Add Python code for couple your code section

Author: kss682

pages/docs/couple-your-code/couple-your-code-defining-mesh-connectivity.md

@@ -14,6 +14,12 @@ For surface coupling in 2D, mesh connectivity boils down to defining edges betwe
 For volume coupling in 2D, mesh connectivity boils down to defining triangles and / or quads between vertices. In 3D, you need to define tetrahedra introduced in version `2.5.0`.
 
 All kind of connectivity can be built up directly from vertices. Triangles and quads also allow us to define them using edge IDs.
+<ul id="apiTabs" class="nav nav-tabs">
+    <li class="active"><a href="#cpp-1" data-toggle="tab">C++</a></li>
+    <li><a href="#python-1" data-toggle="tab">Python</a></li>
+</ul>
+<div class="tab-content">
+<div role="tabpanel" class="tab-pane active" id="cpp-1" markdown="1">
 
 ```cpp
 void setMeshEdge(precice::string_view meshName, VertexID firstVertexID, VertexID secondVertexID);
@@ -22,7 +28,25 @@ void setMeshQuad(precice::string_view meshName, VertexID firstVertexID, VertexID
 void setMeshTetrahedron(precice::string_view meshName, VertexID firstVertexID, VertexID secondVertexID, VertexID thirdVertexID, VertexID fourthVertexID);
 ```
 
+</div>
+<div role="tabpanel" class="tab-pane" id="python-1" markdown="1">
+
+```python
+set_mesh_edge(mesh_name, first_vertex_id, second_vertex_id)
+set_mesh_triangle(mesh_name, first_vertex_id, second_vertex_id, third_vertex_id)
+set_mesh_quad(mesh_name, first_vertex_id, second_vertex_id, third_vertex_id, fourth_vertex_id)
+set_mesh_tetrahedron(mesh_name, first_vertex_id, second_vertex_id, third_vertex_id, fourth_vertex_id)    
+```
+
+</div>
+</div>
 There are also bulk versions of these methods, which can be easier to handle in some cases:
+<ul id="apiTabs" class="nav nav-tabs">
+    <li class="active"><a href="#cpp-2" data-toggle="tab">C++</a></li>
+    <li><a href="#python-2" data-toggle="tab">Python</a></li>
+</ul>
+<div class="tab-content">
+<div role="tabpanel" class="tab-pane active" id="cpp-2" markdown="1">
 
 ```cpp
 void setMeshEdges(precice::string_view meshName, precice::span<const VertexID> vertices);
@@ -31,12 +55,39 @@ void setMeshQuads(precice::string_view meshName, precice::span<const VertexID> v
 void setMeshTetrahedra(precice::string_view meshName, precice::span<const VertexID> vertices);
 ```
 
+</div>
+<div role="tabpanel" class="tab-pane" id="python-2" markdown="1">
+
+```python
+set_mesh_edges(mesh_name, vertices)
+set_mesh_triangles(mesh_name, vertices)
+set_mesh_quads(mesh_name, vertices)
+set_mesh_tetrahedra(mesh_name, vertices)
+```
+
+</div>
+</div>
 If you do not configure any features in the preCICE configuration that require mesh connectivity, all these API functions are [no-ops](https://en.wikipedia.org/wiki/NOP_(code)). Thus, don't worry about performance. If you need a significant workload to already create this connectivity information in your adapter in the first place, you can also explicitly ask preCICE whether it is required:
+<ul id="apiTabs" class="nav nav-tabs">
+    <li class="active"><a href="#cpp-3" data-toggle="tab">C++</a></li>
+    <li><a href="#python-3" data-toggle="tab">Python</a></li>
+</ul>
+<div class="tab-content">
+<div role="tabpanel" class="tab-pane active" id="cpp-3" markdown="1">
 
 ```cpp
 bool requiresMeshConnectivityFor(precice::string_view meshName);
 ```
 
+</div>
+<div role="tabpanel" class="tab-pane" id="python-3" markdown="1">
+
+```python
+requires_mesh_connectivity_for(mesh_name)   
+```
+
+</div>
+</div>
 {% warning %}
 The API function `isMeshConnectivityRequired` is only supported since v2.3.
 {% endwarning %}
@@ -52,6 +103,12 @@ Quads are only supported since v2.1. For older version, the methods only exist a
 {% endwarning %}
 
 The following code shows how mesh connectivity can be defined in our example. For sake of simplification, let's only define one triangle and let's assume that it consists of the first three vertices.
+<ul id="apiTabs" class="nav nav-tabs">
+    <li class="active"><a href="#cpp-4" data-toggle="tab">C++</a></li>
+    <li><a href="#python-4" data-toggle="tab">Python</a></li>
+</ul>
+<div class="tab-content">
+<div role="tabpanel" class="tab-pane active" id="cpp-4" markdown="1">
 
 ```cpp
 /* ... */
@@ -83,6 +140,30 @@ if (precice.requiresMeshConnectivityFor(meshName)) {
 /* ... */
 ```
 
+</div>
+<div role="tabpanel" class="tab-pane" id="python-4" markdown="1">
+
+```python
+# We define the unit square in 2D with vertices A, B, C, D
+coords = np.array([[0, 0], [0, 1], [1, 0], [1, 1]])
+vertex_ids = precice.set_mesh_vertices(mesh_name, coords)
+
+if precice.requires_mesh_connectivity_for(mesh_name):
+
+  # Define triangles ABC and BCD separately
+  precice.set_mesh_triangle(mesh_name, vertex_ids[0], vertex_ids[1],  vertex_ids[2])
+  precice.set_mesh_triangle(mesh_name, vertex_ids[1], vertex_ids[2],  vertex_ids[3])
+
+  # Define triangles in one go
+  triangles = np.array([
+    [vertex_ids[0], vertex_ids[1],  vertex_ids[2]],
+    [vertex_ids[1], vertex_ids[2],  vertex_ids[3]]
+  ])
+  precice.set_mesh_triangles(mesh_name, triangles)
+```
+
+</div>
+</div>
 ## Mesh pre-processing
 
 preCICE pre-processes all provided meshes during initialization, removing duplicates and adding missing hierarchical elements.
@@ -109,6 +190,12 @@ In this case you can save a mapping from Solver ID to preCICE Vertex ID, after d
 When iterating over the faces, get the vertex identifiers of defining points.
 For triangular faces, these would be the 3 corner points.
 Then map these Solver IDs to preCICE IDs, and use those to define your connectivity.
+<ul id="apiTabs" class="nav nav-tabs">
+    <li class="active"><a href="#cpp-5" data-toggle="tab">C++</a></li>
+    <li><a href="#python-5" data-toggle="tab">Python</a></li>
+</ul>
+<div class="tab-content">
+<div role="tabpanel" class="tab-pane active" id="cpp-5" markdown="1">
 
 ```cpp
 Participant participant(...);
@@ -131,6 +218,30 @@ for (auto& tri: solver.triangularFaces) {
 }
 ```
 
+</div>
+<div role="tabpanel" class="tab-pane" id="python-5" markdown="1">
+
+```python
+participant = precice.Participant(...)
+
+id_maps = dict()
+for vertex in solver.vertices:
+  vertex_id = participant.set_mesh_vertex("MyMesh", vertex.coords)
+  # Set the vertex_id as label
+  id_maps[vertex._id] = vertex_id
+
+for tri in solver.triangular_faces:
+  # Lookup the precice vertex id using solver vertex id
+  a = id_maps.get(tri.a._id)
+  b = id_maps.get(tri.b._id)
+  c = id_maps.get(tri.c._id)
+
+  participant.set_mesh_triangle(mesh_name, a, b, c)
+```
+
+</div>
+</div>
+
 ### Solver supports custom attributes
 
 You solver doesn't provide a unique identifier for each vertex.
@@ -145,6 +256,12 @@ Examples of such attributes:
 In this case you can save preCICE Vertex IDs as labels directly in the solver vertices.
 Define the vertices using the preCICE API, then iterate over them and apply the preCICE vertex IDs as labels.
 When iterating over faces, get the preCICE vertex IDs from the point labels, and use those to define your connectivity.
+<ul id="apiTabs" class="nav nav-tabs">
+    <li class="active"><a href="#cpp-6" data-toggle="tab">C++</a></li>
+    <li><a href="#python-6" data-toggle="tab">Python</a></li>
+</ul>
+<div class="tab-content">
+<div role="tabpanel" class="tab-pane active" id="cpp-6" markdown="1">
 
 ```cpp
 Participant participant(...);
@@ -164,6 +281,27 @@ for (auto& tri: solver.triangularFaces) {
 }
 ```
 
+</div>
+<div role="tabpanel" class="tab-pane" id="python-6" markdown="1">
+
+```python
+participant = precice.Participant(...)
+
+for vertex in solver.vertices:
+  vertex_id = participant.set_mesh_vertex("MyMesh", vertex.coords)
+  vertex.label = vertex_id
+
+for tri in solver.triangular_faces:
+  a = tri.a.label
+  b = tri.b.label
+  c = tri.c.label
+
+  participant.set_mesh_triangle("MyMesh", a, b, c)
+```
+
+</div>
+</div>
+
 ### Solver supports coordinates only
 
 Your solver provides coordinates only or labels are already used for another purpose.
@@ -173,6 +311,12 @@ Depending on your solver, coordinates available at various stages may be subject
 Hence, a C++ `std::map` without custom comparator, or python `dict` may not be sufficient.
 
 An alternative would be to use a spatial index as a data structure to store this information.
+<ul id="apiTabs" class="nav nav-tabs">
+    <li class="active"><a href="#cpp-7" data-toggle="tab">C++</a></li>
+    <li><a href="#python-7" data-toggle="tab">Python</a></li>
+</ul>
+<div class="tab-content">
+<div role="tabpanel" class="tab-pane active" id="cpp-7" markdown="1">
 
 ```cpp
 Participant participant(...);
@@ -224,7 +368,8 @@ class IDLookup {
 };
 ```
 
-In python, you could use the rtree package:
+</div>
+<div role="tabpanel" class="tab-pane" id="python-7" markdown="1">
 
 ```py
 import rtree
@@ -242,3 +387,6 @@ for tri in solver.triangularFaces:
   c = index.nearest(tri.c.coords)
   participant.set_mesh_triangle("MyMesh", a, b, c)
 ```
+
+</div>
+</div>

pages/docs/couple-your-code/couple-your-code-gradient-data.md

@@ -11,6 +11,12 @@ This feature is available since version 2.4.0.
 
 When using `nearest-neighbor-gradient` mapping, we require coupling data and additional gradient data. We have seen in [Step 3](couple-your-code-mesh-and-data-access.html) how to write data to the mesh.
 Now, we will learn how to write gradient data to the mesh. For this purpose, we use the following API method:
+<ul id="apiTabs" class="nav nav-tabs">
+    <li class="active"><a href="#cpp-1" data-toggle="tab">C++</a></li>
+    <li><a href="#python-1" data-toggle="tab">Python</a></li>
+</ul>
+<div class="tab-content">
+<div role="tabpanel" class="tab-pane active" id="cpp-1" markdown="1">
 
 ```cpp
 void writeGradientData(
@@ -20,6 +26,15 @@ void writeGradientData(
     precice::span<const double>   gradients);
 ```
 
+</div>
+<div role="tabpanel" class="tab-pane" id="python-1" markdown="1">
+
+```python
+write_gradient_data(mesh_name, data_name, vertex_ids, gradients)
+```
+
+</div>
+</div>
 Let's consider an example for writing block vector gradient data corresponding to the vector data `v0 = (v0x, v0y) , v1 = (v1x, v1y), ... , vn = (vnx, vny)` differentiated in spatial directions x and y.
 The values are passed as following:
 
@@ -31,12 +46,18 @@ The values are passed as following:
 ```
 
 Let's add gradient data to our example code:
+<ul id="apiTabs" class="nav nav-tabs">
+    <li class="active"><a href="#cpp-2" data-toggle="tab">C++</a></li>
+    <li><a href="#python-2" data-toggle="tab">Python</a></li>
+</ul>
+<div class="tab-content">
+<div role="tabpanel" class="tab-pane active" id="cpp-2" markdown="1">
 
 ```cpp
 precice::Participant precice("FluidSolver", "precice-config.xml", rank, size); // constructor
 
 int meshDim = precice.getMeshDimensions("FluidMesh");
-int dataDim = precice.getMeshDimensions("FluidMesh", "Stress");
+int dataDim = precice.getDataDimensions("FluidMesh", "Stress");
 /* ... */
 precice.setMeshVertices("FluidMesh", coords, vertexIDs);
 
@@ -69,6 +90,42 @@ while (not simulationDone()){ // time loop
 /* ... */
 ```
 
+</div>
+<div role="tabpanel" class="tab-pane" id="python-2" markdown="1">
+
+```python
+precice = precice.Participant("FluidSolver", "precice-config.xml", rank, size)
+
+mesh_dim = precice.get_mesh_dimensions("FluidMesh")
+data_dim = precice.get_data_dimensions("FluidMesh", "Stress")
+
+vertex_ids = precice.set_mesh_vertices("FluidMesh", coords)
+
+stress = np.zeros((vertex_size, data_dim))
+stress_gradient = np.zeros((vertex_size, data_dim, mesh_dim))
+precice.initialize()
+
+while not simulation_done():
+  precice_dt = precice.get_max_time_step_size()
+  solver_dt = begin_time_step()
+  dt = min(precice_dt, solver_dt)
+  displacements = precice.read_data("FluidMesh", "Displacements", vertex_ids, dt)
+  set_displacement(displacements)
+  solve_time_step(dt)
+  stress = compute_stress()
+
+  precice.write_data("FluidMesh", "Stress", vertex_ids, stress)
+
+  if precice.requires_gradient_data_for("FluidMesh", "Stress"):
+    stress_gradient = compute_stress_gradient()
+    precice.write_gradient_data("FluidMesh", "Stress", vertex_ids, stress_gradient)
+
+  precice.advance(dt)
+```
+
+</div>
+</div>
+
 {% experimental %}
 This is an experimental feature.
 {% endexperimental %}