Merging next into master for 2.1.8 release

Signed-off-by: amccaskey <mccaskeyaj@ornl.gov>

.project

@@ -10,6 +10,11 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.ds.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.m2e.core.maven2Nature</nature>

ICE Build - Clean and Install.launch

@@ -15,7 +15,8 @@
 <stringAttribute key="M2_USER_SETTINGS" value=""/>
 <booleanAttribute key="M2_WORKSPACE_RESOLUTION" value="false"/>
 <mapAttribute key="org.eclipse.debug.core.environmentVariables">
-<mapEntry key="LD_LIBRARY_PATH" value="/home/bkj/Programs/hdf-java/lib/linux/"/>
+<mapEntry key="LD_LIBRARY_PATH" value="/home/bkj/Programs/hdf-java-2.10/HDF-JAVA-2.10.0-Linux/usr/lib/"/>
 </mapAttribute>
+<booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_START_ON_FIRST_THREAD" value="true"/>
 <stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:/ice}"/>
 </launchConfiguration>

docs/moose/tutorial/.gitignore

@@ -14,3 +14,4 @@
 =======
 >>>>>>> refs/remotes/origin/jay/reflectivity
 >>>>>>> refs/remotes/origin/master
+/ice_moose_2015050.synctex.gz

org.eclipse.ice.analysistool/META-INF/MANIFEST.MF

 Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: ICE Analysis Tool Interface
-Bundle-SymbolicName: org.eclipse.ice.analysistool
+Bundle-SymbolicName: org.eclipse.ice.analysistool;singleton:=true
 Bundle-Version: 2.1.7.20150825
 Bundle-RequiredExecutionEnvironment: JavaSE-1.7
 Export-Package: org.eclipse.ice.analysistool

org.eclipse.ice.analysistool/build.properties

 source.. = src/
 output.. = bin/
 bin.includes = META-INF/,\
-               .
+               schema/,\
+               .,\
+               plugin.xml

org.eclipse.ice.analysistool/plugin.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse version="3.4"?>
+<plugin>
+   <extension-point id="IAnalysisTool" name="Analysis Tool" schema="schema/IAnalysisTool.exsd"/>
+
+</plugin>

org.eclipse.ice.analysistool/schema/IAnalysisTool.exsd

+<?xml version='1.0' encoding='UTF-8'?>
+<!-- Schema file written by PDE -->
+<schema targetNamespace="org.eclipse.ice.analysistool" xmlns="http://www.w3.org/2001/XMLSchema">
+<annotation>
+      <appinfo>
+         <meta.schema plugin="org.eclipse.ice.analysistool" id="IAnalysisTool" name="Analysis Tool"/>
+      </appinfo>
+      <documentation>
+         [Enter description of this extension point.]
+      </documentation>
+   </annotation>
+
+   <element name="extension">
+      <annotation>
+         <appinfo>
+            <meta.element />
+         </appinfo>
+      </annotation>
+      <complexType>
+         <choice minOccurs="1" maxOccurs="unbounded">
+            <element ref="Implementation"/>
+         </choice>
+         <attribute name="point" type="string" use="required">
+            <annotation>
+               <documentation>
+                  
+               </documentation>
+            </annotation>
+         </attribute>
+         <attribute name="id" type="string">
+            <annotation>
+               <documentation>
+                  
+               </documentation>
+            </annotation>
+         </attribute>
+         <attribute name="name" type="string">
+            <annotation>
+               <documentation>
+                  
+               </documentation>
+               <appinfo>
+                  <meta.attribute translatable="true"/>
+               </appinfo>
+            </annotation>
+         </attribute>
+      </complexType>
+   </element>
+
+   <element name="Implementation">
+      <complexType>
+         <attribute name="Class" type="string">
+            <annotation>
+               <documentation>
+                  
+               </documentation>
+               <appinfo>
+                  <meta.attribute kind="java" basedOn=":org.eclipse.ice.analysistool.IAnalysisTool"/>
+               </appinfo>
+            </annotation>
+         </attribute>
+      </complexType>
+   </element>
+
+   <annotation>
+      <appinfo>
+         <meta.section type="since"/>
+      </appinfo>
+      <documentation>
+         [Enter the first release in which this extension point appears.]
+      </documentation>
+   </annotation>
+
+   <annotation>
+      <appinfo>
+         <meta.section type="examples"/>
+      </appinfo>
+      <documentation>
+         [Enter extension point usage example here.]
+      </documentation>
+   </annotation>
+
+   <annotation>
+      <appinfo>
+         <meta.section type="apiinfo"/>
+      </appinfo>
+      <documentation>
+         [Enter API information here.]
+      </documentation>
+   </annotation>
+
+   <annotation>
+      <appinfo>
+         <meta.section type="implementation"/>
+      </appinfo>
+      <documentation>
+         [Enter information about supplied implementation of this extension point.]
+      </documentation>
+   </annotation>
+
+
+</schema>

org.eclipse.ice.caebat.batml.test/src/org/eclipse/ice/caebat/batml/test/BatMLModelTester.java

@@ -147,7 +147,7 @@ public class BatMLModelTester {
 		assertEquals(1, form.getComponents().size());
 
 		// Check the name and description of the item and allowedActions
-		assertEquals("BatML Model Builder", batML.getName());
+		assertEquals("BatML Model", batML.getName());
 		assertEquals("This item builds models based on a BatteryML schema.",
 				batML.getDescription());
 
@@ -175,6 +175,6 @@ public class BatMLModelTester {
 		EMFComponent component = (EMFComponent) batml.getForm().getComponent(1);
 		assertNotNull(component);
 		assertNotNull(component.getEMFTreeComposite());
-		assertTrue("DocumentRoot".equals(component.getEMFTreeComposite().getName()));
+		assertTrue("BatML".equals(component.getEMFTreeComposite().getName()));
 	}
 }

org.eclipse.ice.caebat.batml/META-INF/MANIFEST.MF

 Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: BatteryML
-Bundle-SymbolicName: org.eclipse.ice.caebat.batml
+Bundle-SymbolicName: org.eclipse.ice.caebat.batml;singleton:=true
 Bundle-Version: 2.1.7.20150825
 Service-Component: OSGI-INF/xsdcomponent.xml
 Bundle-RequiredExecutionEnvironment: JavaSE-1.7

org.eclipse.ice.caebat.batml/build.properties

-source.. = src/
+source.. = src/, \
+		   data/
 output.. = bin/
 bin.includes = META-INF/,\
                .,\
                OSGI-INF/,\
                build.properties,\
-               pom.xml
+               pom.xml,\
+               plugin.xml,\
+               data/,\
+               data/BuildingBlockDB.xsd,\
+               data/CellDB.xsd,\
+               data/CellSandwichDB.xsd,\
+               data/DeviceDB.xsd,\
+               data/MaterialDB.xsd,\
+               data/ModelDB.xsd,\
+               data/ModuleDB.xsd,\
+               data/NamedParameters.xsd,\
+               data/PackDB.xsd,\
+               data/PartDB.xsd,\
+               data/SimulationDB.xsd,\
+               data/UnitsDB.xsd,\
+               data/UnitsML-v1.0-csd03.xsd,\
+               data/common_basic_data_types.xsd,\
+               data/electrical.xml,\
+               data/electrical.xsd,\
+               data/matml31.xsd               

org.eclipse.ice.caebat.batml/data/BuildingBlockDB.xsd

+<?xml version="1.0" encoding="utf-8"?>
+<!--
+    Battery BuildingBlock Database Schema, v 10.08.2012
+
+    Copyright (c) 2012 UT-Battelle, LLC All rights reserved.
+    Redistribution and use, with or without modification, are permitted
+    provided that the following conditions are met:
+
+    - Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+
+    - Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in the
+    documentation and/or other materials provided with the distribution.
+
+    - Collection of administrative costs for redistribution of the source
+    code or binary form is allowed. However, collection of a royalty or
+    other fee in excess of good faith amount for cost recovery for such
+    redistribution is prohibited.
+
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+    HOLDER, THE DOE, OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+    INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+    BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
+    OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+    ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+    TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+    USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+    DAMAGE.
+
+ --> 
+<xsd:schema
+   xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+
+   xmlns="BatteryML:2.0"
+   targetNamespace="BatteryML:2.0"
+
+   elementFormDefault="qualified" 
+   attributeFormDefault="unqualified" version="0.2">
+
+
+  <xsd:element name="BuildingBlockDB_Test_Doc">
+    <xsd:annotation>
+      <xsd:documentation>
+	For testing.
+      </xsd:documentation>
+    </xsd:annotation>
+    <xsd:complexType>
+      <xsd:sequence>
+	<xsd:any     namespace="##targetNamespace" minOccurs="0" maxOccurs="unbounded"/>
+      </xsd:sequence>
+    </xsd:complexType>
+  </xsd:element>
+
+<!-- BuildingBlock database -->
+
+  <xsd:element name="BuildingBlockDB">
+    <xsd:annotation>
+      <xsd:documentation>
+	Main database with component definitions. Definitions can exist
+	only in BuildingBlockDB. The component definitions are referenced from
+	other databases by argument ref that is linked to
+	component id.
+      </xsd:documentation>
+    </xsd:annotation>
+    
+    <xsd:complexType>
+      <xsd:sequence>
+	<xsd:choice minOccurs="0" maxOccurs="unbounded">
+	  <xsd:element ref="BuildingBlock"          minOccurs="0" maxOccurs="unbounded"/>
+	  <xsd:element ref="BuildingBlockSet"       minOccurs="0" maxOccurs="unbounded"/>
+	</xsd:choice>
+	<xsd:group   ref="ElementInfoGroup"   minOccurs="0"/>
+      </xsd:sequence>
+      <xsd:attributeGroup ref="OptionalNameGroup"/>
+    </xsd:complexType>
+    <xsd:key name="BuildingBlockIdKey">
+      <xsd:selector xpath="./BuildingBlock | ./BuildingBlockSet"/>
+      <xsd:field xpath="@id"/>
+    </xsd:key>
+  </xsd:element>
+
+  <xsd:element name="BuildingBlock" type="BuildingBlockDBEntryType">
+    <xsd:annotation>
+      <xsd:documentation>
+	BuildingBlock element in BuildingBlockDB.
+      </xsd:documentation>
+    </xsd:annotation>
+  </xsd:element>
+
+  <xsd:complexType name="BuildingBlockAbstractType"  abstract="true">
+    <xsd:annotation>
+      <xsd:documentation>
+	Main instance of component type. Contains all the hierarchical
+	components of the component instance.
+      </xsd:documentation>
+    </xsd:annotation>
+
+    <xsd:sequence>
+      <xsd:element ref="BuildingBlock"          minOccurs="0" maxOccurs="unbounded"/>
+      <xsd:choice minOccurs="0">
+<!--
+	<xsd:element name="Model"           type="BuildingBlockModelType"   minOccurs="0"/>
+-->
+	<xsd:element name="Model"           type="ModelType"   minOccurs="0"/>
+	<xsd:element name="ModelDefinition" type="DefinitionType" minOccurs="0"/>
+      </xsd:choice>
+      <xsd:element ref="Parameters"         minOccurs="0"/>
+      <xsd:any     namespace="##other"          minOccurs="0" maxOccurs="unbounded" processContents="lax"/>
+      <xsd:group   ref="ElementInfoGroup"   minOccurs="0"/>
+    </xsd:sequence>
+    <xsd:attribute name="name"  type="ShortTokenType" use="optional"/>
+    <xsd:attribute name="id"    type="ShortNameType"  use="optional"/>
+    <xsd:attribute name="type"  type="BuildingBlockTypeType"    use="optional"/>
+    <xsd:attribute name="idref" type="ShortNameType"  use="optional"/>
+  </xsd:complexType>
+
+  <xsd:complexType name="BuildingBlockDBEntryType">
+    <xsd:annotation>
+      <xsd:documentation>
+	Main instance of component type. Contains all the hierarchical
+	components of the component instance.
+      </xsd:documentation>
+    </xsd:annotation>
+    
+    <xsd:complexContent>
+      <xsd:restriction base="BuildingBlockAbstractType">
+	<xsd:sequence>
+	  <xsd:element ref="BuildingBlock"          minOccurs="0" maxOccurs="unbounded"/>
+	  <xsd:choice minOccurs="0">
+	    <xsd:element name="Model"           type="ModelType"   minOccurs="0"/>
+	    <xsd:element name="ModelDefinition" type="DefinitionType" minOccurs="0"/>
+	  </xsd:choice>
+	  <xsd:element ref="Parameters"        minOccurs="0"/>
+	  <xsd:any     namespace="##other"         minOccurs="0" maxOccurs="unbounded" processContents="lax"/>
+	  <xsd:group   ref="ElementInfoGroup"  minOccurs="0"/>
+	</xsd:sequence>
+	<xsd:attribute name="name"  type="ShortTokenType" use="optional"/>
+	<xsd:attribute name="id"    type="ShortNameType"  use="required"/>
+	<xsd:attribute name="type"  type="BuildingBlockTypeType"    use="required"/>
+	<xsd:attribute name="idref" type="ShortNameType"  use="prohibited"/>
+      </xsd:restriction>
+    </xsd:complexContent>
+  </xsd:complexType>
+
+  <xsd:complexType name="BuildingBlockRefType">
+    <xsd:annotation>
+      <xsd:documentation>
+	Main instance of battery component type referring to the entry in the component database.
+      </xsd:documentation>
+    </xsd:annotation>
+    
+    <xsd:complexContent>
+      <xsd:restriction base="BuildingBlockAbstractType">
+	<xsd:sequence>
+	  <xsd:group     ref="ElementInfoGroup"   minOccurs="0"/>
+	</xsd:sequence>
+	<xsd:attribute name="name"  type="ShortTokenType" use="prohibited"/>
+	<xsd:attribute name="id"    type="ShortNameType"  use="prohibited"/>
+	<xsd:attribute name="type"  type="BuildingBlockTypeType"    use="prohibited"/>
+	<xsd:attribute name="idref" type="ShortNameType"  use="required"/>
+      </xsd:restriction>
+    </xsd:complexContent>
+  </xsd:complexType>
+
+  <xsd:element name="BuildingBlockSet">
+    <xsd:annotation>
+      <xsd:documentation>
+	BuildingBlock set element in BuildingBlockDB.
+      </xsd:documentation>
+    </xsd:annotation>
+    <xsd:complexType>
+      <xsd:sequence>
+	<xsd:element name="BuildingBlock"     type="BuildingBlockRefType" minOccurs="0" maxOccurs="unbounded"/>
+	<xsd:element name="BuildingBlockSet"  type="BuildingBlockRefType" minOccurs="0" maxOccurs="unbounded"/>
+
+	<xsd:choice minOccurs="0">
+	  <xsd:element name="Model"           type="ModelType"   minOccurs="0"/>
+	  <xsd:element name="ModelDefinition" type="DefinitionType" minOccurs="0"/>
+	</xsd:choice>
+	<xsd:element ref="Parameters"        minOccurs="0"/>
+	<xsd:group   ref="ElementInfoGroup"  minOccurs="0"/>
+      </xsd:sequence>
+      <xsd:attribute name="name"  type="ShortTokenType" use="optional"/>
+      <xsd:attribute name="id"    type="ShortNameType"  use="required"/>
+    </xsd:complexType>
+    <xsd:key name="BuildingBlockSetIdKey">
+      <xsd:selector xpath="./BuildingBlock | ./BuildingBlockSet"/>
+      <xsd:field xpath="@idref"/>
+    </xsd:key>
+  </xsd:element>
+
+
+
+  <xsd:complexType name="BuildingBlockModelType">
+    <xsd:annotation>
+      <xsd:documentation>
+	Model reference to the model specification in the ModelDB.
+      </xsd:documentation>
+    </xsd:annotation>
+    <xsd:attribute name="idref" type="ShortNameType"  use="required"/>
+  </xsd:complexType>
+
+  <xsd:simpleType  name="BuildingBlockTypeType">
+    <xsd:annotation>
+      <xsd:documentation>
+	BuildingBlock type battery. Single choice.
+      </xsd:documentation>
+    </xsd:annotation>
+    <xsd:restriction base="ShortTokenType">
+
+      <xsd:enumeration value="Current Collector">
+	<xsd:annotation>
+	  <xsd:documentation>Current Collector.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Current Collector Positive">
+	<xsd:annotation>
+	  <xsd:documentation>Current Collector Positive.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Current Collector Negative">
+	<xsd:annotation>
+	  <xsd:documentation>Current Collector Negative.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Current Collector Cathode">
+	<xsd:annotation>
+	  <xsd:documentation>Current Collector Cathode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Current Collector Anode">
+	<xsd:annotation>
+	  <xsd:documentation>Current Collector Anode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Anode">
+	<xsd:annotation>
+	  <xsd:documentation>Anode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Cathode">
+	<xsd:annotation>
+	  <xsd:documentation>Cathode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Active Material">
+	<xsd:annotation>
+	  <xsd:documentation>Active Material.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Active Material Anode">
+	<xsd:annotation>
+	  <xsd:documentation>Active Material Anode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Active Material Cathode">
+	<xsd:annotation>
+	  <xsd:documentation>Active Material Cathode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Separator">
+	<xsd:annotation>
+	  <xsd:documentation>Separator.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Coating">
+	<xsd:annotation>
+	  <xsd:documentation>Coating.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Coating Anode">
+	<xsd:annotation>
+	  <xsd:documentation>Coating Anode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Coating Cathode">
+	<xsd:annotation>
+	  <xsd:documentation>Coating Cathode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Electrolyte">
+	<xsd:annotation>
+	  <xsd:documentation>Electrolyte.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Solvent">
+	<xsd:annotation>
+	  <xsd:documentation>Solvent.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Salt">
+	<xsd:annotation>
+	  <xsd:documentation>Salt.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Additives">
+	<xsd:annotation>
+	  <xsd:documentation>Additives.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Binder">
+	<xsd:annotation>
+	  <xsd:documentation>Binder.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Binder Anode">
+	<xsd:annotation>
+	  <xsd:documentation>Binder Anode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Binder Cathode">
+	<xsd:annotation>
+	  <xsd:documentation>Binder Cathode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Conductivity Aid">
+	<xsd:annotation>
+	  <xsd:documentation>Conductivity Aid.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Conductivity Aid Anode">
+	<xsd:annotation>
+	  <xsd:documentation>Conductivity Aid Anode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Conductivity Aid Cathode">
+	<xsd:annotation>
+	  <xsd:documentation>Conductivity Aid Cathode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Tape">
+	<xsd:annotation>
+	  <xsd:documentation>Bonding Tape.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Tab">
+	<xsd:annotation>
+	  <xsd:documentation>Tab.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Tab Anode">
+	<xsd:annotation>
+	  <xsd:documentation>Tab Anode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Tab Cathode">
+	<xsd:annotation>
+	  <xsd:documentation>Tab Cathode.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Insulation">
+	<xsd:annotation>
+	  <xsd:documentation>Insulation.</xsd:documentation>
+	</xsd:annotation>
+      </xsd:enumeration>
+
+      <xsd:enumeration value="Coolant">