Paraview live view tutorial

_data/tutorials.yml

@@ -54,6 +54,10 @@
   - Unsteady_Shape_Opt_NACA0012
   - Species_Transport
 
+- title: Workflow Setup
+  tutorials:
+  - paraview_live
+
 - title: Event Content
   tutorials:
   - event_content

_tutorials/contribute.md

@@ -15,14 +15,14 @@ Do you want to contribute to SU2 with a tutorial? It's easy! Just create a fork
 
 The tutorials in this section of the site are stored under the `_tutorials` folder. To add your contributions:
 
-**1.** Create a new subfolder in `_tutorials/` as `_tutorials/Your_Folder_Name`, where you will store your subgroup of tutorials. You can also add your conribution to an existing folder if it fits better within the existing structure.
+**1.** Create a new subfolder in `_tutorials/` as `_tutorials/Your_Folder_Name`, where you will store your subgroup of tutorials. You can also add your contribution to an existing folder if it fits better within the existing structure.
 
 **2.** Add a new Markdown file inside the subfolder, as `_tutorials/Your_Folder_Name/Your_Tutorial.md`. Add the following [front matter](https://jekyllrb.com/docs/frontmatter/) to your file:
 
 ```
 ---
 title: Your Tutorial Title
-permalink: /docs/Your_Folder_Name/Your_Tutorial/
+permalink: /tutorials/Your_Folder_Name/Your_Tutorial/
 ---
 
 I'm contributing to SU2!
@@ -32,7 +32,7 @@ I'm contributing to SU2!
 
 ```
 - title: Your Subgroup of Tutorials 
-  docs:
+  tutorials:
   - Your_Tutorial
 ```
 

_tutorials/workflow_features/paraview_live/paraview_live.md

@@ -0,0 +1,100 @@
+---
+title: Realtime update of residuals and solution in paraview
+permalink: /tutorials/paraview_live/
+written_by: Nijso Beishuizen
+for_version: 7.5.0
+solver: all
+requires: paraview
+complexity: easy
+---
+
+## Introduction
+
+Often we want to view the solution residuals to see if the solution converges. If the residuals seem to stall or oscillate, this might be an indication that the setup is incorrect. A setting has to be changed or the mesh quality has to be improved to ensure convergence. Sometimes this stalling behavior is temporary, and a look at an intermediate paraview solution can lead to more insight. The intermediate solution can also show if the solution is converging towards the expected solution. In this tutorial we will briefly discuss a paraview setup that will give a live update of the residuals as well as the paraview solution. 
+
+## SU2 Configuration file
+
+We will first discuss some SU2 options that affect our workflow.
+
+The residuals are saved in the history file. The filename is given by the keyword **CONV_FILENAME= history**. Its contents are determined by the keyword **HISTORY_OUTPUT**. We usually store the RMS values of the residuals with the number of iterations, so we set **HISTORY_OUTPUT= ITER RMS_RES**. The file can be saved either in tecplot format or as comma separated values (csv). We use the csv file format because it is very easy to read in paraview. This is the default but can be set explicitly with the keyword **TABULAR_FORMAT= CSV**. The filename  will now be called **history.csv** . The paraview solution is written every x iterations in the filename given by **VOLUME_FILENAME** and x depends on the value of **OUTPUT_WRT_FREQ**. You can save a (2D or 3D) paraview solution using either **OUTPUT_FILES= PARAVIEW** with the extension (suffix) *.vtu* or **OUTPUT_FILES= PARAVIEW_MULTIBLOCK** with extension *.vtm*. To summarize, the following settings are recommended for the paraview live update:
+
+```bash
+TABULAR_FORMAT= CSV
+CONV_FILENAME= history
+OUTPUT_FILES= RESTART, PARAVIEW, PARAVIEW_MULTIBLOCK
+OUTPUT_WRT_FREQ= 100, 10, 10
+VOLUME_FILENAME= flow
+VOLUME_OUTPUT= RESIDUAL, PRIMITIVE, SOLUTION
+HISTORY_OUTPUT= ITER, RMS_RES
+```
+
+## Paraview setup
+
+The paraview live update will simply reload the contents of these files every x seconds, where x is a user defined value. If you haven't installed paraview yet, you can download the latest version here:
+
+[paraview download](https://www.paraview.org/download/)
+
+We open paraview and add a new source. Choose *Live Programmable Source*.
+
+Then choose the *Output Data Set Type* from the list. If you save a regular paraview file, the output filename ends with *.vtu*. Then choose *vtkUnstructuredGrid*. If you save a multiblock paraview file that has the extension *.vtm*, then choose vtkMultiBlockDataSet.
+
+In the *Script* section, copy the following python script:
+
+```python
+# .vtu paraview
+from paraview.vtk.vtkIOXML import vtkXMLUnstructuredGridReader as vtuReader 
+reader = vtuReader() 
+reader.SetFileName('flow.vtu') 
+reader.Update() 
+self.GetOutputDataObject(0).ShallowCopy(reader.GetOutput())
+```
+
+or for a multiblock paraview file:
+
+```python
+# .vtm multiblock
+from paraview.vtk.vtkIOXML import vtkXMLMultiBlockDataReader as vtmreader
+vtmreader = vtmreader()
+vtmreader.SetFileName('flow.vtm')
+vtmreader.Update()
+self.GetOutputDataObject(0).ShallowCopy(vtmreader.GetOutput())
+```
+
+The only thing you need to change here is the filename. Note that this script assumes that you have started paraview in the directory where the paraview filename can be found. The section *Script (RequestInformation)* can be left empty. In the next section, called *Script (CheckNeedsUpdate)*, write the following:
+
+```python
+import time 
+# the update frequency is 30 seconds
+UpdateFrequency = 30
+if not hasattr(self, "_my_time"): 
+  setattr(self, "_my_time", time.time()) 
+
+t = time.time() 
+lastTime = getattr(self, "_my_time") 
+
+if t - lastTime > UpdateFrequency: 
+  setattr(self, "_my_time", t) 
+  self.SetNeedsUpdate(True)
+```
+
+And that's it! You now have a paraview viewer that automatically reads the paraview solution file every 30 seconds! Below the script section you can choose as coloring one of the solution fields, as with a regular paraview session.
+
+You can create a similar setup for the history file to view the residuals. We therefore create a second *Live Programmable Source*. We can keep the *CheckNeedsUpdate* block the same, but since this file gets updated every iteration, we can change the frequency to a lower value, for instance 5 seconds. To load the history file, we set the *Output Data Set Type* to *vtkTable* and add the following code to the *Script* block:
+
+```python
+import numpy as np 
+import pandas as pd 
+
+data = pd.read_csv("history.csv",sep=',') 
+print(data.keys()) 
+print(len(data.columns)) 
+for name in data.keys(): 
+  array = data[name].to_numpy() 
+  output.RowData.append(array, name)
+```
+
+If you now create 2 RenderView windows next to each other (either use *Split Horizontal axis* or use *Split Vertical Axis*) you can visualize the contour in one window and the residuals in the second window. Make sure that when you create the viewing window for the line plot, it is set to *Line Chart View*. The contour plot window uses the default *Render View*. You can now select the residuals from the *Series Parameters* list.
+
+![Screenshot of the setup](../../tutorials_files/workflow_features/paraview_live/images/screenshot_paraview_live.png) 
+Figure (1): screenshot of the paraview live setup.
+