Minor doc changes+roll back of compiler flags and sphinx setup

Author: andersx

Diff for: docs/build/html/.nojekyll

@@ -26,7 +26,7 @@
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #
-needs_sphinx = '1.5.4'
+# needs_sphinx = '1.5.4'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom

Diff for: docs/source/conf.py

@@ -34,6 +34,21 @@
 from .data import NUCLEAR_CHARGE
 
 def generate_coulomb_matrix(nuclear_charges, coordinates, size = 23, sorting = "row-norm"):
+    """ Generates a sorted molecular coulomb, sort either by ``"row-norm"`` or ``"unsorted"``.
+    ``size=`` denotes the max number of atoms in the molecule (thus the size of the resulting square matrix.
+    The resulting matrix is the upper triangle put into the form of a 1D-vector.
+
+    :param coordinates: Input coordinates.
+    :type coordinates: numpy array
+    :param nuclear_charges: List of nuclear charges.
+    :type nuclear_charges: numpy array
+    :param size: Max number of atoms in representation.
+    :type size: integer
+    :param sorting: Matrix sorting scheme, "row-norm" or "unsorted".
+    :type sorting: string
+    :return: 1D Coulomb matrix representation
+    :rtype: numpy array
+    """
 
     if (sorting == "row-norm"):
         return fgenerate_coulomb_matrix(nuclear_charges, \
@@ -48,6 +63,21 @@ def generate_coulomb_matrix(nuclear_charges, coordinates, size = 23, sorting = "
         raise SystemExit
 
 def generate_atomic_coulomb_matrix(nuclear_charges, coordinates, size = 23, sorting = "distance"):
+    """ Generates a list of sorted Coulomb matrices, sorted either by ``"row-norm"`` or ``"distance"``, the latter refers to sorting by distance to each query atom.
+    ``size=`` denotes the max number of atoms in the molecule (thus the size of the resulting square matrix.
+    The resulting matrix is the upper triangle put into the form of a 1D-vector.
+
+    :param coordinates: Input coordinates.
+    :type coordinates: numpy array
+    :param nuclear_charges: List of nuclear charges.
+    :type nuclear_charges: numpy array
+    :param size: Max number of atoms in representation.
+    :type size: integer
+    :param sorting: Matrix sorting scheme, "row-norm" or "distance".
+    :type sorting: string
+    :return: List of 1D Coulomb matrix representations.
+    :rtype: numpy array
+    """
 
     if (sorting == "row-norm"):
         return fgenerate_local_coulomb_matrix(nuclear_charges,
@@ -62,10 +92,38 @@ def generate_atomic_coulomb_matrix(nuclear_charges, coordinates, size = 23, sort
         raise SystemExit
 
 def generate_eigenvalue_coulomb_matrix(nuclear_charges, coordinates, size = 23):
+    """ Generates the eigenvalue-Coulomb matrix representation.
+    ``size=`` denotes the max number of atoms in the molecule (thus the size of the resulting square matrix.
+    The resulting matrix is in the form of a 1D-vector.
+
+    :param coordinates: Input coordinates.
+    :type coordinates: numpy array
+    :param nuclear_charges: List of nuclear charges.
+    :type nuclear_charges: numpy array
+    :param size: Max number of atoms in representation.
+    :type size: integer
+    :return: 1D representation.
+    :rtype: numpy array
+    """
     return fgenerate_eigenvalue_coulomb_matrix(nuclear_charges,
         coordinates, size)
 
 def generate_bob(nuclear_charges, coordinates, atomtypes, asize = {"O":3, "C":7, "N":3, "H":16, "S":1}):
+    """ Generates a bag-of-bonds (BOB) representation of the molecule. ``size=`` denotes the max number of atoms in the molecule (thus relates to the size of the resulting matrix.)
+    ``asize=`` is the maximum number of atoms of each type (necessary to generate bags of minimal sizes).
+    The resulting matrix is the BOB representation put into the form of a 1D-vector.
+
+    :param coordinates: Input coordinates.
+    :type coordinates: numpy array
+    :param nuclear_charges: List of nuclear charges.
+    :type nuclear_charges: numpy array
+    :param size: Max number of atoms in representation.
+    :type size: integer
+    :param asize: Max number of each element type.
+    :type asize: dict
+    :return: 1D BOB representation.
+    :rtype: numpy array
+    """
 
     n = 0
     atoms = sorted(asize, key=asize.get)

Diff for: qml/representations.py

@@ -30,7 +30,7 @@
 
 # Intel
 if any(["intelem" in arg for arg in sys.argv]):
-    COMPILER_FLAGS = ["-fast", "-axCORE-AVX2", "-unroll-aggressive", "-qopenmp"]
+    COMPILER_FLAGS = ["-xHost", "-O3", "-axAVX", "-qopenmp"]
     LINKER_FLAGS = ["-liomp5", " -lpthread", "-lm", "-ldl"]
     MATH_LINKER_FLAGS = ["-L${MKLROOT}/lib/intel64", "-lmkl_rt"]