 299360 Ave neighs/atom = 139.62687 Neighbor list builds = 0 Dangerous builds = 0 2144 -7237.68016758288 eV 2.66409465217928 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04