Merge branch 'develop' of https://github.com/OpenCMISS/documentation …

…into OpenCMISSNotes

_themes/ocmiss/layout.html

@@ -0,0 +1,21 @@
+{% extends 'partials/common_with_sidebar.jinja' %}
+{% set active_nav = "doc" %}
+{% block title %}{{title}} - OpenCMISS{% endblock %}
+{% block sidebar_title %}
+  <h1>Quick Links</h1>
+{% endblock %}
+{% block sidebar_content %}
+  {{ theme_navbar_site_name }}
+  {{ toctree(maxdepth=3, collapse=True) }}
+{% endblock %}
+{% block content %}
+  {% block body %}
+  {% endblock %}
+{% endblock %}
+{% block styles %}
+  {{ super() }}
+  <link rel="stylesheet" href="/documentation/_static/basic.css">
+  <!-- build:css(.tmp) /styles/rst.css -->
+  <link rel="stylesheet" href="/styles/rst.css">
+  <!-- endbuild -->
+{% endblock %}

_themes/ocmiss/theme.conf

@@ -0,0 +1,2 @@
+[theme]
+inherit = basic

conf.py

@@ -21,6 +21,9 @@
 # needed to find the cmake extension (copied to the containing folder by grunt script)
 sys.path.insert(1, os.path.abspath('.'))
 
+# Set numfig on to enable numref
+numfig = True
+
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
@@ -31,6 +34,21 @@
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
     'sphinx.ext.mathjax',
-    'cmake'
+    'sphinxcontrib.rawfiles',
+    'cmake',
+]
+
+# Raw files to copy to destination
+rawfiles = [
+    'videos/oclibs_intro',
+    'videos/oclibs_install_reqs_intro',
+    'videos/oclibs_install_reqs_ubuntu',
+    'videos/oclibs_sdk_intro',
+    'videos/oclibs_sdk_ubuntu',
+    'videos/oclibs_building_intro',
+    'videos/oclibs_building_ubuntu',
 ]
 
+if os.path.exists('_themes/ocmiss/partials/common_with_sidebar.jinja'):
+    html_theme = "ocmiss"
+    html_theme_path = ["_themes"]

contribute.rst

@@ -0,0 +1,6 @@
+
+============
+Contributing
+============
+
+Want to contribute to OpenCMISS projects? Visit the `developers documentation page <developers.html>`_.

contribute/dev_coding_standard.rst

@@ -95,7 +95,7 @@ Fortran 90
 * All features.
 
 Fortran 95
-^^^^^^^^^
+^^^^^^^^^^
 
 * All features.
 

contribute/index.rst

@@ -1,3 +1,5 @@
+
+=========================
 Contributing to OpenCMISS
 =========================
 
@@ -7,6 +9,7 @@ We at OpenCMISS want to make contributing as easy as possible while maintaining
 of quality.
 
 Prior to contributing code:
+
    - Subscribe to the OpenCMISS developer mailing list.
    - Watch the appropriate repo that you wish to develop (e.g. iron, zinc, examples, documentation, or website) in your GitHub account.
 

data_format/cellml.rst

@@ -0,0 +1,12 @@
+.. image:: CellML_Logo_200x100.png
+   :align: right
+   :target: https://www.cellml.org/
+
+CellML in OpenCMISS
+===================
+
+OpenCMISS supports reading and solving models in CellML format, an open standard for representing mathematical models, based on the XML Markup Language.
+
+Detailed documentation and specifications for CellML are given on `cellml.org <https://www.cellml.org/>`_, but its core features are the definition of scalar *variables* and the mathematical equations relating them. CellML is most commonly used to describe lumped parameter (0-D or spatially constant) models which are solved over time, but there are many other applications such as describing material constitutive laws. The open `Physiome Model Repository <https://models.physiomeproject.org/>`_ catalogs a large number of curated CellML models of various types, including representations of a great many important models of biological processes or whole cell function from the literature.
+
+OpenCMISS-Iron allows lumped parameter CellML models to be solved on large numbers of points over spatial domains, and provides facilities for tying CellML variables to spatially varying fields so local CellML and global physics equations are simultaneously solved. Iron uses the code generation facilites of the CellML API Library, with on-the-fly compilation and linking to ensure high performance computation.

data_format/fieldml/cube_pressure.fieldml

@@ -0,0 +1,246 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<Fieldml version="0.5.0" xsi:noNamespaceSchemaLocation="http://www.fieldml.org/resources/xml/0.5/FieldML_0.5.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xlink="http://www.w3.org/1999/xlink">
+ <Region name="/">
+  <Import xlink:href="http://www.fieldml.org/resources/xml/0.5/FieldML_Library_0.5.xml" region="library">
+   <ImportType localName="real.1d" remoteName="real.1d"/>
+   <ImportEvaluator localName="shape.unit.cube" remoteName="shape.unit.cube"/>
+   <ImportEvaluator localName="interpolator.3d.unit.trilinearLagrange" remoteName="interpolator.3d.unit.trilinearLagrange"/>
+   <ImportType localName="parameters.3d.unit.trilinearLagrange" remoteName="parameters.3d.unit.trilinearLagrange"/>
+   <ImportEvaluator localName="parameters.3d.unit.trilinearLagrange.argument" remoteName="parameters.3d.unit.trilinearLagrange.argument"/>
+   <ImportType localName="parameters.3d.unit.trilinearLagrange.component" remoteName="parameters.3d.unit.trilinearLagrange.component"/>
+   <ImportEvaluator localName="parameters.3d.unit.trilinearLagrange.component.argument" remoteName="parameters.3d.unit.trilinearLagrange.component.argument"/>
+   <ImportEvaluator localName="chart.3d.argument" remoteName="chart.3d.argument"/>
+   <ImportType localName="coordinates.rc.3d" remoteName="coordinates.rc.3d"/>
+   <ImportType localName="coordinates.rc.3d.component" remoteName="coordinates.rc.3d.component"/>
+   <ImportEvaluator localName="coordinates.rc.3d.component.argument" remoteName="coordinates.rc.3d.component.argument"/>
+  </Import>
+  <EnsembleType name="nodes">
+   <Members>
+    <MemberRange min="1" max="8"/>
+   </Members>
+  </EnsembleType>
+  <EnsembleType name="node_derivatives">
+   <Members>
+    <MemberRange min="1" max="8"/>
+   </Members>
+  </EnsembleType>
+  <ConstantEvaluator name="node_derivatives.value" value="1" valueType="node_derivatives"/>
+  <ConstantEvaluator name="node_derivatives.d_ds1" value="2" valueType="node_derivatives"/>
+  <ConstantEvaluator name="node_derivatives.d_ds2" value="3" valueType="node_derivatives"/>
+  <ConstantEvaluator name="node_derivatives.d2_ds1ds2" value="4" valueType="node_derivatives"/>
+  <ConstantEvaluator name="node_derivatives.d_ds3" value="5" valueType="node_derivatives"/>
+  <ConstantEvaluator name="node_derivatives.d2_ds1ds3" value="6" valueType="node_derivatives"/>
+  <ConstantEvaluator name="node_derivatives.d2_ds2ds3" value="7" valueType="node_derivatives"/>
+  <ConstantEvaluator name="node_derivatives.d3_ds1ds2ds3" value="8" valueType="node_derivatives"/>
+  <EnsembleType name="node_versions">
+   <Members>
+    <MemberRange min="1" max="1"/>
+   </Members>
+  </EnsembleType>
+  <ConstantEvaluator name="node_versions.1" value="1" valueType="node_versions"/>
+  <ArgumentEvaluator name="nodes.argument" valueType="nodes"/>
+  <ArgumentEvaluator name="node_derivatives.argument" valueType="node_derivatives"/>
+  <ArgumentEvaluator name="node_versions.argument" valueType="node_versions"/>
+  <ArgumentEvaluator name="nodes.parameters" valueType="real.1d">
+   <Arguments>
+    <Argument name="nodes.argument"/>
+    <Argument name="node_derivatives.argument"/>
+    <Argument name="node_versions.argument"/>
+   </Arguments>
+  </ArgumentEvaluator>
+  <MeshType name="mesh3d">
+   <Elements name="elements">
+    <Members>
+     <MemberRange min="1" max="1"/>
+    </Members>
+   </Elements>
+   <Chart name="xi">
+    <Components name="mesh3d.xi.components" count="3"/>
+   </Chart>
+   <Shapes evaluator="shape.unit.cube"/>
+  </MeshType>
+  <ArgumentEvaluator name="mesh3d.argument" valueType="mesh3d"/>
+  <EnsembleType name="mesh3d.eftIndexes">
+   <Members>
+    <MemberRange min="1" max="1"/>
+   </Members>
+  </EnsembleType>
+  <ArgumentEvaluator name="mesh3d.eftIndexes.argument" valueType="mesh3d.eftIndexes"/>
+  <EnsembleType name="mesh3d.eft1.nodes">
+   <Members>
+    <MemberRange min="1" max="8"/>
+   </Members>
+  </EnsembleType>
+  <ArgumentEvaluator name="mesh3d.eft1.nodes.argument" valueType="mesh3d.eft1.nodes"/>
+  <ArgumentEvaluator name="mesh3d.eft1.nodeparameters.argument" valueType="real.1d">
+   <Arguments>
+    <Argument name="node_derivatives.argument"/>
+    <Argument name="node_versions.argument"/>
+    <Argument name="mesh3d.eft1.nodes.argument"/>
+   </Arguments>
+  </ArgumentEvaluator>
+  <ConstantEvaluator name="mesh3d.eft1.nodes.1" value="1" valueType="mesh3d.eft1.nodes"/>
+  <ConstantEvaluator name="mesh3d.eft1.nodes.2" value="2" valueType="mesh3d.eft1.nodes"/>
+  <ConstantEvaluator name="mesh3d.eft1.nodes.3" value="3" valueType="mesh3d.eft1.nodes"/>
+  <ConstantEvaluator name="mesh3d.eft1.nodes.4" value="4" valueType="mesh3d.eft1.nodes"/>
+  <ConstantEvaluator name="mesh3d.eft1.nodes.5" value="5" valueType="mesh3d.eft1.nodes"/>
+  <ConstantEvaluator name="mesh3d.eft1.nodes.6" value="6" valueType="mesh3d.eft1.nodes"/>
+  <ConstantEvaluator name="mesh3d.eft1.nodes.7" value="7" valueType="mesh3d.eft1.nodes"/>
+  <ConstantEvaluator name="mesh3d.eft1.nodes.8" value="8" valueType="mesh3d.eft1.nodes"/>
+  <ReferenceEvaluator name="mesh3d.eft1.nodeparameters.node1.value.v1" evaluator="mesh3d.eft1.nodeparameters.argument" valueType="real.1d">
+   <Bindings>
+    <Bind argument="mesh3d.eft1.nodes.argument" source="mesh3d.eft1.nodes.1"/>
+    <Bind argument="node_derivatives.argument" source="node_derivatives.value"/>
+    <Bind argument="node_versions.argument" source="node_versions.1"/>
+   </Bindings>
+  </ReferenceEvaluator>
+  <ReferenceEvaluator name="mesh3d.eft1.nodeparameters.node2.value.v1" evaluator="mesh3d.eft1.nodeparameters.argument" valueType="real.1d">
+   <Bindings>
+    <Bind argument="mesh3d.eft1.nodes.argument" source="mesh3d.eft1.nodes.2"/>
+    <Bind argument="node_derivatives.argument" source="node_derivatives.value"/>
+    <Bind argument="node_versions.argument" source="node_versions.1"/>
+   </Bindings>
+  </ReferenceEvaluator>
+  <ReferenceEvaluator name="mesh3d.eft1.nodeparameters.node3.value.v1" evaluator="mesh3d.eft1.nodeparameters.argument" valueType="real.1d">
+   <Bindings>
+    <Bind argument="mesh3d.eft1.nodes.argument" source="mesh3d.eft1.nodes.3"/>
+    <Bind argument="node_derivatives.argument" source="node_derivatives.value"/>
+    <Bind argument="node_versions.argument" source="node_versions.1"/>
+   </Bindings>
+  </ReferenceEvaluator>
+  <ReferenceEvaluator name="mesh3d.eft1.nodeparameters.node4.value.v1" evaluator="mesh3d.eft1.nodeparameters.argument" valueType="real.1d">
+   <Bindings>
+    <Bind argument="mesh3d.eft1.nodes.argument" source="mesh3d.eft1.nodes.4"/>
+    <Bind argument="node_derivatives.argument" source="node_derivatives.value"/>
+    <Bind argument="node_versions.argument" source="node_versions.1"/>
+   </Bindings>
+  </ReferenceEvaluator>
+  <ReferenceEvaluator name="mesh3d.eft1.nodeparameters.node5.value.v1" evaluator="mesh3d.eft1.nodeparameters.argument" valueType="real.1d">
+   <Bindings>
+    <Bind argument="mesh3d.eft1.nodes.argument" source="mesh3d.eft1.nodes.5"/>
+    <Bind argument="node_derivatives.argument" source="node_derivatives.value"/>
+    <Bind argument="node_versions.argument" source="node_versions.1"/>
+   </Bindings>
+  </ReferenceEvaluator>
+  <ReferenceEvaluator name="mesh3d.eft1.nodeparameters.node6.value.v1" evaluator="mesh3d.eft1.nodeparameters.argument" valueType="real.1d">
+   <Bindings>
+    <Bind argument="mesh3d.eft1.nodes.argument" source="mesh3d.eft1.nodes.6"/>
+    <Bind argument="node_derivatives.argument" source="node_derivatives.value"/>
+    <Bind argument="node_versions.argument" source="node_versions.1"/>
+   </Bindings>
+  </ReferenceEvaluator>
+  <ReferenceEvaluator name="mesh3d.eft1.nodeparameters.node7.value.v1" evaluator="mesh3d.eft1.nodeparameters.argument" valueType="real.1d">
+   <Bindings>
+    <Bind argument="mesh3d.eft1.nodes.argument" source="mesh3d.eft1.nodes.7"/>
+    <Bind argument="node_derivatives.argument" source="node_derivatives.value"/>
+    <Bind argument="node_versions.argument" source="node_versions.1"/>
+   </Bindings>
+  </ReferenceEvaluator>
+  <ReferenceEvaluator name="mesh3d.eft1.nodeparameters.node8.value.v1" evaluator="mesh3d.eft1.nodeparameters.argument" valueType="real.1d">
+   <Bindings>
+    <Bind argument="mesh3d.eft1.nodes.argument" source="mesh3d.eft1.nodes.8"/>
+    <Bind argument="node_derivatives.argument" source="node_derivatives.value"/>
+    <Bind argument="node_versions.argument" source="node_versions.1"/>
+   </Bindings>
+  </ReferenceEvaluator>
+  <AggregateEvaluator name="mesh3d.eft1.parameters" valueType="parameters.3d.unit.trilinearLagrange">
+   <Bindings>
+    <BindIndex argument="parameters.3d.unit.trilinearLagrange.component.argument" indexNumber="1"/>
+   </Bindings>
+   <ComponentEvaluators>
+    <ComponentEvaluator component="1" evaluator="mesh3d.eft1.nodeparameters.node1.value.v1"/>
+    <ComponentEvaluator component="2" evaluator="mesh3d.eft1.nodeparameters.node2.value.v1"/>
+    <ComponentEvaluator component="3" evaluator="mesh3d.eft1.nodeparameters.node3.value.v1"/>
+    <ComponentEvaluator component="4" evaluator="mesh3d.eft1.nodeparameters.node4.value.v1"/>
+    <ComponentEvaluator component="5" evaluator="mesh3d.eft1.nodeparameters.node5.value.v1"/>
+    <ComponentEvaluator component="6" evaluator="mesh3d.eft1.nodeparameters.node6.value.v1"/>
+    <ComponentEvaluator component="7" evaluator="mesh3d.eft1.nodeparameters.node7.value.v1"/>
+    <ComponentEvaluator component="8" evaluator="mesh3d.eft1.nodeparameters.node8.value.v1"/>
+   </ComponentEvaluators>
+  </AggregateEvaluator>
+  <ReferenceEvaluator name="mesh3d.eft1" evaluator="interpolator.3d.unit.trilinearLagrange" valueType="real.1d">
+   <Bindings>
+    <Bind argument="parameters.3d.unit.trilinearLagrange.argument" source="mesh3d.eft1.parameters"/>
+   </Bindings>
+  </ReferenceEvaluator>
+  <DataResource name="mesh3d.eft1.localtoglobalnodes.data.resource">
+   <DataResourceDescription>
+    <DataResourceString>1 2 3 4 5 6 7 8 
+    </DataResourceString>
+   </DataResourceDescription>
+   <ArrayDataSource name="mesh3d.eft1.localtoglobalnodes.data.source" location="1" rank="2">
+    <RawArraySize>1 8</RawArraySize>
+    <ArrayDataSize>1 8</ArrayDataSize>
+   </ArrayDataSource>
+  </DataResource>
+  <ParameterEvaluator name="mesh3d.eft1.localtoglobalnodes" valueType="nodes">
+   <DenseArrayData data="mesh3d.eft1.localtoglobalnodes.data.source">
+    <DenseIndexes>
+     <IndexEvaluator evaluator="mesh3d.argument.elements"/>
+     <IndexEvaluator evaluator="mesh3d.eft1.nodes.argument"/>
+    </DenseIndexes>
+   </DenseArrayData>
+  </ParameterEvaluator>
+  <ReferenceEvaluator name="mesh3d.eft1.evaluator" evaluator="mesh3d.eft1" valueType="real.1d">
+   <Bindings>
+    <Bind argument="chart.3d.argument" source="mesh3d.argument.xi"/>
+    <Bind argument="mesh3d.eft1.nodeparameters.argument" source="nodes.parameters"/>
+    <Bind argument="nodes.argument" source="mesh3d.eft1.localtoglobalnodes"/>
+   </Bindings>
+  </ReferenceEvaluator>
+  <PiecewiseEvaluator name="mesh3d.fieldtemplate1" valueType="real.1d">
+   <IndexEvaluators>
+    <IndexEvaluator evaluator="mesh3d.argument.elements" indexNumber="1"/>
+   </IndexEvaluators>
+   <EvaluatorMap default="mesh3d.eft1.evaluator"/>
+  </PiecewiseEvaluator>
+  <DataResource name="nodes.coordinates.data.resource">
+   <DataResourceDescription>
+    <DataResourceString>0 0 0 1 0 0 0 1 0 1 1 0 0 0 1 1 0 1 0 1 1 1 1 1 
+    </DataResourceString>
+   </DataResourceDescription>
+   <ArrayDataSource name="nodes.coordinates.data.source" location="0" rank="2">
+    <RawArraySize>8 3</RawArraySize>
+    <ArrayDataSize>8 3</ArrayDataSize>
+   </ArrayDataSource>
+  </DataResource>
+  <ParameterEvaluator name="nodes.coordinates" valueType="real.1d">
+   <DenseArrayData data="nodes.coordinates.data.source">
+    <DenseIndexes>
+     <IndexEvaluator evaluator="nodes.argument"/>
+     <IndexEvaluator evaluator="coordinates.rc.3d.component.argument"/>
+    </DenseIndexes>
+   </DenseArrayData>
+  </ParameterEvaluator>
+  <AggregateEvaluator name="coordinates" valueType="coordinates.rc.3d">
+   <Bindings>
+    <BindIndex argument="coordinates.rc.3d.component.argument" indexNumber="1"/>
+    <Bind argument="nodes.parameters" source="nodes.coordinates"/>
+   </Bindings>
+   <ComponentEvaluators default="mesh3d.fieldtemplate1"/>
+  </AggregateEvaluator>
+  <ContinuousType name="pressure.domain"/>
+  <DataResource name="nodes.pressure.data.resource">
+   <DataResourceDescription>
+    <DataResourceString>80000 100000 100000 80000 100000 80000 80000 100000 
+    </DataResourceString>
+   </DataResourceDescription>
+   <ArrayDataSource name="nodes.pressure.data.source" location="0" rank="1">
+    <RawArraySize>8</RawArraySize>
+    <ArrayDataSize>8</ArrayDataSize>
+   </ArrayDataSource>
+  </DataResource>
+  <ParameterEvaluator name="nodes.pressure" valueType="real.1d">
+   <DenseArrayData data="nodes.pressure.data.source">
+    <DenseIndexes>
+     <IndexEvaluator evaluator="nodes.argument"/>
+    </DenseIndexes>
+   </DenseArrayData>
+  </ParameterEvaluator>
+  <ReferenceEvaluator name="pressure" evaluator="mesh3d.fieldtemplate1" valueType="pressure.domain">
+   <Bindings>
+    <Bind argument="nodes.parameters" source="nodes.pressure"/>
+   </Bindings>
+  </ReferenceEvaluator>
+ </Region>
+</Fieldml>