diff options
Diffstat (limited to 'ml_exp/compound.py')
| -rw-r--r-- | ml_exp/compound.py | 82 |
1 files changed, 48 insertions, 34 deletions
diff --git a/ml_exp/compound.py b/ml_exp/compound.py index 1598fa482..6c8525195 100644 --- a/ml_exp/compound.py +++ b/ml_exp/compound.py @@ -23,7 +23,7 @@ SOFTWARE. import numpy as np from ml_exp.data import NUCLEAR_CHARGE from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\ - first_neighbor_matrix, adjacency_matrix, bag_of_stuff + get_helping_data, adjacency_matrix, bag_of_bonds class Compound: @@ -33,20 +33,31 @@ 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.nc = None self.coordinates = None self.pbe0 = None self.delta = None + # Computed data. self.cm = None self.ljm = None self.am = None - self.bos = None + self.bob = None + self.bo_atoms = None + self.bok_cx = None + self.bof = None + + # Helping data. + self.fnm = None + self.bonds = None + self.bonds_i = None + self.bonds_k = None + self.bonds_f = None if xyz is not None: self.read_xyz(xyz) @@ -62,7 +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) @@ -84,7 +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, @@ -92,42 +103,45 @@ class Compound: as_eig=as_eig, bohr_ru=bohr_ru) - def gen_am(self, - use_forces=False, + def gen_hd(self, size=23, bohr_ru=False): """ + Generate the helping data for use in Adjacency Matrix, for example. + size: compund size. + bohr_ru: if radius units should be in bohr's radius units. + """ + hd = get_helping_data(self.coordinates, + self.atoms, + self.nc, + size=size, + bohr_ru=bohr_ru) + + self.fnm, self.bonds, self.bonds_i, self.bonds_k, self.bonds_f = hd + + def gen_am(self, + use_forces=False, + size=23): + """ 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, - size=size, - use_forces=use_forces, - bohr_ru=bohr_ru) - - # Now, generate the adjacency matrix. - self.am = adjacency_matrix(fnm, - bonds, - forces, + self.am = adjacency_matrix(self.bonds_i, + self.bonds_k, + self.bonds_f, + use_forces=use_forces, size=size) - def gen_bos(self, - size=23, - stuff='bonds'): + def gen_bob(self, + size=23): """ Generate the Bag of Stuff for the compound. size: compound size. - stuff: elements of the bag, by default the known bag of bonds. """ - self.bos = bag_of_stuff(self.cm, + self.bob = bag_of_bonds(self.cm, self.atoms, - size=size, - stuff=stuff) + size=size) def read_xyz(self, filename): @@ -139,15 +153,15 @@ class Compound: lines = f.readlines() self.name = filename.split('/')[-1] - self.n = int(lines[0]) + self.n = np.int32(lines[0]) self.extra = lines[1] self.atoms = [] - self.atoms_nc = np.empty(self.n, dtype=int) - self.coordinates = np.empty((self.n, 3), dtype=float) + 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.coordinates[i] = np.asarray(atom_d[1:4], dtype=float) + self.nc[i] = NUCLEAR_CHARGE[atom_d[0]] + self.coordinates[i] = np.asarray(atom_d[1:4], dtype=np.float64) |