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pymatgen

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FoSpy.plotting.diffraction.engines.pymatgen

cfg module-attribute 

cfg = None

CIF_engine

Source code in FoSpy/plotting/diffraction/engines/_base.py 
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class CIF_engine:
    def _to_frame(self, two_theta, intensity):
        from ....config import values as cfg
        x_label = cfg.diffraction.x_label
        return pd.DataFrame({x_label:two_theta, 'int':intensity})

    def get_pattern(self, **kwargs):
        from ....config import values as cfg

        params = cfg.diffraction.pattern_parameters().copy()
        params.update(kwargs)
        return params

_to_frame 

_to_frame(two_theta, intensity)
Source code in FoSpy/plotting/diffraction/engines/_base.py 
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def _to_frame(self, two_theta, intensity):
    from ....config import values as cfg
    x_label = cfg.diffraction.x_label
    return pd.DataFrame({x_label:two_theta, 'int':intensity})

get_pattern 

get_pattern(**kwargs)
Source code in FoSpy/plotting/diffraction/engines/_base.py 
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def get_pattern(self, **kwargs):
    from ....config import values as cfg

    params = cfg.diffraction.pattern_parameters().copy()
    params.update(kwargs)
    return params

Engine

Bases: CIF_engine

Source code in FoSpy/plotting/diffraction/engines/pymatgen.py 
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class Engine(CIF_engine):
    def __init__(self, cif_path, **kwargs):
        from pymatgen.analysis.diffraction.xrd import XRDCalculator
        from pymatgen.core.structure import Structure
        self.structure = Structure.from_file(cif_path)
        self.sim = XRDCalculator()

    def get_pattern(self,**kwargs):
        import numpy as np

        pattern_config = cfg.get("diffraction.pattern_parameters")
        pattern_config.update(kwargs)

        step = pattern_config.pop('two_theta_step')
        tth_range = pattern_config['two_theta_range']

        peaks = self.get_peaks(**pattern_config)

        two_theta = []
        intensity = []
        for (x,y) in peaks:
            two_theta.append(step*round(x/step))
            intensity.append(y)


        frame =  self._to_frame(two_theta, intensity)
        x_min, x_max = tth_range
        grid = np.arange(x_min, x_max+step, step)

        frame = (frame.
                 set_index(cfg.diffraction.x_label).
                 reindex(grid).
                 fillna(0).
                 reset_index())
        return frame

    def get_peaks(self,two_theta_range=None, normalize=None):

        if two_theta_range is None:
            two_theta_range = cfg.get("diffraction.pattern_parameters.two_theta_range")

        if normalize is None:
            normalize = cfg.get("diffraction.pattern_parameters.normalize")


        pattern = self.sim.get_pattern(self.structure, two_theta_range=two_theta_range, scaled = False)

        if normalize:
            pattern.y = pattern.y / max(pattern.y)

        peaks = tuple((x, y) for x, y in zip(pattern.x, pattern.y))
        return peaks

sim instance-attribute 

sim = XRDCalculator()

structure instance-attribute 

structure = Structure.from_file(cif_path)

__init__ 

__init__(cif_path, **kwargs)
Source code in FoSpy/plotting/diffraction/engines/pymatgen.py 
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def __init__(self, cif_path, **kwargs):
    from pymatgen.analysis.diffraction.xrd import XRDCalculator
    from pymatgen.core.structure import Structure
    self.structure = Structure.from_file(cif_path)
    self.sim = XRDCalculator()

get_pattern 

get_pattern(**kwargs)
Source code in FoSpy/plotting/diffraction/engines/pymatgen.py 
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def get_pattern(self,**kwargs):
    import numpy as np

    pattern_config = cfg.get("diffraction.pattern_parameters")
    pattern_config.update(kwargs)

    step = pattern_config.pop('two_theta_step')
    tth_range = pattern_config['two_theta_range']

    peaks = self.get_peaks(**pattern_config)

    two_theta = []
    intensity = []
    for (x,y) in peaks:
        two_theta.append(step*round(x/step))
        intensity.append(y)


    frame =  self._to_frame(two_theta, intensity)
    x_min, x_max = tth_range
    grid = np.arange(x_min, x_max+step, step)

    frame = (frame.
             set_index(cfg.diffraction.x_label).
             reindex(grid).
             fillna(0).
             reset_index())
    return frame

get_peaks 

get_peaks(two_theta_range=None, normalize=None)
Source code in FoSpy/plotting/diffraction/engines/pymatgen.py 
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def get_peaks(self,two_theta_range=None, normalize=None):

    if two_theta_range is None:
        two_theta_range = cfg.get("diffraction.pattern_parameters.two_theta_range")

    if normalize is None:
        normalize = cfg.get("diffraction.pattern_parameters.normalize")


    pattern = self.sim.get_pattern(self.structure, two_theta_range=two_theta_range, scaled = False)

    if normalize:
        pattern.y = pattern.y / max(pattern.y)

    peaks = tuple((x, y) for x, y in zip(pattern.x, pattern.y))
    return peaks