Updating docs_v7 sections

talbring · talbring · commit 1c35cc097580 · 2019-11-25T14:07:23.000+01:00
diff --git a/_data/docs_v7.yml b/_data/docs_v7.yml
@@ -15,15 +15,24 @@
   docs_v7:
   - Download
   - Installation
-  - Build-SU2-From-Source
+  - SU2-Linux-MacOS
+  - SU2-Windows
   - Test-Cases
 
+- title: Build From Source
+  docs_v7:
+  - Build-SU2-Linux-MacOS
+  - Build-SU2-Windows
+
+- title: Theory
+  docs_v7:
+  - Theory
+
 - title: Users Guide
   docs_v7:
   - Configuration-File
   - Mesh-File
   - Restart-File
-  - Theory
   - Solver-Setup
   - Physical-Definition
   - Markers-and-BC
diff --git a/_docs_v7/Build-SU2-Linux-MacOS.md b/_docs_v7/Build-SU2-Linux-MacOS.md
@@ -1,6 +1,6 @@
 ---
-title: Build SU2 From Source
-permalink: /docs_v7/Build-SU2-From-Source/
+title: Build SU2 on Linux/MacOS
+permalink: /docs_v7/Build-SU2-Linux-MacOS/
 redirect_from: /docs/Build-SU2-From-Source/
 ---
 
@@ -11,20 +11,27 @@ Note that the following guide works only on Linux/MacOS and on Windows using Cyg
 
 ---
 
-## Content ##
 - [Quick Compilation Guide](#quick-compilation-guide)
 - [Requirements](#requirements)
   - [Compilers](#compilers)
+  - [MPI](#mpi)
   - [Python](#python)
   - [Optional: swig and mpi4py](#optional-swig-and-mpi4py)
-- [Automatically Installed Dependencies](#automatically-installed-dependencies)
+- [Automatically installed dependencies](#automatically-installed-dependencies)
   - [Meson and Ninja](#meson-and-ninja)
   - [CoDiPack and MeDiPack](#codipack-and-medipack)
 - [Configuration and Compilation](#configuration-and-compilation)
   - [Basic Configuration](#basic-configuration)
   - [Advanced Configuration](#advanced-configuration)
+    - [Build Type](#build-type)
+    - [Compiler optimizations](#compiler-optimizations)
+    - [Warning level](#warning-level)
+    - [Linear algebra options](#linear-algebra-options)
   - [Compilation](#compilation)
+  - [Setting environment variables](#setting-environment-variables)
 - [Troubleshooting](#troubleshooting)
+  - [MPI installation is not found](#mpi-installation-is-not-found)
+  - [mpi4py library is not found](#mpi4py-library-is-not-found)
 
 ---
 
@@ -174,6 +181,10 @@ Finally to compile and install SU2 use
 ```
 where `build` is again a folder with a configuration created using a call to `meson.py` described in the previous section. By default ninja uses all available cores in your system for the compilation. You can set the number of cores manually by using the `-jN` flag, where `N` is the number of cores you want to use.
 
+
+### Setting environment variables ###
+Set the environment variables to use the executables from any directory without explicity specifying the path as described in the [installation section](/docs_v7/SU2-Linux-MacOS).
+
 ---
 
 ## Troubleshooting ##
diff --git a/_docs_v7/Build-SU2-Windows.md b/_docs_v7/Build-SU2-Windows.md
@@ -43,8 +43,5 @@ In the file browser go to the mingw installation directory and execute the file
 Now you can follow the steps in the [Linux/MacOS Configuration and Compilation section](/docs_v7/Build-SU2-From-Source/#configuration-and-compilation). But make sure to use `python meson.py` and `ninja.exe` instead of `./meson.py` and `./ninja`, respectively.
 
 
-
-
 ## Running the executables
-Add SU2 to the system path. This will allow you to use the executables from any directory without explicitly specifying the path to the executable. To do that access the system variables by typing “environ” in the search/run box of the start menu, select “edit the system environment variables”, and then select “Environment Variables” from the System Properties menu. Edit the “Path” system variable (or select “New” if no “Path” system variable exists) and add the path to the SU2 executables, i.e. the path that you have set with the `--prefix` option (if option was not given, the default is `C:\bin`). When there is more than one directory listed in “Path” they must be separated by semicolons.
-Running SU2 in Windows is identical to running in [Linux or Mac OS environments](/_docs_v7/Execution.md) and is run from the command line (whether cmd.exe or the freely-available Console2 for Windows). However, you may have to use `mpiexec` instead of `mpirun` to execute the code in parallel.
+Follow the [installation guide](/docs_v7/SU2-Windows/).
diff --git a/_docs_v7/Convective-Schemes.md b/_docs_v7/Convective-Schemes.md
@@ -8,15 +8,13 @@ The options listed here do not apply to the high order DG solver.
 
 ---
 
-## Content ##
-
 - [Introduction](#introduction)
 - [Compressible Flow](#compressible-flow)
-  - [Central schemes](#central-schemes)
-  - [Upwind schemes](#upwind-schemes)
+  - [Central Schemes](#central-schemes)
+  - [Upwind Schemes](#upwind-schemes)
 - [Incompressible Flow](#incompressible-flow)
-  - [Central schemes](#central-schemes)
-  - [Upwind schemes](#upwind-schemes)
+  - [Central Schemes](#central-schemes-1)
+  - [Upwind Schemes](#upwind-schemes-1)
 - [Turbulence Equations](#turbulence-equations)
 
 ---
diff --git a/_docs_v7/Custom-Output.md b/_docs_v7/Custom-Output.md
@@ -7,13 +7,15 @@ redirect_from: /docs/Custom-Output/
 With v7.0 we have introduced a new way of customizing the output on screen, in the history file and in the visualization files.
 It is now possible to individually define what you want to have in your output. 
 
-## Content ##
+---
 
 - [Restart and Visualization Files](#restart-and-visualization-files)
   - [Setting Output Fields](#setting-output-fields)
-- [Customizing the Screen and History output](#customizing-the-screen-and-history-output)
+  - [Example](#example)
+- [Customizing the Screen and History Output](#customizing-the-screen-and-history-output)
   - [Screen Output](#screen-output)
   - [History Output](#history-output)
+  - [Example](#example-1)
   
 ---
 
diff --git a/_docs_v7/Execution.md b/_docs_v7/Execution.md
@@ -7,15 +7,14 @@ Once downloaded and installed, and now that you know the basics for setting up y
 
 ---
 
-## Content
 
 - [C++ Modules](#c-modules)
 - [Python Scripts](#python-scripts)
-  - [Parallel Computation Script (parallel-computation.py)](#parallel-computation-script-parallel_computationpy)
-  - [Continuous Adjoint Gradient Calculation (continuous_adjoint.py)](#continuous-adjoint-gradient-calculation-continuous_adjointpy)
-  - [Discrete Adjoint Gradient Calculation (discrete_adjoint.py)](#discrete-adjoint-gradient-calculation-discrete_adjointpy)
-  - [Finite Difference Gradient Calculation (finite_differences.py)](#finite-difference-gradient-calculation-finite_differencespy)
-  - [Shape Optimization Script (shape_optimization.py)](#shape-optimization-script-shape_optimizationpy)
+  - [Parallel Computation Script (parallel_computation.py)](#parallel-computation-script-parallelcomputationpy)
+  - [Continuous Adjoint Gradient Calculation (continuous_adjoint.py)](#continuous-adjoint-gradient-calculation-continuousadjointpy)
+  - [Discrete Adjoint Gradient Calculation (discrete_adjoint.py)](#discrete-adjoint-gradient-calculation-discreteadjointpy)
+  - [Finite Difference Gradient Calculation (finite_differences.py)](#finite-difference-gradient-calculation-finitedifferencespy)
+  - [Shape Optimization Script (shape_optimization.py)](#shape-optimization-script-shapeoptimizationpy)
   
 ---
 
diff --git a/_docs_v7/Guide-to-v7.md b/_docs_v7/Guide-to-v7.md
@@ -6,6 +6,19 @@ redirect_from: /docs/Guide-to-v7/
 
 With v7.0 we have introduced a lot of updates and changes that affect how you interact with the code. This document gives an overview on the most important changes, so that you can quickly update your existing config files to be compatible with v7.0. 
 
+---
+
+- [Definition of the physical problem and solver](#definition-of-the-physical-problem-and-solver)
+- [Definition of the incompressible solver](#definition-of-the-incompressible-solver)
+- [Controlling the solver](#controlling-the-solver)
+- [Output options](#output-options)
+- [ASCII Restart format](#ascii-restart-format)
+- [Grid/mesh movement](#gridmesh-movement)
+- [Setting convergence criteria](#setting-convergence-criteria)
+
+---
+
+
 ### Definition of the physical problem and solver ###
 
 The option `PHYSICAL_PROBLEM` has been renamed to `SOLVER`. The rational behind this change is that we are going to have several different solvers in the future which essentially solve the same physical problems. You can find a list of current solvers in the new [Solver Setup](/docs_v7/Solver-Setup) section.
diff --git a/_docs_v7/Installation.md b/_docs_v7/Installation.md
@@ -3,19 +3,31 @@ title: Installation
 permalink: /docs_v7/Installation/
 ---
 
+---
+
+- [Installing SU2](#installing-su2)
+- [Required Software for Running SU2](#required-software-for-running-su2)
+  - [Command Line Terminal](#command-line-terminal)
+  - [Data Visualization](#data-visualization)
+- [Optional Third-Party Software](#optional-third-party-software)
+  - [Grid Generation](#grid-generation)
+  - [CGNS Library](#cgns-library)
+  - [Parallel Tools](#parallel-tools)
+  - [Python & Python Modules](#python--python-modules)
+  
+---
+
 ## Installing SU2
 
 SU2 has been designed with ease of installation and use in mind. This means that, wherever possible, a conscious effort was made to develop in-house code components rather than relying on third-party packages or libraries to maintain high portability. In simple cases (serial version with no external libraries), the flow solver can be compiled and executed with just a C++ compiler. 
 
 However, the capabilities of SU2 can be extended using externally-provided software. For example, parallel computations require an installed implementation of MPI (Message Passing Interface) for data communication. Again, to facilitate ease of use and to promote the open source nature, whenever external software is required within the SU2 suite, packages that are free or open source have been favored, and we try to ship, build, and link them automatically for you. These dependencies and third-party packages are discussed below.
 
-**Building from source**: refer to the [Source Installation Guide](/docs_v7/Build-SU2-From-Source/). This is the typical install method for Linux/Mac OS X.
-
-The binary executables available on the download page are intended to get new users up and running as quickly as possible. This option is best for new CFD users or those looking to quickly sample some of the features of SU2. To make these binary distributions available to a wide range of potential users, some advanced features requiring external libraries and dependencies have been disabled (most notably the ability to run simulations in parallel). In other words, the pre-compiled binary executables are simply the serial version of the SU2 C++ modules.
+**Building from source**: This is the recommended way to get the best compatibility and performance on your machine. Refer to the guides for building SU2 on [Linux/MacOS](/docs_v7/Build-SU2-Linux-MacOS/) or on [Windows](/docs_v7/Build-SU2-Windows/).
 
-No compilation is required for users who select the binary distribution of SU2. Simply install the binaries, open a terminal, and proceed to the Quick Start Tutorial. Binaries are available for multiple platforms, including installers for Windows.
+The binary executables available on the download page are intended to get new users up and running as quickly as possible. This option is best for new CFD users or those looking to quickly sample some of the features of SU2. To make these binary distributions available to a wide range of potential users, some advanced features requiring external libraries and dependencies have been disabled. For example the Discrete Adjoint method is not available.
 
-**Windows users**: please refer to the [Windows Installation Guide](/docs_v7/Windows-Installation/). 
+No compilation is required for users who select the binary distribution of SU2. Simply extract the binaries, open a terminal, and proceed to the Quick Start Tutorial. Binaries are available for all three platforms. Proceed to the installation guides for [Linux/MacOS](/docs_v7/SU2-Linux-MacOS) or [Windows](/docs_v7/SU2-Windows).
 
 ## Required Software for Running SU2
 
diff --git a/_docs_v7/Linear-Solvers-and-Preconditioners.md b/_docs_v7/Linear-Solvers-and-Preconditioners.md
@@ -9,8 +9,6 @@ As the numerical properties of the linear systems vary significantly with applic
 
 ---
 
-## Content ##
-
 - [Option List](#option-list)
   - [Linear Solvers](#linear-solvers)
   - [Linear Preconditioners](#linear-preconditioners)
diff --git a/_docs_v7/Markers-and-BC.md b/_docs_v7/Markers-and-BC.md
@@ -7,8 +7,6 @@ The term *Marker* refers to a named entity in your mesh file. Boundary condition
 
 ---
 
-## Content ##
-
 - [Euler (Slip) Wall](#euler-slip-wall)
 - [Symmetry Wall](#symmetry-wall)
 - [Constant Heatflux (no-slip) Wall](#constant-heatflux-no-slip-wall)
@@ -23,7 +21,7 @@ The term *Marker* refers to a named entity in your mesh file. Boundary condition
   - [Pressure Outlet (Compressible)](#pressure-outlet-compressible)
   - [Pressure Outlet (Incompressible)](#pressure-outlet-incompressible)
   - [Mass Flow Outlet](#mass-flow-outlet)
-- [Periodic Boundary Condition](#periodic-boundary-condition)
+  - [Periodic Boundary Condition](#periodic-boundary-condition)
 - [Structural Boundary Conditions](#structural-boundary-conditions)
   - [Clamped Boundary](#clamped-boundary)
   - [Displacement Boundary](#displacement-boundary)
diff --git a/_docs_v7/Mesh-File.md b/_docs_v7/Mesh-File.md
@@ -7,8 +7,6 @@ SU2 mainly uses a native mesh file format as input into the various suite compon
 
 ---
 
-## Content ##
-
 - [SU2 Native Format (.su2)](#su2-native-format-su2)
   - [Description](#description)
   - [Specification](#specification)
diff --git a/_docs_v7/Multizone.md b/_docs_v7/Multizone.md
@@ -7,13 +7,11 @@ SU2 is capable of solving physical problems in distinct zones coupled through in
 
 --- 
 
-## Content ##
-
-- [What is Zone ?](#what-is-a-zone-)
+- [What is a Zone ?](#what-is-a-zone)
 - [Multi-zone and Multi-physics](#multi-zone-and-multi-physics)
-  - [How to set up a single-physics Problem](#how-to-set-up-a-single-physics-problem)
-  - [Sub-config files](#sub-config-files)
-  - [How to set up a multi-physics Problem](#how-to-set-up-a-multi-physics-problem)
+  - [How to set up a single-physics problem](#how-to-set-up-a-single-physics-problem)
+    - [Sub-config files](#sub-config-files)
+  - [How to set up a multi-physics problem](#how-to-set-up-a-multi-physics-problem)
   - [Providing mesh information for a multi-zone problem](#providing-mesh-information-for-a-multi-zone-problem)
 
 ---
diff --git a/_docs_v7/Physical-Definition.md b/_docs_v7/Physical-Definition.md
@@ -9,13 +9,11 @@ SU2 offers different ways of setting and computing this definition. This documen
 
 ---
 
-## Content ##
-
 - [Reference Values](#reference-values)
-- [Free-stream Definition (Compressible)](#free-stream-definition-compressible)
+- [Free-Stream Definition (Compressible)](#free-stream-definition-compressible)
   - [Thermodynamic State](#thermodynamic-state)
   - [Mach Number and Velocity](#mach-number-and-velocity)
-  - [Reynolds Number and Viscosity](#reynolds-number-and-viscosity)
+  - [Reynolds Number and Viscosity ###](#reynolds-number-and-viscosity)
   - [Non-Dimensionalization](#non-dimensionalization)
 - [Flow Condition (Incompressible)](#flow-condition-incompressible)
   - [Thermodynamic and Gauge Pressure](#thermodynamic-and-gauge-pressure)
diff --git a/_docs_v7/Quick-Start.md b/_docs_v7/Quick-Start.md
@@ -3,11 +3,27 @@ title: Quick Start
 permalink: /docs_v7/Quick-Start/
 ---
 
-![NACA 0012 Pressure](../../docs_files/naca0012_pressure.png)
+Welcome to the Quick Start Tutorial for the SU2 software suite. This tutorial is intended to demonstrate some of the key features of the analysis and design tools in an easily accessible format. Completion of this tutorial only requires a few minutes. If you haven't done so already, please visit the [Download](/download.html) and [Installation](/docs_v7/Installation/) pages to obtain the most recent stable release of the software and details for installation. This tutorial requires only the SU2_CFD tool from the SU2 suite.
 
-## Introduction
+---
+
+- [Goals](#goals)
+- [Resources](#resources)
+- [Tutorial](#tutorial)
+  - [Background](#background)
+  - [Problem Setup](#problem-setup)
+  - [Mesh Description](#mesh-description)
+  - [Configuration File Options](#configuration-file-options)
+  - [Running SU2](#running-su2)
+  - [Results](#results)
+    - [Flow Solution](#flow-solution)
+    - [Adjoint Solution](#adjoint-solution)
+
+---
+
+
+![NACA 0012 Pressure](../../docs_files/naca0012_pressure.png)
 
-Welcome to the Quick Start Tutorial for the SU2 software suite. This tutorial is intended to demonstrate some of the key features of the analysis and design tools in an easily accessible format. Completion of this tutorial only requires a few minutes. If you haven't done so already, please visit the [Download](/download.html) and [Installation](/docs_v7/Installation/) pages to obtain the most recent stable release of the software and details for installation. This tutorial requires only the SU2_CFD tool from the SU2 suite.
 
 ## Goals
 Upon completing this simple tutorial, the user will be familiar with performing the flow and continuous adjoint simulation of external, inviscid flow around a 2D geometry and be able to plot both the flow solution and the surface sensitivities that result. The specific geometry chosen for the tutorial is the NACA 0012 airfoil. Consequently, the following capabilities of SU2 will be showcased in this tutorial:
diff --git a/_docs_v7/SU2-Linux-MacOS.md b/_docs_v7/SU2-Linux-MacOS.md
@@ -0,0 +1,34 @@
+---
+title: SU2 on Linux/MacOS
+permalink: /docs_v7/SU2-Linux-MacOS/
+---
+
+---
+
+- [Installation](#installation)
+  - [Download and unpack the archive](#download-and-unpack-the-archive)
+  - [Setting Environment variables](#setting-environment-variables)
+  - [Optional: Install MPICH for parallel mode](#optional-install-mpich-for-parallel-mode)
+
+---
+
+## Installation 
+
+### Download and unpack the archive
+[Download](/download/) the .zip for your operating system and unzip it where you want it to be installed. 
+
+### Setting Environment variables
+
+In order to use the executables from any directory without explicitely specifying the path to the executable you should set some environment variables. Either put the following lines to your `~/.bashrc` or `~/.bash_profile` to be permanent, or type the commands into the terminal for temporary use:
+```
+export SU2_RUN=<install_path>
+export PATH=$SU2_RUN:$PATH
+export PYTHONPATH=$SU2_RUN:$PYTHONPATH
+```
+
+where `<install_path>` is the path to the SU2 binaries (i.e. the folder that contains `SU2_CFD` etc.). If you have build [SU2 from source](/docs_v7/Build-SU2-Linux-MacOS/), it will be the path that you specified with the `--prefix` option (default: `/usr/bin`). The `export` commands are also printed after a successful configuration using `meson.py`.
+
+
+### Optional: Install MPICH for parallel mode
+
+If you want to run SU2 in parallel (and you have downloaded the `MPI` version), you need an installation of [MPICH](https://www.mpich.org/downloads/) on your machine. 
diff --git a/_docs_v7/SU2-Windows.md b/_docs_v7/SU2-Windows.md
diff --git a/_docs_v7/Solver-Setup.md b/_docs_v7/Solver-Setup.md
diff --git a/_docs_v7/Theory.md b/_docs_v7/Theory.md
diff --git a/_docs_v7/Windows-Installation.md b/_docs_v7/Windows-Installation.md
