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 = 2.8669658 2.8669658 2.8669658 Created orthogonal box = (0.0000000 -28.672525 0.0000000) to (4.0545019 28.672525 4.0545019) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0545019 2.8669658 4.0545019 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -28.672525 0.0000000) to (4.0545019 28.672525 4.0545019) create_atoms CPU = 0.001 seconds 42 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0545019 2.8669658 4.0545019 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -28.672525 0.0000000) to (4.0545019 28.672525 4.0545019) create_atoms CPU = 0.000 seconds 42 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 = 2 16 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 2 atoms, new total = 82 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_677715648236_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 = 2 16 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) = 4.393 | 4.393 | 4.393 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -123.5798 0 -123.5798 1574654.7 152 0 -332.31335 0 -332.31335 -66531.842 Loop time of 0.530997 on 1 procs for 152 steps with 82 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 = -123.579804144047 -332.313029525036 -332.313348530907 Force two-norm initial, final = 119.05399 0.062612779 Force max component initial, final = 53.192447 0.012360444 Final line search alpha, max atom move = 1.0000000 0.012360444 Iterations, force evaluations = 152 288 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50976 | 0.50976 | 0.50976 | 0.0 | 96.00 Neigh | 0.0020575 | 0.0020575 | 0.0020575 | 0.0 | 0.39 Comm | 0.013446 | 0.013446 | 0.013446 | 0.0 | 2.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005731 | | | 1.08 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2254.00 ave 2254 max 2254 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: 13522.0 ave 13522 max 13522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13522 Ave neighs/atom = 164.90244 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 = 2 16 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 : 152 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.394 | 4.394 | 4.394 Mbytes Step Temp E_pair E_mol TotEng Press Volume 152 0 -332.31335 0 -332.31335 -66531.842 942.69445 195 0 -332.97758 0 -332.97758 -25159.087 911.57993 Loop time of 0.0898895 on 1 procs for 43 steps with 82 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 = -332.313348530907 -332.977311498989 -332.977580213992 Force two-norm initial, final = 44.207584 0.39592653 Force max component initial, final = 43.103524 0.21661878 Final line search alpha, max atom move = 0.0038066272 0.00082458693 Iterations, force evaluations = 43 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.081595 | 0.081595 | 0.081595 | 0.0 | 90.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022228 | 0.0022228 | 0.0022228 | 0.0 | 2.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006071 | | | 6.75 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2226.00 ave 2226 max 2226 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: 13134.0 ave 13134 max 13134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13134 Ave neighs/atom = 160.17073 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 = 2 16 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) = 4.532 | 4.532 | 4.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -332.97758 0 -332.97758 -25159.087 Loop time of 6.235e-06 on 1 procs for 0 steps with 82 atoms 144.3% 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 | | 6.235e-06 | | |100.00 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2226.00 ave 2226 max 2226 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: 13500.0 ave 13500 max 13500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13500 Ave neighs/atom = 164.63415 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 = 2 16 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) = 4.532 | 4.532 | 4.532 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 -332.97758 -332.97758 3.9236486 57.34505 4.0514335 -25159.087 -25159.087 321.78379 -75418.607 -380.43714 2.3585874 151.08793 Loop time of 6.936e-06 on 1 procs for 0 steps with 82 atoms 245.1% 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 | | 6.936e-06 | | |100.00 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2226.00 ave 2226 max 2226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6750.00 ave 6750 max 6750 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13500.0 ave 13500 max 13500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13500 Ave neighs/atom = 164.63415 Neighbor list builds = 0 Dangerous builds = 0 82 -332.977580213992 eV 2.35858742087312 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01