Fix sphere smoothing

[wilfonba]

Description

This PR fixes a bug in the smoothing function for spherical patches that was identified during IGR development. The smoothing was only being applied inside the nominal radius of the patch, resulting in a grid level discontinuity. The old code generates the following IC

Which shows smoothing only on the sphere's interior and a discontinuity on the outer surface. The new code generates the following IC

which shows smoothing on both sides of the nominal radius of the patch. The smoothing coefficient for both ICs is identical.

Fixes #(issue) [optional]

Type of change

• Bug fix (non-breaking change which fixes an issue)

Scope

• This PR comprises a set of related changes with a common goal

[wilfonba]

@haochey Says this is likely an issue for some other patches as well and he's going to resolve it in this PR.

[codecov]

Codecov Report

Attention: Patch coverage is 17.24138% with 24 lines in your changes missing coverage. Please review.

Project coverage is 43.94%. Comparing base (131b41e) to head (12edf88).
Report is 3 commits behind head on master.

Files with missing lines	Patch %	Lines
src/pre_process/m_patches.fpp	14.81%	22 Missing and 1 partial ⚠️
src/pre_process/m_initial_condition.fpp	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #798      +/-   ##
==========================================
+ Coverage   43.74%   43.94%   +0.19%     
==========================================
  Files          65       65              
  Lines       19039    19039              
  Branches     2332     2329       -3     
==========================================
+ Hits         8328     8366      +38     
+ Misses       9303     9262      -41     
- Partials     1408     1411       +3     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[sbryngelson]

@haochey let me know when this is ready

[sbryngelson]

Glad to merge but it's now failing a bunch of tests?

[haochey]

Yeah, I will fix this today.

[haochey]

@sbryngelson This should be ready to merge.

The cuboid patch was not properly initialized for IBM so it breaks all the tests. I updated the 8 golden files for cuboid IBMs with the fix on initialization.

The smooth functions for cylinder and sphere are fixed. They are the only two patches with this issue.