<div dir="ltr">On Sun, Mar 3, 2013 at 7:03 PM, Dharmendar Reddy <span dir="ltr"><<a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Sorry, I will try to present the problem in more detial. <br>So i am trying to mesh a material region. The material is usually a crystal with atoms located as per the lattice defining the crystal. See for example the attached image which has silicon atoms (spheres) in the crystal unit cell which is a cuboid. <br>
<br>Now if i have a cuboid region with 10 unit cells each in x, y and z direction. I need to mesh this region such that I have mesh nodes at atom locations. The can be more mesh nodes than the atom locations. <br></blockquote>
<div><br></div><div style>I believe there is a way to do this in TetGen, but I had not added that to the interface. I will</div><div style>look at it. I think you would just add these as isolated vertices to the boundary DM you pass</div>
<div style>into DMPlexGenerate().</div><div style><br></div><div style> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="gmail_quote">On Sun, Mar 3, 2013 at 5:45 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div>On Sun, Mar 3, 2013 at 6:41 PM, Dharmendar Reddy <span dir="ltr"><<a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a>></span> wrote:<br></div><div class="gmail_extra">
<div class="gmail_quote"><div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Let say I create triangular mesh in a square: (0,0) (0,1) (1,1) (0,1)<br>I want (0,0.25) and (0.25,0) to be among the mesh nodes. It can have other nodes. <br>
</blockquote><div><br></div></div><div>These explanations are too short. From the above, all I understand is that you would get</div><div>a line between (0, 1/4) and (1/4, 0).</div><div><br></div><div> Matt</div><div><div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote">On Sun, Mar 3, 2013 at 5:29 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>On Sun, Mar 3, 2013 at 5:04 PM, Dharmendar Reddy <span dir="ltr"><<a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a>></span> wrote:<br>
</div><div class="gmail_extra"><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello,<div><br> We use cratisian mesh for certain problems only. The user gives the mesh file as one of the inputs. I do not know a-priori what mesh is created. <br>
<br>On a related note, I am solving a system of equations where i need to use a fine cartisian mesh for one equation (Schrodinger) but i would prefer a coarse traiangular or tetrahedral element mesh for another eqaution(Poisson). Is there an interface to interpolate data from one mesh to another? <br>
</div></blockquote><div><br></div><div>There is an interface, which is just a Mat, but there is no infrastructure for calculating it.</div><div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
If i create a DM with a coarse mesh, Can i give the mesh a set of vertices such that after re meshing the DM has the given vertices as mesh nodes ? I tried using the gmsh to create a mesh with give set of vertices inside a region but had no success. <br>
</blockquote><div><br></div></div><div>I do not understand the question.</div><div><div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks<br>Reddy<br><br><div class="gmail_quote">On Sun, Mar 3, 2013 at 3:44 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div>On Sun, Mar 3, 2013 at 3:48 PM, Dharmendar Reddy <span dir="ltr"><<a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a>></span> wrote:<br></div><div class="gmail_extra">
<div class="gmail_quote"><div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">So i should use petsc-dev ? I will try that. <br><br>I there any way i can have access to submesh? Consider a this scenario.<br>
I have a two dimensional mesh in a rectangle with a uniform deltaX and deltaY gridding. Is there any way i can get submesh at say x = (i-1)*deltaX where say i = 1 to N. The dofs on the submesh will should be mapped to dofs on the original mesh. The submesh in this case will be a 1D mesh along y-axis. <br>
</blockquote><div><br></div></div><div>1) If you have a Cartesian mesh, use DMDA. This is no point in an unstructured mesh.</div><div><br></div><div>2) Yes, you can extract a submesh based upon labeled vertices using DMPlexCreateSubmesh(). It will have</div>
<div> a map between points in the submesh and original mesh.</div><div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I can create each DM with input celllist and create maps after that but i am wondering if this can be done via DMgetsubDM kind of call ?<br>
</blockquote><div><br></div></div><div><div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Thanks<br>Reddy <br><br><div class="gmail_quote">
On Sun, Mar 3, 2013 at 2:11 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>On Sun, Mar 3, 2013 at 2:37 PM, Dharmendar Reddy <span dir="ltr"><<a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a>></span> wrote:<br>
</div><div class="gmail_extra"><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Hello,<div><br> Thanks. I will have the code compiled with-cxx and with-sieve.<br>
The error is understandable when i look at the following line from meshcreate.c<br><pre width="80"><a name="13d32b615c8adfcc_13d32a582275dce8_13d32a17e41bacbd_13d32976da79d166_13d32494fcf7d8b7_13d3236f585336e3_13d32039261cf032_13d31e20075baf66_13d31c2c0871858d_line312">312: </a> <font color="#4169E1">if</font> (interpolate) {<a href="http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/SETERRQ.html#SETERRQ" target="_blank">SETERRQ</a>(comm, PETSC_ERR_SUP, <font color="#666666">"Interpolation (creation of faces and edges) is not yet supported."</font>);}<br>
<br><font face="arial,helvetica,sans-serif">Any idea if this feature will be implimented? I am trying to import mesh from gmsh. <br>I have a Fortran code which will genrate list for faces and edges for a given mesh. <br>
Is there a DMMEsh interface through which i can input list of edges and faces ?<br></font></pre></div></blockquote><div><br></div><div>DMMesh was an initial implementation of these ideas, but did not interface well with</div>
<div>solvers, so it has been rewritten in C as DMPlex. The interface is almost exactly the</div><div>same, and if you want increased functionality I would encourage you to switch. For</div><div>example, DMMeshCreateMeshFromAdjacency() becomes</div>
<div><br></div><div> DMPlexCreateFromCellList()</div><div><br></div><div>and you can follow this with</div><div><br></div><div> DMInterpolate()</div><div><br></div><div>to automatically create the edges and faces.</div>
<div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<pre width="80"><font face="arial,helvetica,sans-serif">Thanks<br>Reddy<br></font></pre><br><br><div class="gmail_quote">On Sun, Mar 3, 2013 at 12:23 AM, Satish Balay <span dir="ltr"><<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">BTW: I don't get compile errors with this code using petsc-3.3 built with:<br>
<br>
--with-clanguage=cxx --with-sieve=1 --with-boost=1<br>
<br>
[the code fails to run though..]<br>
<br>
Satish<br>
<br>
---------<br>
<br>
asterix:/home/balay/download-pine>make PETSC_DIR=/home/balay/petsc-dist-test PETSC_ARCH=asterix64-sieve petscDMTest_v2<br>
/home/balay/soft/linux64/mpich2-1.1/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -I/home/balay/petsc-dist-test/include -I/home/balay/petsc-dist-test/asterix64-sieve/include -I/home/balay/petsc-dist-test/include/sieve -I/home/balay/soft/linux64/mpich2-1.1/include -I/home/balay/soft/mpich2-1.5/include -o petscDMTest_v2.o petscDMTest_v2.F90<br>
/home/balay/soft/linux64/mpich2-1.1/bin/mpif90 -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -o petscDMTest_v2 petscDMTest_v2.o -Wl,-rpath,/home/balay/petsc-dist-test/asterix64-sieve/lib -L/home/balay/petsc-dist-test/asterix64-sieve/lib -lpetsc -lX11 -lpthread -llapack -lblas -lm -Wl,-rpath,/home/balay/soft/mpich2-1.5/lib -L/home/balay/soft/mpich2-1.5/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.7.2 -L/usr/lib/gcc/x86_64-redhat-linux/4.7.2 -lmpichf90 -lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lgcc_s -ldl<br>
/usr/bin/rm -f petscDMTest_v2.o<br>
asterix:/home/balay/download-pine>./petscDMTest_v2<br>
[0]PETSC ERROR: --------------------- Error Message ------------------------------------<br>
[0]PETSC ERROR: No support for this operation for this object type!<br>
[0]PETSC ERROR: Interpolation (creation of faces and edges) is not yet supported.!<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 6, unknown<br>
[0]PETSC ERROR: See docs/changes/index.html for recent updates.<br>
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.<br>
[0]PETSC ERROR: See docs/index.html for manual pages.<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: ./petscDMTest_v2 on a asterix64 named asterix by balay Sun Mar 3 00:21:29 2013<br>
[0]PETSC ERROR: Libraries linked from /home/balay/petsc-dist-test/asterix64-sieve/lib<br>
[0]PETSC ERROR: Configure run at Sun Mar 3 00:15:25 2013<br>
[0]PETSC ERROR: Configure options --with-mpi-dir=/home/balay/soft/linux64/mpich2-1.1 --with-shared-libraries=1 --with-clanguage=cxx --with-sieve=1 PETSC_ARCH=asterix64-sieve --with-boost=1<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: DMMeshCreateMeshFromAdjacency() line 312 in /home/balay/petsc-dist-test/src/dm/impls/mesh/meshcreate.c<br>
Surcessfully Loaded mesh into DM<br>
asterix:/home/balay/download-pine><br>
<div><div><br>
<br>
<br>
<br>
<br>
On Sat, 2 Mar 2013, Satish Balay wrote:<br>
<br>
> Fortran compiler doesn't care about presence or absence of interface<br>
> defintions. If they exist - then it does extra prototype checks. If<br>
> they don't exist - it assumes f77 and chugs along].<br>
><br>
> Did you build petsc with sieve [and cxx]? send make.log for this<br>
> petsc build. Also what do you get for:<br>
><br>
> nm -Ao libpetsc.a |grep -i DMMeshCreateMeshFromAdjacency<br>
><br>
> You can followup this issue [with logs] on petsc-maint.<br>
><br>
> Satish<br>
><br>
><br>
> On Sat, 2 Mar 2013, Dharmendar Reddy wrote:<br>
><br>
> > As you said, I do not need, PETSC_USE_FORTRAN_INTERFACES. The interface to<br>
> > dmmeshcreatefromadjacency is not defined in<br>
> ><br>
> > finclude/ftn-custom/petscdmmesh.h90<br>
> ><br>
> > it is only defined in<br>
> ><br>
> > finclude/ftn-auto/petscdmmesh.h90<br>
> ><br>
> ><br>
> > On Sat, Mar 2, 2013 at 7:51 PM, Dharmendar Reddy <<a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a>>wrote:<br>
> ><br>
> > > Hello,<br>
> > > Sorry, I was going to create a test case. Anyways here is the<br>
> > > error message<br>
> > ><br>
> > > petscDMTest_v2.o: In function `MAIN__':<br>
> > > petscDMTest_v2.F90:(.text+0x354): undefined reference to<br>
> > > `dmmeshcreatemeshfromad<br>
> > > jacency_'<br>
> > > make: [testDMMesh] Error 1 (ignored)<br>
> > ><br>
> > > I have attached a test case and makefile. make all should gen rate the<br>
> > > executable.<br>
> > ><br>
> > > Thanks<br>
> > > Reddy<br>
> > ><br>
> > ><br>
> > > On Sat, Mar 2, 2013 at 7:10 PM, Satish Balay <<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>> wrote:<br>
> > ><br>
> > >> On Sat, 2 Mar 2013, Dharmendar Reddy wrote:<br>
> > >><br>
> > >> > Hello,<br>
> > >> > I am trying to use DMMeshCreateMeshFromAdjacency in a Fortran<br>
> > >> code.<br>
> > >> > I get undefined reference error.<br>
> > >><br>
> > >> What error? please copy/paste<br>
> > >><br>
> > >> > I include the following file in my program<br>
> > >> > #include "finclude/petsc.h90"<br>
> > >> ><br>
> > >> > I see that fortran interface to DMMeshCreateMeshFromAdjacency is defined<br>
> > >> > only in<br>
> > >> ><br>
> > >> > finclude/ftn-auto/petscdmmesh.h90<br>
> > >> ><br>
> > >> > I am not able to figure out if PETSC_USE_FORTRAN_INTERFACES is defined.<br>
> > >> I<br>
> > >> > did not compile the code. I am runing the code on TACC stampede. I tried<br>
> > >> > adding<br>
> > >> ><br>
> > >> > #define PETSC_USE_FORTRAN_INTERFACES 1<br>
> > >> > in my program before the petsc inlcude line but i still get error.<br>
> > >><br>
> > >> 1. again 'get error' doesn't tell us anything.<br>
> > >><br>
> > >> And you shouldn't need PETSC_USE_FORTRAN_INTERFACES to use<br>
> > >> DMMeshCreateMeshFromAdjacency<br>
> > >><br>
> > >> Satish<br>
> > >><br>
> > >> ><br>
> > >> ><br>
> > >> > Thanks<br>
> > >> > Reddy<br>
> > >> ><br>
> > >> ><br>
> > >><br>
> > >><br>
> > ><br>
> > ><br>
> > > --<br>
> > > -----------------------------------------------------<br>
> > > Dharmendar Reddy Palle<br>
> > > Graduate Student<br>
> > > Microelectronics Research center,<br>
> > > University of Texas at Austin,<br>
> > > 10100 Burnet Road, Bldg. 160<br>
> > > MER 2.608F, TX 78758-4445<br>
> > > e-mail: <a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a><br>
> > > Phone: <a href="tel:%2B1-512-350-9082" value="+15123509082" target="_blank">+1-512-350-9082</a><br>
> > > United States of America.<br>
> > > Homepage: <a href="https://webspace.utexas.edu/~dpr342" target="_blank">https://webspace.utexas.edu/~dpr342</a><br>
> > ><br>
> ><br>
> ><br>
> ><br>
> ><br>
><br>
><br>
<br><span><font color="#888888">
</font></span></div></div></blockquote></div><span><font color="#888888"><br><br clear="all"><br>-- <br>-----------------------------------------------------<br>Dharmendar Reddy Palle<br>Graduate Student<br>Microelectronics Research center,<br>
University of Texas at Austin,<br>
10100 Burnet Road, Bldg. 160<br>MER 2.608F, TX 78758-4445<br>e-mail: <a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a><br>Phone: <a href="tel:%2B1-512-350-9082" value="+15123509082" target="_blank">+1-512-350-9082</a><br>
United States of America.<br>Homepage: <a href="https://webspace.utexas.edu/~dpr342" target="_blank">https://webspace.utexas.edu/~dpr342</a><br>
</font></span></blockquote></div></div></div><span><font color="#888888"><br><br clear="all"><span><font color="#888888"><div><br></div>-- <br>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
</font></span></font></span></div></div><span><font color="#888888">
</font></span></blockquote></div><span><font color="#888888"><br><br clear="all"><br>-- <br>-----------------------------------------------------<br>Dharmendar Reddy Palle<br>Graduate Student<br>Microelectronics Research center,<br>
University of Texas at Austin,<br>
10100 Burnet Road, Bldg. 160<br>MER 2.608F, TX 78758-4445<br>e-mail: <a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a><br>Phone: <a href="tel:%2B1-512-350-9082" value="+15123509082" target="_blank">+1-512-350-9082</a><br>
United States of America.<br>Homepage: <a href="https://webspace.utexas.edu/~dpr342" target="_blank">https://webspace.utexas.edu/~dpr342</a><br>
</font></span></blockquote></div></div></div><div><div><br><br clear="all"><span><font color="#888888"><div><br></div>-- <br>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
</font></span></div></div></div></div><span><font color="#888888">
</font></span></blockquote></div><span><font color="#888888"><br><br clear="all"><br>-- <br>-----------------------------------------------------<br>Dharmendar Reddy Palle<br>Graduate Student<br>Microelectronics Research center,<br>
University of Texas at Austin,<br>
10100 Burnet Road, Bldg. 160<br>MER 2.608F, TX 78758-4445<br>e-mail: <a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a><br>Phone: <a href="tel:%2B1-512-350-9082" value="+15123509082" target="_blank">+1-512-350-9082</a><br>
United States of America.<br>Homepage: <a href="https://webspace.utexas.edu/~dpr342" target="_blank">https://webspace.utexas.edu/~dpr342</a><br>
</font></span></blockquote></div></div></div><div><div><br><br clear="all"><span><font color="#888888"><div><br></div>-- <br>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
</font></span></div></div></div></div><span><font color="#888888">
</font></span></blockquote></div><span><font color="#888888"><br><br clear="all"><br>-- <br>-----------------------------------------------------<br>Dharmendar Reddy Palle<br>Graduate Student<br>Microelectronics Research center,<br>
University of Texas at Austin,<br>
10100 Burnet Road, Bldg. 160<br>MER 2.608F, TX 78758-4445<br>e-mail: <a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a><br>Phone: <a href="tel:%2B1-512-350-9082" value="+15123509082" target="_blank">+1-512-350-9082</a><br>
United States of America.<br>Homepage: <a href="https://webspace.utexas.edu/~dpr342" target="_blank">https://webspace.utexas.edu/~dpr342</a><br>
</font></span></blockquote></div></div></div><div><div><br><br clear="all"><span class="HOEnZb"><font color="#888888"><div><br></div>-- <br>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
</font></span></div></div></div></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><br>-- <br>-----------------------------------------------------<br>Dharmendar Reddy Palle<br>Graduate Student<br>Microelectronics Research center,<br>
University of Texas at Austin,<br>
10100 Burnet Road, Bldg. 160<br>MER 2.608F, TX 78758-4445<br>e-mail: <a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a><br>Phone: <a href="tel:%2B1-512-350-9082" value="+15123509082" target="_blank">+1-512-350-9082</a><br>
United States of America.<br>Homepage: <a href="https://webspace.utexas.edu/~dpr342" target="_blank">https://webspace.utexas.edu/~dpr342</a><br>
</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>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>