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 Lattice spacing in x,y,z = 4.0515263 4.0515263 4.0515263 Created orthogonal box = (0.0000000 -52.980581 0.0000000) to (24.975285 52.980581 5.7297234) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2579548 6.5063871 5.7297234 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -52.980581 0.0000000) to (24.975285 52.980581 5.7297234) create_atoms CPU = 0.001 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2579548 6.5063871 5.7297234 Created 462 atoms using lattice units in orthogonal box = (0.0000000 -52.980581 0.0000000) to (24.975285 52.980581 5.7297234) create_atoms CPU = 0.001 seconds 462 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 27 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 kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 912 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/MO_109933561507_005#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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.985 | 4.985 | 4.985 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2984.6083 0 -2984.6083 28181.809 58 0 -3053.0269 0 -3053.0269 8856.9504 Loop time of 1.10209 on 1 procs for 58 steps with 912 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2984.60834828111 -3053.02412748955 -3053.02694610738 Force two-norm initial, final = 113.31741 0.15223157 Force max component initial, final = 20.336461 0.015595148 Final line search alpha, max atom move = 1.0000000 0.015595148 Iterations, force evaluations = 58 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0698 | 1.0698 | 1.0698 | 0.0 | 97.07 Neigh | 0.014151 | 0.014151 | 0.014151 | 0.0 | 1.28 Comm | 0.01023 | 0.01023 | 0.01023 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00796 | | | 0.72 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5527.00 ave 5527 max 5527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120920.0 ave 120920 max 120920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120920 Ave neighs/atom = 132.58772 Neighbor list builds = 1 Dangerous builds = 0 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.986 | 4.986 | 4.986 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -3053.0269 0 -3053.0269 8856.9504 15163.199 67 0 -3053.6433 0 -3053.6433 -97.743512 15299.825 Loop time of 0.146458 on 1 procs for 9 steps with 912 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 = -3053.02694610738 -3053.64276640501 -3053.64326434495 Force two-norm initial, final = 169.37191 1.7478809 Force max component initial, final = 152.06820 1.2312843 Final line search alpha, max atom move = 0.00037714913 0.00046437778 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14074 | 0.14074 | 0.14074 | 0.0 | 96.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010527 | 0.0010527 | 0.0010527 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004668 | | | 3.19 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5664.00 ave 5664 max 5664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120880.0 ave 120880 max 120880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120880 Ave neighs/atom = 132.54386 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/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 attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.124 | 5.124 | 5.124 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3053.6433 0 -3053.6433 -97.743512 Loop time of 3.372e-06 on 1 procs for 0 steps with 912 atoms 148.3% 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 | | 3.372e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5664.00 ave 5664 max 5664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120784.0 ave 120784 max 120784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120784 Ave neighs/atom = 132.43860 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/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 attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.124 | 5.124 | 5.124 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 -3053.6433 -3053.6433 25.003367 106.78283 5.7304211 -97.743512 -97.743512 -129.08336 -115.69816 -48.449016 2.7444823 705.21529 Loop time of 3.218e-06 on 1 procs for 0 steps with 912 atoms 186.5% 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 | | 3.218e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5664.00 ave 5664 max 5664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60392.0 ave 60392 max 60392 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120784.0 ave 120784 max 120784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120784 Ave neighs/atom = 132.43860 Neighbor list builds = 0 Dangerous builds = 0 912 -3053.64326433653 eV 2.74448229923141 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01