Merge pull request #131 from aeroamit/patch-1

Update Slope-Limiters-and-Shock-Resolution.md

Author: pcarruscag

_data/docs_v7.yml

@@ -30,6 +30,7 @@
   docs_v7:
   - Theory
   - Streamwise-Periodicity
+  - Thermochemical-Nonequilibrium
 
 - title: Users Guide
   docs_v7:

_docs_v7/Custom-Output.md

@@ -218,6 +218,7 @@ The available types are:
 - `Function`: Introduces a new scalar output that is a function of other scalar outputs, it cannot reference fields (e.g. velocity).
 - `AreaAvg` and `AreaInt`: Computes an area average or integral of a field (the expression) over the list of markers.
 - `MassFlowAvg` and `MassFlowInt`: Computes a mass flow average or integral.
+- `Probe`: Evaluates the expression using the values of the mesh point closest to the coordinates specified inside "[]", [x, y] or [x, y, z] (2 or 3D).
 
 **Note:** Each custom output can only use one type, e.g. it is not possible to write `p_drop : AreaAvg{PRESSURE}[inlet] - AreaAvg{PRESSURE}[outlet]`. This would need to be separated into two `AreaAvg` outputs and one `Function` to compute their difference.
 
@@ -226,7 +227,8 @@ The available types are:
 CUSTOM_OUTPUTS= 'velocity : Macro{sqrt(pow(VELOCITY_X, 2) + pow(VELOCITY_Y, 2) + pow(VELOCITY_Z, 2))};\
                  avg_vel : AreaAvg{$velocity}[z_minus, z_plus];\
                  var_vel : AreaAvg{pow($velocity - avg_vel, 2)}[z_minus, z_plus];\
-                 dev_vel : Function{sqrt(var_vel) / avg_vel}'
+                 dev_vel : Function{sqrt(var_vel) / avg_vel};\
+                 probe1 : Probe{$velocity}[0.005, 0.005, 0.05]'
 ```
 
 To obtain the list of solver variables that can be used, write an invalid expression (e.g. 'x : AreaAvg{INVALID}[]') and run SU2.

_docs_v7/Physical-Definition.md

@@ -19,6 +19,7 @@ SU2 offers different ways of setting and computing this definition. This documen
 - [Free-Stream Definition (Thermochemical Nonequilibrium)](#free-stream-definition-thermochemical-nonequilibrium)
   - [Free-Stream Temperatures](#free-stream-temperatures)
   - [Chemical Composition and Mass Fractions](#chemical-composition-and-mass-fractions)
+- [Transport Coefficient Model (Thermochemical Nonequilibrium)](#transport-coefficient-model-thermochemical-nonequilibrium)
 - [Flow Condition (Incompressible)](#flow-condition-incompressible)
   - [Thermodynamic and Gauge Pressure](#thermodynamic-and-gauge-pressure)
   - [Initial State and Non-Dimensionalization](#initial-state-and-non-dimensionalization)
@@ -128,6 +129,18 @@ A chemistry model, consisting of a set of flow species, thermochemical propertie
 
 Free-stream mass fractions must also be specified in list using the option `GAS_COMPOSITION`. The mass fractions are specified as decimal values in the order of the species in the gas model. For example, an AIR-5 mixture of 77% oxygen and 23% nitrogen would be expressed as (0.77, 0.23, 0.00, 0.00, 0.00).
 
+## Transport Coefficient Model (Thermochemical Nonequilibrium) ##
+
+| Solver | Version |
+| --- | --- |
+| `NEMO_NAVIER_STOKES` | 7.0.0 |
+
+A transport coefficient model must be specified for viscous simulations with the NEMO solver, using the `TRANSPORT_COEFF_MODEL` config option. Available options when using the SU2TCLib thermochemical library are the Wilkes-Blottner-Eucken, Gupta-Yos, and Sutherland viscosity models, specified by `WILKE`, `GUPTA-YOS`, and `SUTHERLAND`, respectively. The default option for transport coefficient model is Wilkes-Blottner-Eucken. 
+
+It should be noted the Sutherland model is only used to evaluate viscosity, and the Wilkes-Blottner-Eucken model is used to evaluate diffusion coefficient and thermal conductivity.
+
+---
+
 ## Flow Condition (Incompressible) ##
 
 | Solver | Version |

_docs_v7/Slope-Limiters-and-Shock-Resolution.md

@@ -96,6 +96,9 @@ The `SLOPE_LIMITER_` options above may each be changed to use different limiters
 | `BARTH_JESPERSEN`       | Barth-Jespersen                                 | This limiter is a smooth version of the commonly seen Barth-Jespersen limiter seen in the literature  |
 | `VENKATAKRISHNAN`       | Venkatakrishnan                                 |  |
 | `VENKATAKRISHNAN_WANG`  | Venkatakrishnan-Wang                            |  |
+| `NISHIKAWA_R3`          | Nishikawa-R3                                    |  |
+| `NISHIKAWA_R4`          | Nishikawa-R4                                    |  |
+| `NISHIKAWA_R5`          | Nishikawa-R5                                    |  |
 | `SHARP_EDGES`           | Venkatakrishnan with sharp-edge modification    | This limiter should not be used for flow solvers |
 | `WALL_DISTANCE`         | Venkatakrishnan with wall distance modification | This limiter should not be used for flow solvers |
 | `VAN_ALBADA_EDGE`       | Van Albada (edge formulation)                   | This limiter is only implemented for flow solvers and does not output limiter values when using the VOLUME_OUTPUT option |
@@ -106,7 +109,7 @@ The default limiter is `VENKATAKRISHNAN`.
 
 The `VENKAT_LIMITER_COEFF` parameter is generally a small constant, defaulting to $$0.05$$, but its specific definition depends on the limiter being used.
 
-For the `VENKATAKRISHNAN`, `SHARP_EDGES`, and `WALL_DISTANCE` limiters, the `VENKAT_LIMITER_COEFF` parameter refers to $$K$$ in $$\epsilon^2=\left(K\bar{\Delta} \right)^3$$, where $$\bar{\Delta}$$ is an average grid size (this is hardcoded as 1m and thus all tuning is via $$K$$).
+For the `VENKATAKRISHNAN`, `SHARP_EDGES`, and `WALL_DISTANCE` limiters, the `VENKAT_LIMITER_COEFF` parameter refers to $$K$$ in $$\epsilon^2=\left(K\bar{\Delta} \right)^3$$, where $$\bar{\Delta}$$ is an average grid size (this is hardcoded as 1m and thus all tuning is via $$K$$). For NISHIKAWA_Rp limiters, $$\epsilon^p=\left(K\bar{\Delta} \right)^{p+1}$$ (p = 3, 4 or 5).
 The $$K$$ parameter defines a threshold, below which oscillations are not damped by the limiter, as described by [Venkatakrishnan](https://doi.org/10.1006/jcph.1995.1084).
 Thus, a large value will approach the case of using no limiter with undamped oscillations, while too small of a value will slow the convergence and add extra diffusion.
 The SU2 implementation of the `BARTH_JESPERSEN` limiter actually uses `VENKATAKRISHNAN` with $$K=0$$.
@@ -115,10 +118,10 @@ The SU2 implementation of the `BARTH_JESPERSEN` limiter actually uses `VENKATAKR
 When using the `VENKATAKRISHNAN_WANG` limiter, `VENKAT_LIMITER_COEFF` is instead $$\varepsilon '$$ in $$\varepsilon = \varepsilon ' (q_{max} - q_{min})$$, where $$q_{min}$$ and $$q_{max}$$ are the respective *global* minimum and maximum of the field variable being limited.
 This global operation incurs extra time costs due to communication between MPI ranks.
 The original work by [Wang](https://doi.org/10.2514/6.1996-2091) suggests using `VENKAT_LIMITER_COEFF` in the range of $$[0.01, 0.20]$$, where again larger values approach the case of using no limiter.
-**Note:** unlike the aforementioned `VENKATAKRISHNAN` limiter, the `VENKATAKRISHNAN_WANG` limiter does not depend directly on the mesh size and can thus be used without non-dimensionalization. If the `VENKATAKRISHNAN` limiter is used outside of non-dimensional mode, the fields with larger values (pressure and temperature) will generally be limited more aggressively than velocity.
+**Note:** unlike the aforementioned `VENKATAKRISHNAN` limiter and NISHIKAWA_Rp limiter, the `VENKATAKRISHNAN_WANG` limiter does not depend directly on the mesh size and can thus be used without non-dimensionalization. If the `VENKATAKRISHNAN` limiter is used outside of non-dimensional mode, the fields with larger values (pressure and temperature) will generally be limited more aggressively than velocity.
 
 
-The `NONE`, `BARTH_JESPERSEN`, `VENKATAKRISHNAN`, and `VENKATAKRISHNAN_WANG` limiter options all have no **geometric modifier**.
+The `NONE`, `BARTH_JESPERSEN`, `VENKATAKRISHNAN`, `VENKATAKRISHNAN_WANG`, and NISHIKAWA_Rp limiter options all have no **geometric modifier**.
 A geometric modifier increases limiting near walls or sharp edges. This is done by multiplying the limiter value by a **geometric factor**. 
 
 For both the `SHARP_EDGES` and `WALL_DISTANCE` limiters, the influence of the geometric modifier is controlled with `ADJ_SHARP_LIMITER_COEFF` which defaults to 3.0.

_docs_v7/Style-Guide.md

@@ -25,6 +25,8 @@ Patch releases cannot break backward compatibility.
 SU2 is written for C++11, the formatting rules are defined in a `clang-format` file located in the root of the repository.
 **New files must follow the formatting rules exactly.**
 
+SU2 uses pre-commit to enforce a consistent formatting. To use, [install pre-commit](https://pre-commit.com/#install) and run `pre-commit install` at the root of the project. You can now force the formatting on all files with `pre-commit run -a`. This will also run all pre-commit hooks before each commit, preventing dirty commits in the repository.
+
 ### Files, functions, and variables
 
 Basic recommendations for creating files, functions, and variables: