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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">That would great if it allows elements with mixed faces,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thank you<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">-Hassan<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Matthew Knepley [mailto:knepley@gmail.com]
<br>
<b>Sent:</b> Thursday, June 29, 2017 10:36 AM<br>
<b>To:</b> Hassan Raiesi <Hassan.Raiesi@aero.bombardier.com><br>
<b>Cc:</b> petsc-users@mcs.anl.gov<br>
<b>Subject:</b> Re: [petsc-users] specifying vertex coordinates using DMPlexCreateFromCellListParallel<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Thu, Jun 29, 2017 at 9:32 AM, Hassan Raiesi <<a href="mailto:Hassan.Raiesi@aero.bombardier.com" target="_blank">Hassan.Raiesi@aero.bombardier.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Ok,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The problem is that the faceSizes varies for pyramids and prisms, they have faces with variable number
of nodes (i.e for pyramids, four triangular faces and one quad face, this I don’t see how to specify?</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">What if I report all faces as quad faces, for triangular faces, there would be a repeated vertex, would
it make any problem?</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">No, you are right, that will not work. The whole interpolation code would have to be rewritten to allow faces with<o:p></o:p></p>
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<p class="MsoNormal">variable size. Its not hard, but it is time-consuming. Since I am moving this summer, this will not be done in a timely<o:p></o:p></p>
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<p class="MsoNormal">manner unfortunately.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Thanks,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Matt<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thank you</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">-Hassan</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Matthew Knepley [mailto:<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>]
<br>
<b>Sent:</b> Thursday, June 29, 2017 10:12 AM<br>
<b>To:</b> Hassan Raiesi <<a href="mailto:Hassan.Raiesi@aero.bombardier.com" target="_blank">Hassan.Raiesi@aero.bombardier.com</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] specifying vertex coordinates using DMPlexCreateFromCellListParallel</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Thu, Jun 29, 2017 at 8:59 AM, Hassan Raiesi <<a href="mailto:Hassan.Raiesi@aero.bombardier.com" target="_blank">Hassan.Raiesi@aero.bombardier.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Matthew,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Not sure if I understood completely, I have the ordering according to the CGNS standard for all cells
in the mesh, or I can change it if needed, but I don’t understand what you mean by reporting all faces as ordered vertices? Do you mean I just define the face connectivity?Could you explain a bit more?</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">For a triangular prism, you would add the case in GetRawFaces() for dim 3, coneSize 6. Lets look at a triangle (dim 2, coneSize 3)<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">
<a href="https://bitbucket.org/petsc/petsc/src/5ebd2cd705b0ffa5a27aee8a08f86795d413b548/src/dm/impls/plex/plexinterpolate.c?at=master&fileviewer=file-view-default#plexinterpolate.c-63" target="_blank">
https://bitbucket.org/petsc/petsc/src/5ebd2cd705b0ffa5a27aee8a08f86795d413b548/src/dm/impls/plex/plexinterpolate.c?at=master&fileviewer=file-view-default#plexinterpolate.c-63</a><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">You see that it returns 3 groups of 2 vertices, which are the edges. For a tetrahedron<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <a href="https://bitbucket.org/petsc/petsc/src/5ebd2cd705b0ffa5a27aee8a08f86795d413b548/src/dm/impls/plex/plexinterpolate.c?at=master&fileviewer=file-view-default#plexinterpolate.c-101" target="_blank">https://bitbucket.org/petsc/petsc/src/5ebd2cd705b0ffa5a27aee8a08f86795d413b548/src/dm/impls/plex/plexinterpolate.c?at=master&fileviewer=file-view-default#plexinterpolate.c-101</a><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">it returns 4 groups of 3 vertices, which are the faces. Note that all faces should be oriented such that the normal is outward.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Thanks,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Matt<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thank you</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">-Hassan</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Matthew Knepley [mailto:<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>]
<br>
<b>Sent:</b> Tuesday, June 27, 2017 1:54 PM<br>
<b>To:</b> Hassan Raiesi <<a href="mailto:Hassan.Raiesi@aero.bombardier.com" target="_blank">Hassan.Raiesi@aero.bombardier.com</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] specifying vertex coordinates using DMPlexCreateFromCellListParallel</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Tue, Jun 27, 2017 at 11:30 AM, Hassan Raiesi <<a href="mailto:Hassan.Raiesi@aero.bombardier.com" target="_blank">Hassan.Raiesi@aero.bombardier.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I meant the interpolation,
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">DMPlex supports those element shapes, however, there are two problems, one, “DMPlexBuildFromCellList_Parallel”
does not take mixed elements (numCorners must be constant for all elements in current implementation), that was easy to fix,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I already extended DMPlexBuildFromCellList_Parallel_Private to take elements with different shapes,
then I realized the interpolation does not work when the mesh has elements other than tets and hex.</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Okay, here is what is needed. You need to<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> a) prescribe an order for the vertices in a prism/pyramid (all input cells must have this order)<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> b) report all faces as sets of ordered vertices<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> - You have to order them matching the Plex vertex order for the lower dimensional shape<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> - They should be oriented as to have outward facing normal<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Regarding the interpolation, I also noticed that the memory requirement is huge if I load the whole
mesh on one core and interpolate (I cannot interpolate a mesh with 9M tets on a machine with 128GB of memory, it ran out of memory, I’ll try to run with petsc memory logs and send).
</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I am not sure what the upper limit is, but in a 3D mesh you could have many times the number of cells in faces and edges. Note that<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">you would need --with-64-bit-indices to go beyond 4GB.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">is there anyways to interpolate the mesh after DMPlexdistribute? The code crashes if I move DMPlexInterpolate
to after calling DMPlexdistribute., I guess what is needed is a DMPlexInterpolate on already distributed meshes.</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">This should work. Maybe try a small example? If that crashes, just send it.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Thanks,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Matt<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thank you</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">-Hassan</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Matthew Knepley [mailto:<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>]
<br>
<b>Sent:</b> Tuesday, June 27, 2017 11:53 AM<br>
<b>To:</b> Hassan Raiesi <<a href="mailto:Hassan.Raiesi@aero.bombardier.com" target="_blank">Hassan.Raiesi@aero.bombardier.com</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] specifying vertex coordinates using DMPlexCreateFromCellListParallel</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Tue, Jun 27, 2017 at 10:08 AM, Hassan Raiesi <<a href="mailto:Hassan.Raiesi@aero.bombardier.com" target="_blank">Hassan.Raiesi@aero.bombardier.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Great, It’s clear now
</span><span style="font-size:11.0pt;font-family:Wingdings;color:#1F497D">J</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">,
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">One more question, any plan to support other element shapes (prism and pyramid) in 3D?, </span>DMPlexGetRawFaces_Internal
o<span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">nly supports tets and hexs in 3D, can prisms and pyramids be used as degenerate hexahedrons?</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">It depends on what you mean "support". Right now, we can represent these shapes in Plex. However, if you<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">want mesh interpolation to work, then yes you need to extend GetRawFaces() to understand that shape. If<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">you want them read out of a file format, other than Gmsh, we would likely have to extend that as well. These<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">are straightforward once I understand what exactly you want to do.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Thanks,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Matt<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thank you</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">-Hassan</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<pre><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></pre>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Matthew Knepley [mailto:<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>]
<br>
<b>Sent:</b> Tuesday, June 27, 2017 10:17 AM<br>
<b>To:</b> Hassan Raiesi <<a href="mailto:Hassan.Raiesi@aero.bombardier.com" target="_blank">Hassan.Raiesi@aero.bombardier.com</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] specifying vertex coordinates using DMPlexCreateFromCellListParallel</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Tue, Jun 27, 2017 at 9:12 AM, Hassan Raiesi <<a href="mailto:Hassan.Raiesi@aero.bombardier.com" target="_blank">Hassan.Raiesi@aero.bombardier.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks for your reply,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Is there any example where each rank owns more than 1 element, i.e for the simple mesh here(attached
png file), how should I pack and pass the coordinates of the vertices owned by rank0, rank1</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="FR-CA" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Rank0:numcells = 2; num nodes=4, cells=[154 245] , nodes=[1 5 2 4]</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">nodes = 1245</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">vertex coords: in what node order ?</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">[coords_n1 coords_n2 coords_n4 coords_n5] or</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">[coords_n2 coords_n4 coords_n1 coords_n5] or …..?</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="FR-CA" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">rank1: numcells = 2; num nodes=2, cells=[532 635], nodes=[6 3]</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">vertexcoords [how to pack the nodes coords here?]</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">should it be [x6y6 x3y3] or [x3y3 x6y6]? In what order?</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I think there is a misunderstanding here.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">There is NO connection between the cell order and the vertex order. Each process gets a contiguous<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">set of cells (in the global numbering) and a contiguous set of vertices (in the global numbering). These<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">two are NOT related. We then move the vertices to the correct processes. In this way, we can load<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">completely in parallel, without requiring any setup in the mesh file.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">If you are worried, you can always arrange the order of vertices to "match" the order of cells.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Thanks,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Matt<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">thanks</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Matthew Knepley [mailto:<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>]
<br>
<b>Sent:</b> Sunday, June 25, 2017 1:04 PM<br>
<b>To:</b> Hassan Raiesi <<a href="mailto:Hassan.Raiesi@aero.bombardier.com" target="_blank">Hassan.Raiesi@aero.bombardier.com</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] specifying vertex coordinates using DMPlexCreateFromCellListParallel</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Tue, Apr 11, 2017 at 9:21 AM, Hassan Raiesi <<a href="mailto:Hassan.Raiesi@aero.bombardier.com" target="_blank">Hassan.Raiesi@aero.bombardier.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hello,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I’m trying to use
<span style="font-family:Consolas">DMPlexCreateFromCellListParallel</span> to create a DM from an already partitioned mesh,
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">It requires an array of numVertices*spaceDim numbers, but how should one order the coordinates of the vertices?<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Global order. Here is the idea. You must read the file in chunks so that each proc can read its own chunk in parallel<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">without talking to anyone else.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">we only pass the global vertex numbers using ‘const int cells[]’ to define the cell-connectivity, so passing the vertex coordinates in local ordering wouldn’t make sense?<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Yes.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">If it needs to be in global ordering, should I sort the global index of the node numbers owned by each rank (as they wont be continuous).<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Nope.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Thanks,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Matt<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thank you<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hassan Raiesi,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Bombardier Aerospace
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><cite><span style="font-family:"Calibri",sans-serif"><a href="http://www.bombardier.com" target="_blank">www.bombardier.com</a></span></cite><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><br>
<br clear="all">
<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">--
<o:p></o:p></p>
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<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="http://www.caam.rice.edu/~mk51/" target="_blank">http://www.caam.rice.edu/~mk51/</a><o:p></o:p></p>
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</div>
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</blockquote>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><br>
<br clear="all">
<o:p></o:p></p>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">--
<o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="http://www.caam.rice.edu/~mk51/" target="_blank">http://www.caam.rice.edu/~mk51/</a><o:p></o:p></p>
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</div>
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</blockquote>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><br>
<br clear="all">
<o:p></o:p></p>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">--
<o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="http://www.caam.rice.edu/~mk51/" target="_blank">http://www.caam.rice.edu/~mk51/</a><o:p></o:p></p>
</div>
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</div>
</div>
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</blockquote>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><br>
<br clear="all">
<o:p></o:p></p>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">--
<o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="http://www.caam.rice.edu/~mk51/" target="_blank">http://www.caam.rice.edu/~mk51/</a><o:p></o:p></p>
</div>
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</blockquote>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><br>
<br clear="all">
<o:p></o:p></p>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">--
<o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="http://www.caam.rice.edu/~mk51/" target="_blank">http://www.caam.rice.edu/~mk51/</a><o:p></o:p></p>
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</blockquote>
</div>
<p class="MsoNormal"><br>
<br clear="all">
<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal">-- <o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><a href="http://www.caam.rice.edu/~mk51/" target="_blank">http://www.caam.rice.edu/~mk51/</a><o:p></o:p></p>
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