Migrate JULES user guide#5
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The github action looks sensible, and the built documentation is rendering sensibly.
I've been unable to review any of your other fixes as the whole change is a single commit. Please can you remember on other occasions to commit the moved code before you modify it. Thanks
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Author
Only in jules/doc: environment.yaml
diff -r jules-lsm.github.io/doc/make.bat jules/doc/make.bat
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< set SPHINXBUILD=sphinx-build
---
> set SPHINXBUILD=sphinx-build
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< 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.https://www.sphinx-doc.org/
< exit /b 1
---
> 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.https://www.sphinx-doc.org/
> exit /b 1
diff -r jules-lsm.github.io/doc/Makefile jules/doc/Makefile
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< # Makefile for Sphinx documentation
---
> # Minimal makefile for Sphinx documentation
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< # You can set these variables from the command line.
< SPHINXOPTS =
< SPHINXBUILD = sphinx-build
< PAPER =
---
> # You can set these variables from the command line, and also
> # from the environment for the first two.
> SPHINXOPTS ?=
> SPHINXBUILD ?= sphinx-build
> SOURCEDIR = source
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< # Internal variables.
< PAPEROPT_a4 = -D latex_paper_size=a4
< PAPEROPT_letter = -D latex_paper_size=letter
< ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
< # the i18n builder cannot share the environment and doctrees with the others
< I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
<
< .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
---
> REPO := $(notdir $(shell git rev-parse --show-toplevel))
> BRANCH := $(shell git rev-parse --abbrev-ref HEAD)
> DEPLOYDIR = $(HOME)/public_html
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> # Put it first so that "make" without argument is like "make help".
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< @echo "Please use \`make <target>' where <target> is one of"
< @echo " html to make standalone HTML files"
< @echo " dirhtml to make HTML files named index.html in directories"
< @echo " singlehtml to make a single large HTML file"
< @echo " pickle to make pickle files"
< @echo " json to make JSON files"
< @echo " htmlhelp to make HTML files and a HTML help project"
< @echo " qthelp to make HTML files and a qthelp project"
< @echo " devhelp to make HTML files and a Devhelp project"
< @echo " epub to make an epub"
< @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
< @echo " latexpdf to make LaTeX files and run them through pdflatex"
< @echo " text to make text files"
< @echo " man to make manual pages"
< @echo " texinfo to make Texinfo files"
< @echo " info to make Texinfo files and run them through makeinfo"
< @echo " gettext to make PO message catalogs"
< @echo " changes to make an overview of all changed/added/deprecated items"
< @echo " linkcheck to check all external links for integrity"
< @echo " doctest to run all doctests embedded in the documentation (if enabled)"
<
< clean:
< -rm -rf $(BUILDDIR)/*
<
< html:
< $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
< @echo
< @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
<
< dirhtml:
< $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
< @echo
< @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
<
< singlehtml:
< $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
< @echo
< @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
<
< pickle:
< $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
< @echo
< @echo "Build finished; now you can process the pickle files."
<
< json:
< $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
< @echo
< @echo "Build finished; now you can process the JSON files."
<
< htmlhelp:
< $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
< @echo
< @echo "Build finished; now you can run HTML Help Workshop with the" \
< ".hhp project file in $(BUILDDIR)/htmlhelp."
<
< qthelp:
< $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
< @echo
< @echo "Build finished; now you can run "qcollectiongenerator" with the" \
< ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
< @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/JULESJointUKLandEnvironmentSimulator.qhcp"
< @echo "To view the help file:"
< @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/JULESJointUKLandEnvironmentSimulator.qhc"
<
< devhelp:
< $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
< @echo
< @echo "Build finished."
< @echo "To view the help file:"
< @echo "# mkdir -p $$HOME/.local/share/devhelp/JULESJointUKLandEnvironmentSimulator"
< @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/JULESJointUKLandEnvironmentSimulator"
< @echo "# devhelp"
<
< epub:
< $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
< @echo
< @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
<
< latex:
< $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
< @echo
< @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
< @echo "Run \`make' in that directory to run these through (pdf)latex" \
< "(use \`make latexpdf' here to do that automatically)."
<
< latexpdf:
< $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
< @echo "Running LaTeX files through pdflatex..."
< $(MAKE) -C $(BUILDDIR)/latex all-pdf
< @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
<
< text:
< $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
< @echo
< @echo "Build finished. The text files are in $(BUILDDIR)/text."
<
< man:
< $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
< @echo
< @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
<
< texinfo:
< $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
< @echo
< @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
< @echo "Run \`make' in that directory to run these through makeinfo" \
< "(use \`make info' here to do that automatically)."
<
< info:
< $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
< @echo "Running Texinfo files through makeinfo..."
< make -C $(BUILDDIR)/texinfo info
< @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
<
< gettext:
< $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
< @echo
< @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
<
< changes:
< $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
< @echo
< @echo "The overview file is in $(BUILDDIR)/changes."
<
< linkcheck:
< $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
< @echo
< @echo "Link check complete; look for any errors in the above output " \
< "or in $(BUILDDIR)/linkcheck/output.txt."
<
< doctest:
< $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
< @echo "Testing of doctests in the sources finished, look at the " \
< "results in $(BUILDDIR)/doctest/output.txt."
---
> @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
>
> .PHONY: help Makefile
>
> # Catch-all target: route all unknown targets to Sphinx using the new
> # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
> %: Makefile
> @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
>
> deploy:
> @$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(DEPLOYDIR)/$(REPO)/$(BRANCH)" $(SPHINXOPTS) $(O)
>
Only in jules/doc: pyproject.toml
Only in jules/doc: README.md
diff -r jules-lsm.github.io/doc/source/building-and-running/considerations.rst jules/doc/source/building-and-running/considerations.rst
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<
< 1. It is machine-independent, so `endianness <http://en.wikipedia.org/wiki/Endianness>`_ is not an issue when moving datasets between machines
< 2. It is self-describing, so as well as containing raw data, NetCDF files also contain metadata describing the data (e.g. variable names, units, origin). Many tools are capable of exploiting this metadata to simplify processing.
---
>
> 1. It is machine-independent, so `endianness <http://en.wikipedia.org/wiki/Endianness>`_ is not an issue when moving datasets between machines
> 2. It is self-describing, so as well as containing raw data, NetCDF files also contain metadata describing the data (e.g. variable names, units, origin). Many tools are capable of exploiting this metadata to simplify processing.
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diff -r jules-lsm.github.io/doc/source/building-and-running/intro.rst jules/doc/source/building-and-running/intro.rst
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diff -r jules-lsm.github.io/doc/source/building-and-running/required-software.rst jules/doc/source/building-and-running/required-software.rst
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< * GFortran, the GNU GCC Fortran compiler - https://www.gnu.org/software/gcc/fortran
< * FCM - http://metomi.github.io/fcm/doc
< * Rose - http://metomi.github.io/rose/doc/html/index.html
< * NetCDF libraries - http://www.unidata.ucar.edu/software/netcdf
---
> * GFortran, the GNU GCC Fortran compiler - https://www.gnu.org/software/gcc/fortran
> * FCM - http://metomi.github.io/fcm/doc
> * Rose - http://metomi.github.io/rose/doc/html/index.html
> * NetCDF libraries - http://www.unidata.ucar.edu/software/netcdf
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diff -r jules-lsm.github.io/doc/source/building-and-running/rose.rst jules/doc/source/building-and-running/rose.rst
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<
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< A Rose suite for JULES will normally contain two applications - an ``fcm_make`` application for building JULES and a ``jules`` application for configuring the namelists and running JULES.
---
> A Rose suite for JULES will normally contain two applications - an ``fcm_make`` application for building JULES and a ``jules`` application for configuring the namelists and running JULES.
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diff -r jules-lsm.github.io/doc/source/building-and-running/running-jules.rst jules/doc/source/building-and-running/running-jules.rst
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diff -r jules-lsm.github.io/doc/source/code/contents.rst jules/doc/source/code/contents.rst
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---
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diff -r jules-lsm.github.io/doc/source/code/io.rst jules/doc/source/code/io.rst
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< The only I/O code that needs to be modified to add new variables for input and output is in ``model_interface_mod`` (the routines in ``src/io/model_interface``). All interaction between the I/O code and the model happens in this module (apart from reading and writing dump files).
---
> The only I/O code that needs to be modified to add new variables for input and output is in ``model_interface_mod`` (the routines in ``src/io/model_interface``). All interaction between the I/O code and the model happens in this module (apart from reading and writing dump files).
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< * Two routines that populate and extract data from the relevant model variables. These are ``populate_var`` and ``extract_var`` respectively.
< * Routines that provide various pieces of information (e.g. string identifiers, number and size of 'levels' dimensions) about the available variables to the input and output layers. Internally, a metadata array that contains information about the available variables is used to implement these 'information providing' routines.
---
> * Two routines that populate and extract data from the relevant model variables. These are ``populate_var`` and ``extract_var`` respectively.
> * Routines that provide various pieces of information (e.g. string identifiers, number and size of 'levels' dimensions) about the available variables to the input and output layers. Internally, a metadata array that contains information about the available variables is used to implement these 'information providing' routines.
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diff -r jules-lsm.github.io/doc/source/conf.py jules/doc/source/conf.py
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< import sys, os
---
> import sys
> import os
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---
> # 'sphinx.ext.todo', 'sphinx.ext.imgmath', 'sphinx.ext.mathjax',
> 'sphinx.ext.todo', 'sphinx.ext.mathjax',
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> # The 'preamble' key allows you to add custom LaTeX commands.
> 'preamble': r'''
> \raggedbottom
> \usepackage{tcolorbox}
> ''',
>
diff -r jules-lsm.github.io/doc/source/examples.rst jules/doc/source/examples.rst
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<
< If you are using a version of JULES since vn5.0, please see the list of standard jobs in the table given `here <https://code.metoffice.gov.uk/trac/jules#ReleaseSchedule>`__ or the
< 'Example configurations' row of the table `here <http://jules.jchmr.org/content/configurations>`__.
---
> If you are using a version of JULES since vn5.0, please see the list of standard
> jobs in the table given `here <https://code.metoffice.gov.uk/trac/jules#ReleaseSchedule>`__
> or the 'Example configurations' row of the table `here <http://jules.jchmr.org/content/configurations>`__.
diff -r jules-lsm.github.io/doc/source/index.rst jules/doc/source/index.rst
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< The Joint UK Land Environment Simulator (JULES) is a computer model that simulates many soil and vegetation processes. This guide primarily describes the format of the input and output files, and does not include detailed descriptions of the science and representation of the processes in the model.
---
> The Joint UK Land Environment Simulator (JULES) is a computer model that
> simulates many soil and vegetation processes. This guide primarily describes the
> format of the input and output files, and does not include detailed descriptions
> of the science and representation of the processes in the model.
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< The first version of JULES was based on the Met Office Surface Exchange System (MOSES), the land surface model used in the `Unified Model <http://www.metoffice.gov.uk/research/modelling-systems/unified-model>`_ (UM) of the `UK Met Office <http://www.metoffice.gov.uk>`_. After that initial split, the MOSES and JULES code bases evolved separately, but with JULES v2.1 these differences were reconciled with the UM. As of JULES v3.1, a single code repository is used for both standalone JULES and JULES in the UM.
---
> The first version of JULES was based on the Met Office Surface Exchange System (MOSES),
> the land surface model used in the
> `Unified Model <http://www.metoffice.gov.uk/research/modelling-systems/unified-model>`_ (UM)
> of the `UK Met Office <http://www.metoffice.gov.uk>`_.
> After that initial split, the MOSES and JULES code bases evolved separately,
> but with JULES v2.1 these differences were reconciled with the UM.
> As of JULES v3.1, a single code repository is used for both
> standalone JULES and JULES in the UM.
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---
>
diff -r jules-lsm.github.io/doc/source/input/ascii.rst jules/doc/source/input/ascii.rst
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< JULES only supports the use of ASCII files for data at a single location. In this case, the input grid can be specified either as a 1D grid with length 1 or as a 2D grid of size 1 x 1. The data should be laid out in columns with one timestep of data per row (with time increasing with the number of rows). For variables with additional 'levels' dimensions (e.g. soil layers), the values for each level should be in consecutive columns.
---
> JULES only supports the use of ASCII files for data at a single location. In this case, the input grid can be specified either as a 1D grid with length 1 or as a 2D grid of size 1 x 1. The data should be laid out in columns with one timestep of data per row (with time increasing with the number of rows). For variables with additional 'levels' dimensions (e.g. soil layers), the values for each level should be in consecutive columns.
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---
> # ...
diff -r jules-lsm.github.io/doc/source/input/file-name-templating.rst jules/doc/source/input/file-name-templating.rst
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< +-----------------------+------------------------------------------------------------------------------------------------+
< | Substitution string | Replaced with |
< +=======================+================================================================================================+
< | ``%y4`` | 4-digit year |
< +-----------------------+------------------------------------------------------------------------------------------------+
< | ``%y2`` | 2-digit year |
< +-----------------------+------------------------------------------------------------------------------------------------+
< | ``%m2`` | 2-digit month |
< +-----------------------+------------------------------------------------------------------------------------------------+
< | ``%m1`` | 1- or 2-digit month |
< +-----------------------+------------------------------------------------------------------------------------------------+
< | ``%mc`` | 3-character month abbreviation |
< +-----------------------+------------------------------------------------------------------------------------------------+
< | ``%d2`` | 2-digit day of month |
< +-----------------------+------------------------------------------------------------------------------------------------+
---
> +-----------------------+----------------------------------+
> | Substitution string | Replaced with |
> +=======================+==================================+
> | ``%y4`` | 4-digit year |
> +-----------------------+----------------------------------+
> | ``%y2`` | 2-digit year |
> +-----------------------+----------------------------------+
> | ``%m2`` | 2-digit month |
> +-----------------------+----------------------------------+
> | ``%m1`` | 1- or 2-digit month |
> +-----------------------+----------------------------------+
> | ``%mc`` | 3-character month abbreviation |
> +-----------------------+----------------------------------+
> | ``%d2`` | 2-digit day of month |
> +-----------------------+----------------------------------+
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diff -r jules-lsm.github.io/doc/source/input/netcdf.rst jules/doc/source/input/netcdf.rst
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< * If using NetCDF for data at a single location, the grid dimensions are still expected to exist with size 1.
\ No newline at end of file
---
> * If using NetCDF for data at a single location, the grid dimensions are still expected to exist with size 1.
diff -r jules-lsm.github.io/doc/source/input/overview.rst jules/doc/source/input/overview.rst
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diff -r jules-lsm.github.io/doc/source/input/principles.rst jules/doc/source/input/principles.rst
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diff -r jules-lsm.github.io/doc/source/input/temporal-interpolation.rst jules/doc/source/input/temporal-interpolation.rst
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<
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< This namelist reads spatially varying parameter values for the TOPMODEL-type parameterisation of runoff. The values are only used if :nml:mem:`JULES_HYDROLOGY::l_top` = TRUE. The description below is very brief. For further details, see the references under :nml:mem:`JULES_HYDROLOGY::l_top`.
---
> This namelist reads spatially varying parameter values for the TOPMODEL-type parametrisation of runoff. The values are only used if :nml:mem:`JULES_HYDROLOGY::l_top` = TRUE. The description below is very brief. For further details, see the references under :nml:mem:`JULES_HYDROLOGY::l_top`.
565c557
< This namelist reads spatially varying parameter values for the PDM-type parameterisation of runoff. The values are only used if :nml:mem:`JULES_HYDROLOGY::l_pdm` = TRUE. The description below is very brief. For further details, see the references under :nml:mem:`JULES_HYDROLOGY::l_pdm`.
---
> This namelist reads spatially varying parameter values for the PDM-type parametrisation of runoff. The values are only used if :nml:mem:`JULES_HYDROLOGY::l_pdm` = TRUE. The description below is very brief. For further details, see the references under :nml:mem:`JULES_HYDROLOGY::l_pdm`.
1026c1018
< * Mathison et al, 'Developing a sequential cropping capability in the JULESvn5.2 land–surface model', Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2019-85, in review, 2019
---
> * Mathison et al, 'Developing a sequential cropping capability in the JULESvn5.2 land-surface model', Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2019-85, in review, 2019
1099d1090
<
1130d1120
<
1133d1122
<
1141d1129
<
1152d1139
<
1546c1533
<
---
> .. |iacute| replace:: í
1552c1539
< * Appx B of Lewis HW, Castillo Sanchez JM, Graham J, Saulter A, Bornemann J, Arnold A, Fallmann J, Harris C, Pearson D, Ramsdale S, Martínez de la Torre A, Bricheno L, Blyth E, Bell VA, Davies H, Marthews TR, O'Neill C, Rumbold H, O'Dea E, Brereton A, Guihou K, Hines A, Butenschon M, Dadson SJ, Palmer T, Holt J, Reynard N, Best M, Edwards J & Siddorn J (2018). The UKC2 regional coupled environmental prediction system. Geoscientific Model Development 11:1-42.
---
> * Appx B of Lewis HW, Castillo Sanchez JM, Graham J, Saulter A, Bornemann J, Arnold A, Fallmann J, Harris C, Pearson D, Ramsdale S, Mart|iacute|nez de la Torre A, Bricheno L, Blyth E, Bell VA, Davies H, Marthews TR, O'Neill C, Rumbold H, O'Dea E, Brereton A, Guihou K, Hines A, Butenschon M, Dadson SJ, Palmer T, Holt J, Reynard N, Best M, Edwards J & Siddorn J (2018). The UKC2 regional coupled environmental prediction system. Geoscientific Model Development 11:1-42.
1683,1692c1670,1679
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | Name | Description |
< +============================+===========================================================================================================+
< | ``conv_loss_frac`` | Fraction of abstracted water that is lost during conveyance from source to user. |
< | | |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``sfc_water_frac`` | Target for the fraction of demand that will be met from surface water (rather than groundwater). |
< | | This is only used if :nml:mem:`JULES_WATER_RESOURCES::partition_method` = 1. |
< | | |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
---
> +----------------------+--------------------------------------------------------------------------------------------------+
> | Name | Description |
> +======================+==================================================================================================+
> | ``conv_loss_frac`` | Fraction of abstracted water that is lost during conveyance from source to user. |
> | | |
> +----------------------+--------------------------------------------------------------------------------------------------+
> | ``sfc_water_frac`` | Target for the fraction of demand that will be met from surface water (rather than groundwater). |
> | | This is only used if :nml:mem:`JULES_WATER_RESOURCES::partition_method` = 1. |
> | | |
> +----------------------+--------------------------------------------------------------------------------------------------+
1811,1836c1798,1822
< +---------------+----------------------------------+-------------------------------------------------------------------------------------+
< | Variable name | Description [#]_ | Notes |
< +===============+==================================+=====================================================================================+
< | ``wrr`` | Repeating width ratio (or canyon | If :nml:mem:`JULES_URBAN::l_urban_empirical` = TRUE |
< | | fraction, W/R) | then this is updated with calculated values. |
< +---------------+----------------------------------+-------------------------------------------------------------------------------------+
< | **The following apply to MORUSES only** |
< +---------------+----------------------------------+-------------------------------------------------------------------------------------+
< | ``hwr`` | Height-to-width ratio (H/W) | See for ``wrr`` above. |
< +---------------+----------------------------------+-------------------------------------------------------------------------------------+
< | ``hgt`` | Building height (H) | See for ``wrr`` above. |
< +---------------+----------------------------------+-------------------------------------------------------------------------------------+
< | ``ztm`` | Effective roughness length of | If :nml:mem:`JULES_URBAN::l_moruses_macdonald` = TRUE |
< | | urban areas | then this is updated with calculated values. |
< +---------------+----------------------------------+-------------------------------------------------------------------------------------+
< | ``disp`` | Displacement height | See for ``ztm`` above. |
< +---------------+----------------------------------+-------------------------------------------------------------------------------------+
< | ``albwl`` | Wall albedo | Data only used if :nml:mem:`JULES_URBAN::l_moruses_albedo` = TRUE. |
< +---------------+----------------------------------+-------------------------------------------------------------------------------------+
< | ``albrd`` | Road albedo | See for ``albwl`` above. |
< +---------------+----------------------------------+-------------------------------------------------------------------------------------+
< | ``emisw`` | Wall emissivity | Data only used if :nml:mem:`JULES_URBAN::l_moruses_emissivity` = TRUE. |
< +---------------+----------------------------------+-------------------------------------------------------------------------------------+
< | ``emisr`` | Road emissivity | See for ``emisw`` above. |
< +---------------+----------------------------------+-------------------------------------------------------------------------------------+
<
---
> +---------------+----------------------------------+------------------------------------------------------------------------+
> | Variable name | Description [#]_ | Notes |
> +===============+==================================+========================================================================+
> | ``wrr`` | Repeating width ratio (or canyon | If :nml:mem:`JULES_URBAN::l_urban_empirical` = TRUE |
> | | fraction, W/R) | then this is updated with calculated values. |
> +---------------+----------------------------------+------------------------------------------------------------------------+
> | **The following apply to MORUSES only** |
> +---------------+----------------------------------+------------------------------------------------------------------------+
> | ``hwr`` | Height-to-width ratio (H/W) | See for ``wrr`` above. |
> +---------------+----------------------------------+------------------------------------------------------------------------+
> | ``hgt`` | Building height (H) | See for ``wrr`` above. |
> +---------------+----------------------------------+------------------------------------------------------------------------+
> | ``ztm`` | Effective roughness length of | If :nml:mem:`JULES_URBAN::l_moruses_macdonald` = TRUE |
> | | urban areas | then this is updated with calculated values. |
> +---------------+----------------------------------+------------------------------------------------------------------------+
> | ``disp`` | Displacement height | See for ``ztm`` above. |
> +---------------+----------------------------------+------------------------------------------------------------------------+
> | ``albwl`` | Wall albedo | Data only used if :nml:mem:`JULES_URBAN::l_moruses_albedo` = TRUE. |
> +---------------+----------------------------------+------------------------------------------------------------------------+
> | ``albrd`` | Road albedo | See for ``albwl`` above. |
> +---------------+----------------------------------+------------------------------------------------------------------------+
> | ``emisw`` | Wall emissivity | Data only used if :nml:mem:`JULES_URBAN::l_moruses_emissivity` = TRUE. |
> +---------------+----------------------------------+------------------------------------------------------------------------+
> | ``emisr`` | Road emissivity | See for ``emisw`` above. |
> +---------------+----------------------------------+------------------------------------------------------------------------+
diff -r jules-lsm.github.io/doc/source/namelists/cable_pftparm.nml.rst jules/doc/source/namelists/cable_pftparm.nml.rst
7c7
< -----------------------------------
---
> ----------------------------------
diff -r jules-lsm.github.io/doc/source/namelists/cable_prognostics.nml.rst jules/doc/source/namelists/cable_prognostics.nml.rst
126c126
< +-------------------------------+-------------------------------------------------------------------------------+
\ No newline at end of file
---
> +-------------------------------+-------------------------------------------------------------------------------+
diff -r jules-lsm.github.io/doc/source/namelists/cable_soilparm.nml.rst jules/doc/source/namelists/cable_soilparm.nml.rst
4d3
<
102,104d100
<
<
<
diff -r jules-lsm.github.io/doc/source/namelists/cable_surface_types.nml.rst jules/doc/source/namelists/cable_surface_types.nml.rst
4d3
<
21,22c20,21
<
<
---
>
>
30,31c29,30
<
<
---
>
>
34c33
<
---
>
36c35
<
---
>
73d71
<
diff -r jules-lsm.github.io/doc/source/namelists/contents.rst jules/doc/source/namelists/contents.rst
5c5,6
< Each run of JULES is controlled by a number of files containing Fortran namelists. These files specify details including:
---
> Each run of JULES is controlled by a number of files containing Fortran
> namelists. These files specify details including:
14,15c15,17
< These files have specific names, and JULES expects all these files to exist for every run (even when their contents are not required). JULES also expects that the namelists within each file appear in the order given below.
<
---
> These files have specific names, and JULES expects all these files to exist for
> every run (even when their contents are not required). JULES also expects that
> the namelists within each file appear in the order given below.
49c51
< red_params.nml
---
> red_parms.nml
diff -r jules-lsm.github.io/doc/source/namelists/crop_params.nml.rst jules/doc/source/namelists/crop_params.nml.rst
1,245c1,244
< ``crop_params.nml``
< ===================
<
<
< This file contains a single namelist called :nml:lst:`JULES_CROPPARM` that sets time- and space-invariant parameters for each crop type.
<
<
< ``JULES_CROPPARM`` namelist members
< -----------------------------------
<
< .. nml:namelist:: JULES_CROPPARM
<
< This namelist reads the values of parameters for each of the crop functional types. These parameters are a function of crop pft only. These parameters are only required if :nml:mem:`JULES_SURFACE_TYPES::ncpft` > 0. The crop pfts should be in the same order as in :doc:`pft_params.nml`.
<
< .. seealso::
< References:
<
< * Osborne et al, `JULES-crop: a parametrisation of crops in the Joint UK Land Environment Simulator <http://www.geosci-model-dev.net/8/1139/2015/gmd-8-1139-2015.html>`_, Geosci. Model Dev., 8, 1139-1155, 2015.
<
< Parameters introduced after the Osborne et al 2015 paper are described in the appendix of
<
< * Williams et al, `Evaluation of JULES-crop performance against site observations of irrigated maize from Mead, Nebraska <https://www.geosci-model-dev.net/10/1291/2017/gmd-10-1291-2017.html>`_, Geosci. Model Dev., 10, 1291-1320, 2017.
<
< .. nml:member:: t_bse_io
<
< :type: real(ncpft)
< :default: None
<
< Base temperature (K).
<
<
< .. nml:member:: t_opt_io
<
< :type: real(ncpft)
< :default: None
<
< Optimum temperature (K).
<
<
< .. nml:member:: tmax_io
<
< :type: real(ncpft)
< :default: None
<
< Maximum temperature (K).
<
<
< .. nml:member:: tt_emr_io
<
< :type: real(ncpft)
< :default: None
<
< Thermal time between sowing and emergence (deg Cd).
<
<
< .. nml:member:: crit_pp_io
<
< :type: real(ncpft)
< :default: None
<
< Critical photoperiod (hours).
<
<
< .. nml:member:: pp_sens_io
<
< :type: real(ncpft)
< :default: None
<
< Sensitivity of development rate to photoperiod (hours\ :sup:`-1`).
<
<
< .. nml:member:: rt_dir_io
<
< :type: real(ncpft)
< :default: None
<
< Coefficient determining relative growth of roots vertically and horizontally.
<
<
< .. nml:member:: alpha1_io
<
< :type: real(ncpft)
< :default: None
<
< Coefficient for determining partitioning.
<
<
< .. nml:member:: alpha2_io
<
< :type: real(ncpft)
< :default: None
<
< Coefficient for determining partitioning.
<
<
< .. nml:member:: alpha3_io
<
< :type: real(ncpft)
< :default: None
<
< Coefficient for determining partitioning.
<
<
< .. nml:member:: beta1_io
<
< :type: real(ncpft)
< :default: None
<
< Coefficient for determining partitioning.
<
<
< .. nml:member:: beta2_io
<
< :type: real(ncpft)
< :default: None
<
< Coefficient for determining partitioning.
<
<
< .. nml:member:: beta3_io
<
< :type: real(ncpft)
< :default: None
<
< Coefficient for determining partitioning.
<
<
< .. nml:member:: gamma_io
<
< :type: real(ncpft)
< :default: None
<
< Coefficient for determining specific leaf area (m\ :sup:`2` kg\ :sup:`-1`).
<
<
< .. nml:member:: delta_io
<
< :type: real(ncpft)
< :default: None
<
< Coefficient for determining specific leaf area (m\ :sup:`2` kg\ :sup:`-1`).
<
<
< .. nml:member:: remob_io
<
< :type: real(ncpft)
< :default: None
<
< Remobilisation factor. Fraction of stem growth partitioned to RESERVEC.
<
<
< .. nml:member:: cfrac_s_io
<
< :type: real(npft)
< :default: None
<
< Carbon fraction of dry matter for stems.
<
<
< .. nml:member:: cfrac_r_io
<
< :type: real(ncpft)
< :default: None
<
< Carbon fraction of dry matter for roots.
<
<
< .. nml:member:: cfrac_l_io
<
< :type: real(ncpft)
< :default: None
<
< Carbon fraction of dry matter for leaves.
<
<
< .. nml:member:: allo1_io
<
< :type: real(ncpft)
< :default: None
<
< Allometric coefficient relating STEMC to CANHT.
<
<
< .. nml:member:: allo2_io
<
< :type: real(ncpft)
< :default: None
<
< Allometric coefficient relating STEMC to CANHT.
<
<
< .. nml:member:: mu_io
<
< :type: real(ncpft)
< :default: None
<
< Allometric coefficient for calculation of senescence. MIN(mu_io * (dvi - sen_dvi_io) ** nu_io, 1.0) is the fraction of leaf carbon that is moved to the harvest pool per day once senescence has started.
<
<
< .. nml:member:: nu_io
<
< :type: real(ncpft)
< :default: None
<
< Allometric coefficient for calculation of senescence. See description for :nml:mem:`mu_io`
<
<
< .. nml:member:: yield_frac_io
<
< :type: real(ncpft)
< :default: None
<
< Fraction of the harvest carbon pool converted to yield carbon (yield is the economically valuable component of the harvest pool e.g. kernel).
<
<
< .. nml:member:: initial_carbon_io
<
< :type: real(ncpft)
< :default: None
<
< Carbon in crop at emergence in kgC/m2.
<
<
< .. nml:member:: initial_c_dvi_io
<
< :type: real(ncpft)
< :default: None
<
< DVI at which the crop carbon is set to :nml:mem:`initial_carbon_io`. Should be at emergence (0.0) or shortly after.
<
<
< .. nml:member:: sen_dvi_io
<
< :type: real(ncpft)
< :default: None
<
< DVI at which leaf senescence begins.
<
<
< .. nml:member:: t_mort_io
<
< :type: real(ncpft)
< :default: None
<
< Soil temperature (second level) at which to kill crop if DVI>1.
---
> ``crop_params.nml``
> ===================
>
> This file contains a single namelist called :nml:lst:`JULES_CROPPARM` that sets time- and space-invariant parameters for each crop type.
>
>
> ``JULES_CROPPARM`` namelist members
> -----------------------------------
>
> .. nml:namelist:: JULES_CROPPARM
>
> This namelist reads the values of parameters for each of the crop functional types. These parameters are a function of crop pft only. These parameters are only required if :nml:mem:`JULES_SURFACE_TYPES::ncpft` > 0. The crop pfts should be in the same order as in :doc:`pft_params.nml`.
>
> .. seealso::
> References:
>
> * Osborne et al, `JULES-crop: a parametrisation of crops in the Joint UK Land Environment Simulator <http://www.geosci-model-dev.net/8/1139/2015/gmd-8-1139-2015.html>`_, Geosci. Model Dev., 8, 1139-1155, 2015.
>
> Parameters introduced after the Osborne et al 2015 paper are described in the appendix of
>
> * Williams et al, `Evaluation of JULES-crop performance against site observations of irrigated maize from Mead, Nebraska <https://www.geosci-model-dev.net/10/1291/2017/gmd-10-1291-2017.html>`_, Geosci. Model Dev., 10, 1291-1320, 2017.
>
> .. nml:member:: t_bse_io
>
> :type: real(ncpft)
> :default: None
>
> Base temperature (K).
>
>
> .. nml:member:: t_opt_io
>
> :type: real(ncpft)
> :default: None
>
> Optimum temperature (K).
>
>
> .. nml:member:: tmax_io
>
> :type: real(ncpft)
> :default: None
>
> Maximum temperature (K).
>
>
> .. nml:member:: tt_emr_io
>
> :type: real(ncpft)
> :default: None
>
> Thermal time between sowing and emergence (deg Cd).
>
>
> .. nml:member:: crit_pp_io
>
> :type: real(ncpft)
> :default: None
>
> Critical photoperiod (hours).
>
>
> .. nml:member:: pp_sens_io
>
> :type: real(ncpft)
> :default: None
>
> Sensitivity of development rate to photoperiod (hours\ :sup:`-1`).
>
>
> .. nml:member:: rt_dir_io
>
> :type: real(ncpft)
> :default: None
>
> Coefficient determining relative growth of roots vertically and horizontally.
>
>
> .. nml:member:: alpha1_io
>
> :type: real(ncpft)
> :default: None
>
> Coefficient for determining partitioning.
>
>
> .. nml:member:: alpha2_io
>
> :type: real(ncpft)
> :default: None
>
> Coefficient for determining partitioning.
>
>
> .. nml:member:: alpha3_io
>
> :type: real(ncpft)
> :default: None
>
> Coefficient for determining partitioning.
>
>
> .. nml:member:: beta1_io
>
> :type: real(ncpft)
> :default: None
>
> Coefficient for determining partitioning.
>
>
> .. nml:member:: beta2_io
>
> :type: real(ncpft)
> :default: None
>
> Coefficient for determining partitioning.
>
>
> .. nml:member:: beta3_io
>
> :type: real(ncpft)
> :default: None
>
> Coefficient for determining partitioning.
>
>
> .. nml:member:: gamma_io
>
> :type: real(ncpft)
> :default: None
>
> Coefficient for determining specific leaf area (m\ :sup:`2` kg\ :sup:`-1`).
>
>
> .. nml:member:: delta_io
>
> :type: real(ncpft)
> :default: None
>
> Coefficient for determining specific leaf area (m\ :sup:`2` kg\ :sup:`-1`).
>
>
> .. nml:member:: remob_io
>
> :type: real(ncpft)
> :default: None
>
> Remobilisation factor. Fraction of stem growth partitioned to RESERVEC.
>
>
> .. nml:member:: cfrac_s_io
>
> :type: real(npft)
> :default: None
>
> Carbon fraction of dry matter for stems.
>
>
> .. nml:member:: cfrac_r_io
>
> :type: real(ncpft)
> :default: None
>
> Carbon fraction of dry matter for roots.
>
>
> .. nml:member:: cfrac_l_io
>
> :type: real(ncpft)
> :default: None
>
> Carbon fraction of dry matter for leaves.
>
>
> .. nml:member:: allo1_io
>
> :type: real(ncpft)
> :default: None
>
> Allometric coefficient relating STEMC to CANHT.
>
>
> .. nml:member:: allo2_io
>
> :type: real(ncpft)
> :default: None
>
> Allometric coefficient relating STEMC to CANHT.
>
>
> .. nml:member:: mu_io
>
> :type: real(ncpft)
> :default: None
>
> Allometric coefficient for calculation of senescence. MIN(mu_io * (dvi - sen_dvi_io) ** nu_io, 1.0) is the fraction of leaf carbon that is moved to the harvest pool per day once senescence has started.
>
>
> .. nml:member:: nu_io
>
> :type: real(ncpft)
> :default: None
>
> Allometric coefficient for calculation of senescence. See description for :nml:mem:`mu_io`
>
>
> .. nml:member:: yield_frac_io
>
> :type: real(ncpft)
> :default: None
>
> Fraction of the harvest carbon pool converted to yield carbon (yield is the economically valuable component of the harvest pool e.g. kernel).
>
>
> .. nml:member:: initial_carbon_io
>
> :type: real(ncpft)
> :default: None
>
> Carbon in crop at emergence in kgC/m2.
>
>
> .. nml:member:: initial_c_dvi_io
>
> :type: real(ncpft)
> :default: None
>
> DVI at which the crop carbon is set to :nml:mem:`initial_carbon_io`. Should be at emergence (0.0) or shortly after.
>
>
> .. nml:member:: sen_dvi_io
>
> :type: real(ncpft)
> :default: None
>
> DVI at which leaf senescence begins.
>
>
> .. nml:member:: t_mort_io
>
> :type: real(ncpft)
> :default: None
>
> Soil temperature (second level) at which to kill crop if DVI>1.
diff -r jules-lsm.github.io/doc/source/namelists/drive.nml.rst jules/doc/source/namelists/drive.nml.rst
4d3
<
26c25
< If total preciption or total rainfall are given, then :nml:mem:`t_for_con_rain` is the near-surface air temperature (K) at or above which rainfall is assumed to be convective in origin. At lower temperatures, all the rainfall is assumed to be large-scale in origin. In this configuration all snow is assumed to be large-scale in origin. The default value used to be 373.15 K but in general this is not recommended as it effectively means all precipitation is large-scale; a value of 293.15 K might be more appropriate.
---
> If total precipitation or total rainfall are given, then :nml:mem:`t_for_con_rain` is the near-surface air temperature (K) at or above which rainfall is assumed to be convective in origin. At lower temperatures, all the rainfall is assumed to be large-scale in origin. In this configuration all snow is assumed to be large-scale in origin. The default value used to be 373.15 K but in general this is not recommended as it effectively means all precipitation is large-scale; a value of 293.15 K might be more appropriate.
56c55
<
---
>
59c58
<
---
>
65,66c64,65
<
<
---
>
>
68c67
<
---
>
73c72
<
---
>
77c76
< Relative humidity is kept constant over day.
---
> Relative humidity is kept constant over day.
81,82c80,81
<
<
---
>
>
89c88
<
---
>
91,92c90,91
<
<
---
>
>
99c98
<
---
>
101,102c100,101
<
<
---
>
>
109c108
<
---
>
111,112c110,111
<
<
---
>
>
119c118
<
---
>
121,123c120,122
<
<
< .. nml:member:: precip_disagg_method
---
>
>
> .. nml:member:: precip_disagg_method
130c129
<
---
>
164c163
<
---
>
179,182c178,181
< :type: logical
< :default: F
<
< Switch to indicate whether ``z1_tq`` (the height (m) at which the temperature and humidity data are valid) should be constant for all points or spatially varying. The height is relative to the zero-plane, not the ground.
---
> :type: logical
> :default: F
>
> Switch to indicate whether ``z1_tq`` (the height (m) at which the temperature and humidity data are valid) should be constant for all points or spatially varying. The height is relative to the zero-plane, not the ground.
184,185c183,184
< TRUE
< Spatially varying ``z1_tq`` will be read from the file specified in :nml:mem:`z1_tq_file`.
---
> TRUE
> Spatially varying ``z1_tq`` will be read from the file specified in :nml:mem:`z1_tq_file`.
187c186
< FALSE
---
> FALSE
198c197
<
---
>
202c201,204
< .. nml:member:: z1_tq_file
---
> .. nml:member:: z1_tq_file
>
> :type: character
> :default: None
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< :type: character
< :default: None
<
208c207
<
---
>
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< .. nml:member:: z1_tq_var_name
---
> .. nml:member:: z1_tq_var_name
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< :type: character
---
> :type: character
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<
---
>
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<
---
>
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<
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>
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<
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>
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>
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>
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>
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>
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>
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---
>
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<
<
---
>
>
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>
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>
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>
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>
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>
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<
---
>
>
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>
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>
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>
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<
---
>
>
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---
>
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>
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>
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>
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>
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>
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---
>
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---
>
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<
<
---
>
>
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<
---
>
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<
---
>
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<
---
>
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<
<
---
>
>
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<
---
>
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<
---
>
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<
---
>
343,344c342,343
<
<
---
>
>
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<
---
>
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<
---
>
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<
---
>
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<
<
---
>
>
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<
---
>
359c358
<
---
>
373,381c372,380
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | Name | Description |
< +============================+===========================================================================================================+
< | ``pstar`` | Air pressure (Pa). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``q`` | Specific humidity (kg kg\ :sup:`-1`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``t`` | Air temperature (K). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
---
> +-----------------+-----------------------------------------+
> | Name | Description |
> +=================+=========================================+
> | ``pstar`` | Air pressure (Pa). |
> +-----------------+-----------------------------------------+
> | ``q`` | Specific humidity (kg kg\ :sup:`-1`). |
> +-----------------+-----------------------------------------+
> | ``t`` | Air temperature (K). |
> +-----------------+-----------------------------------------+
406,420c405,419
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | Name | Description |
< +============================+===========================================================================================================+
< | ``rad_net`` | Net (all wavelength) downward radiation (W m\ :sup:`-2`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``lw_net`` | Net downward longwave radiation (W m\ :sup:`-2`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``sw_net`` | Net downward shortwave radiation (W m\ :sup:`-2`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``lw_down`` | Downward longwave radiation (W m\ :sup:`-2`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``sw_down`` | Downward shortwave radiation (W m\ :sup:`-2`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``diff_rad`` | Diffuse radiation (W m\ :sup:`-2`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
---
> +--------------+-----------------------------------------------------------+
> | Name | Description |
> +==============+===========================================================+
> | ``rad_net`` | Net (all wavelength) downward radiation (W m\ :sup:`-2`). |
> +--------------+-----------------------------------------------------------+
> | ``lw_net`` | Net downward longwave radiation (W m\ :sup:`-2`). |
> +--------------+-----------------------------------------------------------+
> | ``sw_net`` | Net downward shortwave radiation (W m\ :sup:`-2`). |
> +--------------+-----------------------------------------------------------+
> | ``lw_down`` | Downward longwave radiation (W m\ :sup:`-2`). |
> +--------------+-----------------------------------------------------------+
> | ``sw_down`` | Downward shortwave radiation (W m\ :sup:`-2`). |
> +--------------+-----------------------------------------------------------+
> | ``diff_rad`` | Diffuse radiation (W m\ :sup:`-2`). |
> +--------------+-----------------------------------------------------------+
445,461c444,460
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | Name | Description |
< +============================+===========================================================================================================+
< | ``precip`` | Precipitation rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``tot_rain`` | Rainfall rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``tot_snow`` | Snowfall rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``ls_rain`` | Large-scale rainfall rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``con_rain`` | Convective rainfall rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``ls_snow`` | Large-scale snowfall rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``con_snow`` | Convective snowfall rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
---
> +---------------+-------------------------------------------------------------+
> | Name | Description |
> +===============+=============================================================+
> | ``precip`` | Precipitation rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
> +---------------+-------------------------------------------------------------+
> | ``tot_rain`` | Rainfall rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
> +---------------+-------------------------------------------------------------+
> | ``tot_snow`` | Snowfall rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
> +---------------+-------------------------------------------------------------+
> | ``ls_rain`` | Large-scale rainfall rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
> +---------------+-------------------------------------------------------------+
> | ``con_rain`` | Convective rainfall rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
> +---------------+-------------------------------------------------------------+
> | ``ls_snow`` | Large-scale snowfall rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
> +---------------+-------------------------------------------------------------+
> | ``con_snow`` | Convective snowfall rate (kg m\ :sup:`-2` s\ :sup:`-1`). |
> +---------------+-------------------------------------------------------------+
476,484c475,483
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | Name | Description |
< +============================+===========================================================================================================+
< | ``wind`` | Total wind speed (m s\ :sup:`-1`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``u`` | Zonal component of the wind (m s\ :sup:`-1`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | ``v`` | Meridional component of the wind (m s\ :sup:`-1`). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
---
> +------------+----------------------------------------------------------------+
> | Name | Description |
> +============+================================================================+
> | ``wind`` | Total wind speed (m s\ :sup:`-1`). |
> +------------+----------------------------------------------------------------+
> | ``u`` | Zonal component of the wind (m s\ :sup:`-1`). |
> +------------+----------------------------------------------------------------+
> | ``v`` | Meridional component of the wind (m s\ :sup:`-1`). |
> +------------+----------------------------------------------------------------+
492,496c491,495
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
< | Name | Description |
< +============================+===========================================================================================================+
< | ``dt_range`` | Diurnal temperature range (K). |
< +----------------------------+-----------------------------------------------------------------------------------------------------------+
---
> +---------------+-------------------------------------------------------------+
> | Name | Description |
> +===============+=============================================================+
> | ``dt_range`` | Diurnal temperature range (K). |
> +---------------+-------------------------------------------------------------+
586,587d584
<
<
diff -r jules-lsm.github.io/doc/source/namelists/fire.nml.rst jules/doc/source/namelists/fire.nml.rst
25d24
<
diff -r jules-lsm.github.io/doc/source/namelists/imogen.nml.rst jules/doc/source/namelists/imogen.nml.rst
4d3
<
9c8
< IMOGEN uses the netcdf read functions in JULES to load the files to derive the driving data. The driving data is derived from: specific humidity (kg/kg), precipitation (kg/m2/s), wind speed (m/s), incoming shortwave radiation (W/m2), incoming longwave radiation (W/m2), air temeprature (K) and diurnal range of air temperature (K). IMOGEN also needs ``grid_area`` read in via :nml:lst:`JULES_LATLON`.
---
> IMOGEN uses the netcdf read functions in JULES to load the files to derive the driving data. The driving data is derived from: specific humidity (kg/kg), precipitation (kg/m2/s), wind speed (m/s), incoming shortwave radiation (W/m2), incoming longwave radiation (W/m2), air temperature (K) and diurnal range of air temperature (K). IMOGEN also needs ``grid_area`` read in via :nml:lst:`JULES_LATLON`.
13c12
< If :nml:mem:`IMOGEN_RUN_LIST::change_metdata_method` = 2, then use anomalies from the given climatology. Otherwise (:nml:mem:`IMOGEN_RUN_LIST::change_metdata_method` set to 1 or 3) use pattern-scaling (spatial patterns of changes in each meteorological driving variable per degree of global temperature change). Patterns can be derived at the required spatial resolution using ESMValTool <https://esmvaltool.org/>.
---
> If :nml:mem:`IMOGEN_RUN_LIST::change_metdata_method` = 2, then use anomalies from the given climatology. Otherwise (:nml:mem:`IMOGEN_RUN_LIST::change_metdata_method` set to 1 or 3) use pattern-scaling (spatial patterns of changes in each meteorological driving variable per degree of global temperature change). Patterns can be derived at the required spatial resolution using `ESMValTool <https://esmvaltool.org/>`__.
24c23
< * Huntingford, C., et al. (2010),
---
> * Huntingford, C., et al. (2010),
35,36c34,35
< Climate pattern-scaling set for an ensemble of 22
< GCMs–adding uncertainty to the IMOGEN version 2.0 impact system,
---
> Climate pattern-scaling set for an ensemble of 22
> GCMs-adding uncertainty to the IMOGEN version 2.0 impact system,
40c39
< A rapid application emissions-to-impacts tool for scenario assessment:
---
> A rapid application emissions-to-impacts tool for scenario assessment:
63c62
<
---
>
109c108
<
---
>
198a198,205
> .. nml:member:: l_drive_with_global_temps
>
> :type: logical
> :default: F
>
> If TRUE, use imogen to provide jules forcing based on the global mean temperature change and the climate patterns.
>
>
220,221c227,228
< | An additional non-CO2 rdiative forcing can also be prescribed (:nml:mem:`file_non_co2_radf`).
< 2. | Time series of anomaly data provided
---
> | An additional non-CO2 radiative forcing can also be prescribed (:nml:mem:`file_non_co2_radf`).
> 2. | Time series of anomaly data provided
403c410
< Netcdf file containing the patterns. It should be monthly data (12 months total) with the dimension 'imogen_drive' representing time.
---
> Netcdf file containing the patterns. It should be monthly data (12 months total) with the dimension 'imogen_drive' representing time.
420,423d426
<
<
<
<
diff -r jules-lsm.github.io/doc/source/namelists/initial_conditions.nml.rst jules/doc/source/namelists/initial_conditions.nml.rst
4d3
<
diff -r jules-lsm.github.io/doc/source/namelists/intro.rst jules/doc/source/namelists/intro.rst
21c21
<
---
>
27c27
<
---
>
diff -r jules-lsm.github.io/doc/source/namelists/jules_deposition.nml.rst jules/doc/source/namelists/jules_deposition.nml.rst
24c24
<
---
>
64c64
< Note: The Paulot et al. scheme is currently not available in UM-coupled JULES applications.
---
> Note: The Paulot et al. scheme is currently not available in UM-coupled JULES applications.
75c75
< Calculate deposition fluxes. This requires that the concentrations of atmopsheric tracer species are provided as prescribed data (see :ref:`supported-prescribed-variables`).
---
> Calculate deposition fluxes. This requires that the concentrations of atmospheric tracer species are provided as prescribed data (see :ref:`supported-prescribed-variables`).
95c95
< Latitude of southern limit of tundra (radians). This is used to alter the calculation of deposition of certain species in the tundra region (actually for all points north of this limit). Only used if the list of species (see :nml:mem:`JULES_DEPOSITION_SPECIES::dep_species_name_io`) includes one or more of 'CO', 'NO2', 'O3', 'PAN', 'PPAN', 'MPAN' or 'ONITU'.
---
> Latitude of southern limit of tundra (radians). This is used to alter the calculation of deposition of certain species in the tundra region (actually for all points north of this limit). Only used if the list of species (see :nml:mem:`JULES_DEPOSITION_SPECIES::dep_species_name_io`) includes one or more of 'CO', 'NO2', 'O3', 'PAN', 'PPAN', 'MPAN' or 'ONITU'.
103c103
< Constant value for separation of boundary layer levels (m). All layer thicknesses are set to this value. This is used as a simple way to prescribe the layer thicknesses in standalone mode. This value can be overriden by prescribed data - see :nml:lst:`JULES_PRESCRIBED`. This can be considered as the representative depth for tracer concentration and the depth over which the deposition flux is removed.
---
> Constant value for separation of boundary layer levels (m). All layer thicknesses are set to this value. This is used as a simple way to prescribe the layer thicknesses in standalone mode. This value can be overridden by prescribed data - see :nml:lst:`JULES_PRESCRIBED`. This can be considered as the representative depth for tracer concentration and the depth over which the deposition flux is removed.
145c145
< Switch from the UKCA controlling which atmospheric levels in the boundary layer are used for dry deposition. For UM-coupled JULES applications, the UKCA interactive dry deposition switch (l_ukca_intdd in the run_ukca namelist) needs to be true.
---
> Switch from the UKCA controlling which atmospheric levels in the boundary layer are used for dry deposition. For UM-coupled JULES applications, the UKCA interactive dry deposition switch (l_ukca_intdd in the run_ukca namelist) needs to be true.
203c203
< The number of model levels in the boundary layer is required and is set to a default balues of 1. This can be overridden via the namelist variable :nml:mem:`JULES_NLSIZES::bl_levels`. The number of levels is only used to communicate with the atmospheric model (e.g. UKCA).
---
> The number of model levels in the boundary layer is required and is set to a default values of 1. This can be overridden via the namelist variable :nml:mem:`JULES_NLSIZES::bl_levels`. The number of levels is only used to communicate with the atmospheric model (e.g. UKCA).
215c215
< This namelist should occur :nml:mem:`JULES_DEPOSITION::ndry_dep_species` times, with each occurence containing parameters for an atmospheric tracer species that is to be considered in dry deposition.
---
> This namelist should occur :nml:mem:`JULES_DEPOSITION::ndry_dep_species` times, with each occurrence containing parameters for an atmospheric tracer species that is to be considered in dry deposition.
diff -r jules-lsm.github.io/doc/source/namelists/jules_hydrology.nml.rst jules/doc/source/namelists/jules_hydrology.nml.rst
4d3
<
8d6
<
96c94
< Limit the soil conductance to the value when the top layer soil moisture is at the critical soil moisture. Below this threshold, the soil conductance follows Best et al. (2011) equation 7.
---
> Limit the soil conductance to the value when the top layer soil moisture is at the critical soil moisture. Below this threshold, the soil conductance follows Best et al. (2011) equation 7.
202c200
< For slopes calculated from coarser DEM datasets, a lower value might be more appropriate as fine-resolution features of the terrain are not included.
---
> For slopes calculated from coarser DEM datasets, a lower value might be more appropriate as fine-resolution features of the terrain are not included.
diff -r jules-lsm.github.io/doc/source/namelists/jules_irrig.nml.rst jules/doc/source/namelists/jules_irrig.nml.rst
59,60c59,60
< and is available in this release to support beta testing
< activities.
---
> and is available in this release to support beta testing
> activities.
63c63
< feedback where deficiencies are identified.
---
> feedback where deficiencies are identified.
70a71,72
> .. |oumlaut| replace:: ö
>
81c83
< :ref:`Döll & Siebert (2002)<References_irrig>` method. No irrigation
---
> :ref:`D|oumlaut|ll & Siebert (2002)<References_irrig>` method. No irrigation
131c133
< :nml:mem:`nstep_irrig` = NINT(frequency of irrigation update (in sec)) / :nml:mem:`JULES_TIME::timestep_len`)
---
> :nml:mem:`nstep_irrig` = NINT(frequency of irrigation update (in sec)) / :nml:mem:`JULES_TIME::timestep_len`
139c141
< * Döll, P., and Siebert, S., Global modeling of irrigation water
---
> * D|oumlaut|ll, P., and Siebert, S., Global modeling of irrigation water
diff -r jules-lsm.github.io/doc/source/namelists/jules_prnt_control.nml.rst jules/doc/source/namelists/jules_prnt_control.nml.rst
4d3
<
diff -r jules-lsm.github.io/doc/source/namelists/jules_radiation.nml.rst jules/doc/source/namelists/jules_radiation.nml.rst
4d3
<
8d6
<
58,59c56,57
<
<
---
>
>
93c91
<
---
>
106c104
<
---
>
121c119
<
---
>
142,143c140
< .. note:: Observed albedo(s) must be prescribed in
< :doc:`prescribed_data.nml`.
---
> .. note:: Observed albedo(s) must be prescribed in :doc:`prescribed_data.nml`.
204c201
< :nml:mem:`JULES_RADIATION::wght_alb` and
---
> :nml:mem:`JULES_RADIATION::wght_alb` and
206c203
< :nml:mem:`JULES_RADIATION::swdn_frac_albsoil` equal to
---
> :nml:mem:`JULES_RADIATION::swdn_frac_albsoil` equal to
208c205
< :nml:mem:`JULES_RADIATION::wght_alb` :math:`/ \sum_1^4`
---
> :nml:mem:`JULES_RADIATION::wght_alb` :math:`/ \sum_1^4`
210,212c207,209
< However, :nml:mem:`JULES_RADIATION::swdn_frac_albsoil`
< is applied only to bare soil and having a single parameter
< is more transparent to the user, while
---
> However, :nml:mem:`JULES_RADIATION::swdn_frac_albsoil`
> is applied only to bare soil and having a single parameter
> is more transparent to the user, while
241c238
< of the spectrum using :nml:mem:`JULES_RADIATION::ratio_albsoil` and
---
> of the spectrum using :nml:mem:`JULES_RADIATION::ratio_albsoil` and
263c260
< (Ideally, :nml:mem:`JULES_RADIATION::wght_alb` and
---
> (Ideally, :nml:mem:`JULES_RADIATION::wght_alb` and
265c262
< :nml:mem:`JULES_RADIATION::swdn_frac_albsoil` equal to
---
> :nml:mem:`JULES_RADIATION::swdn_frac_albsoil` equal to
267c264
< :nml:mem:`JULES_RADIATION::wght_alb` :math:`/ \sum_1^4`
---
> :nml:mem:`JULES_RADIATION::wght_alb` :math:`/ \sum_1^4`
269,270c266,267
< However, :nml:mem:`JULES_RADIATION::swdn_frac_albsoil` is applied
< only to bare soil and having a single parameter is more transparent
---
> However, :nml:mem:`JULES_RADIATION::swdn_frac_albsoil` is applied
> only to bare soil and having a single parameter is more transparent
275a273,275
> .. |eacute| replace:: é
> .. |ccedil| replace:: ç
>
281c281
< 2213–2223, `doi:10.1175/1520-0442(1995)008<2213:ISOCSS>2.0.CO;2
---
> 2213-2223, `doi:10.1175/1520-0442(1995)008<2213:ISOCSS>2.0.CO;2
285c285
< 1160–1171, `doi:10.1175/1520-0450(1982)021<1160:SADVIC>2.0.CO;2
---
> 1160-1171, `doi:10.1175/1520-0450(1982)021<1160:SADVIC>2.0.CO;2
305,307c305,307
< * Martin Turbet, Jérémy Leconte, Franck Selsis, Emeline Bolmont,
< François Forget, Ignasi Ribas, Sean N. Raymond and Guillem
< Anglada-Escudé (2016), The habitability of Proxima Centauri
---
> * Martin Turbet, J|eacute|r|eacute|my Leconte, Franck Selsis, Emeline Bolmont,
> Fran|ccedil|ois Forget, Ignasi Ribas, Sean N. Raymond and Guillem
> Anglada-Escud|eacute| (2016), The habitability of Proxima Centauri
diff -r jules-lsm.github.io/doc/source/namelists/jules_rivers.nml.rst jules/doc/source/namelists/jules_rivers.nml.rst
90c90
<
---
>
219c219
< * Oki, T. and Sud, Y.C. (1998) Design of Total Runoff Integrating Pathways (TRIP)—A Global River Channel Network. Earth Interactions, 2: 1-37.
---
> * Oki, T. and Sud, Y.C. (1998) Design of Total Runoff Integrating Pathways (TRIP)--A Global River Channel Network. Earth Interactions, 2: 1-37.
333c333
< :suggested: 0.08 (for "several drainages in western Washington State, USA", Cragun 2005)
---
> :suggested: 0.08 (for "several drainages in western Washington State, USA", Cragun 2005)
342c342
< :suggested: 0.95 (for "several drainages in western Washington State, USA", Cragun 2005)
---
> :suggested: 0.95 (for "several drainages in western Washington State, USA", Cragun 2005)
diff -r jules-lsm.github.io/doc/source/namelists/jules_snow.nml.rst jules/doc/source/namelists/jules_snow.nml.rst
4d3
<
8d6
<
180,181c178,179
< These parameters are used as limits at all snow-covered
< grid points.
---
> These parameters are used as limits at all snow-covered
> grid points.
184c182
< These parameters are not used.
---
> These parameters are not used.
187,190c185,188
< Irrespective of whether either of the two previous options
< are selected, these parameters are used to adjust the albedo
< of dense snow to a value more appropriate for firn. See
< also :nml:mem:`aicemax`.
---
> Irrespective of whether either of the two previous options
> are selected, these parameters are used to adjust the albedo
> of dense snow to a value more appropriate for firn. See
> also :nml:mem:`aicemax`.
351,352c349
< Thermal conductivity of lying snow (W m\ :sup:`-1` K\
< :sup:`-1`).
---
> Thermal conductivity of lying snow (W m\ :sup:`-1` K\ :sup:`-1`).
476c473
< infiltration.
---
> infiltration.
542,543c539,540
< (1989)<References_snow>`, with no dependence of the rate of
< growth of small grains on the temperature.
---
> (1989)<References_snow>`, with no dependence of the rate of
> growth of small grains on the temperature.
546,548c543,545
< :ref:`Taillandier et al. (2007)<References_snow>` for
< equitemperature metamorphism. Growth is significantly
< slower than the default scheme at low temperatures.
---
> :ref:`Taillandier et al. (2007)<References_snow>` for
> equitemperature metamorphism. Growth is significantly
> slower than the default scheme at low temperatures.
562c559
< involving the grain size itself.
---
> involving the grain size itself.
564,566c561,563
< is more consistent with conserving the specific surface area
< of snow, though full conservation would require mass
< weighting to be invoked during regridding.
---
> is more consistent with conserving the specific surface area
> of snow, though full conservation would require mass
> weighting to be invoked during regridding.
585,590c582,584
< of the first soil layer is above freezing, until the snow is
< removed or the temperature of soil layer is reduced to
< freezing.
<
<
<
---
> of the first soil layer is above freezing, until the snow is
> removed or the temperature of soil layer is reduced to
> freezing.
619,620d612
<
<
631,632c623
< snow, Geophys. Res. Lett., 38, L23501,
< https://doi.org/10.1029/2011GL049234.
---
> snow, Geophys. Res. Lett., 38, L23501, https://doi.org/10.1029/2011GL049234
636c627
< 11, 899–916, https://doi.org/10.1175/2010JHM1249.1.
---
> 11, 899-916, https://doi.org/10.1175/2010JHM1249.1
639,640c630,631
< National Center for Atmospheric
< Research. https://atmos.washington.edu/~sgw/PAPERS/1989_Marshall.pdf
---
> National Center for Atmospheric Research.
> https://atmos.washington.edu/~sgw/PAPERS/1989_Marshall.pdf
644,645c635
< conditions, J. Geophys. Res., 112, F03003,
< https://doi.org/10.1029/2006JF000514.
---
> conditions, J. Geophys. Res., 112, F03003, https://doi.org/10.1029/2006JF000514
648c638
< 81-10. https://hdl.handle.net/11681/9469
---
> 81-10, https://hdl.handle.net/11681/9469
diff -r jules-lsm.github.io/doc/source/namelists/jules_soil_biogeochem.nml.rst jules/doc/source/namelists/jules_soil_biogeochem.nml.rst
4d3
<
12d10
<
101c99
< * Clark, D. B., Mercado, L. M., Sitch, S., Jones, C. D., Gedney, N., Best, M. J., Pryor, M., Rooney, G. G., Essery, R. L. H., Blyth, E., Boucher, O., Harding, R. J., Huntingford, C., and Cox, P. M.: The Joint UK Land Environment Simulator (JULES), model description – Part 2: Carbon fluxes and vegetation dynamics, Geosci. Model Dev., 4, 701–722, (https://doi.org/10.5194/gmd-4-701-2011), 2011.
---
> * Clark, D. B., Mercado, L. M., Sitch, S., Jones, C. D., Gedney, N., Best, M. J., Pryor, M., Rooney, G. G., Essery, R. L. H., Blyth, E., Boucher, O., Harding, R. J., Huntingford, C., and Cox, P. M.: The Joint UK Land Environment Simulator (JULES), model description - Part 2: Carbon fluxes and vegetation dynamics, Geosci. Model Dev., 4, 701-722, (https://doi.org/10.5194/gmd-4-701-2011), 2011.
143c141
<
---
>
160c158
< * Burke, E. J., Chadburn, S. E., and Ekici, A.: A vertical representation of soil carbon in the JULES land surface scheme (vn4.3_permafrost) with a focus on permafrost regions, Geosci. Model Dev., 10, 959-975, doi:10.5194/gmd-10-959-2017, 2017.
---
> * Burke, E. J., Chadburn, S. E., and Ekici, A.: A vertical representation of soil carbon in the JULES land surface scheme (vn4.3_permafrost) with a focus on permafrost regions, Geosci. Model Dev., 10, 959-975, doi:10.5194/gmd-10-959-2017, 2017.
215c213
< Parameter controlling the depth to which fire burns soil litter carbon in metres. At depths shallower than this value, the fire can burn soil carbon in the two litter pools (dpm and rpm). If z_burn_max falls within a layer only a proportion of the soil carbon is burnt. Only used with layered soil carbon scheme (:nml:mem:`l_layeredc` = TRUE) and fire (either :nml:mem:`JULES_VEGETATION::l_trif_fire` or :nml:mem:`JULES_VEGETATION::l_inferno` or both). In reality the burn depth varies so please check whether the default value of 0.2 is suitable for your application.
---
> Parameter controlling the depth to which fire burns soil litter carbon in metres. At depths shallower than this value, the fire can burn soil carbon in the two litter pools (dpm and rpm). If z_burn_max falls within a layer only a proportion of the soil carbon is burnt. Only used with layered soil carbon scheme (:nml:mem:`l_layeredc` = TRUE) and fire (either :nml:mem:`JULES_VEGETATION::l_trif_fire` or :nml:mem:`JULES_VEGETATION::l_inferno` or both). In reality the burn depth varies so please check whether the default value of 0.2 is suitable for your application.
307,308c305,306
< | :nml:mem:`JULES_VEGETATION::l_triffid` = FALSE, :nml:mem:`const_ch4_cs` = 5.41e-12
< | :nml:mem:`JULES_VEGETATION::l_triffid` = TRUE, :nml:mem:`const_ch4_cs` = 5.41e-10
---
> | :nml:mem:`JULES_VEGETATION::l_triffid` = FALSE, :nml:mem:`const_ch4_cs` = 5.41e-12
> | :nml:mem:`JULES_VEGETATION::l_triffid` = TRUE, :nml:mem:`const_ch4_cs` = 5.41e-10
440c438
< Modeled Microbial Dynamics Explain the Apparent Temperature Sensitivity
---
> Modeled Microbial Dynamics Explain the Apparent Temperature Sensitivity
diff -r jules-lsm.github.io/doc/source/namelists/jules_soil_ecosse.nml.rst jules/doc/source/namelists/jules_soil_ecosse.nml.rst
18c18
< * Clark, D. B., Mercado, L. M., Sitch, S., Jones, C. D., Gedney, N., Best, M. J., Pryor, M., Rooney, G. G., Essery, R. L. H., Blyth, E., Boucher, O., Harding, R. J., Huntingford, C., and Cox, P. M.: The Joint UK Land Environment Simulator (JULES), model description – Part 2: Carbon fluxes and vegetation dynamics, Geosci. Model Dev., 4, 701–722, (https://doi.org/10.5194/gmd-4-701-2011), 2011.
---
> * Clark, D. B., Mercado, L. M., Sitch, S., Jones, C. D., Gedney, N., Best, M. J., Pryor, M., Rooney, G. G., Essery, R. L. H., Blyth, E., Boucher, O., Harding, R. J., Huntingford, C., and Cox, P. M.: The Joint UK Land Environment Simulator (JULES), model description - Part 2: Carbon fluxes and vegetation dynamics, Geosci. Model Dev., 4, 701-722, (https://doi.org/10.5194/gmd-4-701-2011), 2011.
33c33
<
---
>
47c47
<
---
>
88c88
<
---
>
95c95
<
---
>
103c103
<
---
>
196c196
< Note that these default values are also those harwired in the code for use with the 4-pool model (:nml:mem:`JULES_SOIL_BIOGEOCHEM::soil_bgc_model` = 2, :nml:mem:`JULES_SOIL_BIOGEOCHEM::l_q10` = F ).
---
> Note that these default values are also those hardwired in the code for use with the 4-pool model (:nml:mem:`JULES_SOIL_BIOGEOCHEM::soil_bgc_model` = 2, :nml:mem:`JULES_SOIL_BIOGEOCHEM::l_q10` = F ).
215c215
< Note that this default value is also that harwired in the code for use with the 4-pool model (:nml:mem:`JULES_SOIL_BIOGEOCHEM::soil_bgc_model` = 2).
---
> Note that this default value is also that hardwired in the code for use with the 4-pool model (:nml:mem:`JULES_SOIL_BIOGEOCHEM::soil_bgc_model` = 2).
227c227
<
---
>
241c241,242
< The fraction of nitrogen deposition that is aded to the soil nitrate pool. The complement is aded to the ammonium pool.
---
> The fraction of nitrogen deposition that is added to the soil nitrate pool. The complement is added to the ammonium pool.
>
243d243
<
294c294
<
---
>
345c345
<
---
>
369c369
<
---
>
378c378
<
---
>
386c386
<
---
>
391c391
< :default: 0.62, 0.38, 1.74
---
> :default: 0.62, 0.38, 1.74
394c394
<
---
>
402c402
<
---
>
diff -r jules-lsm.github.io/doc/source/namelists/jules_soil.nml.rst jules/doc/source/namelists/jules_soil.nml.rst
4d3
<
8d6
<
23c21
<
---
>
27c25
<
---
>
43c41
<
---
>
54,55c52,53
<
<
---
>
>
104c102
<
---
>
107c105
< * Johansen (1975). Thermal conductivity of soils. PhD thesis. University of Trondheim, Norway
---
> * Johansen (1975). Thermal conductivity of soils. PhD thesis. University of Trondheim, Norway
117c115
<
---
>
119c117
<
---
>
122c120
<
---
>
125c123
<
---
>
216c214
< Depth of the tiled solid-ice bedrock-type layer used underneath individual ice tiles if :nml:mem:`JULES_SURFACE::l_elev_land_ice` is TRUE.
---
> Depth of the tiled solid-ice bedrock-type layer used underneath individual ice tiles if :nml:mem:`JULES_SURFACE::l_elev_land_ice` is TRUE.
229c227
< Setting :nml:mem:`l_tile_soil` = TRUE means a separate soil tile exists for each surface tile (rather than all surface tiles using the same, single soil tile). This also alters the names of many of the soil prognostic and ancillary variables that are used (see elsewhere), with the suffix "_soilt'' being added to indicate the presence of soil tiling. The switches :nml:mem:`l_broadcast_ancils` and :nml:mem:`JULES_INITIAL::l_broadcast_soilt` allow soil tiling to be used with input files that do not contain soil tile information. Setting :nml:mem:`l_broadcast_ancils` = TRUE means that a soil ancillary file that does not contain soil tiles can be used in a tiled run. Setting :nml:mem:`JULES_INITIAL::l_broadcast_soilt` = TRUE means an initital state file that does not contain soil tiles can be used to initialise a run with soil tiles.
---
> Setting :nml:mem:`l_tile_soil` = TRUE means a separate soil tile exists for each surface tile (rather than all surface tiles using the same, single soil tile). This also alters the names of many of the soil prognostic and ancillary variables that are used (see elsewhere), with the suffix "_soilt'' being added to indicate the presence of soil tiling. The switches :nml:mem:`l_broadcast_ancils` and :nml:mem:`JULES_INITIAL::l_broadcast_soilt` allow soil tiling to be used with input files that do not contain soil tile information. Setting :nml:mem:`l_broadcast_ancils` = TRUE means that a soil ancillary file that does not contain soil tiles can be used in a tiled run. Setting :nml:mem:`JULES_INITIAL::l_broadcast_soilt` = TRUE means an initial state file that does not contain soil tiles can be used to initialise a run with soil tiles.
diff -r jules-lsm.github.io/doc/source/namelists/jules_surface.nml.rst jules/doc/source/namelists/jules_surface.nml.rst
4d3
<
8d6
<
207c205
< 1) The meltwater-holding capacity of snow layers reduces as a linear function of their density, becoming zero
---
> #. The meltwater-holding capacity of snow layers reduces as a linear function of their density, becoming zero
209c207
< 2) Where the top few centimetres of the pack has a density appropriate to firn/bare ice
---
> #. Where the top few centimetres of the pack has a density appropriate to firn/bare ice
247c245
< coefficients. On occations when the stability is around neutral it is possible that the iterative calculation does not converge. In this case the larger of the last two calculated transfer coefficients is then used to prevent
---
> coefficients. On occasions when the stability is around neutral it is possible that the iterative calculation does not converge. In this case the larger of the last two calculated transfer coefficients is then used to prevent
diff -r jules-lsm.github.io/doc/source/namelists/jules_surface_types.nml.rst jules/doc/source/namelists/jules_surface_types.nml.rst
2a3
>
24,26c25,27
< made available and are used to check the surface type
< configuration at runtime, they are not yet used by the JULES
< I/O.
---
> made available and are used to check the surface type
> configuration at runtime, they are not yet used by the JULES
> I/O.
74,78c75
< .. nml:member:: urban
<
< :type: integer
< :permitted: -1, npft+1:ntype
< :default: -32768
---
> .. nml:member:: urban
80c77,79
< Index of the urban surface type (#6).
---
> :type: integer
> :permitted: -1, npft+1:ntype
> :default: -32768
82c81
< Can only be used if :nml:mem:`JULES_SURFACE::l_urban2t` = FALSE.
---
> Index of the urban surface type (#6).
83a83
> Can only be used if :nml:mem:`JULES_SURFACE::l_urban2t` = FALSE.
85d84
< .. nml:member:: lake
87,89c86
< :type: integer
< :permitted: npft+1:ntype
< :default: -32768
---
> .. nml:member:: lake
91c88,90
< Index of the lake surface type (#7).
---
> :type: integer
> :permitted: npft+1:ntype
> :default: -32768
92a92
> Index of the lake surface type (#7).
94d93
< .. nml:member:: soil
96,98c95
< :type: integer
< :permitted: npft+1:ntype
< :default: -32768
---
> .. nml:member:: soil
100c97,99
< Index of the soil surface type (#8).
---
> :type: integer
> :permitted: npft+1:ntype
> :default: -32768
102c101
< .. note:: A soil surface type must be given (although the fraction may be set to zero).
---
> Index of the soil surface type (#8).
103a103
> .. note:: A soil surface type must be given (although the fraction may be set to zero).
105d104
< .. nml:member:: ice
107,109c106
< :type: integer
< :permitted: npft+1:ntype
< :default: -32768
---
> .. nml:member:: ice
111c108,110
< Index of the ice surface type (#9).
---
> :type: integer
> :permitted: npft+1:ntype
> :default: -32768
113c112
< .. note:: In the UM the ice surface type must be specified (although the fraction may be set to zero).
---
> Index of the ice surface type (#9).
114a114
> .. note:: In the UM the ice surface type must be specified (although the fraction may be set to zero).
116d115
< .. nml:group:: Multiple ice tiles allowed to exist in an ice gridbox
118,120c117
< These surface types can only be used when multiple ice tiles are
< allowed in a gridbox i.e. when
< :nml:mem:`JULES_SURFACE::l_elev_land_ice` = TRUE.
---
> .. nml:group:: Multiple ice tiles allowed to exist in an ice gridbox
122c119,121
< .. nml:member:: elev_ice
---
> These surface types can only be used when multiple ice tiles are
> allowed in a gridbox i.e. when
> :nml:mem:`JULES_SURFACE::l_elev_land_ice` = TRUE.
124,126c123
< :type: integer
< :permitted: -1,npft+1:ntype
< :default: -32768
---
> .. nml:member:: elev_ice
128c125,127
< Indices of the elevated ice types (#901-925).
---
> :type: integer
> :permitted: -1,npft+1:ntype
> :default: -32768
130,132c129
< Must be grouped together with values ``npft < elev_ice <=
< ntype`` OR ``elev_ice = -1`` to indicate they are not used
< (i.e. all elevated rock instead).
---
> Indices of the elevated ice types (#901-925).
134c131,133
< .. nml:member:: elev_rock
---
> Must be grouped together with values ``npft < elev_ice <=
> ntype`` OR ``elev_ice = -1`` to indicate they are not used
> (i.e. all elevated rock instead).
136,138c135
< :type: integer
< :permitted: -1,npft+1:ntype
< :default: -32768
---
> .. nml:member:: elev_rock
140,141c137,139
< Indices of the elevated non-glaciated bedrock types
< (#926-950).
---
> :type: integer
> :permitted: -1,npft+1:ntype
> :default: -32768
143,145c141,142
< Must be grouped together, with values ``npft < elev_rock <=
< ntype`` OR ``elev_rock = -1`` to indicate they are not used
< (i.e. all elevated ice instead).
---
> Indices of the elevated non-glaciated bedrock types
> (#926-950).
146a144,146
> Must be grouped together, with values ``npft < elev_rock <=
> ntype`` OR ``elev_rock = -1`` to indicate they are not used
> (i.e. all elevated ice instead).
148d147
< .. nml:group:: Two-tile urban schemes including MORUSES
150c149
< These surface types can only be used when :nml:mem:`JULES_SURFACE::l_urban2t` = TRUE.
---
> .. nml:group:: Two-tile urban schemes including MORUSES
152c151
< .. nml:member:: urban_canyon
---
> These surface types can only be used when :nml:mem:`JULES_SURFACE::l_urban2t` = TRUE.
154,156c153
< :type: integer
< :permitted: npft+1:ntype
< :default: -32768
---
> .. nml:member:: urban_canyon
158c155,157
< Index of the urban canyon surface type (#601).
---
> :type: integer
> :permitted: npft+1:ntype
> :default: -32768
159a159
> Index of the urban canyon surface type (#601).
161d160
< .. nml:member:: urban_roof
163,165c162
< :type: integer
< :permitted: npft+1:ntype
< :default: -32768
---
> .. nml:member:: urban_roof
167c164,166
< Index of the urban roof surface type (#602).
---
> :type: integer
> :permitted: npft+1:ntype
> :default: -32768
168a168
> Index of the urban roof surface type (#602).
170c170
< .. note::
---
> .. note::
172c172,177
< When giving urban fraction data (see :nml:lst:`JULES_FRAC`), total *urban* fraction may be given instead of the separate canyon and roof fractions by entering it under the canyon fraction. When initialising if the roof fraction is zero, the canyon fraction will be interpreted as the total *urban* fraction and be partitioned according to the canyon fraction (W/R, see :nml:lst:`URBAN_PROPERTIES`).
---
> When giving urban fraction data (see :nml:lst:`JULES_FRAC`),
> total *urban* fraction may be given instead of the separate canyon and
> roof fractions by entering it under the canyon fraction. When initialising
> if the roof fraction is zero, the canyon fraction will be interpreted as
> the total *urban* fraction and be partitioned according to the canyon
> fraction (W/R, see :nml:lst:`URBAN_PROPERTIES`).
182c187
< .. nml:member:: usr_type
---
> .. nml:member:: usr_type
184,186c189,191
< :type: integer
< :permitted: 1:ntype
< :default: -32768
---
> :type: integer
> :permitted: 1:ntype
> :default: -32768
188c193
< Index of user specified surface type (#10-99).
---
> Index of user specified surface type (#10-99).
190,193c195,198
< A user surface type can be used when experimenting with new
< surface configurations without a code change. These can be
< either vegetated or non-vegetated and are used solely to assign an
< ID number.
---
> A user surface type can be used when experimenting with new
> surface configurations without a code change. These can be
> either vegetated or non-vegetated and are used solely to assign an
> ID number.
195c200
< .. nml:group:: Vegetated surface types
---
> .. nml:group:: Vegetated surface types
197,198c202,203
< A negative value, when permitted, indicates that the surface
< type is not in use.
---
> A negative value, when permitted, indicates that the surface
> type is not in use.
200c205
< .. nml:member:: brd_leaf
---
> .. nml:member:: brd_leaf
202,204c207,209
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
206c211
< Index of the original broadleaf PFT surface type (#1).
---
> Index of the original broadleaf PFT surface type (#1).
208c213
< .. nml:member:: brd_leaf_dec
---
> .. nml:member:: brd_leaf_dec
210,212c215,217
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
214c219
< Index of broadleaf (decidous) PFT surface type (#101)
---
> Index of broadleaf (deciduous) PFT surface type (#101)
216c221
< .. nml:member:: brd_leaf_eg_trop
---
> .. nml:member:: brd_leaf_eg_trop
218,220c223,225
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
222c227
< Index of broadleaf (evergreen tropical) PFT surface type (#102).
---
> Index of broadleaf (evergreen tropical) PFT surface type (#102).
224c229
< .. nml:member:: brd_leaf_eg_temp
---
> .. nml:member:: brd_leaf_eg_temp
226,228c231,233
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
230c235
< Index of broadleaf (evergreen temperate) PFT surface type (#103).
---
> Index of broadleaf (evergreen temperate) PFT surface type (#103).
232c237
< .. nml:member:: ndl_leaf
---
> .. nml:member:: ndl_leaf
234,236c239,241
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
238c243
< Index of original needleleaf PFT surface type (#2).
---
> Index of original needleleaf PFT surface type (#2).
240c245
< .. nml:member:: ndl_leaf_dec
---
> .. nml:member:: ndl_leaf_dec
242,244c247,249
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
246c251
< Index of needleleaf (deciduous) PFT surface type (#201).
---
> Index of needleleaf (deciduous) PFT surface type (#201).
248c253
< .. nml:member:: ndl_leaf_eg
---
> .. nml:member:: ndl_leaf_eg
250,252c255,257
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
254c259
< Index of needleleaf (evergreen) PFT surface type (#202).
---
> Index of needleleaf (evergreen) PFT surface type (#202).
256c261
< .. nml:member:: c3_grass
---
> .. nml:member:: c3_grass
258,260c263,265
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
262c267
< Index of original C3 grass PFT surface type (#3).
---
> Index of original C3 grass PFT surface type (#3).
264c269
< .. nml:member:: c3_crop
---
> .. nml:member:: c3_crop
266,268c271,273
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
270c275
< Index of C3 crop PFT surface type (#301).
---
> Index of C3 crop PFT surface type (#301).
272c277
< .. nml:member:: c3_pasture
---
> .. nml:member:: c3_pasture
274,276c279,281
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
278c283
< Index of C3 pasture PFT surface type (#302).
---
> Index of C3 pasture PFT surface type (#302).
280c285
< .. nml:member:: c4_grass
---
> .. nml:member:: c4_grass
282,284c287,289
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
286c291
< Index of original C4 grass PFT surface type (#4).
---
> Index of original C4 grass PFT surface type (#4).
288c293
< .. nml:member:: c4_crop
---
> .. nml:member:: c4_crop
290,292c295,297
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
294c299
< Index of C4 crop PFT surface type (#401).
---
> Index of C4 crop PFT surface type (#401).
296c301
< .. nml:member:: c4_pasture
---
> .. nml:member:: c4_pasture
298,300c303,305
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
302c307
< Index of C4 pasture PFT surface type (#402).
---
> Index of C4 pasture PFT surface type (#402).
304c309
< .. nml:member:: shrub
---
> .. nml:member:: shrub
306,308c311,313
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
310c315
< Index of original shrub PFT surface type (#5).
---
> Index of original shrub PFT surface type (#5).
312c317
< .. nml:member:: shrub_dec
---
> .. nml:member:: shrub_dec
314,316c319,321
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
318c323
< Index of shrub (deciduous) PFT surface type (#501).
---
> Index of shrub (deciduous) PFT surface type (#501).
320c325
< .. nml:member:: shrub_eg
---
> .. nml:member:: shrub_eg
322,324c327,329
< :type: integer
< :permitted: 1:npft
< :default: -32768
---
> :type: integer
> :permitted: 1:npft
> :default: -32768
326c331
< Index of shrub (evergreen) PFT surface type (#502).
---
> Index of shrub (evergreen) PFT surface type (#502).
diff -r jules-lsm.github.io/doc/source/namelists/jules_vegetation.nml.rst jules/doc/source/namelists/jules_vegetation.nml.rst
4d3
<
21,29c20,28
< Vcmax is calculated based on observed leaf traits. Leaf
< nitrogen (nmass: kgN kgLeaf\ :sup:`-1`) and leaf mass (LMA:
< kgLeaf m\ :sup:`-2`) can be based on observations from the TRY
< database. Vcmax (umol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is based
< on linear regressions as in :ref:`Kattge et al. 2009<References_vegetation>`. Two additional
< parameters are needed: vint and vsl - the intercept and slope,
< respectively, that relate the leaf nitrogen to vcmax. Sigl is
< replaced with LMA (sigl=LMA*Cmass, where Cmass is the
< kgC kgLeaf\ :sup:`-1` and is 0.4).
---
> Vcmax is calculated based on observed leaf traits. Leaf nitrogen
> (nmass: kgN kgLeaf\ :sup:`-1`) and leaf mass (LMA: kgLeaf m\ :sup:`-2`)
> can be based on observations from the TRY database.
> Vcmax (umol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is based on linear
> regressions as in :ref:`Kattge et al. 2009<References_vegetation>`.
> Two additional parameters are needed: vint and vsl - the intercept and
> slope, respectively, that relate the leaf nitrogen to vcmax. Sigl is
> replaced with LMA (sigl=LMA*Cmass, where Cmass is the kgC
> kgLeaf\ :sup:`-1` and is 0.4).
101,103c100,101
< This is hard-wired for 5 PFTs (BT, NT, C3, C4, SH, in that
< order) with co-competition for grasses and trees in
< ``lokta_jls.F90``.
---
> This is hard-wired for 5 PFTs (BT, NT, C3, C4, SH, in that order) with
> co-competition for grasses and trees in ``lokta_jls.F90``.
254,256c252,254
< still in development. Users should ensure that results
< are as expected, and provide feedback where deficiencies
< are identified.
---
> still in development. Users should ensure that results
> are as expected, and provide feedback where deficiencies
> are identified.
275,277c273,275
< respectively will depend on ``sm_wilt`` and ``sm_crit``
< in :nml:lst:`JULES_SOIL_PROPS`, regardless of the setting
< of :nml:mem:`JULES_VEGETATION::fsmc_shape`.
---
> respectively will depend on ``sm_wilt`` and ``sm_crit``
> in :nml:lst:`JULES_SOIL_PROPS`, regardless of the setting
> of :nml:mem:`JULES_VEGETATION::fsmc_shape`.
280,282c278,280
< is still in development. Users should ensure that results
< are as expected, and provide feedback where deficiencies
< are identified.
---
> is still in development. Users should ensure that results
> are as expected, and provide feedback where deficiencies
> are identified.
410c408
< Crop, pasture, and bioenergy crop areas are defined by the :nml:mem:`JULES_AGRIC::frac_agr`, :nml:mem:`JULES_AGRIC::frac_past`, :nml:mem:`JULES_AGRIC::frac_biocrop` variables respectively. Harvests are permitted from any land class and enabled for each PFT separately using the :nml:mem:`JULES_TRIFFID::harvest_type_io` variable. Harvesting may be continuous (as per the existing scheme in :nml:mem:`JULES_VEGETATION::l_trif_crop`, when :nml:mem:`JULES_TRIFFID::harvest_type_io` is 1), or performed at prescribed intervals defined using the :nml:mem:`JULES_TRIFFID::harvest_freq_io` and :nml:mem:`JULES_TRIFFID::harvest_ht_io` variables (when :nml:mem:`JULES_TRIFFID::harvest_type_io` is 2).
---
> Crop, pasture, and bioenergy crop areas are defined by the :nml:mem:`JULES_AGRIC::frac_agr`, :nml:mem:`JULES_AGRIC::frac_past`, :nml:mem:`JULES_AGRIC::frac_biocrop` variables respectively. Harvests are permitted from any land class and enabled for each PFT separately using the :nml:mem:`JULES_TRIFFID::harvest_type_io` variable. Harvesting may be continuous (as per the existing scheme in :nml:mem:`JULES_VEGETATION::l_trif_crop`, when :nml:mem:`JULES_TRIFFID::harvest_type_io` is 1), or performed at prescribed intervals defined using the :nml:mem:`JULES_TRIFFID::harvest_freq_io` and :nml:mem:`JULES_TRIFFID::harvest_ht_io` variables (when :nml:mem:`JULES_TRIFFID::harvest_type_io` is 2).
450,453c448,451
< vegetation canopy. It means that the surface is
< represented as a single entity, rather than having
< distinct surface and canopy levels for the purposes of
< radiative processes.
---
> vegetation canopy. It means that the surface is
> represented as a single entity, rather than having
> distinct surface and canopy levels for the purposes of
> radiative processes.
493,495c491,493
< recommended to use driving data that contains direct and
< diffuse radiation separately rather than a constant
< diffuse fraction.
---
> recommended to use driving data that contains direct and
> diffuse radiation separately rather than a constant
> diffuse fraction.
498,501c496,499
< :ref:`Jogireddy et al. (2006)<References_vegetation>`, and an
< application of option 4 can be found in :ref:`Mercado
< et al. (2007)<References_vegetation>`. Options 1 to 5 are
< described in :ref:`Clark et al (2011)<References_vegetation>`.
---
> :ref:`Jogireddy et al. (2006)<References_vegetation>`, and an
> application of option 4 can be found in :ref:`Mercado
> et al. (2007)<References_vegetation>`. Options 1 to 5 are
> described in :ref:`Clark et al (2011)<References_vegetation>`.
535c533
< * Collatz et al., 1991, Physiological and environmental regulation of stomatal conductance, photosynthesis, and transpiration – a model that includes a laminar boundary layer, Agricultural and Forest Meteorology, https://doi.org/10.1016/0168-1923(91)90002-8.
---
> * Collatz et al., 1991, Physiological and environmental regulation of stomatal conductance, photosynthesis, and transpiration - a model that includes a laminar boundary layer, Agricultural and Forest Meteorology, https://doi.org/10.1016/0168-1923(91)90002-8.
586c584
< Power in sigmodial function used to get competition coefficients.
---
> Power in sigmoidal function used to get competition coefficients.
659,660c657
< This is based on :ref:`Argles, Arthur PK, et al.
< (2020)`.
---
> This is based on :ref:`Argles, Arthur PK, et al. (2020)<References_vegetation>`.
933c930
< Coefficients for the ratio J\ :sub:`25`/V\ :sub:`25` (mol electrons [mol\ :sup:`-1` CO\ :sub:`2`] and (mol electrons [mol\ :sup:`-1` CO\ :sub:`2`] K\ :sup:`-1`). Replaces the use of :nml:mem:`JULES_PFTPARM::jv25_ratio_io`.
---
> Coefficients for the ratio J\ :sub:`25`/V\ :sub:`25` (mol electrons [mol\ :sup:`-1` CO\ :sub:`2`]) and (mol electrons [mol\ :sup:`-1` CO\ :sub:`2`] K\ :sup:`-1`). Replaces the use of :nml:mem:`JULES_PFTPARM::jv25_ratio_io`.
951c948
< Switch that enables sequential cropping (crop rotations).
---
> Switch that enables sequential cropping (crop rotations).
968,971c965,968
< * Argles, A. P. K., Moore, J. R., Huntingford, C., Wiltshire, A. J.,
< Harper, A. B., Jones, C. D., and Cox, P. M.: Robust Ecosystem Demography
< (RED version 1.0): a parsimonious approach to modelling vegetation
< dynamics in Earth system models, Geosci. Model Dev., 13, 4067–4089,
---
> * Argles, A. P. K., Moore, J. R., Huntingford, C., Wiltshire, A. J.,
> Harper, A. B., Jones, C. D., and Cox, P. M.: Robust Ecosystem Demography
> (RED version 1.0): a parsimonious approach to modelling vegetation
> dynamics in Earth system models, Geosci. Model Dev., 13, 4067-4089,
974c971
< model description – Part 1: Energy and water fluxes, Geosci. Model
---
> model description - Part 1: Energy and water fluxes, Geosci. Model
977c974
< model description – Part 2: Carbon fluxes and vegetation dynamics,
---
> model description - Part 2: Carbon fluxes and vegetation dynamics,
983c980
< 1622–1637 https://doi.org/10.1111/nph.16419
---
> 1622-1637 https://doi.org/10.1111/nph.16419
1032c1029
< 553–565, 2007. https://doi.org/10.1111/j.1600-0889.2007.00256.x
---
> 553-565, 2007. https://doi.org/10.1111/j.1600-0889.2007.00256.x
1047c1044
< land–surface model, Geosci. Model Dev. Discuss.,
---
> land-surface model, Geosci. Model Dev. Discuss.,
1049,1051c1046,1048
< * Jones et al., 2020, The impact of a simple representation of
< non-structural carbohydrates on the simulated response of tropical
< forests to drought, Biogeosciences, 17: 3589--3612.
---
> * Jones et al., 2020, The impact of a simple representation of
> non-structural carbohydrates on the simulated response of tropical
> forests to drought, Biogeosciences, 17: 3589--3612.
diff -r jules-lsm.github.io/doc/source/namelists/jules_water_resources.nml.rst jules/doc/source/namelists/jules_water_resources.nml.rst
37c37
<
---
>
86c86
< Consider demand for water for industrial use.
---
> Consider demand for water for industrial use.
diff -r jules-lsm.github.io/doc/source/namelists/model_environment.nml.rst jules/doc/source/namelists/model_environment.nml.rst
4d3
<
42c41
< Any options that are only available to the parent model (e.g. the UM) will be trigger ignored.
---
> Any options that are only available to the parent model (e.g. the UM) will be trigger ignored.
62,65c61,62
< * `src/control/standalone/check_unavailable_options_mod.F90
< <https://code.metoffice.gov.uk/trac/jules/browser/main/trunk/src/control/standalone/check_unavailable_options_mod.F90>`_
< * `src/control/um/check_jules_unavailable_options_mod.F90
< <https://code.metoffice.gov.uk/trac/jules/browser/main/trunk/src/control/um/check_jules_unavailable_options_mod.F90>`_
---
> * `src/control/standalone/check_unavailable_options_mod.F90 <https://github.com/MetOffice/jules/blob/main/src/control/standalone/check_unavailable_options_mod.F90>`_
> * `src/control/um/check_unavailable_options_mod.F90 <https://github.com/MetOffice/jules/blob/main/src/control/um/check_unavailable_options_mod.F90>`_
diff -r jules-lsm.github.io/doc/source/namelists/model_grid.nml.rst jules/doc/source/namelists/model_grid.nml.rst
4d3
<
32c31
< Indicates if the input grid is 1D or 2D.
---
> Indicates if the input grid is 1D or 2D.
48c47
< The name of the single grid dimension.
---
> The name of the single grid dimension.
59c58
< The size of the single grid dimension.
---
> The size of the single grid dimension.
65c64
<
---
>
68,69c67,68
<
< The name of the x dimension (it may, but does not have to, coincide with :nml:mem:`JULES_RIVERS_PROPS::x_dim_name`).
---
>
> The name of the x dimension (it may, but does not have to, coincide with :nml:mem:`JULES_RIVERS_PROPS::x_dim_name`).
72,73c71,72
<
<
---
>
>
75c74
<
---
>
78c77
<
---
>
80c79
<
---
>
82,83c81,82
<
<
---
>
>
85c84
<
---
>
89,92c88,91
<
< The size of the x dimension.
<
<
---
>
> The size of the x dimension.
>
>
94c93
<
---
>
98,99c97,98
<
< The size of the y dimension.
---
>
> The size of the y dimension.
120,121c119,120
<
<
---
>
>
200,201c199,200
<
<
---
>
>
353,376c352,375
< +----------------------------+------------------------------------------------------------------------------------------+
< | Name | Description |
< +============================+==========================================================================================+
< | ``latitude`` | Latitude of each point. Always required. |
< | | |
< +----------------------------+------------------------------------------------------------------------------------------+
< | ``longitude`` | Longitude of each point. Always required. |
< | | Values in the range -180 to 360 are allowed. |
< +----------------------------+------------------------------------------------------------------------------------------+
< | ``projection_x_coord`` | Values of the projection coordinate in the x direction. |
< | | This is only required if :nml:mem:`l_coord_latlon` = FALSE. |
< | | Note that these can have any valid unit. |
< +----------------------------+------------------------------------------------------------------------------------------+
< | ``projection_y_coord`` | Values of the projection coordinate in the y direction. |
< | | This is only required if :nml:mem:`l_coord_latlon` = FALSE. |
< | | Note that these can have any valid unit. |
< +----------------------------+------------------------------------------------------------------------------------------+
< | ``grid_area`` | The area of each gridbox (m\ :sup`2`). |
< | | This is requred if irrigation is being modelled with |
< | | :nml:mem:`JULES_WATER_RESOURCES::l_water_resources` = TRUE and |
< | | :nml:mem:`JULES_WATER_RESOURCES::l_water_irrigation` = TRUE. |
< | | It is also required when using IMOGEN: |
< | | :nml:mem:`IMOGEN_ONOFF_SWITCH::l_imogen` = TRUE |
< +----------------------------+------------------------------------------------------------------------------------------+
---
> +----------------------------+-----------------------------------------------------------------+
> | Name | Description |
> +============================+=================================================================+
> | ``latitude`` | Latitude of each point. Always required. |
> | | |
> +----------------------------+-----------------------------------------------------------------+
> | ``longitude`` | Longitude of each point. Always required. |
> | | Values in the range -180 to 360 are allowed. |
> +----------------------------+-----------------------------------------------------------------+
> | ``projection_x_coord`` | Values of the projection coordinate in the x direction. |
> | | This is only required if :nml:mem:`l_coord_latlon` = FALSE. |
> | | Note that these can have any valid unit. |
> +----------------------------+-----------------------------------------------------------------+
> | ``projection_y_coord`` | Values of the projection coordinate in the y direction. |
> | | This is only required if :nml:mem:`l_coord_latlon` = FALSE. |
> | | Note that these can have any valid unit. |
> +----------------------------+-----------------------------------------------------------------+
> | ``grid_area`` | The area of each gridbox (m\ :sup:`2`). |
> | | This is required if irrigation is being modelled with |
> | | :nml:mem:`JULES_WATER_RESOURCES::l_water_resources` = TRUE and |
> | | :nml:mem:`JULES_WATER_RESOURCES::l_water_irrigation` = TRUE. |
> | | It is also required when using IMOGEN: |
> | | :nml:mem:`IMOGEN_ONOFF_SWITCH::l_imogen` = TRUE |
> +----------------------------+-----------------------------------------------------------------+
390c389
<
---
>
402c401
< The name of the file to read land fraction data from.
---
> The name of the file to read land fraction data from.
410c409
< The name of the variable containing the land fraction data.
---
> The name of the variable containing the land fraction data.
429c428
< TRUE
---
> TRUE
445c444
< TRUE
---
> TRUE
457c456
< TRUE
---
> TRUE
467c466
<
---
>
470,471c469,470
<
< TRUE
---
>
> TRUE
473c472
<
---
>
480,481c479,480
<
<
---
>
>
483c482
<
---
>
485c484
<
---
>
488c487
<
---
>
490,491c489,490
<
<
---
>
>
493c492
<
---
>
496c495
<
---
>
500,501c499,500
<
<
---
>
>
503c502
<
---
>
505c504
<
---
>
509c508
<
---
>
511,512c510,511
<
<
---
>
>
514c513
<
---
>
517c516
<
---
>
523c522
<
---
>
549,551c548,550
< This namelist sets the elevation of each surface tile. Elevations can either be *relative to the gridbox mean* or *have constant elevation bands above sea-level*.
<
< If tile elevations are set relative to the gridbox mean, then the gridbox mean elevation is not required. The gridbox mean elevation is implicit in the near-surface meteorological data that are provided (higher locations will tend to be colder, have lower pressure, etc.). The elevation of each tile is used to alter the values of the air temperature and humidity (and possibly downwelling longwave, see :nml:mem:`JULES_SURFACE::l_elev_lw_down`) over that tile relative to the surface.
---
> This namelist sets the elevation of each surface tile. Elevations can either be *relative to the gridbox mean* or *have constant elevation bands above sea-level*.
>
> If tile elevations are set relative to the gridbox mean, then the gridbox mean elevation is not required. The gridbox mean elevation is implicit in the near-surface meteorological data that are provided (higher locations will tend to be colder, have lower pressure, etc.). The elevation of each tile is used to alter the values of the air temperature and humidity (and possibly downwelling longwave, see :nml:mem:`JULES_SURFACE::l_elev_lw_down`) over that tile relative to the surface.
553c552
< If any tile uses absolute heights (i.e. :nml:mem:`JULES_SURF_HGT::l_elev_absolute_height` has at least one element that is .true.), then the gridbox mean elevation must also be supplied. This is read in from the optional :nml:lst:`JULES_Z_LAND` namelist which is described below. The model calculates elevations relative to the gridbox mean by taking the difference between the absolute elevation and the gridbox mean.
---
> If any tile uses absolute heights (i.e. :nml:mem:`JULES_SURF_HGT::l_elev_absolute_height` has at least one element that is .true.), then the gridbox mean elevation must also be supplied. This is read in from the optional :nml:lst:`JULES_Z_LAND` namelist which is described below. The model calculates elevations relative to the gridbox mean by taking the difference between the absolute elevation and the gridbox mean.
564c563
<
---
>
581,582c580,581
< TRUE
< Heights of surface tiles are absolute values above sea-level. If this option is used, then the elevation of the forcing data must also be provided (see :nml:lst:`JULES_Z_LAND` namelist below).
---
> TRUE
> Heights of surface tiles are absolute values above sea-level. If this option is used, then the elevation of the forcing data must also be provided (see :nml:lst:`JULES_Z_LAND` namelist below).
585c584
< Surface tile heights are relative to the gridbox mean.
---
> Surface tile heights are relative to the gridbox mean.
593c592
< This indicates if surface tile heights relative to the gridbox mean should be read from a specified file or namelist.
---
> This indicates if surface tile heights relative to the gridbox mean should be read from a specified file or namelist.
596,597c595,596
< The variable will be read from a file if the input grid consists of more than location.
<
---
> The variable will be read from a file if the input grid consists of more than location.
>
599c598
< The variable will be read from a namelist if the input grid is for a single location.
---
> The variable will be read from a namelist if the input grid is for a single location.
604c603
<
---
>
607,609c606,608
<
< The name of the file containing surface tile heights relative to the gridbox mean.
<
---
>
> The name of the file containing surface tile heights relative to the gridbox mean.
>
611c610
<
---
>
614,616c613,615
<
< The name of the variable containing surface tile heights relative to the gridbox mean. In the file, the variable must have a single levels dimension of size ``nsurft`` called :nml:mem:`JULES_INPUT_GRID::tile_dim_name`.
<
---
>
> The name of the variable containing surface tile heights relative to the gridbox mean. In the file, the variable must have a single levels dimension of size ``nsurft`` called :nml:mem:`JULES_INPUT_GRID::tile_dim_name`.
>
620c619
<
---
>
623,626c622,625
<
< Surface tile heights relative to the gridbox mean for a single location.
<
<
---
>
> Surface tile heights relative to the gridbox mean for a single location.
>
>
630c629
< This is an optional namelist and only used if any surface tile has :nml:mem:`JULES_SURF_HGT::l_elev_absolute_height` = TRUE. The namelist sets values for the elevation bands and reads the elevation of the forcing data.
---
> This is an optional namelist and only used if any surface tile has :nml:mem:`JULES_SURF_HGT::l_elev_absolute_height` = TRUE. The namelist sets values for the elevation bands and reads the elevation of the forcing data.
635c634
<
---
>
639c638
< Spatially invariant elevation bands for each surface tile. These may be relative to the gridbox mean or absolute elevations above sea-level depending on :nml:mem:`JULES_SURF_HGT::l_elev_absolute_height`.
---
> Spatially invariant elevation bands for each surface tile. These may be relative to the gridbox mean or absolute elevations above sea-level depending on :nml:mem:`JULES_SURF_HGT::l_elev_absolute_height`.
642c641
<
---
>
645c644
<
---
>
647c646
<
---
>
649c648
< The variable will be read from a file if the input grid consists of more than location.
---
> The variable will be read from a file if the input grid consists of more than location.
651c650
< The variable will be read from a namelist if the input grid is for a single location.
---
> The variable will be read from a namelist if the input grid is for a single location.
653c652
< .. nml:group:: Used if :nml:mem:`JULES_Z_LAND::use_file` = TRUE
---
> .. nml:group:: Used if :nml:mem:`JULES_Z_LAND::use_file` = TRUE
656c655
<
---
>
659c658
<
---
>
663c662
<
---
>
666,667d664
<
< The name of the variable containing the elevation of the forcing data. In the file, the variable must have no level dimensions and no time dimensions.
669,670c666,669
< .. nml:group:: Used if :nml:mem:`JULES_Z_LAND::use_file` = FALSE
<
---
> The name of the variable containing the elevation of the forcing data. In the file, the variable must have no level dimensions and no time dimensions.
>
> .. nml:group:: Used if :nml:mem:`JULES_Z_LAND::use_file` = FALSE
>
672c671
<
---
>
675,676c674,675
<
< Elevation of the forcing data for a single location.
---
>
> Elevation of the forcing data for a single location.
681c680
< The following gives an example of how you would set up the namelists to use elevation bands above sea-level.
---
> The following gives an example of how you would set up the namelists to use elevation bands above sea-level.
696c695
< # Set values for the elevation bands.
---
> # Set values for the elevation bands.
721c720
<
---
>
729c728
<
---
>
733c732
<
---
>
763c762
<
---
>
766c765
<
---
>
788c787
<
---
>
801c800
<
---
>
807c806
<
---
>
822c821
<
---
>
835c834
<
---
>
841c840
<
---
>
884c883
<
---
>
907c906
<
---
>
914c913
<
---
>
diff -r jules-lsm.github.io/doc/source/namelists/output.nml.rst jules/doc/source/namelists/output.nml.rst
280,281d279
<
<
diff -r jules-lsm.github.io/doc/source/namelists/pft_params.nml.rst jules/doc/source/namelists/pft_params.nml.rst
191c191
< Leaf reflection coefficient for VIS (photosyntehtically active radiation). See HCTN30 Table 3.
---
> Leaf reflection coefficient for VIS (photosynthetically active radiation). See HCTN30 Table 3.
918,930c918,924
< * Clark et al., 2011, The Joint UK Land Environment Simulator
< (JULES), model description – Part 2: Carbon fluxes and
< vegetation dynamics, Geosci. Model Dev., 4, 701-722,
< https://doi.org/10.5194/gmd-4-701-2011
< * Pinty, B., T. Lavergne, R. E. Dickinson,
< J.-L. Widlowski, N. Gobron, and M. M. Verstraete (2006),
< Simplifying the interaction of land surfaces with radiation
< for relating remote sensing products to climate
< models, J. Geophys. Res., 111, D02116,
< https://doi.org/10.1029/2005JD005952.
<
<
<
---
> * Clark et al., 2011, The Joint UK Land Environment Simulator (JULES),
> model description - Part 2: Carbon fluxes and vegetation dynamics,
> Geosci. Model Dev., 4, 701-722, https://doi.org/10.5194/gmd-4-701-2011
> * Pinty, B., T. Lavergne, R. E. Dickinson, J.-L. Widlowski, N. Gobron,
> and M. M. Verstraete (2006), Simplifying the interaction of
> land surfaces with radiation for relating remote sensing products to
> climate models, J. Geophys. Res., 111, D02116, https://doi.org/10.1029/2005JD005952.
987c981
< If thermal adaptation or acclimation of photosynthesis is selected (:nml:mem:`JULES_VEGETATION::photo_acclim_model` = 1 or 2) together with :nml:mem:`JULES_VEGETATION::photo_jv_model` =2 (J\ :sub:`max`/V\ :sub:`cmax` calculated assuming constant total nitrogen allocation)), this value is used along with parameters :nml:mem:`JULES_VEGETATION::n_alloc_jmax` and :nml:mem:`JULES_VEGETATION::n_alloc_vcmax` to calculate the final value of J\ :sub:`max`/V\ :sub:`cmax`.
---
> If thermal adaptation or acclimation of photosynthesis is selected (:nml:mem:`JULES_VEGETATION::photo_acclim_model` = 1 or 2) together with :nml:mem:`JULES_VEGETATION::photo_jv_model` =2 (J\ :sub:`max`/V\ :sub:`cmax` calculated assuming constant total nitrogen allocation), this value is used along with parameters :nml:mem:`JULES_VEGETATION::n_alloc_jmax` and :nml:mem:`JULES_VEGETATION::n_alloc_vcmax` to calculate the final value of J\ :sub:`max`/V\ :sub:`cmax`.
998c992
< Entropy factor for temperature reponse of J\ :sub:`max` (J mol\ :sup:`-1` K\ :sup:`-1`).
---
> Entropy factor for temperature response of J\ :sub:`max` (J mol\ :sup:`-1` K\ :sup:`-1`).
1006c1000
< Entropy factor for temperature reponse of V\ :sub:`cmax` (J mol\ :sup:`-1` K\ :sup:`-1`).
---
> Entropy factor for temperature response of V\ :sub:`cmax` (J mol\ :sup:`-1` K\ :sup:`-1`).
diff -r jules-lsm.github.io/doc/source/namelists/prescribed_data.nml.rst jules/doc/source/namelists/prescribed_data.nml.rst
4d3
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>
diff -r jules-lsm.github.io/doc/source/namelists/red_parms.nml.rst jules/doc/source/namelists/red_parms.nml.rst
0a1,2
> ``red_parms.nml``
> =================
1a4,7
> This file contains a single namelist called :nml:lst:`RED_PARMS` that sets
> parameters relevant to the Robust Ecosystem Demography submodel
> `(RED version 1.0) <https://gmd.copernicus.org/articles/13/4067/2020/>`_.
> Activate RED in the :nml:mem:`JULES_VEGETATION::l_red`.
3,7c9,10
< This file contains a single namelist called :nml:lst:`JULES_RED` that sets parameters relevant to the Robust Ecosystem Demography submodel (RED version 1.0) <https://gmd.copernicus.org/articles/13/4067/2020/>`_.
< Activate RED in the :nml:mem:`JULES_VEGETATION::l_red.
<
< ``JULES_RED`` namelist members
< ----------------------------------
---
> ``RED_PARMS`` namelist members
> ------------------------------
11c14,18
< This namelist is used to read PFT parameters that are only needed by the Robust Ecosystem Demography (RED). Values are not used if RED is not selected.
---
> This namelist is used to read PFT parameters that are only needed by the Robust
> Ecosystem Demography (RED). Values are not used if RED is not selected.
>
> .. note:: Where a quantity is said to have units of "/360days", this means that
> it is an amount per 360 days.
13c20
< .. note:: Where a quantity is said to have units of "/360days", this means that it is an amount per 360 days.
---
> .. nml:group:: Only used when :nml:mem:`JULES_VEGETATION::l_red` = TRUE
15c22,23
< .. nml:group:: Only used when :nml:mem:`JULES_VEGETATION::l_red = TRUE
---
> This group contains parameters that are only used when RED is enabled in
> JULES_VEGETATION.
39c47,48
< JULES-RED, the higher the value the more dominant: 3 (trees), 2 (shrubs), 1 (grass).
---
> JULES-RED, the higher the value the more dominant: 3 (trees), 2 (shrubs),
> 1 (grass).
55c64,65
< The lowest PFT balanced LAI, which corresponds to the mass0 class (m\ :sup:`2`/m\ :sup:`2`).
---
> The lowest PFT balanced LAI, which corresponds to the mass0 class
> (m\ :sup:`2`/m\ :sup:`2`).
95c105,106
< The allometric/power scaling of PFT mass to PFT crown area (West, G. B., et al 2009 <https://doi.org/10.1073/pnas.0812294106>`_).
---
> The allometric/power scaling of PFT mass to PFT crown area
> (`West, G. B., et al 2009 <https://doi.org/10.1073/pnas.0812294106>`_).
103c114,115
< The allometric/power scaling of PFT mass to PFT mass growth rate (West, G. B., et al., 1997 <https://www.science.org/doi/10.1126/science.276.5309.122>`_).
---
> The allometric/power scaling of PFT mass to PFT mass growth rate
> (`West, G. B., et al., 1997 <https://www.science.org/doi/10.1126/science.276.5309.122>`_).
111c123,124
< The allometric/power scaling of PFT mass to PFT height (Niklas, K. J., et al., 2001 <https://doi.org/10.1073/pnas.041590298>`_).
---
> The allometric/power scaling of PFT mass to PFT height
> (`Niklas, K. J., et al., 2001 <https://doi.org/10.1073/pnas.041590298>`_).
diff -r jules-lsm.github.io/doc/source/namelists/science_fixes.nml.rst jules/doc/source/namelists/science_fixes.nml.rst
4d3
<
38,42c37,41
< This switch improves the calculation of surface air density in the
< surface turbulent fluxes. It includes appropriate use of dry air density
< when the atmospheric water vapour is expressed as a mixing ratio
< (l_mr_physics = .TRUE.), otherwise use the wet air density when
< it is expressed as a specific humidity.
---
> This switch improves the calculation of surface air density in the
> surface turbulent fluxes. It includes appropriate use of dry air density
> when the atmospheric water vapour is expressed as a mixing ratio
> (l_mr_physics = .TRUE.), otherwise use the wet air density when
> it is expressed as a specific humidity.
95c94
< If true, this switch corrects a bug in the surface energy balance
---
> If true, this switch corrects a bug in the surface energy balance
97c96
< (see :nml:mem:`JULES_URBAN::l_moruses_storage`).
---
> (see :nml:mem:`JULES_URBAN::l_moruses_storage`).
115c114
< Overloaded canopies may be produced by changess in the snow amounts or
---
> Overloaded canopies may be produced by changes in the snow amounts or
diff -r jules-lsm.github.io/doc/source/namelists/timesteps.nml.rst jules/doc/source/namelists/timesteps.nml.rst
28,29c28,29
<
<
---
>
>
42c42
<
---
>
56c56
<
---
>
diff -r jules-lsm.github.io/doc/source/namelists/triffid_params.nml.rst jules/doc/source/namelists/triffid_params.nml.rst
47c47
< 3. Bioenergy crops or trees.
---
> 3. Bioenergy crops or trees.
145c145
< .. nml:group:: Only used when :nml:mem:`JULES_VEGETATION::l_trif_biocrop` = TRUE
---
> .. nml:group:: Only used when :nml:mem:`JULES_VEGETATION::l_trif_biocrop` = TRUE
159c159
< .. nml:group:: Only used when :nml:mem:`JULES_TRIFFID::harvest_type_io` = 2
---
> .. nml:group:: Only used when :nml:mem:`JULES_TRIFFID::harvest_type_io` = 2
169c169
< Harvest freqency in years.
---
> Harvest freqency in years.
177c177
< Height [m] to which the PFT is reduced at each harvest cycle.
---
> Height [m] to which the PFT is reduced at each harvest cycle.
179c179
< .. note:: :nml:mem:`lai_min_io` must be set such that PFT height at :nml:mem:`lai_min_io` <= :nml:mem:`harvest_ht_io`, otherwise JULES will not start (the required value will be shown in error output).
---
> .. note:: :nml:mem:`lai_min_io` must be set such that PFT height at :nml:mem:`lai_min_io` <= :nml:mem:`harvest_ht_io`, otherwise JULES will not start (the required value will be shown in error output).
diff -r jules-lsm.github.io/doc/source/namelists/urban.nml.rst jules/doc/source/namelists/urban.nml.rst
4d3
<
9c8
< For all other parameters that MORUSES does not provide, and for any MORUSES parametrisations that are turned off, values from :doc:`nveg_params.nml` will be used instead. See the switches below for more information.
---
> For all other parameters that MORUSES does not provide, and for any MORUSES parameterisations that are turned off, values from :doc:`nveg_params.nml` will be used instead. See the switches below for more information.
15,16c14,15
< * Porson, A., et al. (2010), Implementation of a new urban energy budget scheme in the MetUM. Part I: Description and idealized simulations, Quarterly Journal of the Royal Meteorological Society, 136: 1514-1529. doi: 10.1002/qj.668
< * Porson, A., et al. (2010), Implementation of a new urban energy budget scheme into MetUM. Part II: Validation against observations and model Intercomparison, Quarterly Journal of the Royal Meteorological Society, 136: 1530-1542. doi: 10.1002/qj.572
---
> * Porson, A., et al. (2010), Implementation of a new urban energy budget scheme in the MetUM. Part I: Description and idealized simulations, Quarterly Journal of the Royal Meteorological Society, 136: 1514-1529. doi: 10.1002/qj.668
> * Porson, A., et al. (2010), Implementation of a new urban energy budget scheme into MetUM. Part II: Validation against observations and model Intercomparison, Quarterly Journal of the Royal Meteorological Society, 136: 1530-1542. doi: 10.1002/qj.572
107c106
< MORUSES consists of two surfaces; a canyon (:nml:mem:`JULES_SURFACE_TYPES::urban_canyon`) and a roof (:nml:mem:`JULES_SURFACE_TYPES::urban_roof`). This MORUSES parametrisation calculates the heat capacity of each of these surface types and also modifies how they are coupled with the underlying soil. The heat capacities of the canyon and roof are calculated using the properties of the urban fabric and the geometry of the canyon. The roof has a lower thermal inertia and can respond more rapidly to changes in forcing. The nature of the coupling (radiative, conductive or none) is controlled via :nml:mem:`JULES_NVEGPARM::vf_nvg_io` as descibed below.
---
> MORUSES consists of two surfaces; a canyon (:nml:mem:`JULES_SURFACE_TYPES::urban_canyon`) and a roof (:nml:mem:`JULES_SURFACE_TYPES::urban_roof`). This MORUSES parameterisation calculates the heat capacity of each of these surface types and also modifies how they are coupled with the underlying soil. The heat capacities of the canyon and roof are calculated using the properties of the urban fabric and the geometry of the canyon. The roof has a lower thermal inertia and can respond more rapidly to changes in forcing. The nature of the coupling (radiative, conductive or none) is controlled via :nml:mem:`JULES_NVEGPARM::vf_nvg_io` as descibed below.
110c109
< Consists of two walls and a road where the road only is coupled to the underlying soil. The walls are uncoupled and have a zero-flux boundary condition. The coupling of the road is therefore parametrised using a canyon scaling factor. The nature of the canyon (or road surface) coupling is specified as follows:
---
> Consists of two walls and a road where the road only is coupled to the underlying soil. The walls are uncoupled and have a zero-flux boundary condition. The coupling of the road is therefore parameterised using a canyon scaling factor. The nature of the canyon (or road surface) coupling is specified as follows:
178c177
< If no MORUSES parametrisations are used, i.e. the basic URBAN-2T, then only W/R is required.
---
> If no MORUSES parameterisations are used, i.e. the basic URBAN-2T, then only W/R is required.
diff -r jules-lsm.github.io/doc/source/output.rst jules/doc/source/output.rst
36c36
<
---
>
40c40
<
---
>
42c42
<
---
>
diff -r jules-lsm.github.io/doc/source/output-variables.rst jules/doc/source/output-variables.rst
77c77
< Unlesss stated otherwise these variables have values at both land and sea points.
---
> Unless stated otherwise these variables have values at both land and sea points.
199c199
< -------------------------------------------------------------------
---
> ----------------------------------------------------
249c249
< -------------------------------------------------------------------
---
> -------------------------------------------------------
322c322
< -------------------------------------------------------------------
---
> ---------
416c416
< -------------------------------------------------------------------
---
> ------
487c487
< -------------------------------------------------------------------
---
> ----
578c578
< -------------------------------------------------------------------
---
> ------------------------------------
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< -------------------------------------------------------------------
---
> --------------------------------------
862c862
< -------------------------------------------------------------------
---
> ------------------------------
963c963
< -------------------------------------------------------------------
---
> --------------------------------
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< -------------------------------------------------------------------
---
> ----
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< -------------------------------------------------------------------
---
> -----
1218c1218
< -------------------------------------------------------------------
---
> -----------------------------------
1251c1251
< -------------------------------------------------------------------
---
> ----------------------------------------------
1262c1262
< | ``deposition_rc`` | Surface resistance (Rc) by surface type and chemical tracer (s m\ :sup:`-1`). | ntype, |
---
> | ``deposition_rc`` | Surface resistance (Rc) by surface type and chemical tracer (s m\ :sup:`-1`). | ntype, |
1286c1286
< -------------------------------------------------------------------
---
> ---------------
1404c1404
< -------------------------------------------------------------------
---
> ------
1430c1430
< -------------------------------------------------------------------
---
> ---------------------------
1453d1452
<
diff -r jules-lsm.github.io/doc/source/overview/intro.rst jules/doc/source/overview/intro.rst
4c4,5
< This section provides a brief overview of JULES and an introduction to some of the key switches that determine what the model will simulate in a given run.
---
> This section provides a brief overview of JULES and an introduction to some of
> the key switches that determine what the model will simulate in a given run.
diff -r jules-lsm.github.io/doc/source/overview/key-switches.rst jules/doc/source/overview/key-switches.rst
4,18c4,45
< There are many variables that act together to determine how a run of JULES is set up and these are covered in detail in :doc:`/namelists/contents`. Additionally, `configurations <http://jules.jchmr.org/content/configurations>`__ illustrate suitable combinations of options. Here we highlight a few key switches that select broad areas of science, particularly for the benefit of new users.
<
< The phenology model for natural vegetation can be enabled using :nml:mem:`JULES_VEGETATION::l_phenol` which uses the leaf turnover rate to calculate a time-varying Leaf Area Index (LAI).
<
< To simulate carbon stocks in natural vegetation, the TRIFFID dynamic vegetation model can be enabled via the switch :nml:mem:`JULES_VEGETATION::l_triffid`. When TRIFFID is on, competition between tiles is switched on with :nml:mem:`JULES_VEGETATION::l_veg_compete` and the effect of nitrogen on vegetation growth is enabled via :nml:mem:`JULES_VEGETATION::l_nitrogen`.
<
< The crop model, which is simulates phenology and carbon stocks in crops, can be switched on by setting the number of crop tiles :nml:mem:`JULES_SURFACE_TYPES::ncpft` to a non-zero value.
<
< The crop model and TRIFFID cannot currently be used together. To simulate agricultural areas within TRIFFID, a fraction of the gridbox can be reserved for agricultural Plant Functional Types (PFTs) (as defined by :nml:mem:`JULES_TRIFFID::crop_io` > 0). Agricultural PFT competition and a representation of harvest carbon can be switched on with :nml:mem:`JULES_VEGETATION::l_trif_crop`.
<
< If neither the phenology model nor the crop model are used, LAI for each vegetation tile can be set to a constant (:nml:mem:`JULES_PFTPARM::lai_io`) or a time series or seasonal cycle can be prescribed (:nml:lst:`JULES_PRESCRIBED`).
<
< To simulate carbon and nitrogen stocks in the soil, the 4-pool model should be selected by setting :nml:mem:`JULES_SOIL_BIOGEOCHEM::soil_bgc_model` = 2. This option adds prognostic soil pools and must be used with the TRIFFID vegetation model. If TRIFFID is not used, prescribed soil pools must be invoked via :nml:mem:`JULES_SOIL_BIOGEOCHEM::soil_bgc_model` = 1. Layered soil pools are used if :nml:mem:`JULES_SOIL_BIOGEOCHEM::l_layeredc` = .TRUE..
<
< A multi-layer snow model can be selected using :nml:mem:`JULES_SNOW::nsmax`. Parameterisations of surface and subsurface runoff generation are controlled using :nml:mem:`JULES_HYDROLOGY::l_top` and :nml:mem:`JULES_HYDROLOGY::l_pdm`, while the routing of water in rivers uses :nml:mem:`JULES_RIVERS::l_rivers`.
---
> There are many variables that act together to determine how a run of JULES is
> set up and these are covered in detail in :doc:`/namelists/contents`.
> Additionally, `configurations <http://jules.jchmr.org/content/configurations>`__
> illustrate suitable combinations of options. Here we highlight a few key
> switches that select broad areas of science, particularly for the benefit of
> new users.
>
> The phenology model for natural vegetation can be enabled using
> :nml:mem:`JULES_VEGETATION::l_phenol` which uses the leaf turnover rate to
> calculate a time-varying Leaf Area Index (LAI).
>
> To simulate carbon stocks in natural vegetation, the TRIFFID dynamic vegetation
> model can be enabled via the switch :nml:mem:`JULES_VEGETATION::l_triffid`.
> When TRIFFID is on, competition between tiles is switched on with
> :nml:mem:`JULES_VEGETATION::l_veg_compete` and the effect of nitrogen on
> vegetation growth is enabled via :nml:mem:`JULES_VEGETATION::l_nitrogen`.
>
> The crop model, which is simulates phenology and carbon stocks in crops, can be
> switched on by setting the number of crop tiles
> :nml:mem:`JULES_SURFACE_TYPES::ncpft` to a non-zero value.
>
> The crop model and TRIFFID cannot currently be used together. To simulate
> agricultural areas within TRIFFID, a fraction of the gridbox can be reserved for
> agricultural Plant Functional Types (PFTs)
> (as defined by :nml:mem:`JULES_TRIFFID::crop_io` > 0).
> Agricultural PFT competition and a representation of harvest carbon can be
> switched on with :nml:mem:`JULES_VEGETATION::l_trif_crop`.
>
> If neither the phenology model nor the crop model are used, LAI for each
> vegetation tile can be set to a constant (:nml:mem:`JULES_PFTPARM::lai_io`)
> or a time series or seasonal cycle can be prescribed (:nml:lst:`JULES_PRESCRIBED`).
>
> To simulate carbon and nitrogen stocks in the soil, the 4-pool model should be
> selected by setting :nml:mem:`JULES_SOIL_BIOGEOCHEM::soil_bgc_model` = 2.
> This option adds prognostic soil pools and must be used with the TRIFFID
> vegetation model. If TRIFFID is not used, prescribed soil pools must be
> invoked via :nml:mem:`JULES_SOIL_BIOGEOCHEM::soil_bgc_model` = 1. Layered soil pools are used if :nml:mem:`JULES_SOIL_BIOGEOCHEM::l_layeredc` = .TRUE..
>
> A multi-layer snow model can be selected using :nml:mem:`JULES_SNOW::nsmax`.
> Parametrisations of surface and subsurface runoff generation are controlled
> using :nml:mem:`JULES_HYDROLOGY::l_top` and :nml:mem:`JULES_HYDROLOGY::l_pdm`,
> while the routing of water in rivers uses :nml:mem:`JULES_RIVERS::l_rivers`.
diff -r jules-lsm.github.io/doc/source/overview/overview.rst jules/doc/source/overview/overview.rst
4c4,8
< This section provides a brief overview of JULES, largely so as to provide background information and introduce terms used in the rest of the manual. Further details can be found at the `JULES website <http://jules.jchmr.org/>`_ and in the two `JULES description papers <http://jules.jchmr.org/content/about>`_ (Best et al., 2011, GMD and Clark et al., 2011, GMD).
---
> This section provides a brief overview of JULES, largely so as to provide
> background information and introduce terms used in the rest of the manual.
> Further details can be found at the `JULES website <http://jules.jchmr.org/>`__
> and in the two `JULES description papers <http://jules.jchmr.org/content/about>`__
> (Best et al., 2011, GMD and Clark et al., 2011, GMD).
6c10,20
< For both gridded and single point runs, JULES views each gridbox as consisting of a number of surface types. The fractional area of each surface type is either prescribed by the user or modelled by the TRIFFID sub-model. Each surface type is represented by a surface tile, and a separate energy balance is calculated for each surface tile. The gridbox average energy balance is found by weighting the values from each surface tile. In its standard form, JULES recognises nine surface types: broadleaf trees, needleleaf trees, C3 (temperate) grass, C4 (tropical) grass, shrubs, urban, inland water, bare soil and ice. These 9 types are modelled as 9 surface tiles. A land gridbox is either any mixture of the first 8 surface types, or is land ice. Note that, from version 2.0, one is not limited to these 9 standard surface types (unless running TRIFFID).
---
> For both gridded and single point runs, JULES views each gridbox as consisting
> of a number of surface types. The fractional area of each surface type is either
> prescribed by the user or modelled by the TRIFFID sub-model. Each surface type
> is represented by a surface tile, and a separate energy balance is calculated
> for each surface tile. The gridbox average energy balance is found by weighting
> the values from each surface tile. In its standard form, JULES recognises nine
> surface types: broadleaf trees, needleleaf trees, C3 (temperate) grass,
> C4 (tropical) grass, shrubs, urban, inland water, bare soil and ice.
> These 9 types are modelled as 9 surface tiles. A land gridbox is either any
> mixture of the first 8 surface types, or is land ice. Note that, from
> version 2.0, one is not limited to these 9 standard surface types (unless running TRIFFID).
8c22,27
< Soil processes are modelled in several layers. Each surface tile can be associated with its own soil tile, or all surface tiles can interact with a shared soil column. Each gridbox requires meteorological driving variables (such as air temperature) and variables that describe the soil properties at that location. It is also possible to prescribe certain characteristics of the vegetation, such as Leaf Area Index, to vary between gridboxes.
---
> Soil processes are modelled in several layers. Each surface tile can be
> associated with its own soil tile, or all surface tiles can interact with a
> shared soil column. Each gridbox requires meteorological driving variables
> (such as air temperature) and variables that describe the soil properties at
> that location. It is also possible to prescribe certain characteristics of the
> vegetation, such as Leaf Area Index, to vary between gridboxes.
10c29,37
< JULES can be run for any number of gridboxes from one upwards. The number of gridboxes is limited by the availability of computing power and suitable input data. When run on a grid, JULES models the average state of the land surface within the area of the gridbox and most quantities are taken to be homogeneous within the gridbox (with options to include subgrid-scale variability of a few, such as rainfall). In that case, the input data are also area averages. JULES can also be run "at a point", with inputs that are taken to represent conditions at that point - this configuration might be used when field measurements of meteorological conditions are available.
---
> JULES can be run for any number of gridboxes from one upwards. The number of
> gridboxes is limited by the availability of computing power and suitable
> input data. When run on a grid, JULES models the average state of the land
> surface within the area of the gridbox and most quantities are taken to be
> homogeneous within the gridbox (with options to include subgrid-scale
> variability of a few, such as rainfall). In that case, the input data are also
> area averages. JULES can also be run "at a point", with inputs that are taken
> to represent conditions at that point - this configuration might be used when
> field measurements of meteorological conditions are available.
diff -r jules-lsm.github.io/doc/source/release_notes/JULES3-0.rst jules/doc/source/release_notes/JULES3-0.rst
11c11
<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES3-1.rst jules/doc/source/release_notes/JULES3-1.rst
28a29,30
> .. |eacute| replace:: é
>
33c35
< * A change in the way fresh snow is handled in the multi-layer snow scheme - the density of fresh snow is now prescribed by a new variable (``rho_snow_fresh``). Suggested by Cécile Ménard and implemented by Doug Clark.
---
> * A change in the way fresh snow is handled in the multi-layer snow scheme - the density of fresh snow is now prescribed by a new variable (``rho_snow_fresh``). Suggested by C|eacute|cile M|eacute|nard and implemented by Doug Clark.
diff -r jules-lsm.github.io/doc/source/release_notes/JULES3-3.rst jules/doc/source/release_notes/JULES3-3.rst
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<
---
>
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<
---
>
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<
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>
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<
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>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES3-4.rst jules/doc/source/release_notes/JULES3-4.rst
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES4-0.rst jules/doc/source/release_notes/JULES4-0.rst
28c28
< It also has the advantage that the new namelists are cut-and-paste-able between the UM and JULES, which should make it easier to ensure that the same science is being used in online and offline runs.
---
> It also has the advantage that the new namelists are cut-and-paste-able between the UM and JULES, which should make it easier to ensure that the same science is being used in online and offline runs.
43c43
<
---
>
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES4-1.rst jules/doc/source/release_notes/JULES4-1.rst
6c6
< -----------------
---
> -----------------
10,11c10,11
< There are two schemes that can be used to determine when to irrigate:
<
---
> There are two schemes that can be used to determine when to irrigate:
>
13c13
< 2. Uses development index (dvi) across all tiles from JULES-crop (written by Rutger Dankers). Maximum dvi must exceed -1 (indicates sowing) for irrigation to occur.
---
> 2. Uses development index (dvi) across all tiles from JULES-crop (written by Rutger Dankers). Maximum dvi must exceed -1 (indicates sowing) for irrigation to occur.
diff -r jules-lsm.github.io/doc/source/release_notes/JULES4-8.rst jules/doc/source/release_notes/JULES4-8.rst
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES4-9.rst jules/doc/source/release_notes/JULES4-9.rst
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<
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>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES5-0.rst jules/doc/source/release_notes/JULES5-0.rst
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<
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>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES5-1.rst jules/doc/source/release_notes/JULES5-1.rst
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<
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>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES5-2.rst jules/doc/source/release_notes/JULES5-2.rst
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< * Reduced model overhead when running DrHook profiling. (#782)
---
> * Reduced model overhead when running DrHook profiling. (#782)
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES5-3.rst jules/doc/source/release_notes/JULES5-3.rst
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<
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>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES5-4.rst jules/doc/source/release_notes/JULES5-4.rst
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES5-6.rst jules/doc/source/release_notes/JULES5-6.rst
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES5-7.rst jules/doc/source/release_notes/JULES5-7.rst
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>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES5-8.rst jules/doc/source/release_notes/JULES5-8.rst
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<
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>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES5-9.rst jules/doc/source/release_notes/JULES5-9.rst
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<
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>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES6-0.rst jules/doc/source/release_notes/JULES6-0.rst
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<
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>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES6-1.rst jules/doc/source/release_notes/JULES6-1.rst
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<
---
>
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES6-2.rst jules/doc/source/release_notes/JULES6-2.rst
33c33
<
---
>
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES6-3.rst jules/doc/source/release_notes/JULES6-3.rst
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<
---
>
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES7-0.rst jules/doc/source/release_notes/JULES7-0.rst
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES7-1.rst jules/doc/source/release_notes/JULES7-1.rst
14c14
< * Interactive gas-phase deposition routines from UKCA have been added to JULES, together with a variant version that removes the restriction on the surface tile configuration. See :nml:mem:`JULES_DEPOSITION::dry_dep_model`. (#931)
---
> * Interactive gas-phase deposition routines from UKCA have been added to JULES, together with a variant version that removes the restriction on the surface tile configuration. See :nml:mem:`JULES_DEPOSITION::dry_dep_model`. (#931)
20,30c20,31
< * Added a switch to allow interpretation of times in the model and the driving data as local solar time - see :nml:mem:`JULES_TIME::l_local_solar_time`. (#1327)
< * Added a switch :nml:mem:`IMOGEN_RUN_LIST::l_drive_with_global_temps` so that JULES can be driven with global temperatures and climate patterns. (#1322)
< * Made Medlyn stomatal conductance, Farquhar C\ :sub:`3` photosynthesis, and thermal acclimation available in the UM. (#1246)
< * Further work towards allowing layered soil carbon (:nml:mem:`JULES_SOIL_BIOGEOCHEM::l_layeredc` = TRUE ) in the UM. (#1237)
< * A varying grey tile emissivity has been passed in to JULES - currently only available if selected in LFRic. (#1247)
< * OMP improvements in various routines. (#1310)
< * Enabled a call to CABLE albedo (part of ongoing work to provide access to CABLE). (#1314)
< * MORUSES and anthropogenic heat related metadata migrated to jules-shared to facilitate their implementation in LFRic. The simple two-tile urban scheme now no longer requires W/R as an input unless the total urban fraction only is specified in the ancillary data. (#1255)
< * Included the fab_jules app which builds JULES using Fab software. (#1331, 1364)
< * Updated compiler in JASMIN gfortran platform file. (#1347)
< * Upgraded rose stem testing on Met Office EXZ to use latest availiable CPE, and fixes for EXZ. (#1362, 1358)
---
> * Added a switch to allow interpretation of times in the model and the driving data as local solar time - see :nml:mem:`JULES_TIME::l_local_solar_time`. (#1327)
> * Added a switch :nml:mem:`IMOGEN_RUN_LIST::l_drive_with_global_temps` so that JULES can be driven with global temperatures and climate patterns. (#1322)
> * Made Medlyn stomatal conductance, Farquhar C\ :sub:`3` photosynthesis, and thermal acclimation available in the UM. (#1246)
> * Further work towards allowing layered soil carbon (:nml:mem:`JULES_SOIL_BIOGEOCHEM::l_layeredc` = TRUE ) in the UM. (#1237)
> * A varying grey tile emissivity has been passed in to JULES - currently only available if selected in LFRic. (#1247)
> * OMP improvements in various routines. (#1310)
> * Enabled a call to CABLE albedo (part of ongoing work to provide access to CABLE). (#1314)
> * MORUSES and anthropogenic heat related metadata migrated to jules-shared to facilitate their implementation in LFRic. The simple two-tile urban scheme now no longer requires W/R as an input unless the total urban fraction only is specified in the ancillary data. (#1255)
> * Included the fab_jules app which builds JULES using Fab software. (#1331, 1364)
> * Updated compiler in JASMIN gfortran platform file. (#1347)
> * Upgraded rose stem testing on Met Office EXZ to use latest available CPE, and fixes for EXZ. (#1362, 1358)
>
32d32
<
36,38c36,38
< * Corrected a bug in the `surf_ht_flux` diagnostic when using the Flake lake model. (#1340)
< * Fixing problems in the WARNING output messages. (#1303)
< * Fixed a metadata/rose config error introduced by a bug in Rose. (#1363)
---
> * Corrected a bug in the `surf_ht_flux` diagnostic when using the Flake lake model. (#1340)
> * Fixing problems in the WARNING output messages. (#1303)
> * Fixed a metadata/rose config error introduced by a bug in Rose. (#1363)
44c44
< * Updated NCI rose stem tests. (#1266)
---
> * Updated NCI rose stem tests. (#1266)
50c50
< * Updates associated with many of the above changes and to module leaders file, and release notes. (#1275, 1343)
---
> * Updates associated with many of the above changes and to module leaders file, and release notes. (#1275, 1343)
diff -r jules-lsm.github.io/doc/source/release_notes/JULES7-2.rst jules/doc/source/release_notes/JULES7-2.rst
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES7-3.rst jules/doc/source/release_notes/JULES7-3.rst
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES7-4.rst jules/doc/source/release_notes/JULES7-4.rst
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES7-5.rst jules/doc/source/release_notes/JULES7-5.rst
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES7-6.rst jules/doc/source/release_notes/JULES7-6.rst
13c13
< * Changes to how river ancillary files are processed. (#1512)
---
> * Changes to how river ancillary files are processed. (#1512)
22c22
<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES7-7.rst jules/doc/source/release_notes/JULES7-7.rst
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES7-8.rst jules/doc/source/release_notes/JULES7-8.rst
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES7-9.rst jules/doc/source/release_notes/JULES7-9.rst
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<
---
>
diff -r jules-lsm.github.io/doc/source/release_notes/JULES8-0.rst jules/doc/source/release_notes/JULES8-0.rst
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<
---
>
46a47,51
>
> After migrating to GitHub, the JULES code repository is now available at
> `https://github.com/MetOffice/jules <https://github.com/MetOffice/jules>`_.
> The user guide documentation is also included and can be accessed at
> `https://metoffice.github.io/jules/ <https://metoffice.github.io/jules/>`_.
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Replace #2
Locally built docs: https://wwwspice/~yaswant.pradhan/jules/migrate-docs/html/