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442 changes: 221 additions & 221 deletions dev/_examples/build_1d2dmodel.html
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356 changes: 178 additions & 178 deletions dev/_examples/build_1dmodel.html
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112 changes: 56 additions & 56 deletions dev/_examples/build_2dmodel.html
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2 changes: 1 addition & 1 deletion dev/_examples/plot_dflowfm_mesh.html
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Expand Up @@ -481,7 +481,7 @@ <h2>Read the model<a class="headerlink" href="#Read-the-model" title="Link to th
<span class="c1"># Get the different types of branches in mesh1d</span>
<span class="n">rivers</span> <span class="o">=</span> <span class="n">mod</span><span class="o">.</span><span class="n">rivers</span>
<span class="n">pipes</span> <span class="o">=</span> <span class="n">mod</span><span class="o">.</span><span class="n">pipes</span>
<span class="c1"># Additionnal geometry and structures</span>
<span class="c1"># Additional geometry and structures</span>
<span class="n">manholes</span> <span class="o">=</span> <span class="n">mod</span><span class="o">.</span><span class="n">geoms</span><span class="p">[</span><span class="s2">&quot;manholes&quot;</span><span class="p">]</span>
<span class="n">crosssections</span> <span class="o">=</span> <span class="n">mod</span><span class="o">.</span><span class="n">geoms</span><span class="p">[</span><span class="s2">&quot;crosssections&quot;</span><span class="p">]</span>

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120 changes: 60 additions & 60 deletions dev/_examples/update_refine_2dgrid.html
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Expand Up @@ -466,7 +466,7 @@ <h1>Update a 2D Delft3D FM model: mesh refinements<a class="headerlink" href="#U
<section id="Model-setup-configuration">
<h2>Model setup configuration<a class="headerlink" href="#Model-setup-configuration" title="Link to this heading">#</a></h2>
<p>Updating a bedlevel or infiltration capacity map is an easy step with the command line but sometimes, for example with forcing or grid refinement, you need to update several things at the same time. This is possible by preparing a <strong>configuration file</strong> that includes every methods and settings that you want to do during your update.</p>
<p>The configuration-file contains the model setup configuration and determines which methods are updated and in which sequence and sets optional arguments for each method. This configuration is passed to hydromt using <code class="docutils literal notranslate"><span class="pre">-i</span> <span class="pre">&lt;path_to_ini_file&gt;</span></code>. The supported format are either YAML or INI.</p>
<p>The configuration-file contains the model setup configuration and determines which methods are updated and in which sequence and sets optional arguments for each method. This configuration is passed to hydromt using <code class="docutils literal notranslate"><span class="pre">-i</span> <span class="pre">&lt;path_to_configuration_file&gt;</span></code>.</p>
<p>Each section, before indent, (e.g. setup_mesh2d_refine) corresponds with a model method which are explained in the <a class="reference external" href="https://deltares.github.io/hydromt_delft3dfm/latest/user_guide/dflowfm_model_setup.html">docs (model methods)</a>.</p>
<p>Let’s open the example configuration file <strong>dflowfm_update_mesh2d_refine.yml</strong> from the model repository [examples folder] and have a look at the settings.</p>
<div class="nbinput docutils container">
Expand Down Expand Up @@ -582,65 +582,65 @@ <h2>Update a 1D2D Delft3D FM model to refine the 2D mesh<a class="headerlink" hr
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
2024-10-17 13:32:54,105 - update - log - INFO - HydroMT version: 0.10.0
2024-10-17 13:32:54,106 - update - main - INFO - Updating dflowfm model at /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/dflowfm_piave (r).
2024-10-17 13:32:54,106 - update - main - INFO - Output dir: /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/build/dflowfm_mesh2d_refine
2024-10-17 13:32:54,106 - update - main - INFO - User settings:
2024-10-17 13:32:54,831 - update - model_api - INFO - Initializing dflowfm model from hydromt_delft3dfm (v0.2.1.dev0).
2024-10-17 13:32:54,831 - update - data_catalog - INFO - Parsing data catalog from /usr/share/miniconda/envs/hydromt-delft3dfm/lib/python3.9/site-packages/hydromt_delft3dfm/data/parameters_data.yml
2024-10-17 13:32:54,837 - update - dflowfm - INFO - Reading mdu file at /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/dflowfm_piave/dflowfm/DFlowFM.mdu
2024-10-17 13:32:55,884 - update - dflowfm - INFO - project crs: 3857
2024-10-17 13:32:55,884 - update - dflowfm - INFO - Reading model data from /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/dflowfm_piave
2024-10-17 13:32:55,884 - update - dflowfm - INFO - Reading dimr file at /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/dflowfm_piave/dimr_config.xml
2024-10-17 13:32:57,326 - update - dflowfm - INFO - Reading branches GUI file
2024-10-17 13:32:57,526 - update - dflowfm - INFO - Reading cross-sections files
2024-10-17 13:32:57,570 - update - dflowfm - INFO - Reading manholes file
2024-10-17 13:32:57,675 - update - model_api - WARNING - Replacing result: elevtn
2024-10-17 13:32:57,682 - update - model_api - WARNING - Replacing result: infiltcap
2024-10-17 13:32:57,688 - update - model_api - WARNING - Replacing result: roughness_manning
2024-10-17 13:32:57,694 - update - model_api - WARNING - Replacing geom: region
2024-10-17 13:32:57,694 - update - dflowfm - INFO - Reading cross-sections files
2024-10-17 13:32:57,740 - update - model_api - WARNING - Replacing geom: crosssections
2024-10-17 13:32:57,740 - update - dflowfm - INFO - Reading manholes file
2024-10-17 13:32:57,804 - update - model_api - WARNING - Replacing geom: manholes
2024-10-17 13:32:57,922 - update - model_api - WARNING - Replacing forcing: boundary1d_waterlevelbndbnd
2024-10-17 13:32:57,922 - update - dflowfm - INFO - project crs: 3857
2024-10-17 13:32:57,923 - update - model_api - INFO - setup_mesh2d_refine.polygon_fn: /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/data/refine.geojson
2024-10-17 13:32:57,923 - update - model_api - INFO - setup_mesh2d_refine.sample_fn: None
2024-10-17 13:32:57,923 - update - model_api - INFO - setup_mesh2d_refine.steps: 2
2024-10-17 13:32:57,923 - update - dflowfm - INFO - reading geometry from file /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/data/refine.geojson.
2024-10-17 13:32:57,924 - update - geodataframe - INFO - Reading vector data from /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/data/refine.geojson
2024-10-17 13:32:57,973 - update - mesh - INFO - 2d mesh refined based on polygon.Number of faces before: 460 and after: 828
2024-10-17 13:32:57,975 - update - model_mesh - WARNING - Overwriting grid mesh2d and the corresponding data variables in mesh.
2024-10-17 13:32:58,112 - update - model_api - INFO - setup_link1d2d.link_direction: 1d_to_2d
2024-10-17 13:32:58,112 - update - model_api - INFO - setup_link1d2d.link_type: embedded
2024-10-17 13:32:58,112 - update - model_api - INFO - setup_link1d2d.polygon_fn: None
2024-10-17 13:32:58,112 - update - model_api - INFO - setup_link1d2d.branch_type: None
2024-10-17 13:32:58,112 - update - model_api - INFO - setup_link1d2d.max_length: inf
2024-10-17 13:32:58,112 - update - model_api - INFO - setup_link1d2d.dist_factor: 2.0
2024-10-17 13:32:58,112 - update - dflowfm - WARNING - adding 1d2d links for all branches at non boundary locations.
2024-10-17 13:32:58,112 - update - dflowfm - INFO - setting up 1d_to_2d links.
2024-10-17 13:32:58,412 - update - dflowfm - INFO - Writing model data to /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/build/dflowfm_mesh2d_refine
2024-10-17 13:32:58,413 - update - dflowfm - INFO - Writing maps files to /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/build/dflowfm_mesh2d_refine/maps
2024-10-17 13:32:59,386 - update - dflowfm - INFO - Writting cross-sections files crsdef and crsloc
2024-10-17 13:32:59,955 - update - dflowfm - INFO - Writting friction file(s)
2024-10-17 13:32:59,960 - update - dflowfm - INFO - Writting manholes file.
2024-10-17 13:33:00,316 - update - model_api - WARNING - Replacing geom: mesh1d
2024-10-17 13:33:00,316 - update - model_api - WARNING - Replacing geom: network1d
2024-10-17 13:33:00,317 - update - model_api - WARNING - Replacing geom: mesh2d
2024-10-17 13:33:00,331 - update - model_api - WARNING - Replacing geom: crosssections
2024-10-17 13:33:00,337 - update - model_api - WARNING - Replacing geom: manholes
2024-10-17 13:33:00,338 - update - model_api - WARNING - Replacing geom: rivers
2024-10-17 13:33:00,340 - update - model_api - WARNING - Replacing geom: pipes
2024-10-17 13:33:00,343 - update - model_api - WARNING - Replacing geom: branches
2024-10-17 13:33:00,343 - update - model_api - WARNING - Replacing geom: region
2024-10-17 13:33:00,344 - update - model_api - WARNING - Replacing geom: mesh1d
2024-10-17 13:33:00,344 - update - model_api - WARNING - Replacing geom: network1d
2024-10-17 13:33:00,345 - update - model_api - WARNING - Replacing geom: mesh2d
2024-10-17 13:33:01,790 - update - dflowfm - INFO - Writting branches.gui file
2024-10-17 13:33:01,964 - update - dflowfm - INFO - Writting forcing files.
2024-10-17 13:33:03,099 - update - dflowfm - INFO - Adding dflowfm component to dimr config
2024-10-17 13:33:03,105 - update - dflowfm - INFO - Writing model dimr file to /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/build/dflowfm_mesh2d_refine/dimr_config.xml
2024-10-17 13:39:38,360 - update - log - INFO - HydroMT version: 0.10.0
2024-10-17 13:39:38,360 - update - main - INFO - Updating dflowfm model at /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/dflowfm_piave (r).
2024-10-17 13:39:38,361 - update - main - INFO - Output dir: /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/build/dflowfm_mesh2d_refine
2024-10-17 13:39:38,361 - update - main - INFO - User settings:
2024-10-17 13:39:39,073 - update - model_api - INFO - Initializing dflowfm model from hydromt_delft3dfm (v0.2.1.dev0).
2024-10-17 13:39:39,073 - update - data_catalog - INFO - Parsing data catalog from /usr/share/miniconda/envs/hydromt-delft3dfm/lib/python3.9/site-packages/hydromt_delft3dfm/data/parameters_data.yml
2024-10-17 13:39:39,079 - update - dflowfm - INFO - Reading mdu file at /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/dflowfm_piave/dflowfm/DFlowFM.mdu
2024-10-17 13:39:40,101 - update - dflowfm - INFO - project crs: 3857
2024-10-17 13:39:40,101 - update - dflowfm - INFO - Reading model data from /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/dflowfm_piave
2024-10-17 13:39:40,101 - update - dflowfm - INFO - Reading dimr file at /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/dflowfm_piave/dimr_config.xml
2024-10-17 13:39:41,528 - update - dflowfm - INFO - Reading branches GUI file
2024-10-17 13:39:41,724 - update - dflowfm - INFO - Reading cross-sections files
2024-10-17 13:39:41,771 - update - dflowfm - INFO - Reading manholes file
2024-10-17 13:39:41,878 - update - model_api - WARNING - Replacing result: elevtn
2024-10-17 13:39:41,884 - update - model_api - WARNING - Replacing result: infiltcap
2024-10-17 13:39:41,890 - update - model_api - WARNING - Replacing result: roughness_manning
2024-10-17 13:39:41,896 - update - model_api - WARNING - Replacing geom: region
2024-10-17 13:39:41,896 - update - dflowfm - INFO - Reading cross-sections files
2024-10-17 13:39:41,942 - update - model_api - WARNING - Replacing geom: crosssections
2024-10-17 13:39:41,942 - update - dflowfm - INFO - Reading manholes file
2024-10-17 13:39:42,006 - update - model_api - WARNING - Replacing geom: manholes
2024-10-17 13:39:42,124 - update - model_api - WARNING - Replacing forcing: boundary1d_waterlevelbndbnd
2024-10-17 13:39:42,125 - update - dflowfm - INFO - project crs: 3857
2024-10-17 13:39:42,125 - update - model_api - INFO - setup_mesh2d_refine.polygon_fn: /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/data/refine.geojson
2024-10-17 13:39:42,125 - update - model_api - INFO - setup_mesh2d_refine.sample_fn: None
2024-10-17 13:39:42,125 - update - model_api - INFO - setup_mesh2d_refine.steps: 2
2024-10-17 13:39:42,125 - update - dflowfm - INFO - reading geometry from file /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/data/refine.geojson.
2024-10-17 13:39:42,126 - update - geodataframe - INFO - Reading vector data from /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/data/refine.geojson
2024-10-17 13:39:42,176 - update - mesh - INFO - 2d mesh refined based on polygon.Number of faces before: 460 and after: 828
2024-10-17 13:39:42,178 - update - model_mesh - WARNING - Overwriting grid mesh2d and the corresponding data variables in mesh.
2024-10-17 13:39:42,315 - update - model_api - INFO - setup_link1d2d.link_direction: 1d_to_2d
2024-10-17 13:39:42,315 - update - model_api - INFO - setup_link1d2d.link_type: embedded
2024-10-17 13:39:42,315 - update - model_api - INFO - setup_link1d2d.polygon_fn: None
2024-10-17 13:39:42,315 - update - model_api - INFO - setup_link1d2d.branch_type: None
2024-10-17 13:39:42,315 - update - model_api - INFO - setup_link1d2d.max_length: inf
2024-10-17 13:39:42,315 - update - model_api - INFO - setup_link1d2d.dist_factor: 2.0
2024-10-17 13:39:42,315 - update - dflowfm - WARNING - adding 1d2d links for all branches at non boundary locations.
2024-10-17 13:39:42,315 - update - dflowfm - INFO - setting up 1d_to_2d links.
2024-10-17 13:39:42,601 - update - dflowfm - INFO - Writing model data to /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/build/dflowfm_mesh2d_refine
2024-10-17 13:39:42,601 - update - dflowfm - INFO - Writing maps files to /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/build/dflowfm_mesh2d_refine/maps
2024-10-17 13:39:43,558 - update - dflowfm - INFO - Writting cross-sections files crsdef and crsloc
2024-10-17 13:39:44,118 - update - dflowfm - INFO - Writting friction file(s)
2024-10-17 13:39:44,123 - update - dflowfm - INFO - Writting manholes file.
2024-10-17 13:39:44,474 - update - model_api - WARNING - Replacing geom: mesh1d
2024-10-17 13:39:44,475 - update - model_api - WARNING - Replacing geom: network1d
2024-10-17 13:39:44,475 - update - model_api - WARNING - Replacing geom: mesh2d
2024-10-17 13:39:44,489 - update - model_api - WARNING - Replacing geom: crosssections
2024-10-17 13:39:44,496 - update - model_api - WARNING - Replacing geom: manholes
2024-10-17 13:39:44,496 - update - model_api - WARNING - Replacing geom: rivers
2024-10-17 13:39:44,499 - update - model_api - WARNING - Replacing geom: pipes
2024-10-17 13:39:44,501 - update - model_api - WARNING - Replacing geom: branches
2024-10-17 13:39:44,501 - update - model_api - WARNING - Replacing geom: region
2024-10-17 13:39:44,502 - update - model_api - WARNING - Replacing geom: mesh1d
2024-10-17 13:39:44,503 - update - model_api - WARNING - Replacing geom: network1d
2024-10-17 13:39:44,503 - update - model_api - WARNING - Replacing geom: mesh2d
2024-10-17 13:39:45,945 - update - dflowfm - INFO - Writting branches.gui file
2024-10-17 13:39:46,121 - update - dflowfm - INFO - Writting forcing files.
2024-10-17 13:39:47,259 - update - dflowfm - INFO - Adding dflowfm component to dimr config
2024-10-17 13:39:47,264 - update - dflowfm - INFO - Writing model dimr file to /home/runner/work/hydromt_delft3dfm/hydromt_delft3dfm/docs/_examples/build/dflowfm_mesh2d_refine/dimr_config.xml

</pre></div></div>
</div>
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2 changes: 1 addition & 1 deletion dev/_generated/hydromt_delft3dfm.graph_utils.gpd_to_digraph.html
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<h1>hydromt_delft3dfm.graph_utils.gpd_to_digraph<a class="headerlink" href="#hydromt-delft3dfm-graph-utils-gpd-to-digraph" title="Link to this heading">#</a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="hydromt_delft3dfm.graph_utils.gpd_to_digraph">
<span class="sig-prename descclassname"><span class="pre">hydromt_delft3dfm.graph_utils.</span></span><span class="sig-name descname"><span class="pre">gpd_to_digraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://geopandas.org/en/stable/docs/reference/api/geopandas.GeoDataFrame.html#geopandas.GeoDataFrame" title="(in GeoPandas v1.0.1)"><span class="pre">GeoDataFrame</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">&lt;networkx.classes.digraph.DiGraph</span> <span class="pre">object</span> <span class="pre">at</span> <span class="pre">0x7f7cdedff370&gt;</span></span></span><a class="reference internal" href="../_modules/hydromt_delft3dfm/graph_utils.html#gpd_to_digraph"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hydromt_delft3dfm.graph_utils.gpd_to_digraph" title="Link to this definition">#</a></dt>
<span class="sig-prename descclassname"><span class="pre">hydromt_delft3dfm.graph_utils.</span></span><span class="sig-name descname"><span class="pre">gpd_to_digraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://geopandas.org/en/stable/docs/reference/api/geopandas.GeoDataFrame.html#geopandas.GeoDataFrame" title="(in GeoPandas v1.0.1)"><span class="pre">GeoDataFrame</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">&lt;networkx.classes.digraph.DiGraph</span> <span class="pre">object</span> <span class="pre">at</span> <span class="pre">0x7f9c658ff3a0&gt;</span></span></span><a class="reference internal" href="../_modules/hydromt_delft3dfm/graph_utils.html#gpd_to_digraph"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hydromt_delft3dfm.graph_utils.gpd_to_digraph" title="Link to this definition">#</a></dt>
<dd><p>Convert a <cite>gpd.GeoDataFrame</cite> to a <cite>nx.DiGraph</cite>.</p>
<p>This is done by taking the first and last coordinate in a row as source and target,
respectively.</p>
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2 changes: 1 addition & 1 deletion dev/user_guide/dflowfm_build.html
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<p>Settings to build or update a Delft3DFM model are managed in a configuration file. In this file,
every option from each <a class="reference internal" href="dflowfm_model_setup.html#model-methods"><span class="std std-ref">model method</span></a> can be changed by the user
in its corresponding section.</p>
<p>Note that the order in which the components are listed in the yml/ini file is important:</p>
<p>Note that the order in which the components are listed in the yml file is important:</p>
<ul class="simple">
<li><p>When setting up a 1D model, one of the <cite>setup_rivers</cite>, <cite>setup_channels</cite> and <cite>setup_pipes</cite> should always be run first to determine the model topology.</p></li>
<li><p>When setting up a 2D model, <cite>setup_mesh2d</cite> should always be run first.</p></li>
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2 changes: 1 addition & 1 deletion dev/user_guide/dflowfm_model_setup.html
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The main interactions are available from the HydroMT Command Line Interface and allow you to configure
HydroMT in order to build or update Delft3D FM models.</p>
<p>When building or updating a model from command line a model setup
<a class="reference internal" href="dflowfm_build.html#model-config"><span class="std std-ref">configuration</span></a> (.yml/.ini file) with model methods and options and, optionally,
<a class="reference internal" href="dflowfm_build.html#model-config"><span class="std std-ref">configuration</span></a> (.yml file) with model methods and options and, optionally,
a <a class="reference external" href="https://deltares.github.io/hydromt/latest/user_guide/data_prepare_cat.html">data sources</a> (.yml) file should be prepared.</p>
<section id="model-setup-methods">
<span id="model-methods"></span><h2>Model setup methods<a class="headerlink" href="#model-setup-methods" title="Link to this heading">#</a></h2>
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