Refactor PFLOTRAN interface

LBL-EESA / alquimia-dev

Alquimia is an interface that exposes the capabilities of mature geochemistry codes such as [CrunchFlow](http://www.github.com/cisteefel/crunchtope) and [PFLOTRAN](https://bitbucket.org/pflotran/pflotran-dev).

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Refactor PFLOTRAN interface #89

Closed ghammond86 closed 1 year ago

ghammond86 commented 1 year ago

This PR refactors the following within the PFLOTRAN interface

Several derived types and classes have been revised, renamed, reclassified (class -> type).
The natural ID of the grid cell is now passed to ReactionStepOperatorSpit routine for debugging purposes. This is critical for large problems within ATS where there is little to no information regarding the location of cells that fail to converge for chemistry.

ghammond86 commented 1 year ago

@smolins I believe that we are good. Notice that I am compiling against PFLOTRAN "master" and PETSc "main". After xSDK is released, these will become PFLOTRAN v5.0.0 and PETSc 3.20.0.

smolins commented 1 year ago

Ok, looks good. This is to become 1.1.0 release candidate.

To do for the release:

update the tags used for petsc to 20.0.0 and pflotran to v5.0.0 in the github actions yaml
update readme markdown with correct tags for all codes
update API doc to reflect natural_id addition

To do, not necessarily for the release:

enable gases for pflotran (currently num_gases=0)
see how natural_id can be used in the crunchflow interface (for debugging e.g.)