deploy: 8a58d68

_block_8h_source.html

@@ -456,7 +456,7 @@
 <div class="ttc" id="aclass_d_o_f_handler_html"><div class="ttname"><a href="class_d_o_f_handler.html">DOFHandler</a></div><div class="ttdoc">Degree-of-freedom handler.</div><div class="ttdef"><b>Definition</b> DOFHandler.h:48</div></div>
 <div class="ttc" id="aclass_model_html"><div class="ttname"><a href="class_model.html">Model</a></div><div class="ttdoc">Model of 0D elements.</div><div class="ttdef"><b>Definition</b> Model.h:75</div></div>
 <div class="ttc" id="aclass_node_html"><div class="ttname"><a href="class_node.html">Node</a></div><div class="ttdoc">Node.</div><div class="ttdef"><b>Definition</b> Node.h:53</div></div>
-<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:88</div></div>
+<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:57</div></div>
 <div class="ttc" id="aclass_state_html"><div class="ttname"><a href="class_state.html">State</a></div><div class="ttdoc">State of the system.</div><div class="ttdef"><b>Definition</b> State.h:46</div></div>
 <div class="ttc" id="astruct_triplets_contributions_html"><div class="ttname"><a href="struct_triplets_contributions.html">TripletsContributions</a></div><div class="ttdoc">The number of triplets that the element contributes to the global system.</div><div class="ttdef"><b>Definition</b> Block.h:52</div></div>
 <div class="ttc" id="astruct_triplets_contributions_html_a6d259056f32a5f2bca1366494b78e4fb"><div class="ttname"><a href="struct_triplets_contributions.html#a6d259056f32a5f2bca1366494b78e4fb">TripletsContributions::E</a></div><div class="ttdeci">int E</div><div class="ttdoc">Contributions to E matrix.</div><div class="ttdef"><b>Definition</b> Block.h:83</div></div>

_blood_vessel_8h_source.html

@@ -346,7 +346,7 @@
 <div class="ttc" id="aclass_blood_vessel_html_ad6237cd700152e4b9d9ac64f55d2e4fd"><div class="ttname"><a href="class_blood_vessel.html#ad6237cd700152e4b9d9ac64f55d2e4fd">BloodVessel::setup_dofs</a></div><div class="ttdeci">void setup_dofs(DOFHandler &amp;dofhandler)</div><div class="ttdoc">Set up the degrees of freedom (DOF) of the block.</div><div class="ttdef"><b>Definition</b> BloodVessel.cpp:33</div></div>
 <div class="ttc" id="aclass_d_o_f_handler_html"><div class="ttname"><a href="class_d_o_f_handler.html">DOFHandler</a></div><div class="ttdoc">Degree-of-freedom handler.</div><div class="ttdef"><b>Definition</b> DOFHandler.h:48</div></div>
 <div class="ttc" id="aclass_model_html"><div class="ttname"><a href="class_model.html">Model</a></div><div class="ttdoc">Model of 0D elements.</div><div class="ttdef"><b>Definition</b> Model.h:75</div></div>
-<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:88</div></div>
+<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:57</div></div>
 <div class="ttc" id="astruct_input_parameter_html"><div class="ttname"><a href="struct_input_parameter.html">InputParameter</a></div><div class="ttdoc">Handles the properties of input parameters.</div><div class="ttdef"><b>Definition</b> Parameter.h:127</div></div>
 <div class="ttc" id="astruct_triplets_contributions_html"><div class="ttname"><a href="struct_triplets_contributions.html">TripletsContributions</a></div><div class="ttdoc">The number of triplets that the element contributes to the global system.</div><div class="ttdef"><b>Definition</b> Block.h:52</div></div>
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_blood_vessel_junction_8h_source.html

@@ -339,7 +339,7 @@
 <div class="ttc" id="aclass_blood_vessel_junction_html_ac5f485c4d9dbf15546d6705b9874fc09"><div class="ttname"><a href="class_blood_vessel_junction.html#ac5f485c4d9dbf15546d6705b9874fc09">BloodVesselJunction::update_solution</a></div><div class="ttdeci">virtual void update_solution(SparseSystem &amp;system, std::vector&lt; double &gt; &amp;parameters, const Eigen::Matrix&lt; double, Eigen::Dynamic, 1 &gt; &amp;y, const Eigen::Matrix&lt; double, Eigen::Dynamic, 1 &gt; &amp;dy)</div><div class="ttdoc">Update the solution-dependent contributions of the element in a sparse system.</div><div class="ttdef"><b>Definition</b> BloodVesselJunction.cpp:65</div></div>
 <div class="ttc" id="aclass_d_o_f_handler_html"><div class="ttname"><a href="class_d_o_f_handler.html">DOFHandler</a></div><div class="ttdoc">Degree-of-freedom handler.</div><div class="ttdef"><b>Definition</b> DOFHandler.h:48</div></div>
 <div class="ttc" id="aclass_model_html"><div class="ttname"><a href="class_model.html">Model</a></div><div class="ttdoc">Model of 0D elements.</div><div class="ttdef"><b>Definition</b> Model.h:75</div></div>
-<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:88</div></div>
+<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:57</div></div>
 <div class="ttc" id="astruct_input_parameter_html"><div class="ttname"><a href="struct_input_parameter.html">InputParameter</a></div><div class="ttdoc">Handles the properties of input parameters.</div><div class="ttdef"><b>Definition</b> Parameter.h:127</div></div>
 <div class="ttc" id="astruct_triplets_contributions_html"><div class="ttname"><a href="struct_triplets_contributions.html">TripletsContributions</a></div><div class="ttdoc">The number of triplets that the element contributes to the global system.</div><div class="ttdef"><b>Definition</b> Block.h:52</div></div>
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_chamber_elastance_inductor_8h_source.html

@@ -344,7 +344,7 @@
 <div class="ttc" id="aclass_chamber_elastance_inductor_html_add4b006f8d6484b5c36a9855a4094379"><div class="ttname"><a href="class_chamber_elastance_inductor.html#add4b006f8d6484b5c36a9855a4094379">ChamberElastanceInductor::update_constant</a></div><div class="ttdeci">void update_constant(SparseSystem &amp;system, std::vector&lt; double &gt; &amp;parameters)</div><div class="ttdoc">Update the constant contributions of the element in a sparse system.</div><div class="ttdef"><b>Definition</b> ChamberElastanceInductor.cpp:38</div></div>
 <div class="ttc" id="aclass_d_o_f_handler_html"><div class="ttname"><a href="class_d_o_f_handler.html">DOFHandler</a></div><div class="ttdoc">Degree-of-freedom handler.</div><div class="ttdef"><b>Definition</b> DOFHandler.h:48</div></div>
 <div class="ttc" id="aclass_model_html"><div class="ttname"><a href="class_model.html">Model</a></div><div class="ttdoc">Model of 0D elements.</div><div class="ttdef"><b>Definition</b> Model.h:75</div></div>
-<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:88</div></div>
+<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:57</div></div>
 <div class="ttc" id="adebug_8h_html"><div class="ttname"><a href="debug_8h.html">debug.h</a></div><div class="ttdoc">DEBUG_MSG source file.</div></div>
 <div class="ttc" id="astruct_input_parameter_html"><div class="ttname"><a href="struct_input_parameter.html">InputParameter</a></div><div class="ttdoc">Handles the properties of input parameters.</div><div class="ttdef"><b>Definition</b> Parameter.h:127</div></div>
 <div class="ttc" id="astruct_triplets_contributions_html"><div class="ttname"><a href="struct_triplets_contributions.html">TripletsContributions</a></div><div class="ttdoc">The number of triplets that the element contributes to the global system.</div><div class="ttdef"><b>Definition</b> Block.h:52</div></div>

_closed_loop_coronary_b_c_8h_source.html

@@ -316,7 +316,7 @@
 <div class="ttc" id="aclass_closed_loop_coronary_b_c_html_af8c87a131555bdcc39e8b99e6ec52209"><div class="ttname"><a href="class_closed_loop_coronary_b_c.html#af8c87a131555bdcc39e8b99e6ec52209">ClosedLoopCoronaryBC::im_param_id</a></div><div class="ttdeci">int im_param_id</div><div class="ttdoc">Index of parameter Im.</div><div class="ttdef"><b>Definition</b> ClosedLoopCoronaryBC.h:196</div></div>
 <div class="ttc" id="aclass_d_o_f_handler_html"><div class="ttname"><a href="class_d_o_f_handler.html">DOFHandler</a></div><div class="ttdoc">Degree-of-freedom handler.</div><div class="ttdef"><b>Definition</b> DOFHandler.h:48</div></div>
 <div class="ttc" id="aclass_model_html"><div class="ttname"><a href="class_model.html">Model</a></div><div class="ttdoc">Model of 0D elements.</div><div class="ttdef"><b>Definition</b> Model.h:75</div></div>
-<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:88</div></div>
+<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:57</div></div>
 <div class="ttc" id="astruct_input_parameter_html"><div class="ttname"><a href="struct_input_parameter.html">InputParameter</a></div><div class="ttdoc">Handles the properties of input parameters.</div><div class="ttdef"><b>Definition</b> Parameter.h:127</div></div>
 <div class="ttc" id="astruct_triplets_contributions_html"><div class="ttname"><a href="struct_triplets_contributions.html">TripletsContributions</a></div><div class="ttdoc">The number of triplets that the element contributes to the global system.</div><div class="ttdef"><b>Definition</b> Block.h:52</div></div>
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_closed_loop_heart_pulmonary_8h_source.html

@@ -404,7 +404,7 @@
 <div class="ttc" id="aclass_closed_loop_heart_pulmonary_html_af79757e8bbfaf0209d119ed9950a6f09"><div class="ttname"><a href="class_closed_loop_heart_pulmonary.html#af79757e8bbfaf0209d119ed9950a6f09">ClosedLoopHeartPulmonary::update_constant</a></div><div class="ttdeci">void update_constant(SparseSystem &amp;system, std::vector&lt; double &gt; &amp;parameters)</div><div class="ttdoc">Update the constant contributions of the element in a sparse system.</div><div class="ttdef"><b>Definition</b> ClosedLoopHeartPulmonary.cpp:41</div></div>
 <div class="ttc" id="aclass_d_o_f_handler_html"><div class="ttname"><a href="class_d_o_f_handler.html">DOFHandler</a></div><div class="ttdoc">Degree-of-freedom handler.</div><div class="ttdef"><b>Definition</b> DOFHandler.h:48</div></div>
 <div class="ttc" id="aclass_model_html"><div class="ttname"><a href="class_model.html">Model</a></div><div class="ttdoc">Model of 0D elements.</div><div class="ttdef"><b>Definition</b> Model.h:75</div></div>
-<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:88</div></div>
+<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:57</div></div>
 <div class="ttc" id="astruct_input_parameter_html"><div class="ttname"><a href="struct_input_parameter.html">InputParameter</a></div><div class="ttdoc">Handles the properties of input parameters.</div><div class="ttdef"><b>Definition</b> Parameter.h:127</div></div>
 <div class="ttc" id="astruct_triplets_contributions_html"><div class="ttname"><a href="struct_triplets_contributions.html">TripletsContributions</a></div><div class="ttdoc">The number of triplets that the element contributes to the global system.</div><div class="ttdef"><b>Definition</b> Block.h:52</div></div>
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_closed_loop_r_c_r_b_c_8h_source.html

@@ -288,7 +288,7 @@
 <div class="ttc" id="aclass_closed_loop_r_c_r_b_c_html_aea28d78775993cf4bd04b1e2289cb815"><div class="ttname"><a href="class_closed_loop_r_c_r_b_c.html#aea28d78775993cf4bd04b1e2289cb815">ClosedLoopRCRBC::num_triplets</a></div><div class="ttdeci">TripletsContributions num_triplets</div><div class="ttdoc">Number of triplets of element.</div><div class="ttdef"><b>Definition</b> ClosedLoopRCRBC.h:172</div></div>
 <div class="ttc" id="aclass_d_o_f_handler_html"><div class="ttname"><a href="class_d_o_f_handler.html">DOFHandler</a></div><div class="ttdoc">Degree-of-freedom handler.</div><div class="ttdef"><b>Definition</b> DOFHandler.h:48</div></div>
 <div class="ttc" id="aclass_model_html"><div class="ttname"><a href="class_model.html">Model</a></div><div class="ttdoc">Model of 0D elements.</div><div class="ttdef"><b>Definition</b> Model.h:75</div></div>
-<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:88</div></div>
+<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:57</div></div>
 <div class="ttc" id="astruct_input_parameter_html"><div class="ttname"><a href="struct_input_parameter.html">InputParameter</a></div><div class="ttdoc">Handles the properties of input parameters.</div><div class="ttdef"><b>Definition</b> Parameter.h:127</div></div>
 <div class="ttc" id="astruct_triplets_contributions_html"><div class="ttname"><a href="struct_triplets_contributions.html">TripletsContributions</a></div><div class="ttdoc">The number of triplets that the element contributes to the global system.</div><div class="ttdef"><b>Definition</b> Block.h:52</div></div>
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_flow_reference_b_c_8h_source.html

@@ -248,7 +248,7 @@
 <div class="ttc" id="aclass_flow_reference_b_c_html_aae1023a7f630e44b7936cc97e77421cc"><div class="ttname"><a href="class_flow_reference_b_c.html#aae1023a7f630e44b7936cc97e77421cc">FlowReferenceBC::update_time</a></div><div class="ttdeci">void update_time(SparseSystem &amp;system, std::vector&lt; double &gt; &amp;parameters)</div><div class="ttdoc">Update the time-dependent contributions of the element in a sparse system.</div><div class="ttdef"><b>Definition</b> FlowReferenceBC.cpp:42</div></div>
 <div class="ttc" id="aclass_flow_reference_b_c_html_af76423e0e994859b071fa1066d562aa4"><div class="ttname"><a href="class_flow_reference_b_c.html#af76423e0e994859b071fa1066d562aa4">FlowReferenceBC::num_triplets</a></div><div class="ttdeci">TripletsContributions num_triplets</div><div class="ttdoc">Number of triplets of element.</div><div class="ttdef"><b>Definition</b> FlowReferenceBC.h:133</div></div>
 <div class="ttc" id="aclass_model_html"><div class="ttname"><a href="class_model.html">Model</a></div><div class="ttdoc">Model of 0D elements.</div><div class="ttdef"><b>Definition</b> Model.h:75</div></div>
-<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:88</div></div>
+<div class="ttc" id="aclass_sparse_system_html"><div class="ttname"><a href="class_sparse_system.html">SparseSystem</a></div><div class="ttdoc">Sparse system.</div><div class="ttdef"><b>Definition</b> SparseSystem.h:57</div></div>
 <div class="ttc" id="astruct_input_parameter_html"><div class="ttname"><a href="struct_input_parameter.html">InputParameter</a></div><div class="ttdoc">Handles the properties of input parameters.</div><div class="ttdef"><b>Definition</b> Parameter.h:127</div></div>
 <div class="ttc" id="astruct_triplets_contributions_html"><div class="ttname"><a href="struct_triplets_contributions.html">TripletsContributions</a></div><div class="ttdoc">The number of triplets that the element contributes to the global system.</div><div class="ttdef"><b>Definition</b> Block.h:52</div></div>
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_g_u_i.html

@@ -97,7 +97,7 @@
  <a href="#autotoc_md9">Architecture</a>
  </li>
  <li class="level1">
- <a href="#autotoc_md10">How to Use</a>
+ <a href="#autotoc_md10">User guide</a>
  </li>
 </ul>
 </div>
@@ -112,24 +112,8 @@ <h1><a class="anchor" id="autotoc_md9"></a>
 <li>Backend: Flask app, Node.js for server-side logic, and Cypress for testing. This architecture supports an intuitive user experience for generating and managing 0D input files through a graphical interface.</li>
 </ul>
 <h1><a class="anchor" id="autotoc_md10"></a>
-How to Use</h1>
-<ol type="1">
-<li>Create a virtual environment with the required <code>flask</code> dependency. If using <code>conda</code>, use the below commands: <div class="fragment"><div class="line">conda create -n svZeroDGUI python=3.10 flask</div>
-<div class="line">conda activate svZeroDGUI</div>
-</div><!-- fragment --></li>
-<li>Navigate to the <code>applications</code> folder and then to the <code>create_0dmodel</code> subdirectory.</li>
-<li>Launch the <code>app.py</code> file. <div class="fragment"><div class="line">python applications/svZeroDGUI/app.py</div>
-</div><!-- fragment --></li>
-<li>Select a node type and name the node.<ul>
-<li>For vessels, after drawing the node, click on it to open a form where you can enter details such as vessel length, diameter, and more.</li>
-<li>For junctions, click the node to specify if it’s a Normal Junction or a Blood Vessel Junction.</li>
-</ul>
-</li>
-<li>To draw edges between nodes, toggle the <code>Draw on</code> button on the right. Once active, you can start connecting nodes by drawing edges between them.</li>
-<li>When you wish to stop drawing edges and continue adding or moving nodes, click the <code>Draw off</code> button.</li>
-<li>Once you’ve completed the network, click <code>Export to JSON</code> on the right. If there are any incorrect connections or patterns, an alert will prompt you to make necessary changes so the network can be processed by svZeroDSolver.</li>
-<li>Open the downloaded JSON file and add any additional information, such as boundary condition data, before running it through svZeroDSolver. </li>
-</ol>
+User guide</h1>
+<p>A user guide is available on the <a href="https://simvascular.github.io/documentation/rom_simulation.html#0d-solver-gui">SimVascular website</a>. </p>
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