Dear Oded, The error message from the development version is more useful. Unfortunately there's a bug somewhere in the routine that appears from time-to-time on more complex meshes that I have not been able to track as of yet. This is clearly one of those times... For now you could consider using this python script <https://github.com/dealii/dealii/wiki/Mesh-Input-And-Output> to output your geometry from cubit in a UCD format.
Best, J-P On Friday, October 21, 2016 at 10:47:12 PM UTC+2, Oded Yaakobi wrote: > > Hi Jean-Paul, > > > > I wanted to verify that the issue that I encountered is not related to the > fact that I am using a version of dealii which is not the most updated one, > so I installed the current version of dealii from git. I run two versions > of my code with ‘apply_all_indicators_to_manifolds’ either false or true - > see the attached code. In either case I got similar, although not exactly > the same output. The value of the boundary indicator that is noted > regarding the problematic quad is 1 or 0 respectively. > > > > For ‘apply_all_indicators_to_manifolds’ = false: > > > > Reading block 1 file: > > block 1 file was read successfully > > Reading block 2 file: > > block 2 file was read successfully > > Reading block 1 and 2 file: > > Exception on processing internal UCD data: > > > > -------------------------------------------------------- > > An error occurred in line <3008> of file > </Users/yaakobioy/dealii/dealii_git_21102016/dealii_git_21102016_Source/source/grid/tria.cc> > > in function > > static void > dealii::internal::Triangulation::Implementation::create_triangulation(const > std::vector<Point<spacedim> > &, const std::vector<CellData<3> > &, const > dealii::SubCellData &, Triangulation<3, spacedim> &) [spacedim = 3] > > The violated condition was: > > quad->at_boundary() > > Additional information: > > The input data for creating a triangulation contained information > about a quad with indices 1289, 1398, 1288, and 1397 that is described to > have boundary indicator 1. However, this is an internal quad not located on > the boundary. You cannot assign a boundary indicator to it. > > > > If this happened at a place where you call > Triangulation::create_triangulation() yourself, you need to check the > SubCellData object you pass to this function. > > > > If this happened in a place where you are reading a mesh from a file, then > you need to investigate why such a quad ended up in the input file. A > typical case is a geometry that consisted of multiple parts and for which > the mesh generator program assumes that the interface between two parts is > a boundary when that isn't supposed to be the case, or where the mesh > generator simply assigns 'geometry indicators' to quads at the surface of a > part that are not supposed to be interpreted as 'boundary indicators'. > > -------------------------------------------------------- > > > > > > > > ---------------------------------------------------- > > Exception on processing: > > > > -------------------------------------------------------- > > An error occurred in line <899> of file > </Users/yaakobioy/dealii/dealii_git_21102016/dealii_git_21102016_Source/source/grid/grid_in.cc> > > in function > > void dealii::GridIn<3, 3>::read_abaqus(std::istream &, const bool) > [dim = 3, spacedim = 3] > > The violated condition was: > > false > > Additional information: > > Internal conversion from ABAQUS file to UCD format was unsuccessful. > More information is provided in an error message printed above. Are you > sure that your ABAQUS mesh file conforms with the requirements listed in > the documentation? > > -------------------------------------------------------- > > > > Aborting! > > ---------------------------------------------------- > > > > > > For ‘apply_all_indicators_to_manifolds’ = true: > > > > Reading block 1 file: > > block 1 file was read successfully > > Reading block 2 file: > > block 2 file was read successfully > > Reading block 1 and 2 file: > > Exception on processing internal UCD data: > > > > -------------------------------------------------------- > > An error occurred in line <3008> of file > </Users/yaakobioy/dealii/dealii_git_21102016/dealii_git_21102016_Source/source/grid/tria.cc> > > in function > > static void > dealii::internal::Triangulation::Implementation::create_triangulation(const > std::vector<Point<spacedim> > &, const std::vector<CellData<3> > &, const > dealii::SubCellData &, Triangulation<3, spacedim> &) [spacedim = 3] > > The violated condition was: > > quad->at_boundary() > > Additional information: > > The input data for creating a triangulation contained information > about a quad with indices 1289, 1398, 1288, and 1397 that is described to > have boundary indicator 0. However, this is an internal quad not located on > the boundary. You cannot assign a boundary indicator to it. > > > > If this happened at a place where you call > Triangulation::create_triangulation() yourself, you need to check the > SubCellData object you pass to this function. > > > > If this happened in a place where you are reading a mesh from a file, then > you need to investigate why such a quad ended up in the input file. A > typical case is a geometry that consisted of multiple parts and for which > the mesh generator program assumes that the interface between two parts is > a boundary when that isn't supposed to be the case, or where the mesh > generator simply assigns 'geometry indicators' to quads at the surface of a > part that are not supposed to be interpreted as 'boundary indicators'. > > -------------------------------------------------------- > > > > > > > > ---------------------------------------------------- > > Exception on processing: > > > > -------------------------------------------------------- > > An error occurred in line <899> of file > </Users/yaakobioy/dealii/dealii_git_21102016/dealii_git_21102016_Source/source/grid/grid_in.cc> > > in function > > void dealii::GridIn<3, 3>::read_abaqus(std::istream &, const bool) > [dim = 3, spacedim = 3] > > The violated condition was: > > false > > Additional information: > > Internal conversion from ABAQUS file to UCD format was unsuccessful. > More information is provided in an error message printed above. Are you > sure that your ABAQUS mesh file conforms with the requirements listed in > the documentation? > > -------------------------------------------------------- > > > > Aborting! > > ---------------------------------------------------- > > > > Best, > > Oded > > > On Friday, October 21, 2016 at 1:20:55 PM UTC-4, Jean-Paul Pelteret wrote: >> >> Hi Oded, >> >> I wasn't able to read in the .cub file (clearly its not backwards >> compatible). I did manage to import the .inp file and nothing looks amiss. >> Could you try to set the apply_all_indicators_to_manifolds >> <https://www.dealii.org/developer/doxygen/deal.II/classGridIn.html#a51f7977b217e305d3538574cbd3d3a01> >> flag >> to true? Its possible that one of the boundary id's is being set to an >> internal face. I've had this bug crop up on occasion for unstructured >> meshes, but never for structured ones. If this fixes the problem then >> you'll have to recreate all of the boundary ID's yourself for the time >> being until the bug is fixed. >> >> Regards, >> J-P >> >> >> On Friday, October 21, 2016 at 6:27:07 PM UTC+2, Oded Yaakobi wrote: >>> >>> Hi Jean-Paul, >>> >>> >>> >>> I changed one of the options in the Cubit 15.2 GUI, and now >>> 'gen_input_file' does not appear in the journal file. Reading in my code >>> the resulting abaqus files behaves as before, i.e. this is the output: >>> >>> >>> >>> Reading block 1 file: >>> >>> block 1 file was read successfully >>> >>> Reading block 2 file: >>> >>> block 2 file was read successfully >>> >>> Reading block 1 and 2 file: >>> >>> >>> >>> >>> >>> ---------------------------------------------------- >>> >>> Exception on processing: >>> >>> >>> >>> -------------------------------------------------------- >>> >>> An error occurred in line <864> of file >>> </Users/yaakobioy/dealii/dealii_git_04022016/source/grid/grid_in.cc> in >>> function >>> >>> void dealii::GridIn<3, 3>::read_abaqus(std::istream &) [dim = 3, >>> spacedim = 3] >>> >>> The violated condition was: >>> >>> false >>> >>> The name and call sequence of the exception was: >>> >>> ExcMessage("Internal conversion from ABAQUS file to UCD format was >>> unsuccessful. Are you sure that your >>> ABAQUS mesh file conforms with the >>> requirements listed in the >>> documentation?") >>> >>> Additional Information: >>> >>> Internal conversion from ABAQUS file to UCD format was >>> unsuccessful. Are you sure that your >>> ABAQUS mesh file conforms with the >>> requirements listed in the documentation? >>> >>> -------------------------------------------------------- >>> >>> >>> >>> Aborting! >>> >>> ---------------------------------------------------- >>> >>> >>> >>> For your convenience, I attach here all the files. I hope that you would >>> be able to run the new journal file on your version of Cubit. >>> >>> >>> >>> Thank you, >>> >>> Oded >>> >>> On Friday, October 21, 2016 at 11:09:01 AM UTC-4, Oded Yaakobi wrote: >>>> >>>> Hi Jean-Paul, >>>> >>>> >>>> >>>> Attached is the CUB file of the two-block mesh that I created. >>>> >>>> >>>> >>>> I created the mesh using only Cubit 15.2 GUI. In saving the abaqus >>>> file, I followed the instruction of GridIn::read_abaqus. The journal file >>>> that I attached before reflects the commands that I executed through the >>>> GUI. Probably 'gen_input_file' is not defined in the old version of Cubit >>>> that you have. >>>> >>>> >>>> >>>> According to Cubit 15.2 documentation, 'gen_input_file' is an input >>>> file with the given file name that will be generated when the Sculpt >>>> Parallel command will be executed. This is a text file containing all >>>> sculpt options used in the command. The input file is intended to be used >>>> for batch execution of sculpt. Therefore, in my case, in which I used the >>>> GUI, 'gen_input_file' is actually an output file and not an input file. >>>> >>>> >>>> >>>> Best, >>>> >>>> Oded >>>> >>>> >>>> On Friday, October 21, 2016 at 3:40:32 AM UTC-4, Jean-Paul Pelteret >>>> wrote: >>>>> >>>>> Hi Oded, >>>>> >>>>> Two things: >>>>> 1. The documentation originally stated that "Files generated using >>>>> Cubit 11.x, 12.x and 13.x are valid", but I see that its now been updated >>>>> to include 14.x and 15.x. I personally don't know whether this works with >>>>> newer versions of Cubit, but hopefully it has indeed been tested. >>>>> 2. You've not provided all of the data necessary to recreate your >>>>> geometry: >>>>> >>>>> CUBIT> create sphere radius 1 >>>>>> Successfully created sphere volume 1 >>>>>> Journaled Command: create sphere radius 1 >>>>>> CUBIT> sculpt parallel volume all processors 8 fileroot >>>>>> "sculpt_parallel" gen_input_file "sculpt_parallel.i" overwrite >>>>>> xintervals 8 >>>>>> yintervals 8 zintervals 8 box location position -3 -3 -3 location >>>>>> position >>>>>> 3 3 3 smooth 8 num_laplace 2 max_opt_iters 5 opt_threshold 0.6 >>>>>> max_pcol_iters 100 pcol_threshold 0.2 sideset 2 void adapt_type 1 >>>>>> adapt_levels 2 combine import show clean >>>>>> ERROR: Unrecognized Identifier: 'gen_input_file' >>>>> >>>>> >>>>> Can you please provide all whatever files are necessary to recreate >>>>> the geometry? Either that or provide the actual Cubit file itself. >>>>> Hopefully I can open it in my older version of Cubit. >>>>> >>>>> Regards, >>>>> J-P >>>>> >>>>> >>>>> >>>>> On Thursday, October 20, 2016 at 10:09:47 PM UTC+2, Oded Yaakobi wrote: >>>>>> >>>>>> Hello group, >>>>>> >>>>>> >>>>>> >>>>>> I am interested to test a code that I am developing by solving with >>>>>> it the specific problem of Stokes flow in and around a fluid sphere. >>>>>> >>>>>> >>>>>> >>>>>> I used Cubit 15.2 to create a mesh of a sphere in a box, as shown in >>>>>> the attached picture, and exported it to an abaqus file. The resulting >>>>>> mesh >>>>>> is composed of two blocks - block 1 for the domain inside the sphere and >>>>>> block 2 for the domain outside the sphere. As a first step, I didn’t >>>>>> define >>>>>> different material id’s to each one of the blocks. >>>>>> >>>>>> >>>>>> >>>>>> When I tried to read the file using GridIn::read_abaqus, I received >>>>>> the following Error message: >>>>>> >>>>>> >>>>>> >>>>>> ---------------------------------------------------- >>>>>> >>>>>> Exception on processing: >>>>>> >>>>>> >>>>>> >>>>>> -------------------------------------------------------- >>>>>> >>>>>> An error occurred in line <864> of file >>>>>> </Users/yaakobioy/dealii/dealii_git_04022016/source/grid/grid_in.cc> in >>>>>> function >>>>>> >>>>>> void dealii::GridIn<3, 3>::read_abaqus(std::istream &) [dim = 3, >>>>>> spacedim = 3] >>>>>> >>>>>> The violated condition was: >>>>>> >>>>>> false >>>>>> >>>>>> The name and call sequence of the exception was: >>>>>> >>>>>> ExcMessage("Internal conversion from ABAQUS file to UCD format >>>>>> was unsuccessful. Are you sure that >>>>>> your >>>>>> ABAQUS mesh file conforms with the >>>>>> requirements listed in the >>>>>> documentation?") >>>>>> >>>>>> Additional Information: >>>>>> >>>>>> Internal conversion from ABAQUS file to UCD format was >>>>>> unsuccessful. Are you sure that your >>>>>> ABAQUS mesh file conforms with the requirements >>>>>> listed in the documentation? >>>>>> >>>>>> -------------------------------------------------------- >>>>>> >>>>>> >>>>>> >>>>>> Aborting! >>>>>> >>>>>> ---------------------------------------------------- >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> When I tried to save only one of the blocks (either block 1 or block >>>>>> 2) in separate files, there was no problem in reading the corresponding >>>>>> abaqus files. >>>>>> >>>>>> >>>>>> >>>>>> Have I done something wrong in the way I created the multi-block >>>>>> mesh, or is there a bug with GridIn::read_abaqus? >>>>>> >>>>>> >>>>>> >>>>>> Attached are the abaqus files, the Cubit journal file and my code >>>>>> that fails to read the multi-block mesh file. >>>>>> >>>>>> >>>>>> >>>>>> Thank you, >>>>>> >>>>>> Oded >>>>>> >>>>>> >>>>>> >>>>> -- 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. 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