#This is the readme document for the modeling of climate change impacts in the Hunter River estuary project
#participants: Mat Deiber, Tino Heimhuber + 2/3 CVEN Master’s Thesis Students
#Goal: use state of the art high-resolution climate change projection data (NARCLIM regional climate model ensemble)
 in conjunction with sea level rise scenarios to model the potential impacts of climate change on the hydrodynamics, 
 salinity and temperature (potentially water quality) of the estuary system. 

Folder Structure:

	Modeling
		01_Input
			BC_Generation (this is where all the rainfall runoff modeling etc. is done for generation of the boundary condition input file for RMA)


Key steps:
	The hydrological and hydrodynamic model is already fully set up and calibrated. We basically just need to create a plausible 
	range of future boundary condition scenarios and run them through the model
	
	The first step will be to generate new freshwater inflow time series for the small catchments by using NARcLIM forcing data.
	For each catchment, we’ll use the GRID cell of which the GRID centerpoint is closest to the Catchment centerpoint.
	
	NARCLIM will provide 12 rainfall time series per gridpoint so we need to adjust the python codes to automate the whole workflow even more.
	
	To begin with, we can pick 1-3 scenarios and test how well the “present-day” reanalysis
	data can reproduce the observed catchment flow time series and also how different the NARcLIM ET is from the observed. 
	Once we generated 12 RMA boundary condition files, one for each NARCCLIM ensemble member,
	the next step will be to automate the climate change scenario runs for NARcLIM. 
	
Specific Steps to run RMA2 and RMA11:
	run the 
	Prepare the water quality input time series (they must cover the years specified for the run) 
		For the Hunter, we use temperature at GRETA which is interpolated linearly to fill a few gaps in the record using the R code:
		C:\Users\z5025317\OneDrive - UNSW\WRL_Postdoc_Manual_Backup\WRL_Postdoc\Projects\Paper#1\Analysis\Code\ggplot_time_series_with_trends.R
		For the Hunter at greta, the first few month prior to 01/07/1995 0:00 were set to 10.5 degree manually 
		For seeham old and godswick, we used the same temperature as for the Hunter River
	The python code tide generator is used to generate the tidal boundary condition. The yearly files
	have to be copy pasted into the run directories. 
	Check that the nodes in the Matlab code match the ones generated in the elt file.
		for that we use the matlab code that's in the RMA generator folder
	Once all the run files are generated, start with the RMA2 startup file, wihch will flood the model by 5m and than drop the water level to the starting value. 
	The RMA batch file is used to run all the years in batch mode. The executable names have to be updated there.
		it is run by simply copy pasting the batch file into the windows command line after navigating to the correct
		run directory i.e. /HCC001
	

Download NARCLIM Data for all tributary catchments: