Write MCM/GECKO-A parameters to md file

In generate_wiki.jl, new function write_params to write new MCM/GECKO-A
photolysis parameters to a md file from a markdown. New support function
format_float to return a formatted string with for a float and its
errors. New function lnew to l at 350DU from the new l parameters.
New file src/data/params_header.md with header for the md output file.
In function generate_wiki in TUVtools.jl, renaming kwarg collength to
more concise name MCMcollength. Introducing kwargs parinput and
paroutput for the parameters.csv file from MCMphotolysis
(https://github.com/wacl-york/MCMphotolysis.git) and the output file
name. Calling function write_params from function generate_wiki.

Author: Peter Bräuer

src/TUVtools.jl

@@ -86,12 +86,13 @@ end
 Generate markdown files from templates specified kwarg `wikitemplates`, where
 reactions numbers from TUV in `tuvdir` and in MCM/GECKO-A are listed for every
 reaction listed at the beginning of each template line and written to files specified
-by kwarg `wikioutput`. The table `collength` can be specifief with a kwarg, for nicer
+by kwarg `wikioutput`. The table `MCMcollength` can be specifief with a kwarg, for nicer
 md file formatting. The `MCMversion` needs to be specified for every wiki template.
 """
 function generate_wiki(tuvdir::String; wikitemplates::Union{String, Vector{String}}="",
-  wikioutput::Union{String, Vector{String}}="WIKI.md", collength::Union{Int64,Vector{Int64}}=10,
-  MCMversion::Union{Int64,Vector{Int64}}=4)
+  wikioutput::Union{String, Vector{String}}="WIKI.md", MCMcollength::Union{Int64,Vector{Int64}}=10,
+  MCMversion::Union{Int64,Vector{Int64}}=4, parinput::String="",
+  paroutput::String="../MCM-Photolysis-Parameters.md")
   # Save current directory
   currdir = pwd()
   # Find files related to photolysis mechanism
@@ -100,7 +101,8 @@ function generate_wiki(tuvdir::String; wikitemplates::Union{String, Vector{Strin
   rxnlist = generate_rxns(rxnfiles, callfiles)
 
   # Auto-generate inc files for TUV_DSMACC
-  write_wiki(rxnlist, tuvdir, wikitemplates, wikioutput, collength, MCMversion, currdir)
+  write_wiki(rxnlist, tuvdir, wikitemplates, wikioutput, MCMcollength, MCMversion, currdir)
+  write_params(parinput, paroutput, currdir)
   # Go back to original directory
   cd(currdir)
 end #function generate_wiki

src/data/WIKItemplate_MCMv3.md

@@ -111,6 +111,7 @@ OIO -> I + O2
 ## Additional explanations
 
 <sup>(1)</sup> J(56): NOA photolyses to CH<sub>3</sub>COCH<sub>2</sub>O<sup>•</sup>
- and NO<sub>2</sub> as only products in the MCMv3.3.1 with a quantum yield of 0.9.
- In the MCMv3.2 an additional channel J(57) is assumed leading to
- CH<sub>3</sub>CO<sup>•</sup>, HCHO, and NO<sub>2</sub> with a branching of 0.75:0.25 between J(56) and J(57), respectively.
+and NO<sub>2</sub> as only products in the MCMv3.3.1 with a quantum yield of 0.9.
+In the MCMv3.2 an additional channel J(57) is assumed leading to
+CH<sub>3</sub>CO<sup>•</sup>, HCHO, and NO<sub>2</sub> with a branching of
+0.75:0.25 between J(56) and J(57), respectively.

src/data/params_header.md

@@ -0,0 +1,21 @@
+# MCM photolysis parameterisations
+
+The table below lists improved MCM/GECKO-A photolysis parameterisations,
+which include a dependence on the overlying ozone column.
+At 350DU they are identical the original MCM photolysis parameterisation:
+
+    j(χ) = l·cosᵐ(χ)·exp(-n·sec(χ))
+
+where j is in s<sup>-1</sup>. For other ozone columns `l` is redefined to:
+
+    l([O3]) = l_a0 + l_b0·exp(l_b1/[O3]) + l_c0·exp(l_c1/[O3])
+
+where l, l<sub>a0</sub>, l<sub>b0</sub>, l<sub>c0</sub> are in
+s<sup>-1</sup> and l<sub>b1</sub>, l<sub>c1</sub> are in DU.
+
+Download the parameters as [formatted text file](github.com/pb866) or
+[csv file](github.com/pb866).
+
+
+MCM/GECKO-A | TUV |        l<sub>a0</sub>         |        l<sub>b0</sub>         | l<sub>b1</sub> |        l<sub>c0</sub>         | l<sub>c1</sub> |        l(350DU)        |      m      |      n      | TUV label
+-----------:|----:|:-----------------------------:|:-----------------------------:|:--------------:|:-----------------------------:|:--------------:|:----------------------:|:-----------:|:-----------:|:---------

src/generate_wiki.jl

@@ -69,4 +69,72 @@ function init_wikifiles(ifile, ofile, len, DB, currdir)
   [push!(db, database[i-2]) for i in DB]
 
   return ifile, ofile, collength, db
+end #function init_wikifiles
+
+
+"""
+    write_params(ifile, ofile, pwd)
+
+From `ifile` `parameters.csv` from repository
+[MCMphotolysis](https://github.com/wacl-york/MCMphotolysis.git)
+write a table of the MCM/GECKO-A photolysis parameters to a markdown file `ofile`.
+Use `pwd` to determine absolute paths of the files.
+"""
+function write_params(ifile, ofile, pwd)
+  # Skip routine, if no template is provided
+  if ifile == ""  return  end
+  # Determine absolute paths of I/O files
+  if !isabspath(ifile)  ifile = joinpath(pwd, ifile)  end
+  if !isabspath(ofile)  ofile = joinpath(pwd, ofile)  end
+  # Read header of md file
+  header = readfile(joinpath(@__DIR__, "data/params_header.md"))
+
+  # Open output file
+  open(ofile,"w") do f
+    # print header
+    [println(f, line) for line in header]
+    # Read parameter file from MCMphotolysis
+    param = read_data(ifile, sep = ";", header = 1)
+     # Loop over reactions
+    for i = 1:length(param[1])
+      # Retrieve and format l parameters and errors
+      la0 = format_float(param[1][i], param[8][i])
+      lb0 = format_float(param[2][i], param[9][i])
+      lb1 = @sprintf("%8.2f±%.2f", param[3][i], param[10][i])
+      lc0 = format_float(param[4][i], param[11][i])
+      lc1 = @sprintf("%8.2f±%.2f", param[5][i], param[12][i])
+      # Calculate orignal l parameter at 350 DU and order of magnitude
+      l = lnew(350., param[i,1:5])
+      o = Int(floor(log10(abs(l))))
+      lp = l/10.0^o
+      # Print reaction to md file
+      @printf(f, "%10s  | %3d |%30s |%30s |%s|%30s |",
+        rpad(param[end-2][i],8), param[end-1][i], la0, lb0, rpad(lb1,16), lc0)
+      @printf(f, "%s| %6.3f·10<sup>%d</sup> |%6.3f±%.3f |%6.3f±%.3f | %s\n",
+        rpad(lc1,16),lp, o,
+        param[6][i], param[13][i], param[7][i], param[14][i], param[end][i])
+    end # loop over reactiojns
+    # Inform about number of reactions on screen
+    println("MCM/GECKO-A parameters for $(length(param[1])) reactions ",
+      "written to $(basename(ofile)).")
+  end # close file
+end #function write_params
+
+
+"""
+    format_float(n::AbstractFloat, m::AbstractFloat)
+
+Derive the order of magnitude for float `n` and return `String` in the form
+`"(X.XXX±Y.YYY)·10<sup>Z</sup>"`, where `X` and `Y` are n and m reduced by the
+order of magnitude of `n` and `Z` is the order of magnitude.
+"""
+function format_float(n::AbstractFloat, m::AbstractFloat)
+  o = Int(floor(log10(abs(n))))
+  @sprintf("(%.3f±%.3f)·10<sup>%d</sup>",n/10.0^o, m/10.0^o, o)
 end
+
+
+"""
+    lnew(O3,p) / s^-1 = p[1] + p[2]·exp(-O3/p[3]) + p[4]·exp(-O3/p[5])
+"""
+lnew(O3,p) = (p[1]+p[2]*exp.(-O3/p[3])+p[4]*exp.(-O3/p[5]))[1]

src/setrxns.jl

@@ -273,4 +273,4 @@ function write_incfiles(rxnlist, tuvdir)
       println(f, "  END SELECT")
     end # close file
   end # loop over files
-end #function write_incfiles
+end