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New build system #5

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efbde37
Update for new computation environment routines.
chrispbradley Apr 10, 2018
eb9945a
Merge branch 'develop' of https://github.com/OpenCMISS-Examples/moone…
chrispbradley Apr 11, 2018
700f4d1
Fixes for contexts.
chrispbradley Apr 27, 2018
8011920
Field_MeshDecomposition -> Field_Decomposition
chrispbradley Jun 3, 2018
773ae6c
Changes for decompositions
chrispbradley Sep 15, 2018
0fd0202
Adding OPENCMISS_TOOLCHAIN
chrispbradley Jun 20, 2021
d225807
Fix up control loop type.
chrispbradley Jun 22, 2021
6c16dca
Backup
chrispbradley Nov 16, 2022
66d8f9b
Code style update.
chrispbradley Jan 12, 2023
24501e3
Updates for new build system.
chrispbradley Jul 16, 2024
04f911a
Fixes for Mooney-Rivlin cellml
chrispbradley Aug 5, 2024
b668a35
Fixes for Mooney-Rivlin cellml
chrispbradley Aug 5, 2024
e9f5431
Update
chrispbradley Jan 19, 2025
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13 changes: 11 additions & 2 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
@@ -1,8 +1,17 @@
cmake_minimum_required(VERSION 3.26 FATAL_ERROR)

if(DEFINED OpenCMISS_INSTALL_ROOT)
if(EXISTS "${OpenCMISS_INSTALL_ROOT}/libOpenCMISSSetup.cmake")
set(CMAKE_PROJECT_INCLUDE_BEFORE "${OpenCMISS_INSTALL_ROOT}/libOpenCMISSSetup.cmake")
endif()
endif()

set(ExampleName "mooney_rivlin_cellml")

cmake_minimum_required(VERSION 3.4 FATAL_ERROR)
project(${ExampleName} VERSION 1.0.0 LANGUAGES C Fortran)

find_package(OpenCMISSLibs 1.3.0 COMPONENTS iron REQUIRED CONFIG)
find_package(libOpenCMISS 1.0.0 REQUIRED
COMPONENTS Fortran
)

add_subdirectory(src/fortran)
7 changes: 4 additions & 3 deletions README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,10 @@ Building the example
Instructions on how to configure and build with CMake::

git clone https://github.com/OpenCMISS-Examples/mooney_rivlin_cellml.git
mkdir mooney_rivlin_cellml-build
cd mooney_rivlin_cellml-build
cmake -DOpenCMISSLibs_DIR=/path/to/opencmisslib/install ../mooney_rivlin_cellml
cd mooney_rivlin_cellml
mkdir build
cd build
cmake -DOpenCMISS_INSTALL_ROOT=/path/to/opencmiss/install ../.
make # cmake --build . will also work here and is much more platform agnostic.

Running the example
Expand Down
2 changes: 1 addition & 1 deletion src/fortran/CMakeLists.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
add_executable(${ExampleName} ${ExampleName}.F90)

target_link_libraries(${ExampleName} PRIVATE opencmisslibs)
target_link_libraries(${ExampleName} PRIVATE OpenCMISS::libOpenCMISS_Fortran)

install(TARGETS ${ExampleName} DESTINATION bin)

Expand Down
199 changes: 45 additions & 154 deletions src/fortran/inputs/mooney_rivlin.xml
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Original file line number Diff line number Diff line change
@@ -1,93 +1,6 @@
<?xml version="1.0" encoding="iso-8859-1"?>

<model
name="MooneyRivlin"
cmeta:id="MooneyRivlin"
xmlns="http://www.cellml.org/cellml/1.0#"
xmlns:cellml="http://www.cellml.org/cellml/1.0#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
<model xmlns="http://www.cellml.org/cellml/2.0#" xmlns:cellml="http://www.cellml.org/cellml/2.0#" name="MooneyRivlin" id="MooneyRivlin">

<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
xmlns:bqs="http://www.cellml.org/bqs/1.0#"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">

<!-- metadata about the CellML document itself -->
<rdf:Description rdf:about="">
<dc:creator rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Nickerson</vCard:Family>
<vCard:Given>David</vCard:Given>
</vCard:N>
<vCard:EMAIL rdf:parseType="Resource">
<rdf:value>d.nickerson@auckland.ac.nz</rdf:value>
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet" />
</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>The Bioengineering Institute</vCard:Orgunit>
</vCard:ORG>
</dc:creator>

<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2003-11-28</dcterms:W3CDTF>
</dcterms:created>
</rdf:Description>

<!-- description of the model -->
<rdf:Description rdf:about="#MooneyRivlin">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
This is a CellML version of the Mooney-Rivlin constitutive material law,
defining the relation between the eight independent strain components
and the stress components. It is assumed that the strain components
will be controlled externally by the application using this CellML
model.
</rdf:value>
</cmeta:comment>
<bqs:reference>
<bqs:Pubmed_id>pubmed_id</bqs:Pubmed_id>
<bqs:JournalArticle rdf:parseType="Resource">
<dc:creator>
<rdf:Seq>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Master</vCard:Family>
<vCard:Given>Andre</vCard:Given>
<vCard:Other>T</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Bob</vCard:Family>
<vCard:Given>Billy</vCard:Given>
</vCard:N>
</bqs:Person>
</rdf:li>
</rdf:Seq>
</dc:creator>
<dc:title>
What cool article to reference ??
</dc:title>
<dcterms:issued rdf:parseType="Resource">
<dcterms:W3CDTF>year</dcterms:W3CDTF>
</dcterms:issued>
<bqs:Journal rdf:parseType="Resource">
<dc:title>The Journal of Cool Stuff</dc:title>
</bqs:Journal>
<bqs:volume>volume</bqs:volume>
<bqs:first_page>1</bqs:first_page>
<bqs:last_page>1000</bqs:last_page>
</bqs:JournalArticle>
</bqs:reference>
</rdf:Description>
</rdf:RDF>


<!-- Global units -->
<units name="strain">
Expand All @@ -106,77 +19,55 @@
<unit units="dimensionless"/>
</units>

<component name="interface" cmeta:id="interface">
<component name="interface" id="interface">

<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
<rdf:Description rdf:about="#interface">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
We'll use this component as the "interface" to the model, all
other components are hidden via encapsulation in this component.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>


<!-- Variables we expect to be set/controlled externally -->
<variable name="E11" units="strain" initial_value="0" private_interface="out"/>
<variable name="E22" units="strain" initial_value="0" private_interface="out"/>
<variable name="E33" units="strain" initial_value="0" private_interface="out"/>
<variable name="E12" units="strain" initial_value="0" private_interface="out"/>
<variable name="E13" units="strain" initial_value="0" private_interface="out"/>
<variable name="E23" units="strain" initial_value="0" private_interface="out"/>
<variable name="c1" units="strain" initial_value="2" private_interface="out"/>
<variable name="c2" units="strain" initial_value="6" private_interface="out"/>
<variable name="E11" units="strain" initial_value="0" interface="private"/>
<variable name="E22" units="strain" initial_value="0" interface="private"/>
<variable name="E33" units="strain" initial_value="0" interface="private"/>
<variable name="E12" units="strain" initial_value="0" interface="private"/>
<variable name="E13" units="strain" initial_value="0" interface="private"/>
<variable name="E23" units="strain" initial_value="0" interface="private"/>
<variable name="c1" units="strain" initial_value="2" interface="private"/>
<variable name="c2" units="strain" initial_value="6" interface="private"/>

<!-- Variables we want to make available externally -->
<variable name="Tdev11" units="stress" initial_value="0" public_interface="out" private_interface="in"/>
<variable name="Tdev22" units="stress" initial_value="0" public_interface="out" private_interface="in"/>
<variable name="Tdev33" units="stress" initial_value="0" public_interface="out" private_interface="in"/>
<variable name="Tdev12" units="stress" initial_value="0" public_interface="out" private_interface="in"/>
<variable name="Tdev13" units="stress" initial_value="0" public_interface="out" private_interface="in"/>
<variable name="Tdev23" units="stress" initial_value="0" public_interface="out" private_interface="in"/>
<variable name="Tdev11" units="stress" initial_value="0" interface="public_and_private"/>
<variable name="Tdev22" units="stress" initial_value="0" interface="public_and_private"/>
<variable name="Tdev33" units="stress" initial_value="0" interface="public_and_private"/>
<variable name="Tdev12" units="stress" initial_value="0" interface="public_and_private"/>
<variable name="Tdev13" units="stress" initial_value="0" interface="public_and_private"/>
<variable name="Tdev23" units="stress" initial_value="0" interface="public_and_private"/>

</component> <!--interface-->

<component name="equations" cmeta:id="equations">
<component name="equations" id="equations">

<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
<rdf:Description rdf:about="#equations">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
In this simple model we only have one component, which holds the
six equations.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>


<!-- Inputs -->
<variable name="E11" units="strain" public_interface="in"/>
<variable name="E22" units="strain" public_interface="in"/>
<variable name="E33" units="strain" public_interface="in"/>
<variable name="E12" units="strain" public_interface="in"/>
<variable name="E13" units="strain" public_interface="in"/>
<variable name="E23" units="strain" public_interface="in"/>
<variable name="c1" units="strain" public_interface="in"/>
<variable name="c2" units="strain" public_interface="in"/>
<variable name="E11" units="strain" interface="public"/>
<variable name="E22" units="strain" interface="public"/>
<variable name="E33" units="strain" interface="public"/>
<variable name="E12" units="strain" interface="public"/>
<variable name="E13" units="strain" interface="public"/>
<variable name="E23" units="strain" interface="public"/>
<variable name="c1" units="strain" interface="public"/>
<variable name="c2" units="strain" interface="public"/>

<!-- Outputs computed here -->
<variable name="Tdev11" units="stress" public_interface="out"/>
<variable name="Tdev22" units="stress" public_interface="out"/>
<variable name="Tdev33" units="stress" public_interface="out"/>
<variable name="Tdev12" units="stress" public_interface="out"/>
<variable name="Tdev13" units="stress" public_interface="out"/>
<variable name="Tdev23" units="stress" public_interface="out"/>
<variable name="Tdev11" units="stress" interface="public"/>
<variable name="Tdev22" units="stress" interface="public"/>
<variable name="Tdev33" units="stress" interface="public"/>
<variable name="Tdev12" units="stress" interface="public"/>
<variable name="Tdev13" units="stress" interface="public"/>
<variable name="Tdev23" units="stress" interface="public"/>

<!-- Temporary variables -->

<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="Tdev11_calculation_eq">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Tdev11_calculation"><eq/>
<ci>Tdev11</ci>
<apply><plus/>
Expand All @@ -199,7 +90,7 @@
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="Tdev22_calculation_eq">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Tdev22_calculation"><eq/>
<ci>Tdev22</ci>
<apply><plus/>
Expand All @@ -222,7 +113,7 @@
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="Tdev33_calculation_eq">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Tdev33_calculation"><eq/>
<ci>Tdev33</ci>
<apply><plus/>
Expand All @@ -245,7 +136,7 @@
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="Tdev12_calculation_eq">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Tdev12_calculation"><eq/>
<ci>Tdev12</ci>
<apply><minus/>
Expand All @@ -257,7 +148,7 @@
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="Tdev13_calculation_eq">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Tdev13_calculation"><eq/>
<ci>Tdev13</ci>
<apply><minus/>
Expand All @@ -269,7 +160,7 @@
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="Tdev23_calculation_eq">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Tdev23_calculation"><eq/>
<ci>Tdev23</ci>
<apply><minus/>
Expand All @@ -283,8 +174,8 @@
</math>
</component><!--membrane-->

<connection>
<map_components component_1="interface" component_2="equations"/>
<connection component_1="interface" component_2="equations">

<map_variables variable_1="E11" variable_2="E11"/>
<map_variables variable_1="E22" variable_2="E22"/>
<map_variables variable_1="E33" variable_2="E33"/>
Expand All @@ -301,11 +192,11 @@
<map_variables variable_1="c2" variable_2="c2"/>
</connection>

<group>
<relationship_ref relationship="encapsulation"/>
<encapsulation>

<component_ref component="interface">
<component_ref component="equations"/>
</component_ref>
</group>
</encapsulation>

</model>
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