diff options
| -rw-r--r-- | ml_exp/compound.py | 16 | ||||
| -rw-r--r-- | ml_exp/do_ml.py | 6 | ||||
| -rw-r--r-- | ml_exp/representations.py | 44 |
3 files changed, 38 insertions, 28 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) diff --git a/ml_exp/do_ml.py b/ml_exp/do_ml.py index 5054b2b06..5efd13690 100644 --- a/ml_exp/do_ml.py +++ b/ml_exp/do_ml.py @@ -176,11 +176,13 @@ def do_ml(db_path='data', size=size, as_eig=as_eig, bohr_ru=bohr_ru) + """ if 'AM' in identifiers: compound.gen_hd(size=size, bohr_ru=bohr_ru) compound.gen_am(use_forces=use_forces, size=size) + """ if 'BOB' in identifiers: compound.gen_bob(size=size) @@ -189,8 +191,10 @@ def do_ml(db_path='data', cm_data = np.array([comp.cm for comp in compounds], dtype=np.float64) if 'LJM' in identifiers: ljm_data = np.array([comp.ljm for comp in compounds], dtype=np.float64) + """ if 'AM' in identifiers: am_data = np.array([comp.cm for comp in compounds], dtype=np.float64) + """ if 'BOB' in identifiers: bob_data = np.array([comp.bob for comp in compounds], dtype=np.float64) @@ -218,6 +222,7 @@ def do_ml(db_path='data', opt=opt, identifier='LJM', show_msgs=show_msgs) + """ if 'AM' in identifiers: am_mae, am_tictoc = simple_ml(am_data, energy_pbe0, @@ -227,6 +232,7 @@ def do_ml(db_path='data', opt=opt, identifier='AM', show_msgs=show_msgs) + """ if 'BOB' in identifiers: bob_mae, bob_tictoc = simple_ml(bob_data, energy_pbe0, diff --git a/ml_exp/representations.py b/ml_exp/representations.py index 6b5d26bcb..be567d67a 100644 --- a/ml_exp/representations.py +++ b/ml_exp/representations.py @@ -167,15 +167,15 @@ size. Arrays are not of the right shape.') def get_helping_data(coords, - nc, atoms, + nc, size=23, bohr_ru=False): """ Creates helping data such as the First Neighbor Matrix for the compound. coords: compound coordinates. - nc: nuclear charge data. atoms: list of atoms. + nc: nuclear charge data. size: compund size. bohr_ru: if radius units should be in bohr's radius units. NOTE: Bond distance of carbon to other elements @@ -203,11 +203,11 @@ size. Arrays are not of the right shape.') size = n # Possible bonds. - cc_bond = sorted(['C', 'C']) - ch_bond = sorted(['C', 'H']) - co_bond = sorted(['C', 'O']) - cn_bond = sorted(['C', 'N']) - cs_bond = sorted(['C', 'S']) + cc_bond = ''.join(sorted(['C', 'C'])) + ch_bond = ''.join(sorted(['C', 'H'])) + co_bond = ''.join(sorted(['C', 'O'])) + cn_bond = ''.join(sorted(['C', 'N'])) + cs_bond = ''.join(sorted(['C', 'S'])) pos_bonds = {cc_bond: (1.19, 1.54, 1.0), ch_bond: (1.06, 1.12, 1.0), co_bond: (1.43, 2.15, 0.8), cn_bond: (1.47, 2.19, 1.0), cs_bond: (1.81, 2.55, 0.7)} @@ -221,7 +221,7 @@ size. Arrays are not of the right shape.') for j, xyz_j in enumerate(coords): # Ignore the diagonal. if i != j: - bond = sorted([atoms[i], atoms[j]]) + bond = ''.join(sorted([atoms[i], atoms[j]])) if bond in pos_bonds.keys(): r_min = pos_bonds[bond][0] r_max = pos_bonds[bond][1] @@ -239,21 +239,25 @@ size. Arrays are not of the right shape.') return fnm, bonds, bonds_i, bonds_k, bonds_f -def adjacency_matrix(fnm, - bonds, - forces, +def adjacency_matrix(bonds_i, + bonds_k, + bonds_f, use_forces=False, - size=22): + size=23): """ Calculates the adjacency matrix given the bond list. - fnm: first neighbour matrix. - bonds: list of bonds (tuple of indexes). - forces: list of forces. + bonds: list of bond names. + bonds_i: list of bond indexes (tuple of indexes). + bonds_k: list of k_cx values. + bonds_f: list of force values. use_forces: if the use of forces instead of k_cx should be used. size: compund size. """ - n = len(bonds) + if bonds_i is None: + raise ValueError('The helping data hasn\'t been initialized for\ +the current compound.') + n = len(bonds_i) if size < n: print('Error. Compound size (n) is greater han (size). Using (n)\ instead of (size).') @@ -261,15 +265,15 @@ def adjacency_matrix(fnm, am = np.zeros((size, size), dtype=np.float64) - for i, bond_i in enumerate(bonds): - for j, bond_j in enumerate(bonds): + for i, bond_i in enumerate(bonds_i): + for j, bond_j in enumerate(bonds_i): # Ignore the diagonal. if i != j: if (bond_i[0] in bond_j) or (bond_i[1] in bond_j): if use_forces: - am[i, j] = np.dot(forces[i], forces[j]) + am[i, j] = np.dot(bonds_f[i], bonds_f[j]) else: - am[i, j] = fnm[bond_i[0], bond_i[1]] + am[i, j] = bonds_k[i] return am |