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What is COSMOSS?
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:::info
**COSMOSS** is a **C**oupled **OS**cillator **MO**del **S**pectral **S**imulator
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<figure style="float:right;">
<img src="https://i.imgur.com/HOQWa4m.png" align="right" width="160" height="160">
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Initially COSMOSS was created for my PhD research projects. Using the coupled-oscillators framework, I simulated and extracted information from experimental spectrum[^GoogleScholar], mostly on 2D IR and 2D SFG. As the COSMOSS project moving forward, I couldn't help but wonder if I can make it more general (as its name implied), i.e. works for different molecules, with a user-friendly GUI, support other spectral types, and most important of all, it is **open source**! So here is it, hope you enjoy it.

## What can COSMOSS do?
COSMOSS can help you generate model structures and simulated their vibrational spectrum, currently includes:

- Fourier Transform Infrared spectrum [(FTIR)](https://en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy)
- Sum-Frequency Generation spectrum [(SFG)](https://en.wikipedia.org/wiki/Sum_frequency_generation_spectroscopy)
- Two-Dimensional Infrared spectrum [(2D IR)](https://en.wikipedia.org/wiki/Two-dimensional_infrared_spectroscopy)
- Two-Dimensional Sum-Frequency Generation spectrum [(2D SFG)](https://zanni.chem.wisc.edu/2d-sfg-spectroscopy/)

Besides simple spectral simulations, you can also use it in various ways. For example, I used COSMOSS to study how the peptide orientation affecting the 2D spectral features:[^Ref_Paper_1]

Also, the [coding structure](https://hackmd.io/@jjh/COSMOSS_Code_Structure) is very general! As long as the 'modes' in question can be model as coupled oscillators, you can generate their corresponding spectrum as well. For example, if you are interested in simulating the UV-Vis spectra of a model system, you can repurpose the FTIR core with little modification.

Documentation
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All the notes and tutorials are hosted on the HackMD. Learn more [in the documentation](https://hackmd.io/@jjh/COSMOSS). This documentation will help you understand the coding structure and theoretical background so you can make the best of COSMOSS.

Installation
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[](https://www.mathworks.com/matlabcentral/fileexchange/64433-cosmoss)

Download the source code from either [Matlab file-exchange](https://www.mathworks.com/matlabcentral/fileexchange/64433-cosmoss) or [GitHub](https://github.com/JJ-Ho/COSMOSS).[^Download] Once download, double click on the 'COSMOSS.mlapp' will bring up the main GUI! [^mlapp]

Collaboration
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One of the main reason why COSMOSS is open source is for collaboration! Any contribution is welcomed. The are two branches for potential collaboration:

- Documentation
- Source code

### Documentation
This website is editable if you register an account and sign-in. Learn more about how to edit the page on HackMD here:
- [HeckMD help page (English)](https://hackmd.io/c/tutorials/%2Fs%2Ftutorials).
- [HeckMD help page (Chinese)](https://hackmd.io/c/tutorials-tw/%2Fs%2Ftutorials-tw).

Feel free to write/edit about anything relevant. You are also welcome to send me the link of your personal documentation to my email so I can add a link to your site:

- jhoatgit [at] gmail.com

or leave a comment on the HackMD site.

### Source Code
For the source code, please pull from the [GitHub repo](https://github.com/JJ-Ho/COSMOSS). I also compiled a list of tutorials on "[How to collaborate with Git?](https://hackmd.io/@jjh/Git_Tutorials)".

[^GoogleScholar]: See my publications on [Google Scholar](https://scholar.google.com/citations?user=O8Y6wd8AAAAJ&hl=en&authuser=1)

[^Ref_Paper_1]: [J. Phys. Chem. A 2018, 122, 5, 1270-1282](https://pubs.acs.org/doi/abs/10.1021/acs.jpca.7b11934), see [Running COSMOSS from the workspace](/sQAEQB2PQmS11TNwjUy88Q?both) for example code to generate a movie from COSMOSS.

[^Download]:Since v2.3.1, the [Matlab file-exchange](https://www.mathworks.com/matlabcentral/fileexchange/64433-cosmoss) download page is integrated with the master branch of the [GitHub](https://github.com/JJ-Ho/COSMOSS) repository. No more fooling around!

[^mlapp]: You can modify the GUI elements and the callbacks with the [AppDesinger](https://www.mathworks.com/videos/app-designer-overview-1510748719083.html) in Matlab. See [How to edit COSMOSS GUI](https://hackmd.io/@jjh/EditGUI) for more information.

###### tags: `COSMOSS`