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From: Roy Stogner <roystgnr@ic...>  20110630 15:44:04

On Thu, 30 Jun 2011, Truman Ellis wrote: > How do I access neighbor information using > the DiffSystem framework, FEMContext::elem>neighbor(FEMContext::side) is the neighboring element. > specifically to calculate jumps and averages for calculating fluxes? Currently that's only possible by doing things the same way as nonDiffSystem codes: build a new FEBase (you can get the right type from the FEMContext), initialize it on the neighbor with the inverse_map'ed xyz values that the first FEBase gave you, and calculate values and gradients from that. It would probably be straightforward to fold that code into FEMSystem/FEMContext in the library, though, with a pervariable boolean to determine which variables needed jump information... my suggestion would be to start with it in user code for this DG Poisson system you're trying to get familiar with the APIs, then we'll move it to library code and use that trial system for regression testing, and then you'll have the facility already up and will have the same capability already available for more complex formulations.  Roy 
From: Kirk, Benjamin (JSCEG311) <benjamin.kirk1@na...>  20110630 14:29:46

All  The Parallel CFD 2012 conference will be held in Atlanta, GA USA May 2125 2012. We are planning for a minisymposium titled something like "Leveraging the libMesh Library for Massively Parallel Fluid Dynamics." The focus of the minisymposium will be just that  the application of libMesh to big parallel simulations. More details about the conference can be found at the conference website: http://sites.jsums.edu/parcfd2012 Appropriate presentations would include both enduser applications as well as libraryspecific presentations covering parallelrelevant implementation details. Each session in the minisymposium will be 4 presentations, so the first order of business will be to find out how may sessions we will support. If you are interested in presenting at this conference please reply to me giving a brief synopsis of what you'd plan to talk about so I can work up a count. Abstracts will be due in early February. Thanks, Ben 
From: Truman Ellis <truman@ic...>  20110630 14:28:15

I am trying to implement discontinuous Galerkin to solve the Laplace equation using DiffSystem. Example 21 solves the same problem via the older equation_system method. How do I access neighbor information using the DiffSystem framework, specifically to calculate jumps and averages for calculating fluxes? Thanks,  Truman Ellis 
From: Nachiket Gokhale <gokhalen@gm...>  20110629 20:06:48

On Wed, Jun 29, 2011 at 4:04 PM, John Peterson <jwpeterson@...> wrote: > On Wed, Jun 29, 2011 at 1:56 PM, Omar AlAbbasi <omabbasi@...> wrote: >> Thanks for the suggestions. >> John are you suggesting that within my Libmesh code and prior to specifying >> the position of the spectrum I shall write ... (st_shift .75) and then I >> specify the spectrum to LARGEST_MAGNITUDE ?? > > You specify LARGEST_MAGNITUDE in code, st_type/shift are *command > line* arguments so when you run your code, you pass them there: > > ./a.out st_type sinvert st_shift .75 > > assuming your executable was named a.out. If you want to perform > multiple solves with different shifts during a single run, then you'll > need to do it programmatically, consult the SLEPc docs for more info. You can also specify eps_largest_magnitude on the command line. The manual has other flags as well. Nachiket > >  > John > >  > All of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunkd2dc2 > _______________________________________________ > Libmeshusers mailing list > Libmeshusers@... > https://lists.sourceforge.net/lists/listinfo/libmeshusers > 
From: John Peterson <jwpeterson@gm...>  20110629 20:05:02

On Wed, Jun 29, 2011 at 1:56 PM, Omar AlAbbasi <omabbasi@...> wrote: > Thanks for the suggestions. > John are you suggesting that within my Libmesh code and prior to specifying > the position of the spectrum I shall write ... (st_shift .75) and then I > specify the spectrum to LARGEST_MAGNITUDE ?? You specify LARGEST_MAGNITUDE in code, st_type/shift are *command line* arguments so when you run your code, you pass them there: ./a.out st_type sinvert st_shift .75 assuming your executable was named a.out. If you want to perform multiple solves with different shifts during a single run, then you'll need to do it programmatically, consult the SLEPc docs for more info.  John 
From: Omar AlAbbasi <omabbasi@gm...>  20110629 19:56:22

Thanks for the suggestions. John are you suggesting that within my Libmesh code and prior to specifying the position of the spectrum I shall write ... (st_shift .75) and then I specify the spectrum to LARGEST_MAGNITUDE ?? I would appreciate your help. Omar 
From: John Peterson <jwpeterson@gm...>  20110629 19:17:44

On Wed, Jun 29, 2011 at 1:14 PM, John Peterson <jwpeterson@...> wrote: > On Wed, Jun 29, 2011 at 12:46 PM, Omar AlAbbasi <omabbasi@...> wrote: >> Hi, >> >> I am using Libmesh with Slepc for solving the eigen system that I have. I >> know that in Slepc there is an option to search for eigenvalues around >> specific target (say eigenvalues around 0.75), so is there a way in Libmesh >> to specify this target rather than setting the position of the spectrum to >> Largest or Smallest? > > You can probably use SLEPc's command line arguments (st_type sinvert) > to shift the spectrum by 0.75 (st_shift .75) and then use > SMALLEST_MAGNITUDE. Er, make that LARGEST_MAGNITUDE, because of the inversion.  John 
From: John Peterson <jwpeterson@gm...>  20110629 19:14:40

On Wed, Jun 29, 2011 at 12:46 PM, Omar AlAbbasi <omabbasi@...> wrote: > Hi, > > I am using Libmesh with Slepc for solving the eigen system that I have. I > know that in Slepc there is an option to search for eigenvalues around > specific target (say eigenvalues around 0.75), so is there a way in Libmesh > to specify this target rather than setting the position of the spectrum to > Largest or Smallest? You can probably use SLEPc's command line arguments (st_type sinvert) to shift the spectrum by 0.75 (st_shift .75) and then use SMALLEST_MAGNITUDE.  John 
From: Roy Stogner <roystgnr@ic...>  20110629 18:51:26

On Wed, 29 Jun 2011, Omar AlAbbasi wrote: > I am using Libmesh with Slepc for solving the eigen system that I have. I > know that in Slepc there is an option to search for eigenvalues around > specific target (say eigenvalues around 0.75), so is there a way in Libmesh > to specify this target rather than setting the position of the spectrum to > Largest or Smallest? It looks like right now EigenTimeSolver only supports LARGEST_MAGNITUDE, while EigenSolver only supports {LARGEST,SMALLEST}_{MAGNITUDE,REAL,IMAGINARY}. We'd happily accept patches to improve that, though.  Roy 
From: Omar AlAbbasi <omabbasi@gm...>  20110629 18:46:37

Hi, I am using Libmesh with Slepc for solving the eigen system that I have. I know that in Slepc there is an option to search for eigenvalues around specific target (say eigenvalues around 0.75), so is there a way in Libmesh to specify this target rather than setting the position of the spectrum to Largest or Smallest? Regards, Omar 
From: Ataollah Mesgarnejad <amesga1@ti...>  20110629 17:22:07

Dear all, Is there a way to have tell a TransientLinearImplicitSystem to assemble the matrix then get the SparseMatrix that it has assembled? I want to construct a PetscMatrix out of that to pass to Tao. Best, Ata 
From: Vikram Garg <vikramvgarg@ma...>  20110628 22:05:34

Saumil, If you are using PETSc, you can tack on the command line option ksp_monitor_singular_value and check whether the linear solver is running into trouble. If that is indeed the case, you can try increasing the number of GMRES restart steps or use modified Gram Schmidt. Another approach is to use continuation in parameters, where you start with a smaller Reynolds number and then increment the Reynold number iteratively to the desired value. The solution at Re(i) is used as the starting guess for the solver at Re(i+1). Thanks. On Tue, Jun 28, 2011 at 9:03 AM, Saumil Patel <saumil.patel134@...> wrote: > > Thank You, John. This makes sense. I was able to get results for Re 100. > > I have been trying to get results for Re = 1000. I've tried two approaches: > 1) to multiply the diffusion term by 1/Re and 2) Change the boundary > condition to U=1000. BC's are still based on the Penalty formulation. > > In both cases I'm using a refined mesh of 500 by 500. > > I'm having trouble getting accurate results so I was wondering if the > Kmatrix is becoming illconditioned when I multiply the diffusion term by > .001 (1/Re)? Do you have any suggestions on getting around it this issue? > > Thanks for your help, > > Saumil > > On Mon, Jun 27, 2011 at 10:43 AM, John Peterson <jwpeterson@...>wrote: > > > On Sun, Jun 26, 2011 at 1:37 PM, Saumil Patel <saumil.patel134@...> > > wrote: > > > Hello, > > > > > > I am getting familiar with the LIBMESH code and I was wondering if the > > FEM > > > formulation for the Unsteady NSE in example 13 are in a nondimensional > > > form? If so, I would just need to multiply the diffusion terms in the > > Kuu > > > and Kvv submatrices by the inverse Reynolds number factor, correct? > > > > Well the *dimensional* incompressible NS equations typically contain > > only a single parameter: "nu", the kinematic viscosity, anyway. > > > > So if you multiply the diffusion terms in ex13 by some parameter, you > > can think of it as a dimensional viscosity or an inverse Reynold's > > number. > > > > > Furthermore, I wouldn't need to change the B.C. condition for the top > > lid, > > > correct? > > > > The velocity on the top lid, the size of the domain, and the timestep > > will all take on different physical meaning depending on whether the > > value multiplying the diffusion terms is thought of as the Reynolds > > number or the kinematic viscosity. Consider: > > > > The default values for ex13 are domain size = "1", lid velocity="1". > > > > If the number multiplying the diffusion terms is thought of as the > > kinematic viscosity (in SI units of m^2/s, say) then the domain size > > is 1 meter, the lid velocity 1 m/s. > > > > On the other hand, if the number multiplying the diffusion terms is > > thought of as 1/Re, then setting the lid velocity="1" just means the > > lid velocity is equal to the "characteristic velocity used in defining > > the Reynold's number" and does not imply any particular units. In > > this case, one can always assign a physical value to, for example, the > > lid velocity "U" by specifying particular values for the Re, the > > kinematic viscosity of the fluid, and the domain size "L": > > > > Ex1, air @ 300K (nu=15.68e6 m^2/s) in a L=1cm enclosure, Re=1: U = Re > > * (nu/L) ~ 0.15 cm/s > > > > Ex2, water @ 50C (nu=0.553e6 m^2/s) in a L=1m enclosure, Re=1: U ~ .55 > > micron/s > > > > That is, the same Re=1 solution could represent either of the two > > physical situations (and infinitely many others!) above. > > > >  > > John > > >  > All of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunkd2dc2 > _______________________________________________ > Libmeshusers mailing list > Libmeshusers@... > https://lists.sourceforge.net/lists/listinfo/libmeshusers  Vikram Garg PhD Candidate Institute for Computational and Engineering Sciences The University of Texas at Austin http://users.ices.utexas.edu/~vikram/ http://www.runforindia.org/runners/vikramg 
From: John Peterson <jwpeterson@gm...>  20110628 14:30:56

On Tue, Jun 28, 2011 at 8:03 AM, Saumil Patel <saumil.patel134@...> wrote: > Thank You, John. This makes sense. I was able to get results for Re 100. > > I have been trying to get results for Re = 1000. I've tried two approaches: > 1) to multiply the diffusion term by 1/Re and 2) Change the boundary > condition to U=1000. BC's are still based on the Penalty formulation. > > In both cases I'm using a refined mesh of 500 by 500. > > I'm having trouble getting accurate results so I was wondering if the > Kmatrix is becoming illconditioned when I multiply the diffusion term by > .001 (1/Re)? Do you have any suggestions on getting around it this issue? The matrix condition number goes like h^2 for the Laplacian, so the fine mesh will certainly hurt you there. The cell Reynolds number, Re*(h/L) = 1000/500 = 2 for your case, which is right on the borderline of Galerkin instability. The timestep, linear, and nonlinear tolerances will all need to be different from what they were in the Re=1 case. You'll need to play with those and see which ones work.  John 
From: Saumil Patel <saumil.patel134@gm...>  20110628 14:04:04

Thank You, John. This makes sense. I was able to get results for Re 100. I have been trying to get results for Re = 1000. I've tried two approaches: 1) to multiply the diffusion term by 1/Re and 2) Change the boundary condition to U=1000. BC's are still based on the Penalty formulation. In both cases I'm using a refined mesh of 500 by 500. I'm having trouble getting accurate results so I was wondering if the Kmatrix is becoming illconditioned when I multiply the diffusion term by .001 (1/Re)? Do you have any suggestions on getting around it this issue? Thanks for your help, Saumil On Mon, Jun 27, 2011 at 10:43 AM, John Peterson <jwpeterson@...>wrote: > On Sun, Jun 26, 2011 at 1:37 PM, Saumil Patel <saumil.patel134@...> > wrote: > > Hello, > > > > I am getting familiar with the LIBMESH code and I was wondering if the > FEM > > formulation for the Unsteady NSE in example 13 are in a nondimensional > > form? If so, I would just need to multiply the diffusion terms in the > Kuu > > and Kvv submatrices by the inverse Reynolds number factor, correct? > > Well the *dimensional* incompressible NS equations typically contain > only a single parameter: "nu", the kinematic viscosity, anyway. > > So if you multiply the diffusion terms in ex13 by some parameter, you > can think of it as a dimensional viscosity or an inverse Reynold's > number. > > > Furthermore, I wouldn't need to change the B.C. condition for the top > lid, > > correct? > > The velocity on the top lid, the size of the domain, and the timestep > will all take on different physical meaning depending on whether the > value multiplying the diffusion terms is thought of as the Reynolds > number or the kinematic viscosity. Consider: > > The default values for ex13 are domain size = "1", lid velocity="1". > > If the number multiplying the diffusion terms is thought of as the > kinematic viscosity (in SI units of m^2/s, say) then the domain size > is 1 meter, the lid velocity 1 m/s. > > On the other hand, if the number multiplying the diffusion terms is > thought of as 1/Re, then setting the lid velocity="1" just means the > lid velocity is equal to the "characteristic velocity used in defining > the Reynold's number" and does not imply any particular units. In > this case, one can always assign a physical value to, for example, the > lid velocity "U" by specifying particular values for the Re, the > kinematic viscosity of the fluid, and the domain size "L": > > Ex1, air @ 300K (nu=15.68e6 m^2/s) in a L=1cm enclosure, Re=1: U = Re > * (nu/L) ~ 0.15 cm/s > > Ex2, water @ 50C (nu=0.553e6 m^2/s) in a L=1m enclosure, Re=1: U ~ .55 > micron/s > > That is, the same Re=1 solution could represent either of the two > physical situations (and infinitely many others!) above. > >  > John > 
From: John Peterson <jwpeterson@gm...>  20110627 14:43:56

On Sun, Jun 26, 2011 at 1:37 PM, Saumil Patel <saumil.patel134@...> wrote: > Hello, > > I am getting familiar with the LIBMESH code and I was wondering if the FEM > formulation for the Unsteady NSE in example 13 are in a nondimensional > form? If so, I would just need to multiply the diffusion terms in the Kuu > and Kvv submatrices by the inverse Reynolds number factor, correct? Well the *dimensional* incompressible NS equations typically contain only a single parameter: "nu", the kinematic viscosity, anyway. So if you multiply the diffusion terms in ex13 by some parameter, you can think of it as a dimensional viscosity or an inverse Reynold's number. > Furthermore, I wouldn't need to change the B.C. condition for the top lid, > correct? The velocity on the top lid, the size of the domain, and the timestep will all take on different physical meaning depending on whether the value multiplying the diffusion terms is thought of as the Reynolds number or the kinematic viscosity. Consider: The default values for ex13 are domain size = "1", lid velocity="1". If the number multiplying the diffusion terms is thought of as the kinematic viscosity (in SI units of m^2/s, say) then the domain size is 1 meter, the lid velocity 1 m/s. On the other hand, if the number multiplying the diffusion terms is thought of as 1/Re, then setting the lid velocity="1" just means the lid velocity is equal to the "characteristic velocity used in defining the Reynold's number" and does not imply any particular units. In this case, one can always assign a physical value to, for example, the lid velocity "U" by specifying particular values for the Re, the kinematic viscosity of the fluid, and the domain size "L": Ex1, air @ 300K (nu=15.68e6 m^2/s) in a L=1cm enclosure, Re=1: U = Re * (nu/L) ~ 0.15 cm/s Ex2, water @ 50C (nu=0.553e6 m^2/s) in a L=1m enclosure, Re=1: U ~ .55 micron/s That is, the same Re=1 solution could represent either of the two physical situations (and infinitely many others!) above.  John 
From: Robert <libmesh@ro...>  20110627 13:14:00

Hi, On Fri, Jun 24, 2011 at 10:35:18AM 0500, Roy Stogner wrote: > > On Fri, 24 Jun 2011, Robert wrote: > > > I was trying to build a TransientSystem<FEMSystem> > > Any reason why? FEMSystem already has a mechanism for transient > solves, via the TimeSolver subclasses. I actually want to build a TimeSolver class for a Newmarkstyle solver (I have already a System based on FEMSystem for my problem, so I don't wanted to use the NewmarkSystem) and needed therefore some more variables. TransientSystem<> provides these together with the necessary routines to localize/delocalize the values, so I used this. Robert >  > Roy 
From: Saumil Patel <saumil.patel134@gm...>  20110626 19:38:04

Hello, I am getting familiar with the LIBMESH code and I was wondering if the FEM formulation for the Unsteady NSE in example 13 are in a nondimensional form? If so, I would just need to multiply the diffusion terms in the Kuu and Kvv submatrices by the inverse Reynolds number factor, correct? Furthermore, I wouldn't need to change the B.C. condition for the top lid, correct? Any help you can provide would be much appreciated. Thank You, Saumil Patel 
From: Ataollah Mesgarnejad <amesga1@ti...>  20110625 18:27:51

Dear all, I want to use a PetscVector to update my linear systems solution I tried: *mysystem.solution=*mypetscvec It compiles but then in debug mode fails the assertion: Assertion `this>_type == v._type' failed. [0] src/numerics/petsc_vector.C, line 619 Any idea on how I can do it? Best, Ata 
From: Ataollah Mesgarnejad <amesga1@ti...>  20110625 17:07:04

Dear all, I have two questions regarding reading mesh from exodusII file: 1 When I read my exodusII meshfile number of local elements and local nodes are zero (happens on both one and several processors). How can I distribute the mesh? (I found a work around by doing one uniform refinement !!) 2 Is there a way to read BCs values from exodusII file? (As far as I understand MeshData class doesn't work with exodusII files.) Thanks for your time, Ata 
From: John Peterson <jwpeterson@gm...>  20110624 21:14:26

On Fri, Jun 24, 2011 at 3:10 PM, Vijay S. Mahadevan <vijay.m@...> wrote: > Roy, > > I wanted to ask this to Guido in the deal.ii list but anyway here is > my question. > > Is this journal for papers based on completely open source software > alone that can be replicated/verified by anyone ? What I mean is that > if I use say petsc+libMesh+my own framework, does the journal require > me to make my framework + test code open source in order to be > accepted ? Just clarifying. Yes. Submitted software must have an OSIapproved license.  John 
From: Vijay S. Mahadevan <vijay.m@gm...>  20110624 21:10:59

Roy, I wanted to ask this to Guido in the deal.ii list but anyway here is my question. Is this journal for papers based on completely open source software alone that can be replicated/verified by anyone ? What I mean is that if I use say petsc+libMesh+my own framework, does the journal require me to make my framework + test code open source in order to be accepted ? Just clarifying. IMO, it is a great effort in the right direction and having contributed to the open source initiative in the past, I am happy to see that it is getting a little more structure in the scientific community. Best, Vijay On Fri, Jun 24, 2011 at 3:31 PM, Roy Stogner <roystgnr@...> wrote: > > Dear libMesh users: > > We are pleased to announce the launch of the Archive of Numerical > Software (ANS). ANS is a free, peerreviewed, high quality, openaccess > journal publishing research of numerical methods that are implemented > based on, or extend certain largescale numerical libraries, including > libMesh. > > ANS's distinctive feature  furthering the goal of encouraging the > reuse of software  is that articles must be accompanied by the > computer code (under an OSIapproved open source license) from which > results were obtained. We are committed to establishing and > maintaining high standards of code usability, documentation, and > reproducibility, considering both the code itself as well as > accompanying manuscripts. > > The journal is hosted by the Texas Digital Library and can be found at > http://journals.tdl.org/ans > Its mission statement, policies and submission guidelines can also be > found there. > > Best regards, >  > Roy Stogner > >  > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense.. > http://p.sf.net/sfu/splunkd2dc1 > _______________________________________________ > Libmeshdevel mailing list > Libmeshdevel@... > https://lists.sourceforge.net/lists/listinfo/libmeshdevel > 
From: Truman Ellis <truman@ic...>  20110624 21:08:33

I am working through example 18, and I came across an odd assert. Line 432 of naviersystem.C says: libmesh_assert (c.elem_solution_derivative == 1.0); I don't understand while it is important or even valid to assert this. Any explanation would be helpful. Thanks, Truman 
From: Roy Stogner <roystgnr@ic...>  20110624 20:56:10

On Fri, 24 Jun 2011, John Peterson wrote: > On Fri, Jun 24, 2011 at 2:25 PM, Roy Stogner <roystgnr@...> wrote: >> >> Any preference for what we should name a macro whose behavior is >> essentially "do what libmesh_assert() does even when NDEBUG is >> defined"? > > I think this is called an "if test", right? Heh, zing! Yeah, it'd basically be to replace if (!test) { print "`test' failed"; libmesh_error(); } >> I'm not sure when we'd get around to using such a thing in the library >> (maybe sparingly in the MeshInput subclasses?), but in application >> code at least there's a definite need to always run certain sanity >> checks on input files and input options; the users who provide invalid >> input aren't always going to be kind enough to provide it to a >> develmode program. > > Sorry, I actually don't understand why you need a macro for code that > should essentially always execute? Mostly to turn a bunch of instances of the 35 lines above into oneliners. Using a macro or function prevents having to retype "test" (which can be a long complicated expression returning bool), using a macro keeps the libmesh_here() working right.  Roy 
From: John Peterson <jwpeterson@gm...>  20110624 20:47:03

On Fri, Jun 24, 2011 at 2:25 PM, Roy Stogner <roystgnr@...> wrote: > > Any preference for what we should name a macro whose behavior is > essentially "do what libmesh_assert() does even when NDEBUG is > defined"? I think this is called an "if test", right? > I'm not sure when we'd get around to using such a thing in the library > (maybe sparingly in the MeshInput subclasses?), but in application > code at least there's a definite need to always run certain sanity > checks on input files and input options; the users who provide invalid > input aren't always going to be kind enough to provide it to a > develmode program. Sorry, I actually don't understand why you need a macro for code that should essentially always execute?  John 
From: Roy Stogner <roystgnr@ic...>  20110624 20:31:56

Dear libMesh users: We are pleased to announce the launch of the Archive of Numerical Software (ANS). ANS is a free, peerreviewed, high quality, openaccess journal publishing research of numerical methods that are implemented based on, or extend certain largescale numerical libraries, including libMesh. ANS's distinctive feature  furthering the goal of encouraging the reuse of software  is that articles must be accompanied by the computer code (under an OSIapproved open source license) from which results were obtained. We are committed to establishing and maintaining high standards of code usability, documentation, and reproducibility, considering both the code itself as well as accompanying manuscripts. The journal is hosted by the Texas Digital Library and can be found at http://journals.tdl.org/ans Its mission statement, policies and submission guidelines can also be found there. Best regards,  Roy Stogner 