Abaqus Brain Simulation + Postprocessing

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.

Running the Simulation

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.

Postprocessing

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

Output Summary

• All simulation results go into: simulation_results/<jobname>/
• All plots and processed data are saved alongside the .odb

Requirements

• Abaqus 2022 (or compatible version)
• matplotlib and numpy must be available in the Abaqus Python environment

Notes

• You can change which frame to extract by editing postproc/strain_rate_vs_strain.py or postproc/contour_visualization.py