: block preconditioners only make sense in Bidomain... Add some warning/error message
: #1082 only works if you know about the whole mesh.
#1317 code for saving/loading mSolution is PROBLEM_DIM specific, move it into the save/load methods for Mono and BidomainProblem. (ExtendedBidomain has its own already.)
#1317 is there a reason we can't use PETSc's load/save vector functionality?
#1316 Create a class defining constant tensors to be used when no fibre orientation is provided.
#1316 Create a class defining constant tensors to be used when no fibre orientation is provided.
This may want to go to std::cerr ??
#2017 This code will be needed in the future, not being covered now. Add a test which covers this, e.g. by doing a simulation with a bad stimulus for one of the Purkinje cells - stimulating with the wrong choice of sign say.
(#2578)
should be an exception?
This is a scarily long method; could do with some parts extracted?
consider reducing all stimuli to match this one.
remove magic number? (#1884)
#1319 Template LinearBasisFunction over SPACE_DIM and remove this method?
The name of this method should not include underscores.
The name of this method should not include underscores.
The name of this method should not include underscores.
The name of this method should not include underscores.
The name of this method should not include underscores.
#2057 Make better choices here...
#2057 Make better choices..
move to AbstractParameterisedSystem? (1540)
Should be const
#1322 Mesh should really be const!
#1322 Mesh should be const
#1322 This should be const too
#1322, This should be const too
#1321 This is a horrendously inefficient fix. Perhaps have flag in element object?
does this mean natural radius of a cell? If so at what age? (#1764) Time is in hours.
Which subclasses? Why is the second input argument needed?
this is where to deal with carrying capacity
enable the coarse PDE mesh to change size, e.g. for a growing domain (#630/#1891)
enable this in the case where a coarse PDE mesh is used
Worry about round-off errors (#1891)
#2066 return the time step (mDt) defined in the calculation of the probability of a cell moving to a certain site
#2066 define the time step (dt) defined in the calculation of the probability of a cell moving to a certain site
Should be const
#1930 We should use a reader set iterator for this bit now.
#1730 and we should be able to combine ASCII branch
#1930 We should use a reader set iterator for this bit now.
#1289 assert the node is not considered both owned and halo-owned.
#1957 causes segfaults
#1957 remove when unloading working
: #1361 ComputeContainingElements and related methods, and methods called by that down to here, should really take in const c_vector& rather than ChastePoints.
#1326 This method shouldn't need a new Jacobian inverse for every Xi
The name of this method should not include underscores.
The name of this method should not include underscores.
The name of this method should not include underscores.
The name of this method should not include underscores.
The name of this method should not include underscores.
: which cells are apoptotic? if they get apoptotic during G2-phase then this line has to be changed
This is a little hack that we might want to clean up in the future.
The useMeshWidth is temporary, while we are sorting out 3D stimulus. It is to be removed later (along with StimulusConvergenceTester) scale stimulus depending on space_step of elements
It looks like the value of the stimulus is specific to 3D
#1660 at present this converter is hardcoded to work with "Data" using the below statement
What if the mesh has been scaled, translated or rotated?
- do we assume the vectors are initially empty? The returned std::vectors are all of the same length
There is no set method
- do we assume the vectors are initially empty? The returned std::vectors are all of the same length
When this is implemented, then we require an example in ChasteParametersFullFormat.xml
- do we assume the vectors are initially empty? The returned std::vectors are all of the same length
There is no set method
#2273 - check if this call to Update() is needed
#2273 - investigate whether there is a hard-coded assumption that neighbouring nodes in Potts simulations are unit distance apart
#2273 - check if this call to Update() is needed
#2273 - check if this call is needed
#2273 - check we have correctly dealt with ghost nodes
: if we create a linear system object outside a cardiac solver, these are gonna be the default solver and preconditioner. Not consitent with ChasteDefaults.xml though...
: if we create a linear system object outside a cardiac solver, these are gonna be the default solver and preconditioner. Not consistent with ChasteDefaults.xml though...
: if we create a linear system object outside a cardiac solver, these are gonna be the default solver and preconditioner. Not consitent with ChasteDefaults.xml though...
: #1082 is this the way of defining a null pointer as the default value of pBathNodes?
: #1082 use a single pointer to abstract class
: #1082 use a single pointer to abstract class
: #1082 use a single pointer to abstract class
This is a magic number. Do we want a warning here?
never tested in linalg component
Should it be compulsory for the caller to supply this and manage the memory?
#1695 Store this number in a member variable.
This method is somewhat redundant following the introduction of the method GetVolumeOfCell() (see #1985).
The name of this method should not include underscores.
The name of this method should not include underscores.
The name of this method should not include underscores.
The name of this method should not include underscores.
The name of this method should not include underscores.
Could we search more efficiently by just iterating over edges? (see #2401)
Use iterators to tidy this up (see #2401)
This method currently assumes SPACE_DIM = 2 (see #866)
this could be more efficient (see #2401)
This method seems to be redundant; remove it? (#2401)
Implement ReMesh() in 3D (see #1422)
investigate if moving A and B causes other issues with nearby nodes (see #2401)
currently this assumes a worst case scenario of 3 nodes between A and B could be less movement for other cases (see #1399 and #2401)
currently this assumes a worst case scenario of 3 nodes between A and B; could be less movement for other cases (see #2401)
#1216 change the number 54 below (row nonzero allocation) to be nonmagic
: This assembly is likely to generate many communications. Try to interleave other operations by executing them between Begin() and End().
correct time step? (#2404)
correct time step? (#2404)
correct time step? (#2404)
: #1082 won't work in parallel
: #1082 won't work in parallel
: #1082 assert size(x1) = size(x21) + size(x22)
: #1082 legacy, no need to use the references
: #1082 OK in parallel. Use as an example for the other two blocks
Integrate with other time stepping classes or remove? A small convenience class providing a consistent global time to the PDE solver classes.
The name of this method should not include underscores.
The name of this method should not include underscores.
The name of this method should not include underscores.
The name of this method should not include underscores.
The name of this method should not include underscores.
This method ought to be private and called by the WritePostProcessingFiles method if the user requests for it. This will be possible after modifying the schema and specifying Get and Set methods in HeartConfig to check whether the user wants this file or not
#2359 work out how to get rid of this line needed because PseudoEcgCalculator makes its own Hdf5DataReader.
#2359 work out how to get rid of these lines
Mesh should be const (#1076)
Mesh should be const (#1663)
#1930 Until there is an interator_facade over boundary elements,
#1930 Once there is an interator_facade then we can do: elem_index = pMeshReader->GetFaceData(face_index).ContainingElement;
document these parameters
document these parameters
This should be an exception
This should be an exception
#2452 We need a way of propagating this back to the mesh (and insuring that the mesh is NOT being re-partitioned)
#1949 Readers do not currently support reading of node attributes, so we cannot yet write them from a reader
#1949
#1949 Readers do not currently support reading of node attributes, so we cannot yet write them from a reader
#1949 Will deadlock on GetNode(global ID) in parallel since this code is run on the master process
#1949
#1949
Merge with 3D Voronoi constructor? (see #1075)
Merge with 2D Voronoi constructor? (see #1075)
Mesh should be const (#1076)
Mesh should be const (#1076)
#1322 Mesh should really be const!
#1322 Mesh should be const
This ought to look exactly like the other MakeVtkMesh
#1494 Do we need a barrier?
1.6.2