Merge pull request #140 from maximilianvz/address_issue_113

Merging coord_type into GeneralizedContractionShell Closes #140

Author: FarnazH

gbasis/base.py

@@ -157,12 +157,12 @@ def construct_array_lincomb(self, *transform, coord_type, **kwargs):
             Transformation matrix that will be used for linearly combining the spherical
             contractions.
             Note that multiple instances may be needed to construct the array.
-        coord_type : {"cartesian", "spherical", list/tuple of "cartesian" or "spherical}
-            Types of the coordinate system for the contractions.
-            If "cartesian", then all of the contractions are treated as Cartesian contractions.
-            If "spherical", then all of the contractions are treated as spherical contractions.
-            If list/tuple, then each entry must be a "cartesian" or "spherical" to specify the
-            coordinate type of each `GeneralizedContractionShell` instance.
+        coord_type : list/tuple of str
+            Types of the coordinate system for each GeneralizedContractionShell.
+            Each entry must be one of "cartesian" or "spherical". If multiple
+            instances of GeneralizedContractionShell are given but only one string
+            ("cartesian" or "spherical") is provided in the list/tuple, all of the
+            contractions will be treated according to that string.
         kwargs : dict
             Other keyword arguments that will be used to construct the array.
 

gbasis/base_four_symm.py

@@ -571,12 +571,12 @@ def construct_array_lincomb(self, transform, coord_type, **kwargs):
             Transformation is applied to the left.
             Rows correspond to the linear combinations (i.e. MO) and the columns correspond to the
             contractions (i.e. AO).
-        coord_type : {"cartesian", "spherical", list/tuple of "cartesian" or "spherical}
-            Types of the coordinate system for the contractions.
-            If "cartesian", then all of the contractions are treated as Cartesian contractions.
-            If "spherical", then all of the contractions are treated as spherical contractions.
-            If list/tuple, then each entry must be a "cartesian" or "spherical" to specify the
-            coordinate type of each `GeneralizedContractionShell` instance.
+        coord_type : list/tuple of str
+            Types of the coordinate system for each GeneralizedContractionShell.
+            Each entry must be one of "cartesian" or "spherical". If multiple
+            instances of GeneralizedContractionShell are given but only one string
+            ("cartesian" or "spherical") is provided in the list/tuple, all of the
+            contractions will be treated according to that string.
         kwargs : dict
             Other keyword arguments that will be used to construct the array.
             These keyword arguments are passed directly to `construct_array_spherical`, which will
@@ -595,20 +595,18 @@ def construct_array_lincomb(self, transform, coord_type, **kwargs):
         Raises
         ------
         TypeError
-            If `coord_type` is not one of "cartesian", "spherical", or a list/tuple of these
-            strings.
+            If `coord_type` is not a list/tuple of the strings 'cartesian' or 'spherical'.
 
         """
-        if coord_type == "cartesian":
+        if all(ct == "cartesian" for ct in coord_type):
             array = self.construct_array_cartesian(**kwargs)
-        elif coord_type == "spherical":
+        elif all(ct == "spherical" for ct in coord_type):
             array = self.construct_array_spherical(**kwargs)
         elif isinstance(coord_type, (list, tuple)):
             array = self.construct_array_mix(coord_type, **kwargs)
         else:
             raise TypeError(
-                "`coord_type` must be one of 'cartesian', 'spherical', or a list/tuple of these "
-                "strings."
+                "`coord_type` must be a list/tuple of the strings 'cartesian' or 'spherical'"
             )
         array = np.tensordot(transform, array, (1, 0))
         array = np.tensordot(transform, array, (1, 1))

gbasis/base_one.py

@@ -257,12 +257,12 @@ def construct_array_lincomb(self, transform, coord_type, **kwargs):
             Transformation is applied to the left.
             Rows correspond to the linear combinationes (i.e. MO) and the columns correspond to the
             contractions (i.e. AO).
-        coord_type : {"cartesian", "spherical", list/tuple of "cartesian" or "spherical}
-            Types of the coordinate system for the contractions.
-            If "cartesian", then all of the contractions are treated as Cartesian contractions.
-            If "spherical", then all of the contractions are treated as spherical contractions.
-            If list/tuple, then each entry must be a "cartesian" or "spherical" to specify the
-            coordinate type of each GeneralizedContractionShell instance.
+        coord_type : list/tuple of str
+            Types of the coordinate system for each GeneralizedContractionShell.
+            Each entry must be one of "cartesian" or "spherical". If multiple
+            instances of GeneralizedContractionShell are given but only one string
+            ("cartesian" or "spherical") is provided in the list/tuple, all of the
+            contractions will be treated according to that string.
         kwargs : dict
             Other keyword arguments that will be used to construct the array.
             These keyword arguments are passed directly to `construct_array_spherical`, which will
@@ -278,19 +278,17 @@ def construct_array_lincomb(self, transform, coord_type, **kwargs):
         Raises
         ------
         TypeError
-            If `coord_type` is not one of "cartesian", "spherical", or a list/tuple of these
-            strings.
+            If `coord_type` is not a list/tuple of the strings 'cartesian' or 'spherical'.
 
         """
-        if coord_type == "cartesian":
+        if all(ct == "cartesian" for ct in coord_type):
             array = self.construct_array_cartesian(**kwargs)
-        elif coord_type == "spherical":
+        elif all(ct == "spherical" for ct in coord_type):
             array = self.construct_array_spherical(**kwargs)
         elif isinstance(coord_type, (list, tuple)):
             array = self.construct_array_mix(coord_type, **kwargs)
         else:
             raise TypeError(
-                "`coord_type` must be one of 'cartesian', 'spherical', or a list/tuple of these "
-                "strings."
+                "`coord_type` must be a list/tuple of the strings 'cartesian' or 'spherical'"
             )
         return np.tensordot(transform, array, (1, 0))

gbasis/base_two_asymm.py

@@ -386,18 +386,18 @@ def construct_array_lincomb(
             Array associated with the linear combinations of spherical Gaussians (LCAO's) associated
             with the second index.
             If None, then transformation is skipped.
-        coord_type_one : {"cartesian", "spherical", list/tuple of "cartesian" or "spherical}
+        coord_type_one : list/tuple of string
             Types of the coordinate system for the contractions associated with the first index.
-            If "cartesian", then all of the contractions are treated as Cartesian contractions.
-            If "spherical", then all of the contractions are treated as spherical contractions.
-            If list/tuple, then each entry must be a "cartesian" or "spherical" to specify the
-            coordinate type of each `GeneralizedContractionShell` instance.
-        coord_type_two : {"cartesian", "spherical", list/tuple of "cartesian" or "spherical}
+            Each entry must be one of "cartesian" or "spherical". If multiple
+            instances of GeneralizedContractionShell are given but only one string
+            ("cartesian" or "spherical") is provided in the list/tuple, all of the
+            contractions will be treated according to that string.
+        coord_type_two : list/tuple of string
             Types of the coordinate system for the contractions associated with the second index.
-            If "cartesian", then all of the contractions are treated as Cartesian contractions.
-            If "spherical", then all of the contractions are treated as spherical contractions.
-            If list/tuple, then each entry must be a "cartesian" or "spherical" to specify the
-            coordinate type of each `GeneralizedContractionShell` instance.
+            Each entry must be one of "cartesian" or "spherical". If multiple
+            instances of GeneralizedContractionShell are given but only one string
+            ("cartesian" or "spherical") is provided in the list/tuple, all of the
+            contractions will be treated according to that string.
         kwargs : dict
             Other keyword arguments that will be used to construct the array.
             These keyword arguments are passed directly to `construct_array_spherical`, which will
@@ -420,13 +420,16 @@ def construct_array_lincomb(
         Raises
         ------
         TypeError
-            If `coord_type_one` and `coord_type_two` are not one of "cartesian", "spherical", or a
-            list/tuple of these strings.
+            If `coord_type` is not a list/tuple of the strings 'cartesian' or 'spherical'.
 
         """
-        if coord_type_one == "cartesian" and coord_type_two == "cartesian":
+        if all(ct_one == "cartesian" for ct_one in coord_type_one) and all(
+            ct_two == "cartesian" for ct_two in coord_type_two
+        ):
             array = self.construct_array_cartesian(**kwargs)
-        elif coord_type_one == "spherical" and coord_type_two == "spherical":
+        elif all(ct_one == "spherical" for ct_one in coord_type_one) and all(
+            ct_two == "spherical" for ct_two in coord_type_two
+        ):
             array = self.construct_array_spherical(**kwargs)
         else:
             if coord_type_one in ["cartesian", "spherical"]:
@@ -438,8 +441,7 @@ def construct_array_lincomb(
                 and isinstance(coord_type_two, (list, tuple))
             ):
                 raise TypeError(
-                    "`coord_type` must be one of 'cartesian', 'spherical', or a list/tuple of these"
-                    " strings."
+                    "`coord_type` must be a list/tuple of the strings 'cartesian' or 'spherical'"
                 )
             array = self.construct_array_mix(coord_type_one, coord_type_two, **kwargs)
         if transform_one is not None:

gbasis/base_two_symm.py

@@ -365,12 +365,12 @@ def construct_array_lincomb(self, transform, coord_type, **kwargs):
             Transformation is applied to the left.
             Rows correspond to the linear combinations (i.e. MO) and the columns correspond to the
             contractions (i.e. AO).
-        coord_type : {"cartesian", "spherical", list/tuple of "cartesian" or "spherical}
-            Types of the coordinate system for the contractions.
-            If "cartesian", then all of the contractions are treated as Cartesian contractions.
-            If "spherical", then all of the contractions are treated as spherical contractions.
-            If list/tuple, then each entry must be a "cartesian" or "spherical" to specify the
-            coordinate type of each `GeneralizedContractionShell` instance.
+        coord_type : list/tuple of str
+            Types of the coordinate system for each GeneralizedContractionShell.
+            Each entry must be one of "cartesian" or "spherical". If multiple
+            instances of GeneralizedContractionShell are given but only one string
+            ("cartesian" or "spherical") is provided in the list/tuple, all of the
+            contractions will be treated according to that string.
         kwargs : dict
             Other keyword arguments that will be used to construct the array.
             These keyword arguments are passed directly to `construct_array_spherical`, which will
@@ -389,20 +389,18 @@ def construct_array_lincomb(self, transform, coord_type, **kwargs):
         Raises
         ------
         TypeError
-            If `coord_type` is not one of "cartesian", "spherical", or a list/tuple of these
-            strings.
+            If `coord_type` is not a list/tuple of the strings 'cartesian' or 'spherical'.
 
         """
-        if coord_type == "cartesian":
+        if all(ct == "cartesian" for ct in coord_type):
             array = self.construct_array_cartesian(**kwargs)
-        elif coord_type == "spherical":
+        elif all(ct == "spherical" for ct in coord_type):
             array = self.construct_array_spherical(**kwargs)
         elif isinstance(coord_type, (list, tuple)):
             array = self.construct_array_mix(coord_type, **kwargs)
         else:
             raise TypeError(
-                "`coord_type` must be one of 'cartesian', 'spherical', or a list/tuple of these "
-                "strings."
+                "`coord_type` must be a list/tuple of the strings 'cartesian' or 'spherical'"
             )
         array = np.tensordot(transform, array, (1, 0))
         array = np.tensordot(transform, array, (1, 1))

gbasis/contractions.py

@@ -91,6 +91,8 @@ class GeneralizedContractionShell:
         Contraction coefficients, :math:`\{d_{ij}\}`, of the primitives.
         First axis corresponds to the primitive and the second axis corresponds to the segmented
         contraction shell.
+    coord_type : str
+        Type of the coordinate system used to specify the contractions.
     norm_cont : np.ndarray(M, L)
         Normalization constants of the Cartesian contractions of different angular momentum
         components and segmented contraction shells.
@@ -114,7 +116,7 @@ class GeneralizedContractionShell:
 
     """
 
-    def __init__(self, angmom, coord, coeffs, exps):
+    def __init__(self, angmom, coord, coeffs, exps, coord_type):
         r"""Initialize a GeneralizedContractionShell instance.
 
         Parameters
@@ -134,13 +136,17 @@ def __init__(self, angmom, coord, coeffs, exps):
             dimension.
         exps : np.ndarray(K,)
             Exponents of the primitives, :math:`\{\alpha_i\}_{i=1}^K`.
+        coord_type : str
+            Coordinate type of the contraction. Options include "cartesian" or "c" and
+            "spherical" or "p".
 
         """
         self.angmom = angmom
         self.coord = coord
         self.coeffs = coeffs
         self.exps = exps
         self.assign_norm_cont()
+        self.coord_type = coord_type
 
     @property
     def coord(self):
@@ -479,3 +485,48 @@ def assign_norm_cont(self):
 
         self.norm_cont = np.einsum("ijij->ij", Overlap.construct_array_contraction(self, self))
         self.norm_cont **= -0.5
+
+    @property
+    def coord_type(self):
+        """Return the coordinate type.
+
+        Returns
+        -------
+        coord_type : str
+            Coordinate type of the contraction.
+
+        """
+        return self._coord_type
+
+    @coord_type.setter
+    def coord_type(self, coord_type):
+        """Set the coordinate type.
+
+        Parameters
+        ----------
+        coord_type : str
+            Coordinate type of the contraction.
+
+        Raises
+        ------
+        TypeError
+            If `coord_type` is not a string.
+        ValueError
+            If `coord_type` is not one of the following:
+                - 'c' (cartesian)
+                - 'cartesian'
+                - 'p' (spherical)
+                - 'spherical'
+        """
+
+
+        if not isinstance(coord_type, str):
+            raise TypeError("Coordinate type must be given as a string.")
+        if coord_type not in ["c", "cartesian", "p", "spherical"]:
+            raise ValueError("`coord_type` is incorrectly specified. It must be either 'c' "
+                             "or 'cartesian' for Cartesian coordinates, or 'p' or 'spherical' "
+                             "for spherical coordinates.")
+        self._coord_type = {"c": "cartesian",
+                            "cartesian": "cartesian",
+                            "spherical": "spherical",
+                            "p": "spherical"}[coord_type]