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  Passive Swarm Developer Notes
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* The deformation grid reference file (deformation_grid_ref.vts) is not prefixed
with the PSwarm options prefix.

* deformation_grid_ref.vts uses ascii format -- gasp --

* PSwarmSetUpCoords_FillBox() does not support using -pswarm_box_nx 1,1,1

* Add UpdateMethods for Temperature, and e_plastic.

* Add support for filling GeometryObject with points

* Remove support for -pswarm_coord_layout 0 which utilises a non-prefixed cmd line arg -lattice_layout_N{x,y,z}
Alternatively, modify and wrap SwarmMPntStd_CoordAssignment_LatticeLayout3d() so that it does not call PetscOptionsGetXXX

* PSwarm does not support JSON checkpointing. This is a current design limitation
which needs to be addressed. Models using pswarms will not be able to completely
checkpointed. A restart will simply re-introduce an un-iniitalised set of passive
particles.

* Only ParaView formats are supported by PSwarm. This should be updated to support
the native databucket binary output. Introducing this feature will require a python
tool which can load the native databucket binary output.
[DONE] 52509e3d02f3a58f251919def9778663dde04bb5

