Implement spatial database that can efficiently query for data directly from HDF5 output.

[baagaard-usgs]

Sometimes we want to use output from one PyLith simulation as input in another simulation. The current typical workflow for doing this is to use a Python script to read in data from an HDF5 output file and generate a SimpleDB spatial database.

We should implement a spatial database that provides an efficient way to query data read from the the HDF5 file, so no translation is necessary.

Notes

• We cannot rely on preservation of ordering for efficient queries, because data may be ordered via parallel I/O and a different ordering of the mesh.

• The names of the values in a spatial database do not necessarily match the output. For example, using the stress field as the initial_stress field.

Level of difficulty

Moderate. This is relatively well isolated, but does have some complications and could be difficult to develop an efficient algorithm. Matt suggests we might use the radial basis functions; alternatively we might use a K-D tree to find close points for interpolation.