| [eavp-dev] Comparison between FENICS and ICE mesh formats |
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I have experimented with the FENICS file format to test how it compares to the proposed ICE format found
here.
First it must be noted I had to change our format to account for the fact that the sample FENICS file had boundary conditions on the faces instead of the edges. Thus, the following changes were made to the proposed ICE format:
The Edges block was changed to read EdgeID Vertex1 Vertex2 on each line.
The Faces block was changed to read Face ID FieldVariable1 FieldVariable2...;Edge1 Edge2...;BoundaryCondition1 BoundaryCondition2 on each line. Since the FENICS file did not specify field variables, these are simply omitted for our sample.
A Cells block was added, with the following format: <Cells> CellID Face1 Face2... </Cells>
In reality, it might be more flexible to have a single persisted JaxB object followed by a block of such compressed descriptions. For example:
<Defaults> <Tetrahedron id="0" name="Tetrahedron"> <Defaults>
<Cells> Tetrahedron CellID Face1 Face2 CellID Face1 Face2 </Cells>
This would allow us to unmartial to an arbitrary class without having to persist the entire <Tetrahedron id=...> node for every individual cell of that type.
Also of note is that FENICS stores boundary condition information in a different file. This means that our ICE file is also missing boundary condition definitions, and both files only contain references to boundary condition IDs. A full description for a
problem would involve larger files and longer run times for both formats.
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I ran the test on a 148,970 KB FENICS format file. It took about 11.5-12.5 seconds to parse the file into a set of simple data structures, 5-6.4 seconds of which was spent reading the file in.
After converting to the ICE format, the files was 75.024 KB large. It took about 5-5.5 seconds to parse the file, about .8 seconds of which was spent reading the file in.
The extreme decrease in time is due to the very simple data structures used in the ICE file. When reading the FENICS file, Java will instantiate over a million objects, all of which we read data out of then never use again. By comparison, the ICE file results
in only a few objects, and the vast majority of the data is simply held in very large strings. If we were to actually use the data structures constructed by the XML parser, such as by creating JaxB annoted classes that could parse the FENICS file nodes into
usable data structures directly, then the two may move closer together as the extra work of reading the file is partially made up for by the fact that there is no additional step in which the text strings are converted into data objects, as is in the ICE file.
Robert Smith |