modes in set BCs should be better named

[jgostick]

I'm thinking the following:

• 'add' would added values to existing BCs but only where none are specified
• 'overwrite' would add new ones even where some exist
• 'clear_and_add' would delete ALL existing ones then insert the new ones
• 'clear' (this is already done by remove_BC) would delete all existing BCs. If locations is None, then is removes them all, otherwise only removes the given locations.

'force' 'hard/soft'

[jgostick]

Let's just keep them as they are.

[jgostick]

We should have the following:

• add which adds the new values ONLY to locations which don't already have ones. This used to be called merge
• drop which just removes them from the given locations
• clear which removes ALL bcs
• overwrite which removes bcs from the given locations and replaces with the new ones.

Note that the above is NOT how things currently work.

[jgostick]

Here are the following definitions:

Three 'building blocks':

1. add: Add new ones only to locations that don't already have BCs
2. remove: Removes values from the given locations and leaves the rest
3. clear: Remoes all the values from all locations

Two 'composite' options

1. overwrite: Delete ALL old ones and replace new (clear followed by add)
2. merge: Add new ones to all given locations regardless of what is already there, and keep all others (remove followed by add)

Merge will be the default.

[jgostick]

Some thought is requried regarding other BCs. I have implemented the proposed logic in the current _set_BCs method, which is a subclassed by the transport classes so works ok, but for something like advection diffusion the set_outflow bc does not inherit this. This means we need to implement the logic for each new/unique bc type. I don't know if there is a generic solution, but worth some thought.

[jgostick]

RE my above comment, I think we should implement a policy that all boundary condition arrays are named 'pore.bc_<type>'. This way the _set_BC method can find all types that are defined on the object by searching for the occurance of '.bc_' in the dict name, the ensuring that these are handled accordingly.

Note that I have already done this by creating a _get_bc_types method on the BC mixin, which returns a list of ['rate', 'value'] for instance. This list is iterated on when checking for BCs of other types, for instance.

[jgostick]

So, I turns out I don't like the name 'merge'. When describing how merge works I literally used the word overwrite, which makes me think it should be called overwrite.

Also, when I used 'overwrite' I was surprized that it didn't overwite the values in the 'other' bcs. So if I have some value BCs already set, then I want to set some rate BCs in the same pores, I would expect it to overwrite the value BCs. This is NOT what overwrite does at the moment. So...

Intially I thought about adding a 'force' mode, but after additional consideration, maybe a force=True flag would be better, to indicate that the given mode should be applied everwhere. So when force=False the following works

mode	description
add	Adds the given values to specified locations, but not in any locations which have a bc value of the given type. If force=True, then this will replace any values of the other types if present.
remove	Removes the values of the given type from the specified locations, but only the specified type. If force=True, then this will remove any values of the other types if present.
clear	Removes all BCs of all the given type from all locations. If force=True, then this will also remove any values of the other types if present.
overwrite	Adds the given values to the given locations whether there are values of the given type defined there already. If force=True, then this will also overwrite any values of the other types if present.

[jgostick]

I have removed the force argument on that basis that it added a lot of clutter to the method and required careful reading of the docstring. Basically it was too complicated considering who little it would be used. Basically, the user just needs to set the BCs correctly to start with, and the powers of the force are not needed.

[jgostick]

After too much overthinking we have:

• add: This will put values in all the given pores even if values of the same type are already present.
• overwrite: This will do the same as add, but also put values in pores where values of another type are present, setting those other values to nan or False.
• remove: This will remove values of the given type from the given pores. However, if no type is given, then all types are removed so it acts like overwrite. If no pores are given it will use all pores so acts like a clear method.