this gets rid of the ugly red and green boxes around references. Note
that for some reason, hyperlinks do not seem to work anyway and that
using pdflatex directly does not work either :/
TeXLive 2016 complains about \it and \bf.
Also, this patch adds a simple bash script to create the handbook from
its LaTeX sources. Note that this script does *not* attempt to detect
if all prerequisites (in terms of binaries and LaTeX packages) are
properly available.
because "manager" sounds less religious than "creator" and the
GridCreators did all kinds of other stuff besides creating the grid.
this patch also gets rid of the static function inside these classes,
which should make them easier to understand...
This makes eWoms multi-discretization capable. Along the way, this
fixes some bugs and does a medium sized reorganization of the source tree.
This is a squashed patch of the following commits:
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1st commit message:
add initial version of the element centered finite volume discretization
currently, it is a misnomer as it is just a copy of the vertex
centered discretization plus some renames...
--------
2nd commit message:
rename [VE]cfvModel -> [VE]cfvDiscretization
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3rd commit message:
ecfv: prelimary changes required to make it compile
but not work yet...
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4th commit message:
Rename *FvElementGeometry to *Stencil
"Stencil" seems to be the standard expression for this concept...
(also, it is not specific to finite volume methods and is shorter.)
--------
5th commit message:
refactor the stencil class for the element centered finite volume discretization
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6th commit message:
ECFV: some work on the stencil class
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7th commit message:
ECFV: make the boundary handling code compile
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8th commit message:
rename elemContext() to elementContext()
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9th commit message:
ECFV: make the VTK output modules compile
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10th commit message:
stencil: introduce the concept of primary DOFs
also save an vector of all element pointers in the stencil.
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11th commit message:
ECFV: try to fix assembly; add missing timeIdx arguments to the num*() methods
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12th commit message:
ECFV: fix stupid mistake in the assembler
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13th commit message:
ECFV: remove a few implicit DOF == vertex assumptions
the black-oil example now runs without valgrind complaints until it encounters
a negative oil mole fraction.
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14th commit message:
VCFV: make everything compile again
all vertex centered FV examples should now work again...
--------
15th commit message:
rename [ev]cfvmodel.hh to [ev]cfvdiscretization.hh
the classes have already been renamed.
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16th commit message:
ECFV: make it work to the point where it can write out the initial solution.
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17th commit message:
ECFV: make it work
the local residual/jacobian needed some work in distinguishing primary
and secondary DOFs and there was an minor issue with the serialization
code.
for some reason, it seems still not correct. (-> convergence is too slow.)
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18th commit message:
VCFV: make it compile for the black oil model again
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19th commit message:
VCFV: make it compile with the remaining models again
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20th commit message:
flash model: make it work with ECFV
although this breaks its compatibility with VCFV. (-> next commit)
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21st commit message:
adapt the VCFV to make it compatible with the flash model again
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22nd commit message:
make all models compile with VCFV again
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23rd commit message:
VCFV: more cleanups of the stencil
VcfvStencil now does not have any public attributes anymore. TODO: do
not export attributes in the SubControlVolume and SubControlVolumeFace
classes.
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24th commit message:
VCFV: actually update the element pointer
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25th commit message:
change the blackoil model back to ECFV
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26th commit message:
immiscible model: make it compatible with the ECFV discretization
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27th commit message:
PVS model: make it work with ECFV
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28th commit message:
NCP model: make it work with ECFV
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29th commit message:
rename Vcfv*VelocityModule to *VelocityModule
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30th commit message:
richards model: make it work with ECFV
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31st commit message:
unify the ECFV and the VCFV VTK output modules
and other cleanups
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32nd commit message:
unify the common code of the VCFV and the ECFV disctretizations
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33rd commit message:
unify the element contexts between element and vertex centered finite volumes
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34th commit message:
unify the local jacobian class of the finite volume discretizations
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35th commit message:
replace [VE]vcf(LocalResidual|ElementContext|BoundaryContext|ConstraintsContext) by generic code
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36th commit message:
replace the [EV]cfvLocalResidual by generic code
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37th commit message:
unify the MultiPhaseProblem and Problem classes, introduce NullBorderListCreator
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38th commit message:
remove the discretization specific boundary context
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39th commit message:
unify the [EV]cfvDiscretization classes
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40th commit message:
Unify [EV]cfvMultiPhaseFluxVariables
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41st commit message:
Unify the [EC]cfvNewton* classes
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42nd commit message:
Unify [EV]cfvVolumeVariables
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43rd commit message:
unify [EV]cfvAssembler
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44th commit message:
unified flux variables: fix stupid mistake when calculating pressure gradients
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45th commit message:
unify what's to unify for the [EV]CFV properties
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46th commit message:
make the method to calculate gradients and values at flux approximation points changeable
Currently, this is used by the vertex centered finite volume method to
be able to use P1-finite element gradients instead of two-point
ones...
--------
47th commit message:
make the restart code work correctly, use the correct DofMapper for VCFV
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48th commit message:
actually use the gradient calculator in a model
the immiscible model in this case
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49th commit message:
move some files around to where they belong, use the new gradient calculation code in all models
TODO: proper handling of boundary gradients
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50th commit message:
fix the stokes model
currently it only works with the vertex centered finite volume
discretization, but the plan is to soon move it to a staggered grid
scheme anyway...
--------
51st commit message:
move all models back to using the vertex centered finite volume discretization by default
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52nd commit message:
models: some variable renames and documentation fixes
- scv -> dof
- vert -> dof
- vertex -> dof
- replace 'VCFV'
- fix some typos
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53rd commit message:
don't expect UG anymore
since it is quite non-free and hard to get. we now use ALUGrid instead!
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54th commit message:
temporarily disable jacobian recycling
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55th commit message:
fix writing/reading restart files using the generic code
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56th commit message:
fix bug where fluxes were only counted once in the stencil
this only affected the vertex centered finite volumes discretization...
--------
57th commit message:
boundary gradients: use the center of the sub-control volume adjacent to a boundary segment
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58th commit message:
make it compile on GCC
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59th commit message:
get rid of most hacks
for this, partial reassemble and jacobian recycling was brought
back. For the this and the remaining stuff the main trick is the
introduction of the GridCommHandleFactory concept which constructs
communication handles suited for the respective spatial
discretization...
--------
60th commit message:
fix a few annoying bugs
first, default the convergence criterion for the linear solver did not
honor the initial residual which lead to linear solver breakdowns,
then some debugging code was left in the discrete fracture model and
then there was a bug in the TP gradient approximation class...
this has the consequence that we need a new reference solution for the
discrete fracture problem...
--------
61st commit message:
iterative linear solver: remove the code for the non-default convergence criteria
--------
62nd commit message:
provide the FE cache instead of the local FE
this fixes a segfault in the stokes model caused by the fact that the
local FE was not initialized at this point.
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63rd commit message:
(Navier-)Stokes: fix bug due to the transition to unit normals
now, all tests pass for this branch. The only things which need to be
fixed are some annoying performance regressions compared to master and
some bug in the splices feature of the property system...
--------
64th commit message:
some fix for the local residual of the immiscible model
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65th commit message:
Navier-Stokes: implement SCV center gradients
There seems to be a bug in the previous implementation (the jacobian
inverse transposed is evaluated using the local, not the global
geometry), so the reference solution for the stokes2c test problem has
also been updated...
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66th commit message:
remove the ALUGrid specialization of the LensGridCreator and the YaspGrid one for the fingerproblem
using different grid seems to sometimes cause a different vertex
order, which in turn causes the respective test to fail if the
reference solution was computed using the other grid...
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67th commit message:
VCFV: use the correct BorderListCreator
this makes MPI parallel computations work again. apart from
performance regressions, this branch does not exhibit any known
regressions compared to master anymore...
--------
68th commit message:
make verything compile with the element centered finite volume discretization
except the Navier-Stokes and the two-phase DFM models, of course...
--------
69th commit message:
minor fixes
- make the navier-stokes model slighly more generic by using the
proper (in,ex)teriorIndex() methods on sub-control volumes
- make the signature of the calculateValue() template method of the
common two-point gradient approximator match the one of the vertex
centered finite volume one
--------
70th commit message:
fix fallout from the Big Rebase
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71st commit message:
ECFV: some bugs in the boundary
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72nd commit message:
make computeFlux() compute area-specific quantities
--------
73rd commit message:
fix more bugs in the element centered FV discretization
now eWoms should match Dumux pretty closely...
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74th commit message:
coalesce the common code of the multi phase porous medium models into "MultiPhaseBaseModel"
--------
75th commit message:
update reference solutions
these were changed because of the screw-up with the area of boundary
segments...
--------
76th commit message:
rename "ImplicitBase" to "FvBase"
because in eWoms, everything is implicit and these are currently the
base classes for all finite volume discretizations.
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77th commit message:
make the spatial discretization selectable using a splice
This requires an opm-core with a the patches from
https://github.com/OPM/opm-core/pull/446 merged...
--------
78th commit message:
rename the properties used for splices to *Splice
--------
79th commit message:
move the files in 'tests/models' to 'tests'
since 'tests' was empty except for the 'models' subdirectory...
--------
80th commit message:
improve and fix the tutorial
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81st commit message:
remove the -fno-strict-aliasing flag from the provided option files
seems like recent versions of Dune have been adapted...
--------
82nd commit message:
also compile all CO2 injection simulations using the element centered finite volume discretization
--------
83rd commit message:
PVS model: make it work properly with the element-centered finite volume discretiation
because DOF != number of vertices
we do not have a decoupled tutorial anymore since, well, the decoupled
models have been removed. Also since the move to the Opm CMake based
build system, the "How to create a new folder" section in the handbook
was obsolete.
eWoms hereby declares full independence. Humor aside, the main
technical advantage of this is, that it is now possible to easily
install both, Dumux and eWoms on a system using a package management
system without bad tricks.
the descriptions of the semi-implicit models are imported from dumux
because I suppose that these have been modified manually and the
differences should be negligible anyway...
- adapt the "quick start" chapter to eWoms
- remove the dumux logo from the front page
- remove the "flow of things" and "tipps and tricks" chapters:
- the former was not useful, IMHO but quite a burden to update and
the latter rather belongs to the online documentation (wiki?)
- update the flowchart showing the layout of the source tree
I also removed the deprecation stuff, as IMO it is more confusing than
helpful. (Ever tried to set the
SpatialParameters instead of SpatialParams in your problem?)
Also move the decoupled spatial parameters from dumux/material to
dumux/decoupled because they are specific to the decoupled models.
