Fixed Nek launching bugs

Fixed a bug where the NekReader and NekWriter were using "no" and "yes"
instead of "F" and "T" for parameters. Also fixed a bug causing the
NekWriter to output incorrect coordinates in the Mesh Elements block.
Signed-off-by: r8s <r8s@tnpmbpro.ornl.gov>

org.eclipse.ice.nek5000/src/org/eclipse/ice/nek5000/NekLauncher.java

@@ -167,19 +167,22 @@ public class NekLauncher extends SuiteLauncher {
 		// working directory.
 		String exampleCopyStage = "cp -r " + installDir + "/examples/"
 				+ executable + "/* .;";
-		String rmObjStage = "rm -rf obj/;";
 		String inputCopyStage = "cp ${inputFile} "
 				+ executableMap.get(executable) + ".rea;";
+		String copyNekStep = "cp ${installDir}nek5000 .;";
 
-		// Define the nek and visnek launch stages
+		// Define the nek and visnek launch stages. We attempt to lanch the scripts from two different locations, in order to support both the current and legacy versions of the repo structure.
 		String launchStage = "${installDir}trunk/tools/scripts/nek "
-				+ executableMap.get(executable) + ";";
+				+ executableMap.get(executable) + "; {installDir}bin/nek " + executableMap.get(executable) + ";";
 		String vizStage = "${installDir}trunk/tools/scripts/visnek "
-				+ executableMap.get(executable) + ";";
+				+ executableMap.get(executable) + "; {installDir}bin/visnek " + executableMap.get(executable) + ";";
 
+		//Remove the copy of the nek5000 application we needed to make in the run directory
+		String rmObjStage = "rm -rf nek5000";
+		
 		// Configure the entire launch script
-		String launchCommand = exampleCopyStage + rmObjStage + inputCopyStage
-				+ launchStage + vizStage;
+		String launchCommand = exampleCopyStage + inputCopyStage
+				+ copyNekStep + launchStage + vizStage + rmObjStage ;
 
 		return launchCommand;
 	}

org.eclipse.ice.nek5000/src/org/eclipse/ice/nek5000/NekReader.java

@@ -26,6 +26,7 @@ import org.eclipse.eavp.viz.modeling.factory.IControllerProviderFactory;
 import org.eclipse.eavp.viz.modeling.properties.MeshCategory;
 import org.eclipse.eavp.viz.modeling.properties.MeshProperty;
 import org.eclipse.eavp.viz.modeling.VertexController;
+import org.eclipse.eavp.viz.modeling.base.IController;
 import org.eclipse.eavp.viz.modeling.Vertex;
 import org.eclipse.eavp.viz.service.mesh.datastructures.BoundaryCondition;
 import org.eclipse.eavp.viz.service.mesh.datastructures.BoundaryConditionType;
@@ -840,6 +841,7 @@ public class NekReader {
 						}
 
 						quad.setPolygonProperties(materialId, groupNum);
+						
 
 						// Set the boundary conditions of the quad by edge ID
 						int currEdgeId;
@@ -906,6 +908,7 @@ public class NekReader {
 				}
 			}
 		}
+		
 
 		// Return the Mesh Component containing mesh elements/quads with a
 		// set of (2 + NPSCAL) boundary conditions associated to each edge
@@ -1560,7 +1563,7 @@ public class NekReader {
 		// If entry's value can only be T/F
 		if (isDiscrete) {
 			entry = new DiscreteEntry();
-			entry.setAllowedValues(Arrays.asList("no", "yes"));
+			entry.setAllowedValues(Arrays.asList("NO", "YES"));
 
 			entry.setName("Nek5000 Default Entry");
 			entry.setDescription("");

org.eclipse.ice.nek5000/src/org/eclipse/ice/nek5000/NekWriter.java

@@ -28,6 +28,7 @@ import java.util.HashMap;
 import org.eclipse.eavp.viz.modeling.base.IController;
 import org.eclipse.eavp.viz.modeling.properties.MeshCategory;
 import org.eclipse.eavp.viz.modeling.properties.MeshProperty;
+import org.eclipse.eavp.viz.modeling.EdgeController;
 import org.eclipse.eavp.viz.modeling.VertexController;
 import org.eclipse.eavp.viz.service.mesh.datastructures.BoundaryCondition;
 import org.eclipse.eavp.viz.service.mesh.datastructures.BoundaryConditionType;
@@ -401,7 +402,6 @@ public class NekWriter implements IComponentVisitor {
 		NekPolygonController currQuad;
 		IController currEdge;
 		int currEdgeId;
-		ArrayList<VertexController> currVertices = new ArrayList<VertexController>();
 		String currValue;
 
 		// String buffer used to construct the mesh data, as the MeshComponent
@@ -436,22 +436,11 @@ public class NekWriter implements IComponentVisitor {
 
 			/* --- Construct mesh elements --- */
 
-			// Check each descendent vertex. If it is not yet in the list of
-			// vertices, add it
-			for (IController entity : currQuad
-					.getEntitiesFromCategory(MeshCategory.EDGES)) {
-				for (VertexController v : entity.getEntitiesFromCategory(
-						MeshCategory.VERTICES, VertexController.class)) {
-					if (!currVertices.contains(v)) {
-						currVertices.add(v);
-					}
-				}
-			}
-
-			// Extract the x, y coordinates of the Quad's vertices
-			for (int k = 0; k < 4; k++) {
-				xCoords.add((float) currVertices.get(k).getTranslation()[0]);
-				yCoords.add((float) currVertices.get(k).getTranslation()[1]);
+			// Populate the lists of coordinates, in order, from the start points of the entity's edges.
+			for (EdgeController entity : currQuad
+					.getEntitiesFromCategory(MeshCategory.EDGES, EdgeController.class)) {
+				xCoords.add((float) entity.getStartLocation()[0]); 
+				yCoords.add((float) entity.getStartLocation()[1]); 
 			}
 
 			// Iterate through the Edges of the current Quad