Difference between revisions of "Unstructured mesh-based geometry type"

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(Input Syntax)
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The input format of each of the linked files is based on the OpenFOAM file format.
 
The input format of each of the linked files is based on the OpenFOAM file format.
  
 +
=== Mesh structure/quality ===
  
=== Mesh structure ===
+
The mesh can consist of arbitrary polygons as long as they can be entered in the OpenFOAM file-format and some quality requirements are met:
 +
*The cells must be closed
 +
*The cells must be convex (i.e. all face and body diagonals must be completely within the cell volume)
 +
*Each face must have exactly one owner cell.
 +
*Each face must have exactly one or zero neighbor cells.
 +
 
 +
=== Splitting of polyhedrons ===
 +
 
 +
==== Background ====
 +
 
 +
Serpent will do the final neutron tracking in a tetrahedral mesh, which is automatically generated by splitting other polyhedrons to tetrahedra. Tetrahedrons are used in the neutron tracking as each of their face surfaces is defined by three points (the vertices of the face) this is exactly the number of points required to uniquely define a plane. Since Serpent tests whether a point is inside a cell by testing whether it is on the correct side of each of the surfaces making up the cell, it is important that the surfaces bounding the cell are uniquely defined.
 +
 
 +
Faces with more than three points may not be entirely planar (either due to mesh generation/deformation) or limited numerical precision. To ensure that these kinds of faces are treated in the same way in both the owner cell and the neighbor cell the mesh is split into tetrahedrons before the neutron tracking.
 +
 
 +
==== Smart algorithm ====
 +
 
 +
==== Dumb algorithm ====
 +
 
 +
=== Debugging ===
 +
 
 +
Serpent automatically runs some basic tests for the mesh before and after it has been split to tetrahedra. Serpent tests that each face of the mesh is correctly owned by its owner and neighbored by its neighbor. Serpent also tests that the barycenter of each cell calculated by (in pseudocode)
 +
 
 +
Npoints = 0
 +
 +
for face in cell:
 +
  for point in face:
 +
    baryc.x += point.x
 +
    baryc.y += point.y
 +
    baryc.z += point.z
 +
    Npoints++
 +
 +
baryc.x = baryc.x/Npoints
 +
baryc.y = baryc.y/Npoints
 +
baryc.z = baryc.z/Npoints
 +
 
 +
 
 +
is inside the cell. All of the cells failing this test should be non-convex, but some non-convex cells might not be caught by this test.
 +
 
 +
When reading the unstructured mesh (geometry or interface), Serpent prints out the composition of the mesh:
 +
 
 +
Reading multi-physics interface "./ifc.new"...
 +
Composition of mesh:
 +
Tetrahedrons:      0
 +
Pyramids:          0
 +
Prisms:            0
 +
Hexahedrons:      142400
 +
Other polyhedrons: 0
 +
 
 +
After the initial mesh has been read into memory, Serpent runs the tests and prints out the results:
 +
 
 +
  - Checked neighbority for 420776 surfaces, 0 failed
 +
  - Checked that barycenter is inside tet for 142400 cells, 0 failed
 +
 
 +
Serpent will then divide the mesh to tetrahedra if needed and check the resulting mesh:
 +
 
 +
Dividing hexahedral mesh to tetrahedrons.
 +
Checking divided mesh.
 +
  - Checked neighbority for 1695952 surfaces, 0 failed
 +
  - Checked that barycenter is inside tet for 854400 cells, 0 failed
 +
 
 +
If any of the cells does not pass one of the tests, the simulation will be terminated:
 +
 
 +
Checking initial mesh:
 +
 +
  - Checked neighbority for 1698578 surfaces, 0 failed
 +
  - Checked that barycenter is inside tet for 587520 cells, 15900 failed
 +
 +
***** Fri Feb 26 10:18:49 2016:
 +
 +
  - MPI task        = 0
 +
  - OpenMP thread    = 0
 +
  - RNG parent seed  = 1456474723
 +
 +
Fatal error in function CheckPolyhedMesh:
 +
 +
There were errors in the mesh
 +
 +
Simulation aborted.
 +
 
 +
If the code is compiled in the [[Installing_and_running_Serpent#Compiler_options|DEBUG]]-mode, Serpent will print out warnings for the cells as they fail the tests (there may be a lot of output if many cells are failing):
 +
 
 +
F1 = [ -9.658312E-01 -2.508234E+00 -1.914149E+01; -1.009252E+00 -2.452564E+00 -1.914067E+01; -1.066138E+00 -2.408068E+00 -1.914106E+01; -9.617244E-01 -2.405420E+00 -1.914097E+01; ]
 +
F2 = [ -1.009035E+00 -2.452835E+00 -1.953164E+01; -9.658705E-01 -2.508183E+00 -1.953196E+01; -9.622982E-01 -2.404919E+00 -1.953140E+01; -1.068680E+00 -2.406116E+00 -1.953142E+01; ]
 +
F3 = [ -9.622982E-01 -2.404919E+00 -1.953140E+01; -9.617244E-01 -2.405420E+00 -1.914097E+01; -9.658312E-01 -2.508234E+00 -1.914149E+01; -9.658705E-01 -2.508183E+00 -1.953196E+01; ]
 +
F4 = [ -1.066138E+00 -2.408068E+00 -1.914106E+01; -9.617244E-01 -2.405420E+00 -1.914097E+01; -9.622982E-01 -2.404919E+00 -1.953140E+01; -1.068680E+00 -2.406116E+00 -1.953142E+01; ]
 +
F5 = [ -1.009035E+00 -2.452835E+00 -1.953164E+01; -9.658705E-01 -2.508183E+00 -1.953196E+01; -9.658312E-01 -2.508234E+00 -1.914149E+01; -1.009252E+00 -2.452564E+00 -1.914067E+01; ]
 +
F6 = [ -1.009035E+00 -2.452835E+00 -1.953164E+01; -1.009252E+00 -2.452564E+00 -1.914067E+01; -1.066138E+00 -2.408068E+00  1.914106E+01; -1.068680E+00 -2.406116E+00 -1.953142E+01; ]
 +
figure();
 +
hold on;
 +
fill3(F1(:,1),F1(:,2),F1(:,3),ones(4,1)*1.000000);
 +
fill3(F2(:,1),F2(:,2),F2(:,3),ones(4,1)*0.916667);
 +
fill3(F3(:,1),F3(:,2),F3(:,3),ones(4,1)*-0.833333);
 +
fill3(F4(:,1),F4(:,2),F4(:,3),ones(4,1)*-0.750000);
 +
fill3(F5(:,1),F5(:,2),F5(:,3),ones(4,1)*-0.666667);
 +
fill3(F6(:,1),F6(:,2),F6(:,3),ones(4,1)*-0.583333);
 +
hold off;
 +
title('Cell 23229')
 +
Barycenter (-1.001104E+00 -2.443292E+00 -1.933633E+01)
 +
 +
***** Fri Feb 26 10:22:56 2016 (seed = 1456474964)
 +
Warning message from function CheckPolyhedMesh:
 +
 +
Barycenter not inside cell 23229
 +
 
 +
[[File:Failed_UMSH_cell.png|thumb|250px|A mesh cell failing the barycenter test. The cell is the owner of the blue faces and neighbor to the red faces.]]
 +
As seen above, in case of a failed barycenter test, Serpent will print out the faces as MATLAB/Octave matrices as well as a script-snippet that can be used to plot the failed cell in MATLAB (fill3 is not implemented in Octave at the moment). With a bit of rotating and polishing we can get the plot shown here. The color of each face indicates whether the cell owns or is neighbour to the face. Blue faces are owned by the current cell, the current cell is a neighbor of the red faces. The coordinates of the barycenter are also printed so that the barycenter can be plotted to the figure. If the barycenter falls outside the face, the cell is convex (as is the case here). If the barycenter seems to fall inside the faces, there is most likely something wrong with the owner/neighborship or the ordering of points on one of the faces so that the intended inside of the cell is actually on the wrong side of one or multiple face surfaces.
 +
 
 +
[[Category:Input]]
 +
[[Category:Tutorials]]

Latest revision as of 14:41, 29 November 2017

The unstructured mesh based geometry is a by-product of the unstructured mesh-based multi-physics interface. It can be used to create a geometry universe based on an unstructured mesh.

Input Syntax

The unstructured mesh based geometry can be created by using the solid 1 or solid 3 input card.

Geometry only (solid 1)

solid 1 UNI BGUNI
MESH_SPLIT MESH_DIM SZ1 SZ2 ... SZMESH_DIM
POINTS_FILE
FACES_FILE
OWNER_FILE
NEIGHBOUR_FILE
MATERIALS_FILE

The first solid type creates an unstructured mesh-based geometry universe. Input values are:

UNI  : universe name for the irregular geometry
BGUNI  : name of the background universe filling all undefined space
MESH_SPLIT  : Splitting criterion for the adaptive search mesh (maximum number of geometry cells in search mesh cell)
MESH_DIM  : number of levels in the adaptive search mesh
SZi  : Size of the search mesh at level i
POINTS_FILE  : Path to the unstructured mesh points file
FACES_FILE  : Path to the unstructured mesh faces file
OWNER_FILE  : Path to the unstructured mesh owner file
NEIGHBOUR_FILE  : Path to the unstructured mesh neighbour file
MATERIALS_FILE  : Path to the unstructured mesh materials file

Geometry and multi-physics data (solid 3)

solid 3 UNI BGUNI
INTERFACE_FILE

It is also possible to create the geometry and bring in temperature and/or density data on the same mesh. In this case, most of the parameters are given in a separate multi-physics interface file which can be re-read by Serpent to update the fields between coupled calculation iterations. The input values in the main input file are:

UNI  : universe name for the irregular geometry
BGUNI  : name of the background universe filling all undefined space
POINTS_FILE  : Path to the interface file containing the rest of the parameters


The input format of each of the linked files is based on the OpenFOAM file format.

Mesh structure/quality

The mesh can consist of arbitrary polygons as long as they can be entered in the OpenFOAM file-format and some quality requirements are met:

  • The cells must be closed
  • The cells must be convex (i.e. all face and body diagonals must be completely within the cell volume)
  • Each face must have exactly one owner cell.
  • Each face must have exactly one or zero neighbor cells.

Splitting of polyhedrons

Background

Serpent will do the final neutron tracking in a tetrahedral mesh, which is automatically generated by splitting other polyhedrons to tetrahedra. Tetrahedrons are used in the neutron tracking as each of their face surfaces is defined by three points (the vertices of the face) this is exactly the number of points required to uniquely define a plane. Since Serpent tests whether a point is inside a cell by testing whether it is on the correct side of each of the surfaces making up the cell, it is important that the surfaces bounding the cell are uniquely defined.

Faces with more than three points may not be entirely planar (either due to mesh generation/deformation) or limited numerical precision. To ensure that these kinds of faces are treated in the same way in both the owner cell and the neighbor cell the mesh is split into tetrahedrons before the neutron tracking.

Smart algorithm

Dumb algorithm

Debugging

Serpent automatically runs some basic tests for the mesh before and after it has been split to tetrahedra. Serpent tests that each face of the mesh is correctly owned by its owner and neighbored by its neighbor. Serpent also tests that the barycenter of each cell calculated by (in pseudocode)

Npoints = 0

for face in cell:
  for point in face:
    baryc.x += point.x
    baryc.y += point.y
    baryc.z += point.z
    Npoints++

baryc.x = baryc.x/Npoints
baryc.y = baryc.y/Npoints
baryc.z = baryc.z/Npoints


is inside the cell. All of the cells failing this test should be non-convex, but some non-convex cells might not be caught by this test.

When reading the unstructured mesh (geometry or interface), Serpent prints out the composition of the mesh:

Reading multi-physics interface "./ifc.new"...
Composition of mesh:
Tetrahedrons:      0
Pyramids:          0
Prisms:            0
Hexahedrons:       142400
Other polyhedrons: 0

After the initial mesh has been read into memory, Serpent runs the tests and prints out the results:

 - Checked neighbority for 420776 surfaces, 0 failed
 - Checked that barycenter is inside tet for 142400 cells, 0 failed

Serpent will then divide the mesh to tetrahedra if needed and check the resulting mesh:

Dividing hexahedral mesh to tetrahedrons.
Checking divided mesh.
 - Checked neighbority for 1695952 surfaces, 0 failed
 - Checked that barycenter is inside tet for 854400 cells, 0 failed

If any of the cells does not pass one of the tests, the simulation will be terminated:

Checking initial mesh:

 - Checked neighbority for 1698578 surfaces, 0 failed
 - Checked that barycenter is inside tet for 587520 cells, 15900 failed

***** Fri Feb 26 10:18:49 2016:

 - MPI task         = 0
 - OpenMP thread    = 0
 - RNG parent seed  = 1456474723

Fatal error in function CheckPolyhedMesh:

There were errors in the mesh

Simulation aborted.

If the code is compiled in the DEBUG-mode, Serpent will print out warnings for the cells as they fail the tests (there may be a lot of output if many cells are failing):

F1 = [ -9.658312E-01 -2.508234E+00 -1.914149E+01; -1.009252E+00 -2.452564E+00 -1.914067E+01; -1.066138E+00 -2.408068E+00 -1.914106E+01; -9.617244E-01 -2.405420E+00 -1.914097E+01; ]
F2 = [ -1.009035E+00 -2.452835E+00 -1.953164E+01; -9.658705E-01 -2.508183E+00 -1.953196E+01; -9.622982E-01 -2.404919E+00 -1.953140E+01; -1.068680E+00 -2.406116E+00 -1.953142E+01; ]
F3 = [ -9.622982E-01 -2.404919E+00 -1.953140E+01; -9.617244E-01 -2.405420E+00 -1.914097E+01; -9.658312E-01 -2.508234E+00 -1.914149E+01; -9.658705E-01 -2.508183E+00 -1.953196E+01; ]
F4 = [ -1.066138E+00 -2.408068E+00 -1.914106E+01; -9.617244E-01 -2.405420E+00 -1.914097E+01; -9.622982E-01 -2.404919E+00 -1.953140E+01; -1.068680E+00 -2.406116E+00 -1.953142E+01; ]
F5 = [ -1.009035E+00 -2.452835E+00 -1.953164E+01; -9.658705E-01 -2.508183E+00 -1.953196E+01; -9.658312E-01 -2.508234E+00 -1.914149E+01; -1.009252E+00 -2.452564E+00 -1.914067E+01; ]
F6 = [ -1.009035E+00 -2.452835E+00 -1.953164E+01; -1.009252E+00 -2.452564E+00 -1.914067E+01; -1.066138E+00 -2.408068E+00  1.914106E+01; -1.068680E+00 -2.406116E+00 -1.953142E+01; ]
figure();
hold on;
fill3(F1(:,1),F1(:,2),F1(:,3),ones(4,1)*1.000000);
fill3(F2(:,1),F2(:,2),F2(:,3),ones(4,1)*0.916667);
fill3(F3(:,1),F3(:,2),F3(:,3),ones(4,1)*-0.833333);
fill3(F4(:,1),F4(:,2),F4(:,3),ones(4,1)*-0.750000);
fill3(F5(:,1),F5(:,2),F5(:,3),ones(4,1)*-0.666667);
fill3(F6(:,1),F6(:,2),F6(:,3),ones(4,1)*-0.583333);
hold off;
title('Cell 23229')
Barycenter (-1.001104E+00 -2.443292E+00 -1.933633E+01)

***** Fri Feb 26 10:22:56 2016 (seed = 1456474964)
Warning message from function CheckPolyhedMesh:

Barycenter not inside cell 23229
A mesh cell failing the barycenter test. The cell is the owner of the blue faces and neighbor to the red faces.

As seen above, in case of a failed barycenter test, Serpent will print out the faces as MATLAB/Octave matrices as well as a script-snippet that can be used to plot the failed cell in MATLAB (fill3 is not implemented in Octave at the moment). With a bit of rotating and polishing we can get the plot shown here. The color of each face indicates whether the cell owns or is neighbour to the face. Blue faces are owned by the current cell, the current cell is a neighbor of the red faces. The coordinates of the barycenter are also printed so that the barycenter can be plotted to the figure. If the barycenter falls outside the face, the cell is convex (as is the case here). If the barycenter seems to fall inside the faces, there is most likely something wrong with the owner/neighborship or the ordering of points on one of the faces so that the intended inside of the cell is actually on the wrong side of one or multiple face surfaces.