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 -67.950263 0) to (24.024046 67.950263 5.9143112) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5520125 5.1477472 5.9143112 Created 528 atoms using lattice units in orthogonal box = (0 -67.950263 0) to (24.024046 67.950263 5.9143112) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5520125 5.1477472 5.9143112 Created 530 atoms using lattice units in orthogonal box = (0 -67.950263 0) to (24.024046 67.950263 5.9143112) create_atoms CPU = 0.000 seconds 530 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 34 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 2 atoms, new total = 1056 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 34 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) = 7.333 | 7.333 | 7.333 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3790.7785 0 -3790.7785 33546.55 147 0 -4116.6176 0 -4116.6176 -272.65119 Loop time of 0.941164 on 1 procs for 147 steps with 1056 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 = -3790.77852687253 -4116.61376506498 -4116.61757497047 Force two-norm initial, final = 323.97103 0.17788596 Force max component initial, final = 90.293785 0.028491978 Final line search alpha, max atom move = 1 0.028491978 Iterations, force evaluations = 147 276 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92499 | 0.92499 | 0.92499 | 0.0 | 98.28 Neigh | 0.0053427 | 0.0053427 | 0.0053427 | 0.0 | 0.57 Comm | 0.006494 | 0.006494 | 0.006494 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004335 | | | 0.46 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6380 ave 6380 max 6380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70366 ave 70366 max 70366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70366 Ave neighs/atom = 66.63447 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 : 147 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.333 | 7.333 | 7.333 Mbytes Step Temp E_pair E_mol TotEng Press Volume 147 0 -4116.6176 0 -4116.6176 -272.65119 19309.519 151 0 -4116.6495 0 -4116.6495 42.665526 19292.794 Loop time of 0.0209438 on 1 procs for 4 steps with 1056 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 = -4116.61757497046 -4116.64912125558 -4116.64954464731 Force two-norm initial, final = 18.535253 0.94733637 Force max component initial, final = 17.651752 0.6805719 Final line search alpha, max atom move = 0.00051401022 0.00034982091 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.020323 | 0.020323 | 0.020323 | 0.0 | 97.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013217 | 0.00013217 | 0.00013217 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004885 | | | 2.33 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6384 ave 6384 max 6384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70452 ave 70452 max 70452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70452 Ave neighs/atom = 66.715909 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 34 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) = 6.964 | 6.964 | 6.964 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4116.6495 0 -4116.6495 42.665526 Loop time of 4.71e-07 on 1 procs for 0 steps with 1056 atoms 212.3% 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 | | 4.71e-07 | | |100.00 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6384 ave 6384 max 6384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70446 ave 70446 max 70446 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 = 70446 Ave neighs/atom = 66.710227 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) = 6.964 | 6.964 | 6.964 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 -4116.6495 -4116.6495 23.951083 136.17113 5.915411 42.665526 42.665526 43.229988 56.630859 28.135731 2.7976322 1007.1818 Loop time of 4.41e-07 on 1 procs for 0 steps with 1056 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: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6384 ave 6384 max 6384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70446 ave 70446 max 70446 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 140892 ave 140892 max 140892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140892 Ave neighs/atom = 133.42045 Neighbor list builds = 0 Dangerous builds = 0 1056 -4116.64954464731 eV 2.79763216564787 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01