This repository contains scripts and input files to run a finite element simulation of brain mechanics using Abaqus/Explicit, and postprocess the output. This repo and this README are both a work in progress. Immediate next steps involve full automation of the simulation + post processing pipeline.
Note: See also the SSM simulation workflow.
To submit an Abaqus simulation to the cluster via SGE (qsub
), run:
qsub run_abaqus_simulation_main.sh
This will:
- Run the simulation using
abaqus_simulation_main.inp
- Create a folder in
simulation_results/<jobname>/
- Save all Abaqus output files (
.odb
,.dat
,.sta
, etc.) into that folder
Edit run_abaqus_simulation_main.sh
to change the JOBNAME
or input file path.
Once the simulation completes, submit the postprocessing job:
qsub run_abaqus_simulation_main_postproc.sh
This script:
- Run
postproc/contour_visualization.py
to read the.odb
file and produce a contour plot - Run
postproc/strain_rate_vs_strain.py
to read the.odb
file, extracts max principal strain and strain rate, and generate:- A scatter plot (strain rate vs. strain)
- Histograms of strain and strain rate
- A
.txt
file with raw element-wise data
- All simulation results go into:
simulation_results/<jobname>/
- All plots and processed data are saved alongside the
.odb
- Abaqus 2022 (or compatible version)
matplotlib
andnumpy
must be available in the Abaqus Python environment
- You can change which frame to extract by editing
postproc/strain_rate_vs_strain.py
orpostproc/contour_visualization.py