# TODO list

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

> Last edited: [name=JJHo] [time= Sep 21, 2020] [color=#ff4233]

## Documentations related
- Coding tutorials/documentations:
- [x] Need to update the isotope labeling tutorial
- [x] Write about the analysis tools
- [x] 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](/h-LmPmldSNueBDpyO7SWCQ)
- [ ] 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
- [x] 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
- [x] 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
- [x] 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'](/h-LmPmldSNueBDpyO7SWCQ) 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 $\Delta_{ij->j}$
- 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`