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Re: [Libmesh-users] Defining hanging nodes in the XDA format
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From: Salazar De T. M. <sal...@ll...> - 2018-01-25 20:13:37
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An easier question to make would be: Can I have a parent element with just two children? For instance, the following mesh has two elements and two children for the second element. I am not able to read the mesh attached. The error is:
Program received signal SIGSEGV, Segmentation fault.
0x00002aaaadab14a4 in libMesh::Elem::parent (this=0x0) at ./include/libmesh/elem.h:2357
2357 return _elemlinks[0];
Missing separate debuginfos, use: debuginfo-install blas-3.4.2-8.el7.x86_64 cyrus-sasl-lib-2.1.26-21.el7.x86_64 glpk-4.52.1-2.el7.x86_64 hdf5-1.8.12-8.el7.x86_64 keyutils-libs-1.5.8-3.el7.x86_64 krb5-libs-1.15.1-8.2chaos.ch6.x86_64 lapack-3.4.2-8.el7.x86_64 libX11-1.6.5-1.el7.x86_64 libXau-1.0.8-2.1.el7.x86_64 libcom_err-1.42.9-10.el7.x86_64 libcurl-7.29.0-42.el7_4.1.x86_64 libibverbs-13-7.el7.x86_64 libidn-1.28-4.el7.x86_64 libnl3-3.2.28-4.el7.x86_64 libpsm2-10.2.63-2.el7.x86_64 libselinux-2.5-11.el7.x86_64 libssh2-1.4.3-10.el7_2.1.x86_64 libuuid-2.23.2-43.el7_4.2.x86_64 libxcb-1.12-1.el7.x86_64 nspr-4.13.1-1.0.el7_3.x86_64 nss-3.28.4-15.el7_4.x86_64 nss-softokn-freebl-3.28.3-8.el7_4.x86_64 nss-util-3.28.4-3.el7.x86_64 numactl-libs-2.0.9-6.el7_2.x86_64 openldap-2.4.44-5.el7.x86_64 openssl-libs-1.0.2k-8.el7.x86_64
(gdb) bt
#0 0x00002aaaadab14a4 in libMesh::Elem::parent (this=0x0) at ./include/libmesh/elem.h:2357
#1 0x00002aaaae45ae8a in libMesh::MeshTools::libmesh_assert_valid_refinement_tree (mesh=...) at src/mesh/mesh_tools.C:1682
#2 0x00002aaaae1dd7a5 in libMesh::DistributedMesh::delete_remote_elements (this=0x7fffffffbcd8) at src/mesh/distributed_mesh.C:1363
#3 0x00002aaaae27e2c2 in libMesh::MeshBase::prepare_for_use (this=0x7fffffffbcd8, skip_renumber_nodes_and_elements=false, skip_find_neighbors=false) at src/mesh/mesh_base.C:269
#4 0x00002aaaae4e5705 in libMesh::UnstructuredMesh::read (this=0x7fffffffbcd8, name=..., skip_renumber_nodes_and_elements=false, skip_find_neighbors=false) at src/mesh/unstructured_mesh.C:625
#5 0x0000000000424716 in main (argc=1, argv=0x7fffffffc368) at /g/g92/miguel/code/topsm/test/mwe_restart/mwe_restart.C:49
libMesh-1.3.0
4 # number of elements
10 # number of nodes
. # boundary condition specification file
. # subdomain id specification file
n/a # processor id specification file
n/a # p-level specification file
8 # type size
0 # uid size
0 # pid size
8 # sid size
0 # p-level size
8 # eid size
8 # side size
8 # bid size
0 # subdomain id to name map
2 # n_elem at level 0, [ type sid (n0 ... nN-1) ]
5 0 0 1 2 3
5 0 1 7 9 2
2 # n_elem at level 1, [ type sid (n0 ... nN-1) ]
5 1 0 4 7 8 5
5 1 0 5 8 9 6
5.0000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00
1.0000000000000000e+02 0.0000000000000000e+00 0.0000000000000000e+00
1.0000000000000000e+02 5.0000000000000000e+01 0.0000000000000000e+00
5.0000000000000000e+01 5.0000000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+02 0.0000000000000000e+00 0.0000000000000000e+00
1.2500000000000000e+02 2.5000000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+02 5.0000000000000000e+01 0.0000000000000000e+00
1.3750000000000000e+02 0.0000000000000000e+00 0.0000000000000000e+00
1.3750000000000000e+02 2.5000000000000000e+01 0.0000000000000000e+00
1.3750000000000000e+02 5.0000000000000000e+01 0.0000000000000000e+00
0 # presence of unique ids
0 # sideset id to name map
0 # number of side boundary conditions
0 # nodeset id to name map
0 # number of nodesets
0 # sideset id to name map
0 # number of edge boundary conditions
0 # sideset id to name map
0 # number of shellface boundary conditions
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On 1/24/18, 4:15 PM, "Salazar De Troya, Miguel" <sal...@ll...> wrote:
Attaching a picture. I drew the eight elements I removed. This way you can see how I generated the initial mesh (with two levels of refinement in the outermost elements and one in the interior). Without flattening the mesh, I could not remove those children I drew.
Miguel
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From: "Paul T. Bauman" <ptb...@gm...>
Date: Wednesday, January 24, 2018 at 3:45 PM
To: "Salazar De Troya, Miguel" <sal...@ll...>
Cc: "lib...@li..." <lib...@li...>
Subject: Re: [Libmesh-users] Defining hanging nodes in the XDA format
I'm not sure I'm following (a picture is worth a thousand words here), but it sounds like you're trying to create a child of a quad by only splitting in one direction and not both?
On Tue, Jan 23, 2018 at 7:22 PM, Salazar De Troya, Miguel <sal...@ll...<mailto:sal...@ll...>> wrote:
Hello,
I have the mesh attached below. It is the result of having three quadrangular elements in line, refine the left and right ones, then on their leftmost and rightmost children, do another refinement. After this, I flattened out the mesh and removed the leftmost and rightmost layer of elements. The issue is that I’ve got hanging nodes that libmesh does not recognize. Is there any way to find them or tell libMesh which ones they are?
Is there an alternative way to generate a similar mesh? I was not able to remove the leftmost and rightmost children without flattening the mesh first. It seems as if each parent element must have four elements.
Thanks
Miguel
libMesh-1.3.0
13 # number of elements
26 # number of nodes
n/a # boundary condition specification file
. # subdomain id specification file
n/a # processor id specification file
n/a # p-level specification file
8 # type size
0 # uid size
0 # pid size
8 # sid size
0 # p-level size
0 # eid size
0 # side size
0 # bid size
0 # subdomain id to name map
13 # n_elem at level 0, [ type sid (n0 ... nN-1) ]
5 0 0 1 2 3
5 0 4 0 5 6
5 0 6 5 3 7
5 0 1 8 9 10
5 0 10 9 11 2
5 0 12 4 13 14
5 0 14 13 6 15
5 0 15 6 16 17
5 0 17 16 7 18
5 0 8 19 20 21
5 0 21 20 22 9
5 0 9 22 23 24
5 0 24 23 25 11
5.0000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00
1.0000000000000000e+02 0.0000000000000000e+00 0.0000000000000000e+00
1.0000000000000000e+02 5.0000000000000000e+01 0.0000000000000000e+00
5.0000000000000000e+01 5.0000000000000000e+01 0.0000000000000000e+00
2.5000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00
5.0000000000000000e+01 2.5000000000000000e+01 0.0000000000000000e+00
2.5000000000000000e+01 2.5000000000000000e+01 0.0000000000000000e+00
2.5000000000000000e+01 5.0000000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+02 0.0000000000000000e+00 0.0000000000000000e+00
1.2500000000000000e+02 2.5000000000000000e+01 0.0000000000000000e+00
1.0000000000000000e+02 2.5000000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+02 5.0000000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00
2.5000000000000000e+01 1.2500000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+01 1.2500000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+01 2.5000000000000000e+01 0.0000000000000000e+00
2.5000000000000000e+01 3.7500000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+01 3.7500000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+01 5.0000000000000000e+01 0.0000000000000000e+00
1.3750000000000000e+02 0.0000000000000000e+00 0.0000000000000000e+00
1.3750000000000000e+02 1.2500000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+02 1.2500000000000000e+01 0.0000000000000000e+00
1.3750000000000000e+02 2.5000000000000000e+01 0.0000000000000000e+00
1.3750000000000000e+02 3.7500000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+02 3.7500000000000000e+01 0.0000000000000000e+00
1.3750000000000000e+02 5.0000000000000000e+01 0.0000000000000000e+00
0 # presence of unique ids
0 # sideset id to name map
0 # number of side boundary conditions
0 # nodeset id to name map
0 # number of nodesets
0 # sideset id to name map
0 # number of edge boundary conditions
0 # sideset id to name map
0 # number of shellface boundary conditions
--
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