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 -51.729097 0) to (17.243032 51.729097 4.1820496) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0714801 5.0714801 4.1820496 Created 204 atoms using lattice units in orthogonal box = (0 -51.729097 0) to (17.243032 51.729097 4.1820496) create_atoms CPU = 0.000 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0714801 5.0714801 4.1820496 Created 206 atoms using lattice units in orthogonal box = (0 -51.729097 0) to (17.243032 51.729097 4.1820496) create_atoms CPU = 0.000 seconds 206 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 = 5 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 4 atoms, new total = 406 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 = 5 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) = 7.049 | 7.049 | 7.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1523.6033 0 -1523.6033 21249.334 63 0 -1580.7013 0 -1580.7013 194.29062 Loop time of 0.14948 on 1 procs for 63 steps with 406 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 = -1523.60329530728 -1580.69981309958 -1580.70130496977 Force two-norm initial, final = 91.167562 0.11523042 Force max component initial, final = 25.326607 0.027607457 Final line search alpha, max atom move = 1 0.027607457 Iterations, force evaluations = 63 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14588 | 0.14588 | 0.14588 | 0.0 | 97.59 Neigh | 0.0013216 | 0.0013216 | 0.0013216 | 0.0 | 0.88 Comm | 0.0015257 | 0.0015257 | 0.0015257 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007488 | | | 0.50 Nlocal: 406 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3706 ave 3706 max 3706 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26896 ave 26896 max 26896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26896 Ave neighs/atom = 66.246305 Neighbor list builds = 2 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.05 | 7.05 | 7.05 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -1580.7013 0 -1580.7013 194.29062 7460.4961 68 0 -1580.7204 0 -1580.7204 30.845682 7462.8114 Loop time of 0.00939898 on 1 procs for 5 steps with 406 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 = -1580.70130496977 -1580.72022665329 -1580.72044828786 Force two-norm initial, final = 7.4097906 0.31502896 Force max component initial, final = 6.7904586 0.22334735 Final line search alpha, max atom move = 0.0019240756 0.00042973719 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0090121 | 0.0090121 | 0.0090121 | 0.0 | 95.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.7212e-05 | 8.7212e-05 | 8.7212e-05 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002997 | | | 3.19 Nlocal: 406 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3698 ave 3698 max 3698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26892 ave 26892 max 26892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26892 Ave neighs/atom = 66.236453 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 = 5 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) = 6.681 | 6.681 | 6.681 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1580.7204 0 -1580.7204 30.845682 Loop time of 1.002e-06 on 1 procs for 0 steps with 406 atoms 199.6% 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 | | 1.002e-06 | | |100.00 Nlocal: 406 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3698 ave 3698 max 3698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26888 ave 26888 max 26888 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 = 26888 Ave neighs/atom = 66.226601 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) = 6.681 | 6.681 | 6.681 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 -1580.7204 -1580.7204 17.207704 103.91489 4.1735128 30.845682 30.845682 47.851767 24.553388 20.131892 2.7168211 273.46213 Loop time of 4.31e-07 on 1 procs for 0 steps with 406 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: 406 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3698 ave 3698 max 3698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26888 ave 26888 max 26888 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53776 ave 53776 max 53776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53776 Ave neighs/atom = 132.4532 Neighbor list builds = 0 Dangerous builds = 0 406 -1580.72044828786 eV 2.71682114261879 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00