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 = 2.8669669 2.8669669 2.8669669 Created orthogonal box = (0.0000000 -46.585566 0.0000000) to (16.469471 46.585566 4.0545035) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4916740 3.5289924 4.0545035 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -46.585566 0.0000000) to (16.469471 46.585566 4.0545035) create_atoms CPU = 0.002 seconds 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4916740 3.5289924 4.0545035 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -46.585566 0.0000000) to (16.469471 46.585566 4.0545035) create_atoms CPU = 0.001 seconds 266 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 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 kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 528 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.515 | 4.515 | 4.515 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2060.4853 0 -2060.4853 22324.882 109 0 -2128.2517 0 -2128.2517 -57673.853 Loop time of 2.34699 on 1 procs for 109 steps with 528 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2060.48530297509 -2128.2497693159 -2128.25168989985 Force two-norm initial, final = 93.791943 0.16448518 Force max component initial, final = 24.784274 0.038602855 Final line search alpha, max atom move = 1.0000000 0.038602855 Iterations, force evaluations = 109 208 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.287 | 2.287 | 2.287 | 0.0 | 97.45 Neigh | 0.013605 | 0.013605 | 0.013605 | 0.0 | 0.58 Comm | 0.026731 | 0.026731 | 0.026731 | 0.0 | 1.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01961 | | | 0.84 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5038.00 ave 5038 max 5038 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: 84296.0 ave 84296 max 84296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84296 Ave neighs/atom = 159.65152 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.516 | 4.516 | 4.516 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -2128.2517 0 -2128.2517 -57673.853 6221.5517 141 0 -2132.1291 0 -2132.1291 -21919.828 6005.984 Loop time of 0.352071 on 1 procs for 32 steps with 528 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 = -2128.25168989985 -2132.12740554027 -2132.1291217021 Force two-norm initial, final = 258.09255 1.4763701 Force max component initial, final = 246.92639 0.48547335 Final line search alpha, max atom move = 0.00019044982 9.2458310e-05 Iterations, force evaluations = 32 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33609 | 0.33609 | 0.33609 | 0.0 | 95.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0035693 | 0.0035693 | 0.0035693 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01241 | | | 3.52 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4998.00 ave 4998 max 4998 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: 83532.0 ave 83532 max 83532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83532 Ave neighs/atom = 158.20455 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.655 | 4.655 | 4.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2132.1291 0 -2132.1291 -21919.828 Loop time of 6.254e-06 on 1 procs for 0 steps with 528 atoms 175.9% 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 | | 6.254e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5110.00 ave 5110 max 5110 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: 85752.0 ave 85752 max 85752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85752 Ave neighs/atom = 162.40909 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.655 | 4.655 | 4.655 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 -2132.1291 -2132.1291 15.970112 93.171132 4.0364059 -21919.828 -21919.828 125.57983 -65937.916 52.851235 2.2802102 891.51865 Loop time of 6.976e-06 on 1 procs for 0 steps with 528 atoms 272.4% 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 | | 6.976e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5110.00 ave 5110 max 5110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42876.0 ave 42876 max 42876 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 85752.0 ave 85752 max 85752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85752 Ave neighs/atom = 162.40909 Neighbor list builds = 0 Dangerous builds = 0 528 -2132.1291217021 eV 2.28021024760871 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03