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[hook] Fixed trailing whitespace check.

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bilke committed Aug 7, 2019
1 parent 13e95b7 commit f345850e07a3d273926a71b57cb57f7140ad19cb
Showing with 74 additions and 74 deletions.
  1. +1 −1 ...on/ProjectFile/material/solid/constitutive_relation/LinearElasticOrthotropic/t_poissons_ratios.md
  2. +3 −3 Tests/MathLib/TestGlobalVectorInterface.cpp
  3. +1 −1 web/archetypes/books.pandoc
  4. +4 −4 web/content/_index.pandoc
  5. +1 −1 web/content/books/computational-geotechnics-i.pandoc
  6. +1 −1 web/content/books/computational-hydrology-ii.pandoc
  7. +2 −2 web/content/books/computational-hydrology-iii.pandoc
  8. +1 −1 web/content/books/geoenergy-modeling-i.pandoc
  9. +1 −1 web/content/books/geoenergy-modeling-ii.pandoc
  10. +3 −3 web/content/books/geoenergy-modeling-iii.pandoc
  11. +1 −1 web/content/books/models-of-thermochemical-heat-storage.pandoc
  12. +4 −4 web/content/docs/benchmarks/creep-after-excavation-bgra/CreepAfterExcavation.pandoc
  13. +1 −1 web/content/docs/benchmarks/elliptic/poisson_equation.pandoc
  14. +2 −2 web/content/docs/benchmarks/heat-transport-bhe/3D_Beier_sandbox.pandoc
  15. +3 −3 web/content/docs/benchmarks/hydro-component/contracer/ConTracer.pandoc
  16. +5 −5 web/content/docs/benchmarks/hydro-component/theis/HC_Theis.pandoc
  17. +1 −1 web/content/docs/benchmarks/hydro-mechanics/InjectionProduction.pandoc
  18. +3 −3 web/content/docs/benchmarks/liquid-flow/unconfined-aquifer.pandoc
  19. +4 −4 web/content/docs/benchmarks/thermo-hydro-mechanics/consolidation_pointheatsource.pandoc
  20. +2 −2 web/content/docs/benchmarks/thermo-mechanical-phase-field/thermo-mechanical-phase-field.pandoc
  21. +14 −14 web/content/docs/devguide/advanced/configuration-options.pandoc
  22. +1 −1 web/content/docs/devguide/development-workflows/branching-model.pandoc
  23. +1 −1 web/content/docs/devguide/testing/jenkins.pandoc
  24. +1 −1 web/content/docs/tools/getting-started/overview.pandoc
  25. +1 −1 web/content/docs/tools/meshing/remove-mesh-elements/index.pandoc
  26. +1 −1 web/content/docs/tools/model-preparation/compute-node-areas-from-surface-mesh/index.pandoc
  27. +2 −2 web/content/docs/tools/model-preparation/create-boundary-conditions-along-a-polyline/index.pandoc
  28. +1 −1 web/content/docs/tools/model-preparation/map-geometric-object-to-the-surface-of-a-mesh/index.pandoc
  29. +2 −2 web/content/docs/tools/model-preparation/set-properties-in-polygonal-region/index.pandoc
  30. +4 −4 web/content/docs/tools/workflows/Example-of-a-DGM-to-model-workflow/index.pandoc
  31. +1 −1 web/content/docs/tools/workflows/create-a-simple-parallel-model/index.pandoc
  32. +1 −1 web/content/docs/tools/workflows/create-boundary-condition-in-polygonal-region/index.pandoc
@@ -7,5 +7,5 @@ are calculated by the symmetry property as \f$\nu_{ji} E_i = \nu_{ij} E_j\f$ (no
They also must fulfil following two properties:
\f[|\nu_{ij}| < \sqrt({E_i \over E_j}),\f]
and
\f[1 - \nu_{12}\nu_{21} - \nu_{23}\nu_{32} - \nu_{13}\nu_{31}
\f[1 - \nu_{12}\nu_{21} - \nu_{23}\nu_{32} - \nu_{13}\nu_{31}
- \nu_{12}\nu_{23}\nu{31} - \nu_{32}\nu_{21}\nu{13} > 0.\f]
@@ -208,7 +208,7 @@ void checkGlobalVectorInterfacePETSc()
/*
Assume there is a vector distributed over three processes as
-- rank0 -- --- rank1 --- -- rank2 --
0 1 2 3 4 5 6 7 8 9 10 11
0 1 2 3 4 5 6 7 8 9 10 11
where the numbers are the global entry indices.
In each trunk of entries of a rank, there are ghost entries in
other ranks attached and their global entry indices are:
@@ -224,7 +224,7 @@ void checkGlobalVectorInterfacePETSc()
The above ghost entry embedded vector is realized by the following
test.
*/
*/
std::size_t local_vec_size = 4;
if (mrank == 1)
local_vec_size = 5;
@@ -234,7 +234,7 @@ void checkGlobalVectorInterfacePETSc()
std::vector<double> non_ghost_vals(local_vec_size);
std::size_t nghosts = 3;
if (mrank)
nghosts = 2;
nghosts = 2;
std::vector<GlobalIndexType> ghost_ids(nghosts);
std::vector<double> expected;
switch (mrank)
@@ -9,7 +9,7 @@ book_cover = "[TODO]"

+++

[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/TODO-DONWLOAD-LINK.pdf)
[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/TODO-DONWLOAD-LINK.pdf)

TODO DESCRIPTION

@@ -1,6 +1,6 @@
---
title: OpenGeoSys
authors:
authors:
- Lars Bilke

date: 2017-01-13T14:24:23+01:00
@@ -20,7 +20,7 @@ features:
- headline: Comprehensive Pre-Processing Tools
textline: |
A wide range of helper tools exist to get your model up and running with OpenGeoSys.

Convert your existing data sets into appropriate OGS data formats and structures.

Create meshes approximating geometrically the domain of interest. Analyze mesh quality, cleanup the mesh or adding layers to it.
@@ -42,7 +42,7 @@ features:
permalink: /features/StaggeredCouplingScheme.png
alt: Staggered coupling scheme
layout: right

- headline: Data integration
textline: |
Integrate and visualize data sets for OpenGeoSys by using the OpenGeoSys Data Explorer. It provides functionality to visually assess the data and see possible artefacts, inconsistencies between data sets or missing information.
@@ -113,7 +113,7 @@ features:
alt: Dev workflow
layout: right
# class: inverse

- headline: Get started
textline: |
subfeatures:
@@ -9,7 +9,7 @@ book_cover = "computational-geotechnics-i.png"

+++

[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Comp-Geotechnics-I/Computational_Geotechnics_I.pdf)
[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Comp-Geotechnics-I/Computational_Geotechnics_I.pdf)

In this book, effective computational methods to facilitate those pivotal simulations using open-source software are introduced and discussed with a special focus on the coupled thermo-mechanical behavior of the rock salt. A cohesive coverage of applying geotechnical modeling to the subsurface storage of hydrogen produced from renewable energy sources is accompanied by specific, reproducible example simulations to provide the reader with direct access to this fascinating and important field. Energy carriers such as natural gas, hydrogen, oil, and even compressed air can be stored in subsurface geological formations such as depleted oil or gas reservoirs, aquifers, and caverns in salt rock. Many challenges have arisen in the design, safety and environmental impact assessment of such systems, not the least of which is that large-scale experimentation is not a feasible option. Therefore, simulation techniques are central to the design and risk assessment of these and similar geotechnical facilities.

@@ -9,7 +9,7 @@ book_cover = "computational-hydrology-ii.png"

+++

[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Computational-Hydrology-II/CompHydroII-opt.pdf)
[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Computational-Hydrology-II/CompHydroII-opt.pdf)

This book explores the application of the open-source software OpenGeoSys (OGS) for hydrological numerical simulations concerning conservative and reactive transport modeling. It provides general information on the hydrological and groundwater flow modeling of a real case study and step-by-step model set-up with OGS, while also highlighting related components such as the OGS Data Explorer. The material is based on unpublished manuals and the results of a collaborative project between China and Germany (SUSTAIN H2O). Though the book is primarily intended for graduate students and applied scientists who deal with hydrological modeling, it also offers a valuable source of information for professional geoscientists wishing to expand their knowledge of the numerical modeling of hydrological processes including nitrate reactive transport modeling. This book is the second in a series that showcases further applications of computational modeling in hydrological science.

@@ -8,7 +8,7 @@ book_type = "Tutorial"
book_cover = "Computational-Hydrology-III-Cover.jpg"
+++

[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Computational-Hydrology-III/Computational-Hydrology-III.pdf)
[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Computational-Hydrology-III/Computational-Hydrology-III.pdf)

This tutorial presents the application of the open-source software OpenGeoSys(OGS) with a geochemical solver PHREEQC for ​
​hydrological simulation concerning reactive transport modeling. It contains general information regarding reactive transport modeling and a step-by-step model set-up with OGS and PHREEQC, and related components such as GINA, Data Explorer, and ParaView. A code verification with Engesgaard benchmark and two application examples (Nitrate reduction and Treatment wetland) are presented in detail.
@@ -20,7 +20,7 @@ The tutorial book is intended primarily for graduate students and applied scient

::: {.note}
### <i class="far fa-download"></i> Downloads
- [<i class="far fa-file-archive"></i> Benchmark Input Files](https://ogsstorage.blob.core.windows.net/web/Books/Computational-Hydrology-III/Computational-Hydrology-III-Files.zip)
- [<i class="far fa-file-archive"></i> Benchmark Input Files](https://ogsstorage.blob.core.windows.net/web/Books/Computational-Hydrology-III/Computational-Hydrology-III-Files.zip)
:::

::: {.note}
@@ -12,7 +12,7 @@ aliases = [ "/tutorials/ces-i/e07", "/tutorials/ces-i/e08",

+++

[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Geoenergy-Model-I/Basics-of-Heat-Transport-Processes-in-Geothermal-Systems-opt.pdf)
[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Geoenergy-Model-I/Basics-of-Heat-Transport-Processes-in-Geothermal-Systems-opt.pdf)

This introduction to geothermal modeling deals with flow and heat transport processes in porous and fractured media related to geothermal energy applications. Following background coverage of geothermal resources and utilization in several countries, the basics of continuum mechanics for heat transport processes, as well as numerical methods for solving underlying governing equations are discussed. This examination forms the theoretical basis for five included step-by-step OpenGeoSys exercises, highlighting the most important computational areas within geothermal resource utilization, including heat diffusion, heat advection in porous and fractured media, and heat convection. The book concludes with an outlook on practical follow-up contributions investigating the numerical simulation of shallow and deep geothermal systems.

@@ -11,7 +11,7 @@ aliases = [ "/books/shallow-geothermal-systems" ]

+++

[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Geoenergy-Model-II/ebook_Shao_etal_2016_Geoenergy_Modeling_II.pdf)
[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Geoenergy-Model-II/ebook_Shao_etal_2016_Geoenergy_Modeling_II.pdf)

This book is dedicated to the numerical modeling of shallow geothermal systems. The utilization of shallow geothermal energy involves the integration of multiple Borehole Heat Exchangers (BHE) with Ground Source Heat Pump (GSHP) systems to provide heating and cooling. The modeling practices explained in this book can improve the efficiency of these increasingly common systems. The book begins by explaining the basic theory of heat transport processes in man-made as well as natural media. These techniques are then applied to the simulation of borehole heat exchangers and their interaction with the surrounding soil. The numerical and analytical models are verified against analytical solutions and measured data from a Thermal Response Test, and finally, a real test site is analyzed through the model and discussed with regard to BHE and GSHP system design and optimization.

@@ -9,11 +9,11 @@ book_cover = "geoenergy-modeling-iii.png"

+++

[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Geoenergy-Model-III/GeoenergyModelingIII-EGS.pdf)
[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Geoenergy-Model-III/GeoenergyModelingIII-EGS.pdf)

This tutorial presents the introduction of the open-source software OpenGeoSys for enhanced geothermal reservoir modeling. There are various commercial software tools available to solve complex scientific questions in geothermics. This book will introduce the user to an open source numerical software code for geothermal modeling which can even be adapted and extended based on the needs of the researcher.
This tutorial presents the introduction of the open-source software OpenGeoSys for enhanced geothermal reservoir modeling. There are various commercial software tools available to solve complex scientific questions in geothermics. This book will introduce the user to an open source numerical software code for geothermal modeling which can even be adapted and extended based on the needs of the researcher.

The book explains basic mathematical equations and numerical methods to modeling flow and heat transport in fractured porous rock formations. In order to help readers gain a system-level understanding of the necessary analysis, the authors include two benchmark examples and two case studies of real deep geothermal test-sites located in Germany and France.
The book explains basic mathematical equations and numerical methods to modeling flow and heat transport in fractured porous rock formations. In order to help readers gain a system-level understanding of the necessary analysis, the authors include two benchmark examples and two case studies of real deep geothermal test-sites located in Germany and France.

::: {.clearfix}
:::
@@ -8,7 +8,7 @@ book_cover = "models-of-thermochemical-heat-storage.png"

+++

[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Heat-Storage-I/Models-of-Thermochemical-Heat-Storage.pdf)
[<i class="far fa-file-pdf"></i> Download this book as PDF](https://ogsstorage.blob.core.windows.net/web/Books/Heat-Storage-I/Models-of-Thermochemical-Heat-Storage.pdf)

Thermal energy storage is of high strategic relevance for the establishment of a sustainable energy system. The development of next-generation storage systems like thermochemical solutions is accompanied by major scientific and engineering challenges. Due to the complexity of the considered storage systems and the exceptional efforts for the development of storage materials as well as for the implementation of large-scale experiments, modelling and numerical simulation are of outstanding importance for the prediction of the operational behaviour and the optimization of thermochemical heat storage systems. The deployment of the necessary simulation tools is thus one of the key research topics in the area of thermal energy storage systems.

@@ -14,8 +14,8 @@ author = "Wenqing Wang"
{{< data-link >}}

-------------------------------------------------------------------------
Following up the benchmark about the BGRa creep model described on the
[this page](https://www.opengeosys.org/docs/benchmarks/creepbgra/creepbrga/),
Following up the benchmark about the BGRa creep model described on the
[this page](https://www.opengeosys.org/docs/benchmarks/creepbgra/creepbrga/),
this example represents the creep in the near field of
drift in the deep rock salt after excavation. The domain and the
geometry are shown in the following figure:
@@ -75,9 +75,9 @@ distributed from top to bottom with the boundary values of temperature.
The time step sizes of the simulation are: One step of 0.001 day, 10 steps of 0.1 day, and the
remaining steps of 1 day.

The following three figures are plotted by using the results of the simulation of 1000 days creep.
The following three figures are plotted by using the results of the simulation of 1000 days creep.
The three figures display the distribution of horizontal and vertical stresses at times of
108 days, 409 days and 1000 days, respectively.
108 days, 409 days and 1000 days, respectively.

In theses three figures,
the left sub-figure show the time variations of horizontal and vertical stresses
@@ -166,7 +166,7 @@ info: residual: 5.974447e-17
info: ------------------------------------------------------------------
info: [time] Linear solver took 0.00145817 s.
info: [time] Iteration #1 took 0.0116439 s.
info: [time] Solving process #0 took 0.011662 s in time step #1
info: [time] Solving process #0 took 0.011662 s in time step #1
info: [time] Time step #1 took 0.0116858 s.
info: [time] Output of timestep 1 took 0.000671864 s.
info: The whole computation of the time stepping took 1 steps, in which
@@ -19,7 +19,7 @@ The U-type Borehole Heat Exchanger (BHE) is always utilized to extract the shall

## Model Setup

The numerical model was established using dual continuum method Diersch et al. (2011), in which the BHE is represented by the line element and 3D prism stands for the sand part. The numerical geometry model can be visualized as shown in Figure 1. Thus, there are two material groups in the model distinguishing the soil part and the BHE part. The length of the whole box is 18.5 m with a square cross section of 5 m per side to avoid the impact of boundary conditions on the soil temperature. Detailed parameters for the model configuration are listed in the follwoing table.
The numerical model was established using dual continuum method Diersch et al. (2011), in which the BHE is represented by the line element and 3D prism stands for the sand part. The numerical geometry model can be visualized as shown in Figure 1. Thus, there are two material groups in the model distinguishing the soil part and the BHE part. The length of the whole box is 18.5 m with a square cross section of 5 m per side to avoid the impact of boundary conditions on the soil temperature. Detailed parameters for the model configuration are listed in the follwoing table.

| Parameter | Symbol | Value | Unit |
| ---------------------------------- |:------------------ | -------------------:| --------------------------: |
@@ -43,7 +43,7 @@ In Beier's experiment, the inner diameter of aluminum pipe is 12.6 $\mathrm{cm}$

## OGS-6 Input Files

The detailed input file can be seen from the .prj file. The inflow temperature of the BHE, which was imposed as boundary condition of the BHE can be shown in Figure 2. Initial conditions of inflow and outflow temperature for the BHE were directly obtained from the measurements at t=0. For the initial soil temperature, the average value of all sensors placed in the sand and the borehole wall was set in the numerical model.
The detailed input file can be seen from the .prj file. The inflow temperature of the BHE, which was imposed as boundary condition of the BHE can be shown in Figure 2. Initial conditions of inflow and outflow temperature for the BHE were directly obtained from the measurements at t=0. For the initial soil temperature, the average value of all sensors placed in the sand and the borehole wall was set in the numerical model.

{{< img src="../3D_Beier_sandbox_figures/Inflow_temp.png" width="200">}}

@@ -17,7 +17,7 @@ title = "Conservative tracer transport with time varying source (1D/2D)"

## Overview
This benchmark describes the transport of a conservative tracer through a saturated porous media. Simulations have been performed with OGS-6 and OGS-5 in both, 1D and 2D domains.
Additionally, simulations have been compared with experimental data obtained from a hydraulic tracer experiment conducted in a pilot--scale horizontal flow constructed wetland (Boog, 2013; Boog *et al.*, 2019)
Additionally, simulations have been compared with experimental data obtained from a hydraulic tracer experiment conducted in a pilot--scale horizontal flow constructed wetland (Boog, 2013; Boog *et al.*, 2019)

The experimental system consists of a box of 4.7 m in length, 1.2 m in width and 1.05 m in depth (Nivala *et al.* 2013).
The box was filled with gravel giving an average porosity of 0.38. The initial water level was at 1.0 meter and the outflow was realized by an overflow pipe of 1.0 m height.
@@ -51,7 +51,7 @@ The boundary condition of the tracer ($g_{D,left}^{c_{tracer}}$) at the inlet wa
|$g$ | Gravity acceleration in $y$ direction | 9.81 | m s^-2^ |

---------------------- ---------- ----------- ------------

Table 1: Material Properties

---------------------- ---------- ----------- ------------
@@ -69,7 +69,7 @@ Table 1: Material Properties
|$c_{tracer}(t=0)$ | Initial tracer concentration | 0 | g L^-1^ |

---------------------- ---------- ----------- ------------

Table 2: Initial and boundary conditions for the 1D scenario


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