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added 2d example for edge and vertex connectivity
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project-fluxo-old committed Nov 22, 2023
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65 changes: 47 additions & 18 deletions docs/documentation/userguide/meshformat.md
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Expand Up @@ -57,31 +57,34 @@ name: tab:mesh_file_attributes
| Ngeo $\geq 1$ | INTEGER | Polynomial degree $N_{geo}$ of element mapping, used to determine the number of nodes per element |
| nElems | INTEGER | Total number of elements in mesh |
| nSides | INTEGER | Total number of sides (or element faces) in file |
| nEdges? | INTEGER | Total number of edges in file |
| nNodes | INTEGER | Total number of nodes in file |
| nEdges? | INTEGER | Total number of entries in the EdgeInfo array |
| nVertices? | INTEGER | Total number of entries in the VertexInfo array |
| nNodes | INTEGER | Total number of nodes in file |
| nUniqueSides | INTEGER | Total number of geometrically unique sides in the mesh |
| nUniqueEdges? | INTEGER | Total number of geometrically unique edges in the mesh
| nUniqueEdges? | INTEGER | Total number of geometrically unique edges in the mesh |
| nUniqueNodes | INTEGER | Total number of geometrically unique nodes in the mesh |
| nBCs | INTEGER | Size of the Boundary Condition list |
| nFEMSides? | INTEGER | Total number of topologically (includes periodicity) unique sides in the mesh, needed for a FEM solver |
| nFEMEdges? | INTEGER | Total number of topologically (includes periodicity) unique edges in the mesh, needed for a FEM solver
| nFEMNodes? | INTEGER | Total number of topologically (includes periodicity) unique nodes in the mesh, needed for a FEM solver |
| nFEMSides? | INTEGER | Total number of topologically (includes periodicity) unique sides in the mesh, needed for a FEM solver |
| nFEMEdges? | INTEGER | Total number of topologically (includes periodicity) unique edges in the mesh, needed for a FEM solver |
| nFEMNodes? | INTEGER | Total number of topologically (includes periodicity) unique nodes in the mesh, needed for a FEM solver |
```

### Data Arrays
The mesh information is organized in arrays. The **ElemInfo** array is the first to read, since it contains the data range of each
element in the **SideInfo**, **EdgeInfo**,**VertexInfo** and **NodeCoords** / **GlobalNodeIDs** arrays.
element in the **SideInfo**, **EdgeInfo**, **EdgeConnectInfo**,**VertexInfo**,**VertexConnectInfo** and **NodeCoords** / **GlobalNodeIDs** arrays.

```{table} List of all data arrays in mesh file. Dimensions marked with $^*$ will be distributed in parallel read mode.
---
name: tab:mesh_data_arrays
---
| **Array Name** | **Description** | **Type** | **Size** |
| :-------------------------- | :----------------------- | :--------------- | :--------------- |
| **ElemInfo** | Start \ | End positions of element data in SideInfo / EdgeInfo / VertexInfo / NodeCoords | INTEGER & (1:10?,1:**nElems**$^*$) |
| **SideInfo** | Side Data / Connectivity information | INTEGER | (1:5,1:**nSides**$^*$) |
| **EdgeInfo?** | Element Edge Data / Connectivity information | INTEGER | (1:?,1:**nEdges**$^*$) |
| **VertexInfo?** | Element Vertex Data / Connectivity information (needed for a FEM solver) | INTEGER | (1:?,1:**nNodes**$^*$) |
| **ElemInfo** | Start \ | End positions of element data in SideInfo / EdgeInfo / VertexInfo / NodeCoords | INTEGER & (1:10,1:**nElems**$^*$) |
| **SideInfo** | Side Data / Connectivity information | INTEGER | (1:5,1:**nSides**$^*$) |
| **EdgeInfo?** | Element Edge information and offsets in EdgeConnectInfo | INTEGER | (1:?,1:**nEdges**$^*$) |
| **EdgeConnectInfo?** | Element Edge Connectivity information (needed for a FEM solver) | INTEGER | (1:?,1:**??**$^*$) |
| **VertexInfo?** | Element Vertex Data information and and offsets in EdgeConnectInfo | INTEGER | (1:?,1:**nNodes**$^*$) |
| **VertexConnectInfo?** | Element Vertex Connectivity information (needed for a FEM solver) | INTEGER | (1:?,1:**??**$^*$) |
| **NodeCoords** | Node Coordinates | REAL | (1:3,1:**nNodes**$^*$) |
| **GlobalNodeIDs** | Globally unique node index | INTEGER | (1:**nNodes**$^*$) |
| BCNames | List of user-defined boundary condition names (max. 255 Characters) | STRING | (1:**nBCs**) |
Expand Down Expand Up @@ -130,7 +133,7 @@ name: tab:elem_info
| | |
| :--- | :--- |
| Name in file: | **ElemInfo** |
| Type: | INTEGER, Size: Array(1:6,1:**nElems**$^*$) |
| Type: | INTEGER, Size: Array(1:10,1:**nElems**$^*$) |
| Description: | Array containing elements, one element per row, **row number is elemID**. |
```

Expand All @@ -139,12 +142,12 @@ However, this way, each processor has a defined, non overlapping, range of side
operations, minimizing the need of communication between processors.


| | *Element Type* | *Zone* | *offsetIndSIDE* | *lastIndSIDE* | *offsetIndNODE* | *lastIndNODE* |
| - | - | - | - | - | - | - |
| 1 | 116 | 1 | 0 | 5 | 0 | 6 |
| 2 | 118 | 1 | 5 | 11 | 6 | 14 |
| 3 | 104 | 2 | 11 | 15 | 14 | 18 |
| 4 | 115 | 2 | 15 | 20 | 18 | 23 |
| | *Element Type* | *Zone* | *offsetIndSIDE* | *lastIndSIDE* | *offsetIndNODE* | *lastIndNODE* |*offsetIndEDGE* | *lastIndEDGE* |*offsetIndVERTEX* | *lastIndVERTEX* |
| - | - | - | - | - | - | - | - | - | - | - |
| 1 | 116 | 1 | 0 | 5 | 0 | 6 | 0 | ??? | 0 | ??? |
| 2 | 118 | 1 | 5 | 11 | 6 | 14 | ??? | ??? | ??? | ??? |
| 3 | 104 | 2 | 11 | 15 | 14 | 18 | ??? | ??? | ??? | ??? |
| 4 | 115 | 2 | 15 | 20 | 18 | 23 | ??? | ??? | ??? | ??? |

The example mesh {numref}`fig:exmesh` with 4 elements is summarized in table {numref}`tab:elem_info_array`.

Expand All @@ -158,6 +161,8 @@ name: tab:elem_info_array
| *Zone*: | Element group number. |
| *offsetIndSIDE/lastIndSIDE*: | Each element has a range of sides in the **SideInfo** array. |
| *offsetIndNODE/lastIndNODE*: | Each element has a range of node coordinates in the **NodeCoords** array and **GlobalNodeIDs** array for unique indices. |
| *offsetIndEDGE/lastIndEDGE*: | Each element has a range of edges in the **EdgeInfo** array. |
| *offsetIndVERTEX/lastIndVERTEX*: | Each element has a range of edges in the **VertexInfo** array. |
```

The range and the size are always defined as: *Range=[offset+1,last], Size=last-offset*
Expand Down Expand Up @@ -219,6 +224,30 @@ name: tab:side_info_array
| *BCID*: | Refers to the row index of the Boundary Condition List in **BCNames**/**BCType** array ($\in[1,\dots\text{\texttt{nBCs}}]$). $=0$ for inner sides. Note that $\neq 0$ for periodic and inner boundary conditions, while nbElemID and nbLocSide+Flip are given, see Section {ref}`userguide/meshformat:Boundary Conditions`. |
```

#### Edge Information (EdgeInfo)
```{table} Side Information
---
name: tab:edge_info
---
| | |
| :--- | :--- |
| Name in file: | **EdgeInfo** |
| Type: | INTEGER, Size: Array(1:?,1:**nEdges**$^*$) |
| Description: | Side array, all information of one element is a set of all element sides (CGNS ordering, \rf{fig:CGNS}). |
| | *offsetIndSIDE/lastIndSIDE*in **ElemInfo** refers to the row index of one set of element sides. |
```


```{figure} figures/2d_edge_vertex_connectivity_example.jpg
---
name: fig:exmesh2d
width: 800px
align: center
---
Example 2D mesh with periodic BC, local, unique node IDs and **FEMVertexID** (circles,ellipses) and local, unique edge IDs and their FEMEdgeIDs (trapezoid)
```

#### Node Coordinates and Global Index

```{table} NodeCoords
Expand Down

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