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+# Characteristics of a Canonical Geometry
+
+_Canonical geometries should contain all aspects of the workflow so that
+through the creation of the geometries one encounters all methods and
+considerations necessary to create functional models._
+
+### Basic Models
+
+ * __Simple Model__
+ - Show workflow in a model without complications.
+ - Introduce issues arising from Cubit/Trelis.
+ - Show basic functionality of Cubit/Trelis such as imprinting/merging, assigning materials, and meshing.
+
+ * __Simple Model with Geometric issues__
+ - Go through workflow with a model with geometric complications that are still easy to understand/visualize.
+ - Show basic functionality of SpaceClaim by fixing geometric issues.
+ * Overlaps
+ * Unnecessary details to be removed
+ * Small gaps
+ * Curve coincident to surface
+
+ * __Radial model__
+ - Go through workflow with some applicability, could be a basis to build further complex models
+ - Exemplifies curvilinear CAD issues
+ - Introduces reflecting boundaries
+
+### Auxiliary, Difficult Models (Further design considerations)
+
+* MELCOR geometry (flows that split and recombine)
+* Toroidal geometry with thin walls that may lose particles
+* A radial slice where one encounters boundary conditions
+* Implementation of reflecting boundaries
diff --git a/ComplexAssembly.md b/ComplexAssembly.md
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+# Complex Assembly
+
+#### Procedure Overview
+
+ * A section of FNSF built from .sat file
+ * Void volume (with creation example in both Cubit/Trelis and Solidworks)
+ * Exported as a .h5m file
+
+
+#### Goals of Example
+
+ * Provide a general understanding of what issues could arise on complex models.
+ * Apply the general process to a complex model that has real applicability.
+
+## Procedure
+
+#### In Initial CAD program
+_Any CAD engine should work for this process as long as it can export to a
+format importable by SpaceClaim or Cubit/Trelis. The preferred format is ACIS (.sat)_
+ 1. Download the part titled "FullSectionFNSF.sw" from this page and open in Solidworks.
+ 2. Export the assembly/part to ACIS format (.sat file extension)
+ * ACIS format 22 is preferred (default for Solidworks)
+ * Use save or export feature and select ACIS (.sat) format
+
+ Notes
+- The preferred format is ACIS (.sat). Note that multiple file types could be used, but there is anecdotal evidence that suggests .sat files work the best for this process. Otherwise formats such as STEP and STL are also able to be imported to Trelis/Cubit.
+
+- This step is unnecessary unless you want to explore the model in Solidworks or learn how to save file as .sat.
+
+- To skip this step download the ACIS file titled "FullSectionFNSF.sat" and move onto ANSYS SpaceClaim section.
+
+Descriptions of Basic Issues
+ Gaps: when particles encounter gaps they may lose track of which volume they are in and be lost. In this model there is one obvious gap, but for real models gaps are only an issue when the gap is around 10^-6 units (cm). In many cases small gaps can also be fixed by the imprint/merge step in Trelis/Cubit.
+
+ Overlaps: when particles encounter overlaps between two volumes they may not be able to determine which volume they are in and be lost.
+
+ Edge contacts: there is a possibility that when two volumes are only in contact on a single edge it can cause an issue with surface definitions.
+
+ Unnecessary Detail: all details in the CAD model are included in the meshing process and in the final analysis and small details can greatly increase the amount of computation necessary. The physical threads included in this model are one example. This issue is a problem of optimization and depends on the computing power available as well as the level of detail necessary.
+
+
+ * Visually:
+ - Find one possible example of each type of basic issue.
+ * With SpaceClaim tools:
+ - To identify gaps navigate from __Prepare -> Clearance -> Detect__. In this case to find the gap enter a maximum distance of `1cm` in the Find Options box. The gap will be highlighted in red.
+ - To identify interference navigate from __Prepare -> Interference -> Remove.__ There are technically two volumes of interference and both will be highlighted in red.
+ - The __Imprint__ tool highlights any coincident edges or faces within the part and can make it easier to find edge contacts as well as overlaps. This tool can be found by going __Prepare -> Analysis -> Imprint__.
+ - There are no built-in tools in SpaceClaim to generally identify unnecessary details.
+
+
+ ### In Cubit/Trelis
+ _Cubit and Trelis are basically the same CAD software with Trelis being the commercial version. They are most useful for the meshing of geometries and assigning materials to volumes._
+
+ | Steps | Graphic User Interface | In Command Line |
+ |---|---|---|
+ | __Import the .sat file into Trelis/Cubit__ | - Can be imported using the GUI with __File -> Import__.
- Select the file through file explorer and open.
- One important qualifier to include is `[attributes_on]`. | - In the command line the simple form of the command is `import acis [filepath]`
- This command can be appended with further commands that can be found by typing `help import acis`.
- These qualifiers correspond with the options given when importing files through the GUI.
- One important qualifier to include is `[attributes_on]`. |
+ | __How to save progress for the file as ACIS__ | - Click on file, export, and select the file destination and name.
- Make sure that it is being exported as ACIS (.sat) and press ok to save. | - In command line type `export acis [filepath] overwrite`. |
+ | __Make sure units/distances are correct and if not, fix them__ | - A distance within the model of "X units" should have a metric distance of "X centimeters".
- To check this click on a surface/line with a known metric value and then navigate to the properties page and check the surface area or curve length.
- On the Command Panel click on __Geometry (leftmost option) -> Volume -> Transform -> Scale (from dropdown menu) -> Enter Scale Factor -> Apply__ | - A distance within the model of "X units" should have a metric distance of "X centimeters".
- To check this in the command line the general form is `list [entity name and number] geom`. For example to check the geometry of volume 1 enter `list Volume 1 geom`.
- In command line enter `vol all scale [Scale Factor]`. For example parts from solidworks would require `vol all scale 0.1` to convert the units to centimeters. |
+ | __Inspect models and resolve overlapping volumes__ | - On the Command Panel click on __Geometry (leftmost option) -> Volume -> Modify -> Heal (from dropdown menu) -> check Autoheal -> Apply__
- There are many options within the modify dropdown menu, but none are as robust as SpaceClaim|- In command line one can fix overlaps by typing `validate vol all` and then `healer autoheal [problem vols]`.
- This should work to detect overlaps, but is not as robust as SpaceClaim. |
+
+ Notes
+ - A more general DAGMC based tutorial for Cubit/Trelis basics can be found at https://svalinn.github.io/DAGMC/usersguide/trelis_basics.html.
+
+ - "Command Panel" and "Command Line" are necessary for GUI and command line methods respectively. To enable these select View and switch "Command Line" and/or "Command Panel" to visible.
+
+ - Scale will most likely be off by a factor of 10. For example models from Solidworks will most likely be increased by 10x or 100cm to 1000 units, but this scaling changes based on the initial CAD program. You must scale every entity down or up by that factor to match units to cm.
+
+ _The vacuum and graveyard volumes are not part of the model being analyzed, but play a role in the final analysis. When particles move freely through the vacuum volume and stop once they reach the graveyard volume._
+
+ | Steps | In Graphic User Interface | In Command Line |
+ |---|---|---|
+ | __Create a cube large enough to envelop all other volumes.__ | - Select __Geometry -> Volume -> Create__ and select __Brick__ from the drop down menu.
- Type 500 in each dimension box __(width, height, depth)__ and press __Apply__ to create the block. | - The general form is `create [shape] [dimensions based on shape]`. - For a simple cube 500x500x500 you can enter `create brick x 500`. |
+ | __Create another slightly larger cube to be used for graveyard.__ | - In command panel create another brick in the same way as part 1, using 750 as the new dimension in each dimension box. | - Enter `create brick x 750` |
+ | __Center volumes within the larger cubes.__ | To move the blocks in command panel select __Geometry -> Volume -> Transform__ and select __Move__ from the drop down menu.
- Type "5 6" into the __Volume ID(s)__ box. Then __Select Method -> Distance__ and type 100 into the __X Distance__ box. _This distance/direction may vary._ | - General form is `move vol [volume ids] [axis] [distance along axis]`
- Enter `move vol 5 6 x 100`. |
+ | __Hollow out large cubes to match functionality.__ | - Select __Geometry -> Volume -> Boolean__ and select __Subtract__ from the dropdown menu.
- Select volume 6 as volume A and volume 5 as volume B. Check __Keep Originals__ and click __Apply__.
- You can then delete volume 6 by selecting __Geometry -> Volume -> Delete__ and typing 6 into the __Volume ID(s)__ box and clicking apply.
- Select __Geometry -> Volume -> Boolean__ and select __Subtract__ from the dropdown menu. Select volume 5 as volume A and volumes 1,2,3, and 4 as volume B. Again make sure to check __Keep Originals__ and click __Apply__.
- Then use the delete action to delete volume 5. | - Enter `subtract vol 5 from 6 keep`
- Enter `delete vol 6` to get rid of the original large box.
- Enter `subtract vol 1 2 3 4 from 5 keep` or `subtract vol 1 to 4 from 5 keep`.
- Enter `delete vol 5`. |
+
+ Notes
+ - These volumes could also be created in another CAD program and then assigned a material in the exact same way, but this is an example of how to create these volumes in Trelis and Cubit.
+
+ - Most likely the volumes will be slightly off centered in the x direction, but the larger bricks will be centered with one another. This may vary based on the initial CAD program.
+
+ - To see the blocks better you can select the wireframe option in the top toolbar. It is directly to the right of the undo arrow on the toolbar. Also you can click on the axis on the bottom left of the volume viewing area to get a straight on (x,y) view.
+
Notes
+- The default tolerated distance for imprinting/merging surfaces is 5.0e-4 units.
+
+- Combining surfaces cuts two surfaces and two sets of tetrahedron mesh areas down to one, decreasing computational power required as well as eliminating possible errors where particles exist simultaneously in two surfaces.
+
Notes
+- The preferred format is ACIS (.sat). Note that multiple file types could be used, but there is anecdotal evidence that suggests .sat files work the best for this process. Otherwise formats such as STEP and STL are also able to be imported to Trelis/Cubit.
+
+- This step is unnecessary unless you want to explore the model in Solidworks or learn how to save file as .sat.
+
+- To skip this step download the ACIS file titled "ErrorBlocks.sat" and move onto ANSYS SpaceClaim section.
+
+Descriptions of Basic Issues
+ Gaps: when particles encounter gaps they may lose track of which volume they are in and be lost. In this model there is one obvious gap, but for real models gaps are only an issue when the gap is around 10^-6 units (cm). In many cases small gaps can also be fixed by the imprint/merge step in Trelis/Cubit This gap is made larger in this example so that it can be found visually as well as with the SpaceClaim tool.
+
+ Overlaps: when particles encounter overlaps between two volumes they may not be able to determine which volume they are in and be lost. There is one volume that is obviously overlapping with other volumes.
+
+ Edge contacts: there is a possibility that when two volumes are only in contact on a single edge it can cause an issue with surface definitions. There is one example of an edge contact in this model.
+
+ Unnecessary Detail: all details in the CAD model are included in the meshing process and in the final analysis and small details can greatly increase the amount of computation necessary. The physical threads included in this model are one example. This issue is a problem of optimization and depends on the computing power available as well as the level of detail necessary.
+
+
+ 3. Fix the basic issues with the tools available in SpaceClaim.
+
+
+| __Type of Issue__ | Description | Procedure to fix | Picture Example |
+|---|---|---|---|
+| __Gaps:__ | To fix gaps oftentimes the best option is to use the "Pull" tool and fix any possible overlaps using the "Interference" tool. | - First select one of the two faces on either side of the gap using the "Select" tool. To make it easier to see the face you can hide one of the two components by unchecking the box under the "Structure" toolbar.
- Next click the "Pull" tool and then select the "Up To" option and click any face of the other component that borders the gap. This will extend one of the two components to fill the gap. |  |
+| __Overlaps:__ | The "Interference" tool gives the option to subtract an interfering/overlapping region from one of the two bodies. | - The choice of which to volume to subtract from may be important based on the materials of each volume so be sure to note which component it subtracts from.
- SpaceClaim automatically selects the larger component as the one to subtract from. To switch to the other volume simply check the box labeled "Subtract from smaller body" located in Fix Options. |  |
+| __Edge contacts:__ | There are two main ways to resolve edge contacts, the first is to create a wider edge so that there is a common surface, the second is to cut out the edge so that there is are no shared features between the two components. This is dependent on the nature of the model and the analysis. | - Go to the design tab, sketch section, and select the line option. Create a rectangle that is perpendicular to the edge contact and shares an edge with the top edge of the face that contains the edge contact.
- Select the rectangle using the "Select" tool and then click "Pull". 1. To create a gap select "Cut" from the "Options-Pull" toolbar and then either drag the cut to the bottom of the component, use the "Up To" option and select the bottom face, or use the "Ruler" option and make the pull 100cm.
2. To create a wider edge select "Add" and -similarly to cutting- either drag the cut to the bottom of the component, use the "Up To" option and select the bottom face, or use the "Ruler" option and make the pull 100cm. This method will create interference between the new volume and old which can be resolved using the "Interference" tool. |  |
+| __Unnecessary details:__ | In this particular case the physical threads are an unnecessary detail as they will cause a significant amount of computational load, but have very little effect on the final results. Which details are important to keep and which to delete is dependent on the nature of the model and the analysis. | - This step can be completed in any CAD program and is more of a general suggestion to be considered continuously during the design phase.
- In SpaceClaim one can use a circular pull to flatten the threads off in a similar way to fixing an edge contact. |  |
+
+Notes
+- Most often in real models unnecessary details must be determined intuitively and visually while overlaps, edge contacts, and small gaps cannot be found visually.
+
+- For all of these edits one must work closely with the creator of the model/experiment to determine which complications are important to the end result and which are able to be changed.
+
- Select the file through file explorer and open.
- One important qualifier to include is `[attributes_on]`. | - In the command line the simple form of the command is `import acis [filepath]`
- This command can be appended with further commands that can be found by typing `help import acis`.
- These qualifiers correspond with the options given when importing files through the GUI.
- One important qualifier to include is `[attributes_on]`. |
+| __How to save progress for the file as ACIS__ | - Click on file, export, and select the file destination and name.
- Make sure that it is being exported as ACIS (.sat) and press ok to save. | - In command line type `export acis [filepath] overwrite`. |
+| __Make sure units/distances are correct and if not, fix them__ | - A distance within the model of "X units" should have a metric distance of "X centimeters".
- To check this click on a surface/line with a known metric value and then navigate to the properties page and check the surface area or curve length.
- On the Command Panel click on __Geometry (leftmost option) -> Volume -> Transform -> Scale (from dropdown menu) -> Enter Scale Factor -> Apply__ | - A distance within the model of "X units" should have a metric distance of "X centimeters".
- To check this in the command line the general form is `list [entity name and number] geom`. For example to check the geometry of volume 1 enter `list Volume 1 geom`.
- In command line enter `vol all scale [Scale Factor]`. For example parts from solidworks would require `vol all scale 0.1` to convert the units to centimeters. |
+| __Inspect models and resolve overlapping volumes__ | - On the Command Panel click on __Geometry (leftmost option) -> Volume -> Modify -> Heal (from dropdown menu) -> check Autoheal -> Apply__
- There are many options within the modify dropdown menu, but none are as robust as SpaceClaim|- In command line one can fix overlaps by typing `validate vol all` and then `healer autoheal [problem vols]`.
- This should work to detect overlaps, but is not as robust as SpaceClaim. |
+
+Notes
+- A more general DAGMC based tutorial for Cubit/Trelis basics can be found at https://svalinn.github.io/DAGMC/usersguide/trelis_basics.html.
+
+- "Command Panel" and "Command Line" are necessary for GUI and command line methods respectively. To enable these select View and switch "Command Line" and/or "Command Panel" to visible.
+
+- Scale will most likely be off by a factor of 10. For example models from Solidworks will most likely be increased by 10x or 100cm to 1000 units, but this scaling changes based on the initial CAD program. You must scale every entity down or up by that factor to match units to cm.
+
+_The vacuum and graveyard volumes are not part of the model being analyzed, but play a role in the final analysis. When particles move freely through the vacuum volume and stop once they reach the graveyard volume._
+
+| Steps | In Graphic User Interface | In Command Line |
+|---|---|---|
+| __Create a cube large enough to envelop all other volumes.__ | - Select __Geometry -> Volume -> Create__ and select __Brick__ from the drop down menu.
- Type 500 in each dimension box __(width, height, depth)__ and press __Apply__ to create the block. | - The general form is `create [shape] [dimensions based on shape]`. - For a simple cube 500x500x500 you can enter `create brick x 500`. |
+| __Create another slightly larger cube to be used for graveyard.__ | - In command panel create another brick in the same way as part 1, using 750 as the new dimension in each dimension box. | - Enter `create brick x 750` |
+| __Center volumes within the larger cubes.__ | To move the blocks in command panel select __Geometry -> Volume -> Transform__ and select __Move__ from the drop down menu.
- Type "5 6" into the __Volume ID(s)__ box. Then __Select Method -> Distance__ and type 100 into the __X Distance__ box. _This distance/direction may vary._ | - General form is `move vol [volume ids] [axis] [distance along axis]`
- Enter `move vol 5 6 x 100`. |
+| __Hollow out large cubes to match functionality.__ | - Select __Geometry -> Volume -> Boolean__ and select __Subtract__ from the dropdown menu.
- Select volume 6 as volume A and volume 5 as volume B. Check __Keep Originals__ and click __Apply__.
- You can then delete volume 6 by selecting __Geometry -> Volume -> Delete__ and typing 6 into the __Volume ID(s)__ box and clicking apply.
- Select __Geometry -> Volume -> Boolean__ and select __Subtract__ from the dropdown menu. Select volume 5 as volume A and volumes 1,2,3, and 4 as volume B. Again make sure to check __Keep Originals__ and click __Apply__.
- Then use the delete action to delete volume 5. | - Enter `subtract vol 5 from 6 keep`
- Enter `delete vol 6` to get rid of the original large box.
- Enter `subtract vol 1 2 3 4 from 5 keep` or `subtract vol 1 to 4 from 5 keep`.
- Enter `delete vol 5`. |
+
+Notes
+- These volumes could also be created in another CAD program and then assigned a material in the exact same way, but this is an example of how to create these volumes in Trelis and Cubit.
+
+- Most likely the volumes will be slightly off centered in the x direction, but the larger bricks will be centered with one another. This may vary based on the initial CAD program.
+
+- To see the blocks better you can select the wireframe option in the top toolbar. It is directly to the right of the undo arrow on the toolbar. Also you can click on the axis on the bottom left of the volume viewing area to get a straight on (x,y) view.
+
Notes
+- The default tolerated distance for imprinting/merging surfaces is 5.0e-4 units.
+
+- Combining surfaces cuts two surfaces and two sets of tetrahedron mesh areas down to one, decreasing computational power required as well as eliminating possible errors where particles exist simultaneously in two surfaces.
+