From 85198178482767d2831ddf3762e5e6eeafa990bd Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 22 Feb 2020 18:37:50 -0700
Subject: Fix bug, current errors present on adj matrix
---
ml_exp/__main__.py | 3 ---
ml_exp/representations.py | 16 ++++++++--------
2 files changed, 8 insertions(+), 11 deletions(-)
diff --git a/ml_exp/__main__.py b/ml_exp/__main__.py
index cb8a9a3f1..17119623e 100644
--- a/ml_exp/__main__.py
+++ b/ml_exp/__main__.py
@@ -28,6 +28,3 @@ if __name__ == '__main__':
test = []
for i in range(1, 10):
test.append(Compound(f'/home/luevano/py/ml_exp/data/qm7/000{i}.xyz'))
- test[i-1].gen_cm(size=1, as_eig=False)
- test[i-1].gen_ljm(size=1, as_eig=False)
- test[i-1].gen_am(size=1)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index ae870f3b0..796d15f98 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -48,8 +48,8 @@ def coulomb_matrix(coords,
size. Arrays are not of the right shape.')
if size < n:
- print('Error. Compound size (n) is greater han (size). Using (n)\
- instead of (size).')
+ print('Error. Compound size (n) is greater han (size). Using (n)',
+ 'instead of (size).')
size = n
cm = np.zeros((size, size), dtype=float)
@@ -115,8 +115,8 @@ def lennard_jones_matrix(coords,
size. Arrays are not of the right shape.')
if size < n:
- print('Error. Compound size (n) is greater han (size). Using (n)\
- instead of (size).')
+ print('Error. Compound size (n) is greater han (size). Using (n)',
+ 'instead of (size).')
size = n
lj = np.zeros((size, size), dtype=float)
@@ -137,10 +137,10 @@ def lennard_jones_matrix(coords,
# 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 = np.linalg.norm(rv)/cr
# 1/r^n
- r_2 = 1/r**2
+ r_2 = sigma**2/r**2
r_6 = r_2**3
r_12 = r_6**2
lj[i, j] = (4*epsilon*(r_12 - r_6))
@@ -204,9 +204,9 @@ def first_neighbor_matrix(coords,
cs_bond = sorted(['C', 'S'])
if use_forces:
- fnm = np.empty((n, n), dtype=float)
+ fnm = np.zeros((n, n), dtype=float)
else:
- fnm = np.empty((n, n), dtype=int)
+ fnm = np.zeros((n, n), dtype=int)
bonds = []
forces = []
--
cgit v1.2.3-70-g09d2