Conf Gen

Conf Gen#

autode.conformers.conf_gen.get_simanl_atoms(species: Species, dist_consts: Dict | None = None, conf_n: int = 0, save_xyz: bool = True, also_return_energy: bool = False)#

Use a bonded + repulsive force field to generate 3D structure for a species. If the initial coordinates are reasonable e.g. from a previously generated 3D structure then add random displacement vectors and minimise to generate a conformer. Otherwise add atoms to the box sequentially until all atoms have been added, which generates a qualitatively reasonable 3D geometry which should be optimised using a electronic structure method:

V(x) = Σ_bonds k(d - d0)^2 + Σ_ij c/d^n
Parameters:

  • dist_consts (dict) – Key = tuple of atom indexes, Value = distance

  • conf_n (int) – Number of this conformer

  • save_xyz (bool) – Whether or not to save a .xyz file of the structure for fast reloading

  • also_return_energy (bool) – Whether or not to return the energy

Returns:

Atoms

Return type:

(list(autode.atoms.Atom))

autode.conformers.conf_gen.get_simanl_conformer(species: Species, dist_consts: Dict | None = None, conf_n: int = 0, save_xyz: bool = True) → Conformer#

Generate a conformer of a species using randomise+relax with a simple FF (see get_simanl_atoms). Example

Parameters:

  • dist_consts (dict) – Key = tuple of atom indexes, Value = distance

  • conf_n (int) – Number of this conformer

  • save_xyz (bool) – Whether or not to save a .xyz file of the structure

Returns:

Conformer

Return type:

(autode.conformers.Conformer)

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