Reads crystallographic cif files and simulates diffraction, among other things.
Version 1.8
By Dan Porter, Diamond Light Source 2020
$ 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 [email protected]
Citation: If you use this code (great!), please cite the published DOI: 10.5281/zenodo.3859501
Requirements: Python 2.7+/3+ with packages: Numpy, Matplotlib, Scipy, Tkinter. BuiltIn packages used: sys, os, re, glob, warnings, json, itertools
Stable version from PyPI:
$ pip install Dans-Diffraction
Latest version from GitHub:
$ git clone https://github.com/DanPorter/Dans_Diffraction.git
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.
import Dans_Diffraction as dif
xtl = dif.Crystal('some_file.cif')
xtl.info() # print Crystal structure parametersxtl.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
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')
xtl.Symmetry.load_spacegroup(194) # replaces current symmetry operations
# After adding or changing symmetry operations, regengerate the symmetry matrices
xtl.Symmetry.generate_matrices()Lattice parameters, crystal structure and symmetry operations will be saved to the CIF. If magnetic moments are defined, magnetic symmetry operations and moments will also be saved and format changed to "*.mcif".
xtl.write_cif('edited file.cif')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
Magnetic structures and scattering are currently in development and shouldn't be treated as accurate!
Simple magnetic structures can be loaded from magnetic cif (*.mcif) files. Magnetic moments are stored for each atomic position as a vector. The crystal object has a seperate set of magnetic symmetry operations. Symmetry operations from the tables of magnetic spacegroups can also be loaded. Only simple magnetic structures are allowed. There must be the same number of magnetic symmetry operations as crystal symmetry operations and atomic positions can only have single moments assigned.
xtl = dif.Crystal('some_file.mcif')
xtl.Atoms.mxmymz() # return magnetic moment vectors on each ion
xtl.Symmetry.symmetry_operations_magnetic # magnetic symmetry operations (list of strings)
xtl.Symmetry.print_magnetic_spacegroups() # return str of available magnetic spacegroups, given crystal's spacegroup
xtl.Symmetry.load_magnetic_spacegroup(mag_spg_number) # loads mag. operations given mag. spacegroup numberMagnetic 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)Superstructures can be built using the Superstructure class, requring only a matrix to define the new phase:
su = xtl.generate_superstructure([[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. Superstructures loose their parent crystal and magnetic symmetry, always being defined in P1 symmetry. So su.Atoms == su.Structure.
print(su.parent.info()) # Parent structure
su.P # superstructure matrix
su.superhkl2parent([h, k, l]) # index superstructure hkl with parent cell
su.parenthkl2super([h, k, l]) # index parent hkl with supercellScattering from different crystal structures can be compared using the MultiCrystal class:
xtls = xtl1 + xtl2
xtls.simulate_powder()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.
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)
Start a new GUI, then select a cif file:
$ ipython -i -m Dans_Diffraction gui
Or start the GUI from within the interactive console:
dif.start_gui()Using an already generated crystal:
xtl.start_gui()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 resultsSee class documentation for more information.
Once activated, FDMNES GUI elements become available from the main window, emulating functionality of the classes.
Copyright 2020 Diamond Light Source Ltd.
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Files in this package covered by this licence:
- classes_crystal.py
- classes_scattering.py
- classes_plotting.py
- classes_properties.py
- classes_multicrystal.py
- classes_orbitals.py
- functions_general.py
- functions_plotting.py
- functions_crystallography.py
- tkgui/*.py
Other files are either covered by their own licence or not licenced for other use.
Dr Daniel G Porter, [email protected]
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.