diff options
| author | David Luevano Alvarado <55825613+luevano@users.noreply.github.com> | 2020-02-22 16:36:40 -0700 |
|---|---|---|
| committer | David Luevano Alvarado <55825613+luevano@users.noreply.github.com> | 2020-02-22 16:36:40 -0700 |
| commit | 2572f9581b24547692a5654a1d452690a2cbcad6 (patch) | |
| tree | 82719671bd5a8105c663302313aab19815f1ad98 /ml_exp/compound.py | |
| parent | 4f95e38f1943856f9a0581c06ea603ffb6283d47 (diff) | |
Add adj matrix to compound)
Diffstat (limited to 'ml_exp/compound.py')
| -rw-r--r-- | ml_exp/compound.py | 35 |
1 files changed, 30 insertions, 5 deletions
diff --git a/ml_exp/compound.py b/ml_exp/compound.py index c6d5f8a64..d4dc9b7c0 100644 --- a/ml_exp/compound.py +++ b/ml_exp/compound.py @@ -22,7 +22,8 @@ SOFTWARE. """ import numpy as np from ml_exp.data import NUCLEAR_CHARGE -from ml_exp.representations import coulomb_matrix, lennard_jones_matrix +from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\ + first_neighbor_matrix, adjacency_matrix class Compound: @@ -42,6 +43,7 @@ class Compound: self.cm = None self.ljm = None + self.am = None self.bob = None if xyz is not None: @@ -55,13 +57,13 @@ class Compound: Generate the Coulomb Matrix for the compund. 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. + bohr_ru: if radius units should be in bohr's radius units. """ self.cm = coulomb_matrix(self.coordinates, self.atoms_nc, size=size, as_eig=as_eig, - bhor_ru=bohr_ru) + bohr_ru=bohr_ru) def gen_ljm(self, diag_value=None, @@ -77,7 +79,7 @@ class Compound: 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. + bohr_ru: if radius units should be in bohr's radius units. """ self.ljm = lennard_jones_matrix(self.coordinates, self.atoms_nc, @@ -86,7 +88,30 @@ class Compound: epsilon=epsilon, size=size, as_eig=as_eig, - bhor_ru=bohr_ru) + bohr_ru=bohr_ru) + + def gen_am(self, + use_forces=False, + size=23, + bohr_ru=False): + """ + Generate the Adjacency Matrix for the compund. + use_forces: if the use of forces instead of k_cx should be used. + size: compound size. + bohr_ru: if radius units should be in bohr's radius units. + """ + # First, generate the first neighor matrix. + fnm, bonds, forces = first_neighbor_matrix(self.coordinates, + self.atoms_nc, + self.atoms, + use_forces=use_forces, + bohr_ru=bohr_ru) + + # Now, generate the adjacency matrix. + self.am = adjacency_matrix(fnm, + bonds, + forces, + size=size) def read_xyz(self, filename): |