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Generate diffracted intensities from crystals

Project description

Dans_Diffaction

Reads crystallographic cif files and simulates diffraction

Version 1.x

By Dan Porter, Diamond Light Source 2018

TL;DR:

$ ipython -i -m Dans_Diffraction
import Dans_Diffraction as dif
xtl = dif.Crystal('some_file.cif')
xtl.info() # print Crystal structure parameters

# Print reflection list:
print(xtl.Scatter.print_all_reflections(energy_kev=5)) 

# Plot Powder pattern:
xtl.Plot.simulate_powder(energy_kev=8)
plt.show()

# Start graphical user interface:
xtl.start_gui()

Full code documentation available here.

For comments, queries or bugs - email dan.porter@diamond.ac.uk

Installation

Requirements: Python 2.7+/3+ with packages: Numpy, Matplotlib, Scipy, Tkinter

Stable version from PyPI:

$ pip install Dans-Diffraction

Latest version from GitHub:

$ git clone https://github.com/DanPorter/Dans_Diffraction.git

Operation

Dans_Diffraction is best run within an interactive python environment:

$ ipython -i -m Dans_Diffraction

Dans_Diffraction can also be run in scripts as an import, example scripts are provided in the Examples folder.

Read CIF file

import Dans_Diffraction as dif
xtl = dif.Crystal('some_file.cif')
xtl.info() # print Crystal structure parameters

Alter atomic positions

xtl.Cell.latt([2.85,2.85,10.8,90,90,120]) #  set lattice parameters
xtl.Atoms.info() # Print Symmetric positions
xtl.Structure.info() # Print All positions in P1 symmetry (same structure and functions as xtl.Atoms)
# Symmetric positions
xtl.Atoms.changeatom(idx=0, u=0, v=0, w=0, type='Co', label='Co1')
xtl.Atoms.addatom(idx=0, u=0, v=0, w=0, type='Co', label='Co1')
# After adding or changing an atom in the Atoms class, re-generate the full structure using symmetry arguments:
xtl.generate_lattice()
# Full atomic structure in P1 symmetry
xtl.Structure.changeatom(idx=0, u=0, v=0, w=0, type='Co', label='Co1')
xtl.Structure.addatom(idx=0, u=0, v=0, w=0, type='Co', label='Co1')
# Plot crystal Structure
xtl.Plot.plot_crystal() # 3D plot
xtl.Plot.plot_layers() # 2D plot for layered materials

3D Plot

Alter crystal symmetry

xtl.Symmetry.info() # print symmetry arguments
xtl.Symmetry.addsym('x,y,z+1/2') # adds single symmetry operation
xtl.Symmetry.changesym(0, 'x,y,z+1/4')
# After adding or changing symmetry operations, regengerate the symmetry matrices
xtl.Symmetry.generate_matrices()

Calculate Structure Factors

X-ray or neutron structure factors/ intensities are calculated based on the full unit cell structure, including atomic form-factors (x-rays) or coherent scattering lengths (neutrons).

# Choose scattering options (see help(xtl.Scatter.setup_scatter))
xtl.Scatter.setup_scatter(type='x-ray', energy_keV=8.0)
# Allowed radiation types:
#    'xray','neutron','xray magnetic','neutron magnetic','xray resonant'
xtl.intensity([h,k,l]) # Returns intensity
xtl.print_all_refelctions() # Returns formated string of all allowed reflections
# Plot Experimental Intensities
xtl.Plot.simulate_powder() # Powder pattern
xtl.Plot.simulate_hk0() # Reciprocal space plane

Powder Pattern HK0 Simulation

Magnetic scattering is also available for neutrons and x-rays (both resonant and non-resonant), using the appropriate magnetic form-factors.

Imag = xtl.Scatter.magnetic_neutron(HKL=[0,0,3])
Ires = xtl.Scatter.xray_resonant_magnetic(HKL=[0,0,3], energy_kev=2.838, azim_zero=[1, 0, 0], psi=0, polarisation='s-p', F0=0, F1=1, F2=0)

Multiple Scattering

Simulations of multiple scattering at different azimuths for a particular energy can be simulated. Based on code by Dr Gareth Nisbet.

azimuth, intensity = xtl.Scatter.ms_azimuth([h,k,l], energy_kev=8)

Multiple Scattering

Properties

The Crystal class contains a lot of atomic properties that can be exposed in the Properties class:

xtl.Properties.info()

All the properties are stored in the folder Dans_Diffraction/data.

Superstructures

Superstructures can be built using the Superstructure class, requring only a matrix to define the new phase:

su = xtl.generate_superstructrue([[2,0,0],[0,2,0],[0,0,1]])

Superstucture classes behave like Crystal classes, but have an additional 'Parent' property that references the original crystal structure and additional behaviours partiular to superstructures.

su.parent.info() # Parent structure
su.P # superstructure matrix 

Graphical Front End

All GUI elements

Start a new GUI, then select a cif file:

dif.Startgui()

Using an already generated crystal:

xtl.start_gui()

FDMNES functionality

FDMNES is a powerful tool for simulating resonant x-ray diffraction, created by Y. Joly and O. Bunau.

The Dans_Diffraction FDMNES class allows for the automatic creation of input files and simple analysis of results. The following command should be used to activate these features (only needs to be issued once).

dif.activate_fdmnes()

Once activated, the FDMNES classes become available.

fdm = dif.Fdmnes(xtl) # Create input files and run FDMNES
fdma = dif.FdmnesAnalysis(output_path, output_name) # Load output files and plot results

See class documentation for more information.

Once activated, FDMNES GUI elements become available from the main window, emulating functionality of the classes.

FDMNES Run FDMNES Analyse

Project details


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