### Cell compression by plates.

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7 months ago by
Dear all,
I am trying to reproduce the process of cell compression, as shown below(picture and PP110 in PDF). There is only one big cell for simplicity. An energy term  $E=\frac{1}{2}k\left(z-z_0\right)^2$E=12 k(zz0)2  is introduced to represent the effect of the plates.  $z$z  is the vertical position,  $z_0$z0  the 0 energy position of the plate interface and  $k$k  the stiffness of plate.
I manipulate the energy term in python referring to the manual,
I am meeting some difficulties in realizing the algorithm.
First, the vertical position  $z$z is obtained by calculating the average value of the outmost layer pixels of the plates. I try to use the boundary tracker plugin, but I am not sure whether it can be used in the python plugin.
What's more, the changed energy is  $\bigtriangleup E=\frac{1}{2}k\left(z_{n+1}-z_0\right)^2-\frac{1}{2}k\left(z_n-z_0\right)^2=k\left(\frac{z_{n+1}+z_n}{2}-z_0\right)\left(z_{n+1}-z_n\right)$E=12 k(zn+1z0)212 k(znz0)2=k(zn+1+zn2 z0)(zn+1zn) . It seems that the changed energy is related to the vertical position before and after the pixel flip. How to realize it ?
I have a try and the outcome seems not positive, the imperfect model is attached.
Thank you!

Yuan
File attached: version_finale.pdf (6.24 MB)

File attached: compressionCell.rar (10.01 KB)

Community: CompuCell3D

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7 months ago by
In the figure (labeled 5.7) it doesn't appear that the plates are deformed, only the cell deforms. Do you really want the plates to deform or just the cell?

Looking at your CC3D, there are a couple things if you want the plates to be deformable;
1. You need to define the plates as cells with target volumes and probably target surfaces.
2. When you move the plates (or enlarge the plates) you need to run enough MCS to let the system relax between movements.

If you really want deformable plates you might be able to implement a finite element mesh in CC3D for the plates. The plates would be a set of small cells coupled by springs to their neighbors using focal point plasticity links.
Actually，in the figure the deformation is small, but I think it's okay to neglect the deformation of plates since they are much stiffer than cells.
My question is, are there other methods to move the plates as rigid bodies?
written 7 months ago by Yuan
You can define the plates as fixed cells then add a row of pixels to those fixed cells in python, then relax the system for some number of MCS, then add another row of pixels, ...

In twedit++ use the shortcut at;
CC3D Python -- Visit -- All Lattice Pixels
for how to access all the lattices pixels

You can assign a particular pixel to a cell ("cellA") with;
pt.x=4; pt.y=6; pt.z=0
self.cellField.set(pt,cellA)
or
self.cellField.set((x,y,z),cellA)

The pixels might have been medium or your cell being squashed. That is why you'll need to run some number of MCS to relax things once you've enlarged the wall.
written 7 months ago by James Sluka