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From: Roy Stogner <roy@st...>  20080815 22:10:42

The first release candidate of libMesh 0.6.3 is now available for download. New features include: Continuing experimental ParallelMesh development More internal parallelization Operator overloading on scalar/vector/tensor operations with mixed underlying types Exception throwing, stack trace file output on errors More norm options for some library methods Better PETSc nonlinear solver integration Better line search in libMesh NewtonSolver You can now force LibMesh to use quadrature rules with positive weights GrundmannMoller quadrature rules Changed/added quadrature rules for TRIs at almost every order, preferring rules with fewer points and positive weights QMonomial quadrature class for cheaper integration rules for monomial/XYZ bases on QUADs Recomputed Gauss and Jacobi quadrature rules out to 32 significant digits Updated Exodus library Expanded Exodus I/O support, including subdomain ids, multiple timesteps per file Improved libMesh file formats Assorted bug fixes, compatibility fixes, efficiency improvements A few backwardsincompatible API changes have been made: The macro error() has been replaced with libmesh_error() to avoid name conflicts, and internal assert() calls have been replaced by libmesh_assert() to enable exceptionthrowing and tracefile output on assertion failures. The libMesh::init()/close() methods have been replaced by a libMeshInit object's constructor and destructor, to simplify application code slightly and to provide better cleanup behavior when an uncaught exception is thrown. The old methods are now deprecated and will eventually be removed. 
From: Adam C Powell IV <hazelsct@de...>  20080815 21:20:44

On Fri, 20080815 at 15:30 0500, Roy Stogner wrote: > On Fri, 15 Aug 2008, Adam C Powell IV wrote: > > > I'd like to calculate the integral of (grad u)^2 over my domain, after a > > calculation. > > > > Currently, I assign two new variables, and set up new equations for > > them: Jxdu/dx=0, Jydu/dy=0. Then I just square and add the results of > > calculate_norm (Jx and Jy, L2). It seems to work. But this adds two > > extra field variables and equations to the calculation, multiplying the > > memory usage and slowing things down a good bit. > > > > Alternatively, is it possible to calculate the L2 norm of the field > > derivative or gradient directly, through a method I've missed? > > Well, for future reference in general: it's possible to calculate the > L2 norm of the arctangent cubed of the field gradient directly, if > that's what you want. And what norm is that??? Oh, reading on... > Just loop over all the elements the same way > you would for a residual assembly, calculate whatever function you > need at each quadrature point, and sum the weighted values to > numerically integrate the result. Ah, makes sense. That would do the second separatethederivatives calculation thing. Silly that I didn't think of such a simple loop... > Helper methods like > calculate_norm() are intended to simplify common code, not to be a > straitjacket if you need to do something out of the ordinary. > > Hmm... I didn't mean that last paragraph to sound condescending, but > did it anyway? Apparently karma thinks I deserve to be embarrassed > now. Well, I deserve to be embarrassed for not simply writing a loop. > You see, the next thing I was going to say is that you can (in > the SVN and soon 0.6.3+ libMesh versions) just pass H1_SEMINORM to > calculate_norm() to get the square root of the integral of the > gradient squared, and then square that to get the number you want... Excellent. Somehow I figured that someone might have needed that common variation, and coded it, or part of it. :) > but glancing at the calculate_norm() implementation, I see I never > finished adding that feature; the code currently would give you an > inaccurate result. I'll go fix that now. Thank you! I'll see if I can easily add that patch to my (soontobe) 0.6.3 Debian/Ubuntu package. > > Or if there's nothing quite that convenient, is there a way of > > calculating the derivatives and putting them into a separate vector > > in the system, decoupled from the original calculation? > > All variables in a system are coupled by definition; if you really > needed to keep some postprocessed data around, the way to do it > efficiently would be to add an additional ExplicitSystem to your > EquationSystems object, then put the decoupled variables there. I see, not just another vector but a whole ExplicitSystem. I'll have other uses for that... Thanks again, Adam  GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ 
From: Roy Stogner <roy@st...>  20080815 20:30:37

On Fri, 15 Aug 2008, Adam C Powell IV wrote: > I'd like to calculate the integral of (grad u)^2 over my domain, after a > calculation. > > Currently, I assign two new variables, and set up new equations for > them: Jxdu/dx=0, Jydu/dy=0. Then I just square and add the results of > calculate_norm (Jx and Jy, L2). It seems to work. But this adds two > extra field variables and equations to the calculation, multiplying the > memory usage and slowing things down a good bit. > > Alternatively, is it possible to calculate the L2 norm of the field > derivative or gradient directly, through a method I've missed? Well, for future reference in general: it's possible to calculate the L2 norm of the arctangent cubed of the field gradient directly, if that's what you want. Just loop over all the elements the same way you would for a residual assembly, calculate whatever function you need at each quadrature point, and sum the weighted values to numerically integrate the result. Helper methods like calculate_norm() are intended to simplify common code, not to be a straitjacket if you need to do something out of the ordinary. Hmm... I didn't mean that last paragraph to sound condescending, but did it anyway? Apparently karma thinks I deserve to be embarrassed now. You see, the next thing I was going to say is that you can (in the SVN and soon 0.6.3+ libMesh versions) just pass H1_SEMINORM to calculate_norm() to get the square root of the integral of the gradient squared, and then square that to get the number you want... but glancing at the calculate_norm() implementation, I see I never finished adding that feature; the code currently would give you an inaccurate result. I'll go fix that now. > Or if there's nothing quite that convenient, is there a way of > calculating the derivatives and putting them into a separate vector > in the system, decoupled from the original calculation? All variables in a system are coupled by definition; if you really needed to keep some postprocessed data around, the way to do it efficiently would be to add an additional ExplicitSystem to your EquationSystems object, then put the decoupled variables there.  Roy 
From: Adam C Powell IV <hazelsct@de...>  20080815 19:37:12

Hello, I'd like to calculate the integral of (grad u)^2 over my domain, after a calculation. Currently, I assign two new variables, and set up new equations for them: Jxdu/dx=0, Jydu/dy=0. Then I just square and add the results of calculate_norm (Jx and Jy, L2). It seems to work. But this adds two extra field variables and equations to the calculation, multiplying the memory usage and slowing things down a good bit. Alternatively, is it possible to calculate the L2 norm of the field derivative or gradient directly, through a method I've missed? Or if there's nothing quite that convenient, is there a way of calculating the derivatives and putting them into a separate vector in the system, decoupled from the original calculation? Thanks, Adam  GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/ 