Input file flags and eror handeling

[nedtaylor]

In GitLab by @fhd205 on Oct 26, 2023, 12:35

To make our code clearer, we should change our default input file names to "param.in", "mat.in", and "geom.in". we should also introduce flags that allow users to specify non-default file names and give error messages when the expected files are not present.