Thanks for all your help, Rahul, Vijay and everyone! Vijay, I have 0.6.4. Looked under src, and don't see the get_mesh_data function in system.C, equation_systems.C, equation_systems_io.C, linear_implicit_system.C or explicit_system.C...
Am I missing something? Karen On Sat, Mar 27, 2010 at 12:24 AM, Vijay S. Mahadevan <[email protected]>wrote: > There is a get_mesh_data function in EquationSystems. This should be > accessible from your assemble function through the equation_system > object. > > Vijay > > On Sat, Mar 27, 2010 at 3:13 AM, Karen Lee <[email protected]> wrote: > > Yeah, this makes perfect sense to me. > > > > I'm having difficulty with step 2 though. In main, I define a MeshData > that > > I read in from an input file with the Mesh itself and the associated > data. > > Basically, F_nodal IS mesh_data.get_data(el.get_node(i))[0], but I don't > see > > a get_mesh_data function or something similar in the class doc for > System... > > Nor can I find a way to access the MeshData object associated with the > mesh > > once I have the mesh object pointer... > > > > > > > > > > On Fri, Mar 26, 2010 at 5:38 PM, Rahul Sampath <[email protected] > >wrote: > > > >> Here are the steps to solve Laplacian u(x,y,z) = f(x,y,z): > >> > >> 1. Form A = Assembly( A_elem ) where A_elem = integral(dPhi_i*dPhi_j) > >> 2. Form F_nodal = f(x_i,y_i,z_i) at all mesh nodes > >> 3. Form MassMatrix = Assembly( M_elem ) where M_elem = integral(Phi_k, > >> Phi_j) > >> 4. Form RHS = MassMatrix*F_nodal > >> 5. Solve A U_nodal = RHS for U_nodal > >> > >> > >> > >> On Fri, Mar 26, 2010 at 5:26 PM, Karen Lee <[email protected]> wrote: > >> > This would be for the interpolation only right? > >> > > >> > So if I use this GlobalRHS, and construct my LHS based on the actual > >> problem > >> > I want to solve (just a Poisson, so I would be using dphi), it would > be > >> > equivalent to solving the problem with the RHS being interpolated? > >> > > >> > Karen > >> > > >> > > >> > On Fri, Mar 26, 2010 at 5:23 PM, Rahul Sampath < > [email protected]> > >> > wrote: > >> >> > >> >> To be more precise: > >> >> > >> >> GlobalMassMatrix = Sum_over_elements{ > >> >> integral_over_current_element_using_quadrature(phi_i*phi_j) } > >> >> > >> >> GlobalRHS = GlobalMassMatrix*Nodal_F_Vector > >> >> > >> >> On Fri, Mar 26, 2010 at 5:22 PM, Rahul Sampath < > [email protected] > >> > > >> >> wrote: > >> >> > This is what I meant: > >> >> > > >> >> > MassMatrix = integral(phi_i*phi_j) > >> >> > > >> >> > RHS = MassMatrix*Nodal_F_Vector > >> >> > > >> >> > > >> >> > On Fri, Mar 26, 2010 at 5:11 PM, Karen Lee <[email protected]> > >> wrote: > >> >> >> Sorry, I think I was probably confused. I guess you just meant > that I > >> >> >> can > >> >> >> simply use integral of f_i phi_i phi_j as my RHS, and my original > LHS > >> >> >> as my > >> >> >> LHS, and that would already be effectively an interpolation? > Please > >> let > >> >> >> me > >> >> >> know if this is the correct way to think about it instead of the > long > >> >> >> message I sent with lots of code... > >> >> >> > >> >> >> My 2 questions regarding access to data would still remain: > >> >> >> > >> >> >> 1) I am still having problems accessing MeshData from the > assemble > >> >> >> function. I would like to do something like > >> >> >> mesh_data.get_data(el.get_node(i))[0] to get the first data > variable > >> >> >> for > >> >> >> node i with an element, i from 0 to 3, but I'm not sure how to > access > >> >> >> mesh_data from my System. (I should use Linear Implicit System so > I > >> can > >> >> >> have > >> >> >> the matrix on the lhs right?) > >> >> >> > >> >> >> 2) The other question is, for Fe, do I integrate over all the > >> >> >> quadrature > >> >> >> points of phi_i and phi_j with f_i being a constant? > >> >> >> > >> >> >> Thank you so much!!! > >> >> >> Karen > >> >> >> > >> >> >> > >> >> >> On Fri, Mar 26, 2010 at 4:57 PM, Karen Lee <[email protected]> > >> wrote: > >> >> >>> > >> >> >>> Thanks Rahul. Your responses have clarified things for me. > >> >> >>> > >> >> >>> I am still having problems accessing MeshData from the assemble > >> >> >>> function > >> >> >>> (which is only supposed to have 2 arguments right?) > >> >> >>> > >> >> >>> I can do: > >> >> >>> > >> >> >>> void assemble_load(EquationSystems& es, > >> >> >>> const std::string& system_name) > >> >> >>> { > >> >> >>> > >> >> >>> libmesh_assert (system_name == "load"); > >> >> >>> > >> >> >>> > >> >> >>> const MeshBase& mesh = es.get_mesh(); > >> >> >>> printf("mesh_data obtained"); > >> >> >>> > >> >> >>> ...... > >> >> >>> > >> >> >>> But I'm not sure how I can get the MeshData object that I created > in > >> >> >>> main > >> >> >>> that's attached to the mesh I created. In the look iterating over > >> the > >> >> >>> elements el, I know that I have to use something like > >> >> >>> mesh_data.get_data(el.get_node(i))[0] to get the first data > variable > >> >> >>> for > >> >> >>> node i with an element, i from 0 to 3, but I'm not sure how to > >> access > >> >> >>> mesh_data from my System. (I should use Linear Implicit System so > I > >> >> >>> can have > >> >> >>> the matrix on the lhs right?) > >> >> >>> > >> >> >>> My code is based on example 3, and the relevant part is this (not > >> sure > >> >> >>> if > >> >> >>> it's correct): > >> >> >>> > >> >> >>> for ( ; el != end_el ; ++el) > >> >> >>> { > >> >> >>> const Elem* elem = *el; > >> >> >>> > >> >> >>> dof_map.dof_indices (elem, dof_indices); > >> >> >>> > >> >> >>> fe->reinit (elem); > >> >> >>> > >> >> >>> Ke.resize (dof_indices.size(), > >> >> >>> dof_indices.size()); > >> >> >>> > >> >> >>> Fe.resize (dof_indices.size()); > >> >> >>> > >> >> >>> for (unsigned int qp=0; qp<qrule.n_points(); qp++) > >> >> >>> { > >> >> >>> > >> >> >>> for (unsigned int i=0; i<phi.size(); i++) > >> >> >>> for (unsigned int j=0; j<phi.size(); j++) > >> >> >>> { > >> >> >>> Ke(i,j) += JxW[qp]*(phi[i][qp]*phi[j][qp]); > >> >> >>> } > >> >> >>> > >> >> >>> { > >> >> >>> for (unsigned int i=0; i<phi.size(); i++) > >> >> >>> { > >> >> >>> for (unsigned int k=0; k<phi.size(); k++) > >> >> >>> { > >> >> >>> Fe(i) += > >> >> >>> > JxW[qp]*mesh_data.get_data(el.get_node(k))[0]*phi[i][qp]phi[k][qp]; > >> >> >>> > >> >> >>> } > >> >> >>> } > >> >> >>> } > >> >> >>> .... > >> >> >>> > >> >> >>> The other question is, for Fe, do I integrate over all the > >> quadrature > >> >> >>> points of phi_i and phi_j with f_i being a constant? > >> >> >>> > >> >> >>> Then once I get this solution (the variable name is "R", let's > say), > >> I > >> >> >>> hope to use it in place of mesh_data.get_data(el.get_node(k))[0] > >> and > >> >> >>> do > >> >> >>> something like this (of course this is another system that I'm > >> adding > >> >> >>> to > >> >> >>> EquationSystems): > >> >> >>> > >> >> >>> for (unsigned int qp=0; qp<qrule.n_points(); qp++) > >> >> >>> { > >> >> >>> > >> >> >>> for (unsigned int i=0; i<phi.size(); i++) > >> >> >>> > >> >> >>> > >> >> >>> for (unsigned int j=0; j<phi.size(); j++) > >> >> >>> { > >> >> >>> Ke2(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]); > >> >> >>> > >> >> >>> > >> >> >>> } > >> >> >>> > >> >> >>> { > >> >> >>> const Real x = q_point[qp](0); > >> >> >>> const Real y = q_point[qp](1); > >> >> >>> const Real z = q_point[qp](2); > >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> const Real fxy = R(x,y,z); > >> >> >>> > >> >> >>> for (unsigned int i=0; i<phi.size(); i++) > >> >> >>> > >> >> >>> > >> >> >>> Fe2(i) += JxW[qp]*fxy*phi[i][qp]; > >> >> >>> } > >> >> >>> } > >> >> >>> > >> >> >>> I'm not sure how to access anything in a Variable object > though... > >> >> >>> Let's > >> >> >>> say "R" being a a variable I add to the first system to get the > RHS > >> >> >>> interpolation, and "u" is the variable I add to the second > equation > >> >> >>> system, > >> >> >>> which is the actual solution I'm after... I just know that I can > >> >> >>> output the > >> >> >>> values of the solution at various nodal points in a file, but am > not > >> >> >>> sure > >> >> >>> what to do with the data structure and how I can extract values > at > >> >> >>> different > >> >> >>> arbitrary locations. > >> >> >>> > >> >> >>> Apologies for the lengthy email... > >> >> >>> > >> >> >>> Thanks, > >> >> >>> Karen > >> >> >>> > >> >> >>> > >> >> >>> On Fri, Mar 26, 2010 at 9:15 AM, Rahul Sampath > >> >> >>> <[email protected]> > >> >> >>> wrote: > >> >> >>>> > >> >> >>>> Hi Karen: > >> >> >>>> > >> >> >>>> Take a look at any Nonlinear example problem. Whenever you want > to > >> >> >>>> use > >> >> >>>> any solution vector in your residual computation, you will need > to > >> >> >>>> interpolate the nodal values using the FEM shape functions for > this > >> >> >>>> element and then do the integration. It is very similar to what > you > >> >> >>>> want to do. That is why I suggested the Mass matrix trick. It is > >> very > >> >> >>>> simple to implement and fast too especially if you want to > change f > >> >> >>>> often. You can use the same Mass matrix with differen f. The > catch > >> is > >> >> >>>> that you are using your FE shape functions for your > interpolation. > >> As > >> >> >>>> long as you are happy with linear interpolation for f this > should > >> do. > >> >> >>>> If you want to interpolate f with a higher order polynomial than > >> your > >> >> >>>> FE shape function then this wont work. > >> >> >>>> > >> >> >>>> Btw, if I was not clear earlier: > >> >> >>>> You have to form a global Mass matrix by integrating phi_i phi_j > >> over > >> >> >>>> all elements and doing a typically FEM assembly. Then you can > >> simply > >> >> >>>> multiply this global Mass matrix with you global nodal vector > for > >> f. > >> >> >>>> > >> >> >>>> On Fri, Mar 26, 2010 at 12:51 AM, Karen Lee <[email protected] > > > >> >> >>>> wrote: > >> >> >>>> > Hi Rahul, I'm not completely sure what you mean. > >> >> >>>> > > >> >> >>>> > I would like to form my RHS by integrating f_i Phi_i (I guess > >> >> >>>> > there's > >> >> >>>> > no > >> >> >>>> > need to multiply Phi_j? But you can correct me) for each > element. > >> >> >>>> > > >> >> >>>> > In order to do so, I need values of f at various quadrature > >> points. > >> >> >>>> > I > >> >> >>>> > have f > >> >> >>>> > at various nodal values. The question is, how do I get this > >> linear > >> >> >>>> > interpolation... > >> >> >>>> > > >> >> >>>> > Do you mean that, for each element, I form the mass matrix by > the > >> >> >>>> > xyz > >> >> >>>> > values > >> >> >>>> > of the nodes (and a constant 1) and solve for the coefficient > by > >> >> >>>> > saying > >> >> >>>> > \sum_j A_ij y_j= f_i, where: > >> >> >>>> > > >> >> >>>> > A = [1 x1 y1 z1; > >> >> >>>> > 1 x2 y2 z2; > >> >> >>>> > 1 x3 y3 z3; > >> >> >>>> > 1 x4 y4 z4] and y_j would be my unknown (where j = 1 > >> >> >>>> > corresponds > >> >> >>>> > to > >> >> >>>> > the constant value, and 2, 3, 4 corresponds to the gradient in > >> the > >> >> >>>> > x, > >> >> >>>> > y, z > >> >> >>>> > directions respectively)? > >> >> >>>> > > >> >> >>>> > Thanks, > >> >> >>>> > Karen > >> >> >>>> > > >> >> >>>> > > >> >> >>>> > On Thu, Mar 25, 2010 at 11:44 PM, Rahul Sampath > >> >> >>>> > <[email protected]> > >> >> >>>> > wrote: > >> >> >>>> >> > >> >> >>>> >> If you want to form a RHS by integrating f_i Phi_i Phi_j, You > >> >> >>>> >> could > >> >> >>>> >> form a Mass matrix and then multiply with your vector of > nodal > >> >> >>>> >> values. > >> >> >>>> >> > >> >> >>>> >> Rahul > >> >> >>>> >> > >> >> >>>> >> On Thu, Mar 25, 2010 at 11:40 PM, Karen Lee < > [email protected] > >> > > >> >> >>>> >> wrote: > >> >> >>>> >> > I'm afraid you misunderstood. I don't have the function > that > >> >> >>>> >> > when > >> >> >>>> >> > given > >> >> >>>> >> > x, > >> >> >>>> >> > y, z values gives me the function value. What I do have is > >> just > >> >> >>>> >> > the > >> >> >>>> >> > values > >> >> >>>> >> > at the nodes of the mesh, which need to be linearly > >> interpolated > >> >> >>>> >> > such > >> >> >>>> >> > that I > >> >> >>>> >> > will have something like exact_function. which gives me the > >> >> >>>> >> > value > >> >> >>>> >> > when > >> >> >>>> >> > supplied with any x, y, z. > >> >> >>>> >> > > >> >> >>>> >> > > >> >> >>>> >> > > >> >> >>>> >> > On Thu, Mar 25, 2010 at 10:54 PM, Liang < > [email protected]> > >> >> >>>> >> > wrote: > >> >> >>>> >> > > >> >> >>>> >> >> Karen Lee wrote: > >> >> >>>> >> >> > >> >> >>>> >> >>> I guess I'm not clear how to do this: Load data as a > >> solution > >> >> >>>> >> >>> into > >> >> >>>> >> >>> that, > >> >> >>>> >> >>> and > >> >> >>>> >> >>> query > >> >> >>>> >> >>> it when you're integrating your real system. > >> >> >>>> >> >>> > >> >> >>>> >> >>> I have: > >> >> >>>> >> >>> Mesh mesh(3); > >> >> >>>> >> >>> MeshData mesh_data(mesh); > >> >> >>>> >> >>> mesh_data.activate(); > >> >> >>>> >> >>> mesh.read (mesh_file, &mesh_data); > >> >> >>>> >> >>> mesh_data.read(mesh_file); > >> >> >>>> >> >>> EquationSystems equation_systems (mesh); > >> >> >>>> >> >>> > >> >> >>>> >> >>> > >> >> >>>> >> >>> equation_systems.add_system<ExplicitSystem> ("RHS"); > >> >> >>>> >> >>> equation_systems.get_system("RHS").add_variable("R", > FIRST); > >> >> >>>> >> >>> > >> >> >>>> >> >>> After that, I'm not clear how exactly to load data as a > >> >> >>>> >> >>> solution > >> >> >>>> >> >>> in > >> >> >>>> >> >>> the > >> >> >>>> >> >>> code. My goal is to get a linearly interpolated function > of > >> my > >> >> >>>> >> >>> data on > >> >> >>>> >> >>> the > >> >> >>>> >> >>> nodes (in the form of exact_solution, such that I get the > >> >> >>>> >> >>> function > >> >> >>>> >> >>> value > >> >> >>>> >> >>> out > >> >> >>>> >> >>> when supplying x, y and z). > >> >> >>>> >> >>> > >> >> >>>> >> >>> Hope that clarifies things, and sorry for the multiple > >> >> >>>> >> >>> emails... > >> >> >>>> >> >>> > >> >> >>>> >> >>> Karen > >> >> >>>> >> >>> > >> >> >>>> >> >>> > >> >> >>>> >> >>> > >> >> >>>> >> >>> > >> >> >>>> >> >>> > >> > ------------------------------------------------------------------------------ > >> >> >>>> >> >>> Download Intel® Parallel Studio Eval > >> >> >>>> >> >>> Try the new software tools for yourself. Speed compiling, > >> find > >> >> >>>> >> >>> bugs > >> >> >>>> >> >>> proactively, and fine-tune applications for parallel > >> >> >>>> >> >>> performance. > >> >> >>>> >> >>> See why Intel Parallel Studio got high marks during beta. > >> >> >>>> >> >>> http://p.sf.net/sfu/intel-sw-dev > >> >> >>>> >> >>> _______________________________________________ > >> >> >>>> >> >>> Libmesh-users mailing list > >> >> >>>> >> >>> [email protected] > >> >> >>>> >> >>> > https://lists.sourceforge.net/lists/listinfo/libmesh-users > >> >> >>>> >> >>> > >> >> >>>> >> >>> > >> >> >>>> >> >>> > >> >> >>>> >> >> so you already have the function, which is obtained from > your > >> >> >>>> >> >> discreted > >> >> >>>> >> >> data? > >> >> >>>> >> >> then just put the function as the exact_function. > >> >> >>>> >> >> I think you are trying the 3D case, start from a 2d will > be > >> >> >>>> >> >> easier. > >> >> >>>> >> >> > >> >> >>>> >> >> Liang > >> >> >>>> >> >> > >> >> >>>> >> > > >> >> >>>> >> > > >> >> >>>> >> > > >> >> >>>> >> > > >> > ------------------------------------------------------------------------------ > >> >> >>>> >> > Download Intel® Parallel Studio Eval > >> >> >>>> >> > Try the new software tools for yourself. Speed compiling, > find > >> >> >>>> >> > bugs > >> >> >>>> >> > proactively, and fine-tune applications for parallel > >> >> >>>> >> > performance. > >> >> >>>> >> > See why Intel Parallel Studio got high marks during beta. > >> >> >>>> >> > http://p.sf.net/sfu/intel-sw-dev > >> >> >>>> >> > _______________________________________________ > >> >> >>>> >> > Libmesh-users mailing list > >> >> >>>> >> > [email protected] > >> >> >>>> >> > https://lists.sourceforge.net/lists/listinfo/libmesh-users > >> >> >>>> >> > > >> >> >>>> > > >> >> >>>> > > >> >> >>> > >> >> >> > >> >> >> > >> >> > > >> > > >> > > >> > > > ------------------------------------------------------------------------------ > > Download Intel® Parallel Studio Eval > > Try the new software tools for yourself. Speed compiling, find bugs > > proactively, and fine-tune applications for parallel performance. > > See why Intel Parallel Studio got high marks during beta. > > http://p.sf.net/sfu/intel-sw-dev > > _______________________________________________ > > Libmesh-users mailing list > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/libmesh-users > > > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
