Develop (#29)

* Add python script for mesh conversion to openFOAM

* Update script for openFOAM mesh conversion

* Rename python script for openFOAM grid conversion

* Update script "convert2foam.py" to fix mesh orientation issues in openFOAM's checkMesh routine

* Fix bugs in convert2foam.py

* Fix bugs in convert2foam.py

* Add example parameter file that covers the mesh of a thin fracture

* Add thin fracture example as cpp file

* Update parameter files for examples 02 and 06

The files `input/02_square_in_channel.para`
and `input/06_airfoil_from_csv.para` generated invalid meshes and
have thus be adjusted for it.

* Update example 02 cpp file

* Remove vertex-edge-intersection check in FrontUpdate.h

The call to `vertex.intersects_mesh_edges()`, which checked if a
vertex is placed too close to its surrounding edges has been removed.
This check led to wrong element sizes when choosing quad layers with
very small heights (compared to the global element size).
It was also found that this check is not required to pass the
current meshing tests and thus has been removed.

* Update example 06 to get rid of invalid front edges

* Update Readme

* Update readme

* Update Readme

* Add missing call for facet-connectivity-update to smoothing strategies

* Remove namespace "TQAlgorithm"

* Put includes into TQMesh.h and update examples / application for it

* Add single include to TQMesh.h in for each header file

* Add MeshChecker

* Add input file for ParaReader tests

* Put CppUtils includes into single file. Use again separate includes of headers in algorithm part and testing part

* Add MeshChecker to TQMeshApp.h & Update Readme

* Add CHANGELOG.md

CHANGELOG.md

@@ -0,0 +1,26 @@
+# Changelog
+
+## [1.3.2] - 2024-06-10
+
+### Fixed
+
+- Add missing call to update of face-connectivity prior to mesh smoothing strategies, 
+  which let to invalid meshing attempts in example 2 and example 6 (based on issue [#24](https://github.com/FloSewn/TQMesh/issues/24)) 
+  ([`0ce9393`](https://github.com/FloSewn/TQMesh/commit/0ce9393))
+
+### Changed
+
+- Remove `ve_intersection_` attribute in `src/algorithm/FrontUpdate.h`, which prevented quad layer heights 
+  to be removed adequately in the vicinity of small element sizes and which had no impact on the actual mesh generation
+  ([#26](https://github.com/FloSewn/TQMesh/issues/26)) ([`1762bdd`](https://github.com/FloSewn/TQMesh/commit/1762bdd))
+- Change namespace `TQMesh::TQAlgorithm` simply to `TQMesh`
+- Add single include header files `src/algorithm/TQMesh.h` and `src/utils/CppUtils.h` to reduce include statements 
+  within exampes / TQMesh application
+
+### Added
+
+- **convert2foam.py** to convert the TQMesh text-format to the OpenFOAM compatible mesh format ([#19](https://github.com/FloSewn/TQMesh/issues/19)) ([`df2a078`](https://github.com/FloSewn/TQMesh/commit/df2a078))
+- New example **thin fracture**, which involves merging two meshes that model a thin fraction interface (based on [#26](https://github.com/FloSewn/TQMesh/issues/26)).
+- **MeshChecker** class in `src/algorithm/MeshChecker.h`, which acts as interface for general mesh validity checks ([`7ca7320`](https://github.com/FloSewn/TQMesh/commit/7ca7320))
+  (might be extened in future for mesh quality checks)
+

CMakeLists.txt

@@ -9,7 +9,7 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 project(TQMesh
         LANGUAGES CXX
-        VERSION   1.1)
+        VERSION   1.3.2)
 
 set( BIN ${CMAKE_SOURCE_DIR}/bin )
 if(WIN32)

README.md

@@ -98,17 +98,18 @@ results in the *input/* and *src/examples* directories.
 
 
 <details>
-<summary>Example 1: Local mesh refinement</summary>
+<summary>Local mesh refinement</summary>
 
-This example shows a triangular mesh which features local element refinement. 
-The element size is determined either by the domain's edge segments, 
-through sizing factors that are attributed to boundary vertices or through a size function which is defined by the user.
+**TQMesh** combines a simple definition of mesh domain boundaries with a versatile specification of the 
+element size. The latter is either determined by the domain's edge segments, 
+through sizing factors that are attributed to boundary vertices or via user-defined size functions.
 
 <img src="doc/simple_triangular_mesh.png" alt="TQMesh-simple-triangular-mesh" width="300"/>
+<img src="doc/thin_fracture.png" alt="TQMesh-thin-fracture" width="338"/>
 </details>
 
 <details>
-<summary>Example 2: Quad layers and subdivision</summary>
+<summary>Quad layers and subdivision</summary>
 
 **TQMesh** also features the generation of quadrilateral elements, as well as layers of quad elements in the vicinity of boundaries.
 This example mesh was created by using the paving algorithm (which generates mixed-element meshes that are dominated by quads) and a subsequent quad-refinement of all elements.
@@ -120,7 +121,7 @@ In this way, it is possile to generate elements that consist only of quadrilater
 </details>
 
 <details>
-<summary>Example 3: Boundary shapes</summary>
+<summary>Boundary shapes</summary>
 
 It is possible to create meshes through predefined boundary shapes, such as rectangles, circles or triangles.
 
@@ -130,7 +131,7 @@ It is possible to create meshes through predefined boundary shapes, such as rect
 </details>
 
 <details>
-<summary>Example 4: Local mesh refinement and element coloring</summary>
+<summary>Local mesh refinement and element coloring</summary>
 
 During the meshing process, each element gets an associated color value. 
 These colors can be adjusted during the meshing process, as indicated in this example.
@@ -140,26 +141,25 @@ It also possible to define interior mesh vertices, in order to influence the loc
 </details>
 
 <details>
-<summary>Example 5: Merge meshes</summary>
+<summary>Merge meshes</summary>
 
 **TQMesh** gives the possibility to create and merge several meshes, preserving the conformity of their boundary edges.
 This makes it even easier to assign different color values to different element areas in the domain.
 This example shows the output from a successive mesh generation.
 
 <img src="doc/merge_meshes.png" alt="TQMesh-merge-meshes" width="250"/>
+<img src="doc/multiple_meshes.png" alt="TQMesh-multiple-meshes" width="250"/>
 </details>
 
 <details>
-<summary>Example 6: Import boundaries from CSV files</summary>
+<summary>Import boundaries from CSV files</summary>
 
 In case you want to automate the meshing process, **TQMesh** offers the possibility to import boundary definitions
 via CSV files. This example shows an airfoil that has been meshed in this way.
 
 <img src="doc/airfoil.png" alt="TQMesh-airfoil" width="350"/>
 </details>
 
-
-
 ## Output format
 Currently, **TQMesh** features the VTU output format (which can be read for example by Paraview) or alternatively a simple text output format.
 
@@ -232,13 +232,23 @@ The last entry of the mesh output refers to the size function values at every ve
 
 </details>
 
+## Convert meshes for OpenFOAM
+<img src="doc/banner_3d.jpeg" alt="TQMesh-OpenFOAM-support" width="300"/>
+
+To convert meshes from **TQMesh** to a format that is supported by OpenFOAM
+you can use a script that is provided in `scripts/convert2foam.py`.
+```sh
+python scripts/convert2foam.py [-e EXTRUSION] Mesh.txt export-prefix
+```
+This script simply extrudes the provided mesh into the z-direction and 
+generates the required files which can be used as input for OpenFOAM.
 
 ## Plot your meshes
 A simple python script to plot your mesh is provided under `scripts/plot_mesh.py`.
 It requires the mesh given in the format described above.
 Simply run it with
 ```sh
-python scipts/plot_mesh.py Mesh.txt (-s -v -e -b -f)
+python scripts/plot_mesh.py Mesh.txt (-s -v -e -b -f)
 ```
 Optional flags: 
 * `-s`: Add a contour plot of the underlying size-function
@@ -258,8 +268,9 @@ The following plots show some performance statistics.
 <img src="doc/BenchmarkPlot_QTree.png" alt="TQMesh-QTree-Benchmark" width="400"/> <img src="doc/BenchmarkPlot_Mesh.png" alt="TQMesh-Mesh-Benchmark" width="400"/>
 
 ## To Do's
-* Boundary definition via splines
+* Fixed edges within domains
 * Enhanced quad triangle-to-quad morphing
+* Boundary definition via splines
 * Improved documentation / testing
 
 Feel free to contribute!

auxiliary/test_data/ParaReaderTests.input.para

@@ -0,0 +1,91 @@
+
+# ----------------
+# Mesh 1
+# ----------------
+Define mesh: 
+
+  Define exterior boundary:
+      0.0,   0.0, 1
+    100.0,   0.0, 1
+    100.0, 100.0, 1
+      0.0, 100.0, 1
+  End exterior boundary
+
+  Define interior boundary:
+     10.0,  10.0, 2
+     90.0,  10.0, 2
+     90.0,  90.0, 2
+     10.0,  90.0, 2
+  End interior boundary
+
+End mesh
+
+# ----------------
+# Mesh 2
+# ----------------
+Define mesh:
+
+  Define exterior boundary:
+     10.0,  10.0, 2
+     90.0,  10.0, 2
+     90.0,  90.0, 2
+     10.0,  90.0, 2
+  End exterior boundary
+
+  Define interior boundary:
+     20.0,  20.0, 3
+     80.0,  20.0, 3
+     80.0,  80.0, 3
+     20.0,  80.0, 3
+  End interior boundary
+
+  Define interior boundary:
+     20.0,  20.0, 3
+     80.0,  20.0, 3
+     80.0,  80.0, 3
+     20.0,  80.0, 3
+  End interior boundary
+
+  Define interior boundary:
+     20.0,  20.0, 3
+     80.0,  20.0, 3
+     80.0,  80.0, 3
+     20.0,  80.0, 3
+  End interior boundary
+
+End mesh
+
+# ----------------
+# Mesh 3
+# ----------------
+Define mesh:
+
+  Define exterior boundary:
+     20.0,  20.0, 3
+     80.0,  20.0, 3
+     80.0,  80.0, 3
+     20.0,  80.0, 3
+  End exterior boundary
+
+  Define interior boundary:
+     40.0,  40.0, 4
+     60.0,  40.0, 4
+     60.0,  60.0, 4
+     40.0,  60.0, 4
+  End interior boundary
+
+End mesh
+
+# ----------------
+# Mesh 4
+# ----------------
+Define mesh:
+
+  Define exterior boundary:
+     40.0,  40.0, 4
+     60.0,  40.0, 4
+     60.0,  60.0, 4
+     40.0,  60.0, 4
+  End exterior boundary
+
+End mesh

input/02_square_in_channel.para

@@ -59,10 +59,10 @@ Define mesh:
     4.00, 0.00                 # v1
     4.00, 1.00                 # v2
     0.00, 1.00                 # v3
-    0.35, 0.35,  0.05, 0.20    # v4 
-    0.35, 0.65,  0.05, 0.20    # v5  
-    0.65, 0.65,  0.05, 0.20    # v6
-    0.65, 0.35,  0.05, 0.20    # v7
+    0.35, 0.35,  0.03, 0.25    # v4 
+    0.35, 0.65,  0.03, 0.25    # v5  
+    0.65, 0.65,  0.03, 0.25    # v6
+    0.65, 0.35,  0.03, 0.25    # v7
   End boundary vertices
 
   Define exterior boundary edges:

input/06_airfoil_from_csv.para

@@ -3,7 +3,7 @@
 #===========================================================
 
 #-----------------------------------------------------------
-#                     MESH DEFINITION
+#                   OUTER MESH DEFINITION
 #-----------------------------------------------------------
 Define mesh:
   Element size: 0.003 
@@ -22,13 +22,21 @@ Define mesh:
 
   Define interior boundary from CSV file: ../auxiliary/test_data/Airfoil.csv
 
-  Add quad layers: 0.69132, 0.09754, 0.69132, 0.09754, 10, 0.0003, 1.10
+  Add quad layers: 0.69132, 0.09754, 0.69132, 0.09754, 10, 0.0004, 1.10
+
+  #---------------------------------------------------------
+  #                     LOCAL REFINEMENT     
+  #---------------------------------------------------------
+  Define fixed vertices:
+    0.69095, 0.09625, 0.0020, 0.02
+    0.85985, 0.07582, 0.0008, 0.005
+  End fixed vertices
 
 End mesh
 
 
 #-----------------------------------------------------------
-#                          Mesh #3 
+#                   INNER MESH DEFINITION 
 #-----------------------------------------------------------
 Define mesh:
   Element size: 0.003 

input/08_thin_fracture.para

@@ -0,0 +1,53 @@
+#===========================================================
+#                         TQMESH
+#===========================================================
+
+#-----------------------------------------------------------
+#                     MESH DEFINITION
+#-----------------------------------------------------------
+Define mesh:
+  Element size: 4
+  Element color: 1
+  Meshing algorithm: Tri-to-Quad
+  Number of quad refinements: 1
+  Smooth quad layers: 0
+  Number of smoothing iterations: 3
+
+  # Output formats: COUT, TXT, VTU
+  Output file format: VTU
+  Output file prefix: ./thin_fracture
+
+  #---------------------------------------------------------
+  #                        BOUNDARIES
+  #---------------------------------------------------------
+  Define boundary vertices:
+     55.00,   -140.0000
+     90.00,   -140.0000
+     90.00,   -110.0000
+     55.00,   -110.0000
+    77.03125, -134.0878,  0.1, 0.035 
+    77.04852, -134.0778,  0.1, 0.035 
+    68.49935, -119.4510,  0.1, 0.035 
+    68.48208, -119.4611,  0.1, 0.035 
+  End boundary vertices
+
+  Define exterior boundary edges:
+    0, 1,    1
+    1, 2,    2
+    2, 3,    3
+    3, 0,    4
+  End exterior boundary edges
+
+  Define interior boundary edges:
+    4, 7,    5
+    7, 6,    5
+    6, 5,    5
+    5, 4,    5
+  End interior boundary edges
+
+  #---------------------------------------------------------
+  #                       QUAD-LAYERS
+  #---------------------------------------------------------
+  Add quad layers: 77.03125, -134.0878, 77.03125, -134.0878, 2, 0.1, 1.3
+
+End mesh