build based on 4359d3b

Author: Documenter.jl

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.11.6","generation_timestamp":"2025-08-06T12:21:22","documenter_version":"1.14.1"}}
+{"documenter":{"julia_version":"1.11.6","generation_timestamp":"2025-09-04T05:56:23","documenter_version":"1.14.1"}}

dev/VPLVerse/Ecophys/growth/index.html

@@ -10,4 +10,4 @@
 opt = SimpleOptical(αPAR = 0.80)</code></pre><p>Two models to compute the boundary layer conductance are available. They differ in the amount of information used regarding the geometry of the leaf. A simple model only accounts for the leaf characteristic length and is the most common approach (as before, a version that supports <code>Quantity</code> objects is also available):</p><pre><code class="language-julia hljs">gb = simplegb(d = 0.1)
 gbQ = simplegbQ(d = 0.1m)</code></pre><p>The second model is more complex as it takes into account the aspect ratio (length/width) of the leaf as well as its inclination angle. It will also distinguish between the boundary layer conductance of the front and back side of the leaf. This model relies on unpublished equations fitted to the data reviewed by <a href="https://nph.onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.1993.tb03898.x">Schuepp (1993, New Phyto)</a>:</p><pre><code class="language-julia hljs">gbang = gbAngle(d = 0.1, ang = π/4, ar = 0.1)
 gbangQ = gbAngleQ(d = 0.1m, ang = π/4, ar = 0.1)</code></pre><p>The leaf energy balance is then computed using <code>solve_energy_balance()</code> which will compute the leaf temperature that closes the energy balance as well as the corresponding CO2 assimilationa and transpiration:</p><pre><code class="language-julia hljs">Tleaf, A, Tr = solve_energy_balance(c3; gb = gb, opt = opt, PAR = 100.0, ws = 5.0)
-TleafangQ, AangQ, TrangQ = solve_energy_balance(c3Q; gb = gbangQ, opt = opt, PAR = 100.0μmol/m^2/s, ws = 5.0m/s)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../SkyDomes/API/">« SkyDomes API</a><a class="docs-footer-nextpage" href="photosynthesis/">Photosynthesis API »</a><div class="flexbox-break"></div></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.14.1 on <span class="colophon-date" title="Wednesday 6 August 2025 12:21">Wednesday 6 August 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+TleafangQ, AangQ, TrangQ = solve_energy_balance(c3Q; gb = gbangQ, opt = opt, PAR = 100.0μmol/m^2/s, ws = 5.0m/s)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../SkyDomes/API/">« SkyDomes API</a><a class="docs-footer-nextpage" href="photosynthesis/">Photosynthesis API »</a><div class="flexbox-break"></div></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.14.1 on <span class="colophon-date" title="Thursday 4 September 2025 05:56">Thursday 4 September 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/VPLVerse/Ecophys/index.html

@@ -41,4 +41,4 @@
                      ws = 1.0, RH = 0.75, Tair = 298.0, Ca = 400.0,
                      P = 101.0e3, O2 = 210.0e3, order = Order2(), xatol = 0.01,
                      maxfnevals = 100, net = true)</code></pre><p>Solve the leaf energy balance coupled to photosynthesis and transpiration.</p><p><strong>Arguments</strong></p><ul><li><code>Ags</code>: Photosynthesis and stomatal conductance model</li><li><code>gb</code>: Boundary layer conductance model</li><li><code>opt</code>: Optical properties of the leaf</li><li><code>PAR</code>: Photosynthetically active radiation (umol/m2/s)</li><li><code>NIR</code>: Near-infrared radiation (W/m2)</li><li><code>ws</code>: Wind speed (m/s)</li><li><code>RH</code>: Relative humidity</li><li><code>Tair</code>: Air temperature (K)</li><li><code>Ca</code>: Atmospheric CO2 concentration (μmol/mol)</li><li><code>P</code>: Air pressure (Pa)</li><li><code>O2</code>: Atmospheric O2 concentration (μmol/mol)</li><li><code>order</code>: Order of the root solving algorithm that finds leaf temperature         (see Roots.jl package for more information).</li><li><code>xatol</code>: Absolute tolerance of the root solving algorithm (see Roots.jl package for more information),</li><li><code>maxfnevals</code>: Maximum number of function evaluations of the root solving algorithm (see Roots.jl package for more information).</li><li><code>net</code>: Whether to return net or gross CO2 assimilation.</li></ul><p><strong>Details</strong></p><p>Inputs maybe be either <code>Real</code> or <code>Quantity</code> types from Unitful.jl (i.e., with physical units). If <code>Quantity</code> types are used, the output will be a <code>Quantity</code> type.</p><p><strong>Returns</strong></p><p>A named tuple with net CO2 assimilation (<code>An</code>, μmol/m^2/s), gross CO2 assimilation (<code>Ag</code>, μmol/m^2/s), transpiration (<code>Tr</code>, mol/m^2/s) and leaf temperature (<code>Tleaf</code>, K).</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/VirtualPlantLab/Ecophys.jl/blob/v0.1.1/src/Photosynthesis/EnergyBalance/EnergyBalance.jl#L92-L137">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Ecophys.Photosynthesis.transpiration-Tuple{}" href="#Ecophys.Photosynthesis.transpiration-Tuple{}"><code>Ecophys.Photosynthesis.transpiration</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">transpiration(;gsw = 0.1, gbw = 1.0, Tleaf = 300.0, Tair = 298.0, P = 101e3,
-               RH = 0.75)</code></pre><p>Compute transpiration rate (mol/m^2/s) from conductance to water vapor and environmental variables.</p><p><strong>Arguments</strong></p><ul><li><code>gsw</code>: Stomatal conductance to water vapor (mol/m^2/s)</li><li><code>gbw</code>: Boundary layer conductance to water vapor (mol/m^2/s)</li><li><code>Tleaf</code>: Leaf temperature (K)</li><li><code>Tair</code>: Air temperature (K)</li><li><code>P</code>: Air pressure (Pa)</li><li><code>RH</code>: Relative humidity</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/VirtualPlantLab/Ecophys.jl/blob/v0.1.1/src/Photosynthesis/EnergyBalance/EnergyBalance.jl#L234-L248">source</a></section></article><h2 id="Private"><a class="docs-heading-anchor" href="#Private">Private</a><a id="Private-1"></a><a class="docs-heading-anchor-permalink" href="#Private" title="Permalink"></a></h2><p>Private functions, types or constants from <code>Photosynthesis</code>. These are not exported, so you need to prefix the function name with <code>Ecophys.Photosynthesis</code> to access them. Also bear in mind that these are not part of the public API, so they may change without notice.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Ecophys package</a><a class="docs-footer-nextpage" href="../growth/">Growth API »</a><div class="flexbox-break"></div></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.14.1 on <span class="colophon-date" title="Wednesday 6 August 2025 12:21">Wednesday 6 August 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+               RH = 0.75)</code></pre><p>Compute transpiration rate (mol/m^2/s) from conductance to water vapor and environmental variables.</p><p><strong>Arguments</strong></p><ul><li><code>gsw</code>: Stomatal conductance to water vapor (mol/m^2/s)</li><li><code>gbw</code>: Boundary layer conductance to water vapor (mol/m^2/s)</li><li><code>Tleaf</code>: Leaf temperature (K)</li><li><code>Tair</code>: Air temperature (K)</li><li><code>P</code>: Air pressure (Pa)</li><li><code>RH</code>: Relative humidity</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/VirtualPlantLab/Ecophys.jl/blob/v0.1.1/src/Photosynthesis/EnergyBalance/EnergyBalance.jl#L234-L248">source</a></section></article><h2 id="Private"><a class="docs-heading-anchor" href="#Private">Private</a><a id="Private-1"></a><a class="docs-heading-anchor-permalink" href="#Private" title="Permalink"></a></h2><p>Private functions, types or constants from <code>Photosynthesis</code>. These are not exported, so you need to prefix the function name with <code>Ecophys.Photosynthesis</code> to access them. Also bear in mind that these are not part of the public API, so they may change without notice.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Ecophys package</a><a class="docs-footer-nextpage" href="../growth/">Growth API »</a><div class="flexbox-break"></div></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.14.1 on <span class="colophon-date" title="Thursday 4 September 2025 05:56">Thursday 4 September 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>