Merge branch 'develop' of github.com:NERC-CEH/nanofase into develop

NERC-CEH · Jan 7, 2025 · 5a45fdb · 5a45fdb
2 parents 8a0ff20 + fbad021
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diff --git a/docs/getting-started/building-the-model.md b/docs/getting-started/building-the-model.md
@@ -76,9 +76,3 @@ $ make
 The default target builds the model with debugging enabled. To turn on optimisations, build using `make release` (for `-O3` optimisations) or `make fast` (for `-Ofast` optimsations).
 
 The model will be built into the `build` directory by default (a custom directory can be specified with the `$BUILD_DIR` option, e.g. `make BUILD_DIR=makebuild`). An executable file named `nanofase` will now be available in this directory.
-
-## Other build options
-
-We are also working towards supporting the [Fortran Package Manager](https://fpm.fortran-lang.org/) (FPM), but are not quite there yet. See the [fpm.toml](https://github.com/NERC-CEH/nanofase/blob/develop/fpm.toml) file for the work-in-progress FPM manifest file.
-
-The model can also be compiled using Visual Studio with the Intel Fortran integration. See [](../developers/vs-ifort-setup.md) for a guide on compiling using Visual Studio 2017.
diff --git a/docs/intro.md b/docs/intro.md
@@ -8,7 +8,7 @@ The NanoFASE model is a multimedia spatiotemporal environmental fate and exposur
 
 ## Quickstart guide
 
-The easiest way to install the model is to use the [Fortran Package Manager](https://fpm.fortran-lang.org/en/install/index.html#install), which can be installed using Conda (`conda install -c conda-forge fpm`). The model also requires a recent version of GFortran, NetCDF Fortran and Git installed (see [](./getting-started/building-the-model.md)).
+The easiest way to install the model is to use the [Fortran Package Manager]([https://fpm.fortran-lang.org/en/install/index.html#install](https://fpm.fortran-lang.org/install/index.html#install)), which can be installed using Conda (`conda install -c conda-forge fpm`). The model also requires a recent version of GFortran, NetCDF Fortran and Git installed (see [](./getting-started/building-the-model.md)).
 
 Clone the code (make sure to `--recurse-submodules`) and use *fpm* to install:
 

diff --git a/docs/users/nanofase-data.md b/docs/users/nanofase-data.md
@@ -2,7 +2,7 @@
 
 The *NanoFASE data module* (`nfdata`) is a Python package that is used to compile input data for the model. It is recommended to use this package over and above manually compiling the NetCDF and constants namelist file required by the model, as the data module scripts take care of deriving a variety of [secondary derived variables](netcdf-namelist-input:secondary-derived-variables), amongst other reasons.
 
-The package source code can be [found on GitHub](https://github.com/nerc-ceh/nfdata).
+The package source code can be [found on GitHub](https://github.com/nerc-ceh/nanofase-data).
 
 ## Getting started
 
@@ -263,4 +263,4 @@ We appreciate that the way of specifying point source emissions is currently rat
 
 ### Full parameter schema
 
-The full list of model parameters, including whether they are required by the NanoFASE data module, is given in the [](parameter-reference).
+The full list of model parameters, including whether they are required by the NanoFASE data module, is given in the [](parameter-reference).
diff --git a/docs/users/parameters/sediment-parameters.csv b/docs/users/parameters/sediment-parameters.csv
@@ -1,5 +1,5 @@
 {bdg-dark-line}`group` Name(dimensions),Specified in,Data type,Required or optional,Model units,Description
-{bdg-dark-line}`sediment` `porosity`,{bdg-secondary}`constants.nml` {bdg-danger}`constants.yaml` ,float,Required,\-,Average sediment porosity
+{bdg-dark-line}`sediment` `porosity(sed_l)`,{bdg-secondary}`constants.nml` {bdg-danger}`constants.yaml` ,float,Required,\-,Average sediment porosity
 {bdg-dark-line}`sediment` `initial_mass(spm)`,{bdg-secondary}`constants.nml` {bdg-danger}`constants.yaml` ,float,Required,kg/m<sup>2</sup>,The mass of each sediment size class at the start of the model run.
 {bdg-dark-line}`sediment` `fractional_composition_distribution(fc)`,{bdg-secondary}`constants.nml` {bdg-danger}`constants.yaml` ,float,Required,\-,"The default distribution of sediment mass across fractional compositions, as a percentage."
 {bdg-dark-line}`sediment` `default_spm_size_distribution(spm)`,{bdg-secondary}`constants.nml` {bdg-danger}`constants.yaml` ,float,Required,\-,"The default size distribution applied to sediment particles, as a percentage, when there is no other information, such as from soil erosion yields."

diff --git a/docs/users/parameters/soil-terrestrial-parameters.csv b/docs/users/parameters/soil-terrestrial-parameters.csv
@@ -18,5 +18,5 @@
 `heathland`<br>
 `urban_capped`<br>
 `urban_gardens`<br>
-`urban_parks`                                                                                                                                    ",{bdg-secondary}`constants.nml` {bdg-danger}`constants.yaml` ,float     ,Required                         ,individuals/m3                ,Density of earthworms in each [NanoFASE land use category](nanofase-data:land-use).                                                                                                                                                                                                                                                                                         ,"[See here](netcdf-namelist-input:earthworms) for reasonable estimates for the UK. Could be deduced from earthworm density maps, e.g. [for Europe](https://doi.org/10.1016/j.apsoil.2015.08.015)."
+`urban_parks`                                                                                                                                    ",{bdg-secondary}`constants.nml` {bdg-danger}`constants.yaml` ,float     ,Required                         ,individuals/m2                ,Density of earthworms in each [NanoFASE land use category](nanofase-data:land-use).                                                                                                                                                                                                                                                                                         ,"[See here](netcdf-namelist-input:earthworms) for reasonable estimates for the UK. Could be deduced from earthworm density maps, e.g. [for Europe](https://doi.org/10.1016/j.apsoil.2015.08.015)."
 {bdg-dark-line}`earthworm-densities` `vertical_distribution(soil_l)`                                                                              ,{bdg-secondary}`constants.nml` {bdg-danger}`constants.yaml` ,float     ,Required                         ,\-,"Percentage of the earthworms in each soil layer, used to distribute the densities across the soil profile.                                                                                                                                                                                                                                                                ",