<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Thu, Nov 27, 2014 at 7:06 AM, Olivier Bonnefon <span dir="ltr"><<a href="mailto:olivier.bonnefon@avignon.inra.fr" target="_blank">olivier.bonnefon@avignon.inra.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div text="#000000" bgcolor="#FFFFFF">
    <div>Hello,<br>
      <br>
      Thanks you, it works. If I remove the NullSpaceCondition I get the
      correct solution also with Neumann BC. <br>
      From my point of view, the linear system I get is not singular
      because there is a unique solution. Do you agree ?<br></div></div></blockquote><div><br></div><div>Yes, the non-uniqueness is for the Poisson prblem only.</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"><div text="#000000" bgcolor="#FFFFFF"><div>
      Regards,<br>
      Olivier Bonnefon<div><div class="h5"><br>
      <br>
      <br>
      On 11/25/2014 03:01 PM, Matthew Knepley wrote:<br>
    </div></div></div><div><div class="h5">
    <blockquote type="cite">
      <div dir="ltr">
        <div class="gmail_extra">
          <div class="gmail_quote">On Tue, Nov 25, 2014 at 4:08 AM,
            Olivier Bonnefon <span dir="ltr"><<a href="mailto:olivier.bonnefon@avignon.inra.fr" target="_blank">olivier.bonnefon@avignon.inra.fr</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">
              <div text="#000000" bgcolor="#FFFFFF">
                <div>Hello,<br>
                  <br>
                  Thank you for your answer, I agree with you.<br>
                  <br>
                  I have adapted the ex12 example for the system:<br>
                  <br>
                  -\nabla \nabla u + u + f = 0 in \Omega  (1)<br>
                  <br>
                  with f = 4-x^2-y^2<br>
                  The solution is still x^2-y^2.<br>
                  <br>
                  It consists in adding the following gradient function:<br>
                  <br>
                  void g0_uu(const PetscScalar u[], const PetscScalar
                  u_t[], const PetscScalar u_x[], const PetscScalar a[],
                  const PetscScalar a_t[], const PetscScalar a_x[],
                  const PetscReal x[], PetscScalar g0[])<br>
                  {<br>
                    g0[0] = 1.0;<br>
                  }<br>
                  ...<br>
                  //and set gradient<br>
                  ierr = PetscDSSetJacobian(prob, 0, 0, g0_uu, NULL,
                  NULL, g3_uu);CHKERRQ(ierr);<br>
                  ...<br>
                  Of course, I have modified the f0_u function.<br>
                  <br>
                  <br>
                  With Dirichlet BC, I get the solution.<br>
                  <br>
                  With Neumann BC, the solution is still shifted down
                  (-2/3). The problem (1) with Neumann BC has a unique
                  solution.<br>
                  How remove the condition \int_\Omega u = 0 ?<br>
                </div>
              </div>
            </blockquote>
            <div><br>
            </div>
            <div>That condition is one way of imposing boundary
              conditions for pressure. When I call MatSetNullSpace(), I
              am implying</div>
            <div>this condition. You can take out that call, but the
              system will be singular. You would have to add a condition
              on the</div>
            <div>pressure somehow, like fixing it at a point. This tends
              to make the system more ill-conditioned, but if that is
              appropriate</div>
            <div>for you, then you make a similar call to</div>
            <div><br>
            </div>
            <div>      ierr = DMPlexAddBoundary(cdm, user->bcType ==
              DIRICHLET, "wall", user->bcType == NEUMANN ? "boundary"
              : "marker", 0, user->exactFuncs[0], 1, &id,
              user);CHKERRQ(ierr);</div>
            <div><br>
            </div>
            <div>but for field 1. To test , you can jsut change 0 to 1
              in this call. However, this sets the entire boundary, and
              you really only</div>
            <div>need to set the pressure at one point, so you could
              make another label that only has a single point and use
              that instead.</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-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
              <div text="#000000" bgcolor="#FFFFFF">
                <div> Thanks<span><font color="#888888"><br>
                      Olivier Bonnefon</font></span>
                  <div>
                    <div><br>
                      <br>
                      <br>
                      On 11/06/2014 07:14 AM, Matthew Knepley wrote:<br>
                    </div>
                  </div>
                </div>
                <div>
                  <div>
                    <blockquote type="cite">
                      <div dir="ltr">
                        <div class="gmail_extra">
                          <div class="gmail_quote">On Mon, Nov 3, 2014
                            at 9:46 AM, Olivier Bonnefon <span dir="ltr"><<a href="mailto:olivier.bonnefon@avignon.inra.fr" target="_blank">olivier.bonnefon@avignon.inra.fr</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">
                              <div text="#000000" bgcolor="#FFFFFF">
                                <div>Hello,<br>
                                  <br>
                                  Thank for your answer, I'll explain my
                                  trouble:<br>
                                  <br>
                                  My problem is that the BC Neumann
                                  leads to wrong result.<br>
                                  <br>
                                  With Dirichlet BC, I get:<br>
                                  -------------------------------<br>
                                  <br>
                                  > ./ex12 -run_type full
                                  -refinement_limit 0.0    -bc_type
                                  dirichlet -interpolate 0
                                  -petscspace_order 1 -show_initial
                                  -show_solution -dm_plex_print_fem 1<br>
                                  ...<br>
                                  ...<br>
                                  Solution<br>
                                  Vec Object:potential 1 MPI processes<br>
                                    type: seq<br>
                                  0.5<br>
                                  <br>
                                  This result is correct.<br>
                                  <br>
                                  With Neuman BC, I get:<br>
                                  --------------------------------<br>
                                  <br>
                                  > ./ex12 -run_type full
                                  -refinement_limit 0.0    -bc_type
                                  neumann -interpolate 1
                                  -petscspace_order 1 -show_initial
                                  -dm_plex_print_fem 1 -show_solution
                                  -bd_petscspace_order 1
                                  -snes_linesearch_monitor  
                                  -snes_monitor
                                  -ksp_monitor_true_residual
                                  -snes_converged_reason
                                  -ksp_converged_reason<br>
                                  ....<br>
                                  ....<br>
                                  <br>
                                  <br>
                                  Solution<br>
                                  Vec Object:potential 1 MPI processes<br>
                                    type: seq<br>
                                  -0.75<br>
                                  -0.583333<br>
                                  0.0833333<br>
                                  -0.583333<br>
                                  -0.333333<br>
                                  0.416667<br>
                                  0.0833333<br>
                                  0.416667<br>
                                  1.25<br>
                                  <br>
                                  <br>
                                  That is not the values of the solution
                                  x*x+y*y.<br>
                                </div>
                              </div>
                            </blockquote>
                            <div><br>
                            </div>
                            <div>Sorry, this is poor documentation on my
                              part. I will fix it in the example. The
                              Naumann solution</div>
                            <div>explicitly discards the constant part,
                              meaning</div>
                            <div><br>
                            </div>
                            <div>  \int_\Omega u = 0</div>
                            <div><br>
                            </div>
                            <div>If we look at my solution</div>
                            <div><br>
                            </div>
                            <div>  \int^1_0 dx \int^1_0 dy x^2 + y^2 =
                              2/3</div>
                            <div><br>
                            </div>
                            <div>However, this is for the continuum
                              result, whereas we are enforcing this in
                              the discrete case.</div>
                            <div>Thus, what we really get is 0.75, since
                              we are integrating linear patches instead
                              of quadratic</div>
                            <div>patches. After shifting by that, you
                              still do not get exactly x^2 + y^2 since
                              there is some</div>
                            <div>discretization error. If you run with
                              P2 you should get the exact answer,
                              shifted down to eliminate</div>
                            <div>the DC component.</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-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
                              <div text="#000000" bgcolor="#FFFFFF">
                                <div> <br>
                                  I tried many ksp options. <br>
                                  Moreover, the neumann BC with
                                  "-run_type full" is not cover in the
                                  list <a href="https://bitbucket.org/petsc/petsc/src/fced3c3f9e703542693913793d15321603e40fe6/config/builder.py?at=master#cl-257" target="_blank">https://bitbucket.org/petsc/petsc/src/fced3c3f9e703542693913793d15321603e40fe6/config/builder.py?at=master#cl-257</a><br>
                                  <br>
                                  Do you know what is wrong ?<br>
                                  <br>
                                  Thanks,<br>
                                  <br>
                                  Olivier Bonnefon<br>
                                  <br>
                                  On 10/31/2014 06:50 PM, Matthew
                                  Knepley wrote:<br>
                                </div>
                                <blockquote type="cite">
                                  <div dir="ltr">
                                    <div class="gmail_extra">
                                      <div class="gmail_quote">On Fri,
                                        Oct 31, 2014 at 10:43 AM,
                                        Olivier Bonnefon <span dir="ltr"><<a href="mailto:olivier.bonnefon@avignon.inra.fr" target="_blank">olivier.bonnefon@avignon.inra.fr</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">Hello,<br>
                                          <br>
                                          I'm working on the
                                          snes/examples/tutorial/ex12
                                          version 3.5.2.<br>
                                          <br>
                                          I didn't succed to run the
                                          simplest case with Neumann BC:<br>
                                          <br>
                                          ./ex12 -run_type full
                                          -refinement_limit 0.0   
                                          -bc_type neumann -interpolate
                                          1 -petscspace_order 1
                                          -show_initial
                                          -dm_plex_print_fem 1
                                          -show_solution
                                          -bd_petscspace_order 1
                                          -snes_linesearch_monitor
                                          -snes_monitor
                                          -ksp_monitor_true_residual
                                          -snes_converged_reason
                                          -ksp_converged_reason<br>
                                          <br>
                                          This leads to dofs negatives
                                          values.<br>
                                        </blockquote>
                                        <div><br>
                                        </div>
                                        <div>I do not understand what
                                          you mean. Please always mail
                                          the full error message.</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">Do


                                          you know the options to get a
                                          correct result with Neumann BC
                                          ?<br>
                                        </blockquote>
                                        <div><br>
                                        </div>
                                        <div>There are some tests here:</div>
                                        <div><br>
                                        </div>
                                        <div><a href="https://bitbucket.org/petsc/petsc/src/fced3c3f9e703542693913793d15321603e40fe6/config/builder.py?at=master#cl-257" target="_blank">https://bitbucket.org/petsc/petsc/src/fced3c3f9e703542693913793d15321603e40fe6/config/builder.py?at=master#cl-257</a><br>
                                        </div>
                                        <div><br>
                                        </div>
                                        <div>   Matt</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">Regards,<br>
                                          Olivier Bonnefon<br>
                                          <br>
                                        </blockquote>
                                      </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>
                                    <span><font color="#888888"> </font></span></div>
                                  <span><font color="#888888"> </font></span></blockquote>
                                <span><font color="#888888"> <br>
                                    <br>
                                    <pre cols="72">-- 
Olivier Bonnefon
INRA PACA-Avignon, Unité BioSP
Tel: <a href="tel:%2B33%20%280%294%2032%2072%2021%2058" value="+33432722158" target="_blank">+33 (0)4 32 72 21 58</a></pre>
                                  </font></span></div>
                            </blockquote>
                          </div>
                          <br>
                          <br clear="all">
                          <div><br>
                          </div>
                          -- <br>
                          <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>
                      </div>
                    </blockquote>
                    <br>
                    <br>
                    <pre cols="72">-- 
Olivier Bonnefon
INRA PACA-Avignon, Unité BioSP
Tel: <a href="tel:%2B33%20%280%294%2032%2072%2021%2058" value="+33432722158" target="_blank">+33 (0)4 32 72 21 58</a></pre>
                  </div>
                </div>
              </div>
            </blockquote>
          </div>
          <br>
          <br clear="all">
          <div><br>
          </div>
          -- <br>
          <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>
      </div>
    </blockquote>
    <br>
    <br>
    <pre cols="72">-- 
Olivier Bonnefon
INRA PACA-Avignon, Unité BioSP
Tel: <a href="tel:%2B33%20%280%294%2032%2072%2021%2058" value="+33432722158" target="_blank">+33 (0)4 32 72 21 58</a></pre>
  </div></div></div>

</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature">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></div>