Added configuration to readme

README.md

@@ -22,12 +22,61 @@ options:
 
 ## Bathymetry
 
+Configuration:
+```
+[inp]
+root: input directory
+base: bathymetry database (.xyz)
+hires: 1d hires smoothed breakwater profile (.dat)
+hstru: 1d hires smoothed breakwater porosity height (.dat)
+poro: 1d breakwater porosity (.dat)
+psize: 1d porosity size (.dat)
+hires_step: mesh sizing of 1d profile
+
+[out]
+margin: margin around the buoy and breakwater for subdomain
+no_breakwater: option to remove breakwater
+root: output directory
+sub: output file for subdomain
+out: output file for 1d projection
+step: mesh size
+left: margin for 1d projection (breakwater side)
+right: margin for 1d projection (buoy side)
+
+[artha]
+lat: latitude of the breakwater
+lon: longitude of the breakwater
+
+[buoy]
+lat: latitude of the buoy
+lon: longitude of the buoy
+```
+
 * Insert database in `data/data`
 * Run `processing.subdomain` to generate 2D data in a smaller domain
 * Run `processing.projection` to generate a 1D bathymetry
 
 ## Swash
 
+Configuration:
+```
+[data]
+out: input directory (output of bathymetry)
+
+[swash]
+input: swash input file (.sws)
+path: path to swash directory (should contain swashrun and swash.exe)
+out: output directory for swash (created at the end of the computation)
+mpi: number of mpi threads (omit to use serial)
+
+[post]
+inp: input directory for post-processing (output of sws_npz)
+compare: input directory for post-processing comparison (omit to display results from single case)
+out: output directory for figures
+x0: position of reflection calculations
+t0: minimum time for reflection calculations (necessary because of boundary condition ramping)
+```
+
 * Run `processing.swash` to run the Swash model
 * Run `processing.sws_npz` to convert Swash output to Numpy files
 * Run `processing.post` to plot wave height at a point, water level at an
@@ -37,6 +86,21 @@ options:
 
 ## OlaFlow
 
+Configuration:
+```
+[swash]
+np_out: input of olaflow from swash (output of sws_npz)
+
+[bathy]
+bathy: bathymetry to be used by olaflow
+hstru: height of porous domain (see bathy)
+scale: openscad scaling (mesh sizing in [x,y,z])
+out: output folder for stl bathymetry
+
+[olaflow]
+root: olaflow computation directory
+```
+
 * Run `processing.bathy` to generate stl input files
 * Run `blockMesh`, `snappyHexMesh -overwrite`, copy `0.org` to `0`, `setFields`
 * Run `processing.sws_ola` to convert Swash output to OlaFlow input