From efaa8eeb58d8e19d32f94ec4e91ec794574dfd32 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 18:13:33 -0700
Subject: Coulomb matrix done, fix init
---
ml_exp/__init__.py | 27 ++++-----------------------
ml_exp/compound.py | 28 ++++++++++++++++++++++++----
ml_exp/representations.py | 10 +++++-----
3 files changed, 33 insertions(+), 32 deletions(-)
diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index 06425f6a2..8e803b37e 100644
--- a/ml_exp/__init__.py
+++ b/ml_exp/__init__.py
@@ -20,29 +20,10 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
-from ml_exp.read_qm7_data import read_nc_data, read_db_data, read_qm7_data
-from ml_exp.c_matrix import c_matrix, c_matrix_multiple
-from ml_exp.lj_matrix import lj_matrix, lj_matrix_multiple
-from ml_exp.frob_norm import frob_norm
-from ml_exp.gauss_kernel import gauss_kernel
-from ml_exp.cholesky_solve import cholesky_solve
-from ml_exp.do_ml import do_ml
-from ml_exp.parallel_create_matrices import parallel_create_matrices
-from ml_exp.misc import plot_benchmarks
-
+from ml_exp.compound import Compound
+from ml_exp.representations import coulomb_matrix
# If somebody does "from package import *", this is what they will
# be able to access:
-__all__ = ['read_nc_data',
- 'read_db_data',
- 'read_qm7_data',
- 'c_matrix',
- 'c_matrix_multiple',
- 'lj_matrix',
- 'lj_matrix_multiple',
- 'frob_norm',
- 'gauss_kernel',
- 'cholesky_solve',
- 'do_ml',
- 'parallel_create_matrices',
- 'plot_benchmarks']
+__all__ = ['Compound',
+ 'coulomb_matrix']
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 9536767a7..3ea377826 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -22,10 +22,16 @@ SOFTWARE.
"""
import numpy as np
from ml_exp.data import NUCLEAR_CHARGE
+from ml_exp.representations import coulomb_matrix
class Compound:
- def __init__(self, xyz=None):
+ def __init__(self,
+ xyz=None):
+ """
+ Initialization of the Compound.
+ xyz: (path to) the xyz file.
+ """
# empty_array = np.asarray([], dtype=float)
self.n = None
@@ -41,10 +47,24 @@ class Compound:
if xyz is not None:
self.read_xyz(xyz)
- def gen_cm(self):
- pass
+ def gen_cm(self,
+ size=23,
+ as_eig=True,
+ bohr_ru=False):
+ """
+ Generate the Coulomb Matrix for the compund.
+ size: compound size.
+ as_eig: if the representation should be as the eigenvalues.
+ bhor_ru: if radius units should be in bohr's radius units.
+ """
+ self.coulomb_matrix = coulomb_matrix(self.coordinates,
+ self.atoms_nc,
+ size=size,
+ as_eig=as_eig,
+ bhor_ru=bohr_ru)
- def read_xyz(self, filename):
+ def read_xyz(self,
+ filename):
"""
Reads an xyz file and adds the corresponding data to the Compound.
filename: (path to) the xyz file.
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index bbc538ae6..c503c310d 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -28,16 +28,16 @@ def coulomb_matrix(coords,
nc,
size=23,
as_eig=True,
- bohr_radius_units=False):
+ bhor_ru=False):
"""
Creates the Coulomb Matrix from the molecule data given.
coords: compound coordinates.
nc: nuclear charge data.
size: compound size.
- as_eig: if data should be returned as matrix or array of eigenvalues.
- bohr_radius_units: if units should be in bohr's radius units.
+ as_eig: if the representation should be as the eigenvalues.
+ bhor_ru: if radius units should be in bohr's radius units.
"""
- if bohr_radius_units:
+ if bhor_ru:
cr = 0.52917721067
else:
cr = 1
@@ -54,7 +54,7 @@ def coulomb_matrix(coords,
size = n
nr = range(size)
- cm = np.empty((size, size), dtype=float)
+ cm = np.zeros((size, size), dtype=float)
# Actual calculation of the coulomb matrix.
for i in nr:
--
cgit v1.2.3-70-g09d2