Data types and functions

What do you need

The minimum requirement for PeakPo is 1D diffraction patterns in the chi format. In order to use full functionality of PeakPo, you need the following:

• chi files For example, chi files integrated from DIOPTAS.

• tif or mar345 files Diffraction images files. Basically the raw data files.

• poni file This is the calibration file you make in DIOPTAS.

• jcpds files Diffraction peak position files. Some files are provided in my JCODS GitHub repo. You can also make JCPDS files using JCPDSTools software. Link for the JCPDSTools executables can be found in the JCPDSTools GitHub page.

Where to save data files

The best practice for PeakPo is to copy the chi, tif, and poni files of your dataset all in the same data folder. This data folder can be located anywhere in your hard drive. I strongly recommend not to save any data files in the PeakPo folder because you do not want to mix the PeakPo files with your data files. Note that you will overwrite files in the PeakPo folder when you update PeakPo.

For the jcpds files, I recommend to have them in a folder separate from data files.

What does it plot

PeakPo has the following plot components.

• Base pattern is a 1D diffraction file in the chi format. This is the minimum required component to run PeakPo.

• Cake is a processed 2D diffraction image. PeakPo reads a tif or mar345 file (associated with your base pattern) and a poni file to make cake images and plot them directly above the associated base pattern.

• Waterfall patterns are diffraction files you want to compare with the base pattern. These patterns are stacked above the base pattern in PeakPo.

• Jlist is a list of the JCPDS files which have information on the peak positions and intensities together with the Miller indices of different materials. JCPDS also contains information on equation of state and therefore allow PeakPo to calculate changes in the lattice constants at different pressures and temperatures. Peakpo enables you to tweak the peak positions by changing the axial ratios of the candidate phases. This is particularly important for lower symmetry phases with strong sensitivity of the axial ratios to pressure and temperature.

• Ucfit is a tool that reads peak fitting results in PeakPo (see below) and JCPDS information and then performs unit-cell fitting. It provides advanced statistics for better unit-cell fitting similar to the UnitCell program by T J B Holland and S A T Redfern (1997).

• Background is the internally fitted results to subtract backgrounds in diffraction patterns. Although the background subtraction is convenient and powerful, you should be very careful not to overfit or underfit the background, which can lead to mis-interpretation of peak positions and peak existence. If you uncheck the Bg sub checkbox in the Main tab, PeakPo shows fitted background in dashed line for your inspection.

• Peak fitting allows you to conduct least-square fitting of diffraction peaks. It can take advantage of jlist for finding initial values for peak positions and assigning the Miller indices.