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 -61.463325 0) to (21.730567 61.463325 5.9143112) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6338507 6.8292584 5.9143112 Created 432 atoms using lattice units in orthogonal box = (0 -61.463325 0) to (21.730567 61.463325 5.9143112) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6338507 6.8292584 5.9143112 Created 434 atoms using lattice units in orthogonal box = (0 -61.463325 0) to (21.730567 61.463325 5.9143112) create_atoms CPU = 0.000 seconds 434 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 = 6 30 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 6 atoms, new total = 860 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 = 6 30 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) = 7.267 | 7.267 | 7.267 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3251.8212 0 -3251.8212 15336.176 126 0 -3351.395 0 -3351.395 92.611283 Loop time of 0.652155 on 1 procs for 126 steps with 860 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3251.82122876153 -3351.39193156341 -3351.39503839682 Force two-norm initial, final = 140.7103 0.1612232 Force max component initial, final = 44.181554 0.032613082 Final line search alpha, max atom move = 1 0.032613082 Iterations, force evaluations = 126 237 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63972 | 0.63972 | 0.63972 | 0.0 | 98.09 Neigh | 0.0043928 | 0.0043928 | 0.0043928 | 0.0 | 0.67 Comm | 0.004985 | 0.004985 | 0.004985 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003056 | | | 0.47 Nlocal: 860 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5603 ave 5603 max 5603 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57146 ave 57146 max 57146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57146 Ave neighs/atom = 66.448837 Neighbor list builds = 3 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 : 126 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.267 | 7.267 | 7.267 Mbytes Step Temp E_pair E_mol TotEng Press Volume 126 0 -3351.395 0 -3351.395 92.611283 15798.698 128 0 -3351.3999 0 -3351.3999 31.944277 15800.74 Loop time of 0.0139511 on 1 procs for 2 steps with 860 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3351.39503839682 -3351.39945385852 -3351.39988324752 Force two-norm initial, final = 6.6660216 1.1227642 Force max component initial, final = 4.3687518 0.95743735 Final line search alpha, max atom move = 0.00038407296 0.0003677258 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.013533 | 0.013533 | 0.013533 | 0.0 | 97.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.6182e-05 | 9.6182e-05 | 9.6182e-05 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003216 | | | 2.31 Nlocal: 860 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5603 ave 5603 max 5603 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57164 ave 57164 max 57164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57164 Ave neighs/atom = 66.469767 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 = 6 31 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) = 6.898 | 6.898 | 6.898 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3351.3999 0 -3351.3999 31.944277 Loop time of 5.42e-07 on 1 procs for 0 steps with 860 atoms 0.0% 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 | | 5.42e-07 | | |100.00 Nlocal: 860 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5603 ave 5603 max 5603 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57162 ave 57162 max 57162 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 = 57162 Ave neighs/atom = 66.467442 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) = 6.898 | 6.898 | 6.898 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 -3351.3999 -3351.3999 21.746122 122.99832 5.9074005 31.944277 31.944277 97.152517 -41.025638 39.705952 2.7483531 630.7135 Loop time of 4.7e-07 on 1 procs for 0 steps with 860 atoms 212.8% 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 | | 4.7e-07 | | |100.00 Nlocal: 860 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5603 ave 5603 max 5603 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57162 ave 57162 max 57162 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114324 ave 114324 max 114324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114324 Ave neighs/atom = 132.93488 Neighbor list builds = 0 Dangerous builds = 0 860 -3351.39988324752 eV 2.74835309566684 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00