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MuMFiM

multiscale biological tissue implementation using amsi build

Installation

The easiest way to build mumfim is through spack. See the instructions here

Notes on Problem Setup

  1. In simmodeler you can use val*$t in the dirichlet or neumann boundary condition. This will apply val load linearly accross the number of timesteps you selected. E.g. If you apply a displacement 1*$t, the final displacement will be 1, and if you have 20 timesteps, each step will apply 0.05.
  2. Currently you cannot output the load on a face with a dirichlet boundary condition it will cause a crash.

Microscale Solver

This solver is designed to be a truss/beam solver which can operate on its own, or as part of a biotissue multiscale problem.

Current Limitations

  • Only Truss Networks are implemented
  • Implicit only solver
  • Uses single precicion linear algebra solver

Input Files

Network Input File

The network input file describes the geometry of the fiber network to be read in. It has the following description:

num-nodes num-fibers 0
node-1-x node-1-y node-1-z
...
node-n-x node-n-y node-n-z
fiber-1-node-1 fiber-1-node-2
...
fiber-m-node-1 fiber-m-node-2

The node ids use zero based indexing. See here for an example.

Parameter Input File

The parameter file describes the material parameters of each of the fibers. It should be named the same as the network input file with .params appended to the end. E.g. if the network input file is name test_net.txt the params file should be named test_net.txt.params.

num-parameters num-fibers
reaction-id  fiber-radius  youngs-modulus ... density
fiber-1-parameter
...
fiber-m-parameter

The reaction-id selects the type of reaction you would like to use. Currently there are the following options and parameters:

Reaction Type reaction-id Parameters
Linear 0 fiber-radius, youngs-modulus, density
Linear 0 fiber-radius, youngs-modulus, B, transition-length-ratio, density

See here for an example.

The current version of this input file is limited to linear truss elements. A future version will allow the user to select the element type and enter the appropriate number of parameters as needed.

Microscale only input file

The microscale only input file is a relatively self explanatory yaml input file. See here for an example.

Preparing the Model

  1. Setup model and mesh in simmodeler. Attribute definition template in Simmodeler called macro.
  2. Convert mesh to pumi mesh (requires pumi +simmetrix) 
    $ convert SimmetrixModel.smd SimmetrixMesh.sms OutPumiMesh.smb [--native-model=native_model.x_t]
  3. Convert model to PUMI model (requires pumi +simmetrix) 
    $ mdlConvert SimmetrixModel.smd PumiModel.dmg
  4. Convert model atributes to yaml (requires model-traits +simmetrix) 
    $ smd2yaml SimmetrixModel.smd > ModelTraitsModel.yaml