DISTorX project is a set of scientific programs written as Jupyter notebook, python program with TKinter GUI and Vpython module, and evaluation version of C++ program.

The programs were created for simulation of structural distortion and structural disorder, directly affecting X-Ray powder diffraction patterns.

You can simply distort or disorder physical structures in any direction using user defined function, and generate XRD powder pattern. Programs allows to simply compare simulation results with powder X-Ray diffraction experimental patterns - visualy.

With simple scripting automation you can compare thousands of distorted structures with experiment and choose best mach, fulfilling the imposed conditions.

First read Docs of project and see examples of applications.

DISTorX is Open-Source project! Share, change or use part or whole code for your individual scientific tasks.

DISTorX v1.0

Scientific application to simulation of distortion on complex crystaline structures and its impatc on the XRD patterns.

This repository contains source code of DISTorX v1.0 program written in Python 2.7 with Vpython module and additional sample files.

Program have usage in simulation of distortion caused by Charge-Density-Wave directly affecting XRD patterns.

Instructions how to set up program

Windows Users

Install Python 2.7 (python.org) and Vpython (vpython.org).

Program has been tested on Windows 7, 8.1, 10 and on different computers. After instalation of Python you should install required for the operation of the program libraries (pylab, matplotlib, numpy, tkinter). To install libraries on Windows run CMD and use:

pip install <packagename>

If "pip" is not recognaized, entry full path to script for example:

C:/Python27/Scripts/pip install matplotlib

Python "Idle" - interpreter will inform you wich additional libraries do you need to run program. In Windows you can run program by cmd, directry clicking on DISTorX.py icon, or by python idle. First run takes more time.

Linux Users

Program was also tested on Linux Mint 17.1 'Rebeca' distribution. Istallation of Vpython in this case was by Software manager (graphical linux windowed manager). On Linux there are couple of things you should do manually. Install Python Idle by:

$ apt-get install idle

Idle helps with identification of libraries and its nescesery to operate the program. Installation on linux is more difficult due to the manual installation of libraries. To do that you need to use

$ pip install <library name>

, and also

$ apt-get install <library name>

I encountered a few problems during the installation of matplotlib and after installation of this package reboot is needed (probably depend on linux distribution). One more, linux-python-idle did not recognize:

from matplotlib import style

Comment this line by #. Excuding 'import style' does not affect the operation of the program. In linux terminal program work only when typing

$ python DISTorX\ v1.0.py

, when you try to run program directly in terminal

$ ./DISTorX\ v1.0.py

it doesent work, probably becouse of linux kernel configuration.

Instructions

1. Run program.
2. Select input file *.xyz, with atoms coordinates and elements labels. Program needs the number of line where element is labeled to obtain AFF (Atomic Form Factors). (AFF.txt file)
3. Set simulation parameters. A - an aplitude of distortion, maxTime - maximum time of simulation, dt - time step, a, b, c - lattice parameters, lambda - x-ray wavelength.
4. After initiaze of input structure program can show visualization of structure in time dependency. (Vpython)
5. Program can generate XRD patterns with distortion or without:
6. a) To simulate XRD pattern without distortion just click Simulate XRD. (this gives only one simulation pattern)
7. b) To simulate distortion first run distortion simulation and then dynamic XRD simulation. Time of simulation depends on computer hardware. (this gives set of simulations patterns)
8. Now you can manage results dirctly from ASCII files or use DISTorX to run Dynamic Plot (changes of XRD pattern in time dependency) or compare simulation with experimental results.
9. Program have helping in comparision of simulated and experimental XRD patterns, modules:
10. a) Intensity Match (normalizing intensities of experimental end simulation patterns to 1)
11. b) Set 0 (seting starting level for experimental intensities as 0).

Generated files are all saved in folders. Each new simulation override existing files.

Feel free to testing, at the begining try samples (TETRA.xyz) and experiment sample. Be careful with the input files, program treats input structures as P1 symmetry.

Lech Kalinowski University of Silesia Katowice, Poland

Lech Stanisław Kalinowski, 2017