I Just Started Using SimuSEM, How Do I Get Started?

 Great that you ready to start looking at SEM simulations!  We assume that you have installed Blender and SimuSEM, and we want to give new users a helpful start by asking our developers what they they is most important for new users to know.

Q: What do you want to tell new users to make them feel more comfortable with the Blender interface to SimuSEM?

Doug:  When I fist started working with SimuSEM, I found the Blender GUI overwhelming   Blender is a very powerful tool with lots of features, so my concern is that new users don't know where to start.  I would start by explaining that it is easy to get started and users really only need to be acquainted with a few custom Blender panels to start creating and simulating with SimuSEM..

I would point out the toolbar on the left which is used for interactively transforming shapes, the bottom of the toolbar has useful SimuSEM operations, the Item tab on the right side of the 3D View lets you transform and change properties of the active shape, and sometimes other selected shapes.  The top right is the Outliner that lists all the objects in the 3D View and the bottom right is the Properties Panel which has the Build Sample and Run Control Panels.  Those panels are selected with the 2 tabs just above the red world tab.  

Shari:  I get annoyed when rotating my sample in the 3d view seems wonky because the pivot is some far away point.  The way to fix that is to select an object near the center of the sample to make it the active object and press the . (period) on the numpad (for a PC).  That will switch the rotation pivot to the active object.  On computers without a numpad, press the apostrophe key in the upper left corner of the keyboard to bring up a pie menu and choose "View Selected"(bottom right).  This is also described in this post.

Viewing large scale samples is also annoying.  For instance, if I resize my substrate to 2000nm x 2000nm, it initially looks like this:

and then try to zoom out, it looks like this:

This can happen if you have micron size features and your simulation is in nm (a film that is 1000nm thick, for instance).  Note that you can set units for the sample in the Run Control Panel:

SimuSEM attempts to set view parameters automatically so the sample does not get clipped, but that feature is still a work in progress.  Some ways to fix the view are:

1 Increase the Camera Clip End setting in the View Tab as shown:

2. Make use of the View Preset menu in the Toolbar on the left side of the 3D View:

If you have a large distance between the detector and the sample, the view preset will center the appropriate objects in Blender's 3D View.  Another example is shown here because this is a common user question.

Adding Workers to a Simulation (Windows 11)

One way to speed up your noncharging simulations is to add workers.  If you started your simulation on one computer, another computer (or multiple computers) can be added as workers (depending on the number of CPU ton the second machine).  Here is how to add accomplish adding additional PCs as workers:

1.  Switch your Network profile type to Private if it is set to Public.  

• Right click on the network properties icon in the lower righthand corner of your screen.

 

• Choose Network and internet settings
• Click on Wifi

• Then properties for your network.

• Then make sure Private network is checked.

While you are looking at this section, scroll down to find the IVP4 address.  That is the IP address you need to put in the SimuSEM Progress Window next to the Add Worker button .

• Next, in the tabs on the left side of this window, choose Privacy and Security.  And then Windows Security at the top.  Then click on Firewall and network protection.

• The choose Advanced settings.  You have to allow the app to make changes to your device by clicking Yes.

• Click on Inbound Rules (left) and New rule (right).

•  In the New Inbound Rule Wizard, for Rule Type select Port and Next. Then type in the port numbers and click on Next.

Then click Next through a few more steps.  The defaults are probably fine, including Allow the Connection.  The last step is to assign the rule a name.  I used SimuSEM, which is the name of a new Inbound Rule (see above screenshot).  You can double click on it to open the Properties if you need to modify it.  Note that next time you open the window, the rule you just created will not be at the top of the list.  You have to scroll down to find it.

Now you can click on the Worker tab in the Progress Window and add the computer as a worker using the IP address. 

Reusing Shapes

Reusing shapes saved in another blend file.

1. In File menu, choose Append (or Link if you want changes to the original object to be reflected in this one).

 

2. Choose the blend file with the objects to be used in current sample and click Append.

3.  Then choose Object and click Append

4.  Finally choose the object you want, and click Append

5. The object becomes part of your sample!

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.