[petsc-users] SLEPc iterative solver does not converge but ARPACK does

Hello, i'm using PETSc and SLEPc in Python. I'm trying to calculate eigenvalues for the stokes equations with the following code SHIFT = SLEPc.ST().create() SHIFT.setType(SHIFT.Type.SINVERT) E = SLEPc.EPS().create() E.setST(SHIFT) E.setOperators(K, M) E.setDimensions(25, PETSc.DECIDE)

Re: [petsc-users] SLEPc iterative solver does not converge but ARPACK does

to Which.TARGET_MAGNITUDE). Jose El 6/7/2015, a las 13:26, Julian Andrej j...@tf.uni-kiel.de escribió: Hello, i'm using PETSc and SLEPc in Python. I'm trying to calculate eigenvalues for the stokes equations with the following code SHIFT = SLEPc.ST().create() SHIFT.setType(SHIFT.Type.SINVERT) E

Re: [petsc-users] Parallel ODE solver

There are a variety of algorithms for ODE/DAEs in the PetscTS implementation. For examples see e.g. http://www.mcs.anl.gov/petsc/petsc-current/src/ts/examples/tutorials/index.html Sundials is also capable of parallel solving, even from the Matlab sundialsTB interface, as far as i know. On Tue,

Re: [petsc-users] working-with-submatrix

Especially in eigenproblems, I would suggest using Matthews approach, or applying Dirichlet boundary conditions via the penalty method (penalized robin for example). This would avoid spurious eigenvalues which occur when you use MatZeroRows(). On Wed, Oct 7, 2015 at 2:17 PM, Matthew Knepley

[petsc-users] Solving eigenproblems in the form of Stokes equations

Hi, i'm trying to solve a generalized eigenvalue problem which is the stokes equations discretized by finite elements (with fenics) and producing a banded matrix (reordered structure) of the well known block form [NQ] [QT 0] The domain is the unit square with dirichlet boundary condition

Re: [petsc-users] Solving eigenproblems in the form of Stokes equations

On Sun, Jul 12, 2015 at 1:07 PM, Matthew Knepley knep...@gmail.com wrote: On Fri, Jul 10, 2015 at 4:28 PM, Julian Andrej j...@tf.uni-kiel.de wrote: Hi, i'm trying to solve a generalized eigenvalue problem which is the stokes equations discretized by finite elements (with fenics

[petsc-users] Mass matrix with PetscFE

a mass matrix (the inner product of the function space and the test space)? Regards Julian Andrej

Re: [petsc-users] Mass matrix with PetscFE

reasonable output to stdout. But saving the matrix and analysing it in matlab, results in an all zero matrix. PetscViewerBinaryOpen(PETSC_COMM_WORLD, "Mout",FILE_MODE_WRITE, ); MatView(M, viewer); Any hints? On 24.02.2016 13:58, Matthew Knepley wrote: On Wed, Feb 24, 2016 at 6:47

Re: [petsc-users] Mass matrix with PetscFE

a smaller mass matrix (which is not of size A). Maybe this helps in the discussion. Relevant code starts at line 455. On 2016-02-24 15:03, Julian Andrej wrote: Thanks Matt, I attached the modified example. the corresponding code (and only changes to ex12) is starting at line 832. It also seems

Re: [petsc-users] Mass matrix with PetscFE

Matt On Feb 25, 2016 2:04 AM, "Julian Andrej" <j...@tf.uni-kiel.de> wrote: After a bit of rethinking the problem, the discrepancy between the size of matrix A and the mass matrix M arises because of the Dirichlet boundary conditions. So why aren't the BCs not imposed on the

Re: [petsc-users] A question about DMPlexDistribute

Hi, take a look at slide 10 of [1], there is visually explained what the overlap between partitions is. [1] https://www.archer.ac.uk/training/virtual/files/2015/06-PETSc/slides.pdf On Thu, Aug 11, 2016 at 8:48 AM, leejearl wrote: > Hi, all: > I want to use PETSc to build

Re: [petsc-users] Mass matrix with PetscFE

Hey, yes, this issue was resolved a few weeks after the mail. I just tried again after some DMPlex commits ;). Thanks! On Thu, Jul 21, 2016 at 3:04 PM, Matthew Knepley <knep...@gmail.com> wrote: > On Mon, Mar 7, 2016 at 6:21 PM, Julian Andrej <j...@tf.uni-kiel.de> wrote: >&

Re: [petsc-users] [RFC] Docs: TeX -> HTML

Small suggestion (it also came up at the Meeting) What is the opinion on a "main" documentation in markdown/restructured text or something like that? The conversion from one of these formats into pdf or any other format like html is handled by a variety of tools pretty well. On Sat, Jul 23, 2016

Re: [petsc-users] Segmentation faults: Derived types

You need to generate the TAGS file first using make alletags in ${PETSC_DIR}. Then you need to visit the tags table using emacs. On Sun, Aug 21, 2016 at 12:09 PM, Santiago Ospina De Los Rios wrote: > wow, what a dumb mistake. thank you very much! > > Since you've noticed

Re: [petsc-users] A question about DMPlexDistribute

strata of sizes (5253, 10352, 5298) >> >> Thanks, >> >> Matt >> >>> >>> On 2016年08月11日 23:29, Matthew Knepley wrote: >>> >>> On Thu, Aug 11, 2016 at 3:14 AM, leejearl <leeje...@126.com> wrote: >>>> >&

Re: [petsc-users] PetscFE and TS

like M and J for the stiff ODE with nontrivial mass matrix (see manual section of TS -> F = M u' - f) but i think this should be obsolete right? Appreciate your help. Regards Julian On Mon, Nov 7, 2016 at 10:49 AM, Julian Andrej <j...@tf.uni-kiel.de> wrote: > Hello, > >

Re: [petsc-users] PetscFE and TS

of ideas on my side though :) On Wed, Nov 9, 2016 at 2:33 PM, Matthew Knepley <knep...@gmail.com> wrote: > On Wed, Nov 9, 2016 at 12:32 AM, Julian Andrej <j...@tf.uni-kiel.de> wrote: >> >> I tested a few other things and it turned out that the function added >> as a

Re: [petsc-users] PetscFE and TS

AM, Matthew Knepley <knep...@gmail.com> wrote: >> >> On Wed, Nov 9, 2016 at 7:52 AM, Julian Andrej <j...@tf.uni-kiel.de> wrote: >>> >>> I tried the example with different signs for the forcing, so this >>> might be a mistake by me, yes. it doesn

[petsc-users] PetscFE and TS

Hello, i'm using PetscFE in combination with SNES and a hand written backward euler solver right now and like to hand that over to TS. I have been fiddling quite a while getting TS to work with PetscFE and have encountered a few unclarities. I have looked at examples which are outdated i guess

Re: [petsc-users] Autoconf tests

libMesh provides a m4 test for finding the PETSc library. You can find it here https://github.com/libMesh/libmesh/blob/master/m4/petsc.m4 On Wed, Oct 12, 2016 at 3:18 PM, jeremy theler wrote: > I once made a quick hack, maybe you can start your dirty work from here > >

[petsc-users] PetscFE questions

Hi, i have general question about PetscFE. When i want to assemble certain parts of physics separately, how can i do that? I basically want to assemble matrices/vectors from the weak forms on the same DM (and avoid copying the DM) and use them afterwards. Is there a convenient way for doing that?

Re: [petsc-users] Using PETSc solvers and preconditioners with mfem

on github and was stating that there is some intention to get MFEM working with PETSc but there is no specific timeframe. Regards Julian Andrej On Tue, Oct 25, 2016 at 6:30 PM, Abdullah Ali Sivas <abdullahasi...@gmail.com> wrote: > I will check that. I am preallocating but it may be

Re: [petsc-users] Using PETSc solvers and preconditioners with mfem

timeframe. >> > > There’s currently an open pull request for PETSc solvers inside the private > MFEM repo. > However, I don’t know when the code, if merged, will be released. > > >> Regards >> Julian Andrej >> >> On Tue, Oct 25, 2016 at 6:30 PM, Abdu

Re: [petsc-users] PetscFE questions

On Thu, Oct 20, 2016 at 5:18 PM, Matthew Knepley <knep...@gmail.com> wrote: > On Thu, Oct 20, 2016 at 9:42 AM, Julian Andrej <j...@tf.uni-kiel.de> wrote: >> >> Thanks for the suggestion. I guess DMCreateSubDM can work, but is >> cumbersome to handle for the norma

Re: [petsc-users] PetscFE and TS

-defined state) Norm of matrix ratio 0.0203667, difference 3.06481 (constant state -1.0) Norm of matrix ratio 0.0203667, difference 3.06481 (constant state 1.0) Thanks again On Mon, 14 Nov 2016 07:01:09 -0600 Matthew Knepley <knep...@gmail.com> wrote: > On Mon, Nov 14, 2016 at 3:24 AM, Juli

Re: [petsc-users] PetscFE and TS

com> wrote: > On Mon, Nov 14, 2016 at 7:35 AM, Matthew Knepley <knep...@gmail.com> > wrote: > > > On Mon, Nov 14, 2016 at 3:24 AM, Julian Andrej <j...@tf.uni-kiel.de> > > wrote: > > > >> I think i'm understanding the concept now. Although i h

Re: [petsc-users] PetscFE and TS

t 9:38 AM, Jed Brown <j...@jedbrown.org> wrote: >> >> Matthew Knepley <knep...@gmail.com> writes: >> >> > On Thu, Nov 10, 2016 at 1:31 AM, Julian Andrej <j...@tf.uni-kiel.de> >> > wrote: >> > >> >> I'm getting the correct solut

Re: [petsc-users] PetscFE questions

rds Julian On Wed, Oct 19, 2016 at 11:51 AM, Matthew Knepley <knep...@gmail.com> wrote: > On Tue, Oct 18, 2016 at 7:38 AM, Julian Andrej <j...@tf.uni-kiel.de> wrote: >> >> Hi, >> >> i have general question about PetscFE. When i want to assemble certai

Re: [petsc-users] PetscFE questions

Yeah, thanks for pointing out my mistake. Next time i'm going to think one more time before writing ;) On Fri, Oct 21, 2016 at 12:17 PM, Lawrence Mitchell <lawrence.mitch...@imperial.ac.uk> wrote: > >> On 21 Oct 2016, at 08:26, Julian Andrej <j...@tf.uni-kiel.de> wrote: >&

Re: [petsc-users] SLEPc: Convergence Problems

See this description from Jed http://scicomp.stackexchange.com/questions/3298/appropriate-space-for-weak-solutions-to-an-elliptical-pde-with-mixed-inhomogeneo/3300#3300. In a simpler way you could just scale your diagonal entries which are 1 at the moment with a value that is out of your interest

Re: [petsc-users] SLEPc: Convergence Problems

Do you precondition your eigenvalue problem? If not, you should. Let us know what structure your matrix has and which blocks (if there are any) include which physics. Regards Julian On Mon, Oct 17, 2016 at 5:30 PM, Christopher Pierce wrote: > I've implemented my application

[petsc-users] TAO: Finite Difference vs Continuous Adjoint gradient issues

Hello, we prepared a small example which computes the gradient via the continuous adjoint method of a heating problem with a cost functional. We implemented the text book example and tested the gradient via a Taylor Remainder (which works fine). Now we wanted to solve the optimization

Re: [petsc-users] TAO: Finite Difference vs Continuous Adjoint gradient issues

responses and input again! On 2017-11-23 09:29, Julian Andrej wrote: On 2017-11-22 16:27, Emil Constantinescu wrote: On 11/22/17 3:48 AM, Julian Andrej wrote: Hello, we prepared a small example which computes the gradient via the continuous adjoint method of a heating problem with a cost