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 -51.235426 0.0000000) to (12.076306 51.235426 5.6928251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7090587 5.6928251 5.6928251 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -51.235426 0.0000000) to (12.076306 51.235426 5.6928251) create_atoms CPU = 0.001 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7090587 5.6928251 5.6928251 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -51.235426 0.0000000) to (12.076306 51.235426 5.6928251) create_atoms CPU = 0.001 seconds 218 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 = 3 26 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 2 atoms, new total = 432 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 = 3 26 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) = 7.112 | 7.112 | 7.112 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1426.0483 0 -1426.0483 14670.715 60 0 -1457.2965 0 -1457.2965 4334.0253 Loop time of 0.379143 on 1 procs for 60 steps with 432 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 = -1426.04830451188 -1457.29519574347 -1457.29648622803 Force two-norm initial, final = 50.988604 0.090779954 Force max component initial, final = 14.521800 0.016197891 Final line search alpha, max atom move = 1.0000000 0.016197891 Iterations, force evaluations = 60 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37062 | 0.37062 | 0.37062 | 0.0 | 97.75 Neigh | 0.0020526 | 0.0020526 | 0.0020526 | 0.0 | 0.54 Comm | 0.0037483 | 0.0037483 | 0.0037483 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002717 | | | 0.72 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3965.00 ave 3965 max 3965 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30052.0 ave 30052 max 30052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30052 Ave neighs/atom = 69.564815 Neighbor list builds = 1 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) = 7.112 | 7.112 | 7.112 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1457.2965 0 -1457.2965 4334.0253 7044.6963 69 0 -1457.4316 0 -1457.4316 29.450982 7083.3449 Loop time of 0.0384859 on 1 procs for 9 steps with 432 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1457.29648622803 -1457.43156930255 -1457.43159161329 Force two-norm initial, final = 39.587319 0.33573571 Force max component initial, final = 36.339847 0.27412109 Final line search alpha, max atom move = 0.0020225368 0.00055441998 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.036524 | 0.036524 | 0.036524 | 0.0 | 94.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037299 | 0.00037299 | 0.00037299 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001589 | | | 4.13 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4053.00 ave 4053 max 4053 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30020.0 ave 30020 max 30020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30020 Ave neighs/atom = 69.490741 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 = 3 26 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) = 6.743 | 6.743 | 6.743 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1457.4316 0 -1457.4316 29.450982 Loop time of 1.575e-06 on 1 procs for 0 steps with 432 atoms 127.0% 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 | | 1.575e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4013.00 ave 4013 max 4013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30000.0 ave 30000 max 30000 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 = 30000 Ave neighs/atom = 69.444444 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) = 6.743 | 6.743 | 6.743 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 -1457.4316 -1457.4316 12.049457 103.28998 5.6913161 29.450982 29.450982 26.095021 62.498886 -0.24096199 2.661104 303.20776 Loop time of 2.143e-06 on 1 procs for 0 steps with 432 atoms 140.0% 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 | | 2.143e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4013.00 ave 4013 max 4013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30000.0 ave 30000 max 30000 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 60000.0 ave 60000 max 60000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60000 Ave neighs/atom = 138.88889 Neighbor list builds = 0 Dangerous builds = 0 432 -1457.43159161329 eV 2.6611040307919 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00