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FieldML: concepts and implementation.

Christie GR, Nielsen PM, Blackett SA, Bradley CP, Hunter PJ - Philos Trans A Math Phys Eng Sci (2009)

Bottom Line: It comprises a rich set of operators for defining generalized fields as functions of other fields, starting with basic domain fields including sets of discrete objects and coordinate systems.It is extensible by adding new operators and by their arbitrary combination in expressions, making it well suited for describing the inherent complexity of biological materials and organ systems.It outlines current implementations in established, open source computation and visualization software, both drawing on decades of bioengineering modelling software development experience.

View Article: PubMed Central - PubMed

Affiliation: Auckland Bioengineering Institute, University of Auckland, Auckland 1142, New Zealand. r.christie@auckland.ac.nz

ABSTRACT
The field modelling language FieldML is being developed as a standard for modelling and interchanging field descriptions in software, suitable for a wide range of computation techniques. It comprises a rich set of operators for defining generalized fields as functions of other fields, starting with basic domain fields including sets of discrete objects and coordinate systems. It is extensible by adding new operators and by their arbitrary combination in expressions, making it well suited for describing the inherent complexity of biological materials and organ systems. This paper describes the concepts behind FieldML, including a simple example of a spatially varying finite-element field. It outlines current implementations in established, open source computation and visualization software, both drawing on decades of bioengineering modelling software development experience.

Show MeSH
Connectivity of coordinate field versus material property based on meshes from figure 5. (a) Shaded material property shown on coarse mesh with cut line shown for reference and (b) deformed geometry including cut, defined on highly refined mesh.
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fig6: Connectivity of coordinate field versus material property based on meshes from figure 5. (a) Shaded material property shown on coarse mesh with cut line shown for reference and (b) deformed geometry including cut, defined on highly refined mesh.

Mentions: Figure 6 shows the situation of two fields defined over different mesh refinements from figure 5. The shading indicates the variation of a material property such as stiffness, which can be described throughout a simulation on the original, unrefined mesh, even if the coordinate field is refined several times to accurately describe a detailed deformation involving a cut in the mesh. This shows that one has to be careful when talking about connectivity; it is not a universal property of a hierarchical mesh, but a property of a field at the particular mesh refinement it is defined over at any instant.


FieldML: concepts and implementation.

Christie GR, Nielsen PM, Blackett SA, Bradley CP, Hunter PJ - Philos Trans A Math Phys Eng Sci (2009)

Connectivity of coordinate field versus material property based on meshes from figure 5. (a) Shaded material property shown on coarse mesh with cut line shown for reference and (b) deformed geometry including cut, defined on highly refined mesh.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2665020&req=5

fig6: Connectivity of coordinate field versus material property based on meshes from figure 5. (a) Shaded material property shown on coarse mesh with cut line shown for reference and (b) deformed geometry including cut, defined on highly refined mesh.
Mentions: Figure 6 shows the situation of two fields defined over different mesh refinements from figure 5. The shading indicates the variation of a material property such as stiffness, which can be described throughout a simulation on the original, unrefined mesh, even if the coordinate field is refined several times to accurately describe a detailed deformation involving a cut in the mesh. This shows that one has to be careful when talking about connectivity; it is not a universal property of a hierarchical mesh, but a property of a field at the particular mesh refinement it is defined over at any instant.

Bottom Line: It comprises a rich set of operators for defining generalized fields as functions of other fields, starting with basic domain fields including sets of discrete objects and coordinate systems.It is extensible by adding new operators and by their arbitrary combination in expressions, making it well suited for describing the inherent complexity of biological materials and organ systems.It outlines current implementations in established, open source computation and visualization software, both drawing on decades of bioengineering modelling software development experience.

View Article: PubMed Central - PubMed

Affiliation: Auckland Bioengineering Institute, University of Auckland, Auckland 1142, New Zealand. r.christie@auckland.ac.nz

ABSTRACT
The field modelling language FieldML is being developed as a standard for modelling and interchanging field descriptions in software, suitable for a wide range of computation techniques. It comprises a rich set of operators for defining generalized fields as functions of other fields, starting with basic domain fields including sets of discrete objects and coordinate systems. It is extensible by adding new operators and by their arbitrary combination in expressions, making it well suited for describing the inherent complexity of biological materials and organ systems. This paper describes the concepts behind FieldML, including a simple example of a spatially varying finite-element field. It outlines current implementations in established, open source computation and visualization software, both drawing on decades of bioengineering modelling software development experience.

Show MeSH