- Jia-Jung Ho·Last edited by Jia-Jung Ho on Jun 20, 2021Linked with GitHubContributed by
There is no commentSelect some text and then click Comment, or simply add a comment to this page from below to start a discussion.Coding structure
COSMOSS is a Matlab based program. The Graphic User Interfaces(GUI) end can be break down in to three parts:
- Structure model generation (model_GUIs)
- Spectral simulations (main_GUI)
- Spectral analysis (tool_GUIs)
The simulation procedure end can be summarized in the flow chart:
tags: COSMOSS code
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How to edit COSMOSS GUIs
The Graphic User Interfaces (GUIs) of COSMOSS were written with the appdesigner of Matlb. I used to use GUIDE wordle for the GUIs but found the appdesigner is much scalable. Editing Main GUI To edit the GUIs, you need to call the appdesigner command with the '.mlapp' files. For example, to edit the main GUI, I can type the following in the Matlab working space[^PS]: > appdesigner COSMOSS You should see the appdesigner interface shows up as following: The above figure shows the design view, which allows you to edit the graphical elements. The other tab on the top right named 'Code View' will give you access to the source code for further editing:
Jan 8, 2024TODO 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
Jul 12, 2021What is COSMOSS?
:::info COSMOSS is a Coupled OScillator MOdel Spectral Simulator ::: 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:
Jun 20, 2021Running COSMOSS from the workspace
In this tutorial, I will layout a step-by-step process about how to run COSMOSS from workspace (command line mode). One of the major benefits is to run it in a batch mode. Running in batch mode allows one to explore the "change" from some acting variables. For example, given two molecules, if you want to know how would spectral features change when you pull them away, you can run simulations in a for-loop instead of laborious mouse-clickings. Even better is that you can visualize the result as a movie! :::info Objective: Generating the movie of FTIR spectral change while pulling two molecules away from 3 to 7Å. ::: Constructing the TCO model :::warning Before we start, make sure you've already run COSMOSS at least once so all the paths to relevant function are set!
Mar 25, 2021
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