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From: Roy Stogner <roystgnr@ic...>  20070220 14:26:57

On Tue, 20 Feb 2007, Roy Stogner wrote: > The gripping hand is it's not a .xda/.xdr problem at all. > Uncommenting equation_systems2.reinit() causes the state to remain > unchanged, whereas a call to equation_systems.reinit() causes the > same sort of slight state change before any files are even written. The change appears to be occuring in System::project_vector  but with no elements flagged for refinement or coarsening, that function should just be copying degrees of freedom, not doing anything to change them. I can't figure out yet exactly where anything's being changed  DofMap::enforce_constraints_exactly() gets called at the end of the projection now, but that shouldn't have any effect on a uniform mesh.  Roy 
From: <tim@ce...>  20070220 14:02:59

Dear John, On Tue, 20 Feb 2007, John Peterson wrote: > If we write out only 12 digits of the solution (which I think is true > for xda) could this explain the discrepancy? Yes, but I'm using xdr, not xda (see source code). Best Regards, Tim 
From: Roy Stogner <roystgnr@ic...>  20070220 14:01:39

On Tue, 20 Feb 2007, Tim Kröger wrote: > Hmm. Just to confuse you, I wrote the attached test program. It creates a > grid, solves a simple PDE on it, solves it twice again, then writes > everything to xdr files, reads them in and solves again. Obviously (from the > attached output, produced with ksp_monitor), reading the files in does not > exactly restore the original state. Now that's a tough one. On the one hand, the original state should be restored exactly in your example... I suppose there could be come data that's sitting in cache at 80 bits but gets reread at 64 bits, but I doubt it. On the other hand, I'm finding it hard to get too excited about a state change that's smaller than most linear solver tolerances. The gripping hand is it's not a .xda/.xdr problem at all. Uncommenting equation_systems2.reinit() causes the state to remain unchanged, whereas a call to equation_systems.reinit() causes the same sort of slight state change before any files are even written.  Roy 
From: Kirk, Benjamin \(JSCEG\) <benjamin.kirk1@na...>  20070220 13:58:04

I am too lazy to do this myself  what if you write/read an XDR file instead? It should store a double as a true double and hopefully bypass this issue. Original Message From: libmeshdevelbounces@... [mailto:libmeshdevelbounces@...] On Behalf Of John Peterson Sent: Tuesday, February 20, 2007 7:51 AM To: Tim Kroger Cc: libmeshdevel@...; Roy Stogner Subject: Re: [Libmeshdevel] Two items on my wishlist Hi Tim, If we write out only 12 digits of the solution (which I think is true for xda) could this explain the discrepancy? The residual norm computed from the readin solution looks the same to within about 12 digits. John Tim Kr=1B,bvger writes: > Dear Roy, > > On Mon, 19 Feb 2007, Roy Stogner wrote: > > > My current work with another libMesh user has made me realize that we > > need: > > > > 1. Support for taking .xda/.xdr files which have been written with > > one setting of ENABLE_INFINITE_ELEMENTS and reading them with the > > opposite setting. Currently this seems to break. > > > > However, my recent experiences fixing the "scrambled DoF indices with > > nonLagrange AMR restarts" bug and the "not writing .xda files with > > enough precision" bug have made me realize the importance of: > > > > 2. Me never having to read through the xdr* source code again. > > > > I'd love to dive right in and implement my wishlist item 1, but > > unfortunately that conflicts with wishlist item 2. My hands are tied. > > Hmm. Just to confuse you, I wrote the attached test program. It > creates a grid, solves a simple PDE on it, solves it twice again, then > writes everything to xdr files, reads them in and solves again.=20 > Obviously (from the attached output, produced with ksp_monitor), > reading the files in does not exactly restore the original state.=20 > However, I guess that changing this behaviour, even if it could become > an item 3 of your wishlist, would still conflict with item 2. > > Best Regards, > > Tim./test ksp_monitor > 0 KSP Residual norm 1.733328971787e+01=20 > 1 KSP Residual norm 1.185778941653e+01=20 > 2 KSP Residual norm 1.139134743178e+01=20 > 3 KSP Residual norm 9.913079902632e+00=20 > 4 KSP Residual norm 7.191145025915e+00=20 > 5 KSP Residual norm 5.172029883955e+00=20 > 6 KSP Residual norm 2.147425476520e+00=20 > 7 KSP Residual norm 8.687575748560e01=20 > 8 KSP Residual norm 4.164173667107e01=20 > 9 KSP Residual norm 2.443014766559e01=20 > 10 KSP Residual norm 1.888013690466e01 > 11 KSP Residual norm 1.545632671036e01 > 12 KSP Residual norm 9.547251214559e02 > 13 KSP Residual norm 3.558309380772e02 > 14 KSP Residual norm 2.119986479829e02 > 15 KSP Residual norm 1.472055648826e02 > 16 KSP Residual norm 7.844202526193e03 > 17 KSP Residual norm 4.324782781627e03 > 18 KSP Residual norm 2.537192913599e03 > 19 KSP Residual norm 1.372628313957e03 > 20 KSP Residual norm 7.072639404731e04 > 21 KSP Residual norm 2.981094657572e04 > 22 KSP Residual norm 1.807779624842e04 > 23 KSP Residual norm 1.340784951662e04 > 24 KSP Residual norm 1.088577505522e04 > 25 KSP Residual norm 7.207500151591e05 > 26 KSP Residual norm 3.887867139016e05 > 27 KSP Residual norm 2.190821106975e05 > 28 KSP Residual norm 1.040052415721e05 > 29 KSP Residual norm 3.856840518033e06 > 30 KSP Residual norm 1.989373498593e06 > 31 KSP Residual norm 1.442089144671e06 > 32 KSP Residual norm 8.398949810780e07 > 33 KSP Residual norm 4.613052610992e07 > 34 KSP Residual norm 2.446011262135e07 > 35 KSP Residual norm 1.402013920665e07 > 36 KSP Residual norm 9.288528753379e08 > 37 KSP Residual norm 5.569095323071e08 > 38 KSP Residual norm 3.080619009371e08 > 39 KSP Residual norm 2.149324393284e08 > 40 KSP Residual norm 1.668599996685e08 > 41 KSP Residual norm 1.297303487430e08 > 42 KSP Residual norm 9.127468731142e09 > 43 KSP Residual norm 6.183347158799e09 > 44 KSP Residual norm 4.688102496189e09 > 45 KSP Residual norm 4.418529129665e09 > 46 KSP Residual norm 4.266320304576e09 > 47 KSP Residual norm 4.097419313482e09 > 48 KSP Residual norm 3.918923888652e09 > 49 KSP Residual norm 3.395719439036e09 > 50 KSP Residual norm 2.538813185638e09 > 51 KSP Residual norm 1.415015667448e09 > 52 KSP Residual norm 6.308264312374e10 > 53 KSP Residual norm 3.843345277332e10 > 54 KSP Residual norm 2.514734506456e10 > 55 KSP Residual norm 1.710479832166e10 > 56 KSP Residual norm 1.151796274421e10 > 57 KSP Residual norm 7.714264551552e11 > 58 KSP Residual norm 4.742723602833e11 > 59 KSP Residual norm 3.379626986680e11 > 60 KSP Residual norm 2.548253614890e11 > 61 KSP Residual norm 2.095190091567e11 > 62 KSP Residual norm 1.512617662327e11 >  > 0 KSP Residual norm 1.510050418779e11=20 >  > 0 KSP Residual norm 1.510050418779e11=20 >  > 0 KSP Residual norm 1.611365184359e11=20 > #include <iostream> > #include <algorithm> > #include <math.h> > > #include "libmesh.h" > #include "mesh.h" > #include "mesh_generation.h" > #include "gmv_io.h" > #include "equation_systems.h" > #include "fe.h" > #include "quadrature_gauss.h" > #include "dof_map.h" > #include "sparse_matrix.h" > #include "numeric_vector.h" > #include "dense_matrix.h" > #include "dense_vector.h" > #include "linear_implicit_system.h" > #include "transient_system.h" > #include "perf_log.h" > #include "boundary_info.h" > #include "utility.h" > #include "elem.h" > #include "mesh_refinement.h" > > void assemble(EquationSystems& es, const std::string& system_name) > { > const Mesh& mesh =3D es.get_mesh(); > const unsigned int dim =3D mesh.mesh_dimension(); > LinearImplicitSystem& system =3D = es.get_system<LinearImplicitSystem> ("e"); > const DofMap& dof_map =3D system.get_dof_map(); > FEType fe_type =3D dof_map.variable_type(0); > AutoPtr<FEBase> fe (FEBase::build(dim, fe_type)); > QGauss qrule (dim, FIFTH); > fe>attach_quadrature_rule (&qrule); > const std::vector<Real>& JxW =3D fe>get_JxW(); > const std::vector<std::vector<Real> >& phi =3D fe>get_phi(); > const std::vector<std::vector<RealGradient> >& dphi =3D fe>get_dphi(); > DenseMatrix<Number> Ke; > DenseVector<Number> Fe; > std::vector<unsigned int> dof_indices; >=20 > MeshBase::const_element_iterator el =3D mesh.elements_begin(); > const MeshBase::const_element_iterator end_el =3D mesh.elements_end(); > for ( ; el !=3D end_el ; ++el) > { > const Elem* elem =3D *el; > dof_map.dof_indices (elem, dof_indices); > fe>reinit (elem); > Ke.resize (dof_indices.size(), > dof_indices.size()); > Fe.resize (dof_indices.size()); >=20 > for (unsigned int qp=3D0; qp<qrule.n_points(); qp++) > for (unsigned int i=3D0; i<phi.size(); i++) > { > for (unsigned int j=3D0; j<phi.size(); j++) > { > Ke(i,j) +=3D JxW[qp]*(dphi[i][qp]*dphi[j][qp]+phi[i][qp]*phi[j][qp]); > } > for (unsigned int i=3D0; i<phi.size(); i++) > { > Fe(i) +=3D JxW[qp]*1.0*phi[i][qp]; > } > }=20 > =20 > system.matrix>add_matrix (Ke, dof_indices); > system.rhs>add_vector (Fe, dof_indices); > } > } > > int main (int argc, char** argv) > { > libMesh::init (argc, argv); > { =20 > const unsigned int dim =3D 3; =20 > Mesh mesh (dim); > =20 > MeshTools::Generation::build_cube (mesh, > 4, 4, 4, > 0., 1., > 0., 1., > 0., 1., > HEX27); > MeshRefinement mesh_refinement(mesh); > mesh_refinement.uniformly_refine(1); > EquationSystems equation_systems (mesh); > equation_systems.add_system<LinearImplicitSystem> ("e"); > equation_systems.get_system("e").add_variable("u", SECOND); > equation_systems.get_system("e").attach_assemble_function (assemble); > equation_systems.init(); > equation_systems.get_system("e").solve(); >=20 > std::cout << "" << std::endl; >=20 > equation_systems.get_system("e").solve(); >=20 > std::cout << "" << std::endl; >=20 > equation_systems.get_system("e").solve(); >=20 > std::cout << "" << std::endl; >=20 > mesh.write("mesh.xdr"); > equation_systems.write("systems.xdr", > libMeshEnums::WRITE, > EquationSystems::WRITE_DATAEquationSystems::WRITE_ADDITIONAL_DATA); >=20 > Mesh mesh2(dim); > mesh2.read("mesh.xdr"); > EquationSystems equation_systems2(mesh2); > equation_systems2.read("systems.xdr", > libMeshEnums::READ, > EquationSystems::READ_DATAEquationSystems::READ_ADDITIONAL_DATAEquatio nSystems::READ_HEADER); > equation_systems2.reinit(); > equation_systems2.get_system("e").attach_assemble_function (assemble); > equation_systems2.get_system("e").solve(); > } > =20 > return libMesh::close (); > } > >   > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveysand earn cash > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDE V_______________________________________________ > Libmeshdevel mailing list > Libmeshdevel@... > https://lists.sourceforge.net/lists/listinfo/libmeshdevel 
From: John Peterson <peterson@cf...>  20070220 13:51:50

Hi Tim, If we write out only 12 digits of the solution (which I think is true for xda) could this explain the discrepancy? The residual norm computed from the readin solution looks the same to within about 12 digits. John Tim Kr,bv(Bger writes: > Dear Roy, > > On Mon, 19 Feb 2007, Roy Stogner wrote: > > > My current work with another libMesh user has made me realize that we > > need: > > > > 1. Support for taking .xda/.xdr files which have been written with > > one setting of ENABLE_INFINITE_ELEMENTS and reading them with the > > opposite setting. Currently this seems to break. > > > > However, my recent experiences fixing the "scrambled DoF indices with > > nonLagrange AMR restarts" bug and the "not writing .xda files with > > enough precision" bug have made me realize the importance of: > > > > 2. Me never having to read through the xdr* source code again. > > > > I'd love to dive right in and implement my wishlist item 1, but > > unfortunately that conflicts with wishlist item 2. My hands are tied. > > Hmm. Just to confuse you, I wrote the attached test program. It > creates a grid, solves a simple PDE on it, solves it twice again, then > writes everything to xdr files, reads them in and solves again. > Obviously (from the attached output, produced with ksp_monitor), > reading the files in does not exactly restore the original state. > However, I guess that changing this behaviour, even if it could become > an item 3 of your wishlist, would still conflict with item 2. > > Best Regards, > > Tim./test ksp_monitor > 0 KSP Residual norm 1.733328971787e+01 > 1 KSP Residual norm 1.185778941653e+01 > 2 KSP Residual norm 1.139134743178e+01 > 3 KSP Residual norm 9.913079902632e+00 > 4 KSP Residual norm 7.191145025915e+00 > 5 KSP Residual norm 5.172029883955e+00 > 6 KSP Residual norm 2.147425476520e+00 > 7 KSP Residual norm 8.687575748560e01 > 8 KSP Residual norm 4.164173667107e01 > 9 KSP Residual norm 2.443014766559e01 > 10 KSP Residual norm 1.888013690466e01 > 11 KSP Residual norm 1.545632671036e01 > 12 KSP Residual norm 9.547251214559e02 > 13 KSP Residual norm 3.558309380772e02 > 14 KSP Residual norm 2.119986479829e02 > 15 KSP Residual norm 1.472055648826e02 > 16 KSP Residual norm 7.844202526193e03 > 17 KSP Residual norm 4.324782781627e03 > 18 KSP Residual norm 2.537192913599e03 > 19 KSP Residual norm 1.372628313957e03 > 20 KSP Residual norm 7.072639404731e04 > 21 KSP Residual norm 2.981094657572e04 > 22 KSP Residual norm 1.807779624842e04 > 23 KSP Residual norm 1.340784951662e04 > 24 KSP Residual norm 1.088577505522e04 > 25 KSP Residual norm 7.207500151591e05 > 26 KSP Residual norm 3.887867139016e05 > 27 KSP Residual norm 2.190821106975e05 > 28 KSP Residual norm 1.040052415721e05 > 29 KSP Residual norm 3.856840518033e06 > 30 KSP Residual norm 1.989373498593e06 > 31 KSP Residual norm 1.442089144671e06 > 32 KSP Residual norm 8.398949810780e07 > 33 KSP Residual norm 4.613052610992e07 > 34 KSP Residual norm 2.446011262135e07 > 35 KSP Residual norm 1.402013920665e07 > 36 KSP Residual norm 9.288528753379e08 > 37 KSP Residual norm 5.569095323071e08 > 38 KSP Residual norm 3.080619009371e08 > 39 KSP Residual norm 2.149324393284e08 > 40 KSP Residual norm 1.668599996685e08 > 41 KSP Residual norm 1.297303487430e08 > 42 KSP Residual norm 9.127468731142e09 > 43 KSP Residual norm 6.183347158799e09 > 44 KSP Residual norm 4.688102496189e09 > 45 KSP Residual norm 4.418529129665e09 > 46 KSP Residual norm 4.266320304576e09 > 47 KSP Residual norm 4.097419313482e09 > 48 KSP Residual norm 3.918923888652e09 > 49 KSP Residual norm 3.395719439036e09 > 50 KSP Residual norm 2.538813185638e09 > 51 KSP Residual norm 1.415015667448e09 > 52 KSP Residual norm 6.308264312374e10 > 53 KSP Residual norm 3.843345277332e10 > 54 KSP Residual norm 2.514734506456e10 > 55 KSP Residual norm 1.710479832166e10 > 56 KSP Residual norm 1.151796274421e10 > 57 KSP Residual norm 7.714264551552e11 > 58 KSP Residual norm 4.742723602833e11 > 59 KSP Residual norm 3.379626986680e11 > 60 KSP Residual norm 2.548253614890e11 > 61 KSP Residual norm 2.095190091567e11 > 62 KSP Residual norm 1.512617662327e11 >  > 0 KSP Residual norm 1.510050418779e11 >  > 0 KSP Residual norm 1.510050418779e11 >  > 0 KSP Residual norm 1.611365184359e11 > #include <iostream> > #include <algorithm> > #include <math.h> > > #include "libmesh.h" > #include "mesh.h" > #include "mesh_generation.h" > #include "gmv_io.h" > #include "equation_systems.h" > #include "fe.h" > #include "quadrature_gauss.h" > #include "dof_map.h" > #include "sparse_matrix.h" > #include "numeric_vector.h" > #include "dense_matrix.h" > #include "dense_vector.h" > #include "linear_implicit_system.h" > #include "transient_system.h" > #include "perf_log.h" > #include "boundary_info.h" > #include "utility.h" > #include "elem.h" > #include "mesh_refinement.h" > > void assemble(EquationSystems& es, const std::string& system_name) > { > const Mesh& mesh = es.get_mesh(); > const unsigned int dim = mesh.mesh_dimension(); > LinearImplicitSystem& system = es.get_system<LinearImplicitSystem> ("e"); > const DofMap& dof_map = system.get_dof_map(); > FEType fe_type = dof_map.variable_type(0); > AutoPtr<FEBase> fe (FEBase::build(dim, fe_type)); > QGauss qrule (dim, FIFTH); > fe>attach_quadrature_rule (&qrule); > const std::vector<Real>& JxW = fe>get_JxW(); > const std::vector<std::vector<Real> >& phi = fe>get_phi(); > const std::vector<std::vector<RealGradient> >& dphi = fe>get_dphi(); > DenseMatrix<Number> Ke; > DenseVector<Number> Fe; > std::vector<unsigned int> dof_indices; > > MeshBase::const_element_iterator el = mesh.elements_begin(); > const MeshBase::const_element_iterator end_el = mesh.elements_end(); > 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]*(dphi[i][qp]*dphi[j][qp]+phi[i][qp]*phi[j][qp]); > } > for (unsigned int i=0; i<phi.size(); i++) > { > Fe(i) += JxW[qp]*1.0*phi[i][qp]; > } > } > > system.matrix>add_matrix (Ke, dof_indices); > system.rhs>add_vector (Fe, dof_indices); > } > } > > int main (int argc, char** argv) > { > libMesh::init (argc, argv); > { > const unsigned int dim = 3; > Mesh mesh (dim); > > MeshTools::Generation::build_cube (mesh, > 4, 4, 4, > 0., 1., > 0., 1., > 0., 1., > HEX27); > MeshRefinement mesh_refinement(mesh); > mesh_refinement.uniformly_refine(1); > EquationSystems equation_systems (mesh); > equation_systems.add_system<LinearImplicitSystem> ("e"); > equation_systems.get_system("e").add_variable("u", SECOND); > equation_systems.get_system("e").attach_assemble_function (assemble); > equation_systems.init(); > equation_systems.get_system("e").solve(); > > std::cout << "" << std::endl; > > equation_systems.get_system("e").solve(); > > std::cout << "" << std::endl; > > equation_systems.get_system("e").solve(); > > std::cout << "" << std::endl; > > mesh.write("mesh.xdr"); > equation_systems.write("systems.xdr", > libMeshEnums::WRITE, > EquationSystems::WRITE_DATAEquationSystems::WRITE_ADDITIONAL_DATA); > > Mesh mesh2(dim); > mesh2.read("mesh.xdr"); > EquationSystems equation_systems2(mesh2); > equation_systems2.read("systems.xdr", > libMeshEnums::READ, > EquationSystems::READ_DATAEquationSystems::READ_ADDITIONAL_DATAEquationSystems::READ_HEADER); > equation_systems2.reinit(); > equation_systems2.get_system("e").attach_assemble_function (assemble); > equation_systems2.get_system("e").solve(); > } > > return libMesh::close (); > } > >  > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveysand earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________ > Libmeshdevel mailing list > Libmeshdevel@... > https://lists.sourceforge.net/lists/listinfo/libmeshdevel 
From: <tim@ce...>  20070220 08:13:49

Dear Roy, On Mon, 19 Feb 2007, Roy Stogner wrote: > My current work with another libMesh user has made me realize that we > need: > > 1. Support for taking .xda/.xdr files which have been written with > one setting of ENABLE_INFINITE_ELEMENTS and reading them with the > opposite setting. Currently this seems to break. > > However, my recent experiences fixing the "scrambled DoF indices with > nonLagrange AMR restarts" bug and the "not writing .xda files with > enough precision" bug have made me realize the importance of: > > 2. Me never having to read through the xdr* source code again. > > I'd love to dive right in and implement my wishlist item 1, but > unfortunately that conflicts with wishlist item 2. My hands are tied. Hmm. Just to confuse you, I wrote the attached test program. It creates a grid, solves a simple PDE on it, solves it twice again, then writes everything to xdr files, reads them in and solves again. Obviously (from the attached output, produced with ksp_monitor), reading the files in does not exactly restore the original state. However, I guess that changing this behaviour, even if it could become an item 3 of your wishlist, would still conflict with item 2. Best Regards, Tim 
From: sun <pythonsun@gm...>  20070220 08:13:27

Hi, all, firstly I want to see what the libmesh can work for and try some 'examples' in the download files. Can I do this in Visual Studio? sun 