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+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>declaratron-top</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

File .settings/org.eclipse.m2e.core.prefs

+#Tue Jan 22 17:13:59 GMT 2013
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

File doc/SCS7.pdf

Binary file added.

File doc/amber8.pdf

Binary file added.
+
+==============================
+ATOMS
+==============================
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+ charge :        -0.2001
+ name :          C
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+}
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+ charge :        0.6230999983536656
+ name :          C1
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+}
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+}
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+}
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+}
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+}
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+}
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+}
+
+==============================
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+==============================
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+}
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+}
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+
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
+
+==============================
+ANGLES
+==============================
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+==============================
+DIHEDRALS
+==============================
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+}
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+}
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+}
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+}
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+}
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+}
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+ name :          H1
+ AMBERatomType : hc
+ x, y, z :       -3.974 -1.075 0.924
+}
+       Atom J: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        -0.2001
+ name :          C
+ AMBERatomType : c3
+ x, y, z :       -3.915 -0.493 0.0
+}
+       Atom K: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        0.6230999983536656
+ name :          C1
+ AMBERatomType : c
+ x, y, z :       -2.723 0.415 0.049
+}
+       Atom L: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.485
+ name :          O
+ AMBERatomType : o
+ x, y, z :       -2.788 1.633 0.083
+}
+ barrierHeight: 0.8
+ phase (radians): 0.0
+ periodicity: 1.0
+ current dihedral angle (degrees) -113.86435124481288
+ current potential contribution: (kcal/mol) 0.4763418636650807
+}
+name.mjw.mwmd.Dihedral Object {
+       Atom I: name.mjw.mwmd.Atom Object {
+ mass :          1.008
+ charge :        0.0687
+ name :          H1
+ AMBERatomType : hc
+ x, y, z :       -3.974 -1.075 0.924
+}
+       Atom J: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        -0.2001
+ name :          C
+ AMBERatomType : c3
+ x, y, z :       -3.915 -0.493 0.0
+}
+       Atom K: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        0.6230999983536656
+ name :          C1
+ AMBERatomType : c
+ x, y, z :       -2.723 0.415 0.049
+}
+       Atom L: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.485
+ name :          O
+ AMBERatomType : o
+ x, y, z :       -2.788 1.633 0.083
+}
+ barrierHeight: 0.0
+ phase (radians): 3.141594
+ periodicity: 2.0
+ current dihedral angle (degrees) -113.86435124481288
+ current potential contribution: (kcal/mol) 0.0
+}
+name.mjw.mwmd.Dihedral Object {
+       Atom I: name.mjw.mwmd.Atom Object {
+ mass :          1.008
+ charge :        0.0687
+ name :          H1
+ AMBERatomType : hc
+ x, y, z :       -3.974 -1.075 0.924
+}
+       Atom J: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        -0.2001
+ name :          C
+ AMBERatomType : c3
+ x, y, z :       -3.915 -0.493 0.0
+}
+       Atom K: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        0.6230999983536656
+ name :          C1
+ AMBERatomType : c
+ x, y, z :       -2.723 0.415 0.049
+}
+       Atom L: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.485
+ name :          O
+ AMBERatomType : o
+ x, y, z :       -2.788 1.633 0.083
+}
+ barrierHeight: 0.08
+ phase (radians): 3.141594
+ periodicity: 3.0
+ current dihedral angle (degrees) -113.86435124481288
+ current potential contribution: (kcal/mol) 0.004092947036576513
+}
+name.mjw.mwmd.Dihedral Object {
+       Atom I: name.mjw.mwmd.Atom Object {
+ mass :          1.008
+ charge :        0.0687
+ name :          H1
+ AMBERatomType : hc
+ x, y, z :       -3.974 -1.075 0.924
+}
+       Atom J: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        -0.2001
+ name :          C
+ AMBERatomType : c3
+ x, y, z :       -3.915 -0.493 0.0
+}
+       Atom K: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        0.6230999983536656
+ name :          C1
+ AMBERatomType : c
+ x, y, z :       -2.723 0.415 0.049
+}
+       Atom L: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.5840999983536654
+ name :          O1
+ AMBERatomType : oh
+ x, y, z :       -1.552 -0.259 0.065
+}
+ barrierHeight: 0.0
+ phase (radians): 3.141594
+ periodicity: 2.0
+ current dihedral angle (degrees) 65.53021495051607
+ current potential contribution: (kcal/mol) 0.0
+}
+name.mjw.mwmd.Dihedral Object {
+       Atom I: name.mjw.mwmd.Atom Object {
+ mass :          1.008
+ charge :        0.0687
+ name :          H2
+ AMBERatomType : hc
+ x, y, z :       -3.844 -1.154 -0.868
+}
+       Atom J: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        -0.2001
+ name :          C
+ AMBERatomType : c3
+ x, y, z :       -3.915 -0.493 0.0
+}
+       Atom K: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        0.6230999983536656
+ name :          C1
+ AMBERatomType : c
+ x, y, z :       -2.723 0.415 0.049
+}
+       Atom L: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.485
+ name :          O
+ AMBERatomType : o
+ x, y, z :       -2.788 1.633 0.083
+}
+ barrierHeight: 0.8
+ phase (radians): 0.0
+ periodicity: 1.0
+ current dihedral angle (degrees) 124.2528158915286
+ current potential contribution: (kcal/mol) 0.3497235591412857
+}
+name.mjw.mwmd.Dihedral Object {
+       Atom I: name.mjw.mwmd.Atom Object {
+ mass :          1.008
+ charge :        0.0687
+ name :          H2
+ AMBERatomType : hc
+ x, y, z :       -3.844 -1.154 -0.868
+}
+       Atom J: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        -0.2001
+ name :          C
+ AMBERatomType : c3
+ x, y, z :       -3.915 -0.493 0.0
+}
+       Atom K: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        0.6230999983536656
+ name :          C1
+ AMBERatomType : c
+ x, y, z :       -2.723 0.415 0.049
+}
+       Atom L: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.485
+ name :          O
+ AMBERatomType : o
+ x, y, z :       -2.788 1.633 0.083
+}
+ barrierHeight: 0.0
+ phase (radians): 3.141594
+ periodicity: 2.0
+ current dihedral angle (degrees) 124.2528158915286
+ current potential contribution: (kcal/mol) 0.0
+}
+name.mjw.mwmd.Dihedral Object {
+       Atom I: name.mjw.mwmd.Atom Object {
+ mass :          1.008
+ charge :        0.0687
+ name :          H2
+ AMBERatomType : hc
+ x, y, z :       -3.844 -1.154 -0.868
+}
+       Atom J: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        -0.2001
+ name :          C
+ AMBERatomType : c3
+ x, y, z :       -3.915 -0.493 0.0
+}
+       Atom K: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        0.6230999983536656
+ name :          C1
+ AMBERatomType : c
+ x, y, z :       -2.723 0.415 0.049
+}
+       Atom L: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.485
+ name :          O
+ AMBERatomType : o
+ x, y, z :       -2.788 1.633 0.083
+}
+ barrierHeight: 0.08
+ phase (radians): 3.141594
+ periodicity: 3.0
+ current dihedral angle (degrees) 124.2528158915286
+ current potential contribution: (kcal/mol) 0.0019751945857652497
+}
+name.mjw.mwmd.Dihedral Object {
+       Atom I: name.mjw.mwmd.Atom Object {
+ mass :          1.008
+ charge :        0.0687
+ name :          H2
+ AMBERatomType : hc
+ x, y, z :       -3.844 -1.154 -0.868
+}
+       Atom J: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        -0.2001
+ name :          C
+ AMBERatomType : c3
+ x, y, z :       -3.915 -0.493 0.0
+}
+       Atom K: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        0.6230999983536656
+ name :          C1
+ AMBERatomType : c
+ x, y, z :       -2.723 0.415 0.049
+}
+       Atom L: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.5840999983536654
+ name :          O1
+ AMBERatomType : oh
+ x, y, z :       -1.552 -0.259 0.065
+}
+ barrierHeight: 0.0
+ phase (radians): 3.141594
+ periodicity: 2.0
+ current dihedral angle (degrees) -56.35261791314245
+ current potential contribution: (kcal/mol) 0.0
+}
+name.mjw.mwmd.Dihedral Object {
+       Atom I: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.485
+ name :          O
+ AMBERatomType : o
+ x, y, z :       -2.788 1.633 0.083
+}
+       Atom J: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        0.6230999983536656
+ name :          C1
+ AMBERatomType : c
+ x, y, z :       -2.723 0.415 0.049
+}
+       Atom K: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.5840999983536654
+ name :          O1
+ AMBERatomType : oh
+ x, y, z :       -1.552 -0.259 0.065
+}
+       Atom L: name.mjw.mwmd.Atom Object {
+ mass :          1.008
+ charge :        0.422
+ name :          H3
+ AMBERatomType : ho
+ x, y, z :       -1.658 -1.228 0.039
+}
+ barrierHeight: 1.9
+ phase (radians): 0.0
+ periodicity: 1.0
+ current dihedral angle (degrees) 179.62273797926912
+ current potential contribution: (kcal/mol) 4.118726411211915E-5
+}
+name.mjw.mwmd.Dihedral Object {
+       Atom I: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.485
+ name :          O
+ AMBERatomType : o
+ x, y, z :       -2.788 1.633 0.083
+}
+       Atom J: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        0.6230999983536656
+ name :          C1
+ AMBERatomType : c
+ x, y, z :       -2.723 0.415 0.049
+}
+       Atom K: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.5840999983536654
+ name :          O1
+ AMBERatomType : oh
+ x, y, z :       -1.552 -0.259 0.065
+}
+       Atom L: name.mjw.mwmd.Atom Object {
+ mass :          1.008
+ charge :        0.422
+ name :          H3
+ AMBERatomType : ho
+ x, y, z :       -1.658 -1.228 0.039
+}
+ barrierHeight: 2.3
+ phase (radians): 3.141594
+ periodicity: 2.0
+ current dihedral angle (degrees) 179.62273797926912
+ current potential contribution: (kcal/mol) 1.99471688426589E-4
+}
+name.mjw.mwmd.Dihedral Object {
+       Atom I: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        -0.2001
+ name :          C
+ AMBERatomType : c3
+ x, y, z :       -3.915 -0.493 0.0
+}
+       Atom J: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.485
+ name :          O
+ AMBERatomType : o
+ x, y, z :       -2.788 1.633 0.083
+}
+       Atom K: name.mjw.mwmd.Atom Object {
+ mass :          12.010000000000002
+ charge :        0.6230999983536656
+ name :          C1
+ AMBERatomType : c
+ x, y, z :       -2.723 0.415 0.049
+}
+       Atom L: name.mjw.mwmd.Atom Object {
+ mass :          16.0
+ charge :        -0.5840999983536654
+ name :          O1
+ AMBERatomType : oh
+ x, y, z :       -1.552 -0.259 0.065
+}
+ barrierHeight: 1.1
+ phase (radians): 3.141594
+ periodicity: 2.0
+ current dihedral angle (degrees) -179.33490697695808
+ current potential contribution: (kcal/mol) 2.9639598791725286E-4
+}

File doc/subscript.mml

+<math display = 'block'>
+  <apply>
+  <plus/>
+    <apply>
+      <selector/>
+      <ci>a</ci>
+      <ci>i</ci>
+    </apply>
+    <apply>
+      <selector/>
+      <ci>b</ci>
+      <ci>j</ci>
+      <ci>k</ci>
+    </apply>
+  </apply>
+</math>

File doc/subscript1.mml

+<math display="block" xmlns="http://www.w3.org/1998/Math/MathML">

File doc/subscript1.xml

+<math display="block" xmlns="http://www.w3.org/1998/Math/MathML">
+	<apply>
+		<sum />
+		<bvar>
+			<ci>x</ci>
+		</bvar>
+		<lowlimit>
+			<cn>0</cn>
+		</lowlimit>
+		<uplimit>
+			<cn>5</cn>
+		</uplimit>
+		<apply>
+			<selector>
+				<ci type="vector">R</ci>
+				<ci>x</ci>
+			</selector>
+		</apply>
+	</apply>
+</math>

File doc/subscript2.mml

+<math display = 'block'>
+  <apply>
+    <sum/>
+    <bvar>
+      <ci>x</ci>
+    </bvar>
+    <lowlimit>
+      <cn>0</cn>
+    </lowlimit>
+    <uplimit>
+      <cn>5</cn>
+    </uplimit>
+    <apply>
+      <selector/>
+      <ci>R</ci>
+      <ci>x</ci>
+    </apply>
+  </apply>
+</math>

File doc/subscript2v.mml

+<math display = 'block'>
+  <apply>
+    <sum/>
+    <bvar>
+      <ci>x</ci>
+    </bvar>
+    <lowlimit>
+      <cn>0</cn>
+    </lowlimit>
+    <uplimit>
+      <cn>5</cn>
+    </uplimit>
+    <apply>
+      <selector/>
+      <ci type="vector">R</ci>
+      <ci>x</ci>
+    </apply>
+  </apply>
+</math>

File doc/vdwequation.pdf

Binary file added.
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <parent>
+        <groupId>uk.ac.cam.ch.wwmm</groupId>
+        <artifactId>wwmm-parent</artifactId>
+        <version>3</version>
+    </parent>
+
+    <groupId>cml</groupId>
+    <artifactId>declaratron-top</artifactId>
+    <version>0.1-SNAPSHOT</version>
+    <packaging>pom</packaging>
+    
+
+    <name>Declaratron</name>
+    <description>Semantic scientific processor</description>
+    <url>http://www.xml-cml.org/</url>
+    <developers>
+        <developer>
+            <id>petermr</id>
+            <name>Peter Murray-Rust</name>
+            <email>pm286@cam.ac.uk</email>
+        </developer>
+        <developer>
+            <id>mo_sweph</id>
+            <name>David Murray-Rust</name>
+        </developer>
+    </developers>
+
+    <repositories>
+        <repository>
+            <id>ucc-repo</id>
+            <url>https://maven.ch.cam.ac.uk/m2repo</url>
+        </repository>
+    </repositories>
+
+    <properties>
+      <cmlxom.version>3.2-SNAPSHOT</cmlxom.version>
+        <cml.groupId>cml</cml.groupId>
+        <jumbo.groupId>org.xml-cml</jumbo.groupId>
+        <jumbo.version>6.1-SNAPSHOT</jumbo.version>
+        <cmlxom.version>3.2-SNAPSHOT</cmlxom.version>
+        <jumbotestutil.version>1.1-SNAPSHOT</jumbotestutil.version>
+    
+        <jumboConverters.groupId>org.xml-cml</jumboConverters.groupId>
+<!--         <jumboConverters.version>6.1-SNAPSHOT</jumboConverters.version> -->
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+    </properties>
+
+    <build>
+        <plugins>
+            <plugin>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <configuration>
+                    <forkMode>once</forkMode>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <dependencyManagement>
+        <!-- Keep these alphabetical, please! -->
+        <dependencies>
+            <dependency>
+                <groupId>${jumbo.groupId}</groupId>
+                <artifactId>cmlxom</artifactId>
+                <version>${cmlxom.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>${jumbo.groupId}</groupId>
+                <artifactId>jumbo-testutil</artifactId>
+                <version>${jumbotestutil.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>${jumbo.groupId}</groupId>
+                <artifactId>jumbo</artifactId>
+                <version>${jumbo.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>${jumbo.groupId}</groupId>
+                <artifactId>jumbo-units</artifactId>
+                <version>0.2-SNAPSHOT</version>
+            </dependency>
+            <dependency>
+                <groupId>log4j</groupId>
+                <artifactId>log4j</artifactId>
+                <version>1.2.13</version>
+            </dependency>
+            <dependency>
+                <groupId>xom</groupId>
+                <artifactId>xom</artifactId>
+                <version>1.2.5</version>
+            </dependency>
+
+            <dependency>
+                <groupId>junit</groupId>
+                <artifactId>junit</artifactId>
+                <version>4.8.2</version>
+            </dependency>
+            <dependency>
+                <groupId>org.mockito</groupId>
+                <artifactId>mockito-core</artifactId>
+                <version>1.8.0</version>
+            </dependency>
+
+        </dependencies>
+    </dependencyManagement>
+</project>