diff options
| author | David Luevano Alvarado <55825613+luevano@users.noreply.github.com> | 2020-03-10 12:34:00 -0700 |
|---|---|---|
| committer | David Luevano Alvarado <55825613+luevano@users.noreply.github.com> | 2020-03-10 12:34:00 -0700 |
| commit | 5cbaae0eb1e39a0514424ab0c0005fbb7f78261c (patch) | |
| tree | 64370b4419d76b7074a4186170ec0da9f234c394 | |
| parent | ae4c379f66c42c1e48564ea1bd85aafe6394abff (diff) | |
AM O(n^2) to O((n-1)(n/2-1))
| -rw-r--r-- | ml_exp/representations.py | 37 |
1 files 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 |