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| author | David Luevano Alvarado <55825613+luevano@users.noreply.github.com> | 2020-02-29 07:19:46 -0700 |
|---|---|---|
| committer | David Luevano Alvarado <55825613+luevano@users.noreply.github.com> | 2020-02-29 07:19:46 -0700 |
| commit | 6dd33013265ce38122a623b285e0b39f2496aaf8 (patch) | |
| tree | f86387dc075c138ecda55db49f90e3fb83485eb3 /ml_exp/compound.py | |
| parent | d71927fc791e51bf383b88bd3d943d8e3311ee8a (diff) | |
Rewrite fnm
Diffstat (limited to 'ml_exp/compound.py')
| -rw-r--r-- | ml_exp/compound.py | 33 |
1 files changed, 21 insertions, 12 deletions
diff --git a/ml_exp/compound.py b/ml_exp/compound.py index 98e31532f..ceace6984 100644 --- a/ml_exp/compound.py +++ b/ml_exp/compound.py @@ -33,20 +33,29 @@ class Compound: Initialization of the Compound. xyz: (path to) the xyz file. """ + # General compound data. self.name = None - self.n = None - self.extra = None # In case a comment is in the compound file. + self.extra = None self.atoms = None self.atoms_nc = None self.coordinates = None self.pbe0 = None self.delta = None + # Computed data. self.cm = None self.ljm = None + self.fnm = None self.am = None self.bob = None + self.bo_atoms = None + self.bok_cx = None + self.bof = None + + # Helping data. + self.bonds = None + self.forces = None if xyz is not None: self.read_xyz(xyz) @@ -103,17 +112,17 @@ class Compound: 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, - size=size, - use_forces=use_forces, - bohr_ru=bohr_ru) - + fnm_data = first_neighbor_matrix(self.coordinates, + self.atoms_nc, + self.atoms, + size=size, + use_forces=use_forces, + bohr_ru=bohr_ru) + self.fnm, self.bonds, self.forces = fnm_data # Now, generate the adjacency matrix. - self.am = adjacency_matrix(fnm, - bonds, - forces, + self.am = adjacency_matrix(self.fnm, + self.bonds, + self.forces, size=size) def gen_bob(self, |