Design of the Chimera Code Base

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The Chimera code base will be the centerpiece of the instrumentation for the thesis. Its design needs to be developed considering the goals of the thesis work and the questions that we will want to explore. A design includes clear definition of all packages, TPLs, and functionality.

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Now that Panzer is in Trilinos proper, we can start hammering this out.

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As I work through Panzer, there are a few key components to be concerned with: equation sets, closure models, and boundary conditions. It would then be logical to divide the Chimera source into 3 subpackages: solvers, models, and drivers. This will clearly separate the solvers work from the physics. In addition, separating the models for the drivers will allow for easier code reuse for different problem types. The core Panzer pieces will be contained in models while the interface factories will live in drivers along the executable main.

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I've settled on a core package structure that can be separated at any time as an independent Monte Carlo solvers library. The separate Panzer driver code will sit in another directory. We can also separate each set of numerical experiments in other directories.