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From: Roy Stogner <roy@st...>  20080812 23:06:33

On Mon, 11 Aug 2008, Vijay S. Mahadevan wrote: > But now, when I try to call get_data on MeshData, the assertion > > libmesh_assert (_elem_data_closed); > > fails in /libmesh/include/mesh/mesh_data.h, line 956. > > Of course, I'm out of ideas as to how to close() the mesh_data after > setting the data for elems and nodes. Is there a simple call that > would solve my problem or do I really have to call insert_node_data > and insert_elem_data after building the entire array of data. IMO, the > second method seems tedious and is a big requirement on the user part. I agree. I think the problem is simply that none of the active libMesh developers are MeshData users, so it's about all we can do to keep that functionality from regressing; there's nobody who works with it enough to make informed changes to what may be some flawed API design decisions. Looking over the code, I don't see any better close() method than what you've already identified. We could certainly use one, though; a patch would be appreciated.  Roy 
From: Roy Stogner <roy@st...>  20080812 22:59:05

On Tue, 12 Aug 2008, Nasser Mohieddin Abukhdeir wrote: > I'm trying to implement Dirichlet boundary conditions in a 1D > problem using DiffSystem. There isn't really an example to cover this, > so I just want to verify what I came up with makes sense, where two > variables "B" and "lB" should be zero at the domain boundaries x=0,1 > (note, using numerical jacobians for now): At first glance this looks correct, but it may be overkill. It's actually not necessary to do anything special in 1D. You might not think that a 1D element has "sides" that you can integrate over, but in recent (0.6.0 or so?) libMesh versions we now have a "NodeElem" object whose job is to let you do just that: Dirichlet boundary conditions (or any boundary conditions) expressed as quadrature loops on sides now work correctly even when the side is a single point. I'd add a 1D case to example 18 to make this clear, but 1D incompressible flow is so dull that people would wonder why the option was even there.  Roy 
From: John Peterson <jwpeterson@gm...>  20080812 22:13:09

On Tue, Aug 12, 2008 at 4:59 PM, Nasser Mohieddin Abukhdeir <nasser.abukhdeir@...> wrote: > That works for 1D, for 2D with adaptive meshing should I just project the > solution to a uniform grid and export? For 2D there are several output formats, unfortunately GNUplot is not one of them. May I recommend the General Mesh Viewer (wwwxdiv.lanl.gov/XCM/gmv/GMVHome.html)?  John 
From: Nasser Mohieddin Abukhdeir <nasser.abukhdeir@mc...>  20080812 22:04:06

Hi: I'm trying to implement Dirichlet boundary conditions in a 1D problem using DiffSystem. There isn't really an example to cover this, so I just want to verify what I came up with makes sense, where two variables "B" and "lB" should be zero at the domain boundaries x=0,1 (note, using numerical jacobians for now): const Real penalty = 1.e10; if (elem>contains_point(Point(0.,0.))elem>contains_point(Point(1.,0.))) { for(unsigned int s=0; s<elem>n_sides(); s++) { if(elem>neighbor(s) == NULL) { Number B = side_value(B_var, s), lB = side_value(lB_var, s); Real B_value = 0.; Real lB_value = 0.; for (unsigned int i=0; i != n_B_dofs; i++) { F1(i) += JxW_side[s] * penalty * (B  B_value) * phi_side[i][s]; F2(i) += JxW_side[s] * penalty * (lB  lB_value) * phi_side[i][s]; } } } }  Nasser Mohieddin Abukhdeir Graduate Student (Materials Modeling Research Group) McGill University  Department of Chemical Engineering http://webpages.mcgill.ca/students/nabukh/web/ http://mmrg.chemeng.mcgill.ca/ 
From: Nasser Mohieddin Abukhdeir <nasser.abukhdeir@mc...>  20080812 21:59:52

That works for 1D, for 2D with adaptive meshing should I just project the solution to a uniform grid and export? Nasser Mohieddin Abukhdeir Graduate Student (Materials Modeling Research Group) McGill University  Department of Chemical Engineering http://webpages.mcgill.ca/students/nabukh/web/ http://mmrg.chemeng.mcgill.ca/ John Peterson wrote: > On Tue, Aug 12, 2008 at 9:46 AM, Nasser Mohieddin Abukhdeir > <nasser.abukhdeir@...> wrote: > >> Hi: >> This might be a stupid question, but I cannot figure out how to >> export data from Libmesh for postprocessing into an Octave/Matlab >> compatible format. Right now its a simple problem, I am solving a 1D >> problem with adaptive mesh refinement...there doesn't seem to be >> anything on the lists about this and none of the file formats supported >> by Libmesh seem readable by Octave/Matlab, *please* correct me if I'm wrong. >> > > There is a GnuplotIO output format for 1D. Will that suit your needs? > See ex4 for an example. > > 
From: John Peterson <jwpeterson@gm...>  20080812 16:08:56

On Tue, Aug 12, 2008 at 9:46 AM, Nasser Mohieddin Abukhdeir <nasser.abukhdeir@...> wrote: > Hi: > This might be a stupid question, but I cannot figure out how to > export data from Libmesh for postprocessing into an Octave/Matlab > compatible format. Right now its a simple problem, I am solving a 1D > problem with adaptive mesh refinement...there doesn't seem to be > anything on the lists about this and none of the file formats supported > by Libmesh seem readable by Octave/Matlab, *please* correct me if I'm wrong. There is a GnuplotIO output format for 1D. Will that suit your needs? See ex4 for an example.  John 
From: yunfei zhu <yzhu2009@go...>  20080812 15:16:23

Thanks for your code. I am the beginnder of c++, still trying to understand them. On 8/11/08, Roy Stogner <roy@...> wrote: > > > On Mon, 11 Aug 2008, yunfei zhu wrote: > > Hi, could you guys tell me which function can be used to mesh a >> thickwalled cylinder? In the file of mesh_generation.h, there are >> functions: void build_cube(), void build_line (), void >> build_square(), void build_sphere(). Do you have some function like >> build_cylinder()? or some other method to mesh a cylinder? Many >> thanks. >> > > I've got some code I wrote for another local libMesh user, but I > never tested it enough to want to put it in the library. I'll copy > the relevant parts here, but buyer beware. If you need child element > nodes to be snapped to the correct geometry after refinement, you'll > have to do that yourself. If you need documentation, please write > some and email us a copy. If this code breaks, you get to keep both > pieces. > >  > > else if (param.domaintype == "square"  param.domaintype == "cylinder") > { > if (param.dimension == 1) > MeshTools::Generation::build_line > (mesh, param.coarsegridx, > param.domain_xmin, param.domain_xmin + param.domain_edge_width, > EDGE2); > else if (param.dimension == 2) > { > if (param.elementtype == "unstructured") > { > MeshTools::Generation::build_delaunay_square > (mesh, param.coarsegridx, param.coarsegridy, > param.domain_xmin, param.domain_xmin + > param.domain_edge_width, > param.domain_ymin, param.domain_ymin + > param.domain_edge_length > , > TRI3); > } > else > MeshTools::Generation::build_square > (mesh, param.coarsegridx, param.coarsegridy, > param.domain_xmin, param.domain_xmin + > param.domain_edge_width, > param.domain_ymin, param.domain_ymin + > param.domain_edge_length, > elemtype); > } > else if (param.dimension == 3) > { > if (param.elementtype == "tri") > libmesh_error(); > MeshTools::Generation::build_cube > (mesh, param.coarsegridx, param.coarsegridy, param.coarsegridz, > param.domain_xmin, param.domain_xmin + param.domain_edge_width, > param.domain_ymin, param.domain_ymin + > param.domain_edge_length, > param.domain_zmin, param.domain_zmin + > param.domain_edge_height, > HEX8); > } > else > libmesh_error(); > } > > ... > > if (param.domaintype == "cylinder") > { > if (param.domain_ymin != 0.0  > param.domain_edge_length != 1.0) > { > std::cerr << "Theta must range from 0 to 1" > << std::endl; > libmesh_error(); > } > > PointLocatorTree point_locator(mesh); > > MeshBase::element_iterator el = mesh.elements_begin(); > const MeshBase::element_iterator end_el = mesh.elements_end(); > > for (; el != end_el; ++el) > { > Elem* elem = *el; > > // The boundary we sew up causes problems with BoundaryInfo > // later, so for now remove all boundary ids > mesh.boundary_info>remove(elem); > > for (unsigned int n = 0; n != elem>n_nodes(); ++n) > { > Node &node = *(elem>get_node(n)); > if (std::abs(node(1)  param.domain_edge_length) < TOLERANCE) > { > Point wrapped_point = node; > wrapped_point(1) = 0; > Elem *wrapped_elem = > const_cast<Elem *>(point_locator(wrapped_point)); > libmesh_assert(elem); > > bool found_matching_point = false; > for (unsigned int wn = 0; wn != wrapped_elem>n_nodes(); > ++wn) > { > Node *new_node = wrapped_elem>get_node(wn); > if (new_node>absolute_fuzzy_equals(wrapped_point)) > { > elem>set_node(n) = new_node; > found_matching_point = true; > break; > } > } > libmesh_assert(found_matching_point); > } > } > } > > MeshBase::node_iterator nd = mesh.nodes_begin(); > const MeshBase::node_iterator end_nd = mesh.nodes_end(); > if (param.dimension == 3  param.dimension == 2) > { > for (; nd != end_nd; ++nd) > { > Node &node = **nd; > Real r = node(0), theta = node(1); //, z = node(2); > node(0) = r * cos(2.0*M_PI*theta); > node(1) = r * sin(2.0*M_PI*theta); > // node(2) = z; > > // The boundary we sew up causes problems with > // BoundaryInfo later, so for now remove all boundary > // ids > mesh.boundary_info>remove(&node); > > } > } > else > { > libmesh_error(); > } > } > > 
From: Nasser Mohieddin Abukhdeir <nasser.abukhdeir@mc...>  20080812 14:46:35

Hi: This might be a stupid question, but I cannot figure out how to export data from Libmesh for postprocessing into an Octave/Matlab compatible format. Right now its a simple problem, I am solving a 1D problem with adaptive mesh refinement...there doesn't seem to be anything on the lists about this and none of the file formats supported by Libmesh seem readable by Octave/Matlab, *please* correct me if I'm wrong.  Nasser Mohieddin Abukhdeir Graduate Student (Materials Modeling Research Group) McGill University  Department of Chemical Engineering http://webpages.mcgill.ca/students/nabukh/web/ http://mmrg.chemeng.mcgill.ca/ 