# File Structure

It is very important to me that humans can understand my code and how to get what they want from it. As LLMs get better at parsing codebases, human understanding and decent documentation can seem less important. 
But in my experiance, predominately using LLMs makes gaining an intutive sense for code structure much harder. Then, when you want just one thing from a complicated codebase (or heaven forbid nosense bugs happen), things get messy and LLMs often solve nonoptimally. (That said, I did use LLMs to help build this website and still expect others to use them to understand/use COGITO.) 
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To try and achieve this goal, I have created this interactive visualization of different file inputs and outputs of my different COGITO modules. I hope you enjoy clicking through them and this proves to be a handy reference for understanding the various files of COGITO.
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The boxes are bolded if the input/output file is required. The boxes are colored red for quality accessment files and yellow for debug/developer files. More tags and colors will be added when I get more time for it. This is still a bit underdevelopment and as such there may be small errors here and there. For some ridiculous rendering go click 'bond_cohp_plot.html' in the COGITOpost output section (it may take a second to load).

## COGITO

:::{file-cards} COGITO input
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:::{file-flow} COGITO
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:::{file-cards} COGITO output
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## COGITOpost

:::{file-cards} COGITOpost input
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:::{file-flow} COGITOpost
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:::{file-cards} COGITOpost output
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## COGITOanalyze

:::{file-cards} COGITOanalyze input
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:::{file-flow} COGITOanalyze
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:::{file-cards} COGITOanalyze output
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## COGITOico

:::{file-cards} COGITOico input
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:::{file-flow} COGITOico
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:::{file-cards} COGITOico output
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