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_StarikovLopanitsynaSmirnova_2018_SiAu__SM_985135773293_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.1820496 4.1820496 4.1820496 Created orthogonal box = (0 -65.858983 0) to (40.330226 65.858983 10.243888) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5048751 6.3734499 6.8292584 Created 1485 atoms using lattice units in orthogonal box = (0 -65.858983 0) to (40.330226 65.858983 10.243888) create_atoms CPU = 0.001 seconds 1485 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5048751 6.3734499 6.8292584 Created 1491 atoms using lattice units in orthogonal box = (0 -65.858983 0) to (40.330226 65.858983 10.243888) create_atoms CPU = 0.001 seconds 1491 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 = 10 33 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 0 atoms, new total = 2976 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_985135773293_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 = 8.1961461 ghost atom cutoff = 8.1961461 binsize = 4.0980731, bins = 10 33 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) = 8.545 | 8.545 | 8.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10961.473 0 -10961.473 30026.217 88 0 -11598.836 0 -11598.836 1757.5128 Loop time of 1.39826 on 1 procs for 88 steps with 2976 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 = -10961.4725418965 -11598.8254394368 -11598.836454989 Force two-norm initial, final = 364.80112 0.29017637 Force max component initial, final = 66.11362 0.051449214 Final line search alpha, max atom move = 1 0.051449214 Iterations, force evaluations = 88 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3654 | 1.3654 | 1.3654 | 0.0 | 97.65 Neigh | 0.021109 | 0.021109 | 0.021109 | 0.0 | 1.51 Comm | 0.0051594 | 0.0051594 | 0.0051594 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006564 | | | 0.47 Nlocal: 2976 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9197 ave 9197 max 9197 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 198136 ave 198136 max 198136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198136 Ave neighs/atom = 66.577957 Neighbor list builds = 4 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 : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.548 | 8.548 | 8.548 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -11598.836 0 -11598.836 1757.5128 54417.736 91 0 -11598.995 0 -11598.995 -140.97324 54685.842 Loop time of 0.04696 on 1 procs for 3 steps with 2976 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 = -11598.836454989 -11598.9882997349 -11598.9947562649 Force two-norm initial, final = 105.84723 9.3147113 Force max component initial, final = 78.151812 6.6609397 Final line search alpha, max atom move = 6.4955648e-05 0.00043266566 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.04603 | 0.04603 | 0.04603 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016137 | 0.00016137 | 0.00016137 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000769 | | | 1.64 Nlocal: 2976 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9435 ave 9435 max 9435 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 198166 ave 198166 max 198166 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198166 Ave neighs/atom = 66.588038 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 = 8.1961461 ghost atom cutoff = 8.1961461 binsize = 4.0980731, bins = 10 33 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) = 8.179 | 8.179 | 8.179 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11598.995 0 -11598.995 -140.97324 Loop time of 7.41e-07 on 1 procs for 0 steps with 2976 atoms 135.0% 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 | | 7.41e-07 | | |100.00 Nlocal: 2976 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9407 ave 9407 max 9407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 198040 ave 198040 max 198040 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 = 198040 Ave neighs/atom = 66.545699 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) = 8.179 | 8.179 | 8.179 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 -11598.995 -11598.995 40.374669 132.08899 10.254142 -140.97324 -140.97324 -195.36613 -41.394588 -186.15901 2.7674105 1552.1075 Loop time of 4.31e-07 on 1 procs for 0 steps with 2976 atoms 232.0% 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 | | 4.31e-07 | | |100.00 Nlocal: 2976 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9407 ave 9407 max 9407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 198040 ave 198040 max 198040 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 396080 ave 396080 max 396080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 396080 Ave neighs/atom = 133.0914 Neighbor list builds = 0 Dangerous builds = 0 2976 -11598.9947562649 eV 2.76741046324915 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01