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 -59.571001 0.0000000) to (48.639519 59.571001 9.8602623) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9966530 5.7122878 6.5735082 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -59.571001 0.0000000) to (48.639519 59.571001 9.8602623) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9966530 5.7122878 6.5735082 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -59.571001 0.0000000) to (48.639519 59.571001 9.8602623) create_atoms CPU = 0.002 seconds 1759 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 30 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 6 atoms, new total = 3504 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 30 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) = 8.731 | 8.731 | 8.731 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11182.439 0 -11182.439 24459.965 84 0 -11814.655 0 -11814.655 4926.9293 Loop time of 4.0952 on 1 procs for 84 steps with 3504 atoms 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11182.438817169 -11814.6438408989 -11814.6545982405 Force two-norm initial, final = 428.34467 0.28051092 Force max component initial, final = 57.162111 0.037755438 Final line search alpha, max atom move = 1.0000000 0.037755438 Iterations, force evaluations = 84 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0261 | 4.0261 | 4.0261 | 0.0 | 98.31 Neigh | 0.027882 | 0.027882 | 0.027882 | 0.0 | 0.68 Comm | 0.017002 | 0.017002 | 0.017002 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02424 | | | 0.59 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10642.0 ave 10642 max 10642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243852.0 ave 243852 max 243852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 243852 Ave neighs/atom = 69.592466 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 : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.731 | 8.731 | 8.731 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -11814.655 0 -11814.655 4926.9293 57140.315 93 0 -11815.876 0 -11815.876 89.390427 57495.565 Loop time of 0.309565 on 1 procs for 9 steps with 3504 atoms 95.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11814.6545982405 -11815.8752994474 -11815.8760667279 Force two-norm initial, final = 355.34541 6.1848618 Force max component initial, final = 325.47690 5.1752613 Final line search alpha, max atom move = 0.00015186687 0.00078595076 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28774 | 0.28774 | 0.28774 | 0.0 | 92.95 Neigh | 0.013529 | 0.013529 | 0.013529 | 0.0 | 4.37 Comm | 0.0012454 | 0.0012454 | 0.0012454 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00705 | | | 2.28 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10669.0 ave 10669 max 10669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243771.0 ave 243771 max 243771 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 243771 Ave neighs/atom = 69.569349 Neighbor list builds = 1 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 30 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) = 8.362 | 8.362 | 8.362 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11815.876 0 -11815.876 89.390427 Loop time of 2.042e-06 on 1 procs for 0 steps with 3504 atoms 146.9% 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 | | 2.042e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10669.0 ave 10669 max 10669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243770.0 ave 243770 max 243770 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 = 243770 Ave neighs/atom = 69.569064 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) = 8.362 | 8.362 | 8.362 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 -11815.876 -11815.876 48.579344 120.10437 9.8542568 89.390427 89.390427 37.515865 145.37918 85.276233 2.5640955 2163.248 Loop time of 2.577e-06 on 1 procs for 0 steps with 3504 atoms 232.8% 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 | | 2.577e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10669.0 ave 10669 max 10669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243770.0 ave 243770 max 243770 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 487540.0 ave 487540 max 487540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 487540 Ave neighs/atom = 139.13813 Neighbor list builds = 0 Dangerous builds = 0 3504 -11815.8760667279 eV 2.56409550159616 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04