Update regularization scheme in SR method and add docs

[camelto2]

Please review the developer documentation
on the wiki of this project that contains help and requirements.

Proposed changes

update to SR method. In my previous PR, I accidentally left out applying the regularization to the overlap matrix. This is added back in. Also added control of the CG algorithm via the input file. Some documentation is also added.

What type(s) of changes does this code introduce?

Delete the items that do not apply

• New feature
• Documentation or build script changes

Does this introduce a breaking change?

• No

What systems has this change been tested on?

mac

Checklist

Update the following with a yes where the items apply. If you're unsure about any of them, don't hesitate to ask. This is
simply a reminder of what we are going to look for before merging your code.

• Yes. This PR is up to date with current the current state of 'develop'
• Yes. Code added or changed in the PR has been clang-formatted
• No. This PR adds tests to cover any new code, or to catch a bug that is being fixed
• Yes. Documentation has been added (if appropriate)

[ye-luo]

Test this please