[CIG-SHORT] Issues with cohesive cells in VTK output

[Ravi Kanda]

Thanks, Brad.  Please see below...

> The cohesive cells for kinematic (prescribed slip) ruptures add twice as 
> many nodes, because we add a node for the Lagrange multipliers. 

I went through your implementation outline in Ch. & of the User's manual.  I do 
see that each "kinematic" cohesive cell would add four nodes.  I was confused 
because I thought you were outputting ONLY displacements in the VTK file. 
Please also see my last comment below....


> On the fault, there is fault normal motion where the two sides of the 
> fault move together (so there is no opening or slip in the fault 
> perpendicular direction). This is expected. In the case of the twotri3 
> example, the triangles create the slip by undergoing rigid body 
> rotations, so the result may not look like what you expect, but the 
> solution is correct.

I missed the +/-Z camera orientation there - sorry.  Yes, it does make sense 
that there are fault perpendicular displacements in order to prevent void 
generation.  Does this mean that the illustration in Figure 5.8 of User's Manual 
should be updated (p. 48, TwoQuad4 section: "Color contours and vectors of 
displacement for the kinematic fault example")?  In that figure, the 
displacement vectors are fault parallel.  I was trying to reconcile my output 
with that figure.


> I have never tried probing with ParaView or MayaVi. I suspect the 
> inclusion of the forces associated with the Lagrange multipliers is 
> causing problems. To test this you can try setting the values in the VTK 
> output associated with Lagrange multipliers to zero and see if the 
> probing works.

As I mentioned in my last e-mail, when I look at the ascii VTK output from the 
Line Probe Filter, the interpolation seemed to be OK, but Paraview 2.6.1 (which 
I was using before) could not render the resulting XY-Plots.  I have now 
switched to Paraview 3.2.1, which does the trick.

BTW, in the "twotri3" example, the vector component values listed for the 
Lagrange Multipliers ("nodes" not in the connectivity array) - under both Point 
Data VECTOR & SCALAR attributes - are all close to zero (only the x-components 
are non-zero, but only ~ 1e-19).  In the "twoquad4" case, I can get rid of the 
"third" vector when I zero out these forces.  I guess that takes care of the 
"mysterious" third vector I was seeing in the plots.


> Since we remove the cohesive cells from the VTK output (because VTK 
> doesn't understand cohesive cells), you can zero out the DOF by setting 
> all DOF not associated with a cell to zero. This can be done in two 
> lines of Python code if you get the cells and displacements into Python.

That was what I was thinking of doing if Paraview 3.2.1 had not worked.  I agree 
this is a pretty straightforward fix.

I am attaching the VTK output files for the 2D two-cell examples to this e-mail. 
  When you say you "remove the cohesive cells from the VTK output", do you mean 
just in the connectivity section of the VTK file [where nodes 5 & 7 (tri3) or 7 
& 9 (quad4) are not used]?  Because, the coordinates for the cohesive cells seem 
to be listed under the Dataset POINTS section (the two fault nodes are repeated 
thrice).  Also, all 8 POINTS defined for "twotri3"  (and all 10 for "twoquad4") 
in the VTK output files have corresponding displacement values under the VECTOR 
& SCALAR Dataset attributes.  Do you mean that you are not listing the cohesive 
cell under the CELLS or CELL_TYPES sections [but are including its nodes under 
the POINTS and VECTOR/SCALAR attribute sections]?  Maybe I am missing something 
here....

I am also trying to understand why the "RGB-Alpha" values under the Point Data 
SCALAR Lookup Table have "serial" numbers starting from 2 in the "R" column and 
the vector components in the "G", "B" & "Alpha" columns.  This assignment makes 
"Alpha" = 0 (transparent scalar rendition?).  I would have thought the Point 
Data SCALAR Lookup Table will have RGB values scaled by the magnitude of the 
vector at each point and "Alpha" of 1.0 for each node of the mesh for scalar 
data to be visible.  Is there something I am not getting here?

Maybe all this will become clear with your next documentation release and the 
updated output scheme for the next Pylith release.

Again, thanks for your time!
Ravi.


---------------------------------------------------------------------
Ravi Kanda
Seismological Laboratory, MC 252-21
Division of Geological and Planetary Sciences
California Institute of Technology

1200 E. California Blvd., Pasadena, CA 91125
Phone: 626-395-6971, Fax: 626-564-0715
Web Page: http://www.gps.caltech.edu/~rkanda

----------------------------------------------------------------------

For a human being, the unexamined life is not worth living - SOCRATES

----------------------------------------------------------------------
-------------- next part --------------
# vtk DataFile Version 2.0
Simplicial Mesh Example
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 8 double
-0.5 -0.5 0.0
0.5 -0.5 0.0
-0.5 0.5 0.0
0.5 0.5 0.0
0.5 -0.5 0.0
0.5 -0.5 0.0
-0.5 0.5 0.0
-0.5 0.5 0.0
CELLS 2 8
3  0 4 6
3  1 3 2
CELL_TYPES 2
5
5
POINT_DATA 8
VECTORS displacements_t0.000000 double
0 0 0.0
-0.00707107 -6.85885e-19 0.0
6.85885e-19 0.00707107 0.0
0 0 0.0
-4.37493e-19 -0.00707107 0.0
1.05162e-19 0 0.0
0.00707107 2.17539e-18 0.0
1.05162e-19 0 0.0
SCALARS displacements_verify_t0 double 4
LOOKUP_TABLE default
2 0 0 0.0
3 -0.00707107 -6.85885e-19 0.0
4 6.85885e-19 0.00707107 0.0
5 0 0 0.0
6 -4.37493e-19 -0.00707107 0.0
7 1.05162e-19 0 0.0
8 0.00707107 2.17539e-18 0.0
9 1.05162e-19 0 0.0
CELL_DATA 2
SCALARS replacedCells double 1
LOOKUP_TABLE default
1
-1
-------------- next part --------------
# vtk DataFile Version 2.0
Simplicial Mesh Example
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 10 double
-2 -1 0.0
-2 1 0.0
0 -1 0.0
0 1 0.0
2 -1 0.0
2 1 0.0
0 -1 0.0
0 -1 0.0
0 1 0.0
0 1 0.0
CELLS 2 10
4  0 2 3 1
4  4 5 8 6
CELL_TYPES 2
9
9
POINT_DATA 10
VECTORS displacements_t0.000000 double
0 0 0.0
0 0 0.0
-0.00214286 -0.005 0.0
0.00214286 -0.005 0.0
0 0 0.0
0 0 0.0
-0.00214286 0.005 0.0
-0.00142857 9.11773e-19 0.0
0.00214286 0.005 0.0
-0.00142857 -9.22264e-19 0.0
SCALARS displacements_verify_t0 double 4
LOOKUP_TABLE default
2 0 0 0.0
3 0 0 0.0
4 -0.00214286 -0.005 0.0
5 0.00214286 -0.005 0.0
6 0 0 0.0
7 0 0 0.0
8 -0.00214286 0.005 0.0
9 -0.00142857 9.11773e-19 0.0
10 0.00214286 0.005 0.0
11 -0.00142857 -9.22264e-19 0.0
CELL_DATA 2
SCALARS replacedCells double 1
LOOKUP_TABLE default
-1
1