This directory (3-4-5_Simulations) contains the four modified versions of the groundwater
model from Clark and others (2006)used in this study described by the report in the "7_Report" directory.

Also contained in this directory is the published version of the model (Software.zip) and its related report (sir20065137.pdf).
The model and report are available at http://pubs.usgs.gov/sir/2006/5137/.

The first is in the directory mod158_NL_ML.  This version of the Clark and others (2006) model
has had the nitrogen input modified by UCODE_2005.  UCODE_2005 optimized the nitrogen input 
by applying a single multiplier to the data in CASE_9_LOADINGWELLS.DAT using the python script,
ConFactor.py, written for this study by Kenneth Skinner.  As described in the report, UCODE_2005 
compares the output of the model with groundwater nitrate data collected during the years 2003-2007.
UCODE_2005 then increases or decreases the nitrogen input to the model as a whole with a single 
multiplier using the python script.

Files contained in the mod158_NL_ML directory are described as:
mf2k_gwt files:
	CASE_9*    unmodified model input and output files except for
		CASE_9_LOADINGWELLS is modified from CASE_9_LOADINGWELLSpre.dat using UCODE_2005 and the python script.
	SRNSS.*    unmodified model input files except for
		SRNSS.MOB has been updated to account for the new observation data locations
	InitHead.hed and InitConc_Layer_(1-4).dat are unmodified model input files

UCODE_2005 files:
	UCASE_9_OBA.ins, Ucode*, and UConc* are UCODE_2005 input files
	mod158d_NL.* are UCODE output files
UCODE_2005 was run at the highest verbose level which creates the most output files.  Not all of
the output files were used for analysis.

ConFactor.py is python script called by UCODE_2005 to modify CASE_9_LOADINGWELLSpre.dat

The next three directories contain the previously mentioned model modified for three different
nitrogen loading scenarios: decreasing, constant, and increasing nitrogen input.
The mf2k_gwt files contained in the mod158_NL_dectrend, mod158d_NL_flattrend, and mod158d_NL_inctrend
directories are the same as those described in the mod158d_NL_ML directory except they have been modified
as necessary to have more than one stress period and different nitrogen inputs.  As described in
the report each scenario has the nitrogen input prorated by county from 2003 to 2008 conditions
and then the nitrogen loading scenario runs from 2008 onward.  The decreasing and constant nitrogen
input scenarios thusly have two stress periods while the increasing nitrogen input scenario has six.

No portions of the model files were altered other than stress period information and the
nitrogen inputs.



