Fix rotation and MPI for multiple IBs

[haochey]

Description

Fixes issue #787

This PR fixes two bugs:

1. The rotation of STL patches and STL immersed boundaries.

• Why not working?
  (a) The normal vector of the triangular facets are not rotated with the vertices. The ray-tracing become erroneous when
  the unrotated normal vectors are used.
  (b) The rotation did not consider the original center of the geometry is not at the origin of the coordinate.

• What's the fix?
  (a) Include the normal vector in the process of the model transformation, but skip the scale and translation parts.
  (b) Shift the geometry to the origin before rotation and shift it back to its original position after the rotation.

2. MPI communication for >1 number of IBs. (a two-line fix that's left over from the IBM+STL PR).

Type of change

Please delete options that are not relevant.

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

Scope

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

How Has This Been Tested?

Please describe the tests that you ran to verify your changes.
Provide instructions so we can reproduce.
Please also list any relevant details for your test configuration

• Similar test case mentioned in issue STL immersed boundaries don't work with an applied rotation #787

Test Configuration:

import json
import math
gam_a = 1.4
D = 2
Ma = 4
vel = Ma * math.sqrt(gam_a) 
tStop = 20/vel
print(
    json.dumps(
        {
            "run_time_info": "T",
            "x_domain%beg": -4,
            "x_domain%end": 8,
            "stretch_x" : 'T',
            'a_x': 20,
            'x_a': -10,
            'x_b': 6,
            "y_domain%beg": -3,
            "y_domain%end": 3,
            "stretch_y" : 'T',
            'a_y': 15,
            'y_a': -1.75,
            'y_b': 1.75,
            'loops_y': 2,
            "z_domain%beg": -3,
            "z_domain%end": 3,
            "stretch_z" : 'T',
            'a_z': 15,
            'z_a': -1.75,
            'z_b': 1.75,
            'loops_z': 2,
            "cyl_coord": "F",
            "m": 99,
            "n": 49,
            "p": 49,
            'cfl_adap_dt' : 'F', #'T',
            'n_start'     : 0,
            'cfl_target'  : 0.8,
            't_step_start': 0,
            't_step_stop' : 1, #tStop,
            't_step_save' : 1, #tStop/100,
            'dt' : 1e-9,
            't_stop'      : 1, #tStop,
            't_save'      : 1, #tStop/100,
            "num_patches": 1,
            "model_eqns": 2,
            "alt_soundspeed": "F",
            "num_fluids": 1,
            "mpp_lim": "F",
            "mixture_err": "F",
            "time_stepper": 3,
            "weno_order": 5,
            "weno_eps": 1.0e-16,
            "weno_Re_flux": "F",
            "weno_avg": "T",
            "avg_state": 2,
            "mapped_weno": "F",
            "null_weights": "F",
            "mp_weno": "F",
            "riemann_solver": 2,
            "wave_speeds": 1,
            "viscous": "F",
            "bc_x%beg": -3,
            "bc_x%end": -3,
            "bc_y%beg": -3,
            "bc_y%end": -3,
            "bc_z%beg": -3,
            "bc_z%end": -3,
            "ib": "T",
            "num_ibs": 1,
            "format": 1,
            "precision": 2,
            "prim_vars_wrt":'T',
            "parallel_io": "T",
            "patch_icpp(1)%geometry": 9,
            "patch_icpp(1)%x_centroid": 0.0,
            "patch_icpp(1)%y_centroid": 0.0,
            "patch_icpp(1)%z_centroid": 0.0,
            "patch_icpp(1)%length_x": 100,
            "patch_icpp(1)%length_y": 50,
            "patch_icpp(1)%length_z": 50,
            "patch_icpp(1)%vel(1)": vel,
            "patch_icpp(1)%vel(2)": 0,
            "patch_icpp(1)%vel(3)": 0,
            "patch_icpp(1)%pres": 1,
            "patch_icpp(1)%alpha_rho(1)": 1,
            "patch_icpp(1)%alpha(1)": 1,
            "patch_ib(1)%geometry": 12,
            "patch_ib(1)%model_filepath": "vehicle.stl",
            "patch_ib(1)%model_translate(1)": 3,
            "patch_ib(1)%model_translate(2)": 0,
            "patch_ib(1)%model_translate(3)": 0,
            "patch_ib(1)%model_rotate(3)": -0.5*math.pi,
            "patch_ib(1)%model_spc": 20,
            "patch_ib(1)%model_threshold": 0.01,
            "patch_ib(1)%slip": "F",
            "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),
            "fluid_pp(1)%pi_inf": 0,
        }
    )
)

Without rotation and translation:

With rotation and translation:

• What computers and compilers did you use to test this: MacOS with GCC

Checklist

• I have added comments for the new code
• I ran ./mfc.sh format before committing my code
• New and existing tests pass locally with my changes, including with GPU capability enabled (both NVIDIA hardware with NVHPC compilers and AMD hardware with CRAY compilers) and disabled
• This PR does not introduce any repeated code (it follows the DRY principle)
• I cannot think of a way to condense this code and reduce any introduced additional line count

If your code changes any code source files (anything in src/simulation)

To make sure the code is performing as expected on GPU devices, I have:

• Checked that the code compiles using NVHPC compilers

[codecov]

Codecov Report

Attention: Patch coverage is 44.44444% with 10 lines in your changes missing coverage. Please review.

Project coverage is 43.76%. Comparing base (bae121f) to head (ad01abf).
Report is 3 commits behind head on master.

Files with missing lines	Patch %	Lines
src/common/m_helper.fpp	23.07%	10 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #788      +/-   ##
==========================================
- Coverage   43.79%   43.76%   -0.04%     
==========================================
  Files          65       65              
  Lines       19055    19047       -8     
  Branches     2326     2324       -2     
==========================================
- Hits         8345     8335      -10     
- Misses       9302     9305       +3     
+ Partials     1408     1407       -1     

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