diff --git a/docs/_toc.yml b/docs/_toc.yml index 072e41ca..3f6e4f86 100644 --- a/docs/_toc.yml +++ b/docs/_toc.yml @@ -17,7 +17,6 @@ parts: - file: preprocess - file: simulation - file: postprocess - - file: cluster - file: features - caption: Tutorials diff --git a/docs/cluster.md b/docs/cluster.md deleted file mode 100644 index 21e3cd82..00000000 --- a/docs/cluster.md +++ /dev/null @@ -1 +0,0 @@ -# Running a simulation on an HPC cluster \ No newline at end of file diff --git a/docs/figures/boundary_id.png b/docs/figures/boundary_id.png new file mode 100644 index 00000000..3e19da5b Binary files /dev/null and b/docs/figures/boundary_id.png differ diff --git a/docs/figures/case9_domain_ids.png b/docs/figures/case9_domain_ids.png deleted file mode 100644 index c5812524..00000000 Binary files a/docs/figures/case9_domain_ids.png and /dev/null differ diff --git a/docs/figures/mesh_id.png b/docs/figures/mesh_id.png new file mode 100644 index 00000000..3ebd973b Binary files /dev/null and b/docs/figures/mesh_id.png differ diff --git a/docs/installation.md b/docs/installation.md index ecf5aaa6..09f15650 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -2,9 +2,9 @@ ## Dependencies -The dependencies of `software` are: +The dependencies of `VaSP` are: -* Python >= 3.8 +* Python >= 3.10 * cppimport >= 22.8.2 * pandas >= 2.1.2 * matplotlib >= 3.8.0 @@ -16,12 +16,12 @@ The dependencies of `software` are: ## Installing with `conda` -To install `software` and all its dependencies to a *local environment*, we recommend using `conda`. -Instructions for installing `software` +To install `VaSP` and all its dependencies to a *local environment*, we recommend using `conda`. +Instructions for installing `VaSP` with `conda` can be found [here](install:conda). ## Installing with Docker -To install `software` and all its dependencies to an *isolated environment*, we recommend using the dedicated Docker -container. Instructions for installing `software` with Docker can be found [here](install:docker). +To install `VaSP` and all its dependencies to an *isolated environment*, we recommend using the dedicated Docker +container. Instructions for installing `VaSP` with Docker can be found [here](install:docker). diff --git a/docs/preprocess.md b/docs/preprocess.md index 9a709f48..34d1477e 100644 --- a/docs/preprocess.md +++ b/docs/preprocess.md @@ -10,14 +10,13 @@ vasp-generate-mesh --input-model /[some_path]/my_mesh.vtp which should produce the following files in the same folder as `my_mesh.vtp` - + * `my_mesh.h5`: input mesh for FSI simulation + * `my_mesh.vtu`: default output mesh file from VMTK + * `my_mesh.xml` or `my_mesh.xml.gz` (compressed or not): FEniCS compatible version of the mesh, not used in VaSP + * `my_mesh_edge_length.h5/xmdf`: averaged edge length for each cells. This can be used to check the quality of the mesh + * `my_mesh_boundaries.pvd/vtu`: boundary mesh with IDs for each boundaries. + * `my_mesh_domains.pvd/vtu`: volume mesh with IDs for each domains. + Among the files generated after pre-processing, `my_mesh.h5` will be used as an input to the FSI simulation. However, `.h5` file cannot be viewed by Paraview, and thus we have added other files such as `my_mesh_boundaries.pvd` and `my_mesh_domains.pvd` for viewing the mesh and IDs with Paraview. @@ -31,16 +30,23 @@ vasp-generate-mesh --help To perform FSI simulations, fluid and solid regions need to be generated and marked so that different partial differential equations can be solved on each domain. In `VaSP`, the provided surface mesh will represent the interface of the fluid and solid domain. Then, fluid mesh is created inside the surface mesh to fill the provided surface mesh while solid mesh is created outside the surface mesh to cover the fluid mesh. This mechanism of generating two different mesh works very well for blood vessels. We extended VMTK, a framework for generating mesh based for image-based vascular modelling, to enable the solid mesh generation by utilizing the functionality of adding boundary layer meshing. {numref}`domains` is an example of FSI mesh with fluid and solid regions marked as 1 and 2, respectively. -```{figure} figures/case9_domain_ids.png +```{figure} figures/mesh_id.png --- name: domains --- -Fluid and Solid domain with unique ID +Fluid and Solid domain with unique IDs ``` ## Boundary IDs -Similar to the domains, boundaries also need to be marked separately for applying different boundary conditions. Below is a list of boundaries that are necessary to be identified for performing FSI simulations. +Similar to the domains, boundaries also need to be marked separately for applying different boundary conditions, as shown in {numref}`boundary`. These boundary IDs can be viewed by opening `{your_mesh_name}_boundaries.pvd`. + +```{attention} +While most boundary IDs are fixed, fluid inlet and outlet IDs can vary depending on the input mesh. +Therefore, it is necessary to open the `{your_mesh_name}_boundaries.pvd` and visually check those IDs. +``` + +Below is a list of boundaries that are necessary to be identified for performing FSI simulations.
  1. Fluid inlet
    2. @@ -56,5 +62,9 @@ The third boundary, fluid and solid interface, is required to distinguish static The fourth boundary is usually used to fix the solid inlet and outlet while the last boundary is used to specify Robin boundary condition at the outer wall of the vascular system for representing surrounding environment. -#TODO: insert figure for the boundary - +```{figure} figures/boundary_id.png +--- +name: boundary +--- +Boundaries with unique IDs +```