Merge branch 'master' into doku_dk

docs/html_doku/index.html

@@ -458,7 +458,7 @@ <h2>DataProcessing<a class="headerlink" href="#dataprocessing" title="Permalink
 <dl class="function">
 <dt id="_CPPv3N10GlobalFlow10DataReader26readZeroPointFiveToFiveMinENSt6stringE">
 <span id="_CPPv2N10GlobalFlow10DataReader26readZeroPointFiveToFiveMinENSt6stringE"></span><span id="GlobalFlow::DataReader::readZeroPointFiveToFiveMin__ss"></span><span class="target" id="class_global_flow_1_1_data_reader_1aca2973b0a150f2e0032459115b32bea6"></span>void GlobalFlow::<a class="reference internal" href="#_CPPv3N10GlobalFlow10DataReaderE" title="GlobalFlow::DataReader">DataReader</a><code class="descname">readZeroPointFiveToFiveMin</code><span class="sig-paren">(</span>std::string <em>path</em><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv3N10GlobalFlow10DataReader26readZeroPointFiveToFiveMinENSt6stringE" title="Permalink to this definition">¶</a><br /></dt>
-<dd><p>Creates a mapping of 0.5° ArcIDs to a list of contained 5’ GlobIDs. </p>
+<dd><p>Creates a mapping of 0.5° SpatIDs to a list of contained 5’ GlobIDs. </p>
 <p><dl class="docutils">
 <dt><strong>Parameters</strong></dt>
 <dd><ul class="breatheparameterlist first last simple">

docs/index.md

@@ -2,7 +2,7 @@
 layout: default
 title: Home
 nav_order: 1
-description: "Documentation of the global groundwater modeling framework"
+description: "Documentation of the global groundwater modeling framework."
 permalink: /
 ---
 
@@ -17,17 +17,26 @@ permalink: /
 
 
 # Data and code dois
-[![DOI](https://zenodo.org/badge/109667597.svg)](https://zenodo.org/badge/latestdoi/109667597)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1315471.svg)](https://doi.org/10.5281/zenodo.1315471)
+Code publication in JOSS: [![DOI](https://zenodo.org/badge/109667597.svg)](https://zenodo.org/badge/latestdoi/109667597)
 
-# The global gradient-based groundwater model framework G³M-f
-The global gradient-based groundwater model framework G³M-f is an extensible model framework.
-Its main purpose is to be used as a main building block for the global groundwater mode G³M.
-G³M is a newly developed gradient-based groundwater model which adapts MODFLOW [@harbaugh2005modflow] principles for the globalscale.
-It is written in C++ and intended to be coupled to the global hydrology model WaterGAP (http://watergap.de), but can also be used for regional groundwater models and coupling to other hydrology models.
-While it is intended to be used as a in memory coupled model it is also capable of running a standard standalone groundwater model.
+Outputs of Reinecke et al 2019 in GMD: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1315471.svg)](https://doi.org/10.5281/zenodo.1315471)
+
+# Check out the project on GitHub
+[GitHub](https://github.com/rreinecke/global-gradient-based-groundwater-model)
+
+# The framework G³M-f
+The global gradient-based groundwater model framework (G³M-f) is an extensible program to build groundwater models.
+Its primary purpose is to be used as a central building block for the global groundwater model G³M.
+G³M is a global gradient-based groundwater model which adapts MODFLOW principles for the global scale.
+It is written in C++ and intended to be coupled to the global hydrology model WaterGAP (http://watergap.de).
+While it is intended to be used as a memory coupled model, it can also run a standard standalone groundwater model.
+
+It is mainly intended to be used by developers of global hydrological models (including land surface models and others) who want to simulate groundwater in a gradient-based manner.
+In principle, it can also implement any other, e.g., regional, groundwater model.
+Its main feature compared to MODFLOW is its extensibility, speed, and in-memory coupling capability.
+
+For collaboration on coupling this model to other hydrological models, please contact Dr. Robert Reinecke (rreinecke on github).
 
-TODO why this model is aswesome and which user groups.....
 
 ## Getting Started
 
@@ -44,7 +53,7 @@ libGMP
 libGtest
 lcov
 ```
-### How to compile
+### Build
 ```
 mkdir build
 cd build
@@ -53,13 +62,13 @@ make
 ```
 
 ### Equations
-The three dimensional flow of water through the porous material between the cells is solved as a partial differential equation.
-Where K is the hydraulic conductivity [L/T] along the three axis, S the specific storage and W is the volumentric flux per unit volume in and out of the groundwater system.
-The hydraulic conductivity between two cells is caluclated b yusing the harmonic mean.
+The three-dimensional flow of water through the porous material between the cells is solved as a partial differential equation.
+Where K is the hydraulic conductivity [L/T] along the three axis, S the specific storage, and W is the volumetric flux per unit volume in and out of the groundwater system.
+The hydraulic conductivity between two cells is calculated by using the harmonic mean.
 The equation is solved using a conjugate gradient approach and an Incomplete LUT preconditioner.
 ![](https://latex.codecogs.com/gif.latex?\frac{\partial}{\partial&space;x}\left&space;(&space;K_{x}&space;\frac{\partial&space;h}{\partial&space;x}&space;\right&space;)&space;+&space;\frac{\partial}{\partial&space;y}\left&space;(&space;K_{y}&space;\frac{\partial&space;h}{\partial&space;y}&space;\right&space;)&space;+&space;\frac{\partial}{\partial&space;z}\left&space;(&space;K_{z}&space;\frac{\partial&space;h}{\partial&space;z}&space;\right&space;)&space;+&space;W&space;=&space;S_{s}&space;\frac{\partial&space;h}{\partial&space;t} "Main equation")
 
-Additonal information on the equations can be found in the very detailed MODFLOW documentation: [Modflow 2005](https://water.usgs.gov/ogw/modflow/MODFLOW.html)
+Additional information on the equations can be found in the very detailed MODFLOW documentation: [Modflow 2005](https://water.usgs.gov/ogw/modflow/MODFLOW.html)
 
 ### Boundary Conditions
 G³M support multiple boundary condition types:
@@ -72,8 +81,8 @@ G³M support multiple boundary condition types:
 * Different river approaches
 
 New flows can be defined in Model/ExternalFlows.hpp.
-The domain boundary is currently defined implicitly through the input grid as no-flow for grid files and as ocean boundary for irregual grids.
-This behaviour can be changed in DataProcessing/Neighbouring.hpp.
+The domain boundary is currently defined implicitly through the input grid as no-flow for grid files and as ocean boundary for irregular grids.
+This behavior can be changed in DataProcessing/Neighbouring.hpp.
 
 ## Built With
 
@@ -97,12 +106,12 @@ We use [SemVer](http://semver.org/) for versioning. For the versions available,
 ## Authors and Contributors
 
 * **Robert Reinecke** <span id="badgeCont935"><script type="text/javascript" src="https://publons.com/mashlets?el=badgeCont935&rid=K-3693-2019&size=small"></script></span> - *Initial work* *Maintainer*
-* **Daniel Kretschmer** - *Maintainer*
-* **Sebastian Ackermann** - *Maintainer*
+* **Daniel Kretschmer** - *Variable density flow* *Maintainer*
+* **Sebastian Ackermann** - *WaterGAP coupling* *Maintainer*
 
 ### Past Contributors
 
-* **Alexander Wachholz** - *Documentation review*
+* **Alexander Wachholz** - *Documentation review and NZ model* *Developer*
 * **Christoph Niemann** - *Spatial IDs* *Developer*
 
 ## License

lib/Eigen/Cholesky

@@ -9,6 +9,7 @@
 #define EIGEN_CHOLESKY_MODULE_H
 
 #include "Core"
+#include "Jacobi"
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
@@ -31,10 +32,14 @@
 #include "src/Cholesky/LLT.h"
 #include "src/Cholesky/LDLT.h"
 #ifdef EIGEN_USE_LAPACKE
-#include "src/Cholesky/LLT_MKL.h"
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
+#include "src/misc/lapacke.h"
+#endif
+#include "src/Cholesky/LLT_LAPACKE.h"
 #endif
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_CHOLESKY_MODULE_H
-/* vim: set filetype=cpp et sw=2 ts=2 ai: */