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 -71.950702 0) to (35.975351 71.950702 4.1820496) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8338407 5.8338407 4.1820496 Created 592 atoms using lattice units in orthogonal box = (0 -71.950702 0) to (35.975351 71.950702 4.1820496) create_atoms CPU = 0.000 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8338407 5.8338407 4.1820496 Created 594 atoms using lattice units in orthogonal box = (0 -71.950702 0) to (35.975351 71.950702 4.1820496) create_atoms CPU = 0.000 seconds 594 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 = 9 36 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 0 atoms, new total = 1186 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 = 9 36 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) = 7.345 | 7.345 | 7.345 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4429.433 0 -4429.433 33646.375 77 0 -4621.9634 0 -4621.9634 1523.8546 Loop time of 0.539413 on 1 procs for 77 steps with 1186 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 = -4429.43304862299 -4621.95905483775 -4621.96339673514 Force two-norm initial, final = 157.20127 0.19230885 Force max component initial, final = 27.001932 0.039849281 Final line search alpha, max atom move = 1 0.039849281 Iterations, force evaluations = 77 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53265 | 0.53265 | 0.53265 | 0.0 | 98.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0041955 | 0.0041955 | 0.0041955 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002567 | | | 0.48 Nlocal: 1186 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8404 ave 8404 max 8404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79322 ave 79322 max 79322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79322 Ave neighs/atom = 66.881956 Neighbor list builds = 0 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 : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.346 | 7.346 | 7.346 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -4621.9634 0 -4621.9634 1523.8546 21650.067 83 0 -4622.1004 0 -4622.1004 -15.402967 21739.001 Loop time of 0.0299875 on 1 procs for 6 steps with 1186 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 = -4621.96339673514 -4622.10036303357 -4622.10041367218 Force two-norm initial, final = 51.192855 0.46966701 Force max component initial, final = 46.62563 0.35898537 Final line search alpha, max atom move = 0.0020739775 0.00074452757 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.028919 | 0.028919 | 0.028919 | 0.0 | 96.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022349 | 0.00022349 | 0.00022349 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008446 | | | 2.82 Nlocal: 1186 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8419 ave 8419 max 8419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79138 ave 79138 max 79138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79138 Ave neighs/atom = 66.726813 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 = 9 36 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) = 6.977 | 6.977 | 6.977 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4622.1004 0 -4622.1004 -15.402967 Loop time of 6.11e-07 on 1 procs for 0 steps with 1186 atoms 163.7% 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 | | 6.11e-07 | | |100.00 Nlocal: 1186 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8424 ave 8424 max 8424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79084 ave 79084 max 79084 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 = 79084 Ave neighs/atom = 66.681282 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) = 6.977 | 6.977 | 6.977 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 -4622.1004 -4622.1004 35.88944 144.61029 4.1886466 -15.402967 -15.402967 -7.6508016 -26.587755 -11.970344 2.6910656 439.34744 Loop time of 4.41e-07 on 1 procs for 0 steps with 1186 atoms 226.8% 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 | | 4.41e-07 | | |100.00 Nlocal: 1186 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8424 ave 8424 max 8424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79084 ave 79084 max 79084 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 158168 ave 158168 max 158168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158168 Ave neighs/atom = 133.36256 Neighbor list builds = 0 Dangerous builds = 0 1186 -4622.10041367218 eV 2.69106559885043 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00