Commit last-minute
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221 changed files with 139931 additions and 1 deletions
20
hydroshoot/doc/Makefile
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20
hydroshoot/doc/Makefile
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# Minimal makefile for Sphinx documentation
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||||
#
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||||
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||||
# You can set these variables from the command line.
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||||
SPHINXOPTS =
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SPHINXBUILD = sphinx-build
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SPHINXPROJ = HydroShoot
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SOURCEDIR = .
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||||
BUILDDIR = _build
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||||
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||||
# Put it first so that "make" without argument is like "make help".
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help:
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||||
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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||||
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.PHONY: help Makefile
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||||
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||||
# Catch-all target: route all unknown targets to Sphinx using the new
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||||
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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||||
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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||||
0
hydroshoot/doc/_static/nonempty.txt
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0
hydroshoot/doc/_static/nonempty.txt
vendored
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108
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After Width: | Height: | Size: 11 KiB |
1
hydroshoot/doc/authors.rst
Normal file
1
hydroshoot/doc/authors.rst
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.. include:: ../AUTHORS.rst
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166
hydroshoot/doc/conf.py
Normal file
166
hydroshoot/doc/conf.py
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@ -0,0 +1,166 @@
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|||
# -*- coding: utf-8 -*-
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#
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||||
# Configuration file for the Sphinx documentation builder.
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||||
#
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||||
# This file does only contain a selection of the most common options. For a
|
||||
# full list see the documentation:
|
||||
# http://www.sphinx-doc.org/en/master/config
|
||||
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# -- Path setup --------------------------------------------------------------
|
||||
|
||||
# If extensions (or modules to document with autodoc) are in another directory,
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||||
# add these directories to sys.path here. If the directory is relative to the
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||||
# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import os
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import sys
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sys.path.insert(0, os.path.abspath("..")) # to include the root of the package
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# -- Project information -----------------------------------------------------
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project = u'HydroShoot'
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copyright = u'2021, Rami Albasha'
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author = u'Rami Albasha'
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|
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# The short X.Y version
|
||||
version = u''
|
||||
# The full version, including alpha/beta/rc tags
|
||||
release = u'1.0.0'
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||||
|
||||
# -- General configuration ---------------------------------------------------
|
||||
|
||||
# If your documentation needs a minimal Sphinx version, state it here.
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||||
#
|
||||
# needs_sphinx = '1.0'
|
||||
|
||||
# Add any Sphinx extension module names here, as strings. They can be
|
||||
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
|
||||
# ones.
|
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extensions = [
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"sphinx.ext.autodoc", # support for automatic inclusion of docstring
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||||
"sphinx.ext.autosummary", # generates autodoc summaries
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"sphinx.ext.doctest", # inclusion and testing of doctest code snippets
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"sphinx.ext.intersphinx", # support for linking to other projects
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#"sphinx.ext.imgmath", # support for math equations
|
||||
"sphinx.ext.mathjax", # support for math equations
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||||
"sphinx.ext.ifconfig", # support for conditional content
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||||
"sphinx.ext.viewcode", # support for links to source code
|
||||
"sphinx.ext.coverage", # includes doc coverage stats in the documentation
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"sphinx.ext.todo", # support for todo items
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"sphinx.ext.napoleon", # support for numpy and google style docstrings
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||||
"sphinx_favicon", # support for favicon
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||||
"nbsphinx", # for integrating jupyter notebooks
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"myst_parser", # for parsing .md files
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]
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nbsphinx_allow_errors = True
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# Add any paths that contain templates here, relative to this directory.
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||||
templates_path = ["_templates"]
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autosummary_generate = True
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exclude_patterns = ["_build", "_templates"]
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# The suffix(es) of source filenames.
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# You can specify multiple suffix as a list of string:
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source_suffix = {
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".rst": "restructuredtext",
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".md": "markdown",
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}
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# The master toctree document.
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master_doc = "index"
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# The version info for the project you're documenting, acts as replacement for
|
||||
# |version| and |release|, also used in various other places throughout the
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# built documents.
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||||
#
|
||||
# The language for content autogenerated by Sphinx. Refer to documentation
|
||||
# for a list of supported languages.
|
||||
#
|
||||
# This is also used if you do content translation via gettext catalogs.
|
||||
# Usually you set "language" from the command line for these cases.
|
||||
language = "en"
|
||||
# The name of the Pygments (syntax highlighting) style to use.
|
||||
pygments_style = "sphinx"
|
||||
# If true, `todo` and `todoList` produce output, else they produce nothing.
|
||||
todo_include_todos = False
|
||||
|
||||
# -- Options for HTML output ----------------------------------------------
|
||||
# The theme to use for HTML and HTML Help pages. See the documentation for
|
||||
# a list of builtin themes.
|
||||
html_theme = "pydata_sphinx_theme"
|
||||
# Theme options are theme-specific and customize the look and feel of a theme
|
||||
# further. For a list of options available for each theme, see the
|
||||
# documentation.
|
||||
html_theme_options = {
|
||||
"header_links_before_dropdown": 6,
|
||||
"sidebarwidth": 200,
|
||||
"collapse_navigation": "false",
|
||||
"icon_links": [
|
||||
{
|
||||
"name": "GitHub",
|
||||
"url": "https://github.com/openalea/hydroshoot",
|
||||
"icon": "fa-brands fa-github",
|
||||
},
|
||||
],
|
||||
"show_version_warning_banner": True,
|
||||
"footer_start": ["copyright"],
|
||||
"footer_center": ["sphinx-version"],
|
||||
"secondary_sidebar_items": {
|
||||
"**/*": ["page-toc", "edit-this-page", "sourcelink"],
|
||||
"examples/no-sidebar": [],
|
||||
},
|
||||
}
|
||||
# Add any paths that contain custom static files (such as style sheets) here,
|
||||
# relative to this directory. They are copied after the builtin static files,
|
||||
# so a file named "default.css" will overwrite the builtin "default.css".
|
||||
html_static_path = ["_static"]
|
||||
html_logo = "_static/openalea_web.svg"
|
||||
html_favicon = "_static/openalea_web.svg"
|
||||
# If false, no module index is generated.
|
||||
html_domain_indices = True
|
||||
# If false, no index is generated.
|
||||
html_use_index = True
|
||||
# If true, the index is split into individual pages for each letter.
|
||||
html_split_index = False
|
||||
# If true, links to the reST sources are added to the pages.
|
||||
html_show_sourcelink = True
|
||||
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
|
||||
html_show_sphinx = True
|
||||
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
|
||||
html_show_copyright = True
|
||||
# Output file base name for HTML help builder.
|
||||
htmlhelp_basename = "Hydroshoot_documentation"
|
||||
|
||||
# -- Options for LaTeX output ---------------------------------------------
|
||||
latex_elements = {}
|
||||
latex_documents = [
|
||||
(
|
||||
master_doc,
|
||||
"Hydroshoot.tex",
|
||||
"Hydroshoot Documentation",
|
||||
"INRAE / inria / CIRAD",
|
||||
"manual",
|
||||
),
|
||||
]
|
||||
|
||||
# -- Options for manual page output ---------------------------------------
|
||||
# One entry per manual page. List of tuples
|
||||
# (source start file, name, description, authors, manual section).
|
||||
man_pages = [(master_doc, "hydroshoot", "Hydroshoot Documentation", [author], 1)]
|
||||
|
||||
# -- Options for Texinfo output -------------------------------------------
|
||||
# Grouping the document tree into Texinfo files. List of tuples
|
||||
# (source start file, target name, title, author,
|
||||
# dir menu entry, description, category)
|
||||
texinfo_documents = [
|
||||
(
|
||||
master_doc,
|
||||
"Hydroshoot",
|
||||
"Hydroshoot Documentation",
|
||||
author,
|
||||
"Hydroshoot",
|
||||
"One line description of project.",
|
||||
"Miscellaneous",
|
||||
),
|
||||
]
|
||||
# Example configuration for intersphinx: refer to the Python standard library.
|
||||
intersphinx_mapping = {"python": ("https://docs.python.org/", None)}
|
||||
1
hydroshoot/doc/contributing.rst
Normal file
1
hydroshoot/doc/contributing.rst
Normal file
|
|
@ -0,0 +1 @@
|
|||
.. include:: ../CONTRIBUTING.rst
|
||||
10
hydroshoot/doc/ecophysio.rst
Normal file
10
hydroshoot/doc/ecophysio.rst
Normal file
|
|
@ -0,0 +1,10 @@
|
|||
==========================
|
||||
Ecophysiological processes
|
||||
==========================
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 2
|
||||
|
||||
hydraulic
|
||||
exchange
|
||||
energy
|
||||
55
hydroshoot/doc/ecophysio_solver.rst
Normal file
55
hydroshoot/doc/ecophysio_solver.rst
Normal file
|
|
@ -0,0 +1,55 @@
|
|||
======================
|
||||
Processes interactions
|
||||
======================
|
||||
|
||||
Interactions among the physiological processes occur.
|
||||
|
||||
.. figure:: figs/ecophysio_solver_1.svg
|
||||
:align: center
|
||||
|
||||
Solving the interactions between leaf's water potential, transpiration rate and temperature !
|
||||
|
||||
From the one hand. Leaf water potential (:math:`\Psi`) exerts a control on stomatal conductance to water vapor
|
||||
(:math:`g_{s, \ H_2O}`) and, consequently, on transpiration flux (:math:`E`). However, the latter also determines how much
|
||||
water will flow through the hydraulic segments to be withdrawn from the soil, which affects the distribution of
|
||||
water potential across those segments (Ohm's law). Hence, we have a reciprocity between the distribution of water
|
||||
potential across the shoot (hydraulic structure) and transpiration fluxes from individual leaves.
|
||||
|
||||
From the other hand, leaf temperature (:math:`T`) determines the rate of leaf photosynthesis (Arrhenius functions)
|
||||
and stomatal conductance to both :math:`CO_2` (:math:`g_{s, \ CO_2}`) and water vapor (:math:`g_{s, \ H_2O}`).
|
||||
This means that :math:`T` affects also the transpiration flux :math:`E` which also means that :math:`T` exerts a further
|
||||
control on the hydraulic structure.
|
||||
|
||||
Putting it all together:
|
||||
|
||||
For a given initial temperature (:math:`T_0`) and soil water potential (:math:`\Psi_0`), a leaf can fix :math:`CO_2`
|
||||
with a rate :math:`A_{n, \ 0}` while having a stomatal conductance rate of :math:`g_{s, \ H_2O, \ 0}`.
|
||||
The corresponding water flux transpired by this leaf will be :math:`E_0`. Summed up across all leaves, plant
|
||||
transpiration will withdraw water from the soil, reducing thus soil water potential and resulting in a new :math:`\Psi`
|
||||
value (:math:`\Psi_1`).
|
||||
:math:`\Psi_1`, will hence impose a new stomatal conductance :math:`g_{s, \ H_2O, \ 1}` and consequently a new
|
||||
transpiration flux :math:`E_1`. Yet, this new :math:`E_1` means that leaf temperature is :math:`T_1`... **REWIND**!
|
||||
|
||||
HydroShoot resolve this interactions iteratively until reaching steady rate values of :math:`A_n,` and :math:`E` (
|
||||
implying steady state distribution of water potential cross the shoot). :numref:`fig_2` shows how interactions between
|
||||
the hydraulic, energy and gas-exchange processes is handled in HydroShoot.
|
||||
|
||||
.. _fig_2:
|
||||
|
||||
.. figure:: figs/ecophysio_solver_2.png
|
||||
|
||||
Schematic representation of the numerical resolution of HydroShoot. Meteorological inputs that are common
|
||||
to all leaves are air temperature (:math:`T_{air}, \ K`), air relative humidity (:math:`RH, \ -`), air
|
||||
:math:`CO_2` concentration :math:`[\mu mol\ {mol}^{-1}]`, wind speed (:math:`u, \ m \ s^{-1}`), and atmospheric
|
||||
pressure (:math:`P_a, \ kPa`). Inputs per individual leaves are the absorbed photosynthetic photon flux density
|
||||
(:math:`PPFD, \ \mu mol \ m^{-2} \ s^{-1}`) and :math:`{PPFD}_{10}` the absorbed :math:`PPFD` during the last
|
||||
10 days. :math:`\Psi_u \ [MPa]` is xylem water potential at the nodes between each pair of hydraulic segments.
|
||||
:math:`\Psi_{u, \ init} \ [MPa]` is initial :math:`\Psi_u`. :math:`\Psi_{soil} \ [MPa]` is soil water potential.
|
||||
:math:`T_i \ [K]` is leaf temperature. :math:`T_{i, \ init} \ [K]` is initial :math:`T_i`.
|
||||
:math:`K_{init} \ [kg \ s^{-1} \ m \ {MPa}^{-1}]` is initial hydraulic conductivity of each segment.
|
||||
:math:`\epsilon_x \ [MPa]` is the maximum allowable error of the estimation of xylem water potential. Finally,
|
||||
:math:`\epsilon_T \ [K]` is the maximum allowable error of the estimation of leaf temperature.
|
||||
Circles inside module boxes indicate internal iteration loops. Symbols between curly brackets represent spatially
|
||||
structured variables.
|
||||
|
||||
|
||||
92
hydroshoot/doc/energy.rst
Normal file
92
hydroshoot/doc/energy.rst
Normal file
|
|
@ -0,0 +1,92 @@
|
|||
=============
|
||||
Energy budget
|
||||
=============
|
||||
|
||||
.. figure:: figs/energy_1.png
|
||||
:align: center
|
||||
|
||||
The *energy* module computes the temperature of individual leaves based on a detailed energy balance model (see
|
||||
Supporting Information S3 in **Albasha et al., 2019**).
|
||||
|
||||
Energy gain of each leaf comes from:
|
||||
|
||||
1. the absorbed shortwave;
|
||||
2. thermal longwave radiation from the sky;
|
||||
3. thermal longwave radiation from the sky;
|
||||
4. thermal longwave radiation from the soil;
|
||||
5. thermal longwave radiation from the neighbouring leaves.
|
||||
|
||||
Energy loss of each leaf is due to
|
||||
|
||||
1. thermal longwave radiation emitted by the leaf
|
||||
2. latent heat due to transpiration (evaporative cooling)
|
||||
|
||||
Energy gain or loss may result from heat exchange between the each leaf and the surrounding air by thermal
|
||||
conduction-convection.
|
||||
|
||||
The resulting leaf-scale energy balance equation writes:
|
||||
|
||||
.. math::
|
||||
0 & = \alpha_{i, \ R_g} \cdot \Phi_{i, \ R_g} \\
|
||||
& + \epsilon_{i, \ leaf} \cdot \sigma \cdot
|
||||
\left(
|
||||
k_{i, \ sky} \cdot \epsilon_{sky} \cdot T_{sky}^4
|
||||
+ k_{i, \ soil} \cdot \epsilon_{soil} \cdot T_{soil}^4
|
||||
+ \left[1 - \left(k_{sky} + k_{soil} \right) \right] \cdot T_i^4
|
||||
\right) \\
|
||||
& - 2 \cdot \epsilon_{i, \ leaf} \cdot \sigma \cdot T_i^4 \\
|
||||
& - \lambda \cdot E_i \\
|
||||
& - 2 \cdot K_{air} \cdot \frac{T_i - T_{air}}{\Delta x_i}
|
||||
|
||||
|
||||
where
|
||||
:math:`i` refers to leaf identifier,
|
||||
:math:`j` refers to neighbouring leaves identifier,
|
||||
:math:`\Omega` denotes the upper hemisphere surrounding the leaf :math:`i`,
|
||||
:math:`\alpha_{R_g} \ [-]` is lumped leaf absorptance in the shortwave band,
|
||||
:math:`\Phi_{R_g} \ [W \ m_{leaf}^{-2}]` flux density of shortwave global irradiance,
|
||||
:math:`\epsilon_{leaf} \ [-]` emissivity-absorptivity coefficients of the leaf,
|
||||
:math:`\epsilon_{sky} \ [-]` emissivity-absorptivity coefficients of the leaf,
|
||||
:math:`\epsilon_{soil} \ [-]` emissivity-absorptivity coefficients of the soil,
|
||||
:math:`\lambda \ [W \ s \ {mol}^{-1}]` is latent heat for vaporization,
|
||||
:math:`\sigma \ [W \ m^{-2} \ K^{-4}]` the Stefan-Boltzmann constant,
|
||||
:math:`k_{sky} \ [-]` form factor of the sky,
|
||||
:math:`k_{soil} \ [-]` form factor of the soil,
|
||||
:math:`T \ [K]` leaf temperature,
|
||||
:math:`T_{air}` air temperature,
|
||||
:math:`T_{sky} \ [K]` sky temperature,
|
||||
:math:`T_{soil} \ [K]` soil temperature,
|
||||
:math:`K_{air} \ [W \ m^{-1} \ K^{-1}]` the thermal conductivity of air,
|
||||
:math:`E \ [mol \ m_{leaf}^{-2} \ s^{-1}]` transpiration flux, and
|
||||
:math:`\Delta x_i \ [m]` thickness of the boundary layer.
|
||||
|
||||
|
||||
.. note::
|
||||
Only the forced convective heat transfer is currently considered in HydroShoot since forced convection dominates
|
||||
free convection once wind speed exceeds roughly 0.1 :math:`m \ s^{-1}` **(Nobel 2005)**. This wind speed threshold
|
||||
is generally exceeded during diurnal hours. However, under low wind conditions heat transfer may be underestimated.
|
||||
|
||||
Sky and soil form factors: the *Pirouette Cacahuete* issue!
|
||||
-----------------------------------------------------------
|
||||
|
||||
You may notice once you do your first run something like this:
|
||||
|
||||
.. figure:: figs/energy_2.png
|
||||
:align: center
|
||||
|
||||
|
||||
This refers to the method used to calculate the lumped sky and soil form factors (respectively :math:`k_{sky}` and
|
||||
:math:`k_{soil}`).
|
||||
|
||||
In order to reduce calculation costs, :math:`k_{sky}` and :math:`k_{soil}`) are obtained by flip flopping the canopy:
|
||||
|
||||
.. figure:: figs/energy_3.png
|
||||
:align: center
|
||||
|
||||
At first, the canopy is turned downwards. A unit irradiance is emitted from each sky sector and irradiance that is
|
||||
intercepted by a leaf :math:`i` is assumed equivalent to the form factor between that leaf and the "soil".
|
||||
In the second step, the canopy is turned upwards again and similarly, a unit irradiance is emitted from each sky sector.
|
||||
In this case, irradiance that is intercepted by a leaf :math:`i` is assumed equivalent to the form factor between that
|
||||
leaf and the "sky".
|
||||
|
||||
This method is clearly not 100% precise. It may need further improvements in the future.
|
||||
18
hydroshoot/doc/environment.yml
Normal file
18
hydroshoot/doc/environment.yml
Normal file
|
|
@ -0,0 +1,18 @@
|
|||
name: hydroshoot
|
||||
channels:
|
||||
- conda-forge
|
||||
- openalea3
|
||||
dependencies:
|
||||
- openalea.mtg
|
||||
- openalea.plantgl
|
||||
- alinea.caribu
|
||||
- alinea.astk
|
||||
- numpy
|
||||
- scipy
|
||||
- sympy
|
||||
- pandas
|
||||
- jsonschema
|
||||
- pvlib-python
|
||||
- pip
|
||||
- pip:
|
||||
- -e ..[doc]
|
||||
248
hydroshoot/doc/exchange.rst
Normal file
248
hydroshoot/doc/exchange.rst
Normal file
|
|
@ -0,0 +1,248 @@
|
|||
============
|
||||
Gas exchange
|
||||
============
|
||||
|
||||
.. figure:: figs/exchange.png
|
||||
:align: center
|
||||
|
||||
The *exchange* module computes the rates of net carbon assimilation of C3 plants (:math:`A_n`), stomatal conductance
|
||||
to CO2 (:math:`g_{s, \ CO_2}`) and water vapor (:math:`g_{s, \ H_2O}`), and transpiration (:math:`E`) per unit leaf
|
||||
surface area as a function of micrometeorological conditions and leaf water status.
|
||||
|
||||
|
||||
:math:`A_n` and :math:`g_{s, \ CO_2}` are coupled based on the analytical solution proposed by **Yin et al. (2009)**
|
||||
which also considers mesophyll conductance to CO2 diffusion :math:`g_m`. The solution is based on the following
|
||||
equations (following **Evers et al. 2010** supporting information):
|
||||
|
||||
.. math::
|
||||
\begin{array}{l}
|
||||
A_n = \frac{(C_c - \Gamma) \cdot x_1}{C_c + x_2} - R_d \\
|
||||
C_c = C_i - \frac{A_n}{g_m} \\
|
||||
g_{s, CO_{2}} = g_{s0, CO_{2}} + m_0 \cdot \frac{A_n + R_d}{C_i - \Gamma} \cdot f_w \\
|
||||
g_{s, CO_{2}} = \frac{A_n}{C_a - C_i - A_n \cdot r_{tb}}
|
||||
\end{array}
|
||||
|
||||
where
|
||||
:math:`A_n \ [\mu mol \ m^{-2} \ s^{-1}]` is net carbon assimilation rate,
|
||||
:math:`R_d \ [\mu mol \ m^{-2} \ s^{-1}]` is mitochondrial respiration in the light,
|
||||
:math:`\Gamma \ [\mu bar]` is :math:`CO_2` compensation point in the absence of mitochondrial respiration,
|
||||
:math:`x_1 \ [\mu mol \ m^{-2} \ s^{-1}]` and :math:`x_2 \ [\mu bar]` are intermediate parameters,
|
||||
:math:`g_m \ [\mu mol \ m^{-2} \ s^{-1} \ {\mu bar}^{-1}]` is mesophyll conductance for :math:`CO_2` diffusion,
|
||||
:math:`g_{s, \ CO_2} \ [mol \ m^{-2} \ s^{-1} \ {\mu bar}^{-1}]` is stomatal conductance to :math:`CO_2`,
|
||||
:math:`g_{s0, \ CO_2} \ [mol \ m^{-2} \ s^{-1} \ {\mu bar}^{-1}]` is the residual stomatal conductance to :math:`CO_2`,
|
||||
:math:`m_0 \ [-]` is a shape parameter regulating the slope between :math:`A_n` and :math:`g_{s, \ CO_2}`,
|
||||
:math:`f_w \ [-]` is a dimensionless function representing the response of stomatal conductance to soil or plant water status,
|
||||
:math:`r_{tb} \ [m^2 \ s \ \mu bar \ {\mu mol}^{-1}]` is the combined turbulence and boundary layer resistance for :math:`CO_2`,
|
||||
:math:`C_a \ [\mu bar]` is air :math:`CO_2` partial pressure,
|
||||
:math:`C_i \ [\mu bar]` is intercellular :math:`CO_2` partial pressure, and
|
||||
:math:`C_c \ [\mu bar]` is chloroplast :math:`CO_2` partial pressure.
|
||||
|
||||
|
||||
Net carbon assimilation rate per unit leaf area
|
||||
-----------------------------------------------
|
||||
:math:`A_n` is given as:
|
||||
|
||||
.. math::
|
||||
A_n = V_c \cdot \left(1 - \frac{\Gamma}{C_c} \right) - R_d
|
||||
|
||||
where
|
||||
:math:`V_c \ [\mu mol \ m^{-2} \ s^{-1}]` is carboxylation rate,
|
||||
:math:`\Gamma \ [\mu {mol}_{CO_2} \ {mol}_{CO_2}^{-1}]` :math:`CO_2` compensation point in the absence of mitochondrial
|
||||
respiration,
|
||||
:math:`C_c \ [\mu {mol}_{CO_2} \ {mol}^{-1}]` chloroplast :math:`CO_2` concentration, and
|
||||
:math:`R_d \ [\mu mol \ m^{-2} \ s^{-1}]` is mitochondrial respiration rate in the light.
|
||||
|
||||
:math:`V_c` is given as:
|
||||
|
||||
.. math::
|
||||
V_c = \min \left(W_c, W_j, W_p \right)
|
||||
|
||||
where
|
||||
:math:`W_c`, :math:`W_j`, and :math:`W_p \ [\mu mol \ m^{-2} \ s^{-1}]` are respectively Rubisco-limited carboxylation
|
||||
rate, RuBP-limited carboxylation rate, and Triose phosphates-limited carboxylation rate, given as:
|
||||
|
||||
.. math::
|
||||
\begin{array}{l}
|
||||
W_c = \frac{C_c \cdot V_{c, \max}}{C_c + K_c \cdot \left(1 + \frac{O}{K_o} \right)} \\
|
||||
W_j = \frac{J}{4 + 8 \cdot \frac{\Gamma}{C_c}} \\
|
||||
W_p = \frac{3 \cdot TPU}{\left(1 - \frac{\Gamma}{C_c} \right)}
|
||||
\end{array}
|
||||
|
||||
where
|
||||
:math:`V_{c, \ max} \ [\mu mol \ m^{-2} \ s^{-1}]` is the maximum carboxylation rate,
|
||||
:math:`J \ [\mu mol \ m^{-2} \ s^{-1}]` electron transport rate,
|
||||
:math:`TPU \ [\mu mol \ m^{-2} \ s^{-1}]` Triose phosphates transport rate,
|
||||
:math:`K_c \ [\mu mol \ {mol}^{-1}]` Michaelis-Menten constant for the carboxylase,
|
||||
:math:`K_o \ [mmol \ {mol}^{-1}]` Michaelis-Menten constant for the oxygenase, and
|
||||
:math:`O \ [mmol \ {mol}^{-1}]` oxygen concentration.
|
||||
|
||||
|
||||
Finally, :math:`J` is given as:
|
||||
|
||||
.. math::
|
||||
J = \frac{\alpha \cdot {PPFD}}{\sqrt{1 + \frac{\alpha^2 \cdot {PPFD}^2}{J_{max}^2}}}
|
||||
|
||||
where
|
||||
:math:`J_{max} \ [\mu mol \ m^{-2} \ s^{-1}]` is maximum electron transport rate, and
|
||||
:math:`PPFD \ [\mu mol \ m^{-2} \ s{-1}]` is photosynthetic photon flux density.
|
||||
|
||||
|
||||
The impact of leaf temperature on the photosynthesis parameters is accounted for using Arrhenius functions.
|
||||
For :math:`V_{c, \ max}`, :math:`J_{max}`, :math:`TPU`, and :math:`R_d` temperature dependency writes:
|
||||
|
||||
|
||||
.. math::
|
||||
P = P^{25} \cdot \
|
||||
\frac {\exp \left(c - \frac{\Delta H_a}{R \cdot T_{leaf}} \right)}
|
||||
{1 + \exp \left(\frac {\Delta S \cdot T_{leaf} - \Delta H_d}
|
||||
{R \cdot T_{leaf}} \right)}
|
||||
|
||||
where
|
||||
:math:`P` denotes any of :math:`V_{c, \ max}`, :math:`J_{max}`, :math:`TPU`, and :math:`R_d` parameters,
|
||||
:math:`P^{25}` is the value of :math:`P` at 25 \ :math:`^\circ C`,
|
||||
:math:`c \ [-]` is a shape parameter,
|
||||
:math:`\Delta H_a \ [kJ \ {mol}_{CO_2}^{-1}]` is activation energy of the Arrhenius functions,
|
||||
:math:`\Delta H_d \ [kJ \ {mol}_{CO_2}^{-1}]` is deactivation energy of the Arrhenius functions,
|
||||
:math:`\Delta S \ [kJ \ K^{-1} \ {mol}_{CO_2}^{-1}]` is entropy term,
|
||||
:math:`R \ [kJ \ K^{-1} \ {mol}^{-1}]` is the ideal gas constant, and
|
||||
:math:`T_{leaf} \ [K]` is leaf temperature.
|
||||
|
||||
|
||||
Finally, for :math:`\Gamma`, :math:`K_c`, and :math:`K_o` temperature dependency writes:
|
||||
|
||||
.. math::
|
||||
P = \exp \left(
|
||||
c - \frac{\Delta H_a}{R \cdot T_{leaf}}
|
||||
\right)
|
||||
|
||||
|
||||
Variable intra-canopy photosynthetic capacities
|
||||
-----------------------------------------------
|
||||
Leaf photosynthetic traits (
|
||||
:math:`V_{cmax}`, :math:`J_{max}`, :math:`TPU` and :math:`R_d`; cf. Appendix I in **Albasha et al., 2019**) are set
|
||||
to vary as a function leaf nitrogen content per unit leaf surface area (:math:`N_a, \ g_N \ m^{-2}`) following
|
||||
**Prieto et al. (2012)**:
|
||||
|
||||
.. math::
|
||||
P^{25} = S_{N_a} \ N_a - b_{N_a}
|
||||
|
||||
|
||||
where
|
||||
:math:`P^{25} \ [\mu mol \ m^{-2} \ s^{-1}]` is the value at 25 :math:`^\circ C` for any of the rates
|
||||
of :math:`V_{cmax}`, :math:`J_{max}`, :math:`TPU` or :math:`R_d`,
|
||||
:math:`S_{N_a} \ [\mu mol \ g_N^{-1} \ s^{-1}]` and
|
||||
:math:`b_{N_a} \ [\mu mol \ m^{-2} \ s^{-1}]`
|
||||
are the slope and the intercept of the linear relationship with :math:`N_a` specific to each rate.
|
||||
|
||||
:math:`N_a` is calculated as the product of nitrogen content per unit leaf dry mass (
|
||||
:math:`N_m, \ g_N \ g_{drymatter}^{-1}`) and leaf dry mass per area (:math:`LMA, \ g_{drymatter} \ m^{-2}`).
|
||||
:math:`N_m` linearly varies with plant age, expressed as the thermal time cumulated since budburst, and :math:`LMA`
|
||||
is determined by leaf exposure to light during the last past days **(Prieto et al., 2012)**, as expressed
|
||||
respectively in the two following equations:
|
||||
|
||||
.. math::
|
||||
\begin{array}{l}
|
||||
N_m = a_N \cdot \sum_{i=budburst}^d {\left( \max{\left( 0, T_{air, \i} - T_b \right)} \right)} + b_N \\
|
||||
LMA = a_M \cdot \ \ln{(PPFD_{10})} + b_M
|
||||
\end{array}
|
||||
|
||||
where
|
||||
:math:`T_{air, \ i} \ [^\circ C]` is the mean temperature of the day :math:`i`,
|
||||
:math:`T_b \ [^\circ C]` is the base temperature (minimum required for growth), set to 10 :math:`\ ^\circ C` for
|
||||
grapevine and used for the calculation of thermal time since budburst,
|
||||
:math:`a_N \ [g_N \ g_{drymatter}^{-1} \ ^\circ C \ d^{-1}]` and
|
||||
:math:`b_N \ [g_N \ g_{drymatter}^{-1}]` are the slope and intercept of the linear relationship between :math:`N_m`
|
||||
and accumulated thermal time since budburst,
|
||||
:math:`PPFD_{10} \ [mol_{photon} \ m^{-2} \ d^{-1}]` is the cumulative photosynthetic photon flux density irradiance
|
||||
intercepted by the leaf (output of the energy module) averaged over the past 10 days,
|
||||
:math:`a_M \ [g_{drymatter} \ mol_{photon}^{-1} \ d^{-1}]` and
|
||||
:math:`b_M \ [g_{drymatter} \ m^{-2}]` are the slope and intercept of the linear relationship between :math:`LMA` and
|
||||
the logarithm of :math:`PPFD_{10}`.
|
||||
|
||||
|
||||
Photoinhibition
|
||||
---------------
|
||||
HydroShoot is provided with an empirical photoinhibition model which assumes that combined heat and water
|
||||
stresses inhibit photosynthesis by reducing the electron transport rate (:math:`J`):
|
||||
|
||||
.. math::
|
||||
\begin{array}{l}
|
||||
\Delta H_d = \Delta H_{d, \max} - \max \left( 0, \left( \Delta H_{d, \max} - \Delta H_{d, T} \right) \cdot \min \left( 1, \frac{\Psi_{leaf} - \Psi_{leaf, \max}}{\Psi_{leaf, \min} - \Psi_{leaf, \max}} \right) \right) \\
|
||||
\Delta H_{d, t} = \Delta H_{d, t1} - \left( \Delta H_{d, t1} - \Delta H_{d, t2} \right) \cdot \min \left( 1, \max \left( 0, \frac{T_{leaf} - T_{leaf1}}{T_{leaf2} - T_{leaf1}} \right) \right)
|
||||
\end{array}
|
||||
|
||||
where
|
||||
:math:`\Delta H_d \ [kJ \ mol^{-1}]` is calculated after accounting for the joint effects of leaf water potential
|
||||
:math:`\Psi_{leaf} \ MPa` and temperature :math:`T_{leaf} \ [K]`,
|
||||
:math:`\Delta H_{d, \ max} \ [kJ \ mol^{-1}]` is the value of :math:`\Delta H_d` without accounting for photoinhibition,
|
||||
:math:`\Delta H_{d, \ T} \ [kJ mol^{-1}]` is the value of :math:`\Delta H_d` after accounting for the effect of
|
||||
:math:`T_{leaf}`,
|
||||
:math:`\Psi_{leaf, \ max}` and :math:`\Psi_{leaf, \ min} \ [MPa]` are leaf water potential values at which
|
||||
photoinhibition starts and reaches its maximum effect, respectively, finally,
|
||||
:math:`\Delta H_{d, \ T1}` and :math:`\Delta H_{d, \ T2} \ [kJ mol^{-1}]` are empirical thresholds corresponding to
|
||||
leaf temperatures :math:`T_{leaf1}` and :math:`T_{leaf2}` which are temperatures at which photoinhibition starts and
|
||||
reaches its maximum effect, respectively.
|
||||
|
||||
|
||||
Transpiration rate per unit leaf area
|
||||
-------------------------------------
|
||||
|
||||
The transpiration rate (:math:`E, \ mol \ m^{-2} s^{-1}`) is calculated as:
|
||||
|
||||
.. math::
|
||||
E = \frac{1}{\frac{1}{g_{b, \ H_2O}} + \frac{1}{1.6 \cdot g_{s, \ CO_2}}} \left( \frac{VPD}{P_a} \right)
|
||||
|
||||
|
||||
where
|
||||
:math:`P_a \ [kPa]` is the atmospheric pressure and
|
||||
:math:`g_{b, \ H_2O} \ [mol \ m^{-2} s^{-1}]` is the boundary layer conductance to water vapor derived from
|
||||
**Nobel (2005)** as:
|
||||
|
||||
.. math::
|
||||
g_{b, \ H_2O} = \frac{D_{H_2O} \cdot P_v}{R \cdot T_{leaf} \cdot \Delta x}
|
||||
|
||||
with
|
||||
|
||||
.. math::
|
||||
D_{H_2O} = D_{H_2O, 0} \cdot \frac{P_a}{P_v} \cdot \left( \frac{T_{leaf}}{273} \right)^{1.8}
|
||||
|
||||
where
|
||||
:math:`D_{H_2O}` is the diffusion coefficient of H2O in the air at 0 :math:`^\circ C` (:math:`2.13 \cdot {10}^{-5} \ m^2 s^{-1}`),
|
||||
:math:`P_a \ [MPa]` is the ambient air pressure at 0 :math:`^\circ C`,
|
||||
:math:`P_v \ [MPa]` is water vapor partial pressure, and
|
||||
:math:`\Delta x \ [m]` is the thickness of the boundary layer defined following **Nobel (2005)** as:
|
||||
|
||||
.. math::
|
||||
\Delta x = 0.004 \sqrt{\frac{l}{v}}
|
||||
|
||||
where
|
||||
:math:`l \ [m]` is the mean length of the leaf in the downwind direction (set to 70% of blade length), and
|
||||
:math:`v \ [m \ s^{-1}]` is wind speed in the vicinity of the leaf.
|
||||
|
||||
|
||||
Finally, the impact of water stress on stomatal conductance (i.e. via the :math:`f_w` function) is calculated using
|
||||
one of the following options:
|
||||
|
||||
.. math::
|
||||
f_w =
|
||||
\left\{
|
||||
\begin{array}{cl}
|
||||
\frac{1}{1+\left( \frac{VPD}{D_0} \right)} & (a) \\
|
||||
\frac{1}{1+\left( \frac{\Psi_{leaf}}{\Psi_{crit, \ leaf}} \right)^n} & (b) \\
|
||||
\frac{1}{1+\left( \frac{\Psi_{soil}}{\Psi_{crit, \ leaf}} \right)^n} & (c) \\
|
||||
\end{array}
|
||||
\right.
|
||||
|
||||
|
||||
where
|
||||
:math:`VPD \ [kPa]` is vapor pressure deficit (between the leaf and the air),
|
||||
:math:`D_0 \ [kPa]` shape parameter,
|
||||
:math:`\Psi_{leaf} \ [MPa]` leaf bulk xylem potential,
|
||||
:math:`\Psi_{soil} \ [MPa]` soil bulk water potential (assumed equal to xylem potential at the base of the shoot), and
|
||||
:math:`\Psi_{crit, leaf} \ [MPa]` leaf water potential at which stomatal conductance reduces to half its maximum value.
|
||||
|
||||
|
||||
In case the option :math:`a` is used, stomatal conductance reduction is considered independent from the soil water
|
||||
status (i.e. following **Leuning, 1995**). In contrast, Both options :math:`b` and `c` allow simulating stomatal
|
||||
conductance as a function either of leaf water potential (i.e. regarding shoot hydraulic structure) or soil
|
||||
water potential (i.e. disregarding the hydraulic structure of the shoot).
|
||||
913
hydroshoot/doc/figs/ecophysio_solver_1.svg
Normal file
913
hydroshoot/doc/figs/ecophysio_solver_1.svg
Normal file
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hydroshoot/doc/figs/energy_3.png
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|
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hydroshoot/doc/figs/exchange.png
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|
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|
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hydroshoot/doc/figs/intro_canopy.png
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|
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|
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hydroshoot/doc/figs/intro_irradiance.png
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hydroshoot/doc/figs/intro_net_photosynthesis.png
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|
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|
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1
hydroshoot/doc/history.rst
Normal file
1
hydroshoot/doc/history.rst
Normal file
|
|
@ -0,0 +1 @@
|
|||
.. include:: ../HISTORY.rst
|
||||
46
hydroshoot/doc/hydraulic.rst
Normal file
46
hydroshoot/doc/hydraulic.rst
Normal file
|
|
@ -0,0 +1,46 @@
|
|||
===================
|
||||
Hydraulic structure
|
||||
===================
|
||||
|
||||
The *hydraulic* module computes the distribution of xylem water potential across plant segments by analogy to Ohm’s law
|
||||
(:numref:`fig_1_hydraulic`)
|
||||
|
||||
.. _fig_1_hydraulic:
|
||||
|
||||
.. figure:: figs/hydraulic.png
|
||||
|
||||
Illustration of the variables required to calculate the hydraulic structure: water flux (:math:`F`),
|
||||
hydraulic conductivity (:math:`K`), water pressure at upper (downstream) and lower (upstream) extremities
|
||||
of the conducting element (respectively :math:`H_u` and :math:`H_l`), and the length of the segment (:math:`L`).
|
||||
|
||||
Water flux (:math:`F, \ kg \ s^{-1}`) across the hydraulic segment of length (:math:`L, \ m`)
|
||||
is driven by the difference of xylem pressures across this segment (:math:`H_u - H_l, \ MPa`)
|
||||
and regulated by segment's hydraulic conductivity (:math:`K, \ kgs^{-1} \ m \ MPa^{-1}`):
|
||||
|
||||
.. math::
|
||||
F = - K \cdot \frac{H_u - H_l}{L}
|
||||
|
||||
The hydraulic conductivity varies with water potential as a result of xylem cavitation under water deficit
|
||||
**(Tyree and Sperry, 1989)**. This relationship is described in HydroShoot as:
|
||||
|
||||
.. math::
|
||||
K = K_{max} \cdot \frac{1} {\left( 1 + \left( \frac{\Psi}{\Psi_{crit, \ stem}} \right) ^{c_{x1}} \right)}
|
||||
|
||||
where
|
||||
:math:`K_{max} \ [kg \ s^{-1} \ m \ MPa^{-1}]` is the maximum conductivity of the segment,
|
||||
:math:`\Psi \ [MPa]` is the arithmetic mean of xylem potential of the segment,
|
||||
:math:`\Psi_{crit, \ stem} \ [MPa]` and
|
||||
:math:`c_{x1} \ [-]` are shape parameters.
|
||||
|
||||
:math:`K_{max}` is estimated empirically as proposed by **Tyree and Zimmermann (2002)** as:
|
||||
|
||||
.. math::
|
||||
K_{max} = c_{x2} \cdot D^{c_{x3}}
|
||||
|
||||
where
|
||||
:math:`D \ [m]` is the average diameter of the segment, and
|
||||
:math:`c_{x2}` and
|
||||
:math:`c_{x3}` are shape parameters, mostly given within the ranges of [2.5, 2.8] and [2.0, 5.0], respectively.
|
||||
|
||||
The last two equations apply to all conducting segments (not leaves blades). Water potential of the upper extremity
|
||||
of the petiole is assumed equal to that of the lumped leaf water potential :math:`\Psi_{leaf} \ [MPa]`.
|
||||
27
hydroshoot/doc/index.rst
Normal file
27
hydroshoot/doc/index.rst
Normal file
|
|
@ -0,0 +1,27 @@
|
|||
.. HydroShoot documentation master file, created by
|
||||
sphinx-quickstart on Thu May 30 13:38:38 2019.
|
||||
You can adapt this file completely to your liking, but it should at least
|
||||
contain the root `toctree` directive.
|
||||
|
||||
Welcome to HydroShoot's documentation!
|
||||
======================================
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 3
|
||||
:caption: Contents:
|
||||
|
||||
installation
|
||||
overview
|
||||
model_description
|
||||
usage
|
||||
|
||||
|
||||
|
||||
Further reading
|
||||
===============
|
||||
|
||||
.. toctree::
|
||||
|
||||
authors
|
||||
history
|
||||
contributing
|
||||
13
hydroshoot/doc/installation.rst
Normal file
13
hydroshoot/doc/installation.rst
Normal file
|
|
@ -0,0 +1,13 @@
|
|||
============
|
||||
Installation
|
||||
============
|
||||
|
||||
HydroShoot can be installed automagically using the openalea3 channel from anaconda:
|
||||
|
||||
.. code::
|
||||
|
||||
mamba create -n hydroshoot -c openalea3 -c conda-forge openalea.hydroshoot
|
||||
mamba activate hydroshoot
|
||||
|
||||
|
||||
You're done !
|
||||
36
hydroshoot/doc/make.bat
Normal file
36
hydroshoot/doc/make.bat
Normal file
|
|
@ -0,0 +1,36 @@
|
|||
@ECHO OFF
|
||||
|
||||
pushd %~dp0
|
||||
|
||||
REM Command file for Sphinx documentation
|
||||
|
||||
if "%SPHINXBUILD%" == "" (
|
||||
set SPHINXBUILD=sphinx-build
|
||||
)
|
||||
set SOURCEDIR=.
|
||||
set BUILDDIR=_build
|
||||
set SPHINXPROJ=HydroShoot
|
||||
|
||||
if "%1" == "" goto help
|
||||
|
||||
%SPHINXBUILD% >NUL 2>NUL
|
||||
if errorlevel 9009 (
|
||||
echo.
|
||||
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
|
||||
echo.installed, then set the SPHINXBUILD environment variable to point
|
||||
echo.to the full path of the 'sphinx-build' executable. Alternatively you
|
||||
echo.may add the Sphinx directory to PATH.
|
||||
echo.
|
||||
echo.If you don't have Sphinx installed, grab it from
|
||||
echo.http://sphinx-doc.org/
|
||||
exit /b 1
|
||||
)
|
||||
|
||||
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
|
||||
goto end
|
||||
|
||||
:help
|
||||
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
|
||||
|
||||
:end
|
||||
popd
|
||||
15
hydroshoot/doc/model_description.rst
Normal file
15
hydroshoot/doc/model_description.rst
Normal file
|
|
@ -0,0 +1,15 @@
|
|||
=================
|
||||
Model description
|
||||
=================
|
||||
|
||||
All information in this section are taken from HydroShoot's paper
|
||||
(`Albasha et al., 2019 <https://doi.org/10.1093/insilicoplants/diz007>`_).
|
||||
Please refer to the this paper for a detailed description of model's formulae and evaluation.
|
||||
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
|
||||
ecophysio
|
||||
ecophysio_solver
|
||||
refs
|
||||
53
hydroshoot/doc/overview.rst
Normal file
53
hydroshoot/doc/overview.rst
Normal file
|
|
@ -0,0 +1,53 @@
|
|||
========
|
||||
Overview
|
||||
========
|
||||
|
||||
|
||||
What is HydroShoot about?
|
||||
=========================
|
||||
HydrShoot is a functional-structural plant model that simulates the interactions between shoot's hydraulic structure,
|
||||
gas-exchange and energy-budget, at the organ level.
|
||||
|
||||
.. |fig1| image:: figs/intro_canopy.png
|
||||
:width: 300
|
||||
.. |fig2| image:: figs/intro_irradiance.png
|
||||
:width: 300
|
||||
.. |fig3| image:: figs/intro_hydraulic.png
|
||||
:width: 300
|
||||
.. |fig4| image:: figs/intro_net_photosynthesis.png
|
||||
:width: 300
|
||||
.. |fig5| image:: figs/intro_transpiration.png
|
||||
:width: 300
|
||||
.. |fig6| image:: figs/intro_temperature.png
|
||||
:width: 300
|
||||
|
||||
|
||||
.. table::
|
||||
:align: center
|
||||
|
||||
+--------+--------+
|
||||
| |fig1| | |fig2| |
|
||||
+--------+--------+
|
||||
| |fig3| | |fig4| |
|
||||
+--------+--------+
|
||||
| |fig5| | |fig6| |
|
||||
+--------+--------+
|
||||
|
||||
|
||||
|
||||
|
||||
**Plant shoot is static** to HydroShoot. That is the model does not simulate plant growth nor its development.
|
||||
Its usage would therefore be only sound only if shoot's structure can be assumed constant across a given span of time
|
||||
(let's say a week or so for grapevine).
|
||||
|
||||
|
||||
Why would you be interested in it?
|
||||
==================================
|
||||
HydroShoot may be useful for example if you would like to explore:
|
||||
|
||||
- how leaf net carbon assimilation rate (:math:`A_n`), transpiration rate (:math:`E`), temperature (:math:`T`) and
|
||||
bulk water potential (:math:`\Psi_{leaf}`) interact across the canopy
|
||||
- how soil water status impacts :math:`A_n`, :math:`E`, :math:`T`, and :math:`\Psi_{leaf}`
|
||||
- how the structure of the shoot impacts :math:`A_n`, :math:`E`, :math:`T`, and :math:`\Psi_{leaf}`
|
||||
- how soil water potential (:math:`\Psi_{soil}`) propagates across plant's shoot
|
||||
|
||||
32
hydroshoot/doc/refs.rst
Normal file
32
hydroshoot/doc/refs.rst
Normal file
|
|
@ -0,0 +1,32 @@
|
|||
==========
|
||||
References
|
||||
==========
|
||||
|
||||
Albasha R, Fournier C, Pradal C, Chelle M, Prieto J, Louarn G, Simonneau T, Lebon E. 2019.
|
||||
HydroShoot: a functional-structural plant model for simulating hydraulic structure, gas and energy exchange
|
||||
dynamics of complex plant canopies under water deficit - application to grapevine (Vitisvinifera L.)
|
||||
in silico Plants, diz007, https://doi.org/10.1093/insilicoplants/diz007
|
||||
Evers J, Vos J, Yin X, Romero P, van der Putten P, Struik P. 2010.
|
||||
Simulation of wheat growth and development based on organ-level photosynthesis and assimilate allocation.
|
||||
Journal of Experimental Botany 61: 2203–2216
|
||||
Farquhar G, von Caemmerer S, Berry J. 1980.
|
||||
A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species.
|
||||
Planta 149: 78–90.
|
||||
Leuning R. 1995.
|
||||
A critical appraisal of a combined stomatal-photosynthesis model for C3 plants.
|
||||
Plant, Cell and Environment 18: 339–355.
|
||||
Nobel P. 2005.
|
||||
Temperature and energy budgets. In Nobel S, eds. Physicochemical and Environmental Plant Physiology.
|
||||
Elsevier Academic Press.
|
||||
Prieto J, Louarn G, Perez Peña J, Ojeda H, Simonneau T, Lebon E. 2012.
|
||||
A leaf gas exchange model that accounts for intra-canopy variability by considering leaf nitrogen content and
|
||||
local acclimation to radiation in grapevine (Vitis vinifera L.)
|
||||
Plant, Cell and Environment 35: 1313–1328.
|
||||
Tyree M, Sperry J. 1989.
|
||||
Vulnerability of xylem to cavitation and embolism.
|
||||
Annual review of plant physiology and plant molecular biology 40: 19–38.
|
||||
Tyree M, Zimmermann M. 2002.
|
||||
Xylem structure and the ascent of sap, Springer Series in Wood Science.
|
||||
Yin X, Struik P. 2009.
|
||||
C3 and C4 photosynthesis models: An overview from the perspective of crop modelling.
|
||||
NJAS - Wageningen Journal of Life Sciences 57: 27–38.
|
||||
152
hydroshoot/doc/usage.rst
Normal file
152
hydroshoot/doc/usage.rst
Normal file
|
|
@ -0,0 +1,152 @@
|
|||
=====
|
||||
Usage
|
||||
=====
|
||||
|
||||
.. figure:: figs/usage_fig_1.png
|
||||
:align: center
|
||||
|
||||
Illustration of inputs and outputs of HydroShoot.
|
||||
|
||||
|
||||
Three input files are required in order to run HydroShoot. The first contains all model parameters, the second
|
||||
meteorological data, and the third (optional) soil predawn water potential data. The model returns an undetermined
|
||||
number of files (:math:`\geq 3`) of two types of outputs.
|
||||
|
||||
|
||||
Set the required files up
|
||||
-------------------------
|
||||
|
||||
1. Model parameters
|
||||
|
||||
Almost all model parameters are setup in the **params.json** file.
|
||||
*params.json* is a *JavaScript Object Notation (JSON)* file that contains the following sections:
|
||||
|
||||
* "simulation"
|
||||
* "planting"
|
||||
* "phenology"
|
||||
* "mtg_api"
|
||||
* "numerical_resolution"
|
||||
* "irradiance"
|
||||
* "energy"
|
||||
* "hydraulic"
|
||||
* "exchange"
|
||||
* "soil"
|
||||
|
||||
Each of the above sections refers to its homonym process. An exhaustive and thoroughly detailed description
|
||||
of all the parameters inside each section, their units and their expected values, are given in the
|
||||
`params_schema.json` file (src/hydroshoot/). The reader is encouraged to refer to this file to know how exactly
|
||||
to fill up the *params.json* file.
|
||||
|
||||
2. Meteorological data (time series)
|
||||
|
||||
Meteorological data must be provided using a .csv file whose name must be given in the
|
||||
`params.json` file ("meteo" parameters).
|
||||
This file must contain the following columns:
|
||||
* `time`: a `datetime` string having the format YYYY-MM-DD HH:MM:SS
|
||||
* `Tac`: air temperature :math:`[^\circ C]`
|
||||
* `hs`: relative humidity (%)
|
||||
* `u`: wind speed :math:`[m \ s^{-1}]`
|
||||
* `Rg`: solar radiation (shortwave irradiance) given even in :math:`[W_{global} \ m_{ground}^{-2}]`,
|
||||
:math:`[W_{PAR} \ m_{ground}^{-2}]` or :math:`[{\mu mol}_{PPFD} \ m_{ground}^{-2} \ s^{-1}]`.
|
||||
The user must provide the unit of `Rg` in the `params.json` file ("E_type" parameter).
|
||||
|
||||
|
||||
3. Soil predawn water potential data (time series)
|
||||
|
||||
There are two ways to supply predawn soil water potential (:math:`\Psi_{soil}`) to the model:
|
||||
|
||||
a. using an external file that must be named "psi_soil.input" (the user will be able to give other names to the file
|
||||
in the future).
|
||||
|
||||
b. using the keyword argument "psi_soil" when calling the simulator:
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
from hydroshoot import model
|
||||
|
||||
model.run(g, working_directory, psi_soil=-0.5)
|
||||
|
||||
In this case, the value given in the 'psi_soil' keyword overrides **all values** given in 'psi_soil.input' file.
|
||||
HydroShoot will force soil water potential value **at each time step** to that given by the keyword 'psi_soil'.
|
||||
|
||||
|
||||
Outputs
|
||||
-------
|
||||
|
||||
The first output file is a *comma-separated values* (csv) file named "time_series.output" (only one file is returned)
|
||||
that contains the following time-dependent outputs:
|
||||
|
||||
* **time**: datetime string (YYYY-MM-DD HH:MM:SS)
|
||||
* **An**: net carbon assimilation flux of the whole plant :math:`[\mu mol \ s^{-1}]`
|
||||
* **E**: tranpiration flux of the whole plant :math:`[g \ h^{-1}]`
|
||||
* **Rg**: absorbed shortwave irradiance by the whole plant :math:`[W \ m_{ground}^{-2}]`
|
||||
* **Tleaf**: median leaf temperature :math:`[^\circ C]`
|
||||
|
||||
The second type of outputs is a pickle (pckl) file in which is stored mtg data **for each simulated time step**. Note
|
||||
that **pckl files do not contain geometry data**. Geometry is not currently stored as an output since the model expects
|
||||
it as an input.
|
||||
|
||||
|
||||
Run the model
|
||||
-------------
|
||||
|
||||
Let's take the simple example provided in '~/example/potted_grapevine/'. We will use for this example **architecture**
|
||||
and **display** modules provided with HydroShoot package (these packages may be removed in the future).
|
||||
|
||||
This example runs HydroShoot on a small potted grapevine canopy having two primary shoots.
|
||||
|
||||
Let's build the mock-up using the digitalization data provided in "grapevine_pot.csv" file:
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
from os import getcwd
|
||||
|
||||
from openalea.mtg import traversal
|
||||
from openalea.plantgl.all import Scene
|
||||
from hydroshoot import architecture, display, model
|
||||
|
||||
# Path for plant digitalization data.
|
||||
g = architecture.vine_mtg('grapevine_pot.csv')
|
||||
|
||||
for v in traversal.iter_mtg2(grapevine_mtg, grapevine_mtg.root):
|
||||
architecture.vine_phyto_modular(grapevine_mtg, v)
|
||||
architecture.vine_mtg_properties(grapevine_mtg, v)
|
||||
architecture.vine_mtg_geometry(grapevine_mtg, v)
|
||||
architecture.vine_transform(grapevine_mtg, v)
|
||||
|
||||
Display now the scene using **display** module, you should be having something like :numref:`fig_mockup`:
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
scene = display.visu(g, def_elmnt_color_dict=True, scene=Scene(),
|
||||
view_result=True)
|
||||
|
||||
|
||||
|
||||
.. _fig_mockup:
|
||||
|
||||
.. figure:: figs/usage_fig_2.png
|
||||
|
||||
Screen shot of the mock-up produced by the "potted_grapevine" example.
|
||||
|
||||
You're now ready to run the model using the meteorological data provided in "meteo.input", and forcing soil water
|
||||
potential to a fixed value of -0.5 :math:`MPa`. Ensure first that the model will run over one hour only by setting
|
||||
start and end dates of the simulation in the "params.json" file ("sdate": "2012-08-01 11:00:00",
|
||||
"edate": "2012-08-01 11:00:00").
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
model.run(g, str(getcwd()) + '/', scene, psi_soil=-0.2, gdd_since_budbreak=100.)
|
||||
|
||||
You should now have created the '/output/' folder where output files ("time_series.ouput", "mtg20120801110000.pckl")
|
||||
are stored. "time_series.ouput" file should contain close values to those below:
|
||||
|
||||
|
||||
.. code-block:: none
|
||||
|
||||
time;Rg;An;E;Tleaf
|
||||
2012-08-01 11:00:00;69.83;7.99;179.17;26.05
|
||||
|
||||
|
||||
.. figure:: figs/usage_fig_3.png
|
||||
:align: center
|
||||
Loading…
Add table
Add a link
Reference in a new issue