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(part:GWB_parameter_listings:chap:world_builer_file:sec:index)=
(part:GWB_parameter_listings:chap:world_builder_file:sec:index)=
The World Builder file
======================

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(part:api_manual:chap:API_FFI:sec:CPP_interface:subsec:ASPECT_integration)=
ASPECT intgration
(part:API_manual:chap:API_FFI:sec:CPP_interface:subsec:ASPECT_integration)=
ASPECT integration
=================

```{todo}
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(part:api_manual:chap:API_FFI:sec:CPP_interface:subsec:cpp_integration)=
(part:API_manual:chap:API_FFI:sec:CPP_interface:subsec:CPP_integration)=
C++ interface
=============

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2 changes: 1 addition & 1 deletion doc/sphinx/api_manual/API_FFI/C_interface.md
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(part:api_manual:chap:API_FFI:sec:C_interface)=
(part:API_manual:chap:API_FFI:sec:C_interface)=
C interface
===========

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(part:api_manual:chap:API_FFI:sec:fortran_interface)=
(part:API_manual:chap:API_FFI:sec:Fortran_interface)=
FORTRAN interface
===========

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(part:api_manual:chap:API_FFI:sec:python_interface)=
(part:API_manual:chap:API_FFI:sec:python_interface)=
Python interface
===========

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2 changes: 1 addition & 1 deletion doc/sphinx/api_manual/API_FFI/index.md
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(part:api_manual:chap:API_FFI:sec:index)=
(part:API_manual:chap:API_FFI:sec:index)=
API in different languages (FFI)
==========================================

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2 changes: 1 addition & 1 deletion doc/sphinx/api_manual/api_design.md
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(part:api_manual:chap:api_design)=
(part:API_manual:chap:API_design)=
API design
==========

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2 changes: 1 addition & 1 deletion doc/sphinx/api_manual/available_apis.md
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(part:api_manual:chap:available_apis)=
(part:API_manual:chap:available_APIs)=
Available APIs
==============

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(part:dev_manual:chap:contrib_to_code:sec:code_conventions)=
(part:dev_manual:chap:contribute_to_code:sec:code_conventions)=
Code conventions
================

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(part:dev_manual:chap:contrib_to_code:sec:code_doc_and_doxygen)=
(part:dev_manual:chap:contribute_to_code:sec:code_doc_and_Doxygen)=
Code documentation and Doxygen
==============================

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(part:dev_manual:chap:contrib_to_code:sec:code_style_guide)=
(part:dev_manual:chap:contribute_to_code:sec:code_style_guide)=
Code Style Guide
================

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(part:dev_manual:chap:contrib_to_code:sec:index)=
(part:dev_manual:chap:contribute_to_code:sec:index)=
Contributing to the code
=================================

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(part:dev_manual:chap:contrib_to_code:sec:review_process)=
(part:dev_manual:chap:contribute_to_code:sec:review_process)=
Review process
==============

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(part:dev_manual:chap:contrib_to_code:sec:testing:subsec:index)=
(part:dev_manual:chap:contribute_to_code:sec:testing:subsec:index)=
Testing your code
=================

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(part:dev_manual:chap:contrib_to_code:sec:testing:subsec:integration_testers:subsubsec:app_testers)=
(part:dev_manual:chap:contribute_to_code:sec:testing:subsec:integration_testers:subsubsec:app_testers)=
App tester
==========

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(part:dev_manual:chap:contrib_to_code:sec:testing:subsec:integration_testers:subsubsec:index)=
(part:dev_manual:chap:contribute_to_code:sec:testing:subsec:integration_testers:subsubsec:index)=
Integration testers
===================

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(part:dev_manual:chap:contrib_to_code:sec:testing:subsec:integration_testers:subsubsec:visualization_tester)=
(part:dev_manual:chap:contribute_to_code:sec:testing:subsec:integration_testers:subsubsec:visualization_tester)=
Visualization tester
====================

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(part:dev_manual:chap:contrib_to_code:sec:testing:subsec:integration_testers:subsubsec:wrapper_tester)=
(part:dev_manual:chap:contribute_to_code:sec:testing:subsec:integration_testers:subsubsec:wrapper_tester)=
Wrapper tester
==============

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(part:dev_manual:chap:contrib_to_code:sec:testing:subsec:unit_tests)=
(part:dev_manual:chap:contribute_to_code:sec:testing:subsec:unit_tests)=
Unit tests
==========

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(part:dev_manual:chap:contrib_to_code:sec:tips_tricks)=
(part:dev_manual:chap:contribute_to_code:sec:tips_tricks)=
Tips and tricks
===============

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## Trick 4: Interact with visualization when generating new tests

The tests in the WorldBuilder contain a wb file for the setup and a dat file for the mesh point.
The tests in the World Builder contain a .wb file for the setup and a .dat file for the mesh point.
For example, the mass_conserving_slab_temperature test contains two files:

tests/gwb-dat/mass_conserving_slab_temperature.wb
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tests/gwb-dat/mass_conserving_slab_temperature


The first few lines of the contents in the dat file are:
The first few lines of the contents in the .dat file are:

```{code-block} python
---
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./build/bin/gwb-grid tests/gwb-dat/some_test.wb some_grid.grid

This command is composed of the "gwb-grid" executable in the "bin" subfolder, a wb file for the test, and a grid for the gwb-grid to generate output. There are already a few examples of grids in the tests/gwb-grid folder one could modify from. The output of this command is a vtu file that could be easily visualized in software like Paraview.
This command is composed of the "gwb-grid" executable in the "bin" sub-folder, a wb file for the test, and a grid for the gwb-grid to generate output. There are already a few examples of grids in the tests/gwb-grid folder one could modify from. The output of this command is a vtu file that could be easily visualized in software like Paraview.

For more information, please refer to the manual page for the gwb-grid app:
{ref}`part:user_manual:chap:how_to_use_the_apps:sec:gwb-grid_app`
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(part:dev_manual:chap:contrib_to_doc:sec:doc_style_guide)=
(part:dev_manual:chap:contribute_to_doc:sec:doc_style_guide)=
Documentation style guide
=========================

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(part:dev_manual:chap:contrib_to_doc:sec:doc_testing)=
(part:dev_manual:chap:contribute_to_doc:sec:doc_testing)=
Documentation testing
=====================

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(part:dev_manual:chap:contrib_to_doc:sec:important_syntax)=
Important sytax
(part:dev_manual:chap:contribute_to_doc:sec:important_syntax)=
Important syntax
===============

```{todo}
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(part:dev_manual:chap:contrib_to_doc:sec:index)=
(part:dev_manual:chap:contribute_to_doc:sec:index)=
Contributing to the documentation
=================================

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(part:dev_manual:chap:contrib_to_doc:sec:review_process)=
(part:dev_manual:chap:contribute_to_doc:sec:review_process)=
The review process
================

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(part:dev_manual:chap:contrib_to_doc:sec:tips_and_tricks)=
(part:dev_manual:chap:contribute_to_doc:sec:tips_and_tricks)=
Tips and tricks
================

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(part:dev_manual:chap:developing_for_the_GWB:sec:code_strucuture)=
(part:dev_manual:chap:developing_for_the_GWB:sec:code_structure)=
Code structure
==============

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(part:dev_manual:chap:start_devel_and_contib:sec:contributing_to_gwb:subsec:helping_others)=
(part:dev_manual:chap:start_developing_and_contribute:sec:contributing_to_gwb:subsec:helping_others)=
Helping others
==============

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(part:dev_manual:chap:start_devel_and_contib:sec:contributing_to_gwb:subsec:index)=
Contrbuting to the GWB
(part:dev_manual:chap:start_developing_and_contribute:sec:contributing_to_gwb:subsec:index)=
Contributing to the GWB
======================

```{todo}
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(part:dev_manual:chap:start_devel_and_contib:sec:contributing_to_gwb:subsec:making_a_pull_request)=
(part:dev_manual:chap:start_developing_and_contribute:sec:contributing_to_gwb:subsec:making_a_pull_request)=
Making a pull request
=====================

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(part:dev_manual:chap:start_devel_and_contib:sec:contributing_to_gwb:subsec:pull_request_merging)=
(part:dev_manual:chap:start_developing_and_contribute:sec:contributing_to_gwb:subsec:pull_request_merging)=
Pull request merging
====================

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(part:dev_manual:chap:start_devel_and_contib:sec:contributing_to_gwb:subsec:pull_request_review:subsubsec:benchmarking)=
(part:dev_manual:chap:start_developing_and_contribute:sec:contributing_to_gwb:subsec:pull_request_review:subsubsec:benchmarking)=
Benchmarking
============

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(part:dev_manual:chap:start_devel_and_contib:sec:contributing_to_gwb:subsec:pull_request_review:subsubsec:code_coverage)=
(part:dev_manual:chap:start_developing_and_contribute:sec:contributing_to_gwb:subsec:pull_request_review:subsubsec:code_coverage)=
Code coverage
=======

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(part:dev_manual:chap:start_devel_and_contib:sec:contributing_to_gwb:subsec:pull_request_review:subsubsec:doc_testing)=
(part:dev_manual:chap:start_developing_and_contribute:sec:contributing_to_gwb:subsec:pull_request_review:subsubsec:doc_testing)=
Documentation testing
=====================

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(part:dev_manual:chap:start_devel_and_contib:sec:contributing_to_gwb:subsec:pull_request_review:subsubsec:index)=
(part:dev_manual:chap:start_developing_and_contribute:sec:contributing_to_gwb:subsec:pull_request_review:subsubsec:index)=
Pull request review process
===========================

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(part:dev_manual:chap:start_devel_and_contib:sec:contributing_to_gwb:subsec:pull_request_review:subsubsec:testers)=
(part:dev_manual:chap:start_developing_and_contribute:sec:contributing_to_gwb:subsec:pull_request_review:subsubsec:testers)=
Testers
=======

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(part:dev_manual:chap:start_devel_and_contib:sec:contributing_to_gwb:subsec:pull_request_review:subsubsec:ci)=
(part:dev_manual:chap:start_developing_and_contribute:sec:contributing_to_gwb:subsec:pull_request_review:subsubsec:CI)=
What is continuous integration?
===============================

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(part:dev_manual:chap:start_devel_and_contrib:sec:index)=
(part:dev_manual:chap:start_developing_and_contribute:sec:index)=
How to start developing and contributing
=======================================

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(part:dev_manual:chap:start_devel_and_contrib:sec:tools:subsec:ide)=
(part:dev_manual:chap:start_developing_and_contribute:sec:tools:subsec:IDE)=
IDE
===

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(part:dev_manual:chap:start_devel_and_contrib:sec:tools:subsec:astyle)=
(part:dev_manual:chap:start_developing_and_contribute:sec:tools:subsec:astyle)=
Astyle
=====

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(part:dev_manual:chap:start_devel_and_contrib:sec:tools:subsec:git)=
(part:dev_manual:chap:start_developing_and_contribute:sec:tools:subsec:git)=
Git
===

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(part:dev_manual:chap:start_devel_and_contrib:sec:tools:subsec:index)=
(part:dev_manual:chap:start_developing_and_contribute:sec:tools:subsec:index)=
required and recommended tools
============

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2 changes: 1 addition & 1 deletion doc/sphinx/introduction/gwb_philosophy.md
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(part:introduction:chap:gwb_philosophy)=
(part:introduction:chap:GWB_philosophy)=
GWB philosophy
==============

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2 changes: 1 addition & 1 deletion doc/sphinx/introduction/what_is_the_gwb.md
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(part:introduction:chap:what_is_the_gwb)=
(part:introduction:chap:what_is_the_GWB)=
What is the GWB?
================

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4 changes: 2 additions & 2 deletions doc/sphinx/user_manual/installation/included.md
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Expand Up @@ -8,7 +8,7 @@ When it is downloaded, the folder contains the main library, two programs, and a
The World Builder library
-------------------------

This is the main code of the Geodynamics World Builder.
This is the main code of the Geodynamic World Builder.
In this library is all the code related to setting up and querying the World Builder world.
It also contains the wrapper code to interface with C, Python, and Fortran programs.

Expand All @@ -23,7 +23,7 @@ This data file should contain in the header information on the dimension you wan
The World Builder Visualization program
---------------------------------------

This program helps with visualizing the World Builder file by producing pvd files which can be opened with visualization programs like Paraview.
This program helps with visualizing the World Builder file by producing vtu files which can be opened with visualization programs like Paraview.
It requires a World Builder file and a grid file.
A grid file is a file which contains information about what part of the World Builder domain should be visualized and with what resolution.
For more information on how to use the World Builder visualizer see {ref}`part:user_manual:chap:how_to_use_the_apps:sec:gwb-grid_app`.
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2 changes: 1 addition & 1 deletion doc/sphinx/user_manual/installation/index.md
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Expand Up @@ -4,7 +4,7 @@ Installation

The world builder currently officially supports Linux, OSX, and Windows operating systems.
Each change to the library is tested against these platforms.
The only requirements are a c++ compiler (tested both with GCC and clang) with at minimum c++14 installed together with cmake (<https://cmake.org>).
The only requirements are a c++ compiler (tested both with GCC and clang) with at minimum c++14 installed together with CMake (<https://cmake.org>).

{ref}`part:user_manual:chap:installation:sec:included` will go in depth about what is in the Geodynamic World Builder package when it is downloaded and installed completely.
If you want to skip this explanation, go directly to {ref}`part:user_manual:chap:installation:sec:installing_prerequisites`.
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Installing the prerequisites
============================

When installing the World Builder on a system, make sure cmake is installed.
If you want a Fortran wrapper, then also make sure a Fortran compiler is installed (gFortran is the preferred option, but other Fortran compilers should work as well).
When installing the World Builder on a system, make sure CMake is installed.
If you want a Fortran wrapper, then also make sure a Fortran compiler is installed (GFortran is the preferred option, but other Fortran compilers should work as well).
If you want a Python interface, make sure you have Python 3 installed.

There are many ways to install the prerequisites of the World Builder per operating system.
Expand All @@ -28,15 +28,15 @@ Choose one of the options. "No Fortran compiler" is recommended for normal use:

The world builder can create a Fortran wrapper to be able to link to Fortran programs.
If you don't explicitly need a Fortran wrapper to be built, you can use the following instructions:
1. If not already installed, install homebrew. Run in a terminal: `/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"`
1. If not already installed, install Homebrew. Run in a terminal: `/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"`
2. Run in a terminal `brew install cmake`
3. For a Python wrapper, also run in a terminal `brew install swig`

Note that if you already had a Fortran compiler installed and cmake can find it, the Fortran wrapper will still be built.
Note that if you already had a Fortran compiler installed and CMake can find it, the Fortran wrapper will still be built.
:::

:::{tab-item} Before Xcode 10 with Fortran compiler
1. If not already installed, install homebrew. Run in a terminal: `/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"`
1. If not already installed, install Homebrew. Run in a terminal: `/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"`
2. Run in a terminal `brew install cmake`
3. Run in a terminal `brew install gcc || true && brew link –overwrite gcc`
4. Run in a terminal `export LDFLAGS="-I/usr/local/opt/llvm/lib"`
Expand All @@ -51,7 +51,7 @@ Note that if you already had a Fortran compiler installed and cmake can find it,
You will need to check where clang is installed.
It should be installed in a folder called /Applications/X-code.X.X.app/ or something similar, where the X represents a number.
For Xcode 10 for example, use the following:
1. If not already installed, install homebrew. Run in a terminal: `/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"`
1. If not already installed, install Homebrew. Run in a terminal: `/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"`
2. Run in a terminal `brew install cmake`
3. Run in a terminal `brew install gcc || true && brew link –overwrite gcc`
4. Run in a terminal `export LDFLAGS="-L/Applications/Xcode-10.0.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib"`
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Expand Up @@ -2,7 +2,7 @@
Running the tester
==================

Once you have installed the GWB, it is always a good idea to run the tester to see if the installation works. There are a few ways to call the tester:`make test`, `ninja test` and `ctest`. They can all run the same tests suit, but `ctest` is the most universal and versatile of the option. Running ctest may give you output like below:
Once you have installed the GWB, it is always a good idea to run the tester to see if the installation works. There are a few ways to call the tester:`make test`, `ninja test` and `ctest`. They can all run the same tests suit, but `ctest` is the most universal and versatile of the option. Running CTest may give you output like below:

```
Test project /path/toworld-builder/WorldBuilder/build-rl
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4 changes: 2 additions & 2 deletions doc/sphinx/user_manual/installation/stand_alone_install.md
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Expand Up @@ -11,15 +11,15 @@ Stand-alone installation with all apps

::::{tab-set}
:::{tab-item} For Windows with Visual Studio
6. Run cmake by entering: `cmake MAKE_FILE_GENERATOR="Visual Studio 15 2017 Win64"..`, or the version of Visual Studio you have installed, and make sure cmake finds all the dependencies.
6. Run CMake by entering: `cmake MAKE_FILE_GENERATOR="Visual Studio 15 2017 Win64"..`, or the version of Visual Studio you have installed, and make sure CMake finds all the dependencies.
7. For production runs, set build type to release by entering `-DCMAKE_BUILD_TYPE=Release`.
8. Run make with the amount of threads you want to use (e.g. use 8 processes: `make -j 8`).
9. If you want the Geodynamic World Builder to be installed on your system, run `cmake -build . -target install -j 8`
10. Run the tests to make sure everything installed correctly (`cmake -build . -target run_tests -j 8`).
:::

:::{tab-item} For all other configurations
6. Run cmake by entering: `cmake ..` and make sure cmake finds all the dependencies.
6. Run CMake by entering: `cmake ..` and make sure CMake finds all the dependencies.
7. For production runs, set build type to release by entering `make release`.
8. Run make with the amount of threads you want to use (e.g. use 8 processes: `make -j 8`).
9. If you want the Geodynamic World Builder to be installed on your system, run `sudo make install -j 4`
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