Built site for gh-pages

Deltares · Oct 5, 2023 · c7f72c1 · c7f72c1
1 parent 34ad5f4
commit c7f72c1
Show file tree

Hide file tree

Showing 50 changed files with 1,724 additions and 1,094 deletions.
diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-56a976a2
+c147f9e8
diff --git a/build/index.html b/build/index.html
diff --git a/core/equations.html b/core/equations.html
@@ -83,7 +83,7 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
-<link href="../build/index.html" rel="next">
+<link href="../core/numerics.html" rel="next">
 <link href="../core/usage.html" rel="prev">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
@@ -208,6 +208,12 @@
   <a href="../core/equations.html" class="sidebar-item-text sidebar-link active">
  <span class="menu-text">Equations</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../core/numerics.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Numerical considerations</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -324,7 +330,7 @@ <h1 data-number="1"><span class="header-section-number">1</span> Formal model de
 </div>
 <section id="the-jacobian" class="level2" data-number="1.1">
 <h2 data-number="1.1" class="anchored" data-anchor-id="the-jacobian"><span class="header-section-number">1.1</span> The Jacobian</h2>
-<p>The Jacobian is a <span class="math inline">\(n\times n\)</span> matrix where <span class="math inline">\(n\)</span> is the number of states in the simulation. The computation of the Jacobian for the solver is hardcoded in the Julia core, which is faster and more accurate than using finite difference methods.</p>
+<p>The Jacobian is a <span class="math inline">\(n\times n\)</span> matrix where <span class="math inline">\(n\)</span> is the number of states in the simulation. The Jacobian is computed either using finite difference methods or automatic differentiation. For more details on the computation of the Jacobian and how it is used in the solvers see <a href="../core/numerics.html">numerical considerations</a>.</p>
 <p>The entries of the Jacobian <span class="math inline">\(J\)</span> are given by <span class="math display">\[
 J[i,j] = \frac{\partial f_j}{\partial u_i},
 \]</span></p>
@@ -959,8 +965,8 @@ <h1 data-number="5"><span class="header-section-number">5</span> Performance</h1
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../build/index.html" class="pagination-link">
-        <span class="nav-page-text">API Reference</span> <i class="bi bi-arrow-right-short"></i>
+      <a href="../core/numerics.html" class="pagination-link">
+        <span class="nav-page-text">Numerical considerations</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>

diff --git a/core/index.html b/core/index.html
@@ -152,6 +152,12 @@
   <a href="../core/equations.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Equations</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../core/numerics.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Numerical considerations</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -188,7 +194,7 @@ <h1 class="title">Julia core</h1>
 </header>
 
 <p>With the term “core”, we mean the computational engine of Ribasim. As detailed in the <a href="../core/usage.html">usage</a> documentation, it is generally used as a command line tool.</p>
-<p>The theory is described on the <a href="../core/equations.html">equations</a> page.</p>
+<p>The theory is described on the <a href="../core/equations.html">equations</a> page, and more in-depth numerical considerations are described on the <a href="../core/numerics.html">numerical considerations</a> page.</p>
 <p>The core is implemented in the <a href="https://julialang.org/">Julia programming language</a>, and can be found in the <a href="https://github.com/Deltares/Ribasim">Ribasim repository</a> under the <code>core/</code> folder. For developers we also advise to read the <a href="../contribute/core.html">developer documentation</a>.</p>
 
 

diff --git a/core/numerics.html b/core/numerics.html
diff --git a/core/usage.html b/core/usage.html
@@ -208,6 +208,12 @@
   <a href="../core/equations.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Equations</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../core/numerics.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Numerical considerations</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -227,7 +233,7 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#configuration-file" id="toc-configuration-file" class="nav-link active" data-scroll-target="#configuration-file"><span class="header-section-number">1</span> Configuration file</a>
   <ul class="collapse">
-  <li><a href="#solver-settings" id="toc-solver-settings" class="nav-link" data-scroll-target="#solver-settings"><span class="header-section-number">1.1</span> Solver settings</a></li>
+  <li><a href="#sec-solver-settings" id="toc-sec-solver-settings" class="nav-link" data-scroll-target="#sec-solver-settings"><span class="header-section-number">1.1</span> Solver settings</a></li>
   </ul></li>
   <li><a href="#geopackage-and-arrow-tables" id="toc-geopackage-and-arrow-tables" class="nav-link" data-scroll-target="#geopackage-and-arrow-tables"><span class="header-section-number">2</span> GeoPackage and Arrow tables</a></li>
   <li><a href="#node" id="toc-node" class="nav-link" data-scroll-target="#node"><span class="header-section-number">3</span> Node</a></li>
@@ -345,8 +351,8 @@ <h1 data-number="1"><span class="header-section-number">1</span> Configuration f
 <span id="cb2-41"><a href="#cb2-41" aria-hidden="true" tabindex="-1"></a><span class="co"># defines the logging level of Ribasim</span></span>
 <span id="cb2-42"><a href="#cb2-42" aria-hidden="true" tabindex="-1"></a><span class="dt">verbosity</span> <span class="op">=</span> <span class="st">"info"</span> <span class="co"># optional, default "info", can otherwise be "debug", "warn" or "error"</span></span>
 <span id="cb2-43"><a href="#cb2-43" aria-hidden="true" tabindex="-1"></a><span class="dt">timing</span> <span class="op">=</span> <span class="cn">false</span>     <span class="co"># optional, whether to log debug timing statements</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-<section id="solver-settings" class="level2" data-number="1.1">
-<h2 data-number="1.1" class="anchored" data-anchor-id="solver-settings"><span class="header-section-number">1.1</span> Solver settings</h2>
+<section id="sec-solver-settings" class="level2" data-number="1.1">
+<h2 data-number="1.1" class="anchored" data-anchor-id="sec-solver-settings"><span class="header-section-number">1.1</span> Solver settings</h2>
 <p>The solver section in the configuration file is entirely optional, since we aim to use defaults that will generally work well. Common reasons to modify the solver settings are to adjust the calculation or output stepsizes: <code>adaptive</code>, <code>dt</code>, and <code>saveat</code>. If your model does not converge, or your performance is lower than expected, it can help to adjust other solver settings as well.</p>
 <p>The default solver <code>algorithm = "QNDF"</code>, which is a multistep method similar to Matlab’s <code>ode15s</code> <span class="citation" data-cites="shampine1997matlab">(<a href="#ref-shampine1997matlab" role="doc-biblioref">Shampine and Reichelt 1997</a>)</span>. It is an implicit method that supports the default <code>adaptive = true</code> timestepping. The full list of available solvers is: <code>QNDF</code>, <code>Rosenbrock23</code>, <code>TRBDF2</code>, <code>Rodas5</code>, <code>KenCarp4</code>, <code>Tsit5</code>, <code>RK4</code>, <code>ImplicitEuler</code>, <code>Euler</code>. Information on the solver algorithms can be found on the <a href="https://docs.sciml.ai/DiffEqDocs/stable/solvers/ode_solve/">ODE solvers page</a>.</p>
 <p>The <code>dt</code> controls the stepsize. When <code>adaptive = true</code>, <code>dt</code> only applies to the initial stepsize, and by default it is automatically determined. When <code>adaptive = false</code> a suitable <code>dt</code> must always be provided. The value is in seconds, so <code>dt = 3600.0</code> corresponds to an hourly timestep. When <code>adaptive = true</code>, <code>dtmin</code> and <code>dtmax</code> control the minimum and maximum allowed <code>dt</code>. By default these depend on the problem and algorithm. If a smaller <code>dt</code> than <code>dtmin</code> is needed to meet the set error tolerances, the simulation stops, unless <code>force_dtmin</code> is set to <code>true</code>. <code>force_dtmin</code> is off by default to ensure an accurate solution.</p>

diff --git a/python/examples.html b/python/examples.html
@@ -548,7 +548,7 @@ <h1 data-number="2"><span class="header-section-number">2</span> Update the basi
 <span id="cb26-4"><a href="#cb26-4" aria-hidden="true" tabindex="-1"></a>ax <span class="op">=</span> df_flow.pivot_table(index<span class="op">=</span><span class="st">"time"</span>, columns<span class="op">=</span><span class="st">"edge"</span>, values<span class="op">=</span><span class="st">"flow_m3d"</span>).plot()</span>
 <span id="cb26-5"><a href="#cb26-5" aria-hidden="true" tabindex="-1"></a>ax.legend(bbox_to_anchor<span class="op">=</span>(<span class="fl">1.3</span>, <span class="dv">1</span>), title<span class="op">=</span><span class="st">"Edge"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-display" data-execution_count="26">
-<pre><code>&lt;matplotlib.legend.Legend at 0x7f286a467e90&gt;</code></pre>
+<pre><code>&lt;matplotlib.legend.Legend at 0x7ff7ce42e750&gt;</code></pre>
 </div>
 <div class="cell-output cell-output-display">
 <p><img src="examples_files/figure-html/cell-27-output-2.png" width="727" height="412"></p>

diff --git a/schema/BasinProfile.schema.json b/schema/BasinProfile.schema.json
@@ -1,32 +1,32 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://deltares.github.io/Ribasim/schema/BasinProfile.schema.json",
+    "title": "BasinProfile",
+    "description": "A BasinProfile object based on Ribasim.BasinProfileV1",
+    "type": "object",
     "properties": {
-        "remarks": {
+        "node_id": {
             "format": "default",
-            "default": "",
-            "description": "a hack for pandera",
-            "type": "string"
+            "type": "integer"
         },
         "area": {
             "format": "double",
             "type": "number"
         },
-        "node_id": {
-            "format": "default",
-            "type": "integer"
-        },
         "level": {
             "format": "double",
             "type": "number"
+        },
+        "remarks": {
+            "description": "a hack for pandera",
+            "type": "string",
+            "format": "default",
+            "default": ""
         }
     },
     "required": [
         "node_id",
         "area",
         "level"
-    ],
-    "$id": "https://deltares.github.io/Ribasim/schema/BasinProfile.schema.json",
-    "title": "BasinProfile",
-    "description": "A BasinProfile object based on Ribasim.BasinProfileV1",
-    "type": "object"
+    ]
 }
diff --git a/schema/BasinState.schema.json b/schema/BasinState.schema.json
@@ -1,27 +1,27 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://deltares.github.io/Ribasim/schema/BasinState.schema.json",
+    "title": "BasinState",
+    "description": "A BasinState object based on Ribasim.BasinStateV1",
+    "type": "object",
     "properties": {
-        "remarks": {
-            "format": "default",
-            "default": "",
-            "description": "a hack for pandera",
-            "type": "string"
-        },
         "node_id": {
             "format": "default",
             "type": "integer"
         },
         "level": {
             "format": "double",
             "type": "number"
+        },
+        "remarks": {
+            "description": "a hack for pandera",
+            "type": "string",
+            "format": "default",
+            "default": ""
         }
     },
     "required": [
         "node_id",
         "level"
-    ],
-    "$id": "https://deltares.github.io/Ribasim/schema/BasinState.schema.json",
-    "title": "BasinState",
-    "description": "A BasinState object based on Ribasim.BasinStateV1",
-    "type": "object"
+    ]
 }
diff --git a/schema/BasinStatic.schema.json b/schema/BasinStatic.schema.json
@@ -1,35 +1,39 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://deltares.github.io/Ribasim/schema/BasinStatic.schema.json",
+    "title": "BasinStatic",
+    "description": "A BasinStatic object based on Ribasim.BasinStaticV1",
+    "type": "object",
     "properties": {
-        "remarks": {
+        "node_id": {
             "format": "default",
-            "default": "",
-            "description": "a hack for pandera",
-            "type": "string"
+            "type": "integer"
         },
-        "precipitation": {
+        "drainage": {
             "format": "double",
             "type": "number"
         },
-        "infiltration": {
+        "potential_evaporation": {
             "format": "double",
             "type": "number"
         },
-        "urban_runoff": {
+        "infiltration": {
             "format": "double",
             "type": "number"
         },
-        "node_id": {
-            "format": "default",
-            "type": "integer"
-        },
-        "potential_evaporation": {
+        "precipitation": {
             "format": "double",
             "type": "number"
         },
-        "drainage": {
+        "urban_runoff": {
             "format": "double",
             "type": "number"
+        },
+        "remarks": {
+            "description": "a hack for pandera",
+            "type": "string",
+            "format": "default",
+            "default": ""
         }
     },
     "required": [
@@ -39,9 +43,5 @@
         "infiltration",
         "precipitation",
         "urban_runoff"
-    ],
-    "$id": "https://deltares.github.io/Ribasim/schema/BasinStatic.schema.json",
-    "title": "BasinStatic",
-    "description": "A BasinStatic object based on Ribasim.BasinStaticV1",
-    "type": "object"
+    ]
 }
diff --git a/schema/BasinTime.schema.json b/schema/BasinTime.schema.json
@@ -1,39 +1,43 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://deltares.github.io/Ribasim/schema/BasinTime.schema.json",
+    "title": "BasinTime",
+    "description": "A BasinTime object based on Ribasim.BasinTimeV1",
+    "type": "object",
     "properties": {
-        "remarks": {
+        "node_id": {
             "format": "default",
-            "default": "",
-            "description": "a hack for pandera",
-            "type": "string"
+            "type": "integer"
         },
         "time": {
             "format": "date-time",
             "type": "string"
         },
-        "precipitation": {
+        "drainage": {
             "format": "double",
             "type": "number"
         },
-        "infiltration": {
+        "potential_evaporation": {
             "format": "double",
             "type": "number"
         },
-        "urban_runoff": {
+        "infiltration": {
             "format": "double",
             "type": "number"
         },
-        "node_id": {
-            "format": "default",
-            "type": "integer"
-        },
-        "potential_evaporation": {
+        "precipitation": {
             "format": "double",
             "type": "number"
         },
-        "drainage": {
+        "urban_runoff": {
             "format": "double",
             "type": "number"
+        },
+        "remarks": {
+            "description": "a hack for pandera",
+            "type": "string",
+            "format": "default",
+            "default": ""
         }
     },
     "required": [
@@ -44,9 +48,5 @@
         "infiltration",
         "precipitation",
         "urban_runoff"
-    ],
-    "$id": "https://deltares.github.io/Ribasim/schema/BasinTime.schema.json",
-    "title": "BasinTime",
-    "description": "A BasinTime object based on Ribasim.BasinTimeV1",
-    "type": "object"
+    ]
 }