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Set version to 0.1.0; README; minor updates
Set version to 0.1.0 in Poject.toml. New README including version history. Updated links to parameter files in params_header.md. Updated back-to-top links in wiki templates. New back-to-top link for parameter list at the bottom of the md file. Additional print command in function write_params in generate_wiki.jl.
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‎Project.toml‎

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@@ -2,7 +2,7 @@ name = "TUVtools"
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uuid = "345a537c-f292-11e8-1826-5db092d7553c"
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authors = ["Peter Bräuer <pb866@york.ac.uk>"]
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julia = "≥0.7"
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version = "0.1.0-DEV"
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version = "0.1.0"
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[deps]
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Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"

‎README.md‎

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TUVtools
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========
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TUV developer tools to auto-generate TUV input files, include files to link
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TUV to the boxmodel [DSMACC](https://github.com/pb866/DSMACC-testing.git) or
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generate markdown files for the TUV wiki.
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Installation
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------------
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Go to the package manager and add first the unregistered package
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[filehandling](https://github.com/pb866/filehandling.git) and then TUVtools.
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You may want to `activate` an environment as optional second step, if you
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don't want the project installed in the main julia environment (where `.` can
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be replaced by any path to any existing Project.toml or to a new folder
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creating a new environment).
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```julia
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julia> ]
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pkg> activate .
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pkg> add https://github.com/pb866/filehandling.git
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pkg> add https://github.com/pb866/TUVtools.git
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pkg> instantiate
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pkg> precompile
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```
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Usage
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-----
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Import package with `using` or import `import`:
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```julia
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using Pkg
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Pkg.activate("path/to/Project.toml") #if not in main julia environment
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using TUVtools
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```
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**_Currently all functions work only for the MCM/GECKO-A TUV version 5.2.x., where source code has been moved to a separate source folder!_**
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Additional flags to use with the original TUV version will be introduced in the future.
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### Function setrxns
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Auto-generates The reaction part of the TUV input files from the reaction labels
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defined in the rxn files/subroutines. Options exist to reset flags.
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```julia
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setrxns(tuvdir::String; inputfiles::Union{String,Vector{String}}="", setflags::Int64=-1)
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```
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Specify the location of the TUV main folder with `tuvdir`. TUV input files have to exist
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already and only the mechanisims section is overwritten. By default all files in the `INPUTS`
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folders are re-written. Use keyword argument `inputfiles` to select a subset.
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Use kwarg `setflags` to reset flags for TUV output. By default the same flags are used as
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previously. If you add/delete reactions, you will have to insert/delete flags at the
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corresponding lines (you only need to provide the flag at the first character of the line,
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the remaining line will be auto-filled). Other options are:
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- `0`: Set all flags to false (`F`)
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- `1`: Set all flags to true (`T`)
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- `2`: Set output to `T` for reactions in the MCM/GECKO-A mechanism, remaining flags to `F`
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- `3`: Set output to `T` for reactions in the MCMv3.3.1 (and older) mechanism, remaining flags to `F`
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### Function generate_incfiles
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Auto-generates include files for the boxmodel
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[DSMACC](https://github.com/pb866/DSMACC-testing.git) to link TUV and DSMACC
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reaction numbers in the model.
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```julia
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generate_incfiles(tuvdir::String)
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```
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Specify the main folder of the TUV version you are using
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(needs to be the MCM/GECKO-A TUV version rather than original TUV), from
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which the function will derive the TUV reaction numbers.
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DSMACC reaction numbers are saved in `src/data/MCMv32.db`, `src/data/MCMv331.db`,
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and `src/data/MCM-GECKO-A.db` for the respective MCM versions.
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If you use additonal photolysis reactions or altered the photolysis numbers
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in any way, you need to modify these number either by cloning this repository
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and making sure to load the cloned version into julia or you can `develop` the
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package with the help of the package manager.
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Include files will be auto-generated for every MCM version and written to the
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main folder of the specified TUV version.
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### Function generate_wiki
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This is a more advanced routine for developers of the MCM/GECKO-A TUV version
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to maintain the wiki pages of the repository.
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Function `generate_wiki` can auto-generate wiki pages for the reaction numbers
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used in MCM/GECKO-A and TUV and the improved MCM photolysis parameterisations.
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By default, no wiki files are generated unless you specify a template for the wiki page(s)
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or the `parameter.csv` from [MCMphotolysis](https://github.com/pb866/MCMphotolysis.git).
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```julia
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generate_wiki(tuvdir::String; wikitemplates::Union{String, Vector{String}}="",
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wikioutput::Union{String, Vector{String}}="WIKI.md", MCMcollength::Union{Int64,Vector{Int64}}=10,
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MCMversion::Union{Int64,Vector{Int64}}=4, parinput::String="",
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paroutput::String="../MCM-Photolysis-Parameters.md")
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```
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Specify the main folder of the TUV version used in `tuvdir` to get the TUV
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reaction numbers. If you want to generate wiki page(s) for the reaction numbers,
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make sure the DSMACC reaction numbers are correct in the database files
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(see [function `generate_incfiles`](#function-generate_incfiles)).
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Create templates for all wiki pages using markdown code. Type any text you like
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in the page. Where you want tables with the reaction numbers, only provide the header.
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Put the reaction string starting at the first character of the line for every reaction
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you want in the tables at the correct positon in the template. The script will auto-fill-in
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the correct MCM/GECKO-A and TUV reaction numbers in the first two columns and the
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reaction label in the third. Reaction labels have to be the same as in TUV.
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Examples of templates can be found in `src/data`.
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Specify the templates with the kwarg `wikitemplates` as `String` for single file
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or as `Vector{String}` for multiple files. Define as many output file names as
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templates with `wikioutput` in the same manor. Specify, which version of the MCM
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you are using for each wiki page as `Int64` or `Vector{Int64}` using `3` for
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MCMv3.3.1 or older and `4` for MCM/GECKO-A. Optionally you can specify the column
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length of the MCM/GECKO-A reaction number column for nicer formatting of the table
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in the md files. TUV columns will always be for 3-digit integers.
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If you want to generate the parameter list for the improved MCM/GECKO-A
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photolysis parameterisations, specify the location and file name of the
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`parameters.csv` from [MCMphotolysis](https://github.com/pb866/MCMphotolysis.git)
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with kwarg `parinput`. To specify a location and file name for the
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auto-generated markdown file use kwarg `paroutput`.
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Version history
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===============
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Version 0.1.0
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-------------
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- New function `setrxns` to auto-generate TUV input files
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- New function `generate_incfiles` to auto-generate DSMACC include files
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to link TUV to DSMACC
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- New function `generate_wiki` to auto-generate wiki files for the
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MCM/GECKO-A and TUV reaction numbers and for the improved MCM/GECKO-A
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photolysis parameterisations

‎src/data/WIKItemplate_MCM-GECKO-A.md‎

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@@ -24,7 +24,7 @@ and in TUV 5.2.x for the following compound classes:
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- [Alkyl hydroperoxides](#alkyl-hydroperoxides)
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- [Criegee intermediates](#criegee-intermediates)
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- [Polyfunctionals](#polyfunctional-chromophores)
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- [Halogens](#edwards-et-al-mcm-halogen-extensions)
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- [Halogens](#halogen-extensions)
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Please ensure that `vers` is set to `2` in the `params` file in TUV.
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This should set all cross section and quantum yield options correctly to
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HNO4 -> HO2 + NO2
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HNO4 -> OH + NO3
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## Linear aldehydes
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n-C6H13CHO -> C6H13 + CHO
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## Branched aldehydes
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tALD -> products
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## Unsaturated aldehydes
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## Substituted aldehydes
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intAldOH -> R + CHO
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## Unbranched ketones
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## Branched ketones
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## Unsaturated ketones
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## Cyclic ketones
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## Substituted ketones
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## Ketenes
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## Dicarbonyls
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## Terminal linear alkyl nitrates
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## Internal linear alkyl nitrates
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## Branched alkyl nitrates
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## Substituted alkyl nitrates
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## Further nitrogen compounds
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## Alkyl dinitrates
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## Alkyl hydroperoxides
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## Criegee intermediates
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## Polyfunctional chromophores
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