COMSOL 6.3 - STL Import 1 — Repairing and Combining STL Files

Add a Mesh Part that will be used to import and repair the mesh for the C3 vertebra. It is good practice to repair imported mesh files in separate mesh parts as it makes it easy to ensure that each imported mesh is fully repaired and contains a computational domain before moving on to the next step.

In the window, right-click and choose > .

In the window for , type C3 in the text field.

Locate the section. Select the checkbox.

From the list, choose .

This will set the length unit to mm for this Mesh Part.

In the window, under > > click .

In the window for , locate the section.

Browse to the model’s Application Libraries folder and double-click the file c3_vertebra.stl.

From the list, choose .

This setting is suitable when importing mesh files that have no obvious boundary partitioning, for example, meshes generated by medical imaging techniques. After the import, the mesh will usually consist of only one boundary that you can partition as needed, using the available tools. Use the or settings when importing meshes that contain planar faces and fillets, which can then be detected to partition the mesh accordingly.

Notice that the checkbox is selected by default. Domains are needed before you can generate a tetrahedral mesh in the vertebra. The import checks if the imported surface mesh forms any watertight regions, and if so, it creates domains.

The import automatically generates boundary selections based on the content of the STL file. The selections make it easier to select the proper entities in subsequent mesh operations and later when assigning materials and boundary conditions. If it is successful in creating domains, there will also be domain selections. Rename the boundary selection to something more descriptive.

Locate the section. In the table, enter the following settings:


Name	SOLID section in file
C3	mesh

This information message indicates that the mesh of the vertebra does not form a watertight component. The edge that appears in the selection is an exterior edge that is adjacent to a hole in the mesh.

An node appears reporting that a domain could not be created. Expand the node and click on the subnode to see more details.

In the window, expand the node, then click .

In the window for , locate the section.

In the list, select .

The hole is a slit-like hole with zero or almost zero area. On one side of the slit (on the right side of the green edge in the figure), there is one triangle element, whereas on the other side there are two elements. Since the import functionality cannot partition elements or add new ones, the mesh edges on the two sides of the slit could not be merged even with a larger tolerance.

To repair the slit, you will use the Fill Holes operation, which can introduce new mesh edges in order to merge edges. It searches for holes within a selection of boundaries and will automatically fill all holes smaller than a specified tolerance.

In the toolbar, click

and choose .

In the window for , locate the section.

From the list, choose .

Notice that the checkbox is automatically selected, which means that once all holes are filled and the surface mesh forms a watertight boundary, a domain will be created. Select to create a domain selection and rename the operation to get a more descriptive selection name.

Locate the section. Select the checkbox.

In the text field, type C3.

The slit has been repaired by introducing a mesh edge on the right side of the slit, merging the two sides of the hole, and removing the edge. This makes the mesh watertight and a domain has been created, which is reported in the window.

Next, add a new Mesh Part and import the mesh of the C3-C4 intervertebral disc.

In the window, under right-click and choose .

C3-C4 Disc

In the window for , type C3-C4 Disc in the text field.

Locate the section. Select the checkbox.

From the list, choose .

In the window, under > > click .

In the window for , locate the section.

Browse to the model’s Application Libraries folder and double-click the file intdiscC_3-4.stl.

From the list, choose .

Locate the section. In the table, enter the following settings:


Name	SOLID section in file
C3-C4	mesh

In the window, click .

In the window for , locate the section.

Rotate the mesh and zoom in further to see the view below. For more complex meshes when the coordinates are hidden behind mesh faces, you can also click the button to remove everything except the mesh closest to the coordinates in the view. If you do, click the button to return to the view with the full mesh.

Also in this case, a domain could not be created, this time because there are intersecting mesh elements. To repair the mesh, partition it to create a boundary containing the intersecting elements, delete this boundary, and finally, generate a new mesh face to cover the resulting hole. Here, do the partitioning manually using the Create Edges operation. For a faster workflow, you can also try to use the add-in mesh_partition_with_ball available in the COMSOL Multiphysics Add-in Libraries. See the model Spray Particle Deposition in Human Airways in the Application Gallery on the COMSOL website for an example of how to use the Add-In to clean up an imported STL mesh.

Create Edges 1

In the toolbar, click

and choose .

Select mesh edges around the intersecting elements by clicking them in the window, similar to what is shown in the image below. The selection is most easily done with transparency off. The selected edges can differ from the ones selected in the figure, as long as the edges form a closed loop, include the intersecting elements, and delimit only a small region around the intersecting elements. The last requirement is important when generating a new mesh face that follows the original mesh as close as possible.

In the window for , locate the section.

Select the checkbox to create a selection containing the boundary with the intersecting elements.

to generate the edges and partition the boundary.

Delete Entities 1

In the toolbar, click

and choose .

In the window for , locate the section.

From the list, choose (the boundary with the intersecting elements).

There is now a hole in the surface mesh, so before continuing, the hole must be sealed. Two operations can be used for this purpose: Create Faces and Fill Holes. The Create Faces operation is a manual way of generating mesh faces for holes by selecting edge loops. The Fill Holes operation automatically generates mesh faces to cap several holes at once. Here, use the Fill Holes operation. Note that the mesh faces generated by both of these operations will be minimal faces that strive to be as planar as possible.

C3-C4

In the toolbar, click

and choose .

In the window for , locate the section.

From the list, choose .

Locate the section. Select the checkbox.

In the text field, type C3-C4.

The hole is sealed with a new mesh face and the result is a smooth mesh containing a domain. Check that the domain selection has been added in the Selection List.

Selection List

In the toolbar, click

to open the window.

In the window, click .

button in the toolbar.

Add a third Mesh Part for the C4 vertebra.

In the window, under right-click and choose .

In the window for , type C4 in the text field.

Locate the section. Select the checkbox.

From the list, choose .

In the window, under > > click .

In the window for , locate the section.

Browse to the model’s Application Libraries folder and double-click the file c4_vertebra.stl.

From the list, choose .

Once again, the import failed to create a domain due to a hole in the mesh.

In the window, expand the > > > > node, then click .

In the window for , locate the section.

In the list, select .

Zoom in as much as possible on the tip of the v-shaped edge to see that the hole is caused by a mismatch in coordinates for one of the triangles.

STL files contain a set of triangles that need to be stitched together within a tolerance. In this case, the automatic tolerance is not large enough to connect the vertices of the triangles. This means that this type of hole can be repaired by increasing the Repair tolerance setting for the import.

In the window, under > > click .

In the window for , locate the section.

From the list, choose .

In the text field, type 5e-4[mm].

Using the larger repair tolerance, the element edges are now merged. As a result, the imported mesh is watertight and contains a domain with a corresponding domain selection. Rename the selections to something more descriptive.

Locate the section. In the table, enter the following settings:


Name	SOLID section in file
C4	mesh

Locate the section. In the table, enter the following settings:


Name	SOLID section in file
C4	mesh

button in the toolbar.

Add another mesh part for the C4-C5 intervertebral disc.

In the window, under right-click and choose .

C4-C5 Disc

In the window for , type C4-C5 Disc in the text field.

Locate the section. Select the checkbox.

From the list, choose .

In the window, under > > click .

In the window for , locate the section.

Browse to the model’s Application Libraries folder and double-click the file intdiscC_4-5.stl.

This mesh has been prepared to not contain anything that needs repairing.

Locate the section. In the table, enter the following settings:


Name	SOLID section in file
C4-C5	mesh

Locate the section. In the table, enter the following settings:


Name	SOLID section in file
C4-C5	mesh

Next, add a mesh part for the C5 vertebra.

In the window, under right-click and choose .

In the window for , locate the section.

Browse to the model’s Application Libraries folder and double-click the file c5_vertebra.stl.

From the list, choose .

This mesh has been prepared to fit perfectly with the adjacent vertebrae so here we want the import to partition the boundaries automatically. It is also prepared not to need repair.

Locate the section. In the table, enter the following settings:


Name	SOLID section in file
C5	mesh

Locate the section. In the table, enter the following settings:


Name	SOLID section in file
C5	mesh

In the window, click .

In the window for , type C5 in the text field.

Locate the section. Select the checkbox.

From the list, choose .

Next, add a Mesh Part where the meshes will be combined into one.

In the window, under right-click and choose .

Combined Mesh

In the window for , type Combined Mesh in the text field.

Locate the section. Select the checkbox.

From the list, choose .

In the window, under > > click .

In the window for , locate the section.

From the list, choose .

Select the checkbox to also import the domain you created earlier for the volume enclosed by the mesh. Domains are needed for most physics interfaces when running simulations in the volumes inside.

Import 2

In the toolbar, click

In the window for , locate the section.

From the list, choose .

Select the checkbox.

The information message states that the mesh has intersecting elements and gives the suggestion to use the Union operation to compute the intersection. Rotate the mesh and zoom in on the coordinates to see where they are located.

button in the toolbar.

In the window, click .

In the window for , locate the section.

From the list, choose .

Zooming in on the intersecting elements confirms that the mesh of the vertebra intersects that of the intervertebral disc. Before resolving the intersection with a Union operation, you will also import the rest of the meshes into this mesh part.

Import 3

In the toolbar, click

In the window for , locate the section.

From the list, choose .

Select the checkbox.

The C4 vertebra does not intersect the intervertebral disc, in fact there is a gap between the two.

In the window, click .

Import 3

To adjust the position of the C4 vertebra you can use a Transform attribute to the Import node. This allows for moving, rotating, and scaling an imported mesh. You can add several Transform attributes to an Import node, to, for example, rotate the mesh around more than one axis.

Transform 1

In the toolbar, click

and choose .

In the window for , locate the section.

In the text field, type 1[mm].

Import 4

In the toolbar, click

In the window for , locate the section.

From the list, choose .

Select the checkbox.

In the window, click .

In the window for , locate the section.

The C4-C5 disc and the C5 vertebra have been prepared with identical meshes on the touching boundaries. These boundaries only need to be merged.

button in the toolbar.

Import 5

In the toolbar, click

In the window for , locate the section.

From the list, choose .

Select the checkbox.

Add a Clip Plane to see inside the mesh and inspect how the meshes are intersecting.

button in the toolbar.

In the window toolbar, click

next to

, then choose .

In the window, hover over the frame for and right-click to open up the Graphics context menu. Select to rotate to be parallel with the xz plane.

In the window, hover over the frame for and right-click to open up the Graphics context menu. Select to view the part of the mesh that is positioned on the positive side of the y axis.

It is possible to click and drag the frame of the Clip Plane in the graphics to pan through the volumes. If you do, move the frame back to somewhere close to y=0 before continuing.

button in the toolbar.

In the window toolbar, click

next to

, then choose to show the cross-sectional faces of the domains that are cut with the Clip Plane. Since the cross-sectional faces can only be visualized where domains exists, this is one way to check if the mesh operations were actually able to create domains after repairing the holes. Note that the cross-sectional faces are not shown, even if there are domains, if the option is enabled in the toolbar, so remember to check the status of that option if you do not see any cross-sections.

In the window toolbar, click

next to

, then choose to disable the colors of the domains. This gives a more clear view of the overlaps between the imported meshes.

Zoom in on the cross section of the C3-C4 intervertebral disc.

The red areas show where the domains of the imported meshes intersect. In this view you can see that these meshes are not even close to match up no matter how careful you are at positioning the meshes in relation to each other. The black edges on top of the disc indicate that there is a gap between the disc and the C3 vertebra. First unite the meshes and then resolve the intersections and the gap.

Union 1

In the toolbar, click

and choose .

In the window for , locate the section.

From the list, choose .

Select Domains 1–3 only.

Locate the section. From the list, choose .

In the text field, type 6e-4[mm].

Lowering the tolerance usually helps when calculating a complex intersection. In some cases, when the element size differs too much between the input meshes, it can be necessary to remesh the boundaries before the Union operation to obtain similar sized elements. This can help with a successful computation of a mesh union, but is not needed for our vertebra mesh.

From the list, choose .

Switching to a linear placement of the mesh vertices helps here as the curved surfaces almost coincide at some locations.