From 5cbaae0eb1e39a0514424ab0c0005fbb7f78261c Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 10 Mar 2020 12:34:00 -0700
Subject: AM O(n^2) to O((n-1)(n/2-1))
---
ml_exp/representations.py | 37 ++++++++++++++++++-------------------
1 file changed, 18 insertions(+), 19 deletions(-)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index ab2dcdd21..937268d0c 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -189,29 +189,28 @@ size. Arrays are not of the right shape.')
co_bond: (1.43, 2.15, 0.8), cn_bond: (1.47, 2.19, 1.0),
cs_bond: (1.81, 2.55, 0.7)}
- fnm = np.zeros((size, size), dtype=bool)
+ fnm = np.zeros((n, n), dtype=bool)
bonds = []
bonds_i = []
bonds_k = []
bonds_f = []
- for i, xyz_i in enumerate(coords):
- for j, xyz_j in enumerate(coords):
- # Ignore the diagonal.
- if i != 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]
- rv = xyz_i - xyz_j
- r = np.linalg.norm(rv)/cr
- if r >= r_min and r <= r_max:
- fnm[i, j] = True
- # Only add to the list if in the upper triangle.
- if j > i:
- bonds.append(bond)
- bonds_i.append((i, j))
- bonds_k.append(pos_bonds[bond][2])
- bonds_f.append(rv*nc[i]*nc[j]/r**3)
+ for i in range(n - 1):
+ for j in range(i + 1, n):
+ 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]
+ rv = coords[i] - coords[j]
+ r = np.linalg.norm(rv)/cr
+ if r >= r_min and r <= r_max:
+ fnm[i, j] = True
+ fnm[j, i] = True
+ bonds.append(bond)
+ bonds_i.append((i, j))
+ bonds_k.append(pos_bonds[bond][2])
+ bonds_f.append(rv*nc[i]*nc[j]/r**3)
+
+ fnm = np.pad(fnm, ((0, size - n), (0, size - n)), 'constant')
return fnm, bonds, bonds_i, bonds_k, bonds_f
--
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