LAMMPS (30 Jul 2021) 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_StarikovGordeevLysogorskiy_2020_SiAuAl__SM_113843830602_000 # For Simulator : LAMMPS 3 Mar 2020 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 4.0254352 4.0254352 4.0254352 Created orthogonal box = (0.0000000 -60.782739 0.0000000) to (42.979887 60.782739 5.6928251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7862979 5.8650011 5.6928251 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -60.782739 0.0000000) to (42.979887 60.782739 5.6928251) create_atoms CPU = 0.003 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7862979 5.8650011 5.6928251 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -60.782739 0.0000000) to (42.979887 60.782739 5.6928251) create_atoms CPU = 0.002 seconds 916 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 = 11 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 12 atoms, new total = 1816 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_113843830602_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:189) 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 = 11 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) = 7.959 | 7.959 | 7.959 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6015.9688 0 -6015.9688 9207.3428 89 0 -6129.5604 0 -6129.5604 -68.45246 Loop time of 2.41896 on 1 procs for 89 steps with 1816 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6015.96880453847 -6129.55503674306 -6129.56040932697 Force two-norm initial, final = 124.17147 0.17837725 Force max component initial, final = 27.435819 0.019327686 Final line search alpha, max atom move = 1.0000000 0.019327686 Iterations, force evaluations = 89 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.368 | 2.368 | 2.368 | 0.0 | 97.89 Neigh | 0.014958 | 0.014958 | 0.014958 | 0.0 | 0.62 Comm | 0.019357 | 0.019357 | 0.019357 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01667 | | | 0.69 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9524.00 ave 9524 max 9524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126640.0 ave 126640 max 126640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126640 Ave neighs/atom = 69.735683 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.959 | 7.959 | 7.959 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -6129.5604 0 -6129.5604 -68.45246 29744.273 91 0 -6129.5944 0 -6129.5944 -186.85434 29748.537 Loop time of 0.0586904 on 1 procs for 2 steps with 1816 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6129.56040932697 -6129.58911520143 -6129.5944338184 Force two-norm initial, final = 29.291099 6.2157880 Force max component initial, final = 20.733244 4.4380615 Final line search alpha, max atom move = 9.2654168e-05 0.00041120490 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.056875 | 0.056875 | 0.056875 | 0.0 | 96.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031046 | 0.00031046 | 0.00031046 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001505 | | | 2.56 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9552.00 ave 9552 max 9552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126520.0 ave 126520 max 126520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126520 Ave neighs/atom = 69.669604 Neighbor list builds = 0 Dangerous builds = 0 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 = 11 30 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) = 7.591 | 7.591 | 7.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6129.5944 0 -6129.5944 -186.85434 Loop time of 2.313e-06 on 1 procs for 0 steps with 1816 atoms 172.9% 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 | | 2.313e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9568.00 ave 9568 max 9568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126500.0 ave 126500 max 126500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126500 Ave neighs/atom = 69.658590 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.591 | 7.591 | 7.591 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 -6129.5944 -6129.5944 42.921691 121.78375 5.6911422 -186.85434 -186.85434 -199.9563 -121.65528 -238.95144 2.6805425 944.06676 Loop time of 2.459e-06 on 1 procs for 0 steps with 1816 atoms 244.0% 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 | | 2.459e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9568.00 ave 9568 max 9568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126500.0 ave 126500 max 126500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 253000.0 ave 253000 max 253000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253000 Ave neighs/atom = 139.31718 Neighbor list builds = 0 Dangerous builds = 0 1816 -6129.5944338184 eV 2.6805425222136 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02