Simulation of the diffraction pattern#

This notebook shows how we can create a sample (phase) from atoms and calculate diffraction profile using constant wavelength experiment type.

# EasyScience, technique-independent
from easyCore import np
from easyCore.Fitting.Fitting import Fitter

# EasyScience, diffraction
from easyDiffractionLib import Site, Phase, Phases
from easyDiffractionLib.Jobs import Powder1DCW

# Vizualization
import py3Dmol
from bokeh.io import show, output_notebook
from bokeh.plotting import figure

# Misc
import xarray as xr

Warning: GSAS-2 is not installed

output_notebook()
FIGURE_WIDTH = 700
FIGURE_HEIGHT = 300

Loading BokehJS ...

Sample#

Create an atom using `Site` interface#

atom = Site.from_pars(label="Cl",
                      specie="Cl",
                      fract_x=0.0,
                      fract_y=0.0,
                      fract_z=0.0)

Create a phase, set space group, add atom#

phase = Phase(name="salt")

phase.spacegroup.space_group_HM_name = "F m -3 m"

phase.add_atom(atom)

Add another atom (using `Phase` interface)#

phase.add_atom('Na', 'Na', 0.5, 0.5, 0.5)

Visualise the structure#

viewer = py3Dmol.view()
viewer.addModel(phase.to_cif_str(),'cif',{'doAssembly':True,'duplicateAssemblyAtoms':True,'normalizeAssembly':True})
viewer.setStyle({'sphere':{'colorscheme':'Jmol','scale':.2},'stick':{'colorscheme':'Jmol', 'radius': 0.1}})
viewer.addUnitCell()
viewer.replicateUnitCell(2,2,2)
viewer.zoomTo()

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

<py3Dmol.view at 0x7f87af50b370>

Create Phases object#

phases = Phases()
phases.append(phase)

Experiment#

Create `Dataset`#

data = xr.Dataset()

Create `Job`#

job = Powder1DCW('NaCl', data, phases=phases)

Modify instrumental parameters#

job.parameters.resolution_u = 0.1447
job.parameters.resolution_v = -0.4252
job.parameters.resolution_w = 0.3864
job.parameters.resolution_x = 0.0
job.parameters.resolution_y = 0.0

Modify pattern parameters#

job.pattern.zero_shift = 0.0
job.pattern.scale = 100.0

Create calculator#

calculator = job.interface # CrysPy is default

print(f"Current calculator engine: {calculator.current_interface_name}")

Current calculator engine: CrysPy

print(f"Available calculator engines: {calculator.available_interfaces}")
print(f"Available calculators for CW: {calculator.interface_compatability('Npowder1DCWunp')}")

Available calculator engines: ['CrysPy', 'CrysFML']
Available calculators for CW: ['CrysPy', 'CrysFML']

Analysis#

Calculate the profile using the calculator we defined previously.#

x_data = np.linspace(20, 170, 500)
_ = job.create_simulation(x_data)
y_data = np.array(data['sim_NaCl'])

fig = figure(width=FIGURE_WIDTH, height=FIGURE_HEIGHT)
fig.line(x_data, y_data, legend_label='CW Simulation', color='orangered', line_width=2)
show(fig)

Simulation of the diffraction pattern

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