Changed README to markdown format. Changed output file names to be consistent

README.md

+Everything is super simple right now. We can complicate it more if we want.
+
+I made a single .cc file with three functions:
+
+
+cutZDCoutput(string fileName, int rodNum)
+  Arguments:
+    fileName - The input .root file
+    rodNum   - The transmission spectrum you would like to use. Uses the old
+               numbering scheme. I will change that as soon as I figure out
+               the conversion.
+  Description:
+    Takes an input .root file with photon data from the top of the ZDC and
+    cuts it based on the transmission spectrum for the selected rod.
+
+  Output:
+    .root file and .txt file with photon data after cuts. Named the same as the input
+    file prepended with Out_
+
+
+
+PMTcuts(string fileName, int PMTmodel = 6091)
+  Arguments:
+    fileName - The input .root file
+    PMTmodel - Loads the Quantum efficiency curve for the given PMT model #.
+               Currently we only have data for the 6091. Waiting on datasheets
+               from Peter for the other options.
+
+  Description:
+    Takes an input .root file with photon data from the top of the ZDC light guide
+    and cuts it based on the Quantum Efficiency for the selected PMT model.
+
+  Output:
+    .txt file with photon data after cuts. Named the same as the input file
+    prepended with Out_
+
+SetBranches()
+  Arguments:
+    None
+  Description:
+    Does like it sounds. The input and output files and variables are global
+    so we can reuse this section of code.

outputDigitization.cc

@@ -53,7 +53,7 @@ void cutZDCoutput(string fileName, int rodNum){
 	int EventNo;
 	double energy,X,Y,Z,Px,Py,Pz;
 	TRandom rnd;
-	ofstream outputFile( Form("%s_Out.txt",fileName.c_str() ) );
+	ofstream outputFile( Form("Out_%s.txt",fileName.c_str() ) );
 
 	//// Get the transmission data
 	////