<jupyter_start><jupyter_text>Visualization<jupyter_code>from eminus import Atoms, read_xyz, SCF, write_cube, write_xyz
from eminus.addons import get_fods, view_grid, view_mol;
## View the initial xyz file
view_mol('CH4.xyz')
## Do the DFT calculation
atoms = Atoms(*read_xyz('CH4.xyz'), center=True)
scf = SCF(atoms)
scf.run();
## Calculate FODs and write them to a xyz file
fods = get_fods(atoms)
write_xyz(atoms, 'CH4_fods.xyz', fods);
## View molecule with FODs
view_mol('CH4_fods.xyz')
## Write the density to a cube file
write_cube(scf, scf.n, 'CH4_density.cube');
## Display the cube file
view_mol('CH4_density.cube')
## Use a smaller grid and display it along with the atom positions
atoms.s = 10
atoms.update()
view_grid(atoms.r, atoms.X)<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.12242268041237113, 'fraction_numerical': 0.010309278350515464, 'mean_word_length': 6.4, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '1', 'dir': 'jupyter-structured-clean-dedup', 'id': '252861', 'license': 'Apache-2.0', 'n_tokens_mistral': 327, 'n_tokens_neox': 298, 'n_words': 81, 'path': 'examples/08_visualizer_addon/08_visualizer_addon.ipynb', 'repo_name': 'wangenau/eminus', 'size': '776'}