<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 28 Jun 2016, at 23:45, Matthew Knepley <<a href="mailto:knepley@gmail.com" class="">knepley@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class="gmail_extra"><div class="gmail_quote">On Tue, Jun 28, 2016 at 6:47 PM, Sander Arens<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:Sander.Arens@ugent.be" target="_blank" class="">Sander.Arens@ugent.be</a>></span><span class="Apple-converted-space"> </span>wrote:<br class=""><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 dir="ltr" class="">Please reply to all, so that other people can also read this discussion on the mailing list.<br class=""><br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div class="">I do currently have problems understanding the inner workings of PetscFE. For example how the element matrix is assembled. As far as I could deduce from your example, g3_uu_3d is the fourth-order elasticity tensor which means that we should form the double-dot product of it with the strain for it to be the integrand of the gradient of the basis functions ( int_omega [g3:epsilon]•grad(v) d omega). So for a linear elastic problem, according to my understanding, g3<span class="Apple-converted-space"> </span><u class="">should</u><span class="Apple-converted-space"> </span>be the elasticity tensor and g0,g1,g2 = NULL if there is no volumetric force. And the residual should be f0 = 0 ; f1= the cauchy stress tensor.</div><div class=""><br class=""></div></blockquote><div class="">Yes, that seems correct. </div></div></blockquote><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 dir="ltr" class=""><div class=""><br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">I also have troubles understanding how to apply boundary conditions. There seems to be the concept of DMAddBoundary() and the PetscDSSetBdJacobian() and PetscDSSetBdResidual(). I struggle to understand what sets them apart from each other. My impression is that DMAddBoundary() is for Dirichlet and Neumann conditions and that PetscDSSetBdJacobian() and PetscDSSetBdResidual() are for BC types that do not fall in those categories?</blockquote><div class="">Note that you can also use PetscDSAddBoundary now (if you use the master branch). DMAddBoundary is basically used to tell which boundary region to apply which bc. If it's a Dirichlet bc you have to provide a function to prescribe the values on the boundary, if it's a Neumann bc you just give it NULL. PetscDSSetBdJacobian() and PetscDSSetBdResidual() are for Neumann bcs.<span class="Apple-converted-space"> </span><br class="">The reason why there's this difference for Dirichlet and Neumann bcs is because for finite elements you need to assemble stuff for non-zero Neumann bcs while for Dirichlet you set some dofs to some prescribed value.<br class=""></div></div></div></blockquote></div></div></div></div></blockquote>Ok, that makes sense. I did not find documentation on PetscDSAddBoundary but I managed to use the old functions to impose the correct BC.<br class=""><blockquote type="cite" class=""><div class=""><div dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><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;"><div dir="ltr" class=""><div class=""><div class=""><br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div class="">ex77 works with the options you provided me with. However the solver does not seem to converge.</div></blockquote><div class="">What do you mean that it works but it doesn't converge? Did you use all the options I provided you? In case not, you should send the output of -snes_view.<br class=""></div></div></div></div></blockquote><div class=""><br class=""></div><div class="">The output of -ksp_view -ksp_monitor_true_residual -ksp_converged_reason</div></div></div></div></div></blockquote><div>I must have made some changes without noticing when i tried to follow the workings of the ex77 sourcecode, my apologies. I copied the example again and it runs and converges fine now with the options you provided. If I change -dim to 2 however it does not converge and / or produce the correct Jacobian. But as far as I understand, ex77 is not intended to run in 2D.</div><blockquote type="cite" class=""><div class=""><div dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class="gmail_extra"><div class="gmail_quote"><div class=""> </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 dir="ltr" class=""><div class=""><div class=""><div class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">The problem I have with the documentation online so far is that I fail to fully understand how to apply petscFE. I did for example not know that you had to set the order of the finite element space and I have the feeling that there is much more I am missing.<span class="Apple-converted-space"> </span><br class=""></blockquote></div><br class=""></div><div class="">I don't really understand what you mean with "applying PetscFE".<br class=""></div><div class="">I think the simplest way to learn how to use it is to start from one of the examples and if you don't understand what a function does you look it up in the documentation. If you want to see what kind of options there are for some object, for example petscspace, you add "-help|grep petscspace" to the command line.<br class=""></div></div></div></blockquote><div class=""><br class=""></div><div class="">PetscFE is a Ciarlet triple (P, P', K) meaning a PetscSpace for the primal space P, PetscDualSpace for the dual space P', and reference</div><div class="">cell K which is a DM. The main function of PetscFE is to tabulate the basis at quadrature points, and to act with dual space basis vectors</div><div class="">on functions.</div><div class=""><br class=""></div></div></div></div></div></blockquote>I have troubles to understand what you mean with “tabulate the basis” and I am not too familiar with the concept of dual spaces. My intention is to use the PetscFE infrastructure to construct the global Jacobian to give to the nonlinear solver. As a simple example, I tried using snes for solving a linear elastic problem in 2D and PetscFE to create the Jacobian and to impose the BC.</div><div>I do now have a program that runs and gives the correct solution if I use the matrix-free SNES solver. -snes_type test gives a ratio of 0.45 however and I am almost certain that the stiffness tensor I create is correct (I checked the assembly algorithm in numpy and it gives the expected cauchy stress tensor). The only explanation I have left is some misunderstanding on my side about how the double contraction works in Petsc.</div><div><br class=""></div><div>Thank you,</div><div><br class=""></div><div>M. Hartig<br class=""><blockquote type="cite" class=""><div class=""><div dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class="gmail_extra"><div class="gmail_quote"><div class=""> <span class="Apple-converted-space"> </span>Thanks,</div><div class=""><br class=""></div><div class=""> Matt</div><div class=""> </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 dir="ltr" class=""><div class=""><div class=""></div><div class="">Thanks,<br class=""></div><div class="">Sander<span class="Apple-converted-space"> </span><br class=""></div></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On 28 June 2016 at 17:47,<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:rickcha@googlemail.com" target="_blank" class="">rickcha@googlemail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br class=""><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 style="word-wrap: break-word;" class="">Yes, that was vague, I should have formulated that better. <div class="">What I’m trying to accomplish is writing a FEM code to calculate deformation and stress of structure. As a first step analysing a linear elastic and static problem in 2D, which I plan to extend to a elastic-plastic transient analysis for a 3D case. <div class=""><br class=""></div><div class="">I do currently have problems understanding the inner workings of PetscFE. For example how the element matrix is assembled. As far as I could deduce from your example, g3_uu_3d is the fourth-order elasticity tensor which means that we should form the double-dot product of it with the strain for it to be the integrand of the gradient of the basis functions ( int_omega [g3:epsilon]•grad(v) d omega). So for a linear elastic problem, according to my understanding, g3<span class="Apple-converted-space"> </span><u class="">should</u><span class="Apple-converted-space"> </span>be the elasticity tensor and g0,g1,g2 = NULL if there is no volumetric force. And the residual should be f0 = 0 ; f1= the cauchy stress tensor.</div><div class=""><br class=""></div><div class="">I also have troubles understanding how to apply boundary conditions. There seems to be the concept of DMAddBoundary() and the PetscDSSetBdJacobian() and PetscDSSetBdResidual(). I struggle to understand what sets them apart from each other. My impression is that DMAddBoundary() is for Dirichlet and Neumann conditions and that PetscDSSetBdJacobian() and PetscDSSetBdResidual() are for BC types that do not fall in those categories?</div><div class=""><br class=""></div><div class="">ex77 works with the options you provided me with. However the solver does not seem to converge.</div><div class=""><br class=""></div><div class="">The problem I have with the documentation online so far is that I fail to fully understand how to apply petscFE. I did for example not know that you had to set the order of the finite element space and I have the feeling that there is much more I am missing. </div><div class=""><br class=""></div><div class="">Thank you for your precious time,</div><div class=""><br class=""></div><div class="">M. Hartig</div><div class=""><div class="h5"><div class=""><div class=""><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On 28 Jun 2016, at 14:30, Sander Arens <<a href="mailto:Sander.Arens@ugent.be" target="_blank" class="">Sander.Arens@ugent.be</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">What are you trying to do with it? I don't think there's more documentation on how to use PetscFE than what's already in the online documentation and in the examples.<br class=""></div>What do you mean with "grasp the concept"?<br class=""><br class=""></div>Thanks,<br class=""></div>Sander<br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On 27 June 2016 at 17:41,<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:rickcha@googlemail.com" target="_blank" class="">rickcha@googlemail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br class=""><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 style="word-wrap: break-word;" class="">That did do the trick with the examples, thank you. I am still struggling with my own simple example however. Is there any documentation available on how to use petscFE? I could not find anything besides the three examples. And I yet have to grasp the concept.<div class=""><br class=""></div><div class=""><br class=""></div><div class="">Thanks in advance,</div><div class="">M. Hartig<div class=""><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On 27 Jun 2016, at 15:49, Sander Arens <<a href="mailto:Sander.Arens@ugent.be" target="_blank" class="">Sander.Arens@ugent.be</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><div class=""><div class="">I think you forgot to set the order of the finite element spaces, which default to 0. Does it work if you try for example ex77 with the following options found<span class="Apple-converted-space"> </span><a href="https://bitbucket.org/petsc/petsc/src/8bc5349a152c81f25b59a9592e1e5936c01866af/config/builder.py?at=master&fileviewer=file-view-default#builder.py-562" target="_blank" class="">here?</a><br class=""><br class=""></div>Thanks,<br class=""></div>Sander<br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On 27 June 2016 at 15:28,<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:rickcha@googlemail.com" target="_blank" class="">rickcha@googlemail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br class=""><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;">Dear Petsc developer team,<br class=""><br class="">while learning the ways of the petscFE I came across a curiosity I’d like to point out to you. The Jacobians that are created from the petscFE object seem to have only 0-entries (apart from the obviously empty regions) in examples 12 and 77. That might be due to a limited understanding from my side on how exactly petscFE and the mentioned examples work, but it struck me as unusual.<br class=""><br class="">Thanks in advance,<br class=""><br class="">M. Hartig</blockquote></div><br class=""></div></div></blockquote></div><br class=""></div></div></div></div></blockquote></div><br class=""></div></div></blockquote></div><br class=""></div></div></div></div></div></div></div></blockquote></div><br class=""></div></blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>--<span class="Apple-converted-space"> </span><br class=""><div class="gmail_signature" data-smartmail="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 class="">-- Norbert Wiener</div></div></div></div></blockquote></div><br class=""></body></html>