diff options
| author | David Luevano Alvarado <55825613+luevano@users.noreply.github.com> | 2020-03-02 12:01:58 -0700 |
|---|---|---|
| committer | David Luevano Alvarado <55825613+luevano@users.noreply.github.com> | 2020-03-02 12:01:58 -0700 |
| commit | 62cef5f1782caf4ff379cd021744b98be4be6c8b (patch) | |
| tree | dd42fddfb03f1ff201d6f770bb92c3f32cae9329 /ml_exp/compound.py | |
| parent | 4a3f602aab73bb0304a237ddca5d9f3fa8867001 (diff) | |
Fix bug
Diffstat (limited to 'ml_exp/compound.py')
| -rw-r--r-- | ml_exp/compound.py | 16 |
1 files changed, 8 insertions, 8 deletions
diff --git a/ml_exp/compound.py b/ml_exp/compound.py index 4428e9164..6c8525195 100644 --- a/ml_exp/compound.py +++ b/ml_exp/compound.py @@ -38,7 +38,7 @@ class Compound: self.n = None self.extra = None self.atoms = None - self.atoms_nc = None + self.nc = None self.coordinates = None self.pbe0 = None self.delta = None @@ -73,7 +73,7 @@ class Compound: bohr_ru: if radius units should be in bohr's radius units. """ self.cm = coulomb_matrix(self.coordinates, - self.atoms_nc, + self.nc, size=size, as_eig=as_eig, bohr_ru=bohr_ru) @@ -95,7 +95,7 @@ class Compound: bohr_ru: if radius units should be in bohr's radius units. """ self.ljm = lennard_jones_matrix(self.coordinates, - self.atoms_nc, + self.nc, diag_value=diag_value, sigma=sigma, epsilon=epsilon, @@ -112,8 +112,8 @@ class Compound: bohr_ru: if radius units should be in bohr's radius units. """ hd = get_helping_data(self.coordinates, - self.nc, self.atoms, + self.nc, size=size, bohr_ru=bohr_ru) @@ -127,8 +127,8 @@ class Compound: use_forces: if the use of forces instead of k_cx should be used. size: compound size. """ - self.am = adjacency_matrix(self.fnm, - self.bonds, + self.am = adjacency_matrix(self.bonds_i, + self.bonds_k, self.bonds_f, use_forces=use_forces, size=size) @@ -156,12 +156,12 @@ class Compound: self.n = np.int32(lines[0]) self.extra = lines[1] self.atoms = [] - self.atoms_nc = np.empty(self.n, dtype=np.int64) + self.nc = np.empty(self.n, dtype=np.int64) self.coordinates = np.empty((self.n, 3), dtype=np.float64) for i, atom in enumerate(lines[2:self.n + 2]): atom_d = atom.split() self.atoms.append(atom_d[0]) - self.atoms_nc[i] = NUCLEAR_CHARGE[atom_d[0]] + self.nc[i] = NUCLEAR_CHARGE[atom_d[0]] self.coordinates[i] = np.asarray(atom_d[1:4], dtype=np.float64) |