From fb4307513ddda06742bbe4d542c2716c0d67c06d Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 22 Feb 2020 16:56:05 -0700
Subject: Refactor code
---
ml_exp/representations.py | 93 +++++++++++++----------------------------------
1 file changed, 26 insertions(+), 67 deletions(-)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 483da2898..354611190 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -20,7 +20,6 @@ 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
@@ -53,36 +52,17 @@ def coulomb_matrix(coords,
instead of (size).')
size = n
- nr = range(size)
cm = np.zeros((size, size), dtype=float)
# Actual calculation of the coulomb matrix.
- for i in nr:
- if i < 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 nr:
- if j < 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] = (cr*Z_i*Z_j/math.sqrt(x + y + z))
+ for i, xyz_i in enumerate(coords):
+ for j, xyz_j in enumerate(coords):
+ rv = xyz_i - xyz_j
+ r = np.linalg.norm(rv)/cr
+ if i == j:
+ cm[i, j] = (0.5*nc[i]**2.4)
else:
- break
+ cm[i, j] = nc[i]*nc[j]/r
# Now the value will be returned.
if as_eig:
@@ -139,52 +119,31 @@ def lennard_jones_matrix(coords,
instead of (size).')
size = n
- nr = range(size)
lj = np.zeros((size, size), dtype=float)
# Actual calculation of the lennard-jones matrix.
- for i in nr:
- if i < 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 nr:
- if j < n:
- x_j = coords[j, 0]
- y_j = coords[j, 1]
- z_j = coords[j, 2]
- # Never really used because when needed it is equal to Z_i.
- # 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:
- if diag_value is None:
- lj[i, j] = (0.5*Z_i**2.4)
- else:
- lj[i, j] = diag_value
+ for i, xyz_i in enumerate(coords):
+ for j, xyz_j in enumerate(coords):
+ if i == j:
+ if diag_value is None:
+ lj[i, j] = (0.5*nc[i]**2.4)
else:
- # Calculations are done after i==j is checked
- # so no division by zero is done.
-
- # A little play with r exponents
- # so no square root is calculated.
- # Conversion factor is included in r^2.
+ lj[i, j] = diag_value
+ else:
+ # Calculations are done after i==j is checked
+ # so no division by zero is done.
- # 1/r^2
- r_2 = sigma**2/(cr**2*(x + y + z))
+ # A little play with r exponents
+ # so no square root is calculated.
+ # Conversion factor is included in r^2.
+ rv = xyz_i - xyz_j
+ r = sigma*np.linalg.norm(rv)/cr
- r_6 = math.pow(r_2, 3)
- r_12 = math.pow(r_6, 2)
- lj[i, j] = (4*epsilon*(r_12 - r_6))
- else:
- break
+ # 1/r^n
+ r_2 = 1/r**2
+ r_6 = r_2**3
+ r_12 = r_6**2
+ lj[i, j] = (4*epsilon*(r_12 - r_6))
# Now the value will be returned.
if as_eig:
--
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