TUVtools

TUV developer tools to auto-generate TUV input files, include files to link TUV to the boxmodel DSMACC or generate markdown files for the TUV wiki.

Installation

Go to the package manager and add first the unregistered package filehandling and then TUVtools. You may want to activate an environment as optional second step, if you don't want the project installed in the main julia environment (where . can be replaced by any path to any existing Project.toml or to a new folder creating a new environment).

julia> ]
pkg> activate .
pkg> add https://github.com/pb866/filehandling.git
pkg> add https://github.com/pb866/TUVtools.git
pkg> instantiate
pkg> precompile

Usage

Import package with using or import import:

using Pkg
Pkg.activate("path/to/Project.toml") #if not in main julia environment
using TUVtools

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! Additional flags to use with the original TUV version may be introduced in the future.

Function setrxns

Auto-generates the reaction part of the TUV input files from the reaction labels defined in the rxn files/subroutines. Options exist to reset flags.

setrxns(tuvdir::String; inputfiles::Union{String,Vector{String}}="", setflags::Int64=-1)

Specify the location of the TUV main folder with tuvdir. TUV input files have to exist already and only the mechanisims section is overwritten. By default all files in the INPUTS folders are re-written. Use keyword argument inputfiles to select a subset.

Use kwarg setflags to reset flags for TUV output. By default the same flags are used as previously. If you add/delete reactions, you will have to insert/delete flags at the corresponding lines (you only need to provide the flag at the first character of the line, the remaining line will be auto-filled). Other options are:

• 0: Set all flags to false (F)
• 1: Set all flags to true (T)
• 2: Set output to T for reactions in the MCM/GECKO-A mechanism, remaining flags to F
• 3: Set output to T for reactions in the MCMv3.3.1 (and older) mechanism, remaining flags to F

Function generate_incfiles

Auto-generates include files for the boxmodel DSMACC to link TUV and DSMACC reaction numbers in the model.

generate_incfiles(tuvdir::String)

Specify the main folder of the TUV version you are using (needs to be the MCM/GECKO-A TUV version rather than original TUV), from which the function will derive the TUV reaction numbers. DSMACC reaction numbers are saved in data/MCMv32.db, data/MCMv331.db, and data/MCM-GECKO-A.db for the respective MCM versions.

If you use additonal photolysis reactions or altered the photolysis numbers in any way, you need to modify these number either by cloning this repository and making sure to load the cloned version into julia or you can develop the package with the help of the package manager.

Include files will be auto-generated for every MCM version and written to the main folder of the specified TUV version.

Function generate_wiki

This is a more advanced routine for developers of TUV_MG — the MCM/GECKO-A version of TUV 5.2 – to maintain the wiki pages of the repository.

Function generate_wiki can auto-generate wiki pages for the reaction numbers used in MCM/GECKO-A and TUV and the improved MCM photolysis parameterisations.

By default, no wiki files are generated unless you specify a template for the wiki page(s) or the parameter.csv from MCMphotolysis.

generate_wiki(tuvdir::String; wikitemplates::Union{String, Vector{String}}="",
  wikioutput::Union{String, Vector{String}}="WIKI.md",
  wikidir::String=joinpath(@__DIR__, "../data"), parinput::String="",
  paroutput::String="../MCM-Photolysis-Parameters.md",
  MCMcollength::Union{Int64,Vector{Int64}}=10,
  MCMversion::Union{Int64,Vector{Int64}}=4)

Specify the main folder of the TUV version in tuvdir to get the TUV reaction numbers. If you want to generate wiki page(s) for the reaction numbers, make sure the DSMACC reaction numbers are correct in the database files (see function generate_incfiles).

Create templates for all wiki pages using markdown code. Type any text you like in the page. Where you want tables with the reaction numbers, only provide the header. Put the reaction string starting at the first character of the line for every reaction you want in the tables at the correct positon in the template. The script will auto-fill-in the correct MCM/GECKO-A and TUV reaction numbers in the first two columns and the reaction label in the third. Reaction labels have to be the same as in TUV. Examples of templates can be found in ./data. Use these templates (select with wikitemplates) or save different templates to folder wikidir.

Specify the templates with the kwarg wikitemplates as String for single file or as Vector{String} for multiple files. Define as many output file names as templates with wikioutput (in the same manor). Specify, which version of the MCM you are using for each wiki page as Int64 or Vector{Int64} using 3 for MCMv3.3.1 or older and 4 for MCM/GECKO-A. Optionally, you can specify the column length of the MCM/GECKO-A reaction number column for nicer formatting of the table in the md files. TUV columns will always be for 3-digit integers.

If you want to generate the parameter list for the improved MCM/GECKO-A photolysis parameterisations, specify the location and file name of the parameters.csv from MCMphotolysis with kwarg parinput. To specify a location and file name for the auto-generated markdown file use kwarg paroutput.

Version history

Version 0.1.2

• Use import for filehandling (as fh) rather than using
• Add support for line breaks in j labels in the reaction files
• Move data folder from src to main folder
• New kwarg wikidir to specify the directory of the wiki templates
• Bug fixes

Version 0.1.1

• Fix #5 (BoundsError)
• Fix name of O(3P) in database files and wiki pages

Version 0.1.0

• New function setrxns to auto-generate TUV input files
• New function generate_incfiles to auto-generate DSMACC include files to link TUV to DSMACC
• New function generate_wiki to auto-generate wiki files for the MCM/GECKO-A and TUV reaction numbers and for the improved MCM/GECKO-A photolysis parameterisations