Commit 508bc973 authored by Chris Cantwell's avatar Chris Cantwell

Merge branch 'fix/cardiac-examples' into 'master'

Fix/cardiac examples

This MR fixes the example session files included with the cardiac solver so that they will actually execute.

See merge request !418
parents c9490c9a cd05adb4
......@@ -501,24 +501,27 @@
</COMPOSITE>
<DOMAIN> C[0] </DOMAIN>
</GEOMETRY>
<EXPANSIONS>
<E COMPOSITE="C[0]" NUMMODES="5" FIELDS="u,v" TYPE="MODIFIED" />
</EXPANSIONS>
<CONDITIONS>
<PARAMETERS>
<P> TimeStep = 0.001 </P>
<P> NumSteps = 100000 </P>
<P> FinTime = TimeStep*NumSteps </P>
<P> IO_CheckSteps = 100 </P>
<P> IO_InfoSteps = 10 </P>
<P> initialwavetype = 0 </P>
<P> duration = 1 </P>
<P> UseDirDeriv = 0 </P>
<P> k = 8.0 </P>
<P> a = 0.15 </P>
<P> eps = 0.002 </P>
<P> mu1 = 0.2 </P>
<P> mu2 = 0.3 </P>
<P> TimeStep = 0.001 </P>
<P> FinTime = 100 </P>
<P> NumSteps = FinTime/TimeStep </P>
<P> IO_CheckSteps = 1/TimeStep </P>
<P> IO_InfoSteps = 10 </P>
<P> initialwavetype = 0 </P>
<P> Chi = 28 </P>
<P> Cm = 0.125 </P>
<P> Substeps = 4 </P>
<P> k = 8.0 </P>
<P> a = 0.15 </P>
<P> eps = 0.002 </P>
<P> mu1 = 0.2 </P>
<P> mu2 = 0.3 </P>
</PARAMETERS>
<SOLVERINFO>
......@@ -527,7 +530,6 @@
<I PROPERTY="Projection" VALUE="Continuous" />
<I PROPERTY="DiffusionAdvancement" VALUE="Implicit" />
<I PROPERTY="TimeIntegrationMethod" VALUE="IMEXdirk_3_4_3" />
<I PROPERTY="GlobalSysSoln" VALUE="DirectMultiLevelStaticCond" />
</SOLVERINFO>
<VARIABLES>
......@@ -538,6 +540,7 @@
<BOUNDARYREGIONS>
<B ID="0"> C[1] </B>
</BOUNDARYREGIONS>
<BOUNDARYCONDITIONS>
<REGION REF="0">
<N VAR="u" VALUE="0.0" />
......@@ -546,7 +549,7 @@
</BOUNDARYCONDITIONS>
<FUNCTION NAME="InitialConditions">
<E VAR="u" VALUE="1.0/(1.0 + exp( 32*(x-2.0)))" />
<E VAR="u" VALUE="0" />
<E VAR="v" VALUE="0" />
</FUNCTION>
......@@ -554,8 +557,8 @@
<FILTERS>
<FILTER TYPE="HistoryPoints">
<PARAM NAME="OutputFile">ap.his</PARAM>
<PARAM NAME="OutputFrequency">10</PARAM>
<PARAM NAME="OutputFile"> ap.his </PARAM>
<PARAM NAME="OutputFrequency"> 10 </PARAM>
<PARAM NAME="Points">
1 0.5 0
2 0.5 0
......@@ -569,5 +572,24 @@
</PARAM>
</FILTER>
</FILTERS>
<STIMULI>
<STIMULUS ID="0" TYPE = "StimulusRect">
<p_x1> 0.2</p_x1>
<p_y1> 0.2</p_y1>
<p_z1> 0.0</p_z1>
<p_x2> 0.8</p_x2>
<p_y2> 0.8</p_y2>
<p_z2> 0.0</p_z2>
<p_is> 1.0</p_is>
<p_strength> 2.0 </p_strength>
<PROTOCOL TYPE = "ProtocolSingle">
<START> 0.0 </START>
<DURATION> 1.0 </DURATION>
</PROTOCOL>
</STIMULUS>
</STIMULI>
</NEKTAR>
......@@ -523,10 +523,10 @@
<SOLVERINFO>
<I PROPERTY="EQTYPE" VALUE="Monodomain" />
<I PROPERTY="CellModel" VALUE="CourtemancheRamirezNattel98" />
<I PROPERTY="CellModelVariant" VALUE="Original" />
<I PROPERTY="Projection" VALUE="Continuous"/>
<I PROPERTY="DiffusionAdvancement" VALUE="Implicit"/>
<I PROPERTY="TimeIntegrationMethod" VALUE="IMEXdirk_3_4_3"/>
<I PROPERTY="GlobalSysSoln" VALUE="IterativeStaticCond" />
</SOLVERINFO>
<VARIABLES>
......
......@@ -743,10 +743,11 @@
<SOLVERINFO>
<I PROPERTY="EQTYPE" VALUE="Monodomain" />
<I PROPERTY="CellModel" VALUE="CourtemancheRamirezNattel98" />
<I PROPERTY="CellModelVariant" VALUE="Original" />
<I PROPERTY="Projection" VALUE="Continuous"/>
<I PROPERTY="DiffusionAdvancement" VALUE="Implicit"/>
<I PROPERTY="TimeIntegrationMethod" VALUE="IMEXdirk_3_4_3"/>
<I PROPERTY="GlobalSysSoln" VALUE="DirectStaticCond" />
<I PROPERTY="GlobalSysSoln" VALUE="IterativeStaticCond" />
</SOLVERINFO>
<VARIABLES>
......@@ -782,7 +783,7 @@
<p_y2> 0.8</p_y2>
<p_z2> 0.0</p_z2>
<p_is> 1.0</p_is>
<p_strength> 3.0 </p_strength>
<p_strength> 300.0 </p_strength>
<PROTOCOL TYPE = "ProtocolSingle">
<START> 0.0 </START>
......
......@@ -512,27 +512,18 @@
<P> IO_CheckSteps = 1/TimeStep </P>
<P> IO_InfoSteps = 1 </P>
<P> IO_HistorySteps = 0.05/TimeStep </P>
<P> StimulusDuration = 2.0 </P> <!-- ms -->
<P> StimulusStrength = 3 </P>
<P> ix = 1.0 </P>
<P> iy = 0.5 </P>
<P> iz = 0.0 </P>
<P> ir = 0.05 </P>
<P> is = 1 </P>
<P> C = StimulusStrength </P>
<P> D = StimulusDuration/4.0 </P>
<P> IterativeSolverTolerance = 1e-05 </P>
<P> Chi = 28 </P> <!-- larger: wavefront moves slower -->
<P> Cm = 0.125 </P> <!-- smaller: higher peak mag. of act. -->
<P> Chi = 28 </P>
<P> Cm = 0.125 </P>
</PARAMETERS>
<SOLVERINFO>
<I PROPERTY="EQTYPE" VALUE="Monodomain" />
<I PROPERTY="CellModel" VALUE="TenTusscher06Endo" />
<I PROPERTY="CellModel" VALUE="TenTusscher06" />
<I PROPERTY="CellModelVariant" VALUE="Endocardium" />
<I PROPERTY="Projection" VALUE="Continuous"/>
<I PROPERTY="DiffusionAdvancement" VALUE="Implicit"/>
<I PROPERTY="TimeIntegrationMethod" VALUE="IMEXdirk_3_4_3"/>
<I PROPERTY="GlobalSysSoln" VALUE="IterativeStaticCond" />
<I PROPERTY="TimeIntegrationMethod" VALUE="IMEXOrder1"/>
</SOLVERINFO>
<VARIABLES>
......@@ -553,32 +544,32 @@
<E VAR="u" VALUE="-85.23" />
</FUNCTION>
<FUNCTION NAME="d00">
<FUNCTION NAME="IsotropicConductivity">
<E VAR="intensity" VALUE="0.13341" />
</FUNCTION>
<FUNCTION NAME="d11">
<E VAR="intensity" VALUE="0.13341" />
</FUNCTION>
<FUNCTION NAME="d22">
<E VAR="intensity" VALUE="0.13341" />
</FUNCTION>
<EXPRESSIONS>
<E NAME="P" VALUE="1.0/(1.0 + exp( 32*(x-1)))" />
<E NAME="Q" VALUE="(-tanh((is*x-ix+ir)*(is*x-ix-ir)+(is*y-iy+ir)* (is*y-iy-ir)+(is*z-iz+ir)*(is*z-iz-ir))/2.0+0.5)" />
<E NAME="R" VALUE="exp(-4*(t-D)*(t-D))" />
</EXPRESSIONS>
<FUNCTION NAME="Stimulus">
<E VAR="u" VALUE="C*P" />
<!--<E VAR="u" VALUE="(-tanh((is*x-ix+ir)*(is*x-ix-ir)+(is*y-iy+ir)*
(is* y-iy-ir)+(is*z-iz+ir)*(is*z-iz-ir))/2.0+0.5)*100-81" />-->
<!--<E VAR="u" VALUE="100.0/(1.0 + exp( 32*(x-2.0)))" />-->
</FUNCTION>
</CONDITIONS>
<STIMULI>
<STIMULUS ID="0" TYPE = "StimulusRect">
<p_x1> 0.3</p_x1>
<p_y1> 0.3</p_y1>
<p_z1> 0.0</p_z1>
<p_x2> 0.7</p_x2>
<p_y2> 0.7</p_y2>
<p_z2> 0.0</p_z2>
<p_is> 1.0</p_is>
<p_strength> 300.0 </p_strength>
<PROTOCOL TYPE = "ProtocolS1S2">
<START> 2.0 </START>
<DURATION> 2.0 </DURATION>
<S1CYCLELENGTH> 300.0 </S1CYCLELENGTH>
<NUM_S1> 2.0 </NUM_S1>
<S2CYCLELENGTH>100.0 </S2CYCLELENGTH>
</PROTOCOL>
</STIMULUS>
</STIMULI>
<FILTERS>
<FILTER TYPE="HistoryPoints">
<PARAM NAME="OutputFile">tt06endo.his</PARAM>
......
......@@ -512,27 +512,18 @@
<P> IO_CheckSteps = 1/TimeStep </P>
<P> IO_InfoSteps = 1 </P>
<P> IO_HistorySteps = 0.05/TimeStep </P>
<P> StimulusDuration = 2.0 </P> <!-- ms -->
<P> StimulusStrength = 3 </P>
<P> ix = 1.0 </P>
<P> iy = 0.5 </P>
<P> iz = 0.0 </P>
<P> ir = 0.05 </P>
<P> is = 1 </P>
<P> C = StimulusStrength </P>
<P> D = StimulusDuration/4.0 </P>
<P> IterativeSolverTolerance = 1e-05 </P>
<P> Chi = 28 </P> <!-- larger: wavefront moves slower -->
<P> Cm = 0.125 </P> <!-- smaller: higher peak mag. of act. -->
<P> Chi = 28 </P>
<P> Cm = 0.125 </P>
</PARAMETERS>
<SOLVERINFO>
<I PROPERTY="EQTYPE" VALUE="Monodomain" />
<I PROPERTY="CellModel" VALUE="TenTusscher06Epi" />
<I PROPERTY="CellModel" VALUE="TenTusscher06" />
<I PROPERTY="CellModelVariant" VALUE="Epicardium" />
<I PROPERTY="Projection" VALUE="Continuous"/>
<I PROPERTY="DiffusionAdvancement" VALUE="Implicit"/>
<I PROPERTY="TimeIntegrationMethod" VALUE="IMEXdirk_3_4_3"/>
<I PROPERTY="GlobalSysSoln" VALUE="IterativeStaticCond" />
<I PROPERTY="TimeIntegrationMethod" VALUE="IMEXOrder1"/>
</SOLVERINFO>
<VARIABLES>
......@@ -553,35 +544,35 @@
<E VAR="u" VALUE="-85.23" />
</FUNCTION>
<FUNCTION NAME="d00">
<FUNCTION NAME="IsotropicConductivity">
<E VAR="intensity" VALUE="0.13341" />
</FUNCTION>
<FUNCTION NAME="d11">
<E VAR="intensity" VALUE="0.13341" />
</FUNCTION>
<FUNCTION NAME="d22">
<E VAR="intensity" VALUE="0.13341" />
</FUNCTION>
<EXPRESSIONS>
<E NAME="P" VALUE="1.0/(1.0 + exp( 32*(x-1)))" />
<E NAME="Q" VALUE="(-tanh((is*x-ix+ir)*(is*x-ix-ir)+(is*y-iy+ir)* (is*y-iy-ir)+(is*z-iz+ir)*(is*z-iz-ir))/2.0+0.5)" />
<E NAME="R" VALUE="exp(-4*(t-D)*(t-D))" />
</EXPRESSIONS>
<FUNCTION NAME="Stimulus">
<E VAR="u" VALUE="C*P" />
<!--<E VAR="u" VALUE="(-tanh((is*x-ix+ir)*(is*x-ix-ir)+(is*y-iy+ir)*
(is* y-iy-ir)+(is*z-iz+ir)*(is*z-iz-ir))/2.0+0.5)*100-81" />-->
<!--<E VAR="u" VALUE="100.0/(1.0 + exp( 32*(x-2.0)))" />-->
</FUNCTION>
</CONDITIONS>
<STIMULI>
<STIMULUS ID="0" TYPE = "StimulusRect">
<p_x1> 0.3</p_x1>
<p_y1> 0.3</p_y1>
<p_z1> 0.0</p_z1>
<p_x2> 0.7</p_x2>
<p_y2> 0.7</p_y2>
<p_z2> 0.0</p_z2>
<p_is> 1.0</p_is>
<p_strength> 300.0 </p_strength>
<PROTOCOL TYPE = "ProtocolS1S2">
<START> 2.0 </START>
<DURATION> 2.0 </DURATION>
<S1CYCLELENGTH> 300.0 </S1CYCLELENGTH>
<NUM_S1> 2.0 </NUM_S1>
<S2CYCLELENGTH>100.0 </S2CYCLELENGTH>
</PROTOCOL>
</STIMULUS>
</STIMULI>
<FILTERS>
<FILTER TYPE="HistoryPoints">
<PARAM NAME="OutputFile">tt06epi.his</PARAM>
<PARAM NAME="OutputFile">tt06endo.his</PARAM>
<PARAM NAME="OutputFrequency">10</PARAM>
<PARAM NAME="Points">
1 0.5 0
......@@ -597,4 +588,5 @@
</FILTER>
</FILTERS>
</NEKTAR>
......@@ -512,27 +512,18 @@
<P> IO_CheckSteps = 1/TimeStep </P>
<P> IO_InfoSteps = 1 </P>
<P> IO_HistorySteps = 0.05/TimeStep </P>
<P> StimulusDuration = 2.0 </P> <!-- ms -->
<P> StimulusStrength = 3 </P>
<P> ix = 1.0 </P>
<P> iy = 0.5 </P>
<P> iz = 0.0 </P>
<P> ir = 0.05 </P>
<P> is = 1 </P>
<P> C = StimulusStrength </P>
<P> D = StimulusDuration/4.0 </P>
<P> IterativeSolverTolerance = 1e-05 </P>
<P> Chi = 28 </P> <!-- larger: wavefront moves slower -->
<P> Cm = 0.125 </P> <!-- smaller: higher peak mag. of act. -->
<P> Chi = 28 </P>
<P> Cm = 0.125 </P>
</PARAMETERS>
<SOLVERINFO>
<I PROPERTY="EQTYPE" VALUE="Monodomain" />
<I PROPERTY="CellModel" VALUE="TenTusscher06M" />
<I PROPERTY="CellModel" VALUE="TenTusscher06" />
<I PROPERTY="CellModelVariant" VALUE="Mid" />
<I PROPERTY="Projection" VALUE="Continuous"/>
<I PROPERTY="DiffusionAdvancement" VALUE="Implicit"/>
<I PROPERTY="TimeIntegrationMethod" VALUE="IMEXdirk_3_4_3"/>
<I PROPERTY="GlobalSysSoln" VALUE="IterativeStaticCond" />
<I PROPERTY="TimeIntegrationMethod" VALUE="IMEXOrder1"/>
</SOLVERINFO>
<VARIABLES>
......@@ -553,35 +544,35 @@
<E VAR="u" VALUE="-85.23" />
</FUNCTION>
<FUNCTION NAME="d00">
<FUNCTION NAME="IsotropicConductivity">
<E VAR="intensity" VALUE="0.13341" />
</FUNCTION>
<FUNCTION NAME="d11">
<E VAR="intensity" VALUE="0.13341" />
</FUNCTION>
<FUNCTION NAME="d22">
<E VAR="intensity" VALUE="0.13341" />
</FUNCTION>
<EXPRESSIONS>
<E NAME="P" VALUE="1.0/(1.0 + exp( 32*(x-1)))" />
<E NAME="Q" VALUE="(-tanh((is*x-ix+ir)*(is*x-ix-ir)+(is*y-iy+ir)* (is*y-iy-ir)+(is*z-iz+ir)*(is*z-iz-ir))/2.0+0.5)" />
<E NAME="R" VALUE="exp(-4*(t-D)*(t-D))" />
</EXPRESSIONS>
<FUNCTION NAME="Stimulus">
<E VAR="u" VALUE="C*P" />
<!--<E VAR="u" VALUE="(-tanh((is*x-ix+ir)*(is*x-ix-ir)+(is*y-iy+ir)*
(is* y-iy-ir)+(is*z-iz+ir)*(is*z-iz-ir))/2.0+0.5)*100-81" />-->
<!--<E VAR="u" VALUE="100.0/(1.0 + exp( 32*(x-2.0)))" />-->
</FUNCTION>
</CONDITIONS>
<STIMULI>
<STIMULUS ID="0" TYPE = "StimulusRect">
<p_x1> 0.3</p_x1>
<p_y1> 0.3</p_y1>
<p_z1> 0.0</p_z1>
<p_x2> 0.7</p_x2>
<p_y2> 0.7</p_y2>
<p_z2> 0.0</p_z2>
<p_is> 1.0</p_is>
<p_strength> 300.0 </p_strength>
<PROTOCOL TYPE = "ProtocolS1S2">
<START> 2.0 </START>
<DURATION> 2.0 </DURATION>
<S1CYCLELENGTH> 300.0 </S1CYCLELENGTH>
<NUM_S1> 2.0 </NUM_S1>
<S2CYCLELENGTH>100.0 </S2CYCLELENGTH>
</PROTOCOL>
</STIMULUS>
</STIMULI>
<FILTERS>
<FILTER TYPE="HistoryPoints">
<PARAM NAME="OutputFile">tt06m.his</PARAM>
<PARAM NAME="OutputFile">tt06endo.his</PARAM>
<PARAM NAME="OutputFrequency">10</PARAM>
<PARAM NAME="Points">
1 0.5 0
......@@ -597,4 +588,5 @@
</FILTER>
</FILTERS>
</NEKTAR>
......@@ -8,8 +8,13 @@
</PARAMETERS>
<SOLVERINFO>
<I PROPERTY="CellModel" VALUE="CourtemancheRamirezNattel98cAF" />
<I PROPERTY="CellModel" VALUE="CourtemancheRamirezNattel98" />
<I PROPERTY="CellModelVariant" VALUE="Original" />
</SOLVERINFO>
<FUNCTION NAME="InitialConditions">
<E VAR="u" VALUE="0" />
</FUNCTION>
</CONDITIONS>
<STIMULI>
......
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