Add cylinder manifold (#1167)

Description
Added cylindrical manifold option to manifolds.cc.
Modified the parameter file input (arg1, arg2, ... arg6 became point coordinates and vector coordinates).
Added a some documentation to explain how the manifold subsection works.
Coarsest meshes were too coarse and lead to geometrical errors even when refined. A manifold makes it possible for the refinements to follow a particular geometry.

Testing
New 3D application test using a cylinder manifold.

Documentation
Modified existing simulation parameters which were unclear. Manifolds can now be described with a center point (spherical/cylindrical) and a direction vector (cylindrical)

Former-commit-id: dabcf1f

CHANGELOG.md

@@ -3,6 +3,12 @@
 All notable changes to the Lethe project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/).
 
+## [Master] - 2024-06-05
+
+### Added
+
+- MINOR A cylindrical manifold type has been added in the manifold parameter file option. Input arguments arg1, arg2, arg3, etc. used to describe the manifold geometry were modified to point coordinates and direction vector. A manifold section has been added to the documentation [#1167](https://github.com/chaos-polymtl/lethe/pull/1167)
+
 ## [Master] - 2024-05-27
 
 ### Changed

applications_tests/lethe-fluid/CMakeLists.txt

@@ -7,6 +7,7 @@ file(COPY square.msh DESTINATION "${CMAKE_CURRENT_BINARY_DIR}")
 file(COPY cylinder_structured.msh DESTINATION "${CMAKE_CURRENT_BINARY_DIR}")
 file(COPY taylorCouette.msh DESTINATION "${CMAKE_CURRENT_BINARY_DIR}")
 file(COPY box.msh DESTINATION "${CMAKE_CURRENT_BINARY_DIR}")
+file(COPY cylinder_manifold.msh DESTINATION "${CMAKE_CURRENT_BINARY_DIR}")
 
 file(COPY cavity_ht_average_velocity_restart_files/restart.averagevelocities DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/cavity_ht_average_velocity_restart.${_build_type}/mpirun=1/")
 file(COPY cavity_ht_average_velocity_restart_files/restart.pvdhandler DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/cavity_ht_average_velocity_restart.${_build_type}/mpirun=1/")

applications_tests/lethe-fluid/cylinder_manifold.mpirun=2.output

@@ -0,0 +1,12 @@
+Running on 2 MPI rank(s)...
+   Number of active cells:       80
+   Number of degrees of freedom: 500
+   Volume of triangulation:      2.83
+Pressure drop: 0 Pa
+Total pressure drop: 0 Pa
+
+*****************************
+Steady iteration:        1/1
+*****************************
+Pressure drop: 5.07 Pa
+Total pressure drop: 5.03 Pa

applications_tests/lethe-fluid/cylinder_manifold.msh

@@ -0,0 +1,68 @@
+$MeshFormat
+2.2 0 8
+$EndMeshFormat
+$Nodes
+24
+ 1 -1 0 0
+ 2 -6.123233995736766e-17 0 1
+ 3 1 0 1.224646799147353e-16
+ 4 1.83697019872103e-16 0 -1
+ 5 0.5 0 0
+ 6 0 0 0.5
+ 7 0 0 -0.5
+ 8 -0.5 0 0
+ 9 -6.123233995736766e-17 1 1
+10 0 1 0.5
+11 0 0.5 0.5
+12 -6.123233995736766e-17 0.5 1
+13 0.5 1 0
+14 0.5 0.5 0
+15 0 1 -0.5
+16 0 0.5 -0.5
+17 -0.5 1 0
+18 -0.5 0.5 0
+19 -1 1 0
+20 -1 0.5 0
+21 1 1 1.224646799147353e-16
+22 1 0.5 1.224646799147353e-16
+23 1.83697019872103e-16 1 -1
+24 1.83697019872103e-16 0.5 -1
+$EndNodes
+$Elements
+28
+ 1  5 2 1 1  2  6  8  1 12 11 18 20
+ 2  5 2 1 1  6  5  7  8 11 14 16 18
+ 3  5 2 1 1 12 11 18 20  9 10 17 19
+ 4  5 2 1 1 11 14 16 18 10 13 15 17
+ 5  5 2 1 1  2  3  5  6 12 22 14 11
+ 6  5 2 1 1  3  4  7  5 22 24 16 14
+ 7  5 2 1 1  4  1  8  7 24 20 18 16
+ 8  5 2 1 1 12 22 14 11  9 21 13 10
+ 9  5 2 1 1 22 24 16 14 21 23 15 13
+10  5 2 1 1 24 20 18 16 23 19 17 15
+11  3 2 2 2  2  1 20 12
+12  3 2 2 2 12 20 19  9
+13  3 2 2 2  2 12 22  3
+14  3 2 2 2 12  9 21 22
+15  3 2 2 2  3 22 24  4
+16  3 2 2 2 22 21 23 24
+17  3 2 2 2  4 24 20  1
+18  3 2 2 2 24 23 19 20
+19  3 2 3 3  6  5  7  8
+20  3 2 3 3  2  6  8  1
+21  3 2 3 3  4  1  8  7
+22  3 2 3 3  3  4  7  5
+23  3 2 3 3  2  3  5  6
+24  3 2 4 4  9 19 17 10
+25  3 2 4 4 10 17 15 13
+26  3 2 4 4  9 10 13 21
+27  3 2 4 4 21 13 15 23
+28  3 2 4 4 23 15 17 19
+$EndElements
+$PhysicalNames
+4
+3 1 "Unspecified"
+2 2 "cylinder-manifold"
+2 3 "inlet"
+2 4 "outlet"
+$EndPhysicalNames

applications_tests/lethe-fluid/cylinder_manifold.prm

@@ -0,0 +1,99 @@
+# Listing of Parameters
+#----------------------
+
+set dimension = 3
+
+#---------------------------------------------------
+# Simulation Control
+#---------------------------------------------------
+
+subsection simulation control
+  set method            = steady
+  set output name       = output
+  set output frequency  = 0
+  set log precision     = 3
+end
+
+#---------------------------------------------------
+# Mesh
+#---------------------------------------------------
+
+subsection mesh
+  set type               = gmsh
+  set file name          = ../../cylinder_manifold.msh
+  set initial refinement = 1
+end
+
+#---------------------------------------------------
+# Boundary Conditions
+#---------------------------------------------------
+
+subsection boundary conditions
+  set number = 3
+  subsection bc 0
+    set id   = 2
+    set type = noslip
+  end
+  subsection bc 1
+    set id   = 4
+    set type = outlet
+  end
+  subsection bc 2
+    set id   = 3
+    set type = function
+    subsection u
+      set Function expression = 0
+    end
+    subsection v
+      set Function expression = 1
+    end
+  end
+end
+
+#---------------------------------------------------
+# Non-Linear Solver Control
+#---------------------------------------------------
+
+subsection non-linear solver
+  subsection fluid dynamics
+    set tolerance = 1e-12
+    set verbosity = quiet
+  end
+end
+
+#---------------------------------------------------
+# Linear Solver Control
+#---------------------------------------------------
+
+subsection linear solver
+  subsection fluid dynamics
+    set verbosity = quiet
+  end
+end
+
+#---------------------------------------------------
+# Manifolds
+#---------------------------------------------------
+
+subsection manifolds
+    set number = 1
+    subsection manifold 0
+        set id = 2
+        set type = cylindrical
+    end
+end
+
+#---------------------------------------------------
+# Post-processing
+#---------------------------------------------------
+
+subsection post-processing
+  set verbosity                        = verbose
+  set output frequency                 = 1
+
+  # Pressure drop calculation
+  set calculate pressure drop          = true
+  set pressure drop name               = cylinder_manifold_pressure_drop
+  set inlet boundary id                = 3
+  set outlet boundary id               = 4
+end

applications_tests/lethe-fluid/taylorcouette-unstructured_gls.prm

@@ -101,14 +101,12 @@ subsection manifolds
   subsection manifold 0
     set id   = 0
     set type = spherical
-    set arg1 = 0
-    set arg2 = 0
+    set point coordinates = 0,0
   end
   subsection manifold 1
     set id   = 1
     set type = spherical
-    set arg1 = 0
-    set arg2 = 0
+    set point coordinates = 0,0
   end
 end
 

doc/source/examples/incompressible-flow/2d-flow-around-cylinder/2d-flow-around-cylinder.rst

@@ -114,15 +114,19 @@ All the deal.II meshes supported by Lethe that correspond to the `GridGenerator
       subsection manifold 0
         set id   = 0
         set type = spherical
-        set arg1 = 8
-        set arg2 = 8
+        set point coordinates = 8, 8
       end
     end
 
 
-First the number of manifolds is specified by the ``set number`` command. Then a subsection for each of the manifolds is created starting with the ``manifold 0``. The boundary ``id`` is in this case set to ``0`` as we want to set a cylinder manifold and this is the corresponding id in this example. Then the ``type`` of the manifold is specified. In Lethe, there are two types supported:
+First the number of manifolds is specified by the ``set number`` command. Then a subsection for each of the manifolds is created starting with the ``manifold 0``. The boundary ``id`` is in this case set to ``0`` as we want to set a spherical manifold and this is the corresponding id in this example. Then the ``type`` of the manifold is specified. In Lethe, there are three types supported:
 
-* ``spherical`` manifold: The former can be used to describe any sphere, circle, hypesphere or hyperdisc in two or three dimensions and requires as arguments two or three geometrical locations depending on the dimension, that are used to create the circle center where the manifold will be build. In this example we set ``arg1`` and ``arg2`` to ``8``. 
+* ``spherical`` manifold: The former can be used to describe any sphere, circle, hypesphere or hyperdisc in two or three dimensions and requires the center of the geometry as an input argument. In this example we set ``point coordinates`` to ``8, 8``.
+
+* ``cylindrical`` manifold: Used to describe cylinders in three dimensions. It uses the coordinates of a point and a direction vector located on the axis of the cylinder.
+
+  .. caution::
+    Cylindrical manifolds are not supported in 2D.
 
 * ``iges`` manifold corresponding to a CAD geometry: the last two lines of the ``manifold 0`` subsection are replaced by the following command ``set cad file = file_name.iges`` where the path to the cad file is specified. 
 

doc/source/parameters/cfd/cfd.rst

@@ -20,6 +20,7 @@ General, CFD and Multiphysics
    initial_conditions
    laser_heat_source
    linear_solver_control
+   manifolds
    mesh
    mesh_adaptation_control
    multiphysics

doc/source/parameters/cfd/manifolds.rst

@@ -0,0 +1,64 @@
+==========
+Manifolds
+==========
+Linking parts of the mesh to manifolds is an interesting way to factor the real geometry of the mesh during refinements. This mesh treatment can lead to reduced geometric approximation error.
+
+.. code-block:: text
+
+  subsection manifolds
+
+    # Sets the total number of specified manifolds
+    set number = 0
+
+    subsection manifold 0
+
+        # Boundary mesh id specified in the .gmsh file
+        set id                 = 0
+
+        # Type of manifold. Choices are <spherical|cylindrical|iges|none>
+        set type               = none
+
+        # Center of the sphere or a point along the cylinder's axis (x, y, z)
+        set point coordinates  = 0, 0, 0  #for 2D, set point coordinates = 0, 0
+
+        # Direction vector used only for the cylinder (x, y, z)
+        set direction vector   = 0, 1, 0
+
+    end
+
+  end
+
+First the number of manifolds is specified by the ``set number`` command. Then a subsection for each of the manifolds is created starting with the ``manifold 0``. The boundary ``id`` is in this case set to ``0`` corresponding to the mesh boundary to which the manifold will be applied. Then the ``type`` of the manifold is specified.
+
+* Lethe supports three types of manifolds:
+
+  * ``spherical`` manifold: The former can be used to describe any sphere, circle, hypesphere or hyperdisc in two or three dimensions and requires the center of the geometry to set the manifold.
+  * ``cylindrical`` manifold: Used to describe cylinders in three dimensions. It uses the coordinates of a point and a direction vector located on the axis of the cylinder.
+
+    .. caution::
+        Cylindrical manifolds are not supported in 2D.
+
+  * ``iges``: manifold corresponding to a CAD geometry: the last two lines of the ``manifold 0`` subsection are replaced by the following command ``set cad file = file_name.iges`` where the path to the cad file is specified.
+
+.. note::
+    For more information about manifolds and the reasons behind them, we invite you to read the documentation page of deal.II: `Manifold description for triangulations <https://www.dealii.org/developer/doxygen/deal.II/group__manifold.html>`_.
+
+------------------------
+Understanding Manifolds
+------------------------
+
+We can clearly see that the geometry is more similar to an octagon than to a circle. This is a problem because the cells composing the mesh are not aware that they should morph to shape a cylinder. After every refinement, an extra node is added between the existing nodes in order to generate new cells. The octagonal shape is therefore conserved as it is illustrated below:
+
+A really coarse mesh of a cylinder viewed from the top looks like this:
+
+.. image:: images/coarse_cylinder.png
+    :align: center
+    :width: 400
+
+Manifolds are added to the geometry in order to solve this issue. Using a point and a direction vector along the axis of the cylinder, the cells of a part of the mesh are restricted to respect a certain geometry while refining the mesh. On the image below, the geometry on the left is obtained by adding a cylindrical manifold to the mesh. The geometry on the right is obtained if no manifold are specified.
+
+.. image:: images/fine_cylinder_manifold.png
+    :align: center
+    :width: 800
+
+

examples/incompressible-flow/2d-flow-around-cylinder/cylinder.prm

@@ -111,8 +111,7 @@ subsection manifolds
   subsection manifold 0
     set id   = 0
     set type = spherical
-    set arg1 = 8
-    set arg2 = 8
+    set point coordinates = 8, 8
   end
 end
 

examples/incompressible-flow/2d-transient-flow-around-cylinder/cylinder.prm

@@ -122,8 +122,7 @@ subsection manifolds
   subsection manifold 0
     set id   = 0
     set type = spherical
-    set arg1 = 8
-    set arg2 = 8
+    set point coordinates = 8,8
   end
 end
 

examples/incompressible-flow/3d-flow-around-sphere/sphere-0.1.prm

@@ -99,9 +99,7 @@ subsection manifolds
   subsection manifold 0
     set id   = 0
     set type = spherical
-    set arg1 = 0 # Co-ordinates of sphere centre
-    set arg2 = 0
-    set arg3 = 0
+    set point coordinates = 0,0,0
   end
 end
 

examples/incompressible-flow/3d-flow-around-sphere/sphere-150.prm

@@ -112,9 +112,7 @@ subsection manifolds
   subsection manifold 0
     set id   = 0
     set type = spherical
-    set arg1 = 0 # Co-ordinates of sphere centre
-    set arg2 = 0
-    set arg3 = 0
+    set point coordinates = 0, 0, 0
   end
 end
 

examples/incompressible-flow/3d-flow-around-sphere/sphere-adapt.prm

@@ -112,9 +112,7 @@ subsection manifolds
   subsection manifold 0
     set id   = 0
     set type = spherical
-    set arg1 = 0 # Co-ordinates of sphere centre
-    set arg2 = 0
-    set arg3 = 0
+    set point coordinates = 0,0,0
   end
 end