Merge branch 'master' into runners

Author: sbryngelson

.github/workflows/test.yml

@@ -49,6 +49,8 @@ jobs:
       - name: Setup MacOS
         if:   matrix.os == 'macos'
         run:  |
+          brew update
+          brew upgrade
           brew install coreutils python cmake fftw hdf5 gcc@14 boost open-mpi
           echo "FC=gfortran-14" >> $GITHUB_ENV
           echo "BOOST_INCLUDE=/opt/homebrew/include/" >> $GITHUB_ENV

CMakeLists.txt

@@ -165,6 +165,7 @@ elseif (CMAKE_Fortran_COMPILER_ID STREQUAL "Cray")
         )
         add_link_options("SHELL: -K trap=fp" "SHELL: -G2")
     endif()
+
 elseif (CMAKE_Fortran_COMPILER_ID STREQUAL "Flang")
     add_compile_options(
         $<$<COMPILE_LANGUAGE:Fortran>:-Mfreeform>
@@ -188,13 +189,14 @@ elseif ((CMAKE_Fortran_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_Fortran_COMPILER_
     if (CMAKE_BUILD_TYPE STREQUAL "Debug")
         add_compile_options(
             $<$<COMPILE_LANGUAGE:Fortran>:-O0>
+            $<$<COMPILE_LANGUAGE:Fortran>:-C> 
+            $<$<COMPILE_LANGUAGE:Fortran>:-g>
+            $<$<COMPILE_LANGUAGE:Fortran>:-traceback> 
+            $<$<COMPILE_LANGUAGE:Fortran>:-Minform=inform> 
+            $<$<COMPILE_LANGUAGE:Fortran>:-Mbounds>
         )
     endif()
 
-    if (CMAKE_BUILD_TYPE STREQUAL "Debug")
-        add_compile_options(-C -g -O0 -traceback -Minform=inform -Mbounds)
-    endif()
-
     if (DEFINED ENV{MFC_CUDA_CC})
         string(REGEX MATCHALL "[0-9]+" MFC_CUDA_CC $ENV{MFC_CUDA_CC})
         message(STATUS "Found $MFC_CUDA_CC specified. GPU code will be generated for compute capability(ies) ${MFC_CUDA_CC}.")

README.md

@@ -37,19 +37,25 @@ MFC has high-level documentation, visualizations, and more on [its website](http
 ## An example
 
 We keep many examples.
-Here's one!
+Here are some of them!
 MFC can execute high-fidelity simulations of shock-droplet interaction (see `examples/3d_shockdroplet`)
 
 <p align="center">
     <img src="docs/res/shockdrop.png" alt="Shock Droplet Example" width="700"/>
 </p>
 
-Another example is the high-Mach flow over an airfoil, shown below.
+This one simulates high-Mach flow over an airfoil, shown below.
 
 <p align="center">
     <img src="docs/res/airfoil.png" alt="Airfoil Example" width="700"/><br/>
 </p>
 
+This one simulates high amplitude acoustic wave through a circular orifice opening, shown below.
+
+<p align="center">
+    <img src="docs/res/orifice.png" alt="Orifice Example" width="700"/><br/>
+</p>
+
 
 ## Getting started
 

docs/documentation/case.md

@@ -166,12 +166,12 @@ MPI topology is automatically optimized to maximize the parallel efficiency for
 | `vel(i)` *           | Real    | Supported             | Velocity in direction $i$.                                   |
 | `hcid` *             | Integer | N/A                   | Hard coded patch id                                          |
 | `cf_val` *           | Real    | Supported             | Surface tension color function value                         |
-| `model%%filepath`     | String  | Not Supported         | Path to an STL or OBJ file (not all OBJs are supported).     |
-| `model%%scale(i)`     | Real    | Not Supported         | Model's (applied) scaling factor for component $i$.          |
-| `model%%rotate(i)`    | Real    | Not Supported         | Model's (applied) angle of rotation about axis $i$.          |
-| `model%%translate(i)` | Real    | Not Supported         | Model's $i$-th component of (applied) translation.           |
-| `model%%spc`          | Integer | Not Supported         | Number of samples per cell when discretizing the model into the grid. |
-| `model%%threshold`    | Real    | Not Supported         | Ray fraction inside the model patch above which the fraction is set to one.|
+| `model_filepath`     | String  | Not Supported         | Path to an STL or OBJ file (not all OBJs are supported).     |
+| `model_scale(i)`     | Real    | Not Supported         | Model's (applied) scaling factor for component $i$.          |
+| `model_rotate(i)`    | Real    | Not Supported         | Model's (applied) angle of rotation about axis $i$.          |
+| `model_translate(i)` | Real    | Not Supported         | Model's $i$-th component of (applied) translation.           |
+| `model_spc`          | Integer | Not Supported         | Number of samples per cell when discretizing the model into the grid. |
+| `model_threshold`    | Real    | Not Supported         | Ray fraction inside the model patch above which the fraction is set to one.|
 
 *: These parameters should be prepended with `patch_icpp(j)%` where $j$ is the patch index.
 
@@ -263,7 +263,11 @@ Optimal choice of the value of `smooth_coeff` is case-dependent and left to the
 - `patch_icpp(j)alpha(i)`, `patch_icpp(j)alpha_rho(i)`, `patch_icpp(j)pres`, and `patch_icpp(j)vel(i)` define for $j$-th patch the void fraction of `fluid(i)`, partial density of `fluid(i)`, the pressure, and the velocity in the $i$-th coordinate direction.
 These physical parameters must be consistent with fluid material's parameters defined in the next subsection.
 
-- `model%%scale`, `model%%rotate` and `model%%translate` define how the model should be transformed to domain-space by first scaling by `model%%scale`, then rotating about the Z, X, and Y axes (using `model%%rotate`), and finally translating by `model%%translate`.
+- `model_filepath` defines the root directory of the STL or OBJ model file.
+
+- `model_scale`, `model_rotate` and `model_translate` define how the model should be transformed to domain-space by first scaling by `model_scale`, then rotating about the Z, X, and Y axes (using `model_rotate`), and finally translating by `model_translate`.
+
+- `model_spc` and `model_threshold` are ray-tracing parameters. `model_spc` defines the number of rays per cell to render the model. `model_threshold` defines the ray-tracing threshold at which the cell is marked as the model.
 
 ### 4. Immersed Boundary Patches
 
@@ -279,6 +283,12 @@ These physical parameters must be consistent with fluid material's parameters de
 | `m`                    | Real    | NACA airfoil parameters (see below) |
 | `p`                    | Real    | NACA airfoil parameters (see below) |
 | `slip`                 | Logical | Apply a slip boundary |
+| `model_filepath`      | String  | Path to an STL or OBJ file (not all OBJs are supported).     |
+| `model_scale(i)`      | Real    | Model's (applied) scaling factor for component $i$.          |
+| `model_rotate(i)`     | Real    | Model's (applied) angle of rotation about axis $i$.          |
+| `model_translate(i)`  | Real    | Model's $i$-th component of (applied) translation.           |
+| `model_spc`           | Integer | Number of samples per cell when discretizing the model into the grid. |
+| `model_threshold`     | Real    | Ray fraction inside the model patch above which the fraction is set to one.|
 
 These parameters should be prepended with `patch_ib(j)%` where $j$ is the patch index.
 
@@ -301,6 +311,8 @@ Additional details on this specification can be found in [The Naca Airfoil Serie
 
 - `slip` applies a slip boundary to the surface of the patch if true and a no-slip boundary condition to the surface if false.
 
+- Please see [Patch Parameters](#3-patches) for the descriptions of `model_filepath`, `model_scale`, `model_rotate`, `model_translate`, `model_spc`, and `model_threshold`.
+
 ### 5. Fluid Material’s
 
 | Parameter | Type   | Description                                    |

docs/res/orifice.png

@@ -42,7 +42,7 @@
     # ==========================================================================
 
     # Formatted Database Files Structure Parameters ============================
-    'format'                       : 2,
+    'format'                       : 1,
     'precision'                    : 2,
     'prim_vars_wrt'                :'T',
     'rho_wrt'                      :'T',

examples/0D_qbmm/case.py

@@ -42,7 +42,7 @@
     # ==========================================================================
 
     # Formatted Database Files Structure Parameters ============================
-    'format'                       : 2,
+    'format'                       : 1,
     'precision'                    : 2,
     'prim_vars_wrt'                :'T',
     'rho_wrt'                      :'T',

examples/1D_acoustic_dipole/case.py

@@ -42,7 +42,7 @@
     # ==========================================================================
 
     # Formatted Database Files Structure Parameters ============================
-    'format'                       : 2,
+    'format'                       : 1,
     'precision'                    : 2,
     'prim_vars_wrt'                :'T',
     'rho_wrt'                      :'T',

examples/1D_acoustic_gauss_sigmadist/case.py

@@ -42,7 +42,7 @@
     # ==========================================================================
 
     # Formatted Database Files Structure Parameters ============================
-    'format'                       : 2,
+    'format'                       : 1,
     'precision'                    : 2,
     'prim_vars_wrt'                :'T',
     'rho_wrt'                      :'T',