diff options
| -rw-r--r-- | ml_exp/compound.py | 41 |
1 files changed, 33 insertions, 8 deletions
diff --git a/ml_exp/compound.py b/ml_exp/compound.py index 3ea377826..d74f1230a 100644 --- a/ml_exp/compound.py +++ b/ml_exp/compound.py @@ -22,7 +22,7 @@ SOFTWARE. """ import numpy as np from ml_exp.data import NUCLEAR_CHARGE -from ml_exp.representations import coulomb_matrix +from ml_exp.representations import coulomb_matrix, lennard_jones_matrix class Compound: @@ -40,8 +40,8 @@ class Compound: self.coordinates = None self.energy = None - self.coulomb_matrix = None - self.lennard_jones_matrix = None + self.c_matrix = None + self.lj_matrix = None self.bob = None if xyz is not None: @@ -57,11 +57,36 @@ class Compound: as_eig: if the representation should be as the eigenvalues. bhor_ru: if radius units should be in bohr's radius units. """ - self.coulomb_matrix = coulomb_matrix(self.coordinates, - self.atoms_nc, - size=size, - as_eig=as_eig, - bhor_ru=bohr_ru) + self.c_matrix = coulomb_matrix(self.coordinates, + self.atoms_nc, + size=size, + as_eig=as_eig, + bhor_ru=bohr_ru) + + def gen_lj(self, + diag_value=None, + sigma=1.0, + epsilon=1.0, + size=23, + as_eig=True, + bohr_ru=False): + """ + Generate the Lennard-Jones Matrix for the compund. + diag_value: if special diagonal value is to be used. + sigma: sigma value. + epsilon: epsilon value. + size: compound size. + as_eig: if the representation should be as the eigenvalues. + bhor_ru: if radius units should be in bohr's radius units. + """ + self.lj_matrix = lennard_jones_matrix(self.coordinates, + self.atoms_nc, + diag_value=diag_value, + sigma=sigma, + epsilon=epsilon, + size=size, + as_eig=as_eig, + bhor_ru=bohr_ru) def read_xyz(self, filename): |