146 openfoam example

.gitignore

@@ -10,3 +10,4 @@ opendaTestReports/
 **/MANIFEST.MF
 **/tests/*.log
 OpenDATimings_*.txt
+*.*~

.travis.yml

@@ -4,7 +4,6 @@ sudo: required
 
 jdk:
   - openjdk11
-  - oraclejdk11
 
 before_install:
   - sudo apt-get update
@@ -18,7 +17,7 @@ before_install:
 
 
 install: ./travis_install.sh
-script: ./travis_test.sh 
+script: ./travis_test.sh
 
 #after_script:
 #  - java -cp ~/codacy-coverage-reporter-assembly-latest.jar com.codacy.CodacyCoverageReporter -l Java -r build/reports/jacoco/test/jacocoTestReport.xml

algorithms/java/algorithms.iml

@@ -17,24 +17,6 @@
     <orderEntry type="module" module-name="core" />
     <orderEntry type="module" module-name="models" />
     <orderEntry type="module" module-name="observers" />
-    <orderEntry type="module-library">
-      <library>
-        <CLASSES>
-          <root url="jar://$MODULE_DIR$/../../core/java/resources/xom/xom-1.2.6.jar!/" />
-        </CLASSES>
-        <JAVADOC />
-        <SOURCES />
-      </library>
-    </orderEntry>
-    <orderEntry type="module-library">
-      <library>
-        <CLASSES>
-          <root url="jar://$MODULE_DIR$/../../core/java/resources/junit/junit-3.8.2.jar!/" />
-        </CLASSES>
-        <JAVADOC />
-        <SOURCES />
-      </library>
-    </orderEntry>
     <orderEntry type="module-library">
       <library>
         <CLASSES>
@@ -53,5 +35,6 @@
         <SOURCES />
       </library>
     </orderEntry>
+    <orderEntry type="library" name="CoreResources" level="project" />
   </component>
 </module>

algorithms/java/src/org/openda/algorithms/AbsoluteAveragePerLocationStopCriterion.java

@@ -18,7 +18,7 @@
 * along with OpenDA.  If not, see <http://www.gnu.org/licenses/>.
 */
 package org.openda.algorithms;
-import org.openda.interfaces.IPrevExchangeItem;
+import org.openda.interfaces.IExchangeItem;
 import org.openda.interfaces.IObservationDescriptions;
 import org.openda.interfaces.IVector;
 
@@ -72,17 +72,16 @@ public boolean checkForStop(IVector parameters, IVector residuals, double cost,
     public boolean checkForStop(IVector parameters, IVector residuals, IObservationDescriptions descriptions, double cost, double threshold) {
         boolean isStop = false;
         this.threshold = threshold;
-        List<IPrevExchangeItem> items = descriptions.getExchangeItems();
+        List<IExchangeItem> items = descriptions.getExchangeItems();
         this.nLoc = items.size();
         this.isSatisfied = new boolean[this.nLoc];
         this.Ids = new String[this.nLoc];
         int indFirst = 0;
         int indLast = 0;
         double absAvg = 0.0;
         double maxAbsAvg = Double.NEGATIVE_INFINITY;
-//        for(IPrevExchangeItem item : items){ // assume the exchangeItems are in the
         for (int i=0; i<nLoc; i++) {
-            IPrevExchangeItem item = items.get(i);
+            IExchangeItem item = items.get(i);
             String id = item.getId();
             this.Ids[i] = id.trim();
             int n = 1;

algorithms/java/src/org/openda/algorithms/BFGS.java

@@ -22,11 +22,10 @@
 package org.openda.algorithms;
 
 import org.openda.interfaces.*;
-import org.openda.utils.Results;
+import org.openda.utils.ConfigTree;
 import org.openda.utils.Instance;
-import org.openda.utils.Vector;
+import org.openda.utils.Results;
 import org.openda.utils.io.CalRestartSettings;
-import org.openda.utils.ConfigTree;
 
 import java.io.File;
 
@@ -44,7 +43,7 @@ public class BFGS extends Instance implements IAlgorithm {
 	private IStochModelFactory stochModelFactory;
     protected ConfigTree bfgsConf;
 
-    private IStochModelInstance bestEstimate = null;
+    protected IStochModelInstance bestEstimate = null;
 
     private SimulationKwadraticCostFunctionWithGradient J=null;
     private PreconditionedCostFunctionWithGradient Jc=null;

algorithms/java/src/org/openda/algorithms/BaseDudCoreOptimizer.java

@@ -72,6 +72,7 @@ public abstract class BaseDudCoreOptimizer {
 	public boolean add_constraints = false;
 	public String lower = null;
 	public String upper = null;
+	private double[] stdValues;
 
 	protected int numberOfSearchDirections() {
 		IStochVector parameterUncertainty = f.getParameterUncertainty();
@@ -1004,7 +1005,8 @@ void next() {
 
 			// now make this pretty for treeVectors
 			IVector stdWithStructure = pTry.clone();
-			stdWithStructure.setValues(std.getValues());
+			stdValues = std.getValues();
+			stdWithStructure.setValues(stdValues);
 			Results.putMessage("Error estimate for this outer iteration");
 			Results.putValue(	"parameterErrorEstimateStd", stdWithStructure, stdWithStructure.getSize(), 
 								"outer iteration "+imain, IResultWriter.OutputLevel.Verbose,
@@ -1141,5 +1143,9 @@ public IVector[] getPredCurrent() {
 		}
 		return result;
 	}
+
+	public double[] getStdValues() {
+		return stdValues;
+	}
 }
 

algorithms/java/src/org/openda/algorithms/ConjugateGradient.java

@@ -22,11 +22,10 @@
 package org.openda.algorithms;
 
 import org.openda.interfaces.*;
-import org.openda.utils.Results;
+import org.openda.utils.ConfigTree;
 import org.openda.utils.Instance;
-import org.openda.utils.Vector;
+import org.openda.utils.Results;
 import org.openda.utils.io.CalRestartSettings;
-import org.openda.utils.ConfigTree;
 
 import java.io.File;
 
@@ -44,7 +43,7 @@ public class ConjugateGradient extends Instance implements IAlgorithm {
     private IStochModelFactory stochModelFactory;
 	protected ConfigTree conjugateGradientConf;
 
-    private IStochModelInstance bestEstimate = null;
+    protected IStochModelInstance bestEstimate = null;
 
     private SimulationKwadraticCostFunctionWithGradient J=null;
     private PreconditionedCostFunctionWithGradient Jc=null;

algorithms/java/src/org/openda/algorithms/DischargeDependentFilter.java

@@ -18,7 +18,7 @@
 * along with OpenDA.  If not, see <http://www.gnu.org/licenses/>.
 */
 package org.openda.algorithms;
-import org.openda.interfaces.IPrevExchangeItem;
+import org.openda.interfaces.IExchangeItem;
 import org.openda.interfaces.IObservationDescriptions;
 import org.openda.interfaces.IStochObserver;
 import org.openda.observers.DischargeDependentSelector;
@@ -77,13 +77,13 @@ public ObservationSpace applyFilter(ObservationSpace input) {
 
 	private void stopIfNoSelectedData(IStochObserver observer) {
         IObservationDescriptions descr = observer.getObservationDescriptions();
-        List<IPrevExchangeItem> items;
+        List<IExchangeItem> items;
         try{
             items = descr.getExchangeItems();
         }catch (Exception e) {
-            items = new ArrayList<IPrevExchangeItem>(); //Empty list
+            items = new ArrayList<IExchangeItem>(); //Empty list
         }
-        for(IPrevExchangeItem item : items){ // assume the exchangeItems are in the
+        for(IExchangeItem item : items){ // assume the exchangeItems are in the
             String id = item.getId();
             double times[] = item.getTimes();
             if (times == null) {
@@ -143,11 +143,11 @@ public void initialize(File workingDir, String[] arguments) {
 	}
 
 	private void logObservationSpace(ObservationSpace observationSpace) throws IOException {
-		List<IPrevExchangeItem> observationItems =
+		List<IExchangeItem> observationItems =
 				observationSpace.observer.getObservationDescriptions().getExchangeItems();
 		String idLine = "obs.EI id's/size";
 		List<Double> obsValues = new ArrayList<Double>();
-		for	(IPrevExchangeItem exchangeItem : observationItems) {
+		for	(IExchangeItem exchangeItem : observationItems) {
 			double[] eiValues = exchangeItem.getValuesAsDoubles();
 			idLine += "," + exchangeItem.getId() + "=" + eiValues.length;
 			for (double eiValue : eiValues) {

algorithms/java/src/org/openda/algorithms/GLUE.java

@@ -39,7 +39,7 @@ public class GLUE extends Instance implements IAlgorithm {
 	private IStochModelFactory stochModelFactory;
     protected ConfigTree glueConf;
 
-    private IStochModelInstance bestEstimate = null;
+    protected IStochModelInstance bestEstimate = null;
     private IStochObserver stochObserver = null;
     private IVector pInit=null;
 

algorithms/java/src/org/openda/algorithms/GriddedFullSearch.java

@@ -40,7 +40,7 @@ public class GriddedFullSearch extends Instance implements IAlgorithm {
 	private IStochModelFactory stochModelFactory;
     protected ConfigTree gfsConf;
 
-    private IStochModelInstance bestEstimate = null;
+    protected IStochModelInstance bestEstimate = null;
     private IStochObserver stochObserver = null;
 
     private SimulationKwadraticCostFunction J=null;

algorithms/java/src/org/openda/algorithms/Powell.java

@@ -40,7 +40,7 @@ public class Powell extends Instance implements IAlgorithm {
 	private IStochModelFactory stochModelFactory;
     protected ConfigTree powellConf;
 
-    private IStochModelInstance bestEstimate = null;
+    protected IStochModelInstance bestEstimate = null;
 
     private SimulationKwadraticCostFunction J=null;
     private PowellCoreOptimizer powellOptimizer;

algorithms/java/src/org/openda/algorithms/RMSECostFunction.java

@@ -383,15 +383,15 @@ public double evaluate(IVector p, String context) {
 	private IVector removeBias(IStochObserver obsSelection, IVector lastPredicted) {
         IVector prd = lastPredicted.clone();
         IObservationDescriptions descr = obsSelection.getObservationDescriptions();
-        List<IPrevExchangeItem> items;
+        List<IExchangeItem> items;
         try{
-            items = (List<IPrevExchangeItem>) descr.getExchangeItems();
+            items = (List<IExchangeItem>) descr.getExchangeItems();
         }catch (Exception e) {
             throw new RuntimeException("No observation data is available.");
         }
         int firstIndex=0;
         int lastIndex;
-        for(IPrevExchangeItem item : items){
+        for(IExchangeItem item : items){
             String id = item.getId();
             double times[] = item.getTimes();
             if (times == null) {

algorithms/java/src/org/openda/algorithms/SCE.java

@@ -29,7 +29,6 @@
 import org.openda.utils.io.CalRestartSettings;
 
 import java.io.File;
-import java.util.ArrayList;
 import java.util.Random;
 
 
@@ -44,7 +43,7 @@ public class SCE extends Instance implements IAlgorithm {
 	private IStochModelFactory stochModelFactory;
     protected ConfigTree sceConf;
 
-    private IStochModelInstance bestEstimate = null;
+    protected IStochModelInstance bestEstimate = null;
     //config
     public double initStep=1.0; //scaling factor for initial perturbations of parameters
     //workspace

algorithms/java/src/org/openda/algorithms/Simplex.java

@@ -38,12 +38,12 @@ public class Simplex extends Instance implements IAlgorithm {
 	private IStochModelFactory stochModelFactory;
     protected ConfigTree simplexConf;
 
-    private IStochModelInstance bestEstimate = null;
+    protected IStochModelInstance bestEstimate = null;
     //config
     public double initStep=1.0; //scaling factor for initial perturbations of parameters
     //workspace
     private SimulationKwadraticCostFunction J=null;
-    private SimplexCoreOptimizer simplexOptimizer = null;
+    protected SimplexCoreOptimizer simplexOptimizer = null;
 
     private File workingDir=null;
     private String[] arguments=null;

algorithms/java/src/org/openda/algorithms/SimplexCoreOptimizer.java

@@ -58,9 +58,10 @@ public class SimplexCoreOptimizer{
 	//stopping
 	private boolean moreToDo = true;         // is this optimization finished
 	private int imain=0;                     // main iterations done
+	private double[] stdValues;
 
 
-    /**
+	/**
      * Constructor for Simplex minimization
      * @param f : cost function to be minimized
      */
@@ -475,7 +476,8 @@ void next(){
 					std.sqrt();
 					// now make this pretty for treeVectors
 					IVector stdWithStructure = this.pCurrent[0].clone();
-					stdWithStructure.setValues(std.getValues());
+					stdValues = std.getValues();
+					stdWithStructure.setValues(stdValues);
 					Results.putMessage("Error estimate for this outer iteration");
                     Results.putValue(	"parameterErrorEstimateStd", stdWithStructure, stdWithStructure.getSize(),
                                         "outer iteration "+imain, IResultWriter.OutputLevel.Verbose,
@@ -589,4 +591,7 @@ private IVector vectorSum(IVector[] vs){
 		return result;
 	}
 
+	public double[] getStdValues() {
+		return stdValues;
+	}
 }

algorithms/java/src/org/openda/algorithms/SimulationKwadraticCostFunction.java

@@ -462,13 +462,13 @@ private void logDebugInfo(String modelInstanceName, IStochObserver observationSe
 				// Add model instance identifier to evaluation
 				String message = "Evaluation:," + numberEvaluation + "," + modelInstanceName;
 				debugFileWriter.write(message + "\n");
-				List<IPrevExchangeItem> observationItems =
+				List<IExchangeItem> observationItems =
 						observationSelection.getObservationDescriptions().getExchangeItems();
 				debugFileWriter.write("obs.id's,size,startIndex\n");
 				List<Double> obsValues = new ArrayList<Double>();
 				List<Double> obsTimes = new ArrayList<Double>();
 				int startIndex = 1;
-				for	(IPrevExchangeItem exchangeItem : observationItems) {
+				for	(IExchangeItem exchangeItem : observationItems) {
 					double[] eiValues = exchangeItem.getValuesAsDoubles();
 					double[] eiTimes = exchangeItem.getTimes();
 					debugFileWriter.write(exchangeItem.getId() + "," + eiValues.length + "," + startIndex + "\n");
@@ -508,15 +508,15 @@ private void logDebugInfo(String modelInstanceName, IStochObserver observationSe
 	private IVector removeBias(IStochObserver obsSelection, IVector lastPredicted) {
         IVector prd = lastPredicted.clone();
         IObservationDescriptions descr = obsSelection.getObservationDescriptions();
-        List<IPrevExchangeItem> items;
+        List<IExchangeItem> items;
         try{
             items = descr.getExchangeItems();
         }catch (Exception e) {
             throw new RuntimeException("No observation data is available through the exchangeItems.");
         }
         int firstIndex=0;
         int lastIndex;
-        for(IPrevExchangeItem item : items){
+        for(IExchangeItem item : items){
             String id = item.getId();
             double times[] = item.getTimes();
             if (times == null) {
@@ -555,15 +555,15 @@ private IVector removeBias(IStochObserver obsSelection, IVector lastPredicted) {
 	private IVector removeStd(IStochObserver obsSelection, IVector lastPredicted) {
         IVector prd = lastPredicted.clone();
         IObservationDescriptions descr = obsSelection.getObservationDescriptions();
-        List<IPrevExchangeItem> items;
+        List<IExchangeItem> items;
         try{
             items = descr.getExchangeItems();
         }catch (Exception e) {
             throw new RuntimeException("No observation data is available through exchangeItems.");
         }
         int firstIndex=0;
         int lastIndex;
-        for(IPrevExchangeItem item : items){
+        for(IExchangeItem item : items){
             String id = item.getId();
             double times[] = item.getTimes();
             if (times == null) {

algorithms/java/src/org/openda/algorithms/SparseDud.java

@@ -66,7 +66,7 @@ private int[][] findNonZeros( boolean verbose) {
 		}
 
 		ConfigTree[] subTrees = configtree.getSubTrees("dependencies/obs");
-		List<IPrevExchangeItem> exchangeItems = stochObserver.getObservationDescriptions().getExchangeItems();
+		List<IExchangeItem> exchangeItems = stochObserver.getObservationDescriptions().getExchangeItems();
 		checkDependenciesForAllExchangeItems(subTrees, exchangeItems);
 
 		boolean[] allParsFound = new boolean[npar];
@@ -97,7 +97,7 @@ private int[][] findNonZeros( boolean verbose) {
 						if ( predFound==0) {
 							String allObservations="";
 							if (exchangeItems != null) {
-								for (IPrevExchangeItem exchangeItem : exchangeItems) {
+								for (IExchangeItem exchangeItem : exchangeItems) {
 									allObservations +=  "\t'" + exchangeItem.getId() + "'\n";
 								}
 							} else {
@@ -150,9 +150,9 @@ private void checkDependenciesForAllParameters(ArrayList<String> parameterNames,
 			throw new RuntimeException(parsNotFound + " parameter(s) found without any dependency");
 	}
 
-	private void checkDependenciesForAllExchangeItems(ConfigTree[] subTrees, List<IPrevExchangeItem> exchangeItems) {
+	private void checkDependenciesForAllExchangeItems(ConfigTree[] subTrees, List<IExchangeItem> exchangeItems) {
 		boolean anyExchangeItemNotFound = false;
-		for (IPrevExchangeItem exchangeItem : exchangeItems) {
+		for (IExchangeItem exchangeItem : exchangeItems) {
 			String exchangeItemId = exchangeItem.getId();
 			boolean exchangeItemFound = false;
 			for (ConfigTree subTree : subTrees) {

algorithms/java/src/org/openda/algorithms/kalmanFilter/EnKFSeq.java

@@ -142,7 +142,7 @@ private MinimalObservationDescriptions(double x, double y) {
 			this.y = y;
 		}
 
-		public List<IPrevExchangeItem> getExchangeItems() {
+		public List<IExchangeItem> getExchangeItems() {
 			throw new UnsupportedOperationException(getClass().getName() + ".getExchangeItems() not implemented.");
 		}