<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Thu, Jan 18, 2018 at 6:10 AM, 서승진 (기계항공및원자력공학부) <span dir="ltr"><<a href="mailto:mistloin@unist.ac.kr" target="_blank">mistloin@unist.ac.kr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p style="margin-top:0px;margin-bottom:0px">Dear petsc-user.</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px">Hi. I am trying several parts of example code, (SNES ex12.c : Poisson Problem in 2d and 3d with simplicial finite element)</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px">and I have several problems to understand.
</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px">I appologize to sent a long and boring email to you...</p>
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</p>
<p style="margin-top:0px;margin-bottom:0px"><strong>1) About setting of geometry</strong><br>
</p>
<p style="margin-top:0px;margin-bottom:0px"><img width="320" height="116" id="gmail-m_-9079360143004781812775157_rs|3" style="width: 320px; height: 115.8px;" size="74067" src="cid:009d718e-c50b-4bd9-8d2c-714321b9fc46"></p>
<p style="margin-top:0px;margin-bottom:0px"><img width="470" height="73" id="gmail-m_-9079360143004781812983726_rs|3" style="width: 470px; height: 73.01px;" size="43510" src="cid:7e0f732c-ecad-4ea7-a3f3-8d6a09bc5cc9"></p>
<p style="margin-top:0px;margin-bottom:0px"><img width="385" height="24" id="gmail-m_-9079360143004781812504697_rs|3" style="width: 385px; height: 24.41px;" size="24165" src="cid:40e3a7a8-4191-4693-bc97-84a550d5152f"></p>
<p style="margin-top:0px;margin-bottom:0px">I referred the "DMPlexCreateBoxMesh" function to make simplicial box mesh.
</p>
<p style="margin-top:0px;margin-bottom:0px">I found that lower[] and upper[] are factors to set the size of the box mesh. Is it right?</p>
<p style="margin-top:0px;margin-bottom:0px">Actually, I want to make a rectangular geometry with size of 3m x 1m, and four boundary (two dirichlet and two neumann condition). </p>
<p style="margin-top:0px;margin-bottom:0px">If I wrong, please give me some tip to make a good geometry.</p></div></div></div></blockquote><div><br></div><div>Yes, you can use <span style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">DMPlexCreateBoxMesh() </span>to make that. </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div id="gmail-m_-9079360143004781812divtagdefaultwrapper" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:12pt" dir="ltr"><div id="gmail-m_-9079360143004781812divtagdefaultwrapper" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:12pt" dir="ltr"><p style="margin-top:0px;margin-bottom:0px">
</p>
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</p>
<p style="margin-top:0px;margin-bottom:0px"><strong>2) About application boundary condition</strong><br>
</p>
<p style="margin-top:0px;margin-bottom:0px"><img width="532" height="221" id="gmail-m_-9079360143004781812471282_rs|3" style="width: 532px; height: 220.79px;" size="109380" src="cid:c6eed790-070c-4e66-8dbb-8b461fb06f10"></p>
<p style="margin-top:0px;margin-bottom:0px"><img width="602" height="148" id="gmail-m_-9079360143004781812929361_rs|3" style="width: 602px; height: 148.29px;" size="134256" src="cid:37a6abda-13a5-45bd-b751-2d193f784071"></p>
<p style="margin-top:0px;margin-bottom:0px">I reffered the example "SNES ex69.c" to set a label and condition for the four boundarys.
</p>
<p style="margin-top:0px;margin-bottom:0px">First part of code is about label of boundary condition,</p></div></div></div></blockquote><div><br></div><div>This is wrong. You should not have DMPlexMarkBoundaryFaces() in there. What did you want it to do?</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div id="gmail-m_-9079360143004781812divtagdefaultwrapper" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:12pt" dir="ltr"><div id="gmail-m_-9079360143004781812divtagdefaultwrapper" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:12pt" dir="ltr"><p style="margin-top:0px;margin-bottom:0px"> and second part is about setting of boundary condition.
</p>
<p style="margin-top:0px;margin-bottom:0px">However, due to second part, error occurs.</p></div></div></div></blockquote><div><br></div><div>Always, always, always send the full error message. Otherwise, I am just guessing.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div id="gmail-m_-9079360143004781812divtagdefaultwrapper" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:12pt" dir="ltr"><div id="gmail-m_-9079360143004781812divtagdefaultwrapper" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:12pt" dir="ltr"><p style="margin-top:0px;margin-bottom:0px">
</p>
<p style="margin-top:0px;margin-bottom:0px">Is there any wrong argument?</p></div></div></div></blockquote><div><br></div><div>If they are homogeneous Neumann conditions, there is no need to mark them. If they are inhomogeneous, you</div><div>must specify a part of the weak form, as is done in SNES ex12 and ex77.</div><div><br></div><div>Second, for the Dirichlet conditions, are you sure you only want to constrain the components that I am in ex69?</div><div>What would help is to fully specify your problem, so that we know what you want to do.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div id="gmail-m_-9079360143004781812divtagdefaultwrapper" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:12pt" dir="ltr"><div id="gmail-m_-9079360143004781812divtagdefaultwrapper" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:12pt" dir="ltr"><p style="margin-top:0px;margin-bottom:0px"> Please give me some tip to applied four boundary conditions on the mesh. </p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px"><strong>3) About input parameters of DSSetJacobian()</strong></p>
<p style="margin-top:0px;margin-bottom:0px">In DSSetJacobian (prob, f, g, g0, g1, g2, g3), I have a problem to understand g0~g3
</p>
<p style="margin-top:0px;margin-bottom:0px"> g0 : integrand for test function and basis function</p>
<p style="margin-top:0px;margin-bottom:0px"> g1 : integrand for test function gradient and basis function</p>
<p style="margin-top:0px;margin-bottom:0px"> g2 : integrand for test function and basis function gradient
</p>
<p style="margin-top:0px;margin-bottom:0px"> g3 : integrand for test function gradient and basis function gradient</p>
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</p>
<p style="margin-top:0px;margin-bottom:0px">I have studied the FEM before one month, but I am very confused by above four terms.</p></div></div></div></blockquote><div><br></div><div>There is a short explanation here:</div><div><br></div><div> <a href="http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DT/PetscDSSetJacobian.html">http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DT/PetscDSSetJacobian.html</a></div><div><br></div><div>and here you can see the four terms which are being integrated to arrive at the element matrix:</div><div><br></div><div> <a href="http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DT/PetscFEIntegrateJacobian.html">http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DT/PetscFEIntegrateJacobian.html</a></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div id="gmail-m_-9079360143004781812divtagdefaultwrapper" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:12pt" dir="ltr"><div id="gmail-m_-9079360143004781812divtagdefaultwrapper" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:12pt" dir="ltr">
<p style="margin-top:0px;margin-bottom:0px">I should study this in my self, but I need to some tip or internet address which include a helpful description about above terms.</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px">(I think this issue is not good at this email, but I have been really suffered by above term...) <br>
</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px"><strong>4) About useful tool to visualize the result and geometry<br>
</strong></p>
<p style="margin-top:0px;margin-bottom:0px"><img id="gmail-m_-9079360143004781812img348174" style="max-width: 99.9%;" size="8003" src="cid:80900b60-6b68-4c72-8f3e-df0d475795d7"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px">I also have searched the tool which can express the visualized result and geometry.</p></div></div></div></blockquote><div><br></div><div>I use Paraview from KitWare, which is free. I output HDF5, using the generic PETSc Viewer options detailed in the manual,</div><div><br></div><div> -dm_view hdf5:lap.h5 -vec_view hdf5:lap.h5::append</div><div><br></div><div>and then I automatically create an XDMF file lap.xmf, describing the HDF5, which can be read by Paraview,</div><div><br></div><div> $PETSC_DIR/bin/petsc_gen_xdmf.py lap.h5</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div id="gmail-m_-9079360143004781812divtagdefaultwrapper" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:12pt" dir="ltr"><div id="gmail-m_-9079360143004781812divtagdefaultwrapper" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:12pt" dir="ltr">
<p style="margin-top:0px;margin-bottom:0px">Could you give me a tip to select the visualizing tool for better analysis?</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
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</p>
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</p>
<p style="margin-top:0px;margin-bottom:0px">Thanks you for reading my email.</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px">Best regards,</p>
<p style="margin-top:0px;margin-bottom:0px">Seungjin Seo<br>
</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
</div>
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<div id="gmail-m_-9079360143004781812divRplyFwdMsg" dir="ltr"><font color="#000000" face="Calibri, sans-serif" style="font-size:11pt"><b>보낸 사람:</b> Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>><br>
<b>보낸 날짜:</b> 2018년 1월 16일 화요일 오후 8:48:16<br>
<b>받는 사람:</b> 서승진 (기계항공및원자력공학부)<br>
<b>참조:</b> Smith, Barry F.; <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>제목:</b> Re: [petsc-users] I have a question for PETSc example</font>
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<div class="gmail-m_-9079360143004781812x_gmail_quote">On Mon, Jan 15, 2018 at 8:28 PM, 서승진 (기계항공및원자력공학부) <span dir="ltr">
<<a href="mailto:mistloin@unist.ac.kr" target="_blank">mistloin@unist.ac.kr</a>></span> wrote:<br>
<blockquote class="gmail-m_-9079360143004781812x_gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left:1px solid rgb(204,204,204)">
<div dir="ltr">
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<p style="margin-top:0px;margin-bottom:0px">sorry, I mean that</p>
<p style="margin-top:0px;margin-bottom:0px"><span><strong>My geometry is a rectangle</strong>.</span></p>
<p style="margin-top:0px;margin-bottom:0px">That means, geometry is just rectangle box shape with four boundary.</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px">My question is that, how can I set the four boundary condition individually in example 12 of SNES?</p>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>You put a different marker on each side. The easiest way to do it is to give the</div>
<div><br>
</div>
<div> -dm_plex_separate_marker</div>
<div><br>
</div>
<div>option. This is done in SNES ex69.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail-m_-9079360143004781812x_gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left:1px solid rgb(204,204,204)">
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<p style="margin-top:0px;margin-bottom:0px">(I think that the boundary condition should be added in right side of the weak form, where load vector f and test function term is included. However, in example of petsc, boundary condition is applied as general
form.)</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px">Seungjin Seo<br>
</p>
</div>
<hr style="width:98%;display:inline-block">
<div id="gmail-m_-9079360143004781812x_gmail-m_7279604020525382251divRplyFwdMsg" dir="ltr"><font color="#000000" face="Calibri, sans-serif" style="font-size:11pt"><span class="gmail-m_-9079360143004781812x_gmail-"><b>보낸 사람:</b> Smith, Barry F. <<a href="mailto:bsmith@mcs.anl.gov" target="_blank">bsmith@mcs.anl.gov</a>><br>
</span><b>보낸 날짜:</b> 2018년 1월 15일 월요일 오후 11:06:18<br>
<b>받는 사람:</b> 서승진 (기계항공및원자력공학부)<br>
<b>참조:</b> Smith, Barry F.; <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">
petsc-users@mcs.anl.gov</a>
<div>
<div class="gmail-m_-9079360143004781812x_gmail-h5"><br>
<b>제목:</b> Re: [petsc-users] I have a question for PETSc example</div>
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The term "rectangular mesh" usually refers to a "structured grid mesh" so it is not clear if you truly need an unstructured grid. Take a look at src/snes/examples/tutorials/ex<wbr>19.c
<br>
<br>
Barry<br>
<br>
<br>
> On Jan 15, 2018, at 1:03 AM, 서승진 (기계항공및원자력공학부) <<a href="mailto:mistloin@unist.ac.kr" target="_blank">mistloin@unist.ac.kr</a>> wrote:<br>
> <br>
> Dear PETSc-user<br>
> <br>
> I am Seungjin Seo, researcher of Korean Advanced Institute of Science and Technology, South Korea.<br>
> <br>
> I am tring to understand the ex12.c in SNES examples, and I have a problem...<br>
> Could you give me some advise? Is there any good description or materials for PetscFE and DMPlex?<br>
> <br>
> I will make a code with unstructured grid with PetscFE and SNES. My geometry is a rectangle mesh (the size is not fixed so I think this is unstructured grid).<br>
> The equation is <br>
> I will set boundry conditions as follow;<br>
> 1. (Top-side boundary) Neumann boundary<br>
> 2. (Bottom-side boundary) Neumann boundary<br>
> 3. (Left-side boundary) Dirichlet boundary<br>
> 4. (Right-side boundary) Dirichlet boundary<br>
> <br>
> In example ex12.c in SNES, load vector f is defiend as f_0, and neumann boundary condition is defined as f_bd_0. f_1 means the test function gradient term. The example set general type of neumann boundary condition on f_bd_0, but I want to set each boundary
condition individually. Could you give me some advise?<br>
> <br>
> Thansk for reading my email.<br>
> <br>
> Best regard,<br>
> Seungjin Seo<br>
> <br>
> <br>
> <br>
> 보낸 사람: Smith, Barry F. <<a href="mailto:bsmith@mcs.anl.gov" target="_blank">bsmith@mcs.anl.gov</a>><br>
> 보낸 날짜: 2017년 12월 21일 목요일 오후 3:46:42<br>
> 받는 사람: 서승진 (기계항공및원자력공학부)<br>
> 참조: <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
> 제목: Re: [petsc-users] I have a question for PETSc example<br>
> <br>
> <br>
> In deed you can, yes many PETSc examples only feature a single field for simplicity, but multiple fields are fine. You simple provide your FormFunction and FormJacobian to handle both degrees of freedom per cell/node at the same time. You use SNES or TS
depending on if your problem is time dependent and then use -pc_type lu to start. Once you have the physics correct come back and ask us about optimizing the linear solver with preconditioners; but until you have the physics correct it is absurd to waste time
worrying about making the linear solver efficient. What you want to do, many people do and is not a big deal.<br>
> <br>
> Barry<br>
> <br>
> <br>
> > On Dec 21, 2017, at 12:27 AM, 서승진 (기계항공및원자력공학부) <<a href="mailto:mistloin@unist.ac.kr" target="_blank">mistloin@unist.ac.kr</a>> wrote:<br>
> > <br>
> > Dear PETSc-user<br>
> > <br>
> > <br>
> > I am Seungjin Seo, researcher of Korean Advanced Institute of Science and Technology, South Korea.<br>
> > <br>
> > <br>
> > <br>
> > I am trying to solve thermal and fluid equations within a porous structure.<br>
> > The thermal equation includes a non-linear term of pressure and the fluid equation has a boundary condition using temperature gradient.<br>
> > Is there any way I can solve these two equations at the same time, instead of solving temperature first with previous pressure distribution and then pressure and update temperature?<br>
> > Many examples solve only one PDF instead of coupling several physics.<br>
> > Please recommend me which solver is appropriate for my case?<br>
> > <br>
> > Best regards,<br>
> > Seungjin Seo<br>
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<div>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</div>
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<div><a href="http://www.caam.rice.edu/~mk51/" target="_blank">https://www.cse.buffalo.edu/~<wbr>knepley/</a><br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>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</div><div><br></div><div><a href="http://www.caam.rice.edu/~mk51/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div>
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