update links in svfsi

cdarve245 · cdarve245 · commit 26a553eac670 · 2023-07-31T14:16:29.000-07:00
diff --git a/documentation/svfsi/fluid/prescribed_input/readme.md b/documentation/svfsi/fluid/prescribed_input/readme.md
@@ -4,7 +4,7 @@ To set up the input file, set the equation to be FSI to allow the mesh to move u
 
 ```
     Add BC: moving_wall {
-        Type: Dirichlet 
+        Type: Dirichlet
         Time dependence: General
         Temporal and spatial values file path: wall_motion.dat
         Profile: Flat
@@ -23,7 +23,7 @@ It is recommended to include remeshing if the wall motion is such that the domai
         Min dihedral angle: 10.0
         Max radius ratio: 1.1
         Remesh frequency: 100
-        Frequency for copying data: 1  
+        Frequency for copying data: 1
     }
 ```
 
@@ -42,10 +42,10 @@ Under the mesh equation, we similarly add the motion file.
         Output: Spatial {
             Displacement: t
         }
-        
+
         #---------- Add the BC for the moving_wall to the mesh equation as well ------
         Add BC: moving_wall {
-            Type: Dirichlet 
+            Type: Dirichlet
             Time dependence: General
             Temporal and spatial values file path: wall_motion.dat
             Profile: Flat
@@ -56,4 +56,4 @@ Under the mesh equation, we similarly add the motion file.
     }
 ```
 
-Follow this [instruction](http://simvascular.github.io/docssvFSI.html#app_restart_after_remesh) if you need to restart your simulation after stoppage.
+Follow this [instruction](svfsi.html#app_restart_after_remesh) if you need to restart your simulation after stoppage.
diff --git a/documentation/svfsi/fluid/prescribed_wall_motion/readme.md b/documentation/svfsi/fluid/prescribed_wall_motion/readme.md
@@ -1,6 +1,6 @@
 ### Wall motion
 
-There are many established pipelines to obtain the wall motion from CT/MR scans<a href="#ref-3">[3-5]</a>. Here, we would recommend using the [cardiac geometric modeling tool](http://simvascular.github.io/docsSimCardio.html#automatic-cardiac-modeling) developed in the **SimCardio** project.
+There are many established pipelines to obtain the wall motion from CT/MR scans<a href="#ref-3">[3-5]</a>. Here, we would recommend using the [cardiac geometric modeling tool](simcardio.html#automatic-cardiac-modeling) developed in the **SimCardio** project.
 
 For the wall motion file, the file format is as follows. First, specify the dimension of the problem (three), the number of times at which to specify the displacements, and the number of vertices in the moving wall mesh. Then specify the times at which the displacements occur. Next, for each vertex, specify its index and then the prescribed displacements for each time. Note that in the case of multiple moving faces, these numbers may not start at one for any given face, as indexing is global. If a vertex is on an edge between two faces, it should have the same index and displacement fields, specified redundantly in both files.
 
@@ -15,12 +15,12 @@ displacement_1_vertex_1
 displacement_2_vertex_1
 ...
 displacement_n_vertex_1
-vertex_2_index 
+vertex_2_index
 displacement_1_vertex_2
 displacement_2_vertex_2
 ...
 displacement_n_vertex_2
-... 
+...
 ```
 
 For example,
@@ -49,50 +49,50 @@ For example,
 7.220E-1
 7.600E-1
 1
-0.000000   0.000000   0.000000   
-2.800E-1   -8.99E-2   -1.00E-2   
-8.799E-1   -2.09E-1   -8.10E-1   
-1.339999   -1.59E-1   -1.43000   
-1.509999   7.000E-2   -1.59000   
-1.310000   3.100E-1   -1.52000   
-1.069999   5.100E-1   -1.41000   
-1.009999   6.000E-1   -1.28000   
-9.699E-1   3.600E-1   -1.10000   
-1.049999   -1.09E-1   -8.80E-1   
-1.169999   -6.69E-1   -7.60E-1   
-1.169999   -1.17999   -7.90E-1   
-1.129999   -1.31999   -9.69E-1   
-1.049999   -1.25999   -1.34000   
-1.000000   -9.39E-1   -1.64000   
-9.899E-1   -4.29E-1   -1.96000   
-1.000000   3.000E-2   -2.15000   
-9.299E-1   3.600E-1   -1.90000   
-6.599E-1   4.200E-1   -1.14000   
-1.999E-1   1.500E-1   -3.50E-1   
-0.000000   0.000000   0.000000   
+0.000000   0.000000   0.000000
+2.800E-1   -8.99E-2   -1.00E-2
+8.799E-1   -2.09E-1   -8.10E-1
+1.339999   -1.59E-1   -1.43000
+1.509999   7.000E-2   -1.59000
+1.310000   3.100E-1   -1.52000
+1.069999   5.100E-1   -1.41000
+1.009999   6.000E-1   -1.28000
+9.699E-1   3.600E-1   -1.10000
+1.049999   -1.09E-1   -8.80E-1
+1.169999   -6.69E-1   -7.60E-1
+1.169999   -1.17999   -7.90E-1
+1.129999   -1.31999   -9.69E-1
+1.049999   -1.25999   -1.34000
+1.000000   -9.39E-1   -1.64000
+9.899E-1   -4.29E-1   -1.96000
+1.000000   3.000E-2   -2.15000
+9.299E-1   3.600E-1   -1.90000
+6.599E-1   4.200E-1   -1.14000
+1.999E-1   1.500E-1   -3.50E-1
+0.000000   0.000000   0.000000
 2
-0.000000   0.000000   0.000000   
-2.700E-1   -8.99E-2   0.000000   
-8.500E-1   -1.99E-1   -6.80E-1   
-1.280000   -1.59E-1   -1.16999   
-1.430000   5.000E-2   -1.28000   
-1.230000   2.599E-1   -1.19999   
-1.010000   4.499E-1   -1.09000   
-9.500E-1   5.099E-1   -9.69E-1   
-9.100E-1   2.400E-1   -8.19E-1   
-1.000000   -2.59E-1   -6.70E-1   
-1.120000   -8.29E-1   -5.69E-1   
-1.130000   -1.31999   -5.89E-1   
-1.090000   -1.44999   -7.50E-1   
-1.000000   -1.36000   -1.06999   
-9.400E-1   -1.00999   -1.31000   
-9.300E-1   -4.69E-1   -1.56999   
-9.500E-1   0.000000   -1.72999   
-8.900E-1   3.299E-1   -1.53999   
-6.200E-1   3.999E-1   -9.39E-1   
-1.900E-1   1.399E-1   -2.90E-1   
-0.000000   0.000000   0.000000  
-... 
+0.000000   0.000000   0.000000
+2.700E-1   -8.99E-2   0.000000
+8.500E-1   -1.99E-1   -6.80E-1
+1.280000   -1.59E-1   -1.16999
+1.430000   5.000E-2   -1.28000
+1.230000   2.599E-1   -1.19999
+1.010000   4.499E-1   -1.09000
+9.500E-1   5.099E-1   -9.69E-1
+9.100E-1   2.400E-1   -8.19E-1
+1.000000   -2.59E-1   -6.70E-1
+1.120000   -8.29E-1   -5.69E-1
+1.130000   -1.31999   -5.89E-1
+1.090000   -1.44999   -7.50E-1
+1.000000   -1.36000   -1.06999
+9.400E-1   -1.00999   -1.31000
+9.300E-1   -4.69E-1   -1.56999
+9.500E-1   0.000000   -1.72999
+8.900E-1   3.299E-1   -1.53999
+6.200E-1   3.999E-1   -9.39E-1
+1.900E-1   1.399E-1   -2.90E-1
+0.000000   0.000000   0.000000
+...
 ```
 
-Note that in this example, we wish the mesh motion to be periodic in time, and thus the final displacement is zero.
+Note that in this example, we wish the mesh motion to be periodic in time, and thus the final displacement is zero.
diff --git a/documentation/svfsi/fsi/appendix_creating_fluid_geometry/readme.md b/documentation/svfsi/fsi/appendix_creating_fluid_geometry/readme.md
@@ -1,6 +1,6 @@
 ### Creating the geometry for the fluid domain
 
-For most cardiovascular modeling applications, the geometry of the fluid domain is generated by segmenting blood vessels out of medical image data. This process is described on the main SimVascular documentation: http://simvascular.github.io/modeling.html. We now want delete all the caps off the model. Once you have done that, export it by right-clicking the model from the left-hand menu and selecting ``Export as Solid Model''. When SimVascular prompts you for a name and location for the exported model, make sure to add an .stl extension to make sure the exported model is in .stl format. We will perform the next step in Meshmixer, and Meshmixer only takes in .stl format surfaces.
+For most cardiovascular modeling applications, the geometry of the fluid domain is generated by segmenting blood vessels out of medical image data. This process is described [here](modeling.html). We now want delete all the caps off the model. Once you have done that, export it by right-clicking the model from the left-hand menu and selecting ``Export as Solid Model''. When SimVascular prompts you for a name and location for the exported model, make sure to add an .stl extension to make sure the exported model is in .stl format. We will perform the next step in Meshmixer, and Meshmixer only takes in .stl format surfaces.
 
 <figure>
   <img class="svImg svImgMd" src="/documentation/svfsi/fsi/imgs/SV_Export_as_stl1.png" style="width:100%;height:auto;max-width: 30vw;">
diff --git a/documentation/svfsi/fsi/appendix_creating_solid_mesh/readme.md b/documentation/svfsi/fsi/appendix_creating_solid_mesh/readme.md
@@ -1,14 +1,14 @@
 ### Create the solid domain mesh
 
-Similar to the way we create the mesh for the fluid domain in SimVascular (see: http://simvascular.github.io/meshing.html) we can now create the mesh for the solid domain.
+Similar to the way we [create the mesh](meshing.html) for the fluid domain in SimVascular, we can now create the mesh for the solid domain.
 
 1.  Import the .stl of the structural domain geometry into SimVascular
 
     Right-click on the "Models" button and choose "Import solid Model", then select the .stl model you just exported from Meshmixer:
 
     <figure>
       <img class="svImg svImgLg" src="/documentation/svfsi/fsi/imgs/importing_solid_into_SV.png" style="width:100%;height:auto;max-width: 30vw;">
-      <figcaption class="svCaption" >Importing .stl model into SimVascular.</figcaption>
+      <figcaption class="svCaption">Importing .stl model into SimVascular.</figcaption>
     </figure>
 
 2.  Extract faces, rename them if wanted
diff --git a/documentation/svfsi/fsi/mesh_adam_bl/readme.md b/documentation/svfsi/fsi/mesh_adam_bl/readme.md
@@ -2,7 +2,7 @@
 
 To run an FSI simulation we need a mesh for both the structural domain and the fluid domain. These two meshes must have their interface nodes coincide exactly in order to satisfy the interfacial conditions that result from conservation of mass and momentum. The coincident nodes of the fluid mesh are mapped onto the corresponding nodes on the structural mesh and the solution of velocity, displacement, pressure, etc. are treated as equal in the structural and fluid domains.
 
-The fluid domain geometry for patient-specific anatomies are generated using the usual [SimVascular modeling pipeline](http://simvascular.github.io/modeling.html). To create the geometry for the structural domain, we will make use of the [boundary layer meshing feature](https://simvascular.github.io/meshing.html#tetgenboundarylayer) in the `Meshing` module. The usual case for boundary layer meshing involves extruding this thin layer of elements _inwards_, starting from the walls and going into the direction of the vessel centers. To make a wall mesh, we will instead use the boundary layer meshing feature to extrude elements _outwards_ to effectively make a new mesh with a specified thickness that surrounds our fluid domain. This new mesh will form the geometry of our structural domain.
+The fluid domain geometry for patient-specific anatomies are generated using the usual [SimVascular modeling pipeline](modeling.html). To create the geometry for the structural domain, we will make use of the [boundary layer meshing feature](meshing.html#tetgenboundarylayer) in the `Meshing` module. The usual case for boundary layer meshing involves extruding this thin layer of elements _inwards_, starting from the walls and going into the direction of the vessel centers. To make a wall mesh, we will instead use the boundary layer meshing feature to extrude elements _outwards_ to effectively make a new mesh with a specified thickness that surrounds our fluid domain. This new mesh will form the geometry of our structural domain.
 
 Before we use the boundary layer meshing to extrude outwards, it is extremely important that we thoroughly smooth our model. The outward extrusion of elements has the potential to cause some elements to extrude into each other and overlap, which will cause the extrusion to fail. This is especially true at bifurcations, where the extruded elements from the two daughter branches could easily run into each other near the junction if not properly smoothed. We will therefore make thorough use of the local smoothing tools in the Models module before meshing. Below is an example of a bifurcation that would normally occur after lofting segmentations together without smoothing. If we try to extrude a boundary layer mesh from this, the elements at the sharp corner will intersect with each other and cause it to fail.
 
diff --git a/documentation/svfsi/main/input/readme.md b/documentation/svfsi/main/input/readme.md
@@ -1,6 +1,6 @@
 ## Input file format
 
-**svFSI** uses plain-text input file. This input file will define the physics solved, mesh, linear solver, boundary conditions and general simulation parameters. An overview of the syntax could be found <a href=https://sites.google.com/site/memt63/tools/MUPFES/mupfes-scripting>here</a>. The input file for svFSI is a scripting code that sets values to specific parameters. A colon ":" is used as a separator between the keyword or key phrase and its value. If the parameters being set are single-valued constants, you may use a **single line structure** as,
+**svFSI** uses plain-text input file. This input file will define the physics solved, mesh, linear solver, boundary conditions and general simulation parameters. An overview of the syntax could be found <a href="https://sites.google.com/site/memt63/tools/MUPFES/mupfes-scripting">here</a>. The input file for svFSI is a scripting code that sets values to specific parameters. A colon ":" is used as a separator between the keyword or key phrase and its value. If the parameters being set are single-valued constants, you may use a **single line structure** as,
 
 ```
 <keyword or key phrase>: 1.3
@@ -57,7 +57,7 @@ Increment in saving restart files: 200
 
 <a id="mesh_info"> <h4> Mesh information </h4></a>
 
-Mesh data is provided in the second part. It mainly includes the paths to volumetric meshes and boundary meshes. There may also be additional information such as domains, fiber orientation, initial values, prestress, etc. Multiples meshes can be loaded for the same or different equations within svFSI. svFSI supports reading multiple mesh formats as mentioned [here](http://simvascular.github.io/docssvFSI.html#mesh). Regardless of the mesh format, the mesh information is provided using the block structure. Nested keywords "Add mesh" and "Add face" could be used to provide paths to the mesh and face files. The users should also provide a string-based name for each mesh and face immediately after the colon. This name will be useful when when setting boundary conditions later. For example:
+Mesh data is provided in the second part. It mainly includes the paths to volumetric meshes and boundary meshes. There may also be additional information such as domains, fiber orientation, initial values, prestress, etc. Multiples meshes can be loaded for the same or different equations within svFSI. svFSI supports reading multiple mesh formats as mentioned [here](svfsi.html#mesh). Regardless of the mesh format, the mesh information is provided using the block structure. Nested keywords "Add mesh" and "Add face" could be used to provide paths to the mesh and face files. The users should also provide a string-based name for each mesh and face immediately after the colon. This name will be useful when when setting boundary conditions later. For example:
 
 ```
 Add mesh: mesh_name {
diff --git a/documentation/svfsi/structure/mesh_gen/readme.md b/documentation/svfsi/structure/mesh_gen/readme.md
@@ -1,6 +1,6 @@
-## Mesh Generation ##
+## Mesh Generation
 
-Mesh generation for cardiac mechanics modeling are quite standard and can be achieved following the general guide <a href="http://simvascular.github.io/docssvFSI.html#mesh">here</a>.
+Mesh generation for cardiac mechanics modeling are quite standard and can be achieved following the general guide <a href="svfsi.html#mesh">here</a>.
 
 On the other hand, the heart wall is a composite of layers (or sheets) of parallel myocytes, which are the predominant fiber types. These fiber and sheet directions enable defining a local orthonormal coordinate system inside the cardiac muscle. This local coordinate system is crucial for using a structurally-based constitutive relation for the cardiac muscle <a href="#ref-9">[9]</a>. For 3D problems, the users are required to prescribe fiber and sheet directions in the computational domain for certain constitutive relations. Users are provided an option to define a constant fiber direction through the following input directives,
 
@@ -22,4 +22,4 @@ Fiber direction file path: fibersLong.vtu
 Fiber direction file path: fibersSheet.vtu
 ```
 
-In the latter approach, the vtu file should have the local coordinate system stored as a vector with the name "FIB_DIR" at the centroid of each element. An example is provided <a href="https://github.com/SimVascular/svFSI-Tests/blob/master/06-ustruct/03-LV-Guccione-active/mesh/P1/fibersLong.vtu">here</a>.
+In the latter approach, the vtu file should have the local coordinate system stored as a vector with the name "FIB_DIR" at the centroid of each element. An example is provided <a href="https://github.com/SimVascular/svFSI-Tests/blob/master/06-ustruct/03-LV-Guccione-active/mesh/P1/fibersLong.vtu">here</a>.
