add a distance() function and subtract off problem::center in position()

[zhichen3]

PR summary

1. Adds a separate function to calculate distance, mainly because the old way gets the 2d spherical case wrong.
2. Also subtracts off problem::center in position(). I think that's done in all cases where we call position except in rad_util.H, but that happens only in nonCartesian coordinate, and problem::center should be 0 at those cases. So I think it doesn't affect things.
3. Most places calculate the position separately, I changed it to using position()
4. Also make sure problem::center is 0 for spherical2d

PR motivation

PR checklist

• test suite needs to be run on this PR
• this PR will change answers in the test suite to more than roundoff level
• all newly-added functions have docstrings as per the coding conventions
• the CHANGES file has been updated, if appropriate
• if appropriate, this change is described in the docs

[zingale]

a lot of failures: http://groot.astro.sunysb.edu/Castro/test-suite/gfortran/2024-11-07-002/index.html

[zhichen3]

will separate this out into separate prs