Merge branch 'master' into dimension

Author: sbryngelson

.github/workflows/lint-toolchain.yml

@@ -42,5 +42,21 @@ jobs:
 
     - name: Validate example cases
       run: |
-        ./mfc.sh validate examples/1D_sodshocktube/case.py
-        ./mfc.sh validate examples/2D_shockbubble/case.py
+        failed=0
+        passed=0
+        for case in examples/*/case.py; do
+          [ -f "$case" ] || continue
+          output=$(./mfc.sh validate "$case" 2>&1)
+          if [ $? -eq 0 ]; then
+            passed=$((passed + 1))
+          else
+            echo "FAIL: $case"
+            echo "$output"
+            failed=$((failed + 1))
+          fi
+        done
+        echo ""
+        echo "Results: $passed passed, $failed failed"
+        if [ "$failed" -ne 0 ]; then
+          exit 1
+        fi

.gitignore

@@ -44,6 +44,7 @@ docs/*/result*
 docs/documentation/*-example.png
 docs/documentation/examples.md
 docs/documentation/case_constraints.md
+docs/documentation/physics_constraints.md
 
 examples/*batch/*/
 examples/**/D/*

CMakeLists.txt

@@ -660,16 +660,19 @@ if (MFC_DOCUMENTATION)
         VERBATIM
     )
 
-    # Generate case_constraints.md from case_validator.py and examples/
+    # Generate case_constraints.md and physics_constraints.md together.
+    # Both are produced by gen_constraints.sh, so a single command avoids races.
     add_custom_command(
         OUTPUT  "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/case_constraints.md"
+                "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/physics_constraints.md"
         DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/toolchain/mfc/gen_case_constraints_docs.py"
+                "${CMAKE_CURRENT_SOURCE_DIR}/toolchain/mfc/gen_physics_docs.py"
                 "${CMAKE_CURRENT_SOURCE_DIR}/toolchain/mfc/case_validator.py"
                 "${CMAKE_CURRENT_SOURCE_DIR}/toolchain/mfc/params/definitions.py"
                 "${examples_DOCs}"
         COMMAND "bash" "${CMAKE_CURRENT_SOURCE_DIR}/docs/gen_constraints.sh"
                        "${CMAKE_CURRENT_SOURCE_DIR}"
-        COMMENT "Generating case_constraints.md"
+        COMMENT "Generating case_constraints.md and physics_constraints.md"
         VERBATIM
     )
 
@@ -732,11 +735,13 @@ if (MFC_DOCUMENTATION)
 
         set(opt_example_dependency "")
         set(opt_constraints_dependency "")
+        set(opt_physics_dependency "")
         set(opt_cli_reference_dependency "")
         set(opt_parameters_dependency "")
         if (${target} STREQUAL documentation)
             set(opt_example_dependency "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/examples.md")
             set(opt_constraints_dependency "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/case_constraints.md")
+            set(opt_physics_dependency "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/physics_constraints.md")
             set(opt_cli_reference_dependency "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/cli-reference.md")
             set(opt_parameters_dependency "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/parameters.md")
         endif()
@@ -749,6 +754,7 @@ if (MFC_DOCUMENTATION)
             DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/${target}-Doxyfile"
                     "${opt_example_dependency}"
                     "${opt_constraints_dependency}"
+                    "${opt_physics_dependency}"
                     "${opt_cli_reference_dependency}"
                     "${opt_parameters_dependency}"
                     "${${target}_SRCs}" "${${target}_DOCs}"

docs/custom.css

@@ -3,6 +3,22 @@
  * Overrides for doxygen-awesome theme
  */
 
+/* Seamless split <code> tags for Fortran % struct accessors.
+ * Doxygen consumes %<word> even inside code spans, so we split around %
+ * into adjacent <code> elements and remove internal borders/padding. */
+code.f90l {
+    border-right: 0;
+    border-top-right-radius: 0;
+    border-bottom-right-radius: 0;
+    padding-right: 0;
+}
+code.f90r {
+    border-left: 0;
+    border-top-left-radius: 0;
+    border-bottom-left-radius: 0;
+    padding-left: 0;
+}
+
 /* Fix inline code visibility in colored admonition blocks (warning, attention, important, note, etc.) */
 
 /* Warning/Attention/Important blocks (red/pink background) */

docs/documentation/case.md

@@ -65,7 +65,7 @@ To run such a case, use the following format:
 For example, to run the `scaling` case in "weak-scaling" mode:
 
 ```shell
-./mfc.sh run examples/scaling/case.py -t pre_process -j 8 -- --scaling weak
+./mfc.sh run examples/scaling/benchmark.py -t pre_process -j 8 -- --scaling weak
 ```
 
 ## Parameters
@@ -281,12 +281,12 @@ For instance, in a 2D simulation, when a cylindrical `patch(2)` is immersed in a
 
 - `smoothen` activates smoothening of the boundary of the patch that alters the existing patch.
 When smoothening occurs, fluids of the two patches are mixed in the region of the boundary.
-For instance, in the aforementioned case of the cylindrical patch immersed in the rectangular patch, smoothening occurs when ``patch_icpp(2)smoothen = 'T'``.
+For instance, in the aforementioned case of the cylindrical patch immersed in the rectangular patch, smoothening occurs when ``patch_icpp(2)%%smoothen = 'T'``.
 `smooth_coeff` controls the thickness of the region of smoothening (sharpness of the mixture region).
 The default value of `smooth_coeff` is unity. The region of smoothening is thickened with decreasing the value.
 Optimal choice of the value of `smooth_coeff` is case-dependent and left to the user.
 
-- `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.
+- `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_filepath` defines the root directory of the STL or OBJ model file.
@@ -297,7 +297,7 @@ These physical parameters must be consistent with fluid material's parameters de
 
 #### Elliptic Smoothing
 
-Initial conditions in which not all patches support the `patch_icpp(j)%smoothen` parameter can still be smoothed by applying iterations of the heat equation to the initial condition.
+Initial conditions in which not all patches support the `patch_icpp(j)%%smoothen` parameter can still be smoothed by applying iterations of the heat equation to the initial condition.
 This is enabled by adding `'elliptic_smoothing': "T",` and `'elliptic_smoothing_iters': N,` to the case dictionary, where `N` is the number of smoothing iterations to apply.
 
 ### 4. Immersed Boundary Patches {#sec-immersed-boundary-patches}
@@ -463,10 +463,10 @@ Boundary condition patches can be used with non-characteristic boundary conditio
 Their use is detailed in [Boundary Condition Patches](#boundary-condition-patches).
 
 - `bc_[x,y,z]%%vb[1,2,3]` specifies the velocity in the (x,1), (y,2), (z,3) direction applied to `bc_[x,y,z]%%beg` when using `bc_[x,y,z]%%beg = -16`.
-Tangential velocities require viscosity, `weno_avg = T`, and `bc_[x,y,z]%%beg = -16` to work properly. Normal velocities require `bc_[x,y,z]%%end = -15` or `\bc_[x,y,z]%%end = -16` to work properly.
+Tangential velocities require viscosity, `weno_avg = T`, and `bc_[x,y,z]%%beg = -16` to work properly. Normal velocities require `bc_[x,y,z]%%end = -15` or `bc_[x,y,z]%%end = -16` to work properly.
 
 - `bc_[x,y,z]%%ve[1,2,3]` specifies the velocity in the (x,1), (y,2), (z,3) direction applied to `bc_[x,y,z]%%beg` when using `bc_[x,y,z]%%end = -16`.
-Tangential velocities require viscosity, `weno_avg = T`, and `bc_[x,y,z]%%end = 16` to work properly. Normal velocities require `bc_[x,y,z]%%end = -15` or `\bc_[x,y,z]%%end = -16` to work properly.
+Tangential velocities require viscosity, `weno_avg = T`, and `bc_[x,y,z]%%end = 16` to work properly. Normal velocities require `bc_[x,y,z]%%end = -15` or `bc_[x,y,z]%%end = -16` to work properly.
 
 - `model_eqns` specifies the choice of the multi-component model that is used to formulate the dynamics of the flow using integers from 1 through 3.
 `model_eqns = 1`, `2`, and `3` correspond to \f$\Gamma\f$-\f$\Pi_\infty\f$ model (\cite Johnsen08), 5-equation model (\cite Allaire02), and 6-equation model (\cite Saurel09), respectively.
@@ -531,7 +531,7 @@ If this option is false, velocity gradient is computed using finite difference s
 - `weno_avg` it activates the arithmetic average of the left and right, WENO-reconstructed, cell-boundary values.
 This option requires `weno_Re_flux` to be true because cell boundary values are only utilized when employing the scalar divergence method in the computation of velocity gradients.
 
-- `surface_tension` activates surface tension when set to ``'T'``. Requires `sigma` to be set and `num_fluids`. The color function in each patch should be assigned such that `patch_icpp(i)%cf_val = 1` in patches where `patch_icpp(i)%alpha = 1 - eps` and `patch_icpp(i)%cf_val = 0` in patches where `patch_icpp(i)%alpha = eps`.
+- `surface_tension` activates surface tension when set to ``'T'``. Requires `sigma` to be set and `num_fluids`. The color function in each patch should be assigned such that `patch_icpp(i)%%cf_val = 1` in patches where `patch_icpp(i)%%alpha = 1 - eps` and `patch_icpp(i)%%cf_val = 0` in patches where `patch_icpp(i)%%alpha = eps`.
 
 - `viscous` activates viscosity when set to ``'T'``. Requires `Re(1)` and `Re(2)` to be set.
 
@@ -620,8 +620,8 @@ To restart the simulation from $k$-th time step, see @ref running "Restarting Ca
 | `num_probes`            | Integer | Number of probes	|
 | `probe(i)%[x,y,z]`      | Real	  | Coordinates of probe $i$	|
 | `output_partial_domain` | Logical | Output part of the domain |
-| `[x,y,z]_output%beg`    | Real    | Beginning of the output domain in the [x,y,z]-direction |
-| `[x,y,z]_output%end`    | Real    | End of the output domain in the [x,y,z]-direction |
+| `[x,y,z]_output%%beg`    | Real    | Beginning of the output domain in the [x,y,z]-direction |
+| `[x,y,z]_output%%end`    | Real    | End of the output domain in the [x,y,z]-direction |
 | `lag_txt_wrt`           | Logical | Write Lagrangian bubble data to `.dat` files |
 | `lag_header`            | Logical | Write header to Lagrangian bubble `.dat` files |
 | `lag_db_wrt`            | Logical | Write Lagrangian bubble data to silo/hdf5 database files |
@@ -667,7 +667,7 @@ If `file_per_process` is true, then pre_process, simulation, and post_process mu
 
 - `probe_wrt` activates the output of state variables at coordinates specified by `probe(i)%[x;y,z]`.
 
-- `output_partial_domain` activates the output of part of the domain specified by `[x,y,z]_output%beg` and `[x,y,z]_output%end`.
+- `output_partial_domain` activates the output of part of the domain specified by `[x,y,z]_output%%beg` and `[x,y,z]_output%%end`.
 This is useful for large domains where only a portion of the domain is of interest.
 It is not supported when `precision = 1` and `format = 1`.
 It also cannot be enabled with `flux_wrt`, `heat_ratio_wrt`, `pres_inf_wrt`, `c_wrt`, `omega_wrt`, `ib`, `schlieren_wrt`, `qm_wrt`, or 'liutex_wrt'.
@@ -991,30 +991,30 @@ Note: For relativistic flow, the conservative and primitive densities are differ
 
 When ``cyl_coord = 'T'`` is set in 3D the following constraints must be met:
 
-- `bc_y%beg = -14`  enables the axis boundary condition
+- `bc_y%%beg = -14`  enables the axis boundary condition
 
-- `bc_z%beg = bc_z%end = -1`  enables periodic boundary conditions in the azimuthal direction
+- `bc_z%%beg = bc_z%%end = -1`  enables periodic boundary conditions in the azimuthal direction
 
-- `z_domain%beg = 0`  sets the azimuthal starting point to 0
+- `z_domain%%beg = 0`  sets the azimuthal starting point to 0
 
-- `z_domain%end = 2*math.pi` to set the azimuthal ending point to \f$2\pi\f$ (note, requires `import math` in the case file)
+- `z_domain%%end = 2*math.pi` to set the azimuthal ending point to \f$2\pi\f$ (note, requires `import math` in the case file)
 
 When ``cyl_coord = 'T'`` is set in 2D the following constraints must be met:
 
-- `bc_y%beg = -2` to enable reflective boundary conditions
+- `bc_y%%beg = -2` to enable reflective boundary conditions
 
 ### 17. Chemistry
 
 | Parameter                     | Type    | Description                                              |
 | ---:                          | :---:   | :---                                                     |
 | `chemistry`                   | Logical | Enable chemistry simulation                              |
-| `chem_params%diffusion`       | Logical | Enable multispecies diffusion                            |
-| `chem_params%reactions`       | Logical | Enable chemical reactions                                |
-| `chem_params%gamma_method`    | Integer | Methodology for calculating the heat capacity ratio      |
-| `chem_params%transport_model` | Integer | Methodology for calculating the diffusion coefficients   |
+| `chem_params%%diffusion`       | Logical | Enable multispecies diffusion                            |
+| `chem_params%%reactions`       | Logical | Enable chemical reactions                                |
+| `chem_params%%gamma_method`    | Integer | Methodology for calculating the heat capacity ratio      |
+| `chem_params%%transport_model` | Integer | Methodology for calculating the diffusion coefficients   |
 | `cantera_file`                | String  | Cantera-format mechanism file (e.g., .yaml)              |
 
-- `chem_params%transport_model` specifies the methodology for calculating diffusion coefficients and other transport properties, `1` for mixture-average, `2` for Unity-Lewis
+- `chem_params%%transport_model` specifies the methodology for calculating diffusion coefficients and other transport properties, `1` for mixture-average, `2` for Unity-Lewis
 
 - `cantera_file` specifies the chemical mechanism file. If the file is part of the standard Cantera library, only the filename is required. Otherwise, the file must be located in the same directory as your `case.py` file
 
@@ -1051,15 +1051,15 @@ The entries labeled "Characteristic." are characteristic boundary conditions bas
 
 | Parameter                     | Type    | Description |
 | ---:                          | :----:  | :--- |
-| `bc_[x,y,z]%grcbc_in`         | Logical | Enable grcbc for subsonic inflow |
-| `bc_[x,y,z]%grcbc_out`        | Logical | Enable grcbc for subsonic outflow (pressure)|
-| `bc_[x,y,z]%grcbc_vel_out`    | Logical | Enable grcbc for subsonic outflow (pressure + normal velocity) |
-| `bc_[x,y,z]%vel_in`           | Real Array | Inflow velocities in x, y and z directions |
-| `bc_[x,y,z]%vel_out`          | Real Array | Outflow velocities in x, y and z directions |
-| `bc_[x,y,z]%pres_in`          | Real    | Inflow pressure |
-| `bc_[x,y,z]%pres_out`         | Real    | Outflow pressure |
-| `bc_[x,y,z]%alpha_rho_in`     | Real Array | Inflow density |
-| `bc_[x,y,z]%alpha_in`         | Real Array | Inflow void fraction |
+| `bc_[x,y,z]%%grcbc_in`         | Logical | Enable grcbc for subsonic inflow |
+| `bc_[x,y,z]%%grcbc_out`        | Logical | Enable grcbc for subsonic outflow (pressure)|
+| `bc_[x,y,z]%%grcbc_vel_out`    | Logical | Enable grcbc for subsonic outflow (pressure + normal velocity) |
+| `bc_[x,y,z]%%vel_in`           | Real Array | Inflow velocities in x, y and z directions |
+| `bc_[x,y,z]%%vel_out`          | Real Array | Outflow velocities in x, y and z directions |
+| `bc_[x,y,z]%%pres_in`          | Real    | Inflow pressure |
+| `bc_[x,y,z]%%pres_out`         | Real    | Outflow pressure |
+| `bc_[x,y,z]%%alpha_rho_in`     | Real Array | Inflow density |
+| `bc_[x,y,z]%%alpha_in`         | Real Array | Inflow void fraction |
 
 This boundary condition can be used for subsonic inflow (`bc_[x,y,z]%[beg,end]` = -7) and subsonic outflow (`bc_[x,y,z]%[beg,end]` = -8) characteristic boundary conditions. These are based on \cite Pirozzoli13. This enables to provide inflow and outflow conditions outside the computational domain.