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 -49.791884 0.0000000) to (23.472119 49.791884 5.6928251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9035644 6.8341801 5.6928251 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -49.791884 0.0000000) to (23.472119 49.791884 5.6928251) create_atoms CPU = 0.002 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9035644 6.8341801 5.6928251 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -49.791884 0.0000000) to (23.472119 49.791884 5.6928251) create_atoms CPU = 0.001 seconds 412 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 25 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 = 816 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 = 6 25 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) = 7.232 | 7.232 | 7.232 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2561.4365 0 -2561.4365 30591.929 37 0 -2752.3051 0 -2752.3051 4386.1662 Loop time of 0.36478 on 1 procs for 37 steps with 816 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2561.43645728546 -2752.3027415503 -2752.30507969259 Force two-norm initial, final = 241.41421 0.12228415 Force max component initial, final = 50.454448 0.011915887 Final line search alpha, max atom move = 1.0000000 0.011915887 Iterations, force evaluations = 37 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35614 | 0.35614 | 0.35614 | 0.0 | 97.63 Neigh | 0.0031299 | 0.0031299 | 0.0031299 | 0.0 | 0.86 Comm | 0.0029274 | 0.0029274 | 0.0029274 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002579 | | | 0.71 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5222.00 ave 5222 max 5222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56956.0 ave 56956 max 56956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56956 Ave neighs/atom = 69.799020 Neighbor list builds = 1 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 : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.232 | 7.232 | 7.232 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -2752.3051 0 -2752.3051 4386.1662 13306.649 44 0 -2752.5061 0 -2752.5061 -69.543523 13382.447 Loop time of 0.0552365 on 1 procs for 7 steps with 816 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 = -2752.30507969259 -2752.50518176007 -2752.50612543596 Force two-norm initial, final = 72.636293 1.0369021 Force max component initial, final = 65.804895 0.70917886 Final line search alpha, max atom move = 0.00031950333 0.00022658501 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053217 | 0.053217 | 0.053217 | 0.0 | 96.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037962 | 0.00037962 | 0.00037962 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00164 | | | 2.97 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5208.00 ave 5208 max 5208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56864.0 ave 56864 max 56864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56864 Ave neighs/atom = 69.686275 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 = 6 25 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) = 6.863 | 6.863 | 6.863 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2752.5061 0 -2752.5061 -69.543523 Loop time of 2.228e-06 on 1 procs for 0 steps with 816 atoms 179.5% 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 | | 2.228e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5208.00 ave 5208 max 5208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56848.0 ave 56848 max 56848 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 = 56848 Ave neighs/atom = 69.666667 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) = 6.863 | 6.863 | 6.863 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 -2752.5061 -2752.5061 23.464148 100.22913 5.6903212 -69.543523 -69.543523 -68.889085 -54.874348 -84.867136 2.7223875 631.49978 Loop time of 2.649e-06 on 1 procs for 0 steps with 816 atoms 226.5% 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 | | 2.649e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5208.00 ave 5208 max 5208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56848.0 ave 56848 max 56848 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113696.0 ave 113696 max 113696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113696 Ave neighs/atom = 139.33333 Neighbor list builds = 0 Dangerous builds = 0 816 -2752.50612543596 eV 2.72238754925409 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00