Fix physics storage bug

[elynnwu]

Purpose

Physics state phii and tendency variables need to be reset to zero in between steps. These variables are first used as read before writing, so they need to be reset back to zero.

Code changes:

• physics: set phii and *_dt to zero first

Checklist

Before submitting this PR, please make sure:

• You have followed the coding standards guidelines established at Code Review Checklist.
• Docstrings and type hints are added to new and updated routines, as appropriate
• All relevant documentation has been updated or added (e.g. README, CONTRIBUTING docs)
• For each public change and fix in pace-util, HISTORY has been updated
• Unit tests are added or updated for non-stencil code changes

[twicki]

Great find, this is awesome