Move cmatrix to representations

1 files changed, 0 insertions, 146 deletions

diff --git a/ml_exp/c_matrix.py b/ml_exp/c_matrix.py
deleted file mode 100644
index ac942d473..000000000
--- a/ml_exp/c_matrix.py
+++ /dev/null
@@ -1,146 +0,0 @@
-"""MIT License
-
-Copyright (c) 2019 David Luevano Alvarado
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-import math
-import numpy as np
-from numpy.linalg import eig
-
-
-def c_matrix(mol_data,
-             nc_data,
-             max_len=25,
-             as_eig=True,
-             bohr_radius_units=False):
-    """
-    Creates the Coulomb Matrix from the molecule data given.
-    mol_data: molecule data, matrix of atom coordinates.
-    nc_data: nuclear charge data, array of atom data.
-    max_len: maximum amount of atoms in molecule.
-    as_eig: if data should be returned as matrix or array of eigenvalues.
-    bohr_radius_units: if units should be in bohr's radius units.
-    """
-    if bohr_radius_units:
-        conversion_rate = 0.52917721067
-    else:
-        conversion_rate = 1
-
-    mol_n = len(mol_data)
-    mol_nr = range(mol_n)
-
-    if not mol_n == len(nc_data):
-        print(''.join(['Error. Molecule matrix dimension is different ',
-                       'than the nuclear charge array dimension.']))
-    else:
-        if max_len < mol_n:
-            print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
-                           'greater than max_len. Using mol_n.']))
-            max_len = None
-
-        if max_len:
-            cm = np.zeros((max_len, max_len))
-            ml_r = range(max_len)
-
-            # Actual calculation of the coulomb matrix.
-            for i in ml_r:
-                if i < mol_n:
-                    x_i = mol_data[i, 0]
-                    y_i = mol_data[i, 1]
-                    z_i = mol_data[i, 2]
-                    Z_i = nc_data[i]
-                else:
-                    break
-
-                for j in ml_r:
-                    if j < mol_n:
-                        x_j = mol_data[j, 0]
-                        y_j = mol_data[j, 1]
-                        z_j = mol_data[j, 2]
-                        Z_j = nc_data[j]
-
-                        x = (x_i-x_j)**2
-                        y = (y_i-y_j)**2
-                        z = (z_i-z_j)**2
-
-                        if i == j:
-                            cm[i, j] = (0.5*Z_i**2.4)
-                        else:
-                            cm[i, j] = (conversion_rate*Z_i*Z_j/math.sqrt(x
-                                                                          + y
-                                                                          + z))
-                    else:
-                        break
-
-            # Now the value will be returned.
-            if as_eig:
-                cm_sorted = np.sort(eig(cm)[0])[::-1]
-                # Thanks to SO for the following lines of code.
-                # https://stackoverflow.com/a/43011036
-
-                # Keep zeros at the end.
-                mask = cm_sorted != 0.
-                f_mask = mask.sum(0, keepdims=1) >\
-                    np.arange(cm_sorted.shape[0]-1, -1, -1)
-
-                f_mask = f_mask[::-1]
-                cm_sorted[f_mask] = cm_sorted[mask]
-                cm_sorted[~f_mask] = 0.
-
-                return cm_sorted
-
-            else:
-                return cm
-
-        else:
-            cm_temp = []
-            # Actual calculation of the coulomb matrix.
-            for i in mol_nr:
-                x_i = mol_data[i, 0]
-                y_i = mol_data[i, 1]
-                z_i = mol_data[i, 2]
-                Z_i = nc_data[i]
-
-                cm_row = []
-                for j in mol_nr:
-                    x_j = mol_data[j, 0]
-                    y_j = mol_data[j, 1]
-                    z_j = mol_data[j, 2]
-                    Z_j = nc_data[j]
-
-                    x = (x_i-x_j)**2
-                    y = (y_i-y_j)**2
-                    z = (z_i-z_j)**2
-
-                    if i == j:
-                        cm_row.append(0.5*Z_i**2.4)
-                    else:
-                        cm_row.append(conversion_rate*Z_i*Z_j/math.sqrt(x
-                                                                        + y
-                                                                        + z))
-
-                cm_temp.append(np.array(cm_row))
-
-            cm = np.array(cm_temp)
-            # Now the value will be returned.
-            if as_eig:
-                return np.sort(eig(cm)[0])[::-1]
-            else:
-                return cm