Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Feature/curvature compartments fpp tutorial #30

Open
wants to merge 11 commits into
base: master
Choose a base branch
from
Open

Feature/curvature compartments fpp tutorial #30

Changes from 1 commit
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
0797174
added elongated cell tutorial - w.i.p
maciekswat Aug 24, 2024
7e74d86
added elongated cell tutorial - w.i.p
maciekswat Aug 25, 2024
12930d7
added new content
maciekswat Aug 31, 2024
3c1c774
finished case study of how to build elongated cells
maciekswat Aug 31, 2024
be7f6ec
Addressed most PR comments
maciekswat Sep 14, 2024
4200895
fixing index for real-world examples
maciekswat Sep 14, 2024
557e0d9
Updated the tutorial to highlight the ability to use <InternalMaxTot…
maciekswat Sep 15, 2024
b1492f2
updated FPP plugin manual to include :
maciekswat Sep 15, 2024
c21d398
fixing the "Real World Examples" section
maciekswat Sep 28, 2024
e85fb2b
Implementing PR changes
maciekswat Sep 28, 2024
c40d75e
addressing PR comments
maciekswat Sep 28, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
28 changes: 28 additions & 0 deletions docs/focal_point_plasticity.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,34 @@ example):
</Plugin>


The total number of links a given cell can form is computed as a sum of ``<MaxNumberOfJunctions>`` values coming from ``<Parameters>``
or ``<InternalParameters>`` sections where a given cell type appears. In the example above ``Center`` can form maximum of 2 internal links (between compartments)

CompuCell3D gives you ability to override this default algorithm by adding additional tag that control the total number of links:
Copy link
Collaborator

@fyffep fyffep Sep 18, 2024 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

nitpick: This could say, ". . . the total number of links of a given cell type." It took me a moment to realize that it's not possible to control the global, simulation-wide number of links. Instead, "total" just pertains to each cell.



.. code-block:: xml

<Plugin Name="FocalPointPlasticity">

<MaxTotalNumberOfLinks CellType="Center">1</MaxTotalNumberOfLinks>
<InternalMaxTotalNumberOfLinks CellType="Center">1</InternalMaxTotalNumberOfLinks>


<Parameters Type1="Top" Type2="Top">
<Lambda>10.0</Lambda>
...

In this example we are limiting the maximum number of links ``Center`` cells can form with Center cells of another cluster to 1
``<MaxTotalNumberOfLinks CellType="Center">1</MaxTotalNumberOfLinks>`` and do the same for number of links the ``Center`` cells can form
with cells that are members of the same cluster: ``<InternalMaxTotalNumberOfLinks CellType="Center">1</InternalMaxTotalNumberOfLinks>``



where we can override this default algorithm. This feature can be useful when working with "elongated" compartmental cells where
you do not want Center cells to form more than two links


We can also specify link constituent law and change it to different form
that "spring relation". To do this we use the following syntax inside
FocalPointPlasticity CC3DML plugin:
Expand Down