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Remove the CFD Simulation section.
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documentation/getting_started.html

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@@ -195,7 +195,6 @@ <h4 class="skipTo tutorial">Tutorial</h4>
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<p class="skipTo tutorial_create_segmentations">Create Segmentations</p>
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<p class="skipTo tutorial_create_solid_model">Create Solid Model</p>
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<p class="skipTo tutorial_create_finite_element_mesh">Create Finite Element Mesh</p>
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<p class="skipTo tutorial_create_simulation">Create CFD Simulation</p>
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<p class="skipTo tutorial_summary">Summary</p>
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</div>
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</div>

documentation/getting_started/tutorial/create_finite_element_mesh/readme.md

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<h2 id="tutorial_create_finite_element_mesh">Create Finite Element Mesh</h2>
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The continuous volume enclosed by a solid model of vascular anatomy is subdivided into discrete tetrahedral elements using mesh
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generation software. This finite element mesh is used by the SimVascular <i>svSolver</i> and <i>svFsi</i> computational fluid
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dynamics programs to simulate blood flow in a vascular network.
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generation software. This finite element mesh is used by the SimVascular <i>svMultiPhysics</i> program to simulate blood flow in a vascular network.
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A good mesh is integral to finite element CFD simulation techniques. It enables computers to numerically solve the
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underlying governing fluid equations and simulate physical effects. The mesh quality influences the accuracy, convergence,

documentation/getting_started/tutorial/create_simulation/readme.md renamed to documentation/getting_started/tutorial/create_simulation.not-used/readme.md

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@@ -5,7 +5,7 @@ models of the human vasculature. CFD solvers used for such simulations must acco
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conditions, physiologic models and physics specific to cardiovascular modeling.
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The <i>Simulations Tool</i> has functionality to assign boundary conditions, material properties, and set parameters for the
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SimVascular <i>svSolver</i> CFD solver. <i>svSolver</i> can be run through the GUI for testing a simulation setup. However,
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SimVascular <i>svMultiPhysics</i> solver. The <i>svMultiPhysics</i> can be run through the GUI for testing a simulation setup. However,
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for simulating physiological relevant time scales the simulation files are generated on a desktop, copied to a high performance
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computing (HPC) cluster, and run in parallel there.
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<br>
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<div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #e6e600; border-left: 6px solid #e6e600">
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The <i>svSolver</i> CFD solver does not use any predefined units. All values used for physical parameters (e.g. fluid density)
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The <i>svMultiPhysics</i> solver does not use any predefined units. All values used for physical parameters (e.g. fluid density)
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and boundary conditions must be consistent with the spatial dimensions of the finite element mesh.
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</div>
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<br>
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The following sections demonstrate how to setup a CFD simulation for <i>svSolver</i> using the <b>aorta-iliacs</b> solid model
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The following sections demonstrate how to setup a CFD simulation for <i>svMultiPhysics</i> using the <b>aorta-iliacs</b> solid model
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and finite element mesh. A detailed discussion about CFD simulations can be found in the SimVascular
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<a href="flowsolver.html">Simulation Guide</a> documentation.
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<a href="flowsolver.html">CFD Simulation Guide</a> documentation.
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<h3 id="tutorial_create_simulation_1"> Create an instance of a <i>Simulations Tool</i> for the <b>aorta-iliacs</b> model. </h3>
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<tr>
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<td><img src="/documentation/getting_started/tutorial/images/create-simulation-12.png" width="512" height="360"> </td>
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<td> The <i>ToolBox</i> <b>Solver Parameters</b> page is used to set the parameters controlling <i>svSolver</i>
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<td> The <i>ToolBox</i> <b>Solver Parameters</b> page is used to set the parameters controlling <i>svMultiPhysics</i>
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solution and output. Parameter values are entered by clicking with the left mouse button on the appropriate
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<i>TextBox</i>.
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<br><br>
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<h3 id="tutorial_create_simulation_4"> Run the simulation. </h3>
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This section demonstrates how run the simulation.
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The <i>svSolver</i> program can be run as a single process using one processor (core) or in parallel using two or more processors.
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<i>svSolver</i> uses the <i>Open MPI</i> implementation of the Message Passing Interface (MPI) to run in parallel. The <i>Open MPI</i>
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libraries must be installed in order to run <i>svSolver</i> in parallel. In this demonstration the <i>svSolver</i> program is run
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The <i>svMultiPhysics</i> program can be run as a single process using one processor (core) or in parallel using two or more processors.
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<i>svMultiPhysics</i> uses the <i>Open MPI</i> implementation of the Message Passing Interface (MPI) to run in parallel. The <i>Open MPI</i>
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libraries must be installed in order to run <i>svMultiPhysics</i> in parallel. In this demonstration the <i>svMultiPhysics</i> program is run
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on a single processor.
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<div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #d0d0d0; border-left: 6px solid #d0d0d0">
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The SimVascular <i>svSolver</i> program is included in the Windows SimVascular application installer. For MacOS and Ubuntu
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platforms it must be installed using a separate <i>svSolver</i> installer downloaded from
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The SimVascular <i>svMultiPhysics</i> program is included in the Windows SimVascular application installer. For MacOS and Ubuntu
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platforms it must be installed using a separate <i>svMultiPhysics</i> installer downloaded from
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<a href="https://simtk.org/frs/?group_id=188"> SimTK </a>
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</div>
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<td><img src="/documentation/getting_started/tutorial/images/create-simulation-13.png" width="512" height="360"> </td>
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<td> The <i>ToolBox</i> <b>Create Files and Run Simulation</b> page is used to run <i>svSolver</i>.
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<td> The <i>ToolBox</i> <b>Create Files and Run Simulation</b> page is used to run <i>svMultiPhysics</i>.
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<br><br>
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Select the <b>aorta-iliacs</b> from the <b>Choose Mesh:</b> <i>ComboBox</i>.
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<br><br>
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Press the <b>Run Simulation</b> <i>Button</i>.
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<br><br>
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The <i>svSolver</i> program is run on a single processor and should take several minutes to complete.
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The <i>svMultiPhysics</i> program is run on a single processor and should take several minutes to complete.
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<br><br>
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<div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #d0d0d0; border-left: 6px solid #d0d0d0">
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The <i>svSolver</i> program can be run in parallel by selecting the <b>Use MPI</b> <i>CheckBox</i> and setting the
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The <i>svMultiPhysics</i> program can be run in parallel by selecting the <b>Use MPI</b> <i>CheckBox</i> and setting the
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<b>Number of Processors</b> <i>Slider</i> to 2 or larger.
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</div>
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</td>
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<td><img src="/documentation/getting_started/tutorial/images/create-simulation-17.png" width="512" height="360"> </td>
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<td> The <i>ToolBox</i> <b>Convert Results</b> page is used to convert <i>svSolver</i> results files into VTK format files.
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<td> The <i>ToolBox</i> <b>Convert Results</b> page is used to convert <i>svMultiPhysics</i> results files into VTK format files.
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<br><br>
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GUI controls:
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<br><br>

documentation/getting_started/tutorial/intro/readme.md

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<h1 id="tutorial"> Tutorial </h1>
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This section demonstrates how to use the SimVascular image-based modeling pipeline to create a patient-specific geometric model
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of the human vasculature and perform a finite element computational fluid dynamics (CFD) simulation of blood flow for that model.
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A model of an aorta with left and right iliac arteries is created from an MR image volume.
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This section demonstrates how to use the SimVascular image-based modeling pipeline to create a patient-specific geometric model of the human vasculature. A finite element mesh is then created from that model that can later be used for a computational fluid dynamics (CFD) simulation of blood flow for that model. A model of an aorta with left and right iliac arteries is created from an MR image volume.
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<!-- The following lists the sections in this tutorial
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