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<p class="MsoNormal"><span style="color:#1F497D">Hi again,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">I have examined my mesh (which you can find in the attachment) with Salome and gmsh – there are no flat faces at the boundaries. But there are line elements! So I am relieved as far as my worried
questions in the last mail are concerned – mesher and the FEM solver are doing their work as they should.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">But IMO it makes no sense to compute the derivatives over the line elements and average it with the derivatives over the face elements. Is it possible that this is exactly what happens in the gradient
filter (and in the computederivative + celldatatopointdata filters)? If so, why? And can that be switched off, as IMO it should?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Or, to put it differently: Apparently ParaView does not make a difference between a line and a face. Why is this so? Shouldn’t it do that?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Thanks for a clarification,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Matthias<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Zenker, Dr. Matthias
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<b>Gesendet:</b> Dienstag, 27. September 2016 17:00<br>
<b>An:</b> 'Moreland, Kenneth'<br>
<b>Cc:</b> paraview@paraview.org<br>
<b>B</b></span><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">etreff:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> AW: [Paraview] Gradient filter: boundary effects<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Ken,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US">thank you for pointing this out! I was not aware that boundary lines are also inifinitely flat cells. This seems true for all boundaries, also the internal boundaries between the two faces.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The question for me is now: Is this normal, or does that mean that the whole FEM simulation is corrupt? Should I have a mesh that does not have those line cells? The mesh has been calculated by the Salome mesher, which
uses netgen. The boundaries were declared as groups. The mesh has then been exported as unv, imported by Elmer which has done the FEM calculations, and saved the results as vtu. If those line cells represent a problem, where in this chain do I have to look
for the mistake?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Matthias<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Moreland, Kenneth [<a href="mailto:kmorel@sandia.gov">mailto:kmorel@sandia.gov</a>]
<br>
<b>Gesendet:</b> Dienstag, 27. September 2016 16:41<br>
<b>An:</b> Zenker</span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">, Dr. Matthias<br>
<b>Cc:</b> <a href="mailto:paraview@paraview.org">paraview@paraview.org</a><br>
<b>Betreff:</b> Re: [Paraview] Gradient filter: boundary effects<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US">Matthias,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">As I suspected, your data has some boundary elements that are throwing off the gradient calculation. The data you sent me has line cells around the boarder of the data. The easiest way to see these line cells is to go
to the Properties panel and change the “Line Width” parameter to something large. (Attached is an image that shows the boundary cells by setting the line width to 20.)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">So in the example you gave, the gradient is computed correctly in the triangles, but the finite differences computation for the line cells can only compute the gradient in the direction of the line. Thus, there is no
y component for the gradient in these line cells. Because the line cells share the points of the triangles along the bottom, the gradient average becomes incorrect.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-Ken<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="color:black">From: </span></b><span lang="EN-US" style="color:black">"Zenker, Dr. Matthias" <<a href="mailto:Matthias.Zenker@erbe-med.com">Matthias.Zenker@erbe-med.com</a>><br>
<b>Date: </b>Tuesday, September 27, 2016 at 9:51 AM<br>
<b>To: </b>"Moreland, Kenneth" <<a href="mailto:kmorel@sandia.gov">kmorel@sandia.gov</a>><br>
<b>Cc: </b>"<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>" <<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>><br>
<b>Subject: </b>[EXTERNAL] AW: [Paraview] Gradient filter: boundary effects</span><span lang="EN-US" style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Hi Ken,</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">if you want to have a look – here is a simple test file. At the bottom side, there are 4 adjacent cells having grad(y)~7900 from computederivatives, but all 3 nodes on the bottom side have grad(y)
~ 5300 from celldatatopointdata.</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Thanks,</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Matthias</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Moreland, Kenneth [<a href="mailto:kmorel@sandia.gov">mailto:kmorel@sandia.gov</a>]
<br>
<b>Gesendet:</b> Dienstag, 27. September 2016 15:40<br>
<b>An:</b> Zenker, Dr. Matthias<br>
<b>Cc:</b> <a href="mailto:paraview@paraview.org">paraview@paraview.org</a><br>
<b>Betreff:</b> Re: [Paraview] Gradient filter: boundary effects</span><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Matthias,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">If values are being pulled from 7900 units down to 5300 units, there must be some neighbor with lower values. Why that is happening for you I cannot say without looking at your data. Perhaps on the boundary there are
some malformed or 2D cells with invalid gradients.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-Ken<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="color:black">From: </span></b><span lang="EN-US" style="color:black">"Zenker, Dr. Matthias" <<a href="mailto:Matthias.Zenker@erbe-med.com">Matthias.Zenker@erbe-med.com</a>><br>
<b>Date: </b>Tuesday, September 27, 2016 at 9:06 AM<br>
<b>To: </b>"Moreland, Kenneth" <<a href="mailto:kmorel@sandia.gov">kmorel@sandia.gov</a>><br>
<b>Cc: </b>"<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>" <<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>><br>
<b>Subject: </b>[EXTERNAL] AW: [Paraview] Gradient filter: boundary effects</span><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Hi Ken,</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">what I don’t understand is that the cell gradients are correct, but their average at the border is not. (Example: All cell gradients adjacent to one node at the border have approx. 7900 units in
y direction, the node has approx. 5300)</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">So it seems I cannot determine the gradient in the postprocessing step, but have to calculate it in the FEM solver (where I do get correct results now – I didn’t initially, which was the reason why
I tried it with ParaView).</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Thank you anyway, I have learned new bits of ParaView again (which is great software BTW)!</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Have a nice holiday (if I interpret your autoreply correctly)!</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Matthias</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Moreland, Kenneth [<a href="mailto:kmorel@sandia.gov">mailto:kmorel@sandia.gov</a>]
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<b>Gesendet:</b> Dienstag, 27. September 2016 14:36<br>
<b>An:</b> Zenker, Dr. Matthias; <a href="mailto:paraview@paraview.org">paraview@paraview.org</a><br>
<b>Betreff:</b> Re: [Paraview] Gradient filter: boundary effects</span><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">You could run the results through the point to cell filter, but that would give you the same answer as the gradient of unstructured dataset filter with the faster approximation option on.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-Ken<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="color:black">From: </span></b><span lang="EN-US" style="color:black">"Zenker, Dr. Matthias" <<a href="mailto:Matthias.Zenker@erbe-med.com">Matthias.Zenker@erbe-med.com</a>><br>
<b>Date: </b>Tuesday, September 27, 2016 at 8:28 AM<br>
<b>To: </b>"Moreland, Kenneth" <<a href="mailto:kmorel@sandia.gov">kmorel@sandia.gov</a>>, "<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>" <<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>><br>
<b>Subject: </b>[EXTERNAL] AW: [Paraview] Gradient filter: boundary effects</span><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">Hi Kenneth,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">thank you for the quick answer!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">So it seems not that trivial to calculate an electrical field between a rod and a plane given the potential…<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The compute derivatives filter does not give me the problem at the boundary indeed. Instead it gives a value per cell, not per node, which does not look nice.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Is there a friendly filter or switch which would give me the smoothed surface representation back?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Matthias<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Moreland, Kenneth [<a href="mailto:kmorel@sandia.gov">mailto:kmorel@sandia.gov</a>]
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<b>Gesendet:</b> Dienstag, 27. September 2016 14:14<br>
<b>An:</b> Zenker, Dr. Matthias; <a href="mailto:paraview@paraview.org">paraview@paraview.org</a><br>
<b>Betreff:</b> Re: [Paraview] Gradient filter: boundary effects</span><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Matthias,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The gradient is estimated with finite differences. Thus, it is not wholly unexpected that there could be differences at the boundaries. However, the algorithm does
<i>not</i> assume zero for adjacent cells at the boundaries.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The way the unstructured gradient filter works is that it computes the local gradient in each cell at each of the cell’s points. Then for every point it averages the gradient from all incident cells at that point. (If
you have the Faster Approximation option on, then the filter only computes one gradient per cell in the center and averages those. Faster, but more artifacts, particularly at the edges.)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">If this averaging is causing you an issue, you might try the Compute Derivatives filter. This does a wholly local operation within each cell, so you should not see any artifacts (unless the field itself has artifacts
at the boundaries).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-Ken<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="color:black">From: </span></b><span lang="EN-US" style="color:black">ParaView <<a href="mailto:paraview-bounces@paraview.org">paraview-bounces@paraview.org</a>> on behalf of "Zenker, Dr. Matthias" <<a href="mailto:Matthias.Zenker@erbe-med.com">Matthias.Zenker@erbe-med.com</a>><br>
<b>Date: </b>Tuesday, September 27, 2016 at 5:45 AM<br>
<b>To: </b>"<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>" <<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>><br>
<b>Subject: </b>[EXTERNAL] [Paraview] Gradient filter: boundary effects</span><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">when I use the gradient filter (unstructured dataset), I observe edge effects which are IMO unphysical. For the nodes on the outer boundary of my domain, the gradient magnitude is smaller than I would expect. The behavior
is like the filter tries to use the adjacent nodes to calculate the gradient, and since there are none outside the domain, it assumes zero and finds a lower result.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">If so, I would consider this a bug – is there a fix or workaround?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Matthias<o:p></o:p></span></p>
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