ued.py

aimsprop.ued

Functions

compute_ued_simple(bundle: Bundle, key: str, R: ndarray, alpha: float, ABpairs = None) -> Bundle

Compute the simple pairwise-distance form of the UED cross section, with Gaussian blurring in R.

Parameters:

Name	Type	Description	Default
bundle	Bundle	the Bundle object to compute the property for (modified in place)	required
key	str	the name of the property	required
R	ndarray	the distances to collocate the UED cross section to.	required
alpha	float	the Guassian blurring exponent	required
ABpairs		a restricted list of atom pair indices to include in the computation, or None for all atom pairs.	None

Returns:

Type	Description
Bundle	bundle: reference to the input Bundle object. The property key is set to computed UED property.

Source code in aimsprop/ued.py

def compute_ued_simple(
    bundle: Bundle,
    key: str,
    R: np.ndarray,
    alpha: float,
    ABpairs=None,
) -> Bundle:
    """Compute the simple pairwise-distance form of the UED cross section,
        with Gaussian blurring in R.

    Params:
        bundle: the Bundle object to compute the property for (modified in
            place)
        key: the name of the property
        R: the distances to collocate the
            UED cross section to.
        alpha: the Guassian blurring exponent
        ABpairs: a restricted list of atom pair indices
            to include in the computation, or None for all atom pairs.
    Return:
        bundle: reference to the input Bundle object. The property
            key is set to computed UED property.
    """

    for frame in bundle.frames:
        N = frame.N
        xyz = frame.xyz
        # Which pair indices?
        if ABpairs is None:
            ABpairs2 = []
            for A in range(len(N)):
                for B in range(A):
                    ABpairs2.append((A, B))
        else:
            ABpairs2 = ABpairs
        # Compute UED cross section
        V = np.zeros_like(R)
        for A, B in ABpairs2:
            rAB = xyz[A, :] - xyz[B, :]
            RAB = math.sqrt(sum(rAB ** 2))
            SAB = math.sqrt(_ued_cross_sections[N[A]] * _ued_cross_sections[N[B]]) / RAB
            V += SAB * math.sqrt(alpha / math.pi) * np.exp(-alpha * (R - RAB) ** 2)
        frame.properties[key] = V
    return bundle