On 23 June 2015 at 14:02, Martin Sandve Alnæs <[email protected]> wrote: > On 23 June 2015 at 14:13, Jan Blechta <[email protected]> wrote: >> >> On Tue, 23 Jun 2015 12:18:05 +0100 >> "Garth N. Wells" <[email protected]> wrote: >> >> > On 23 June 2015 at 10:43, Martin Sandve Alnæs <[email protected]> >> > wrote: >> > > On 23 June 2015 at 11:00, Jan Blechta <[email protected]> >> > > wrote: >> > >> >> > >> On Tue, 23 Jun 2015 08:54:03 +0000 >> > >> Anders Logg <[email protected]> wrote: >> > >> >> > >> > Yes exactly, that's the point, but it would get rid of a few >> > >> > lines of code and look simpler. Users who want to write more >> > >> > lines of code are free to do this: >> > >> > >> > >> > BoundingBoxTree tree; >> > >> > tree.build(mesh); >> > >> > const std::size_t cell_index = >> > >> > tree.compute_first_entity_collision(x); // this may fail and >> > >> > give a non-context related error message Cell cell(mesh, >> > >> > cell_index); function.eval(values, x, cell); >> > >> > >> > >> > Compare with: >> > >> > >> > >> > AutoCell cell; // we don't even need to supply the mesh here >> > >> > function.eval(values, x, cell); >> > >> >> > >> Ok, I'm just saying that this is equivalent to >> > >> >> > >> BoundingBoxTree tree(mesh); >> > >> function.eval(values, x, tree); >> > >> >> > >> while not introducing new class. But if it creates some benefit >> > >> that AutoCell inherits from Cell, then why not... >> > >> >> > >> Jan >> > > >> > > >> > > Because it's a strange abstraction and doesn't solve any problems >> > > that needs solving, but introduces new hidden pitfalls: >> > > >> > > AutoCell cell; // we don't even need to supply the mesh here >> > > function.eval(values, x, cell); // but the mesh is secretly >> > > attached here >> > > >> > > So now cell contains a big data structure (the tree) and a >> > > reference to the mesh, >> > > and the user still needs to carry the AutoCell object around to >> > > avoid to gain >> > > any benefits related to reuse of the tree. Why not just carry the >> > > tree around? >> > > >> > > With Jan's example, it's much clearer how the data flows: >> > > BoundingBoxTree tree(mesh); >> > > function.eval(values, x, tree); >> > > and now the user has a reusable tree in the same amount of code. >> > > >> > >> > I like having the user manage the tree. What about >> > >> > tree = BoundingBoxTree(mesh) >> > cell = tree.find_cell(x) >> > function.eval(values, x, cell) >> > >> > This way Function::eval doesn't need to be parallel-aware. If x is not >> > inside cell, Function::eval can throw and error. >> >> Yes, but what would be the interface for other situations which may >> trigger non-matching eval internally, like interpolate, assemble, ...? >> >> Jan > > > > If the inside check can be kept outside Function::eval, I think it's > best if Function::eval can assume that x is contained in the given > cell to keep things efficient: >
I think we should have an (optional) check that x is contained in the cell. The check could be in debug mode only, or turned on/off via a function argument. > tree = BoundingBoxTree(mesh) > cell = tree.find_cell(x) > status = not cell.empty() > if status: > function.eval(values, x, cell) > > In addition there can be a wrapper: > status = function.eval(values, x, tree) > > which does: > cell = tree.find_cell(x) > status = not cell.empty() > if status: > function.eval(values, x, cell) > return status > > So if you have a tree, you can avoid recreating it, > and if you have a cell, you can avoid searching for it. > I like the first, and I'm not bothered either way with the second. Garth > Martin > > >> >> > >> > Garth >> > >> > >> > > Martin >> > > >> > > >> > >> > >> > >> > -- >> > >> > Anders >> > >> > >> > >> > >> > >> > tis 23 juni 2015 kl 10:48 skrev Jan Blechta >> > >> > <[email protected]>: >> > >> > >> > >> > > On Tue, 23 Jun 2015 08:42:49 +0000 >> > >> > > Anders Logg <[email protected]> wrote: >> > >> > > >> > >> > > > How about something like this: >> > >> > > > >> > >> > > > 1. Require additional Cell& cell argument to Function::eval >> > >> > > > >> > >> > > > 2. Add new class AutoCell handling this for users who don't >> > >> > > > want to explicitly work with a BoundingBoxTree >> > >> > > > >> > >> > > > class AutoCell : public Cell >> > >> > > > { >> > >> > > > public: >> > >> > > > AutoCell(Mesh &mesh); >> > >> > > > BoundingBoxTree tree; >> > >> > > > } >> > >> > > > >> > >> > > > AutoCell cell(mesh); >> > >> > > > function.eval(values, x, cell); >> > >> > > > >> > >> > > > 3. If the mesh moves, a user can do something like: >> > >> > > > >> > >> > > > cell.invalidate() >> > >> > > >> > >> > > This is semantically equivalent to passing bounding box. >> > >> > > AutoCell would be just a wrapper for BoundingBoxTree, not >> > >> > > doing anything new. >> > >> > > >> > >> > > Jan >> > >> > > >> > >> > > > >> > >> > > > -- >> > >> > > > Anders >> > >> > > > >> > >> > > > >> > >> > > > >> > >> > > > tis 23 juni 2015 kl 10:30 skrev Garth N. Wells >> > >> > > > <[email protected]>: >> > >> > > > >> > >> > > > > On 22 June 2015 at 18:00, Anders Logg >> > >> > > > > <[email protected]> wrote: >> > >> > > > > > The challenge in moving the bounding box tree outside of >> > >> > > > > > the mesh is >> > >> > > > > that it >> > >> > > > > > has always been part of the mesh (it replaced an earlier >> > >> > > > > > data structure >> > >> > > > > that >> > >> > > > > > was there) so a user expects to be able to do >> > >> > > > > > >> > >> > > > > > v = Function(V) >> > >> > > > > > print v(x) >> > >> > > > > > >> > >> > > > > >> > >> > > > > This is fine for Expressions, but for a Function I don't >> > >> > > > > think it's bad for the interface to make obvious to the >> > >> > > > > user that they are performing a potentially expensive >> > >> > > > > operation. If the user was required to pass the cell, all >> > >> > > > > would be fine. It would also fix the issues with Function >> > >> > > > > evaluations in parallel. >> > >> > > > > >> > >> > > > > > without needing to instantiate some cryptic >> > >> > > > > > BoundingBoxTree data >> > >> > > > > structure. >> > >> > > > > > Furthermore, a user expects that on subsequent calls >> > >> > > > > > v(x) is fast since >> > >> > > > > the >> > >> > > > > > tree has already been built. >> > >> > > > > > >> > >> > > > > > I don't see a way around automatic handling of building >> > >> > > > > > the search tree. >> > >> > > > > Are >> > >> > > > > > there some clever suggestions? >> > >> > > > > > >> > >> > > > > >> > >> > > > > We have a fundamental problem/flaw that MeshGeometery is >> > >> > > > > mutable and a Mesh owns a bounding box object. One of the >> > >> > > > > two needs to give. >> > >> > > > > >> > >> > > > > Garth >> > >> > > > > >> > >> > > > > >> > >> > > > > > Handling this for PointSource and MultiMesh is >> > >> > > > > > unproblematic. (But for MultiMesh, I would rather want >> > >> > > > > > to move it myself.) >> > >> > > > > > >> > >> > > > > > -- >> > >> > > > > > Anders >> > >> > > > > > >> > >> > > > > > >> > >> > > > > > mån 22 juni 2015 kl 17:54 skrev Marco Morandini < >> > >> > > > > [email protected]>: >> > >> > > > > >> >> > >> > > > > >> >>> Besides, the mesh bounding_box_tree used to find the >> > >> > > > > >> >>> colliding mesh entity is cached. I fear this could >> > >> > > > > >> >>> be a source of "strange" results, because its use >> > >> > > > > >> >>> is here completely transparent to the user, who may >> > >> > > > > >> >>> be unaware of the need to update it. >> > >> > > > > >> >>> >> > >> > > > > >> >> >> > >> > > > > >> >> I really don't like magical caching. How about having >> > >> > > > > >> >> >> > >> > > > > >> >> PointSource::apply(GenericVector& b, Cell& c, double >> > >> > > > > >> >> magnitude); >> > >> > > > > >> >> >> > >> > > > > >> >> The user is responsible for finding the cell, and >> > >> > > > > >> >> thereby also responsible for handling meshes that >> > >> > > > > >> >> move, etc. >> > >> > > > > >> >> >> > >> > > > > >> >> PointSource::apply(...) presently uses >> > >> > > > > >> >> Mesh::bounding_box_tree(), which I would like to get >> > >> > > > > >> >> rid of from Mesh since mesh geometry is mutable. If >> > >> > > > > >> >> the search tools are not cached, the user takes >> > >> > > > > >> >> responsibility for managing the bounding boxes. >> > >> > > > > >> > >> > >> > > > > >> > For the record, this issue is filed as >> > >> > > > > >> > https://bitbucket.org/fenics-project/dolfin/issue/89 >> > >> > > > > >> > >> > >> > > > > >> >> > >> > > > > >> Right now Mesh::bounding_box_tree() is used by >> > >> > > > > >> >> > >> > > > > >> void PointSource::apply(GenericVector& b) >> > >> > > > > >> void Function::eval(Array<double>& values, const >> > >> > > > > >> Array<double>& x) const >> > >> > > > > >> >> > >> > > > > >> and >> > >> > > > > >> >> > >> > > > > >> MultiMesh ( + MultiMeshDirichletBC ) >> > >> > > > > >> >> > >> > > > > >> It would be pretty easy to change PointSource and >> > >> > > > > >> Function. But I think that, for MultiMesh, I should >> > >> > > > > >> move the bboxes there, and leave MultiMesh::build() >> > >> > > > > >> unchanged. >> > >> > > > > >> >> > >> > > > > >> I can go this route if there is consensus. >> > >> > > > > >> >> > >> > > > > >> Marco >> > >> > > > > >> >> > >> > > > > >> >> > >> > > > > >> >> > >> > > > > >> _______________________________________________ >> > >> > > > > >> fenics mailing list >> > >> > > > > >> [email protected] >> > >> > > > > >> http://fenicsproject.org/mailman/listinfo/fenics >> > >> > > > > _______________________________________________ >> > >> > > > > fenics mailing list >> > >> > > > > [email protected] >> > >> > > > > http://fenicsproject.org/mailman/listinfo/fenics >> > >> > > > > >> > >> > > >> > >> > > _______________________________________________ >> > >> > > fenics mailing list >> > >> > > [email protected] >> > >> > > http://fenicsproject.org/mailman/listinfo/fenics >> > >> > > >> > >> >> > >> _______________________________________________ >> > >> fenics mailing list >> > >> [email protected] >> > >> http://fenicsproject.org/mailman/listinfo/fenics >> > > >> > > >> > > >> > > _______________________________________________ >> > > fenics mailing list >> > > [email protected] >> > > http://fenicsproject.org/mailman/listinfo/fenics >> > > >> > _______________________________________________ >> > fenics mailing list >> > [email protected] >> > http://fenicsproject.org/mailman/listinfo/fenics >> > _______________________________________________ fenics mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics
