update tikz pictures

SimVascular · Oct 28, 2023 · 5323d1b · 5323d1b
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diff --git a/docs/pages/main.md b/docs/pages/main.md
@@ -34,12 +34,19 @@ reflect the hemodynamics and physiology of different cardiovascular
 anatomies. These 0D models are governed by differential algebraic equations
 (DAEs).
 
-For more background information on 0D models, have a look at SimVascular's
-[ROM Simulation Guide](http://simvascular.github.io/docsROMSimulation.html).
+For more background information on 0D models, have a look at the detailed documentation:
+- System of equations: SparseSystem
+- Time integration: Integrator
+- Overview of available 0D elements (blocks): Block
 
-* <a href="https://github.com/StanfordCBCL/svZeroDPlus">Source
-repository</a>
-* <a href="https://simvascular.github.io">About SimVascular</a>
+You can find more details about governing equations in individual blocks, for example:
+- BloodVessel
+- BloodVesselJunction
+- WindkesselBC
+
+For implementation details, have a look at the [source code](https://github.com/StanfordCBCL/svZeroDPlus).
+
+[About SimVascular](https://simvascular.github.io)
 
 # Installation
 

diff --git a/docs/png/blood_vessel.png b/docs/png/blood_vessel.png
diff --git a/docs/png/blood_vessel_dark.png b/docs/png/blood_vessel_dark.png
diff --git a/docs/png/blood_vessel_junction.png b/docs/png/blood_vessel_junction.png
diff --git a/docs/png/blood_vessel_junction_dark.png b/docs/png/blood_vessel_junction_dark.png
diff --git a/docs/png/blood_vessel_junction_individual.png b/docs/png/blood_vessel_junction_individual.png
diff --git a/docs/png/blood_vessel_junction_individual_dark.png b/docs/png/blood_vessel_junction_individual_dark.png
diff --git a/docs/png/closed_loop_coronary_b_c.png b/docs/png/closed_loop_coronary_b_c.png
diff --git a/docs/png/closed_loop_coronary_b_c_dark.png b/docs/png/closed_loop_coronary_b_c_dark.png
diff --git a/docs/png/closed_loop_r_c_r_b_c.png b/docs/png/closed_loop_r_c_r_b_c.png
diff --git a/docs/png/closed_loop_r_c_r_b_c_dark.png b/docs/png/closed_loop_r_c_r_b_c_dark.png
diff --git a/docs/png/flow_reference_b_c.png b/docs/png/flow_reference_b_c.png
diff --git a/docs/png/flow_reference_b_c_dark.png b/docs/png/flow_reference_b_c_dark.png
diff --git a/docs/png/junction.png b/docs/png/junction.png
diff --git a/docs/png/junction_dark.png b/docs/png/junction_dark.png
diff --git a/docs/png/open_loop_coronary_b_c.png b/docs/png/open_loop_coronary_b_c.png
diff --git a/docs/png/open_loop_coronary_b_c_dark.png b/docs/png/open_loop_coronary_b_c_dark.png
diff --git a/docs/png/pressure_reference_b_c.png b/docs/png/pressure_reference_b_c.png
diff --git a/docs/png/pressure_reference_b_c_dark.png b/docs/png/pressure_reference_b_c_dark.png
diff --git a/docs/png/resistance_b_c.png b/docs/png/resistance_b_c.png
diff --git a/docs/png/resistance_b_c_dark.png b/docs/png/resistance_b_c_dark.png
diff --git a/docs/png/resistive_junction.png b/docs/png/resistive_junction.png
diff --git a/docs/png/resistive_junction_dark.png b/docs/png/resistive_junction_dark.png
diff --git a/docs/png/windkessel_b_c.png b/docs/png/windkessel_b_c.png
diff --git a/docs/png/windkessel_b_c_dark.png b/docs/png/windkessel_b_c_dark.png
diff --git a/src/model/BloodVessel.h b/src/model/BloodVessel.h
@@ -44,19 +44,7 @@
  *
  * Models the mechanical behavior of a bloodvessel with optional stenosis.
  *
- * \f[
- * \begin{circuitikz} \draw
- * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
- * \draw (1,0) node[anchor=south]{$P_{in}$}
- * to [R, l=$R$, *-] (3,0)
- * to [R, l=$S$, -] (5,0)
- * (5,0) to [L, l=$L$, -*] (7,0)
- * node[anchor=south]{$P_{out}$}
- * (5,0) to [C, l=$C$, -] (5,-1.5)
- * node[ground]{};
- * \draw [-latex] (7.2,0) -- (8,0) node[right] {$Q_{out}$};
- * \end{circuitikz}
- * \f]
+ * \image html blood_vessel_dark.png
  *
  * ### Governing equations
  *
@@ -141,6 +129,19 @@
  * * `3` Stenosis coefficient
  *
  */
+//  * \f[
+//  * \begin{circuitikz} \draw
+//  * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
+//  * \draw (1,0) node[anchor=south]{$P_{in}$}
+//  * to [R, l=$R$, *-] (3,0)
+//  * to [R, l=$S$, -] (5,0)
+//  * (5,0) to [L, l=$L$, -*] (7,0)
+//  * node[anchor=south]{$P_{out}$}
+//  * (5,0) to [C, l=$C$, -] (5,-1.5)
+//  * node[ground]{};
+//  * \draw [-latex] (7.2,0) -- (8,0) node[right] {$Q_{out}$};
+//  * \end{circuitikz}
+//  * \f]
 class BloodVessel : public Block {
  public:
   /**

diff --git a/src/model/BloodVesselJunction.h b/src/model/BloodVesselJunction.h
@@ -40,39 +40,16 @@
 #include "SparseSystem.h"
 
 /**
- * @brief BloodVesselJunction
+ * @brief Junction between blood vessels
  *
  * Models a junction with one inlet and arbitrary outlets using
  * modified blood vessel elements between each inlet and outlet pair.
  *
- * \f[
- * \begin{circuitikz}
- * \draw node[left] {$Q_\text{in}$} [-latex] (0,0) -- (0.8,0);
- * \draw (1,0.1) node[anchor=south]{$P_\text{in}$};
- * \draw (1,0) to [short, *-] (2.5,0.75);
- * \draw (1,0) to [short, *-] (2.5,-0.75);
- * \draw (2.5,0.75) node[anchor=south]{} to [generic, l_=$BV_{1}$, -*]
- * (4.5,0.75); \draw (2.4,0.75) node[anchor=south]{}; \draw (4.6,0.75)
- * node[anchor=south] {$P_{out,1}$}; \draw (2.5,-0.75) node[anchor=south]{} to
- * [generic, l^=$BV_{2}$, -*] (4.5,-0.75); \draw (2.4,-0.75)
- * node[anchor=north]{}; \draw (4.6,-0.75) node[anchor=north]
- * {$P_{out,2}$}; \draw [-latex] (4.7,0.75) -- (5.5,0.75) node[right]
- * {$Q_{out,1}$}; \draw [-latex] (4.7,-0.75) -- (5.5,-0.75) node[right]
- * {$Q_{out,2}$}; \end{circuitikz} \f]
+ * \image html blood_vessel_junction_dark.png
  *
  * Each blood vessel is modelled as:
  *
- * \f[
- * \begin{circuitikz} \draw
- * node[left] {$Q_\text{in}$} [-latex] (0,0) -- (0.8,0);
- * \draw (1,0) node[anchor=south]{$P_\text{in}$}
- * to [R, l=$R$, *-] (3,0)
- * to [R, l=$S$, -] (5,0)
- * (5,0) to [L, l=$L$, -*] (7,0)
- * node[anchor=south]{$P_\text{out}$};
- * \draw [-latex] (7.2,0) -- (8,0) node[right] {$Q_\text{out}$};
- * \end{circuitikz}
- * \f]
+ * \image html blood_vessel_junction_individual_dark.png
  *
  * ### Governing equations
  *
@@ -140,6 +117,33 @@
  * * `i+2*num_outlets` Stenosis coefficient for inner blood vessel `i`
  *
  */
+//  * \f[
+//  * \begin{circuitikz}
+//  * \draw node[left] {$Q_\text{in}$} [-latex] (0,0) -- (0.8,0);
+//  * \draw (1,0.1) node[anchor=south]{$P_\text{in}$};
+//  * \draw (1,0) to [short, *-] (2.5,0.75);
+//  * \draw (1,0) to [short, *-] (2.5,-0.75);
+//  * \draw (2.5,0.75) node[anchor=south]{} to [generic, l_=$BV_{1}$, -*]
+//  * (4.5,0.75); \draw (2.4,0.75) node[anchor=south]{}; \draw (4.6,0.75)
+//  * node[anchor=south] {$P_{out,1}$}; \draw (2.5,-0.75) node[anchor=south]{} to
+//  * [generic, l^=$BV_{2}$, -*] (4.5,-0.75); \draw (2.4,-0.75)
+//  * node[anchor=north]{}; \draw (4.6,-0.75) node[anchor=north]
+//  * {$P_{out,2}$}; \draw [-latex] (4.7,0.75) -- (5.5,0.75) node[right]
+//  * {$Q_{out,1}$}; \draw [-latex] (4.7,-0.75) -- (5.5,-0.75) node[right]
+//  * {$Q_{out,2}$}; \end{circuitikz}
+//  * \f]
+// 
+//  * \f[
+//  * \begin{circuitikz} \draw
+//  * node[left] {$Q_\text{in}$} [-latex] (0,0) -- (0.8,0);
+//  * \draw (1,0) node[anchor=south]{$P_\text{in}$}
+//  * to [R, l=$R$, *-] (3,0)
+//  * to [R, l=$S$, -] (5,0)
+//  * (5,0) to [L, l=$L$, -*] (7,0)
+//  * node[anchor=south]{$P_\text{out}$};
+//  * \draw [-latex] (7.2,0) -- (8,0) node[right] {$Q_\text{out}$};
+//  * \end{circuitikz}
+//  * \f]
 class BloodVesselJunction : public Block {
  public:
   // Inherit constructors

diff --git a/src/model/ClosedLoopCoronaryBC.h b/src/model/ClosedLoopCoronaryBC.h
@@ -44,21 +44,7 @@ enum class Side { LEFT, RIGHT, NONE };
  * @brief Closed loop coronary boundary condition (connected to other blocks on
  * both sides).
  *
- * \f[
- * \begin{circuitikz} \draw
- * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
- * \draw (1,0) node[anchor=south]{$P_{in}$}
- * to [R, l=$R_a$, *-] (3,0)
- * to [R, l=$R_{am}$, -] (5,0)
- * to [R, l=$R_v$, *-*] (7,0)
- * node[anchor=south]{$P_{out}$}
- * (5,0) to [C, l=$C_{im} \;V_{im}$, -*] (5,-1.5)
- * node[left]{$P_{im}$}
- * (3,0) to [C, l=$C_a$, -*] (3,-1.5)
- * node[left]{$P_a$};
- * \draw [-latex] (7.2,0) -- (8.0,0) node[right] {$Q_{out}$};
- * \end{circuitikz}
- * \f]
+ * \image html closed_loop_coronary_b_c_dark.png
  *
  * ### Governing equations
  *
@@ -116,6 +102,21 @@ enum class Side { LEFT, RIGHT, NONE };
  * * `4` Cim
  *
  */
+//  * \f[
+//  * \begin{circuitikz} \draw
+//  * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
+//  * \draw (1,0) node[anchor=south]{$P_{in}$}
+//  * to [R, l=$R_a$, *-] (3,0)
+//  * to [R, l=$R_{am}$, -] (5,0)
+//  * to [R, l=$R_v$, *-*] (7,0)
+//  * node[anchor=south]{$P_{out}$}
+//  * (5,0) to [C, l=$C_{im} \;V_{im}$, -*] (5,-1.5)
+//  * node[left]{$P_{im}$}
+//  * (3,0) to [C, l=$C_a$, -*] (3,-1.5)
+//  * node[left]{$P_a$};
+//  * \draw [-latex] (7.2,0) -- (8.0,0) node[right] {$Q_{out}$};
+//  * \end{circuitikz}
+//  * \f]
 class ClosedLoopCoronaryBC : public Block {
  public:
   explicit ClosedLoopCoronaryBC(int id, const std::vector<int> &param_ids,

diff --git a/src/model/ClosedLoopRCRBC.h b/src/model/ClosedLoopRCRBC.h
@@ -43,18 +43,7 @@
  * Models the mechanical behavior of a Windkessel boundary condition that is
  * connected to other blocks on both sides.
  *
- * \f[
- * \begin{circuitikz} \draw
- * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
- * \draw (1,0) node[anchor=south]{$P_{in}$}
- * to [R, l=$R_p$, *-] (3,0)
- * to [R, l=$R_d$, *-*] (5,0)
- * node[anchor=south]{$P_{out}$}
- * (3,0) to [C, l=$C$, *-] (3,-1.5)
- * node[ground]{$P_{C}$};
- * \draw [-latex] (5.2,0) -- (6.0,0) node[right] {$Q_{out}$} ;
- * \end{circuitikz}
- * \f]
+ * \image html closed_loop_r_c_r_b_c_dark.png
  *
  * ### Governing equations
  *
@@ -108,6 +97,18 @@
  * * `2` Distal resistance
  *
  */
+//  * \f[
+//  * \begin{circuitikz} \draw
+//  * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
+//  * \draw (1,0) node[anchor=south]{$P_{in}$}
+//  * to [R, l=$R_p$, *-] (3,0)
+//  * to [R, l=$R_d$, *-*] (5,0)
+//  * node[anchor=south]{$P_{out}$}
+//  * (3,0) to [C, l=$C$, *-] (3,-1.5)
+//  * node[ground]{$P_{C}$};
+//  * \draw [-latex] (5.2,0) -- (6.0,0) node[right] {$Q_{out}$} ;
+//  * \end{circuitikz}
+//  * \f]
 class ClosedLoopRCRBC : public Block {
  public:
   // Inherit constructors

diff --git a/src/model/FlowReferenceBC.h b/src/model/FlowReferenceBC.h
@@ -43,13 +43,7 @@
  *
  * Applies a prescribed flow to a boundary.
  *
- * \f[
- * \begin{circuitikz} \draw
- * node[left] {$\hat{Q}$} [-latex] (0,0) -- (0.8,0);
- * \draw (1,0) node[anchor=south]{$P$} to [short, *-] (1.2,0) ;
- * \draw [-latex] (1.4,0) -- (2.2,0) node[right] {$Q$};
- * \end{circuitikz}
- * \f]
+ * \image html flow_reference_b_c_dark.png
  *
  * ### Governing equations
  *
@@ -78,6 +72,13 @@
  * * `0` Flow
  *
  */
+//  * \f[
+//  * \begin{circuitikz} \draw
+//  * node[left] {$\hat{Q}$} [-latex] (0,0) -- (0.8,0);
+//  * \draw (1,0) node[anchor=south]{$P$} to [short, *-] (1.2,0) ;
+//  * \draw [-latex] (1.4,0) -- (2.2,0) node[right] {$Q$};
+//  * \end{circuitikz}
+//  * \f]
 class FlowReferenceBC : public Block {
  public:
   // Inherit constructors

diff --git a/src/model/Junction.h b/src/model/Junction.h
@@ -43,18 +43,7 @@
  * Models a junction with arbitrary inlets and outlets. Across all inlets and
  * outlets of the junction, mass is conserved and pressure is continuous.
  *
- * \f[
- * \begin{circuitikz}
- * \draw node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
- * \draw (1,0) node[anchor=south]{$P_{in}$} to [short, *-*] (3.0,0);
- * \draw (3,0) node[anchor=south]{} to [short, -*] (4.5,1.0);
- * \draw (4.3,1.1) node[anchor=south] {$P_{out,1}$};
- * \draw (3,0) node[anchor=south]{} to [short, -*] (4.5,-1.0);
- * \draw (4.3,-1.1) node[anchor=north] {$P_{out,2}$};
- * \draw [-latex] (4.65,1.1) -- (5.25,1.5) node[right] {$Q_{out,1}$};
- * \draw [-latex] (4.65,-1.1) -- (5.25,-1.5) node[right] {$Q_{out,2}$};
- * \end{circuitikz}
- * \f]
+ * \image html junction_dark.png
  *
  * ### Governing equations
  *
@@ -85,6 +74,18 @@
  * \quad \mathrm{with} \quad i \neq j \f]
  *
  */
+//  * \f[
+//  * \begin{circuitikz}
+//  * \draw node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
+//  * \draw (1,0) node[anchor=south]{$P_{in}$} to [short, *-*] (3.0,0);
+//  * \draw (3,0) node[anchor=south]{} to [short, -*] (4.5,1.0);
+//  * \draw (4.3,1.1) node[anchor=south] {$P_{out,1}$};
+//  * \draw (3,0) node[anchor=south]{} to [short, -*] (4.5,-1.0);
+//  * \draw (4.3,-1.1) node[anchor=north] {$P_{out,2}$};
+//  * \draw [-latex] (4.65,1.1) -- (5.25,1.5) node[right] {$Q_{out,1}$};
+//  * \draw [-latex] (4.65,-1.1) -- (5.25,-1.5) node[right] {$Q_{out,2}$};
+//  * \end{circuitikz}
+//  * \f]
 class Junction : public Block {
  public:
   using Block::Block;

diff --git a/src/model/OpenLoopCoronaryBC.h b/src/model/OpenLoopCoronaryBC.h
@@ -41,20 +41,7 @@
 /**
  * @brief Open loop coronary boundary condition based on \cite kim_coronary.
  *
- * \f[
- * \begin{circuitikz} \draw
- * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
- * \draw (1,0) node[anchor=south]{$P_{in}$}
- * to [R, l=$R_a$, *-] (3,0)
- * to [R, l=$R_{am}$, -] (5,0)
- * to [R, l=$R_v$, *-*] (7,0)
- * node[anchor=south]{$P_{v}$}
- * (5,0) to [C, l=$C_{im} \;V_{im}$, -*] (5,-1.5)
- * node[left]{$P_{im}$}
- * (3,0) to [C, l=$C_a$, -*] (3,-1.5)
- * node[left]{$P_a$};
- * \end{circuitikz}
- * \f]
+ * \image html open_loop_coronary_b_c_dark.png
  *
  * ### Governing equations
  *
@@ -104,6 +91,20 @@
  * * `6` Pv
  *
  */
+//  * \f[
+//  * \begin{circuitikz} \draw
+//  * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
+//  * \draw (1,0) node[anchor=south]{$P_{in}$}
+//  * to [R, l=$R_a$, *-] (3,0)
+//  * to [R, l=$R_{am}$, -] (5,0)
+//  * to [R, l=$R_v$, *-*] (7,0)
+//  * node[anchor=south]{$P_{v}$}
+//  * (5,0) to [C, l=$C_{im} \;V_{im}$, -*] (5,-1.5)
+//  * node[left]{$P_{im}$}
+//  * (3,0) to [C, l=$C_a$, -*] (3,-1.5)
+//  * node[left]{$P_a$};
+//  * \end{circuitikz}
+//  * \f]
 class OpenLoopCoronaryBC : public Block {
  public:
   // Inherit constructors

diff --git a/src/model/PressureReferenceBC.h b/src/model/PressureReferenceBC.h
@@ -43,14 +43,7 @@
  *
  * Applies a predefined pressure at a boundary.
  *
- * \f[
- * \begin{circuitikz}
- * \draw (1,0) node[anchor=south]{$P$} to [short, *-] (1.2,0) ;
- * \draw [-latex] (1.4,0) -- (2.2,0) node[right] {$Q$};
- * \draw (1,0) to [short, l=, *-] (1,-1)
- * node[ground]{$\hat{P}$};
- * \end{circuitikz}
- * \f]
+ * \image html pressure_reference_b_c_dark.png
  *
  * ### Governing equations
  *
@@ -79,6 +72,14 @@
  * * `0` Pressure
  *
  */
+//  * \f[
+//  * \begin{circuitikz}
+//  * \draw (1,0) node[anchor=south]{$P$} to [short, *-] (1.2,0) ;
+//  * \draw [-latex] (1.4,0) -- (2.2,0) node[right] {$Q$};
+//  * \draw (1,0) to [short, l=, *-] (1,-1)
+//  * node[ground]{$\hat{P}$};
+//  * \end{circuitikz}
+//  * \f]
 class PressureReferenceBC : public Block {
  public:
   // Inherit constructors

diff --git a/src/model/ResistanceBC.h b/src/model/ResistanceBC.h
@@ -41,13 +41,7 @@
 /**
  * @brief Resistance boundary condition.
  *
- * \f[
- * \begin{circuitikz} \draw
- * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
- * \draw (1.0,0) to [R, l=$R$, *-*] (3,0)
- * node[anchor=south]{$P_{d}$};
- * \end{circuitikz}
- * \f]
+ * \image html resistance_b_c_dark.png
  *
  * ### Governing equations
  *
@@ -77,6 +71,13 @@
  * * `1` Distal pressure
  *
  */
+//  * \f[
+//  * \begin{circuitikz} \draw
+//  * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
+//  * \draw (1.0,0) to [R, l=$R$, *-*] (3,0)
+//  * node[anchor=south]{$P_{d}$};
+//  * \end{circuitikz}
+//  * \f]
 class ResistanceBC : public Block {
  public:
   // Inherit constructors