Science Scripts

Collection of Scripts for Handling Scientific Data

XRD

1. xrd_converter (GUI and CLI): Convert xrd data in complex csv or xrdml formats into simple csv format for plotting, or archiving. Bot GUI and command line versions available.

2. xrd_plotter: Plot one or more XRD data files (csv or xrdml format). Available both as a local python script (with GUI) or as a stand-alone web script (running either locally or in remote server).

   Functionality of the plotter:

   • Curve fitting
   • Curve normalization to peak
   • Cropping to view
   • Search of theoretical xrd based on formula or peak selection via Materials Genome (python version only).
   • Search of theoretical xrd based on formula or peak selection via Chrystallographic Open Database.
   • Search of experimental xrd minerals based on peak selection Rruff.
   • Smoothing curves
   • Background subtraction (via regularization or through reference diffractogram).
   • Correct angular offsets with reference data.

Raman

1. raman_plotter: Plot one or more FTIR data files (H5, xml, or txt formats from Horiba Labspec). Available both as a local python script (with GUI, and ability the Rruff database for Raman reference data) or as a stand-alone web script (running either locally or in remote server).

   Functionality of the plotter:

   • Curve fitting
   • Curve normalization to peak
   • Cropping to view
   • Search of experimental raman spectra of minerals based on peak selection Rruff.
   • Search of theoretical raman based peak selection via Rruff.
   • Smoothing curves
   • Background subtraction (via regularization or through reference spectra).

FTIR

1. ftir_plotter: Plot one or more Raman data files (jdx or csv formats from Thermo Nicolet). Available both as a local python script (with GUI, and ability to access the Rruff databased for FTIR reference data) or as a stand-alone web script (running either locally or in remote server)

   Functionality of the plotter:

   • Curve fitting
   • Curve normalization to peak
   • Cropping to view
   • Search of experimental FTIR spectra of minerals based on peak selection Rruff.
   • Smoothing curves
   • Background subtraction (via regularization or through reference spectra).

SEM/EDS

1. Summarizer: Create a summary given the spectra and the images.

PyMol Plotter

1. plot_pymol_structures: Plot a 'necklace' of spherical particles from a PACKMOL-style PDB file.

Build GMSH

1. Build_gmsh: Bash script to compile GMSH for older system via miniconda3.