Meshing a Sample, Part 1

Meshing a Sample, Part I

Now that charging is available in SimuSEM 3.0, generating a proper mesh is essential for charging simulations.  It can also be used for generating some complex shapes that may be difficult in a non meshed sample.  

This tutorial will discuss basics of creating a meshed sample, including generating a mesh.  We aim to make generating a mesh as pain-free as possible, but as of now, SimuSEM can not automatically adjust the sample to deal with meshing conflicts.

For our first meshed sample, we will create a sample of silicon dioxide lines on a silicon substrate:

1.  Start with a new meshed project.  My project name is sio2_lines

2. Add an SiO2 Trapezoidal Line

3.  Next add an SiO2  Cylinder.  Note that the cylinder is rotated 90 degrees, so the height of the original unrotated cylinder is the same as the line length.  The dimensions refer to the original unrotated shape for cylinders, cones and spheres.

4. Now your sample should look like this:

5. We would like to align the cylinder on top of the trapezoidal line.  To do that, select the line, and choose Cursor To Top on the left side of the 3D View/

6.  Now to the outliner (on the right side of the Blender window) and click on the Cylinder to make it the active shape.

If we want to align a whole cylinder with the 3D cursor that is now centered on the top of the line, we can just choose "center" and check x,y and z  and then click on OK to create a curved top to the line.  In my picture, I did not choose the radius of the circle correctly to get a smooth transition from line to curved top, so I changed the x-dimension to 27nm to get a smooth profile with an elliptical top.

7.  Note that we have a cylinder overlapping another the line.  In general, it is important to define how the shapes overlap so that the simulation will know apply the correct material model in the overlapping region.  In this case since the two shapes are the same material, so for a non meshed sample overlapping shapes of the same material is usually acceptable.  For a meshed sample, the mesh generation sometimes has trouble with overlapping shapes or shapes with a shared boundary.    In this case, the cylinder on top could be defined as a union (if the material of the shape are the same) with the line or a Difference Filled Hole.

In this case, it turns out that a union of the cylinder with the line will mesh correctly.

So, to change the cylinder, press the Get Props button, make the cylinder a Union with the Trapezoidal Line.

Then press Modify Cylinder at the bottom of the panel.

8.  Finally. press Generate Mesh. If the mesh generation is successful, the bottom of the panel will say "Mesh File Saved" and indicate the number of volumes and elements in the mesh.  The number of volumes is greater than the number of shapes because the number of volumes includes a meshed vacuum region around the sample and often shapes are split into 2 or more volumes during the meshing process.  We recommend keeping the number of elements under around 2 million to keep the simulation time manageable.

If the mesh generation is not successful, either the number of volumes and elements will be zero or the panel will give a list of shapes that gave problems during the meshing process.

If problems occur with the union of the cylinder and the line, we could use a half cylinder instead.

Coming soon: tutorials about 1. using a half cylinder on top of the line and creating multiple lines using Array and 2. dealing with error messages from gmsh, the mesh generation program.

9.  Now that a mesh has been generated, I like to check it.  If you have installed gmsh, press View in GMSH  below Generate Mesh.

When gmsh opens, you will see the top of the vacuum mesh boundary around the sample:

Rotate the sample by pressing the left mouse button while moving the mouse pointer.  Pan the view by pressing the right mouse button while moving the mouse pointer.

Look at individual shapes using Tools -- Visibility. Then you can check out individual shapes by highlighting the shapes in the Visibility window and press Apply.

You can check that shapes are properly touching each other to be electrically connected by checking the surface.  This screenshot shows that the section of the silicon dioxide line that is touching the substrate share a common surface so are electrically connected.

Why is the Run button disabled? How do I create a scan region?

With the release of SimuSEM 3.0, defining a scan region has changed significantly!

I can help! I created a small project with four shapes and no scan region (yet). The “Run” button is disabled:

Now I will add a scan region, which specifies the size and shape of the region to be scanned, and the settings for the electron beam. In the bottom right panel:

Scroll down through the scan region properties. The defaults are probably fine to start: a “Gaussian Beam” electron gun perpendicular to the surface of the sample with a circular beam cross-section. Scroll down in the panel and do the following:

  

One thing to note is that the “Run” button will remain disabled until you enter a project “Name” and “Folder” for it to save its results in.

What happened to my move widget? Why can't I select any objects in Blender?

 Is the move widget on your shape in Blender partially or completely missing?

In the above image, notice that the move widget on the selected shape has only one arrow instead of 3 allowing movement only in that direction.  Look to the right of the selected shape in the Location section of the panel, and notice that the y and z locations are locked.  That keeps you from accidentally moving it in the 3d View.  If you clock on the locks, those directions will be unlocked and the other two arrows on the move widget will return

Sometimes the SimuSEM extension will lock one or more axes in location and/or rotation on a particular shape by default, if it is likely that it should not be moved.  For instance, the location of the substrate layers are locked in all 3 axes by default.  However, if you want to move a shape in a direction that is locked, you can either unlock it or type in a new location in that panel.  Or if you don't want to accidentally transform an object, you can lock the location, rotation and/or scale of any axis manually.

Why can't I select any objects?

If you are trying to select an object, but you can't, one likely cause is that you are in Edit Mode.  You need to be in Object mode to select an object.  Edit mode will allow you to select a part of an object, which is sometimes useful in SimuSEM.  Whenever you are asked to select a vertex, edge or face of an object,  you are in Edit Mode in Blender.  SimuSEM always has a Cancel button next to buttons that switch to Edit Mode, such as Choose a Pixel or Cursor to Face buttons.  However, you can always switch back to Object mode by click in the field circled in the above figure.  You can not add new shape in Edit Mode.

Fix Sample Rotation Pivot

 SimuSEM Tip:  Rotating Sample 

When using the rotation widget in the upper right corner, does the sample seem to rotate around a point far away from the center?  Fix, by telling Blender to use a selected object as the center of rotation.  First, select a small enough shape in the sample.  Then press the period key in the numpad on a PC keyboard.  Blender calls this Orbit Around Selection.

If you end up with a large shape as the rotation pivot and have trouble rotating the 3d view, just select a relatively small object and press the numpad (.) key.  Look here or in the Blender manual for more information.