Hi Jean-Paul, The last journal file that you sent me run successfully. I was able to read the file that it generated using GridIn::read_ucd. By the way, it would be more clear if the suffix of the generated file will be "ucd" and not "inp" which is the suffix that is affiliated with abaqus file format.
Thanks, Oded On Monday, October 24, 2016 at 4:39:57 PM UTC-4, Jean-Paul Pelteret wrote: > > Hi Oded, > > Hmm... I didn't have much luck with the script either. That was > unexpected! I've dug up an older version from many year ago and attached > it. Please give it a go! I know that this one doesn't output material IDs, > but I'll try to see if I can refactor it so that it does. > > Regards, > J-P > > On Monday, October 24, 2016 at 9:21:21 PM UTC+2, Oded Yaakobi wrote: >> >> Hi Jean-Paul, >> >> I tried to run the python script that you noted, but got various error >> messages. >> Were you able to run it successfully on my mesh? >> >> Best, >> Oded >> >> >> On Monday, October 24, 2016 at 11:05:36 AM UTC-4, Jean-Paul Pelteret >> wrote: >>> >>> 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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