TODO list

Here is a list of tasks to improve COSMOSS in various aspects:

Last edited: JJHo Sep 21, 2020

Documentations related

• Coding tutorials/documentations:

  • Need to update the isotope labeling tutorial
  • Write about the analysis tools
  • Note that Cuts analysis function need image processing tool box!
  • Write about each Model_GUIs
  • Document Structure Data Class
  • Make a figure to summarize the steps to apply orientation and ensemble average
  • Write about how the Jansen map is only applied on Amide modes
  • Document the 2D grid construction model

• Generic tutorials:

  • How vibrational spectroscopies are used in peptide studies?
  • What is 2D spectroscopies and how to add another dimension?
  • What are the spectral features in 2D?
  • Explain Feynman pathways

• Other documentations

  • Add a gallery note to present what can be done by COSMOSS
  • COSMOSS related paper abstracts

Coding related

• Reorganizing data structure

  • Move the implementation of the Jensen map from the H_handler to the model construction stage.
  • Rename some of the properties so it make much intuitive sense. Leave coding details within codes.
  • Unify 1D spectral data
  • Rename the molecular response from beta to Gamma to match: Theoretical background of COSMOSS
  • Where is the 'SD.Extra.AmideModeIndex' used? Check all the amideI related code. I am suspecting that is deprecated.
  • Generate the coupling matrix and H when building molecular model
    • Make Coupling as SD_method? By including it into the SD_1ExH?
    • I don't like how Coupling take inputs, how about consolidate it? So does SD_Comb2, need to fix it

• Appdesigner related

  • Considering update figure on the existing axes to avoid blowing up desktop space
  • Updating sub-GUI names
  • Adding a 'SaveStrutureData' function and push buttons on each Model_GUIs
  • Place a GUI input to specify distant cut-off when using nearest-neighbor coupling model
  • There are two figures generated when simulating 2D spectrum with random sampling option toggled. Should be one only
  • Unify the SD_Connectivity method the stand alone Connectivity function

• Reorganizing main_GUI

  • Add a GUI input to modify figure titles
  • Add GUI input of the memory cut-off
  • Move Model related codes out of the appdesigner (use MVC model)
  • Add toggle to flip 2D
    ${\omega }_1/{\omega }_2$ axes, from Hochstrasser style to Fayer style.

• Upgrade Plot_Mode analysis GUI

  • Figure out how to visualize 2 quantum modes' eigenvectors, specifically, how to set center position?
  • Add sorting for 2D paths to tell if it is a diagonal or cross peak
  • Add a GUI element to select different pathways

• Upgrades in Model_2D_grid

  • Fix the labeling function
  • Distinguish mode center and molecule center in 2D grid
  • Add a GUI input to set translational center

• Visualizing 'EJLR' parts

  • Implementing Garth Simpson's way (histogram) to visualize contributions of
    ${\beta }_{ijk}$ and
    ${\chi }_{ijk}$
  • Figure out what's the benefit to plot response intensity for each ijk terms
  • How to implement the Fresnel coefficient code.

Theoretical topics

• Review my note of Hamiltonian generation. Conclude the importance of
  ${\mathrm{\Delta }}_{ij->j}$
• Need to understand the long tail effect in the Feynman pathway Cutoff. Is this long tail effect real?
• Think about what is the incident angle change in 2DIR spectrum. Does it has the incident angle dependence?

tags: COSMOSS todo code