From 9b26afc10f47866ddb176d9e2c8609b9b180105d Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Thu, 26 Mar 2020 15:58:22 -0700
Subject: Add flattening to cm and ljm
---
ml_exp/representations.py | 16 ++++++++++++++--
1 file changed, 14 insertions(+), 2 deletions(-)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 3e44d626c..b0a5d8553 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -28,6 +28,7 @@ from ml_exp.data import POSSIBLE_BONDS
def coulomb_matrix(coords,
nc,
size=23,
+ flatten=True,
as_eig=True,
bohr_ru=False):
"""
@@ -35,6 +36,7 @@ def coulomb_matrix(coords,
coords: compound coordinates.
nc: nuclear charge data.
size: compound size.
+ flatten: if the representation should be 1D.
as_eig: if the representation should be as the eigenvalues.
bohr_ru: if radius units should be in bohr's radius units.
"""
@@ -75,7 +77,11 @@ size. Arrays are not of the right shape.')
return np.pad(cm_eigs, (0, size - n), 'constant')
else:
- return np.pad(cm, ((0, size - n), (0, size - n)), 'constant')
+ if flatten:
+ return np.pad(cm, ((0, size - n), (0, size - n)),
+ 'constant').flatten()
+ else:
+ return np.pad(cm, ((0, size - n), (0, size - n)), 'constant')
def lennard_jones_matrix(coords,
@@ -84,6 +90,7 @@ def lennard_jones_matrix(coords,
sigma=1.0,
epsilon=1.0,
size=23,
+ flatten=True,
as_eig=True,
bohr_ru=False):
"""
@@ -94,6 +101,7 @@ def lennard_jones_matrix(coords,
sigma: sigma value.
epsilon: epsilon value.
size: compound size.
+ flatten: if the representation should be 1D.
as_eig: if the representation should be as the eigenvalues.
bohr_ru: if radius units should be in bohr's radius units.
"""
@@ -141,7 +149,11 @@ size. Arrays are not of the right shape.')
return np.pad(lj_eigs, (0, size - n), 'constant')
else:
- return np.pad(lj, ((0, size - n), (0, size - n)), 'constant')
+ if flatten:
+ return np.pad(lj, ((0, size - n), (0, size - n)),
+ 'constant').flatten()
+ else:
+ return np.pad(lj, ((0, size - n), (0, size - n)), 'constant')
def get_helping_data(coords,
--
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