fstonedahl · fstonedahl · Jul 28, 2017 · Jul 28, 2017 · Jul 30, 2017 · Aug 2, 2017
diff --git a/.classpath b/.classpath
@@ -13,5 +13,7 @@
 	<classpathentry kind="lib" path="/home/forrest/.ivy2/cache/org.ow2.asm/asm-all/jars/asm-all-5.0.4.jar"/>
 	<classpathentry kind="lib" path="/home/forrest/.ivy2/cache/com.novocode/junit-interface/jars/junit-interface-0.11.jar"/>
 	<classpathentry kind="lib" path="/home/forrest/.ivy2/cache/org.scala-lang.modules/scala-parser-combinators_2.12/bundles/scala-parser-combinators_2.12-1.0.4.jar"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/MOEAFramework"/>
+	<classpathentry kind="lib" path="/home/forrest/.ivy2/cache/com.google.code.gson/gson/jars/gson-1.7.1.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,6 @@
+*tmp.nlogo
+
 /bin/
 target/
 /test/tmp
+/test/tmptmp
diff --git a/CREDITS.TXT b/CREDITS.TXT
@@ -1,4 +1,4 @@
-Copyright 2013 Forrest Stonedahl & Uri Wilensky
+Copyright 2013-2017 Forrest Stonedahl & Uri Wilensky
 
 The BehaviorSearch software was initially developed as part of Forrest Stonedahl's doctoral thesis research, with adviser Uri Wilensky at the Center for Connected Learning and Computer-Based Modeling at Northwestern University.
 It is an open source project, and new contributors/developers are welcome (contact feedback@behaviorsearch.org if interested).

diff --git a/build.sbt b/build.sbt
@@ -18,7 +18,11 @@ libraryDependencies ++= Seq(
   "org.scala-lang.modules" %% "scala-parser-combinators" % "1.0.4",
   "org.ow2.asm" % "asm-all" % "5.0.4",
   "org.parboiled" %% "parboiled" % "2.1.3",
-  "com.novocode" % "junit-interface" % "0.11" % "test"
+  "com.novocode" % "junit-interface" % "0.11" % "test",
+  "com.google.code.gson" % "gson" % "1.7.1"
+// libraryDependencies += "org.moeaframework" % "moeaframework" % "2.12"
+// PROBLEM: MOEA 2.12 isn't good enough, since I need my custom contributions (already merged to master, but not released) 
+
 )
 
 libraryDependencies ++= {

diff --git a/documentation/tutorialFx.html b/documentation/tutorialFx.html
@@ -9,6 +9,28 @@
 	<title>BehaviorSearch Documentation</title>
 </head>
 
+
+<!--MULTI-OBJ NOTES:
+* Need to document:
+
+measureIf can either be Netlogo reporter OR the special value "@DONE"
+
+
+ Raw (step-by-step) measures are collected throughout the simulation run 
+ (although you can use the measureIf condition to only collect a subset, which may be faster and more memory-efficient)
+ all turtles are cleared (necessary for technical reasons), and single run condensers get evaluated
+ with the outputs from the raw  measures (which are LISTS -- although note that they might contain 0 or 1 data elements).  
+ The condensing is done in your model workspace, so you can use custom procedures that you wrote)...)
+ Combining across runs happens in one of the workspaces where your model has been loaded, but you should not assume
+ anything about the model state (e.g. that it is at the end of a run, etc)...
+
+ The condensed or combined results should ONLY consist of lists or primitive data (numbers, strings), 
+ not agents or any of the more complex data types (arrays, tables, etc)  
+
+ -->
+
+
+
 <body>
 <div id="container">
 	<div id="header">

diff --git a/examples/Example_Fire_Burn_Variance.bsearch2 b/examples/Example_Fire_Burn_Variance.bsearch2
@@ -0,0 +1,43 @@
+{
+  "bsearchVersionNumber": 2.0,
+  "infoTab": "Write notes here...",
+  "modelDCInfo": {
+    "modelFileName": "../../models/Sample Models/Earth Science/Fire.nlogo",
+    "setupCommands": "setup",
+    "stepCommands": "go",
+    "stopCondition": "not any? turtles",
+    "measureIfReporter": "@DONE",
+    "maxModelSteps": 10000,
+    "rawMeasureReporters": {
+      "RAW1": "(burned-trees / initial-trees) * 100"
+    },
+    "singleRunCondenserReporters": {
+      "CONDENSED1": "last @{RAW1}"
+    },
+    "fitnessSamplingReplications": 5,
+    "bestCheckingNumReplications": 20
+  },
+  "paramSpecStrings": [
+    "[\"density\" [1 \"C\" 99]]"
+  ],
+  "objectives": [
+    {
+      "name": "objective1",
+      "objectiveType": "MAXIMIZE",
+      "fitnessCombineReplications": "standard-deviation @{CONDENSED1}",
+      "fitnessDerivativeParameter": "",
+      "fitnessDerivativeDelta": 0.0,
+      "fitnessDerivativeUseAbs": false
+    }
+  ],
+  "searchAlgorithmInfo": {
+    "searchMethodType": "MutationHillClimber",
+    "searchMethodParams": {
+      "mutation-rate": "1.0",
+      "restart-after-stall-count": "0"
+    },
+    "chromosomeType": "MixedTypeChromosome",
+    "caching": false,
+    "evaluationLimit": 500
+  }
+}
diff --git a/examples/Example_Fire_Derivative.bsearch2 b/examples/Example_Fire_Derivative.bsearch2
@@ -0,0 +1,43 @@
+{
+  "bsearchVersionNumber": 2.0,
+  "infoTab": "Write notes here...",
+  "modelDCInfo": {
+    "modelFileName": "../../models/Sample Models/Earth Science/Fire.nlogo",
+    "setupCommands": "setup",
+    "stepCommands": "go",
+    "stopCondition": "not any? turtles",
+    "measureIfReporter": "@DONE",
+    "maxModelSteps": 10000,
+    "rawMeasureReporters": {
+      "RAW1": "(burned-trees / initial-trees) * 100"
+    },
+    "singleRunCondenserReporters": {
+      "CONDENSED1": "last @{RAW1}"
+    },
+    "fitnessSamplingReplications": 2,
+    "bestCheckingNumReplications": 4
+  },
+  "paramSpecStrings": [
+    "[\"density\" [2 \"C\" 99]]"
+  ],
+  "objectives": [
+    {
+      "name": "objective1",
+      "objectiveType": "MAXIMIZE",
+      "fitnessCombineReplications": "mean @{CONDENSED1}",
+      "fitnessDerivativeParameter": "density",
+      "fitnessDerivativeDelta": 1.0,
+      "fitnessDerivativeUseAbs": false
+    }
+  ],
+  "searchAlgorithmInfo": {
+    "searchMethodType": "MutationHillClimber",
+    "searchMethodParams": {
+      "mutation-rate": "1.0",
+      "restart-after-stall-count": "0"
+    },
+    "chromosomeType": "MixedTypeChromosome",
+    "caching": false,
+    "evaluationLimit": 600
+  }
+}
diff --git a/examples/Example_Flocking_Convergence.bsearch2 b/examples/Example_Flocking_Convergence.bsearch2
@@ -0,0 +1,51 @@
+{
+  "bsearchVersionNumber": 2.0,
+  "infoTab": "Write notes here...",
+  "modelDCInfo": {
+    "modelFileName": "../../models/Sample Models/Biology/Flocking.nlogo",
+    "setupCommands": "setup",
+    "stepCommands": "go",
+    "stopCondition": "",
+    "measureIfReporter": "ticks >= 75",
+    "maxModelSteps": 100,
+    "rawMeasureReporters": {
+      "RAW1": "standard-deviation [dx] of turtles + standard-deviation [dy] of turtles"
+    },
+    "singleRunCondenserReporters": {
+      "CONDENSED1": "mean @{RAW1}"
+    },
+    "fitnessSamplingReplications": 5,
+    "bestCheckingNumReplications": 10
+  },
+  "paramSpecStrings": [
+    "[\"population\" 50]",
+    "[\"vision\" [0 0.25 10]]",
+    "[\"minimum-separation\" [0 0.25 5]]",
+    "[\"max-align-turn\" [0 0.25 20]]",
+    "[\"max-separate-turn\" [0 0.25 20]]",
+    "[\"max-cohere-turn\" [0 0.25 20]]"
+  ],
+  "objectives": [
+    {
+      "name": "objective1",
+      "objectiveType": "MINIMIZE",
+      "fitnessCombineReplications": "mean @{CONDENSED1}",
+      "fitnessDerivativeParameter": "",
+      "fitnessDerivativeDelta": 0.0,
+      "fitnessDerivativeUseAbs": false
+    }
+  ],
+  "searchAlgorithmInfo": {
+    "searchMethodType": "StandardGA",
+    "searchMethodParams": {
+      "mutation-rate": "0.05",
+      "population-size": "30",
+      "crossover-rate": "0.7",
+      "population-model": "generational",
+      "tournament-size": "3"
+    },
+    "chromosomeType": "GrayBinaryChromosome",
+    "caching": true,
+    "evaluationLimit": 12000
+  }
+}
diff --git a/mySearchOutput.bestHistory.csv b/mySearchOutput.bestHistory.csv
diff --git a/mySearchOutput.finalBests.csv b/mySearchOutput.finalBests.csv
diff --git a/mySearchOutput.modelRunHistory.csv b/mySearchOutput.modelRunHistory.csv
diff --git a/mySearchOutput.objectiveFunctionHistory.csv b/mySearchOutput.objectiveFunctionHistory.csv
diff --git a/mySearchOutput.searchConfig.xml b/mySearchOutput.searchConfig.xml
diff --git a/resources/SearchMethodList.txt b/resources/SearchMethodList.txt
@@ -1,5 +1,17 @@
+-- Legacy single-objective --
 RandomSearch
 SimulatedAnnealing
 MutationHillClimber
 StandardGA
 
+-- Single objective from MOEA --
+Random
+GA
+
+-- Multi-objective from MOEA --
+DBEA
+SPEA2
+NSGA-II
+NSGA-III
+e-NSGA-II
+eMOEA
diff --git a/src/bsearch/MOEAlink/BSProblem.java b/src/bsearch/MOEAlink/BSProblem.java
@@ -0,0 +1,70 @@
+package bsearch.MOEAlink;
+
+import java.util.List;
+
+import org.moeaframework.core.Solution;
+import org.moeaframework.core.Variable;
+import org.moeaframework.problem.AbstractProblem;
+import org.moeaframework.util.distributed.FutureSolution;
+import org.nlogo.api.MersenneTwisterFast;
+
+import bsearch.app.BehaviorSearchException;
+import bsearch.datamodel.SearchProtocolInfo;
+import bsearch.evaluation.SearchManager;
+import bsearch.space.SearchSpace;
+
+public class BSProblem extends AbstractProblem {
+	private SearchProtocolInfo protocol;
+	private SearchSpace space;
+	private SearchManager searchManager; 
+	private long evaluationRequestCounter = 0; 
+	private int uncorrelatedSearchSeed;
+
+	public BSProblem(SearchProtocolInfo protocol, SearchManager searchManager, int searchSeed) {
+		super(protocol.paramSpecStrings.size(), protocol.objectives.size());
+		this.protocol = protocol;
+		this.searchManager = searchManager;
+		this.space = new SearchSpace(protocol.paramSpecStrings);
+		// we choose a seed that is deterministically derived from the search seed,
+		// but is not correlated with it, so that we don't get the same NetLogo model
+		// runs for searches numbered N and N+1. 
+		this.uncorrelatedSearchSeed = new MersenneTwisterFast(searchSeed).nextInt();
+	}
+
+	@Override
+	public void evaluate(Solution solution) {
+
+		MOEASolutionWrapper solWrapper = new MOEASolutionWrapper(solution, space, protocol.objectives);
+//		int rand; 
+//		synchronized (otherRng) {
+//			rand = otherRng.nextInt();
+//			GeneralUtils.debug(rand + solWrapper.getParameterSettings().toString());
+//		}
+		long evaluationCount;
+		if (solution instanceof FutureSolution) {
+			evaluationCount = ((FutureSolution) solution).getDistributedEvaluationID();
+		} else {
+			// we must be running single threaded, so no need to synchronize to avoid race condition
+			evaluationCount = evaluationRequestCounter++; 
+		}
+//		GeneralUtils.debug(evaluationCount + ": " + solWrapper.getParameterSettings().toString().hashCode());
+
+		MersenneTwisterFast rng = new MersenneTwisterFast(uncorrelatedSearchSeed + evaluationCount);
+		try {
+			//TODO: Pass evaluationCount into computeFitnessSingle, so we can use that for getting perfectly replicable output?
+			searchManager.computeFitnessSingle(solWrapper, protocol.modelDCInfo.fitnessSamplingReplications, rng);
+		} catch (BehaviorSearchException e) {
+			e.printStackTrace();
+		}
+	}
+
+	@Override
+	public Solution newSolution() {
+		List<Variable> vars = space.getMOEAVariables();
+		Solution solution = new Solution(this.numberOfVariables, this.numberOfObjectives);
+		for (int i = 0; i < vars.size(); i++) {
+			solution.setVariable(i, vars.get(i));
+		}
+		return solution;
+	}
+}