/usr/lib/python3/dist-packages/periodictable/cromermann.py

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# Copyright (c) 2009 Trustees of the Columbia University
# in the City of New York.  All rights reserved.
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# DANSE Diffraction group, Simon J. L. Billinge
#
# File coded by:    Pavol Juhas
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"""
Cromer-Mann formula for calculating x-ray scattering factors.
"""

# module version
__id__ = "$Id: cromermann.py 1051 2010-01-30 01:01:43Z juhas $"

import os
import logging
import numpy
from periodictable import core


def getCMformula(symbol):
    """
    Obtain Cromer-Mann formula and coefficients for a specified element.

    *symbol* : string
        symbol of an element

    Return instance of CromerMannFormula.
    """
    if not _cmformulas:
        _update_cmformulas()
    return _cmformulas[symbol]


def fxrayatq(symbol, Q, charge=None):
    """
    Return x-ray scattering factors of an element at a given Q.

    *symbol* : string
         symbol of an element or ion, e.g., "Ca", "Ca2+"
    *Q* : float or [float] | |1/Ang|
         Q value
    *charge* : int
         ion charge, overrides any valence suffixes such as "-", "+", "3+".

    Return float or numpy array.
    """
    stol = numpy.array(Q) / (4 * numpy.pi)
    rv = fxrayatstol(symbol, stol, charge)
    return rv


def fxrayatstol(symbol, stol, charge=None):
    """
    Calculate x-ray scattering factors at specified sin(theta)/lambda

    *symbol* : string
        symbol of an element or ion, e.g., "Ca", "Ca2+"
    *stol* : float or [float] | |1/Ang|
        sin(theta)/lambda
    *charge* : int
        ion charge, overrides any valence suffixes such as "-", "+", "3+".

    Return float or numpy.array.
    """
    # resolve lookup symbol smbl, by default symbol
    smbl = symbol
    # build standard element or ion symbol
    if charge is not None:
        smbl = symbol.rstrip('012345678+-')
        if charge:
            smbl += ("%+i" % charge)[::-1]
    # convert Na+ or Cl- to Na1+, Cl1-
    elif symbol[-1:] in '+-' and not symbol[-2:-1].isdigit():
        smbl = (symbol[:-1] + "1" + symbol[-1:])
    # smbl is resolved here
    cmf = getCMformula(smbl)
    rv = cmf.atstol(stol)
    return rv


class CromerMannFormula(object):
    """
    Cromer-Mann formula for x-ray scattering factors.
    Coefficient storage and evaluation.

    Class data:

    *stollimit* : float | |1/Ang|
        maximum sin(theta)/lambda for which the formula works

    Attributes:

    *symbol* : string
        symbol of an element
    *a* : [float]
        a-coefficients
    *b* : [float]
        b-coefficients
    *c* : float
        c-coefficient
    """

    # obtained from tables/f0_WaasKirf.dat and the associated reference
    # D. Waasmaier, A. Kirfel, Acta Cryst. (1995). A51, 416-413
    # http://dx.doi.org/10.1107/S0108767394013292
    stollimit = 6

    def __init__(self, symbol, a, b, c):
        """
        Create a new instance of CromerMannFormula for specified element.

        No return value
        """
        self.symbol = symbol
        self.a = numpy.asarray(a, dtype=float)
        self.b = numpy.asarray(b, dtype=float)
        self.c = float(c)
        return


    def atstol(self, stol):
        """
        Calculate x-ray scattering factors at specified sin(theta)/lambda

        *stol* : float or [float] | |1/Ang|
            sin(theta)/lambda

        Return float or numpy.array.
        """
        stolflat = numpy.array(stol).flatten()
        n = len(stolflat)
        stol2row = numpy.reshape(stolflat ** 2, (1, n))
        bcol = self.b.reshape((len(self.a), 1))
        bstol2 = numpy.dot(bcol, stol2row)
        adiag = numpy.diag(self.a)
        rvrows = numpy.dot(adiag, numpy.exp(-bstol2))
        rvflat = rvrows.sum(axis=0) + self.c
        rvflat[stolflat > self.stollimit] = numpy.nan
        # when stol is scalar, addition of zero converts the rv array to float
        rv = rvflat.reshape(numpy.shape(stol)) + 0.0
        return rv

# class CromerMannFormula


def _update_cmformulas():
    """
    Update the static dictionary of CromerMannFormula instances.
    """
    data_path = core.get_data_path('xsf')
    filename = os.path.join(data_path, 'f0_WaasKirf.dat')
    fp = open(filename)
    lineiter = iter(fp)
    for line in lineiter:
        w = line.split()
        if w[0] == "#S":
            smbl = w[2]
            continue
        if w[0] == "#L":
            assert smbl is not None
            line1 = next(lineiter)
            w1 = line1.split()
            assert len(w1) == 11
            a = list(map(float, w1[0:5]))
            b = list(map(float, w1[6:11]))
            c = float(w1[5])
            cmf = CromerMannFormula(smbl, a, b, c)
            _cmformulas[cmf.symbol] = cmf
            smbl = None
    return
_cmformulas = {}

# End of file
python3-periodictable 1.5.0-3 / usr / lib / python3 / dist-packages / periodictable / cromermann.py
