diff options
| author | David Luevano Alvarado <55825613+luevano@users.noreply.github.com> | 2020-03-26 15:58:22 -0700 |
|---|---|---|
| committer | David Luevano Alvarado <55825613+luevano@users.noreply.github.com> | 2020-03-26 15:58:22 -0700 |
| commit | 9b26afc10f47866ddb176d9e2c8609b9b180105d (patch) | |
| tree | 81361f3b02108c85213bbdcf5e9248c9cd0701dd | |
| parent | 1d7ea44f8b5dba01ad2660b8014002b989dff464 (diff) | |
Add flattening to cm and ljm
| -rw-r--r-- | ml_exp/representations.py | 16 |
1 files 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, |