Re: [deal.II] Condition number and Eigen Values of a Matrix
Thank you so much Jean-Paul. I was able to use SolverCG::connect_condition_number_slot() successfully in my code. Best, Reza On Thursday, December 3, 2020 at 10:57:23 AM UTC-8 Jean-Paul Pelteret wrote: > If it's of any help, our CG and GMRES solvers (and maybe some of the > others?) can return the estimated condition number during / after a call > to solve(). > > https://dealii.org/developer/doxygen/deal.II/classSolverCG.html#a52f1fd3d41765ec06d2d0add1a74a37c > > < > https://dealii.org/developer/doxygen/deal.II/classSolverCG.html#a52f1fd3d41765ec06d2d0add1a74a37c > > > > https://dealii.org/developer/doxygen/deal.II/classSolverGMRES.html#a3025d81c3d7db3e1a1b0114bef794202 > > < > https://dealii.org/developer/doxygen/deal.II/classSolverGMRES.html#a3025d81c3d7db3e1a1b0114bef794202 > > > > Jean-Paul > > On 03.12.20 05:46, Wolfgang Bangerth wrote: > > On 12/2/20 9:30 PM, Reza Rastak wrote: > >> > >> I am trying to calculate the condition number of a Trilinos Block > >> Sparse matrix. Is there an example of that in the documentation that > >> you can point me to? > > > > No, and that's actually a quite difficult task because you have to > > estimate eigenvalues. The easiest way is probably to use the power > > iteration and inverse power iteration to estimate largest and smallest > > eigenvalues -- see the EigenPower and EigenInverse classes. > > > > Best > > W. > > > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/9f45c49f-19e4-4a06-85d6-a187e1a9033en%40googlegroups.com.
Re: [deal.II] Strange floating point error
On 12/4/20 11:44 AM, Corbin Foucart wrote: Does anyone have any idea 1. Why this exception occurs only at certain refinement levels? Floating point exceptions happen when you try to do arithmetic on numbers called "signaling NaNs" that are used as "invalid values" and because the processor aborts the program when they are used, they're a good way to make sure that uninitialized values are never used. Some compilers/operating systems support them, and others don't, so they are not available on every system. That might explain the difference between the two systems you are using. Where the actual exception actually happens in the code is not overly relevant -- the question is why you give that function uninitialized memory. So in your case, run the program in a debugger like you're already doing. Look at the backtrace and go to the last function you were in inside your own program -- then inspect the values of all of the arguments you pass to the function being called in that place and try to understand why one of these will have these NaNs in them. Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/68b2b035-6c8c-8b2c-a43f-93b0537a4c90%40colostate.edu.
Re: [deal.II] Re: Error in Compilation
On 12/4/20 3:16 AM, pushkar...@gmail.com wrote: Well that was not a problem it was my silly mistake that I for some reason commented out the main() function in hurry and raninto such an error but now I encountered other errors while compilation as : Pushkar, what is your specific question? Start with reading through the error messages (and also the warnings!) top to bottom and address them one-by-one. The compiler actually provides you with fairly good descriptions of what is wrong. Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/55d8263f-43d3-256b-f680-bd5db842fef2%40colostate.edu.
Re: [deal.II] Clearing a particle properties without getting properties for each particle
Hello Shahab, I would wait before trying to do some changes. Rene has started looking more deeply into the particle structure (see : https://github.com/dealii/dealii/pull/11314) and this will, most likely, fix your problem. On Friday, December 4, 2020 at 8:18:11 a.m. UTC-5 shahab.g...@gmail.com wrote: > Not here, but it other functions it would be very useful to be able to map > back to the owning particle. > In fact, I have to treat local and ghost particles differently. In terms > of updating properties, I only need to update the properties of local > particles. When the maximum displacement of a particles reaches half of the > cell length in the triangulation, I call > sort_particles_into_subdomains_and_cells() to update the list of local and > ghost particles. I can explain the algorithm in more details if you want. > Thanks again. > Shahab > > On Thursday, December 3, 2020 at 10:54:42 PM UTC-5 Wolfgang Bangerth wrote: > >> On 12/3/20 4:13 PM, shahab.g...@gmail.com wrote: >> > I want to iterate through all the particles in each iteration of my >> solver and >> > update some of the properties. The problem is iterating through >> particles >> > using particle_handler() is rather computationally expensive. I am >> looking for >> > a way to update the properties without iterating through the >> particle_handler. >> >> I see. >> >> So you'd need to iterate through the the blocks of properties stored in >> the >> PropertyPool? We could write such an interface, but let me ask a couple >> of >> questions first: >> * Do you need to map back from block of memory to the owning particle? >> * Will you somehow need to treat ghost particles differently than the >> locally >> owned ones? How will you make sure that locally owned particles on one >> processor stay in sync with the corresponding ghost particles on the >> other >> processor(s)? >> >> Best >> W. >> >> -- >> >> Wolfgang Bangerth email: bang...@colostate.edu >> www: http://www.math.colostate.edu/~bangerth/ >> >> -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/5e92a68f-bd8c-4877-bfad-047b8a4fc86cn%40googlegroups.com.
[deal.II] Re: Error in Compilation
Pushkar, Have you done any modifications to step-26? Best, Bruno On Friday, December 4, 2020 at 5:16:15 AM UTC-5 pushkar...@gmail.com wrote: > Well that was not a problem it was my silly mistake that I for some reason > commented out the main() function in hurry and raninto such an error but > now I encountered other errors while compilation as : > > [ 50%] Building CXX object CMakeFiles/step-26.dir/step-26.cc.o > In file included from > /home/pushkar/examples/step-26/point_comparison_operator.h:8, > from /home/pushkar/examples/step-26/step-26.cc:52: > /usr/local/include/deal.II/base/tensor_base.h:3:2: warning: #warning This > file is deprecated. Use instead. [-Wcpp] > 3 | #warning This file is deprecated. Use > instead. > | ^~~ > /home/pushkar/examples/step-26/step-26.cc: In instantiation of > ‘Step26::HeatEquation::HeatEquation() [with int dim = 2]’: > /home/pushkar/examples/step-26/step-26.cc:1023:23: required from here > /home/pushkar/examples/step-26/step-26.cc:108:23: warning: > ‘Step26::HeatEquation<2>::quadrature_collection’ will be initialized after > [-Wreorder] > 108 | Quadrature quadrature_collection; > | ^ > /home/pushkar/examples/step-26/step-26.cc:107:26: warning: > ‘dealii::hp::DoFHandler<2, 2> Step26::HeatEquation<2>::dof_handler’ > [-Wreorder] > 107 | hp::DoFHandler dof_handler; > | ^~~ > /home/pushkar/examples/step-26/step-26.cc:201:3: warning: when > initialized here [-Wreorder] > 201 | HeatEquation::HeatEquation () > | ^ > /home/pushkar/examples/step-26/step-26.cc:132:20: warning: > ‘Step26::HeatEquation<2>::heat_conductivity’ will be initialized after > [-Wreorder] > 132 | const double heat_conductivity; > |^ > /home/pushkar/examples/step-26/step-26.cc:109:26: warning: > ‘dealii::Quadrature<1> Step26::HeatEquation<2>::face_quadrature_collection’ > [-Wreorder] > 109 | Quadratureface_quadrature_collection; > | ^~ > /home/pushkar/examples/step-26/step-26.cc:201:3: warning: when > initialized here [-Wreorder] > 201 | HeatEquation::HeatEquation () > | ^ > /home/pushkar/examples/step-26/step-26.cc:201:3: error: uninitialized > const member in ‘const double’ [-fpermissive] > /home/pushkar/examples/step-26/step-26.cc:135:21: note: ‘const double > Step26::HeatEquation<2>::part_height’ should be initialized > 135 | const doublepart_height; > | ^~~ > /home/pushkar/examples/step-26/step-26.cc: In instantiation of ‘void > Step26::HeatEquation::run() [with int dim = 2]’: > /home/pushkar/examples/step-26/step-26.cc:1024:32: required from here > /home/pushkar/examples/step-26/step-26.cc:796:24: error: no matching > function for call to ‘project(dealii::hp::DoFHandler<2, 2>&, > dealii::ConstraintMatrix&, dealii::Quadrature<2>&, > Step26::InitialCondition<2>&, dealii::Vector&, bool, > dealii::Quadrature<1>&)’ > 796 |VectorTools::project(dof_handler, > |^ > 797 |constraints, > | > 798 | quadrature_collection, > | ~~ > 799 | initial_condition, > | ~~ > 800 | old_solution, > | ~ > 801 | false, > | ~~ > 802 | face_quadrature_collection); > | ~~~ > In file included from /home/pushkar/examples/step-26/step-26.cc:44: > /usr/local/include/deal.II/numerics/vector_tools.h:813:8: note: candidate: > ‘template void > dealii::VectorTools::project(const dealii::Mapping&, const > dealii::DoFHandler&, const dealii::ConstraintMatrix&, const > dealii::Quadrature&, const dealii::Function VectorType::value_type>&, VectorType&, bool, const dealii::Quadrature<(dim > - 1)>&, bool)’ > 813 | void project (const Mapping, > |^~~ > /usr/local/include/deal.II/numerics/vector_tools.h:813:8: note: template > argument deduction/substitution failed: > /home/pushkar/examples/step-26/step-26.cc:796:24: note: > ‘dealii::hp::DoFHandler<2, 2>’ is not derived from ‘const > dealii::Mapping’ > 796 |VectorTools::project(dof_handler, > |^ > 797 |constraints, > | > 798 | quadrature_collection, > | ~~ > 799 | initial_condition, > | ~~ > 800 | old_solution, > | ~ > 801 | false, > | ~~ > 802 | face_quadrature_collection); > |
Re: [deal.II] Clearing a particle properties without getting properties for each particle
Not here, but it other functions it would be very useful to be able to map back to the owning particle. In fact, I have to treat local and ghost particles differently. In terms of updating properties, I only need to update the properties of local particles. When the maximum displacement of a particles reaches half of the cell length in the triangulation, I call sort_particles_into_subdomains_and_cells() to update the list of local and ghost particles. I can explain the algorithm in more details if you want. Thanks again. Shahab On Thursday, December 3, 2020 at 10:54:42 PM UTC-5 Wolfgang Bangerth wrote: > On 12/3/20 4:13 PM, shahab.g...@gmail.com wrote: > > I want to iterate through all the particles in each iteration of my > solver and > > update some of the properties. The problem is iterating through > particles > > using particle_handler() is rather computationally expensive. I am > looking for > > a way to update the properties without iterating through the > particle_handler. > > I see. > > So you'd need to iterate through the the blocks of properties stored in > the > PropertyPool? We could write such an interface, but let me ask a couple of > questions first: > * Do you need to map back from block of memory to the owning particle? > * Will you somehow need to treat ghost particles differently than the > locally > owned ones? How will you make sure that locally owned particles on one > processor stay in sync with the corresponding ghost particles on the other > processor(s)? > > Best > W. > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > www: http://www.math.colostate.edu/~bangerth/ > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/2796d59e-3e02-4888-91d5-2b9dc148ec5en%40googlegroups.com.
[deal.II] Re: Error in Compilation
Well that was not a problem it was my silly mistake that I for some reason commented out the main() function in hurry and raninto such an error but now I encountered other errors while compilation as : [ 50%] Building CXX object CMakeFiles/step-26.dir/step-26.cc.o In file included from /home/pushkar/examples/step-26/point_comparison_operator.h:8, from /home/pushkar/examples/step-26/step-26.cc:52: /usr/local/include/deal.II/base/tensor_base.h:3:2: warning: #warning This file is deprecated. Use instead. [-Wcpp] 3 | #warning This file is deprecated. Use instead. | ^~~ /home/pushkar/examples/step-26/step-26.cc: In instantiation of ‘Step26::HeatEquation::HeatEquation() [with int dim = 2]’: /home/pushkar/examples/step-26/step-26.cc:1023:23: required from here /home/pushkar/examples/step-26/step-26.cc:108:23: warning: ‘Step26::HeatEquation<2>::quadrature_collection’ will be initialized after [-Wreorder] 108 | Quadrature quadrature_collection; | ^ /home/pushkar/examples/step-26/step-26.cc:107:26: warning: ‘dealii::hp::DoFHandler<2, 2> Step26::HeatEquation<2>::dof_handler’ [-Wreorder] 107 | hp::DoFHandler dof_handler; | ^~~ /home/pushkar/examples/step-26/step-26.cc:201:3: warning: when initialized here [-Wreorder] 201 | HeatEquation::HeatEquation () | ^ /home/pushkar/examples/step-26/step-26.cc:132:20: warning: ‘Step26::HeatEquation<2>::heat_conductivity’ will be initialized after [-Wreorder] 132 | const double heat_conductivity; |^ /home/pushkar/examples/step-26/step-26.cc:109:26: warning: ‘dealii::Quadrature<1> Step26::HeatEquation<2>::face_quadrature_collection’ [-Wreorder] 109 | Quadratureface_quadrature_collection; | ^~ /home/pushkar/examples/step-26/step-26.cc:201:3: warning: when initialized here [-Wreorder] 201 | HeatEquation::HeatEquation () | ^ /home/pushkar/examples/step-26/step-26.cc:201:3: error: uninitialized const member in ‘const double’ [-fpermissive] /home/pushkar/examples/step-26/step-26.cc:135:21: note: ‘const double Step26::HeatEquation<2>::part_height’ should be initialized 135 | const doublepart_height; | ^~~ /home/pushkar/examples/step-26/step-26.cc: In instantiation of ‘void Step26::HeatEquation::run() [with int dim = 2]’: /home/pushkar/examples/step-26/step-26.cc:1024:32: required from here /home/pushkar/examples/step-26/step-26.cc:796:24: error: no matching function for call to ‘project(dealii::hp::DoFHandler<2, 2>&, dealii::ConstraintMatrix&, dealii::Quadrature<2>&, Step26::InitialCondition<2>&, dealii::Vector&, bool, dealii::Quadrature<1>&)’ 796 |VectorTools::project(dof_handler, |^ 797 |constraints, | 798 | quadrature_collection, | ~~ 799 | initial_condition, | ~~ 800 | old_solution, | ~ 801 | false, | ~~ 802 | face_quadrature_collection); | ~~~ In file included from /home/pushkar/examples/step-26/step-26.cc:44: /usr/local/include/deal.II/numerics/vector_tools.h:813:8: note: candidate: ‘template void dealii::VectorTools::project(const dealii::Mapping&, const dealii::DoFHandler&, const dealii::ConstraintMatrix&, const dealii::Quadrature&, const dealii::Function&, VectorType&, bool, const dealii::Quadrature<(dim - 1)>&, bool)’ 813 | void project (const Mapping, |^~~ /usr/local/include/deal.II/numerics/vector_tools.h:813:8: note: template argument deduction/substitution failed: /home/pushkar/examples/step-26/step-26.cc:796:24: note: ‘dealii::hp::DoFHandler<2, 2>’ is not derived from ‘const dealii::Mapping’ 796 |VectorTools::project(dof_handler, |^ 797 |constraints, | 798 | quadrature_collection, | ~~ 799 | initial_condition, | ~~ 800 | old_solution, | ~ 801 | false, | ~~ 802 | face_quadrature_collection); | ~~~ In file included from /home/pushkar/examples/step-26/step-26.cc:44: /usr/local/include/deal.II/numerics/vector_tools.h:830:8: note: candidate: ‘template void dealii::VectorTools::project(const dealii::DoFHandler&, const dealii::ConstraintMatrix&, const dealii::Quadrature&, const dealii::Function&, VectorType&, bool, const
[deal.II] Error in Compilation
Dear deal.II community, I ran into error while compilation which I am not able to decipher in which case I look forward to your help . The output I encountered on executing "make all" : 15:24:23 Build of project step-26-Debug@step-26 /usr/bin/make all /snap/cmake/715/bin/cmake -S/home/pushkar/examples/step-26 -B/home/pushkar/examples/step-26 --check-build-system CMakeFiles/Makefile.cmake 0 /snap/cmake/715/bin/cmake -E cmake_progress_start /home/pushkar/examples/step-26/CMakeFiles /home/pushkar/examples/step-26//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/home/pushkar/examples/step-26' /usr/bin/make -f CMakeFiles/step-26.dir/build.make CMakeFiles/step-26.dir/depend make[2]: Entering directory '/home/pushkar/examples/step-26' cd /home/pushkar/examples/step-26 && /snap/cmake/715/bin/cmake -E cmake_depends "Unix Makefiles" /home/pushkar/examples/step-26 /home/pushkar/examples/step-26 /home/pushkar/examples/step-26 /home/pushkar/examples/step-26 /home/pushkar/examples/step-26/CMakeFiles/step-26.dir/DependInfo.cmake --color= make[2]: Leaving directory '/home/pushkar/examples/step-26' /usr/bin/make -f CMakeFiles/step-26.dir/build.make CMakeFiles/step-26.dir/build make[2]: Entering directory '/home/pushkar/examples/step-26' [ 50%] Linking CXX executable step-26 /snap/cmake/715/bin/cmake -E cmake_link_script CMakeFiles/step-26.dir/link.txt --verbose=1 /usr/bin/c++ -rdynamic -rdynamic -fuse-ld=gold -pthread -ggdb CMakeFiles/step-26.dir/step-26.cc.o -o step-26 -Wl,-rpath,/usr/local/lib /usr/local/lib/libdeal_II.g.so.9.0.0 -lpthread -lm -ldl -lopenblas -lgfortran -lquadmath -lm -lc -lgcc_s -lgcc -ldl -lz -lrt /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/Scrt1.o:function _start: error: undefined reference to 'main' collect2: error: ld returned 1 exit status make[2]: *** [CMakeFiles/step-26.dir/build.make:106: step-26] Error 1 make[1]: *** [CMakeFiles/Makefile2:183: CMakeFiles/step-26.dir/all] Error 2 make: *** [Makefile:103: all] Error 2 make[2]: Leaving directory '/home/pushkar/examples/step-26' make[1]: Leaving directory '/home/pushkar/examples/step-26' "/usr/bin/make all" terminated with exit code 2. Build might be incomplete. 15:24:23 Build Failed. 3 errors, 0 warnings. (took 615ms) Any help in this regard will be beneficial Regards Pushkar -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/72bfcdd4-ba69-4cb4-a1d9-6627c26874dbn%40googlegroups.com.
