[doc] fix some stuff in handbook and doxygen

Handbook:
- don't use deprecated Latex commands \it and \bf
- use the \Cplusplus macro consistently

Doxygen:
- put FluidStates group to the right hierarchy level
- improve wording

See merge request !140

Handbook:
- don't use deprecated Latex commands \it and \bf
- use the \Cplusplus macro consistently

Doxygen:
- put FluidStates group to the right hierarchy level
- improve wording

Cleanup/3pparkervangenuchten

* clean up 3p Parker-vanGenuchten
* replace MaterialParam by auto in 2p volvars
* improve tortuosity code


See merge request !139

* Clarify program flow
* Drop unused variables
* Remove superfluous semicolons
* White space changes

[fix][fvelementgeometry][box] Replace double bracket with single bracket

For the one-dimensional case the double curly brackets seem to result in
an error because it actually tries to assign an initializer list of size
2 to a GlobalPosition of size 1. For larger FieldVectors the double
bracket operator seems to be required by the compiler.

See merge request !138

For the one-dimensional case the double curly brackets seem to result in
an error because it actually tries to assign an initializer list of size
2 to a GlobalPosition of size 1. For larger FieldVectors the double
bracket operator seems to be required by the compiler.

[pointsource] fix pointsource constructor



See merge request !137

This fixes all the sequential 2p2c tests.

[sequential pressure-module] make EntryType, rhs and matrix protected instead of private to use it in derived class
This is similar to what is done in the non-adaptive pressure module.

Fix/1p model

* Remove permeability output (make 1p work with tensor permeabilities)
* Only compute velocity when needed for output

See merge request !136

The current implementation does not work with tensor permeabilities.
Not outputting the permeability as standard is suboptimal so we should
think about a better solution in the future.

* Remove permeability from the reference vtu files

[freeflow][multidomain] Remove deprecated functions



See merge request !135

Feature/improve pointsources

* Make convenience assignment operators work for the classes derived from PointSource
* Make the PointSourceHelper (computing in which scv a point source falls) a property to be able to exchange implementations (the current default uses the bounding box tree. This is however a waste of resources if one already knows more about where the point source is.)
* Rename PointSourceHelper to BoundingBoxTreePointSourceHelper

See merge request !134

The class computing in which sub control volume a point source falls
gets a property. Thus it can be exchanged with custom implementations
e.g. not making use of the bounding box tree. The default implementation
is the BoundingBoxTreePointSourceHelper using the axis-aligned bounding
box volume hierachy to find in which scv a point source falls.

Deprecate the old class. The deprecation warning seems not to be thrown for the
class template. Thus this uses a bit ugly workaround of deprecating the member
function... The message should however state it clearly.

Assignment operators get inherited technically but are overwritten by the
default assignment operator. The special assignment operators taking a
Scalar or a PrimaryVariable vector that gets assigned to the values member
of point source has thus to be overloaded in every derived class too.

This commit makes direct assignment of values to point source classes
derived from the base point source possible.

The number of embeddings of a point source (number of sub
control volumes the point source belongs to) can now be
set from outside. PointSourceHelper doesn't need to be a
friend class of PointSource anymore. The default number
of embeddings is 1 (a point source with no embeddings, e.g.
outside the grid boundary will be discarded anyway).

[implicit] Remove the shouldWriteOutput check inside writeOutput

When calling writeOutput one would expect that the output is actually
written to file. Instead this might not have happened in the old version.
This commit makes the implicit problem consistent with the sequential
models. Before calling writeOutput one should ask if shouldWriteOutput
is true. This is already consistently done all over dumux, so this
commit removes the double checking.

See merge request !133

Feature/cleanup after 2.9



See merge request !118

They were moved or deprecated in 2.9

They were reanmed and moved in 2.9

They were renamed in 2.9

They were renamed in 2.9

It's content was moved and renamed in 2.9

They were deprecated in 2.9

They were moved and renamed in 2.9

When calling writeOutput one would expect that the output is actually
written to file. Instead this might not have happened in the old version.
This commit makes the implicit problem consistent with the sequential
models. Before calling writeOutput one should ask if shouldWriteOutput
is true. This is already consistently done all over dumux, so this
commit removes the double checking.

Feature/bump up version



See merge request !132

Kilian Weishaupt authored 9 years ago and Timo Koch committed 9 years ago

(cherry picked from commit b208b98f)

Kilian Weishaupt authored 9 years ago and Timo Koch committed 9 years ago

(cherry picked from commit 0c643665)