I am trying to read the code of siesta, which includes maybe thousands of lines of code. So the first thing is to read and understand the architecture of the code, I try to find some tools to help me read the code, but I am not sure what is the mainstream method for this kind of job. My question is: What is the best option or toolchain to analyze the code architecture of a large program?

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A very good start would be to run the source code through DoxyGen it can analyse and document code in a number of languages including Fortran - if you also have Graphviz installed then you can also generate a number of diagrams for you and embed them into the documentation.

Both are Free, gratis & Open Source, and are available for most platforms including Windows, OS-X and Linux.

DoxyGen has a DoxyWizard GUI to allow you to set things up but can then be run from the command line. Note that you will probably want to select the All Entities option on Page 2 of the Wizard. Initial ViewPage 2 Page 3Page 4

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