materials.json

Named file: config/system/materials.json

Purpose

Stores default material and tissue properties in the pipeline for use in the 3D FEM.

Syntax

To declare this entity in config/system/materials.json, use the following syntax:

{
  "conductivities": {
    "endoneurium": { // example syntax for anisotropic medium
      "value": "anisotropic",
      "sigma_x": String,
      "sigma_y": String,
      "sigma_z": String,
      "unit": "String",
      "references": {
        "1": String,
        ...,
        "n": String
      }
    },
    "epineurium": { // example syntax for isotropic medium
      "value": "String",
      "unit": "String",
      "references": {
        "1": String,
        ...,
        "n": String
      }
    }
  }
}

Properties

"<material>": The value is a JSON Object containing the conductivity value and units as Strings. Though using strings may seem odd for storing conductivity values, we do this because we read them directly into COMSOL to define materials, and COMSOL expects a string (which it evaluates as expression).

• "value": The conductivity of the material (if not “anisotropic”, the value must be in units S/m). If the value is “anisotropic”, the system is expecting additional keys for the values in each Cartesian direction:

  • "sigma_x": The value (String) is the conductivity in the x-direction (unit: S/m)

  • "sigma_y": The value (String) is the conductivity in the y-direction (unit: S/m)

  • "sigma_z":  The value (String) is the conductivity in the z-direction (unit: S/m)

• "unit": The unit of the associated conductivity in square brackets (must be “[S/m]”)

• "references": The value (Dictionary) contains citations to the source of the material conductivity used. The contents are non-functional (i.e., they are not used in any of the code), but they serve as a point of information reference for good bookkeeping. Each reference used is assigned its own key-value pair (Optional).

Example

See: config/system/materials.json to see all built-in material definitions, which the user may add to.

Note

Perineurium can be represented in the pipeline as either a meshed domain with a finite thickness or as a thin layer approximation, but the conductivity value used for either method is defined in materials.json unless the "PerineuriumResistivityMode" is "MANUAL" and the conductivity is defined explicitly in Model (Perineurium Properties).