biodesign_joint_morphogenesis

https://github.com/sarroyavet/biodesign_joint_morphogenesis

Science Score: 57.0%

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Repository

Basic Info

Host: GitHub
Owner: sarroyavet
License: gpl-3.0
Language: Python
Default Branch: master
Size: 280 KB

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Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 4

Created over 3 years ago · Last pushed 9 months ago

Metadata Files

Readme License Citation Authors

BioDesign - script for morphogenesis-inspired design

This project was developed at Aix Marseille Univ, CNRS, ISM, Marseille, France, and was supported by French Research National Agency (ANR) Grant No. ANR-20-CE10-0008.

This repository contains the implementation of a bio-inspired algorithm for the design of unilateral contact surfaces based on the morphogenesis of synovial joint principles. It is meant to be used with CODE_ASTER 14.4, GMSH 4.9.3, and Paraview 5.9 (for result visualization).

This Python module was created by Kalenia MARQUEZ-FLOREZ. It allows obtaining a bio-inspired contact surface profile for two axi-symmetric bodies in unilateral contact.

Requisites

Python 3.x
Salome-Meca 2019 (and all its prerequisites)
Code_Aster 14.4 
Gmsh 4.9.3
Paraview 4.9

Python libraries used: matplotlib, json, csv, numpy, math, psutil, logging, os, subprocess, shutil, sys

General instructions

The main python file to run the script is runall.py which has as input the path of the cases .csv file (see example README) and the path of the workdirectory (where all the results of the simulations are stored). Then, the runall.py script calls the gen.py which is the general script that manages the whole process. It is gen.py which calls the mesh module (supported in GMSH) to generate the .unv meshes for the simulations and each of the CODEASTER command files (for morphogenesis and to monitor contact variables, i.e. stresses). At each growth step, the results are written in format .vtk by the module resVTK.py.

code structure

Use:

import runall from runall

runall('csv_file_path', 'work_directory_file_path')

NOTE: Change the CODE_ASTER path in mecaNO.comm, growNO.comm and gen.py accordingly to your system

Research

The scripts of this repository were first used in Marquez-Florez, K., Arroyave-Tobon, S., & Linares, J. M. (2023). From biological morphogenesis to engineering joint design: a bio-inspired algorithm. Materials & Design, 225, 111466.

Owner

Login: sarroyavet
Kind: user

Repositories: 2
Profile: https://github.com/sarroyavet

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Marquez-Florez
  given-names: Kalenia
  orcid: https://orcid.org/0000-0001-6388-3208
title: "Bio-inspired algorithm for the design of unilateral contact surfaces based on the morphogenesis of synovial joint principles:parameter optimisation with DOE"
version: V1.3
identifiers:
  - type: doi
    value: 10.5281/zenodo.7584068
date-released: 2025-06-20

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