From 02cb17d411e9a1bc2fe5c6bcf75695f23f340648 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 17:44:34 -0700
Subject: Add exception
---
ml_exp/representations.py | 158 +++++++++++++++++++++++-----------------------
1 file changed, 79 insertions(+), 79 deletions(-)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 830e51707..50b78e548 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -42,83 +42,34 @@ def coulomb_matrix(coords,
else:
conversion_rate = 1
- mol_n = len(coords)
- mol_nr = range(mol_n)
+ n = coords.shape[0]
+ nr = range(n)
- if not mol_n == len(nc):
- print(''.join(['Error. Molecule matrix dimension is different ',
- 'than the nuclear charge array dimension.']))
- else:
- if size < mol_n:
- print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
- 'greater than size. Using mol_n.']))
- size = None
-
- if size:
- cm = np.zeros((size, size))
- ml_r = range(size)
-
- # Actual calculation of the coulomb matrix.
- for i in ml_r:
- if i < mol_n:
- x_i = coords[i, 0]
- y_i = coords[i, 1]
- z_i = coords[i, 2]
- Z_i = nc[i]
- else:
- break
-
- for j in ml_r:
- if j < mol_n:
- x_j = coords[j, 0]
- y_j = coords[j, 1]
- z_j = coords[j, 2]
- Z_j = nc[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(np.linalg.eig(cm)[0])[::-1]
- # Thanks to SO for the following lines of code.
- # https://stackoverflow.com/a/43011036
+ if not n == nc.shape[0]:
+ raise ValueError('Compound size is different than the nuclear charge\
+ size. Arrays are not of the right shape.')
- # 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)
+ if size < n:
+ print(''.join(['Error. Molecule matrix dimension (n) is ',
+ 'greater than size. Using n.']))
+ size = None
- f_mask = f_mask[::-1]
- cm_sorted[f_mask] = cm_sorted[mask]
- cm_sorted[~f_mask] = 0.
+ if size:
+ cm = np.zeros((size, size))
+ ml_r = range(size)
- return cm_sorted
-
- else:
- return cm
-
- else:
- cm_temp = []
- # Actual calculation of the coulomb matrix.
- for i in mol_nr:
+ # Actual calculation of the coulomb matrix.
+ for i in ml_r:
+ if i < n:
x_i = coords[i, 0]
y_i = coords[i, 1]
z_i = coords[i, 2]
Z_i = nc[i]
+ else:
+ break
- cm_row = []
- for j in mol_nr:
+ for j in ml_r:
+ if j < n:
x_j = coords[j, 0]
y_j = coords[j, 1]
z_j = coords[j, 2]
@@ -129,17 +80,66 @@ def coulomb_matrix(coords,
z = (z_i-z_j)**2
if i == j:
- cm_row.append(0.5*Z_i**2.4)
+ cm[i, j] = (0.5*Z_i**2.4)
else:
- cm_row.append(conversion_rate*Z_i*Z_j/math.sqrt(x
- + y
- + z))
+ cm[i, j] = (conversion_rate*Z_i*Z_j/math.sqrt(x
+ + y
+ + z))
+ else:
+ break
- cm_temp.append(np.array(cm_row))
+ # Now the value will be returned.
+ if as_eig:
+ cm_sorted = np.sort(np.linalg.eig(cm)[0])[::-1]
+ # Thanks to SO for the following lines of code.
+ # https://stackoverflow.com/a/43011036
- cm = np.array(cm_temp)
- # Now the value will be returned.
- if as_eig:
- return np.sort(np.linalg.eig(cm)[0])[::-1]
- else:
- return cm
+ # 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 nr:
+ x_i = coords[i, 0]
+ y_i = coords[i, 1]
+ z_i = coords[i, 2]
+ Z_i = nc[i]
+
+ cm_row = []
+ for j in nr:
+ x_j = coords[j, 0]
+ y_j = coords[j, 1]
+ z_j = coords[j, 2]
+ Z_j = nc[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(np.linalg.eig(cm)[0])[::-1]
+ else:
+ return cm
--
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