From b02bdb661b1a9320fb95c6f75d04808101f56f0c Mon Sep 17 00:00:00 2001 From: Sam Harrison Date: Wed, 4 Sep 2024 11:56:44 +0100 Subject: [PATCH 1/5] Update nanofase-data.md --- docs/users/nanofase-data.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/users/nanofase-data.md b/docs/users/nanofase-data.md index 71e3459..076d8ae 100644 --- 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). \ No newline at end of file +The full list of model parameters, including whether they are required by the NanoFASE data module, is given in the [](parameter-reference). From c0993ebfe5e6fa3717c34c6cde96c0a79138e7d9 Mon Sep 17 00:00:00 2001 From: Sam Harrison Date: Thu, 3 Oct 2024 09:50:13 +0100 Subject: [PATCH 2/5] Correct docs for sediment parameters --- docs/users/parameters/sediment-parameters.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/users/parameters/sediment-parameters.csv b/docs/users/parameters/sediment-parameters.csv index 9cbaa2d..a9d5018 100644 --- 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/m2,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." From 8b68573afda6f32b9612412d7a7d1de001723861 Mon Sep 17 00:00:00 2001 From: Sam Harrison Date: Thu, 3 Oct 2024 15:17:43 +0100 Subject: [PATCH 3/5] Update soil-terrestrial-parameters.csv --- docs/users/parameters/soil-terrestrial-parameters.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/users/parameters/soil-terrestrial-parameters.csv b/docs/users/parameters/soil-terrestrial-parameters.csv index 47802e8..944198c 100644 --- a/docs/users/parameters/soil-terrestrial-parameters.csv +++ b/docs/users/parameters/soil-terrestrial-parameters.csv @@ -18,5 +18,5 @@ `heathland`
`urban_capped`
`urban_gardens`
-`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. ", From a83cdeee43c65c0cab37b27c4a9aafa756913124 Mon Sep 17 00:00:00 2001 From: Sam Harrison Date: Wed, 13 Nov 2024 13:20:07 +0000 Subject: [PATCH 4/5] Updating docs link to fpm --- docs/intro.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/intro.md b/docs/intro.md index 81ac20e..20f2f11 100644 --- 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: From fbad021ec26700131cac12f0c7e43139b04de5bb Mon Sep 17 00:00:00 2001 From: Sam Harrison Date: Wed, 13 Nov 2024 13:27:31 +0000 Subject: [PATCH 5/5] Updating build instruction docs --- docs/getting-started/building-the-model.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/docs/getting-started/building-the-model.md b/docs/getting-started/building-the-model.md index dbc879d..68b6dcf 100644 --- 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.