Metadata-Version: 2.1
Name: Dans-Diffraction
Version: 2.2.3
Summary: Generate diffracted intensities from crystals
Home-page: https://github.com/DanPorter/Dans_Diffraction
Author: Dan Porter
Author-email: d.g.porter@outlook.com
License: UNKNOWN
Description: # Dans_Diffaction
        Reads crystallographic cif files and simulates diffraction, among other things.
        
        **Version 2.2**
        
        [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3859501.svg)](https://doi.org/10.5281/zenodo.3859501)
        
        By Dan Porter, Diamond Light Source
        2022
        
        #### TL;DR:
        ```text
        $ ipython -i -m Dans_Diffraction
        ```
        
        ```python
        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](https://danporter.github.io/Dans_Diffraction/).
        
        For comments, queries or bugs - email [dan.porter@diamond.ac.uk](mailto:dan.porter@diamond.ac.uk)
        
        **Citation:** If you use this code (great!), please cite the published DOI: [10.5281/zenodo.3859501](https://doi.org/10.5281/zenodo.3859501)
        
        # Installation
        **Requirements:** 
        Python 3+ with packages: *Numpy*, *Matplotlib*, *Tkinter*.
        BuiltIn packages used: *sys*, *os*, *re*, *glob*, *warnings*, *json*, *itertools*
        
        Stable version from PyPI:
        ```text
        $ pip install Dans-Diffraction
        ```
        
        Download latest version from GitHub:
        ```text
        $ git clone https://github.com/DanPorter/Dans_Diffraction.git
        ```
        Or install latest version direct from GitHub:
        ```text
        $ pip install git+https://github.com/DanPorter/Dans_Diffraction.git
        ```
        
        
        # Operation
        Dans_Diffraction is best run within an interactive python environment:
        ```text
        $ ipython -i -m Dans_Diffraction
        ```
        
        Dans_Diffraction can also be run in scripts as an import, example scripts are provided in the [Examples](https://github.com/DanPorter/Dans_Diffraction/blob/master/Examples) folder.
        ### Read CIF file
        ```python
        import Dans_Diffraction as dif
        xtl = dif.Crystal('some_file.cif')
        xtl.info() # print Crystal structure parameters
        help(xtl)  # all functions (nearly!) are documented
        ```
        
        ### Alter atomic positions
        ```python
        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](https://github.com/DanPorter/Dans_Diffraction/blob/master/Screenshots/3Dstructrue_Ca3CoMnO6.png?raw=true)
        
        
        ### Alter crystal symmetry
        ```python
        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()
        ```
        
        ### Save structure as CIF
        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".
        ```python
        xtl.write_cif('edited file.cif')
        ```
        
        ### 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).
        ```python
        # 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.Scatter.print_all_refelctions() # Returns formated string of all allowed reflections
        inten = xtl.Scatter.intensity([h,k,l]) # Returns intensity
        twotheta, iten, reflections = xtl.Scatter.powder(units='twotheta')
        # Plot Experimental Intensities
        xtl.Plot.simulate_powder() # Powder pattern
        xtl.Plot.simulate_hk0() # Reciprocal space plane
        ```
        ![Powder Pattern](https://github.com/DanPorter/Dans_Diffraction/blob/master/Screenshots/powder_diamond.png?raw=true)
        ![HK0 Simulation](https://github.com/DanPorter/Dans_Diffraction/blob/master/Screenshots/supercell_diffraction.png?raw=true)
        
        
        ### Magnetic Structrues
        *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.
        ```python
        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 number
        ```
        Magnetic scattering is also available for neutrons and x-rays (both resonant and non-resonant), using the appropriate magnetic form-factors.
        ```python
        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
        Superstructures can be built using the Superstructure class, requring only a matrix to define the new phase:
        ```python
        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.
        
        ```python
        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 supercell
        ```
        
        ### Multi-phase
        Scattering from different crystal structures can be compared using the MultiCrystal class:
        ```python
        xtls = xtl1 + xtl2
        xtls.simulate_powder()
        ```
        
        
        ### Properties
        The Crystal class contains a lot of atomic properties that can be exposed in the Properties class:
        ```python
        xtl.Properties.info()
        ```
        
        Calculated properties include:
         - Molecular weight
         - Density
         - Diamagnetic suscpetibility 
         - x-ray absorption coefficient, attenuation length, transmission and refractive index
         - Molecular charge balance
         - Molecular mass fraction
         - Atomic orbitals
         - Magnetic exchange paths (in progress...)
        
        Properties are calulated using the atomic structure along with atomic data stored in the folder [Dans_Diffraction/data](data).
        
        
        ### Multiple Scattering
        Simulations of multiple scattering at different azimuths for a particular energy can be simulated. Based on [code by Dr Gareth Nisbet](https://journals.iucr.org/a/issues/2015/01/00/td5022/).
         [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12866.svg)](https://doi.org/10.5281/zenodo.12866).
        
        ```python
        azimuth, intensity = xtl.Scatter.ms_azimuth([h,k,l], energy_kev=8)
        ```
        
        ![Multiple Scattering](https://github.com/DanPorter/Dans_Diffraction/blob/master/Screenshots/ms_azimuth_silicon.png?raw=true)
        
        
        ### Graphical Front End
        ![All GUI elements](https://github.com/DanPorter/Dans_Diffraction/blob/master/Screenshots/GUI_all.png?raw=true)
        
        Start a new GUI, then select a cif file:
        ```text
        $ ipython -i -m Dans_Diffraction gui
        ```
        Or start the GUI from within the interactive console:
        ```python
        dif.start_gui()
        ```
        Using an already generated crystal:
        ```python
        xtl.start_gui()
        ```
        
        ### FDMNES functionality
        FDMNES is a powerful tool for simulating resonant x-ray diffraction, created by [Y. Joly and O. Bunau.](http://neel.cnrs.fr/spip.php?rubrique1007&lang=en)
        
        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). 
        ```python
        dif.activate_fdmnes()
        ```
        Once activated, the FDMNES classes become available.
        ```python
        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](https://github.com/DanPorter/Dans_Diffraction/blob/master/Screenshots/GUI_08.png?raw=true)
        ![FDMNES Analyse](https://github.com/DanPorter/Dans_Diffraction/blob/master/Screenshots/GUI_09.png?raw=true)
        
        
        -----------------------------------------------------------------------------
           Copyright 2022 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_orientation.py
        * classes_orbitals.py
        * functions_general.py
        * functions_plotting.py
        * functions_scattering.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, [dan.porter@diamond.ac.uk](mailto:dan.porter@diamond.ac.uk)
         
         [www.diamond.ac.uk](www.diamond.ac.uk)
         
         Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.
Keywords: crystal,cif,diffraction,crystallography,science,x-ray,neutron,resonant,magnetic,magnetism,multiple scattering,fdmnes,super structure,spacegroup,space group
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.7
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Development Status :: 3 - Alpha
Description-Content-Type: text/markdown
