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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -55.454933 0.0000000) to (33.959072 55.454933 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4772697 5.3666064 5.7504086 Created 1488 atoms using lattice units in orthogonal box = (0.0000000 -55.454933 0.0000000) to (33.959072 55.454933 8.6256130) create_atoms CPU = 0.002 seconds 1488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4772697 5.3666064 5.7504086 Created 1494 atoms using lattice units in orthogonal box = (0.0000000 -55.454933 0.0000000) to (33.959072 55.454933 8.6256130) create_atoms CPU = 0.002 seconds 1494 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2976 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_115454747503_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.661 | 5.661 | 5.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12262.935 0 -12262.935 67269.29 86 0 -13197.64 0 -13197.64 7934.2918 Loop time of 20.3152 on 1 procs for 86 steps with 2976 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 = -12262.9346589558 -13197.6297362952 -13197.6398698415 Force two-norm initial, final = 871.66860 0.37453517 Force max component initial, final = 147.03755 0.034100325 Final line search alpha, max atom move = 1.0000000 0.034100325 Iterations, force evaluations = 86 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.201 | 20.201 | 20.201 | 0.0 | 99.44 Neigh | 0.070883 | 0.070883 | 0.070883 | 0.0 | 0.35 Comm | 0.017685 | 0.017685 | 0.017685 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02584 | | | 0.13 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8521.00 ave 8521 max 8521 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: 262080.0 ave 262080 max 262080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262080 Ave neighs/atom = 88.064516 Neighbor list builds = 3 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.669 | 5.669 | 5.669 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -13197.64 0 -13197.64 7934.2918 32487.475 92 0 -13198.393 0 -13198.393 -15.654969 32624.918 Loop time of 1.26893 on 1 procs for 6 steps with 2976 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 = -13197.6398698415 -13198.3924852288 -13198.3931631584 Force two-norm initial, final = 333.82168 1.9662719 Force max component initial, final = 304.80146 1.6764610 Final line search alpha, max atom move = 9.8900890e-05 0.00016580349 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2633 | 1.2633 | 1.2633 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072419 | 0.00072419 | 0.00072419 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004946 | | | 0.39 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8661.00 ave 8661 max 8661 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: 261744.0 ave 261744 max 261744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261744 Ave neighs/atom = 87.951613 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.807 | 5.807 | 5.807 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13198.393 0 -13198.393 -15.654969 Loop time of 2.408e-06 on 1 procs for 0 steps with 2976 atoms 166.1% 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 | | 2.408e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8698.00 ave 8698 max 8698 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: 260844.0 ave 260844 max 260844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260844 Ave neighs/atom = 87.649194 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.807 | 5.807 | 5.807 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 -13198.393 -13198.393 33.970124 111.46986 8.6157847 -15.654969 -15.654969 -82.356087 -5.1686947 40.559875 2.2482454 920.39751 Loop time of 2.217e-06 on 1 procs for 0 steps with 2976 atoms 270.6% 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 | | 2.217e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8698.00 ave 8698 max 8698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130422.0 ave 130422 max 130422 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 260844.0 ave 260844 max 260844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260844 Ave neighs/atom = 87.649194 Neighbor list builds = 0 Dangerous builds = 0 2976 -13198.3931631584 eV 2.24824535022475 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22