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 -55.340585 0.0000000) to (15.061799 55.340585 9.8602623) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4550569 6.1489539 6.5735082 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -55.340585 0.0000000) to (15.061799 55.340585 9.8602623) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4550569 6.1489539 6.5735082 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -55.340585 0.0000000) to (15.061799 55.340585 9.8602623) create_atoms CPU = 0.001 seconds 507 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 = 4 28 3 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 2 atoms, new total = 1008 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 = 4 28 3 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) = 7.316 | 7.316 | 7.316 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3244.9295 0 -3244.9295 23367.564 60 0 -3399.0585 0 -3399.0585 4703.2764 Loop time of 0.869509 on 1 procs for 60 steps with 1008 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3244.92952321175 -3399.0557376927 -3399.05854963892 Force two-norm initial, final = 184.38411 0.12912860 Force max component initial, final = 31.038339 0.029490640 Final line search alpha, max atom move = 1.0000000 0.029490640 Iterations, force evaluations = 60 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85122 | 0.85122 | 0.85122 | 0.0 | 97.90 Neigh | 0.0079507 | 0.0079507 | 0.0079507 | 0.0 | 0.91 Comm | 0.0052255 | 0.0052255 | 0.0052255 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005113 | | | 0.59 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5425.00 ave 5425 max 5425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70157.0 ave 70157 max 70157 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70157 Ave neighs/atom = 69.600198 Neighbor list builds = 2 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.316 | 7.316 | 7.316 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -3399.0585 0 -3399.0585 4703.2764 16437.625 68 0 -3399.3552 0 -3399.3552 33.760551 16535.615 Loop time of 0.075966 on 1 procs for 8 steps with 1008 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 = -3399.05854963892 -3399.35492843413 -3399.35515975279 Force two-norm initial, final = 95.973983 0.64710551 Force max component initial, final = 85.155442 0.38339448 Final line search alpha, max atom move = 0.00075933779 0.00029112592 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.073493 | 0.073493 | 0.073493 | 0.0 | 96.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041442 | 0.00041442 | 0.00041442 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002059 | | | 2.71 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5451.00 ave 5451 max 5451 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70257.0 ave 70257 max 70257 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70257 Ave neighs/atom = 69.699405 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 = 4 28 3 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) = 6.948 | 6.948 | 6.948 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3399.3552 0 -3399.3552 33.760551 Loop time of 7.717e-06 on 1 procs for 0 steps with 1008 atoms 25.9% 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 | | 7.717e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5490.00 ave 5490 max 5490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70168.0 ave 70168 max 70168 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 = 70168 Ave neighs/atom = 69.611111 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) = 6.948 | 6.948 | 6.948 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 -3399.3552 -3399.3552 15.071578 111.47653 9.8418821 33.760551 33.760551 31.030241 37.414986 32.836426 2.59482 507.70623 Loop time of 2.225e-06 on 1 procs for 0 steps with 1008 atoms 179.8% 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 | | 2.225e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5490.00 ave 5490 max 5490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70168.0 ave 70168 max 70168 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 140336.0 ave 140336 max 140336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140336 Ave neighs/atom = 139.22222 Neighbor list builds = 0 Dangerous builds = 0 1008 -3399.35515975279 eV 2.59481995486672 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01