secretory-cleft-ibamr

This project uses IBAMR and VisIt to simulate secretory clefts in CD8+ T-Cells.

Examples

Rigidity 30x Rigidity 100x

Installation

Installing Docker

Windows, Linux, MacOS (Binary Package)

https://docs.docker.com/get-docker/

MacOS

Recommended install with cask: brew cask install docker

Pulling Docker Image from Docker Hub

docker pull ericlee3141/ibamr_secretory_cleft:latest
docker image ls # Note <IMAGE ID>
docker tag <IMAGE ID> <YOUR IMAGE NAME>:latest
docker rmi ericlee3141/ibamr_secretory_cleft:latest
docker run -n <YOUR CONTAINER NAME> -it <YOUR IMAGE NAME>

Usage

Generate Simulation Input data

cd /PATH/TO/FOLDER
git clone https://github.com/ericlovesmath/secretory-cleft-ibamr
cd secretory-cleft-ibamr
python CircleTest.py # Requires Python 3.6+

Edit secretory-cleft-ibamr/CircleTest.py following the instructions written in the code.

secretory-cleft-ibamr/fila_256 will be generated holding FILA_256.xxx files for IBAMR.

Running Simulation

docker start -i <YOUR CONTAINER NAME>
cd /usr/test/sfw/ibamr/ibamr-objs-opt/examples/IB/explicit/test

Replace all FILA_256.xxx from the Python script

Leave preexisting FILA_256.xxx files not generated from the Python script alone

./main2d input2d
exit

Exporting Simulation Data

cd /PATH/TO/FOLDER
docker cp <YOUR CONTAINER NAME>:/usr/test/sfw/ibamr/ibamr-objs-opt/examples/IB/explicit/test/viz_IB2d/ .

Visualizing Data

Installing VisIt (Binary Package)

https://wci.llnl.gov/simulation/computer-codes/visit/executables

Navigating VisIt

Open > secretory-cleft-ibamr/viz_IB2d > lag_data.visit

Add > Subset > fila_256_mesh

Open > dumps.visit

dumps.visit:Subset - levels > Delete

Add > Pseudocolor > P

dumps.visit:Pseudocolor - P > Pseudocolor > Opacity > Constant > 20%

Draw