Re: [deal.II] Understanding slightly cryptic warnings from modified Step-52 code

2020-06-24 Thread Krishnakumar Gopalakrishnan
, Krishna On Wed, 24 Jun 2020 at 23:54, Wolfgang Bangerth wrote: > On 6/24/20 3:14 PM, Krishnakumar Gopalakrishnan wrote: > > Hi, > > > > I am solving the basic diffusion equation using the direct method (based > on > > Step-52). > > > > I have made t

[deal.II] Understanding slightly cryptic warnings from modified Step-52 code

2020-06-24 Thread Krishnakumar Gopalakrishnan
Hi, I am solving the basic diffusion equation using the direct method (based on Step-52). I have made the following changes from Step-52 tutorial 1. The domain is now 1D (as opposed to 2D in step-52) 2. We have Neumann BCs on both ends (left NeumannBC = 0.5, right NeumannBC= 0) 3. Removes the

Re: [deal.II] How to apply a spatially variable non-zero initial condition in step-52?

2020-06-07 Thread Krishnakumar Gopalakrishnan
. Krishna On Tue, 14 Apr 2020 at 01:24, Wolfgang Bangerth wrote: > On 4/13/20 6:00 PM, Krishnakumar Gopalakrishnan wrote: > > I am currently working on Step-52, which solves the diffusion equation. > > > > I now want to disable the Method of Manufactured Solutions

[deal.II] How to apply a spatially variable non-zero initial condition in step-52?

2020-04-13 Thread Krishnakumar Gopalakrishnan
I am currently working on Step-52, which solves the diffusion equation. I now want to disable the Method of Manufactured Solutions (MMS) i.e. get rid of the forcing function which produces an expected analytical solution, in the direction towards solving my real-world problem. I also have set

Re: [deal.II] Installation with spack - no access to adol-c

2020-03-17 Thread Krishnakumar Gopalakrishnan
I did a spack-based install of deal.ii on a 64-bit Linux machine as well as on a macbook pro, and didn't encounter any issues. Krishna On Tuesday, March 17, 2020 at 9:58:48 PM UTC, Jean-Paul Pelteret wrote: > > Hi Konrad, > > Yes, we need some version of ADOL-C greater than 2.6.3, as we

Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-17 Thread Krishnakumar Gopalakrishnan
on VTK library by the way which allows easy (relatively) > opening of vtk file and conversion into numpy arrays. It can be pretty > handy, although the documentation is poor. > > :)! > > > On Monday, 16 March 2020 13:00:57 UTC-4, Wolfgang Bangerth wrote: >> >

Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Krishnakumar Gopalakrishnan
gt; > Bruno > On 3/16/20 12:14 PM, Krishnakumar Gopalakrishnan wrote: > > Hi Bruno, > > Thanks for this information. > > I am genuinely curious to know about these other programs that are capable > of reading .vtk and .vtu files. Everyone says that these files are

Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Krishnakumar Gopalakrishnan
. Why should we restrict the output because two visualization tools > don't support 1D? > > Best, > > Bruno > > On Monday, March 16, 2020 at 11:37:57 AM UTC-4, Krishnakumar > Gopalakrishnan wrote: >> >> Hi Praveen, >> >> Thank you. That really helps. I

Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Krishnakumar Gopalakrishnan
. If the FE space is continuous, you will > get a plot which is globally continuous. > > Best > praveen > > On 16-Mar-2020, at 8:50 PM, Krishnakumar Gopalakrishnan > wrote: > > Hi Praveen, > > Thanks for your reply. Yes, I had success with gnuplot, but the fol

Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Krishnakumar Gopalakrishnan
lot format > > > https://www.dealii.org/current/doxygen/deal.II/classDataOutInterface.html#a85407e870a68179ebe62410d9efc153f > > and use gnuplot to visualize it. > > Best > praveen > > On 16-Mar-2020, at 8:33 PM, Krishnakumar Gopalakrishnan > wrote: > >

Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Krishnakumar Gopalakrishnan
on results. Regards, Krishna On Mon, 16 Mar 2020 at 00:22, Wolfgang Bangerth wrote: > On 3/15/20 1:50 PM, Krishnakumar Gopalakrishnan wrote: > > > > It looks like both paraview and VTK can only visualise 2D/3D meshes? > What's > > the best way to visualise 1D outpu

[deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-15 Thread Krishnakumar Gopalakrishnan
Using deal.ii, I got the results of a time-dependent 1D diffusion equation written to disk as a set of .vtu files (one per time-step). It looks like both paraview and VTK can only visualise 2D/3D meshes? What's the best way to visualise 1D outputs? Regards, Krishna -- The deal.II project is

Re: [deal.II] Accessing a particular boundary in one-dimensional case

2020-03-15 Thread Krishnakumar Gopalakrishnan
2020 at 23:47, Wolfgang Bangerth wrote: > On 3/13/20 5:34 PM, Krishnakumar Gopalakrishnan wrote: > > > > Looking at step-7 and adapting it a little bit, does the following code > look > > reasonable to mark the boundary ID of the left edge as '1' for later > setting >

[deal.II] Accessing a particular boundary in one-dimensional case

2020-03-13 Thread Krishnakumar Gopalakrishnan
For a one-dimensional unit domain (0,1), if one needs to set non-homogenous Neumann BC at a particular end of the domain (say the left end, x=0), Looking at step-7 and adapting it a little bit, does the following code look reasonable to mark the boundary ID of the left edge as '1' for later

Re: [deal.II] Linearizing a non-linear diffusion equation by using value from previous-time step for the non-linear part (Rothe method)

2020-03-13 Thread Krishnakumar Gopalakrishnan
:59 PM, Krishnakumar Gopalakrishnan wrote: > > I have a non-linear diffusion equation of the form > > > > du/dt = \nabla.( D(u) \grad u) > > > > The non-linearity appears because of the dependence of the diffusion > > coefficient on the solution. > > >

[deal.II] Linearizing a non-linear diffusion equation by using value from previous-time step for the non-linear part (Rothe method)

2020-03-13 Thread Krishnakumar Gopalakrishnan
I have a non-linear diffusion equation of the form du/dt = \nabla.( D(u) \grad u) The non-linearity appears because of the dependence of the diffusion coefficient on the solution. When discretising by the Rothe method, applying backward Euler method in the strictest sense: (u^n -

Re: [deal.II] Initial guidance/starting point for solving a non-linear diffusion equation with double neumann BCs

2020-03-13 Thread Krishnakumar Gopalakrishnan
ent problems to get started. > Let us know if you have more specific questions. > > Best, > Daniel > > Am Do., 12. März 2020 um 17:38 Uhr schrieb Krishnakumar Gopalakrishnan < > krish...@vt.edu>: > >> I need to solve the following non-linear diffusion equation on a

[deal.II] Initial guidance/starting point for solving a non-linear diffusion equation with double neumann BCs

2020-03-12 Thread Krishnakumar Gopalakrishnan
I need to solve the following non-linear diffusion equation on a unit 1D domain: du/dt = \nabla \dot ( D(u) \grad u) subject to Neumann bcs at both ends. D(u)*grad(u) = f(t) at x=0, and D(u)*grad(u) = 0 at x=1, with a constant initial condition u(x,0) = u0 The difficulty with this problem is

Re: [deal.II] Question on copyright, licensing, authorship & attribution for reuse of (parts of) tutorial programs

2020-03-12 Thread Krishnakumar Gopalakrishnan
Thank you so much for your kind explanation. I thought that maybe the common landing page for all the tutorials (the one with the graphviz dot-diagram relationship) is a possible candidate. But I understand why its probably also not the best since most pages have already lengthy content and

Re: [deal.II] Question on copyright, licensing, authorship & attribution for reuse of (parts of) tutorial programs

2020-03-12 Thread Krishnakumar Gopalakrishnan
Thank you so much for your answers. *"But they're all licensed under the same LGPL license."* Ah. I get it now. The library includes the tutorials as well, right? So LGPL should apply everywhere. * In particular, that's why we came up with the code gallery:

Re: [deal.II] Question about the advice about regularity of the stokes' equations in Step-22

2020-03-12 Thread Krishnakumar Gopalakrishnan
rch 11, 2020 at 9:20:56 PM UTC, Wolfgang Bangerth wrote: > > On 3/10/20 12:59 PM, Krishnakumar Gopalakrishnan wrote: > > Step-22 has a strong-sounding stub-like statement:/"In practice, one > > wants to impose as little regularity on the pressure variable as > possi

[deal.II] Question on copyright, licensing, authorship & attribution for reuse of (parts of) tutorial programs

2020-03-12 Thread Krishnakumar Gopalakrishnan
While, I understand that deal.Ii (the library itself) is licensed under LGPL 2.1 or above, this question is about reuse of tutorial programs in own research. I see that some later tutorial programs have dois on Zenodo and certain open licences attached to them. However, most of the earlier

Re: [deal.II] How to determine the saddle-point nature of PDEs like those in Step-20, 21?

2020-03-11 Thread Krishnakumar Gopalakrishnan
ich consists of only symbolic notations, can one somehow infer the definiteness/symmetry of the matrix? Regards, Krishna On Wed, 11 Mar 2020 at 17:17, Wolfgang Bangerth wrote: > On 3/11/20 7:57 AM, Krishnakumar Gopalakrishnan wrote: > > In Step-21 tutorial, we have a statement that starts wit

[deal.II] How to determine the saddle-point nature of PDEs like those in Step-20, 21?

2020-03-11 Thread Krishnakumar Gopalakrishnan
In Step-21 tutorial, we have a statement that starts with the following (emphasis is mine): *"Given the saddle point structure of the first two equations and their similarity to the mixed Laplace formulation we have introduced in step-20

[deal.II] Question about the advice about regularity of the stokes' equations in Step-22

2020-03-10 Thread Krishnakumar Gopalakrishnan
Step-22 has a strong-sounding stub-like statement: * "In practice, one wants to impose as little regularity on the pressure variable as possible". * The above one-liner (fairly enough) assumes domain knowledge. As a new entrant to deal.ii (haven't studied fluid mechanics before), may I ask the

[deal.II] Updated link to Jack Poulson's PhD thesis (in the landing page of video lecture 34)

2020-03-10 Thread Krishnakumar Gopalakrishnan
The link to Jack Poulson's text currently in the landing page of Video Lecture 34 https://www.math.colostate.edu/~bangerth/videos.676.34.html has become out of date. For the benefit of those following the video lectures, the updated

[deal.II] Question on how MatrixTools::MatrixCreator sets the appropriate flags of FeValues?

2020-02-18 Thread Krishnakumar Gopalakrishnan
In the tutorials, Step-23 suddenly gets rid of the assemble_system() function and introduces MatrixTools::MatrixCreator::create_mass_matrix and MatrixTools::MatrixCreator::create_laplace_matrix However, there is no discussion whatsoever of how the appropriate update flags (bitfields) of the

[deal.II] Open vs closed notation for time-interval of the heat equation

2020-02-15 Thread Krishnakumar Gopalakrishnan
I am slightly confused by the use of open vs closed interval for denoting the time-interval of the heat equation. For example in lecture 27 (https://www.math.colostate.edu/~bangerth/videos.676.27.html), both the video lecture and the slides seem to convey that the PDE holds for the closed

Re: [deal.II] Question about the definiteness of the system matrix in Step-20

2020-02-01 Thread Krishnakumar Gopalakrishnan
o > it cannot be positive definite. > > Thanks, > David Wells > > On Sat, Feb 1, 2020 at 9:49 AM Krishnakumar Gopalakrishnan > > wrote: > > > > I realize that this question is not exactly about the code/concepts > behind deal.II library itself, but rather

[deal.II] Question on the operator matrix (system matrix) of Step-20

2020-02-01 Thread Krishnakumar Gopalakrishnan
Once again, apologies for asking questions which are more oriented towards vector calculus than the deal.II library/code itself. In Step-20, under the introduction section on solvers, it says: "If we sort our degrees of freedom so that all velocity come before all pressure variables, then we

[deal.II] Question about the definiteness of the system matrix in Step-20

2020-02-01 Thread Krishnakumar Gopalakrishnan
I realize that this question is not exactly about the code/concepts behind deal.II library itself, but rather about a mathematical statement from step-20. *"After assembling the linear system we are faced with the task of solving it. The problem here is: the matrix has a zero block at the

[deal.II] Question on references for locally conservative discretization of the Laplace equation such as in Step-20

2020-01-31 Thread Krishnakumar Gopalakrishnan
Step-20 tutorial says that: *"It turns out that the usual discretizations of the Laplace equation (such as those used in step-3 , step-4 , or step-6

[deal.II] IterativeInverse function appears to have disappeared between v8.5.0 and v9.0.0?

2020-01-20 Thread Krishnakumar Gopalakrishnan
I was just finishing Prof Bangerth's video lecture 21 wherein the concept of Schur Complement is introduced. For computing the inverse of the mass matrix (M), it looks like Dealii uses the facilities of the IterativeInverse class. The latest notes in the webpage for the lecture,

Re: [deal.II] Facilities for computing the "goodness" of a mesh (i.e. something like a mesh-quality indicator)

2020-01-15 Thread Krishnakumar Gopalakrishnan
Kronbichler wrote: > > Dear Krishna, > > We have recently added one such function, namely > GridTools::compute_aspect_ratio_of_cells(), > > > https://dealii.org/developer/doxygen/deal.II/namespaceGridTools.html#a2a9d8801d952ea8afa9ec1573229a329 > > Best, > Martin

[deal.II] Facilities for computing the "goodness" of a mesh (i.e. something like a mesh-quality indicator)

2020-01-15 Thread Krishnakumar Gopalakrishnan
In the results/extension section of Step-6 as well in Step-49, there is a great deal of discussion about obtaining good meshes are for a problem, with the caveat that this is a highly specialized topic. Step-49 is full of warnings about things that can go wrong when applying certain

[deal.II] Possible minor error in a graphic for MATH676 video lecture 15

2020-01-11 Thread Krishnakumar Gopalakrishnan
I don't know if this is the right place to discuss this, but it might possibly be of relevance to new users of deal.ii There might be a minor error in a graphic used in the slides corresponding to video lecture 15 of MATH676 (topic: cell refinement introduction) In the longest edge refinement

Re: [deal.II] Re: Why did the developers of deal.ii choose templates over variadic arguments?

2019-12-20 Thread Krishnakumar Gopalakrishnan
Friday, December 20, 2019 at 8:12:56 AM UTC-5, Krishnakumar > Gopalakrishnan wrote: >> >> With the highest deference to the amazing quality of software development >> that deal.ii developers follow, I wish to ask a question about the >> particular development

[deal.II] Why did the developers of deal.ii choose templates over variadic arguments?

2019-12-20 Thread Krishnakumar Gopalakrishnan
With the highest deference to the amazing quality of software development that deal.ii developers follow, I wish to ask a question about the particular development paradigm chosen (with no disrespect to any of the developers intended). This question is just out of personal curiosity. deal.ii