Templates added to VIBE Key-Value Pair Item

The VIBE Key-Value Pair Item's Form now features a section to select a
template for either NTG or DualFoil problems, which will reset the table
to the correct format for that problem type.
Signed-off-by: Robert Smith <smithrw@ornl.gov>

org.eclipse.ice.vibe/data/DualFoil.conf

+BIN_DIR= $CAEBAT_ROOT/bin
+
+OUTPUT_PREFIX = 
+
+SIM_NAME = case10                                    # Name of current simulation
+SIM_ROOT =$CAEBAT_ROOT/../examples/$SIM_NAME  # Where to put results from this simulation
+
+PLASMA_STATE_WORK_DIR = $SIM_ROOT/work/battery_state # Where to put state files as the simulation evolves 
+
+CURRENT_STATE = cphit.cgns
+PRINT_DEBUG = 0
+
+RUN_COMMENT = Coupled CAEBAT Module simulation	     # A run comment picked up by the portal
+
+TAG = ElectroChemElectricalThermal                   # A tag that enables related runs to be retrieved together
+USER  = batsim                                          # Optional, if missing the unix username is used
+
+NUM_CCP_ZONES = 84 
+NUM_CCN_ZONES = 80
+NUM_CHARTRAN_ZONES = 136
+NUM_POUCH_ZONES = 8
+NUM_ZONES = 308
+
+PLASMA_STATE_FILES = $CURRENT_STATE 
+
+SIMULATION_MODE = NORMAL                             # Simulation mode 
+
+LOG_LEVEL = WARNING
+LOG_FILE = $SIM_ROOT/${SIM_NAME}.log
+
+[PORTS]
+   NAMES = INIT DRIVER CHARTRAN THERMAL
+   
+   [[DRIVER]]                                       # REQUIRED Port section 
+      IMPLEMENTATION = CHARTRAN_THERMAL_DRIVER
+                                                    
+                                                    # How is the simulation initialized 
+                                                    # (generate the very first state - if needed)
+   [[INIT]]                                         # REQUIRED Port section (check currently 
+      IMPLEMENTATION = INIT_STATE 
+     
+  [[THERMAL]]
+      IMPLEMENTATION = AMPERES_THERMAL 
+
+  [[CHARTRAN]]
+      IMPLEMENTATION = DUALFOIL 
+
+# Individual configuration sections
+
+# Component sepcification (entries similar for all components)
+# NAME entry MUST match the name of the python class that implements the component
+[INIT_STATE]
+    CLASS = DRIVERS
+    SUB_CLASS = 
+    NAME = InitialState
+    NPROC = 1
+    BIN_PATH = $CAEBAT_ROOT/bin
+    INPUT_DIR = 
+    INPUT_FILES = 
+    OUTPUT_FILES = $CURRENT_STATE
+    VARIABLES = 'lumped_source', 'lumped_temperature'
+    INIT_VALUES = '0.0', '298.0'
+    SCRIPT = $BIN_PATH/init_state.py
+
+[CHARTRAN_THERMAL_DRIVER]
+    CLASS = DRIVERS
+    SUB_CLASS = CHARTRAN_THERMAL
+    NAME = Driver
+    NPROC = 1
+    BIN_PATH = $CAEBAT_ROOT/bin
+    INPUT_DIR = 
+    INPUT_FILES =
+    OUTPUT_FILES = $CURRENT_STATE 
+    SCRIPT = $BIN_PATH/thermal_chartran_driver_n.py
+
+[AMPERES_THERMAL]
+    CLASS = THERMAL
+    SUB_CLASS = 
+    NAME = Amperes
+    NPROC = 1
+    BIN_PATH = $CAEBAT_ROOT/bin
+    INPUT_DIR = $SIM_ROOT/input
+    INPUT_FILES = 'input_keyvalue', 'FarasisModule_4P.e'
+    OUTPUT_FILES = $CURRENT_STATE
+    INPUT_VAR = 'lumped_source'
+    OUTPUT_VAR = 'lumped_temperature' 
+    SCRIPT = $BIN_PATH/amperes_thermal.py
+
+ [DUALFOIL]
+    CLASS = CHARTRAN
+    SUB_CLASS = 
+    NAME = DualFoil 
+    NPROC = 1
+    BIN_PATH = $CAEBAT_ROOT/bin
+    INPUT_DIR = $SIM_ROOT/input
+    INPUT_FILES = 'input_keyvalue', 'dualfoil5.in' , 'li-ion-ebar.in'
+    OUTPUT_FILES = 'df_caebat.out'
+    INPUT_VAR    = 'lumped_temperature'
+    OUTPUT_VAR   = 'lumped_source', 'lumped_resistance'
+    SCRIPT = $BIN_PATH/dualfoil_chartran.py
+   
+# Time loop sepecification (two modes for now) EXPLICIT | REGULAR
+# For MODE = REGULAR, the framework uses the variables START, FINISH, and NSTEP
+# For MODE = EXPLICIT, the frame work uses the variable VALUES (space separated list of time values)
+
+[TIME_LOOP]
+   MODE = EXPLICIT
+   START = 0.0
+   FINISH = 0.0
+   NSTEP  = 0
+   VALUES = 0.0 0.4 0.8 1.2 1.6

org.eclipse.ice.vibe/data/DualFoil.dat

+ELECTRICAL=1 
+XCONDUCTIVITY=3.07
+YCONDUCTIVITY=3.07
+ZCONDUCTIVITY=1.7899
+HEATCAPACITY=1100
+ICSHORT=0
+NUMBCS=2
+BCTYPE=1,1
+BCIDS=3,4
+AMBIENTTEMP=320,298 
+CONVECTIVERATE=15.0,55.0
+
+ICSHORT=0
+CurrentFlux=268750000.00 
+
+CRATE=1
+NUMSEG=5
+CURRDEN=0.0,30.0,0.0,-22.,0.
+MODESEG=1,1,0,1,0
+CUTOFFL=2.0,2.0,2.0,2.0,2.0
+CUTOFFH=4.3,4.3,4.3,4.3,4.3
+
+
+THICKNESS=135e-6
+YPolyCoefficients =3.6433e+02,-2.0629e+03,1.1248e+04,-2.8978e+04,4.0999e+04,-3.1353e+04,9.8589e+03
+UPolyCoefficients =4.1210,-1.0206,-1.1902,8.2938,-20.6735,24.8684,-11.0442
+YPolyDegrees =6,0
+UPolyDegrees =6,0

org.eclipse.ice.vibe/data/NTG.conf

+
+BIN_DIR = $CAEBAT_ROOT/bin
+OUTPUT_PREFIX = 
+RUN_ID = prismatic_cell_20141110060439
+SIM_NAME = case6
+SIM_ROOT = $CAEBAT_ROOT/../examples/${SIM_NAME}
+PLASMA_STATE_WORK_DIR = $SIM_ROOT/work/battery_state
+CURRENT_STATE = cphit.cgns
+RUN_COMMENT = A run comment picked up by the portal.
+TAG = ElectroChemElectricalThermal
+USER = <username>
+NUM_CHARTRAN_ZONES = 34
+NUM_CCP_ZONES = 19
+NUM_CCN_ZONES = 18
+NUM_ZONES = 73
+NUM_POUCH_ZONES = 2
+PLASMA_STATE_FILES = $CURRENT_STATE
+SIMULATION_MODE = NORMAL
+LOG_LEVEL = WARNING
+LOG_FILE = $SIM_ROOT/${SIM_NAME}.log
+PRINT_DEBUG = 0
+
+[PORTS]
+    NAMES = INIT DRIVER THERMAL ELECTRICAL CHARTRAN
+
+    [[INIT]]
+        IMPLEMENTATION = INIT_STATE
+    [[DRIVER]]
+        IMPLEMENTATION = CHARTRAN_ELECTRICAL_THERMAL_DRIVER
+    [[THERMAL]]
+        IMPLEMENTATION = AMPERES_THERMAL
+    [[ELECTRICAL]]
+        IMPLEMENTATION = AMPERES_ELECTRICAL
+    [[CHARTRAN]]
+        IMPLEMENTATION = NTG
+
+[CHARTRAN_ELECTRICAL_THERMAL_DRIVER]
+    CLASS = DRIVERS
+    SUB_CLASS = CHARTRAN_THERMAL
+    NAME = Driver
+    NPROC = 1
+    BIN_PATH = $CAEBAT_ROOT/bin
+    INPUT_DIR = $SIM_ROOT/
+    INPUT_FILES = 
+    OUTPUT_FILES = $CURRENT_STATE
+    SCRIPT = $BIN_PATH/thermal_electrical_chartran_driver_n.py
+
+[AMPERES_THERMAL]
+    CLASS = THERMAL
+    SUB_CLASS = 
+    NAME = Amperes
+    NPROC = 1
+    BIN_PATH = $CAEBAT_ROOT/bin
+    INPUT_DIR = $SIM_ROOT/input
+    INPUT_FILES = 'input_keyvalue','FarasisWSingleTab.e'
+    OUTPUT_FILES = $CURRENT_STATE
+    SCRIPT = $BIN_PATH/amperes_thermal.py
+    INPUT_VAR = 'lumped_source'
+    OUTPUT_VAR = 'lumped_temperature'
+[AMPERES_ELECTRICAL]
+    CLASS = ELECTRICAL
+    SUB_CLASS = 
+    NAME = Amperes
+    NPROC = 1
+    BIN_PATH = $CAEBAT_ROOT/bin
+    INPUT_DIR = $SIM_ROOT/input
+    INPUT_FILES = 'input_keyvalue','FarasisWSingleTab.e'
+    OUTPUT_FILES = $CURRENT_STATE
+    SCRIPT = $BIN_PATH/amperes_electrical.py
+    INPUT_VAR = 'lumped_resistance'
+    OUTPUT_VAR = 'lumped_source'
+
+[NTG]
+    CLASS = CHARTAN
+    SUB_CLASS = 
+    NAME = NTG
+    NPROC = 1
+    BIN_PATH = $CAEBAT_ROOT/bin
+    INPUT_DIR = $SIM_ROOT/input
+    INPUT_FILES = 'input_keyvalue'
+    OUTPUT_FILES = $CURRENT_STATE
+    SCRIPT = $BIN_PATH/ntg_chartran.py
+    INPUT_VAR = 'lumped_temperature'
+    OUTPUT_VAR = 'lumped_source','lumped_resistance'
+
+[INIT_STATE]
+    CLASS = DRIVERS
+    SUB_CLASS = 
+    NAME = InitialState
+    NPROC = 1
+    BIN_PATH = $CAEBAT_ROOT/bin
+    INPUT_DIR = $SIM_ROOT/
+    INPUT_FILES = 
+    OUTPUT_FILES = $CURRENT_STATE
+    SCRIPT = $BIN_PATH/init_state.py
+    VARIABLES = 'lumped_source', 'lumped_resistance', 'lumped_temperature'
+    INIT_VALUES = '0.0', '0.0', '298.'
+
+
+[TIME_LOOP]
+    MODE = REGULAR
+    START = 0.0
+    FINISH = 10.0
+    NSTEP = 3
+    VALUES = 0.1 0.2 0.3 0.4 0.5 0.6 1.5 3.5 6.5 8.5 8.6 8.7 8.8 8.9 9.0 9.1 9.2 9.3 9.4 9.5
+    

org.eclipse.ice.vibe/data/NTG.dat

+ELECTRICAL=1 
+XCONDUCTIVITY=1.7899
+YCONDUCTIVITY=1.7899
+ZCONDUCTIVITY=1.7899
+HEATCAPACITY=1100
+ICSHORT=0
+NUMBCS=6
+BCTYPE=1,1,2,2,1,1
+BCIDS=3,4,5,6,7,8
+AMBIENTTEMP=300,300,298,328,300,300 
+CONVECTIVERATE=0.0,0.0,5.0,5.0,1.0,1.0
+
+ICSHORT=0
+CurrentFlux=3602431. 
+
+CRATE=5
+CURRDEN=79.26 
+CUTOFF=2.8
+THICKNESS=135e-6
+YPolyCoefficients = 3.6433e+02, -2.0629e+03, 1.1248e+04, -2.8978e+04, 4.0999e+04, -3.1353e+04, 9.8589e+03
+UPolyCoefficients = 4.1210, -1.0206, -1.1902, 8.2938, -20.6735, 24.8684, -11.0442
+YPolyDegrees = 6, 0 
+UPolyDegrees = 6, 0 

org.eclipse.ice.vibe/src/org/eclipse/ice/vibe/kvPair/VibeKVPair.java

@@ -37,8 +37,11 @@ import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.core.runtime.Path;
 import org.eclipse.ice.datastructures.ICEObject.Component;
+import org.eclipse.ice.datastructures.ICEObject.IUpdateable;
+import org.eclipse.ice.datastructures.entry.DiscreteEntry;
 import org.eclipse.ice.datastructures.entry.IEntry;
 import org.eclipse.ice.datastructures.entry.StringEntry;
+import org.eclipse.ice.datastructures.form.DataComponent;
 import org.eclipse.ice.datastructures.form.Form;
 import org.eclipse.ice.datastructures.form.FormStatus;
 import org.eclipse.ice.datastructures.form.TableComponent;
@@ -52,27 +55,51 @@ import org.eclipse.ice.item.Item;
  * This class is a Model Item that configures a set of data components that
  * represent key-value pairs for VIBE input.
  * 
- * @author Jay Jay Billings, Andrew Bennett
+ * @author Jay Jay Billings, Andrew Bennett, Robert Smith
  * 
  */
 @XmlRootElement(name = "VibeKVPair")
 public class VibeKVPair extends Item implements IReader, IWriter {
 
+	/**
+	 * The index for the template component in the list of components.
+	 */
+	private static final int TEMPLATE_COMPONENT_ID = 0;
+
 	/**
 	 * Keep track of everything that we can do with the KV Pair Item
 	 */
 	private ArrayList<String> actionItems;
 
+	/**
+	 * The name of the default template to load.
+	 */
+	private static String defaultTemplate = "NTG";
+
 	/**
 	 * The tag that indicates this file should be exported to kv pairs.
 	 */
 	private String customTaggedExportString = "Export to key-value pair output";
 
+	/**
+	 * The component for the table of editable key value pairs.
+	 */
+	TableComponent kvTable;
+
+	/**
+	 * The name of the last template used to initialize the table component.
+	 */
+	private String templateName;
+
 	/**
 	 * The nullary constructor.
 	 */
 	public VibeKVPair() {
 		this(null);
+
+		// Initialize the template name
+		templateName = defaultTemplate;
+
 		return;
 	}
 
@@ -85,9 +112,60 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 	public VibeKVPair(IProject projectSpace) {
 		// Punt to the base class.
 		super(projectSpace);
+
+		// Initialize the template name
+		templateName = defaultTemplate;
 		return;
 	}
 
+	/**
+	 * This operation returns a data component that contains the list of
+	 * reafiles that may be selected by a user from the Nek5000_Model_Builder
+	 * directory. This component will be empty if there are no files and contain
+	 * an Entry that says "No problems available."
+	 *
+	 * @param files
+	 *            The set of Nek reafiles available to be loaded
+	 * @return the data component
+	 */
+	private DataComponent createSelectorComponent() {
+
+		// Local Declaration
+		DataComponent caseComp = new DataComponent();
+
+		// The list of available templates
+		ArrayList<String> templateNames = new ArrayList<String>();
+		templateNames.add("NTG");
+		templateNames.add("DualFoil");
+
+		// Setup the data component
+		caseComp.setName("Problem Type Templates");
+		caseComp.setDescription("The following is a list of VIBE Key-Value "
+				+ "Pair input type templates for editing.");
+		caseComp.setId(0);
+
+		// Create an Entry for the template names
+		DiscreteEntry templatesEntry = new DiscreteEntry();
+		templatesEntry.setAllowedValues(templateNames);
+		templatesEntry.setDefaultValue(defaultTemplate);
+		templatesEntry.setValue(defaultTemplate);
+
+		// Setup the file Entry's descriptive information
+		templatesEntry.setName("Available Templates");
+		templatesEntry.setDescription("A list of the templates available "
+				+ "for populating the VIBE Key-Value Pair table component");
+		templatesEntry.setId(1);
+
+		// Add the Entry to the Component
+		caseComp.addEntry(templatesEntry);
+
+		// Register this Item as a listener of templatesEntry
+		templatesEntry.register(this);
+
+		return caseComp;
+
+	}
+
 	/**
 	 * This operation overrides the base class' operation to create a Form with
 	 * Entries that will be used to generate the VIBEkey-value pair file. It has
@@ -98,10 +176,13 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 		// Create the form
 		form = new Form();
 
+		// Add the template selector component
+		form.addComponent(createSelectorComponent());
+
 		// If loading from the new item button we should just
 		// load up the default case 6 file by passing in null
 		if (project != null) {
-			loadDefault();
+			loadDefault(defaultTemplate);
 		}
 	}
 
@@ -153,6 +234,12 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 					+ "Could not find any data to write out");
 			retStatus = FormStatus.InfoError;
 		}
+
+		// Get the selection from the template component
+		DataComponent templateComp = (DataComponent) components
+				.get(TEMPLATE_COMPONENT_ID);
+		String template = templateComp.retrieveAllEntries().get(0).getValue();
+
 		return retStatus;
 	}
 
@@ -203,7 +290,7 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 					// Complain
 					System.err.println("VibeKVPair Generator Message: "
 							+ "Failed to refresh the project space.");
-					logger.error(getClass().getName() + " Exception!",e);
+					logger.error(getClass().getName() + " Exception!", e);
 				}
 				// return a success
 				retStatus = FormStatus.Processed;
@@ -233,7 +320,8 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 	@Override
 	public void loadInput(String name) {
 		IFile inputFile = inputFile = project.getFile(name);
-		logger.info("VibeKVPair Message: Loading" + inputFile.getFullPath().toOSString());
+		logger.info("VibeKVPair Message: Loading"
+				+ inputFile.getFullPath().toOSString());
 		form = read(inputFile);
 		form.setName(getName());
 		form.setDescription(getDescription());
@@ -244,8 +332,12 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 
 	/**
 	 * Loads a default dataset that's embedded in the plugin
+	 * 
+	 * @param caseName
+	 *            The name of the file containing the default case that will be
+	 *            used to populate the table
 	 */
-	public void loadDefault() {
+	public void loadDefault(String caseName) {
 		IFile inputFile = null;
 		File temp = null;
 		try {
@@ -254,13 +346,13 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 			// Create a filepath for the default file
 			if (project != null) {
 				defaultFilePath = project.getLocation().toOSString()
-						+ System.getProperty("file.separator")
-						+ "case_6.dat";
+						+ System.getProperty("file.separator") + caseName
+						+ ".dat";
 			} else {
 				defaultFilePath = ResourcesPlugin.getWorkspace().getRoot()
 						.getLocation().toOSString()
-						+ System.getProperty("file.separator")
-						+ "case_6.dat";
+						+ System.getProperty("file.separator") + caseName
+						+ ".dat";
 			}
 
 			// Create a temporary location to load the default file
@@ -270,8 +362,8 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 			}
 
 			// Pull the default file from inside the plugin
-			URI uri = new URI(
-					"platform:/plugin/org.eclipse.ice.vibe/data/case_6.dat");
+			URI uri = new URI("platform:/plugin/org.eclipse.ice.vibe/data/"
+					+ caseName + ".dat");
 			InputStream reader = uri.toURL().openStream();
 			FileOutputStream outStream = new FileOutputStream(temp);
 
@@ -283,13 +375,15 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 			}
 			outStream.close();
 			if (project != null) {
-				inputFile = project.getFile("case_6.dat");
+				inputFile = project.getFile(caseName + ".dat");
 				project.refreshLocal(IResource.DEPTH_INFINITE, null);
 			} else {
 				inputFile = ResourcesPlugin.getWorkspace().getRoot()
 						.getFile(new Path(defaultFilePath));
 			}
-			logger.info("VibeKVPair Message: Loading" + inputFile.getFullPath().toOSString());
+			logger.info("VibeKVPair Message: Loading"
+					+ inputFile.getFullPath().toOSString());
+
 			form = read(inputFile);
 			form.setName(getName());
 			form.setDescription(getDescription());
@@ -310,10 +404,10 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 					+ " Vibe case data!");
 		} catch (CoreException e) {
 			// TODO Auto-generated catch block
-			logger.error(getClass().getName() + " Exception!",e);
+			logger.error(getClass().getName() + " Exception!", e);
 		}
 	}
-	
+
 	/**
 	 * Reads in the KV Pair file to a form.
 	 * 
@@ -328,14 +422,18 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 		if (ifile == null) {
 			return null;
 		}
-		Form form = new Form();
+
+		// Initialize the form if it does not exist
+		if (form == null) {
+			form = new Form();
+		}
 
 		// Read in the ini file to an ArrayList<String>
 		ArrayList<String> lines = new ArrayList<String>();
 		BufferedReader reader = null;
 		try {
-			reader = new BufferedReader(new InputStreamReader(
-					ifile.getContents()));
+			reader = new BufferedReader(
+					new InputStreamReader(ifile.getContents()));
 
 			// Read the FileInputStream and append to a StringBuffer
 			StringBuffer buffer = new StringBuffer();
@@ -358,8 +456,8 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 					+ "Error! Could not find file for loading.");
 			return null;
 		} catch (IOException e) {
-			logger.error("VibeKVPair Message: "
-					+ "Error! Trouble reading file.");
+			logger.error(
+					"VibeKVPair Message: " + "Error! Trouble reading file.");
 			return null;
 		} catch (CoreException e) {
 			logger.error("VibeKVPair Message: "
@@ -367,8 +465,14 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 			return null;
 		}
 
-		//
-		TableComponent kvTable = new TableComponent();
+		// Create the table if it doesn't exist or empty it if it does
+		if (kvTable == null) {
+			kvTable = new TableComponent();
+		} else {
+			for (int i : kvTable.getRowIds()) {
+				kvTable.deleteRow(0);
+			}
+		}
 		ArrayList<IEntry> row;
 		ArrayList<IEntry> kvEntries = new ArrayList<IEntry>();
 		IEntry key = new StringEntry();
@@ -379,16 +483,145 @@ public class VibeKVPair extends Item implements IReader, IWriter {
 		kvEntries.add(value);
 		kvTable.setRowTemplate(kvEntries);
 
+		// The list of keys whose rows will be dependent on another row
+		ArrayList<String> dependentKeys = new ArrayList<String>();
+		dependentKeys.add("MODESEG");
+		dependentKeys.add("CUTOFFL");
+		dependentKeys.add("CUTOFFH");
+
+		// The list of rows dependent on another row
+		ArrayList<VibeKVPairRow> dependentRows = new ArrayList<VibeKVPairRow>();
+
+		// The row for the NUMSEG key
+		VibeKVPairRow numsegRow = null;
+
 		for (String line : lines) {
 			if (line.contains("=")) {
 				String[] keyValue = line.split("=");
 				int rowID = kvTable.addRow();
 				row = kvTable.getRow(rowID);
-				row.get(0).setValue(keyValue[0]);
-				row.get(1).setValue(keyValue[1]);
+
+				// The new row under construction
+				VibeKVPairRow entryRow = null;
+
+				// For most keys, create a standard row
+				if (!dependentKeys.contains(keyValue[0])) {
+
+					entryRow = new VibeKVPairRow((StringEntry) row.get(0),
+							(StringEntry) row.get(1));
+
+					if ("NUMSEG".equals(keyValue[0])) {
+						numsegRow = entryRow;
+
+						// The prescence of NUMSEG means that this is a DualFoil
+						// problem. We must set the template name appropriately,
+						// in case this function was invoked by importing a
+						// key-value file directly.
+						templateName = "DualFoil";
+						((DataComponent) form
+								.getComponent(TEMPLATE_COMPONENT_ID))
+										.retrieveAllEntries().get(0)
+										.setValue("DualFoil");
+					}
+				}
+
+				else {
+
+					// TODO If we ever want to create more complex relationships
+					// between rows,