Regions and Geometry in GSSF

Geometry

A specific simulation workflow has certain overarching geometrical information. These are provided in the <geometry> section of the GSSF-XML file. In particular, there are:

Property (Type)	Entry in geometry dictionary	Description
Centre (x, y, z)	centre	Focal point of the simulation. Often a needle tip. Other locations generally expressed as an offset from this location. Default centre of simulation extent
Needle axis (x, y, z)	needleaxis	Primary/default axis for the simulation. May or may not be an actual axis of a needle, but will be used as a fallback if a needle axis is not provided.
Simulation scaling factor (r)	simulationscaling	The (multiplicative) ratio going from input surface length scales (e.g. mm) to simulation length scales (e.g. m)

These may be referred to, and assumed to exist, in any component.

Regions

Regions are geometric entities. They may be either 2D subdomains (boundary subdomains) or 3D subdomains. They are specified in the GSSF-XML by one of the three tags:

    <surface name="REGIONNAME" input="INPUTLOCATION" groups="GROUP1; GROUP2;..." />
    <zone name="REGIONNAME" input="INPUTLOCATION" groups="GROUP1; GROUP2;..." />
    <both name="REGIONNAME" input="INPUTLOCATION" groups="GROUP1; GROUP2;..." />

The REGIONNAME may be any string used to refer to the region elsewhere in the configuration (such as the mesher) and the INPUTLOCATION is usually the filename of the STL surface defining the region. This may be given relative to the working directory. Generally, STL files are kept in an input/ subdirectory.

The Needle Library may add regions representing needles, as NEEDLE_[NEEDLEID] (and NEEDLE_[NEEDLEID]_ACTIVE, NEEDLE_[NEEDLEID]_INACTIVE if appropriate).

Labelling

Regions will be labelled by integers in the final mesh, which are used in the Elmer SIF file to assign properties, boundary conditions and so forth. The relationship between labels and regions is hard to predict if possible at all, as it is dependent on the volumetric meshing, number of subdomains appearing in the simulation domain and ordering of assignment.

As such, the parameter dictionary accessible in the SIF template contains region entries. For example:

<regions>
  <surface name="organ" input... />
  ...

is used in the SIF template as follows:

!===================
Boundary Condition 3
!===================
Target Boundary = Integer {{ p.REGION_ORGAN }}
Temperature = {{ p.CONSTANT_BODY_TEMPERATURE|typed }}
...

The conversion from region name to corresponding constant name uses slugify.

Groups

As several regions can all effectively represent the same subdomain, or related subdomains, groups allow you to indicate this in GSSF-XML. This is by far the more common way to include mesh indexes in the SIF template, as it future proofs against multiple related region entries, even if you currently only use one.

Groups are notated, for example:

<surface name="organ" input="input/organ.stl" groups="organs; outer-surfaces" />

In this case, entries BOUNDARIES_ORGANS and BOUNDARIES_OUTER_SURFACES will be created in the global parameter dictionary. These actually include the whole target boundary line in the SIF file, so if they are not present, the line is omitted and no syntax error occurs.

!===================
Boundary Condition 3
!===================
{{ p.BOUNDARIES_ORGANS }}
Temperature = {{ p.CONSTANT_BODY_TEMPERATURE|typed }}
...

Similarly, this is true for the needles in their parameter dictionaries, with needles[id].BOUNDARIES_NEEDLE_ACTIVE and needles[id].BOUNDARIES_NEEDLE_INACTIVE.