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 = 3.3024436 3.3024436 3.3024436 Created orthogonal box = (0.0000000 -42.804561 0.0000000) to (24.713225 42.804561 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2956910 5.0957810 5.7200000 Created 336 atoms using lattice units in orthogonal box = (0.0000000 -42.804561 0.0000000) to (24.713225 42.804561 5.7200000) create_atoms CPU = 0.001 seconds 336 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2956910 5.0957810 5.7200000 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -42.804561 0.0000000) to (24.713225 42.804561 5.7200000) create_atoms CPU = 0.001 seconds 339 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 8 26 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 672 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_072689718616_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.507 | 4.507 | 4.507 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4930.8356 0 -4930.8356 21764.79 44 0 -4993.9563 0 -4993.9563 7880.4511 Loop time of 1.68952 on 1 procs for 44 steps with 672 atoms 97.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4930.83562880851 -4993.95190426568 -4993.95634419449 Force two-norm initial, final = 73.149341 0.22737737 Force max component initial, final = 16.605812 0.030923261 Final line search alpha, max atom move = 1.0000000 0.030923261 Iterations, force evaluations = 44 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6823 | 1.6823 | 1.6823 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0035992 | 0.0035992 | 0.0035992 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00367 | | | 0.22 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3284.00 ave 3284 max 3284 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: 39384.0 ave 39384 max 39384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39384 Ave neighs/atom = 58.607143 Neighbor list builds = 0 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.507 | 4.507 | 4.507 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -4993.9563 0 -4993.9563 7880.4511 12101.675 47 0 -4994.087 0 -4994.087 -2.3988066 12150.474 Loop time of 0.118393 on 1 procs for 3 steps with 672 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 = -4993.95634419449 -4994.08458637779 -4994.08695375202 Force two-norm initial, final = 104.86787 0.68508034 Force max component initial, final = 68.289033 0.50669441 Final line search alpha, max atom move = 0.00011985377 6.0729235e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11738 | 0.11738 | 0.11738 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016966 | 0.00016966 | 0.00016966 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008415 | | | 0.71 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3273.00 ave 3273 max 3273 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: 40848.0 ave 40848 max 40848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40848 Ave neighs/atom = 60.785714 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.645 | 4.645 | 4.645 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4994.087 0 -4994.087 -2.3988066 Loop time of 2.009e-06 on 1 procs for 0 steps with 672 atoms 149.3% 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 | | 2.009e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3273.00 ave 3273 max 3273 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: 40162.0 ave 40162 max 40162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40162 Ave neighs/atom = 59.764881 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.645 | 4.645 | 4.645 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 -4994.087 -4994.087 24.723147 85.772846 5.7298025 -2.3988066 -2.3988066 8.4180042 51.313426 -66.92785 2.6662158 672.10813 Loop time of 2.045e-06 on 1 procs for 0 steps with 672 atoms 146.7% 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 | | 2.045e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3273.00 ave 3273 max 3273 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20081.0 ave 20081 max 20081 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40162.0 ave 40162 max 40162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40162 Ave neighs/atom = 59.764881 Neighbor list builds = 0 Dangerous builds = 0 672 -4994.08695375202 eV 2.6662158144577 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02