Whoops! Good catch!! I had fixed this in a local version... but it never made
it back out to the main repo. It's committed now.
Derek
On Feb 9, 2010, at 11:38 AM, Rahul Sampath wrote:
> Hi:
>
> I am sorry if I was not clear in my earlier e-mail. I generated a
> simple HEX8 mesh using Cubit. The geometry is a simple cube and I
> specify a simple node-based boundary condition on all surfaces (all
> displacements are 0.0 on all surfaces). I have attached the sample
> Cubit file, the mesh exported in ExodusII format and the ASCII form of
> the Exodus file generated using the publicly available ncdump program.
> The Exodus format uses a 1-based numbering for its nodes. Libmesh uses
> a 0-based numbering. So in the Libmesh function ExodusII_IO::read()
> you have to read the node ids (for element-to-node connectivities and
> boundary sets) from the exodus file in 1-based numbering subtract 1
> from it and store it in the Libmesh data stuctures. The problem is
> that you are subtracting 1 only when reading the element-to-node map
> and not when reading node-based boundary conditions.
>
> The following is taken from the Libmesh source code:
>
> In the function ExodusII_IO::read()
>
> // Read nodeset info
> 00215 {
> 00216 exio_helper.read_nodeset_info();
> 00217
> 00218 for (int nodeset=0; nodeset<exio_helper.get_num_node_sets();
> nodeset++)
> 00219 {
> 00220 int nodeset_id = exio_helper.get_nodeset_id(nodeset);
> 00221
> 00222 exio_helper.read_nodeset(nodeset);
> 00223
> 00224 const std::vector<int>& node_list = exio_helper.get_node_list();
> 00225
> 00226 for(unsigned int node=0; node<node_list.size(); node++)
> 00227 mesh.boundary_info->add_node(node_list[node], nodeset_id);
> 00228 }
> 00229 }
> 00230
>
> In Line 222, exio_helper::node_list is populated from the input file
> and this uses 1-based numbering. In line 227 this is passed to the
> function boundary_info->add_node which expects 0-based numbering.
> As a result, when boundary_info->add_node calls SerialMesh::node_ptr
> the following assertion failed error is thrown: "i < this->n_nodes() "
> at line 108 of serial_mesh.C
>
> Could you kindly take a look into this problem.
>
> Thanks.
>
> Regards,
>
> Rahul
>
> On Mon, Feb 8, 2010 at 3:26 PM, Derek Gaston <[email protected]> wrote:
>> I don't think there is a bug with ExodusII_IO. Just make sure that your
>> mesh doesn't contain any blocks, sidesets or nodesets that are _0_.
>>
>> This is done on purpose so the numbering matches what gets generated with
>> Cubit.
>>
>> What are you using to generate your meshes?
>>
>> Derek
>>
>> This is
>> On Feb 8, 2010, at 12:14 PM, Rahul Sampath wrote:
>>
>>> Hi:
>>>
>>> I believe that there is a bug in the function ExodusII_IO::read(). I
>>> have attached a sample program and the input file to demonstrate this.
>>> The ASCII version of the exodus file was generated using the tool
>>> ncdump. You can see the ExodusII uses a 1-based numbering scheme.
>>> However, when trying to add nodes to boundary_info using nodesets the
>>> ExodusII_IO::read() function assumes a 0-based numbering scheme. As a
>>> result an assertion error is thrown at line 108 in serial_mesh.C in
>>> function SerialMesh::node_ptr, which is called from
>>> BoundaryInfo::add_node, which is in turn called from
>>> ExodusII_IO::read.
>>>
>>> Regards,
>>>
>>> Rahul
>>> <cubeMesh.txt>------------------------------------------------------------------------------
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>>
>>
> <sampleCube.txt><sampleCube.e><testReadMesh.cc><sampleCube.cub>
------------------------------------------------------------------------------
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