Metadata-Version: 2.1
Name: Dans_Diffraction
Version: 1.7.0
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
        
        **Version 1.7**
        
        By Dan Porter, Diamond Light Source
        2020
        
        #### 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
        
        # Installation
        **Requirements:** 
        Python 2.7+/3+ with packages: *Numpy*, *Matplotlib*, *Scipy*, *Tkinter*
        
        Stable version from PyPI:
        ```text
        $ pip install Dans-Diffraction
        ```
        
        Latest version from GitHub:
        ```text
        $ git clone 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](Examples) folder.
        ### Read CIF file
        ```python
        import Dans_Diffraction as dif
        xtl = dif.Crystal('some_file.cif')
        xtl.info() # print Crystal structure parameters
        ```
        
        ### 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](Screenshots/3Dstructrue_Ca3CoMnO6.png)
        
        
        ### 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')
        # 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).
        ```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.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](Screenshots/powder_diamond.png)
        ![HK0 Simulation](Screenshots/supercell_diffraction.png)
        
        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)
        ```
        
        ### Multiple Scattering
        Simulations of multiple scattering at different azimuths for a particular energy can be simulated. Based on code by Dr Gareth Nisbet.
        
        ```python
        azimuth, intensity = xtl.Scatter.ms_azimuth([h,k,l], energy_kev=8)
        ```
        
        ![Multiple Scattering](Screenshots/ms_azimuth_silicon.png)
        
        ### Tensor Scattering
        Simulations of resonant scattering using tensors. Resonant x-ray azimuths can be simulated. Based on code by Prof. Steve Collins.
        
        ```python
        ss, sp, ps, pp = xtl.Scatter.tensor_scattering('Ru1', [h,k,l], energy_kev=2.838, azir=[0,1,0], psideg=90)
        ```
        
        ![Tensor Scattering](Screenshots/ts_azimuth_ZnO.png)
        
        ### Properties
        The Crystal class contains a lot of atomic properties that can be exposed in the Properties class:
        ```python
        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:
        ```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.
        
        ```python
        su.parent.info() # Parent structure
        su.P # superstructure matrix 
        ```
        
        ### Multi-phase
        Scattering from different crystal structures can be compared using the MultiCrystal class:
        ```python
        xtls = xtl1 + xtl2
        xtls.simulate_powder()
        plt.show()
        ```
        
        ### Graphical Front End
        ![All GUI elements](Screenshots/GUI_all.png)
        
        Start a new GUI, then select a cif file:
        ```python
        dif.Startgui()
        ```
        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](Screenshots/GUI_08.png)
        ![FDMNES Analyse](Screenshots/GUI_09.png)
        
Keywords: crystal,cif,diffraction,crystallography,science,x-ray,neutron,resonant,magnetic,magnetism,multiple scattering,fdmnes,super structure
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.7
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Development Status :: 3 - Alpha
Description-Content-Type: text/markdown
