Add Libcint bindings

.gitignore

@@ -116,3 +116,7 @@ venv.bak/
 
 # PyCharm
 .idea/
+
+# Libcint
+gbasis/integrals/lib/
+gbasis/integrals/include/

README.md

@@ -46,6 +46,24 @@ git clone https://github.com/theochem/gbasis.git
 cd gbasis
 pip install --user -e .[dev,iodata]
 ```
+To use `gbasis.integrals.libcint`, the user must run the following script to build
+and install `libcint` into the `gbasis/integrals` directory,
+```bash
+tools/install_libcint.sh
+```
+This script depends on the following packages:
+* CMake
+* Git
+* Python 3
+* a C compiler (gcc or clang are recommended)
+* a Common Lisp interpreter (sbcl or clisp are recommended)
+By default, the x86-optimized `qcint` package is used for `libcint`.
+If this doesn't work on your computer, then run the script with the environment
+variable `USE_LIBCINT=1` to use the regular `libcint` package:
+```bash
+USE_LIBCINT=1 tools/install_libcint.sh
+```
+
 Note that `iodata` must be installed separately. `cython` is a dependency of `iodata`.
 
 To test the installation,

docs/notes.tex

@@ -811,7 +811,7 @@ \subsubsection{Gradient of density}
 with respect to atomic orbitals,
 \begin{lstlisting}[xleftmargin=-25pt]
 	from gbasis.evals.density import evaluate_density_gradient
-	
+
 	output = evaluate_density_gradient(one_dm, basis, grid_3d, deriv_type="direct")
 \end{lstlisting}
 \item To evaluate the gradient of the density using density matrix expressed

gbasis/contractions.py

@@ -1,6 +1,7 @@
 """Data class for contractions of Gaussian-type primitives."""
-from gbasis.utils import factorial2
+from numbers import Integral
 import numpy as np
+from gbasis.utils import factorial2
 
 
 class GeneralizedContractionShell:
@@ -83,8 +84,6 @@ class GeneralizedContractionShell:
         Tuple of magnetic quantum numbers of the contractions that specifies the ordering after
         transforming the contractions from the Cartesian to spherical coordinate system.
         Property of `GeneralizedContractionShell`.
-    charge : float
-        Charge at the center of the Gaussian primitives.
     exps : np.ndarray(K,)
         Exponents of the primitives, :math:`\{\alpha_i\}_{i=1}^K`.
     coeffs : np.ndarray(K, M)
@@ -113,10 +112,11 @@ class GeneralizedContractionShell:
     assign_norm_contr(self)
         Assign normalization constants for the contractions.
 
-
     """
 
-    def __init__(self, angmom, coord, coeffs, exps, coord_type, tol=1e-15, ovr_screen=False):
+    def __init__(
+        self, angmom, coord, coeffs, exps, coord_type, icenter=None, tol=1e-15, ovr_screen=False
+    ):
         r"""Initialize a GeneralizedContractionShell instance.
 
         Parameters
@@ -139,11 +139,12 @@ def __init__(self, angmom, coord, coeffs, exps, coord_type, tol=1e-15, ovr_scree
         coord_type : str
             Coordinate type of the contraction. Options include "cartesian" or "c" and
             "spherical" or "p".
+        icenter : np.int64 or None (optional)
+            Index for the atomic center for the contraction
         ovr_tol : float
             Tolerance used in overlap screening.
         ovr_screen : boolean
             Flag used for activating overlap screening.
-
         """
         self.angmom = angmom
         self.coord = coord
@@ -153,6 +154,41 @@ def __init__(self, angmom, coord, coeffs, exps, coord_type, tol=1e-15, ovr_scree
         self.ovr_screen = ovr_screen
         self.assign_norm_cont()
         self.coord_type = coord_type
+        self.icenter = icenter
+
+    @property
+    def icenter(self):
+        """Atom center index for the contractions.
+
+        Returns
+         -------
+         icenter : int or None
+             Index for the corresponding atom center of the contractions.
+
+        """
+        return self._icenter
+
+    @icenter.setter
+    def icenter(self, icenter):
+        """Atom center index for the contractions.
+
+        Parameters
+        ----------
+        icenter : int or None
+            Index for the corresponding atom center of the contractions.
+
+        Raises
+        ------
+        TypeError
+            If `center` is not an `Integral` or `None` type.
+
+        """
+        if isinstance(icenter, Integral):
+            self._icenter = int(icenter)
+        elif icenter is None:
+            self._icenter = None
+        else:
+            raise TypeError(f"Center should be of `numbers.Integral` type. Got {type(icenter)}")
 
     @property
     def coord(self):