updated readme

README.md

@@ -12,7 +12,7 @@ The ABM requires two additional commands to run: the number of years, and the sp
 
 	java -jar ABM.jar -year 5 -modelName WEEDCONTROL -uncertainty 1
 
-will start the ABM for five years running with the WEEDCONTROL gams model. The uncertainty flag set to 1 runs the normal simulation. When the uncertainty flag is set to 0 it only uses the model satisfaction when making the decisions. 
+will start the ABM for five years running with the WEEDCONTROL gams model on . The uncertainty flag set to 1 runs the normal simulation. When the uncertainty flag is set to 0 it only uses the model satisfaction when making the decisions. 
 
 ### ABM Requirements
 1. /data/ folder containing input data files:
@@ -21,18 +21,6 @@ will start the ABM for five years running with the WEEDCONTROL gams model. The u
 
 2. /projdir/ folder containing the MP optimization model
 
-<!--Additional commands to fine tune the ABM simulation are available. The following flags turn off portions of the default simulation:
-
--uncertainty :: if set to 0, then ABM will not use the dissimilarity calculations during simulations
-
--individual_learning :: if set to 0, then the ABM will not use individual learning for activities during simulation
-
--social_learning :: if set to 0, then the ABM will not use social learning for activities during simulation
-
--activity_preference :: if set to 0, then the ABM will not use activity preference during simulation
-
--->
-
 ### Java JAR File Extraction
 To extract the required JAR file for the external MP model integration in eclipse do the following:
 
@@ -44,7 +32,6 @@ To extract the required JAR file for the external MP model integration in eclips
 
 4. Choose a file location and hit 'Finish'.
 
-
 ### Library Installation in Eclipse
 All of the those libraries should already be downloaded and included in the /lib/ directory. 
 
@@ -68,6 +55,17 @@ The libraries can be downloaded here if required:
 2. Download commons-math3-3.6.1-bin.zip from here: http://commons.apache.org/proper/commons-math/download_math.cgi
 3. Download the apache command line interface (cli) tool used for reading the input parameters: http://commons.apache.org/proper/commons-cli/
 
+### Eclipse Development Environment
+The code is developed and debugged using eclipse 4.7 or greater using JUnit5 for unit testing. 
+
+1. Clone the github repository to your computer
+
+2. After opening eclipse, right click on the command window (left side) and select "Import"
+
+3. Under "General" select "Projects from folders or archives" and select the git repository. 
+
+4. Install libraries in eclipse from the \lib folder and compile. 
+
 ### Troubleshooting Guide
 1. Issue related to graph library:
 
@@ -103,4 +101,8 @@ If the issue persists, try removing the libraries and reinstalling them again.
 	 
 	 -year <arg>                  ABM simulation years
 	 
-	 Make sure you are running the full command to start the ABM jar file. Three commands are necessary when starting. 
+	 Make sure you are running the full command to start the ABM jar file. Three commands are necessary when starting. 
+	 
+6. Error relating to JNI issues when running jar file OR issues related to library usage. 
+
+	JNI issues come from incorrect library settings. The easiest option to fix library issues is usually to uninstall all user libraries and re-add the libraries.