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From: Subramanya Gautam Sadasiva <ssadasiv@pu...>  20130222 19:41:44

Sorry about this mail . I see there is a really stupid error in what I am doing. Subramanya Sadasiva "But memory eventually fades. Turbulences damp out, internal strains yield to plastic flow, concentration inhomogeneities diffuse to uniformity. Systems tend to subside to very simple states,independent of their specific history." Herbert Callen . Thermodynamics and an Introduction to Thermostatics.  Original Message  From: "Subramanya Gautam Sadasiva" <ssadasiv@...> To: "libmeshusers" <libmeshusers@...> Sent: Friday, February 22, 2013 2:22:42 PM Subject: [Libmeshusers] Forcing the solver to use a particular solver. Hi, I want to use the petsc_dm solver without passing usepetscdm at the command line. I did this in the constructor of my class that derives from nonlinearimplicitsystem . AutoPtr<PetscNonlinearSolver<Number> > petsc_solver = AutoPtr<PetscNonlinearSolver<Number> > (new PetscNonlinearSolver<Number> (*this)); // Attach the R & J calculation object petsc_solver>residual_object = this; petsc_solver>jacobian_object = this; // Attach the bounds calculation object petsc_solver>bounds_object = this; // Get a petsc error . this is an alias for a integer PetscErrorCode ierr; petsc_solver>PetscNonlinearSolver<Number>::init(); // The prefix is ch_solve_. I need to figure out how to // put it into the documentation ierr = SNESSetOptionsPrefix(petsc_solver>_snes,"ch_solve_"); // Set from options file for the solve ierr = SNESSetFromOptions(petsc_solver>_snes); // Now put petsc solver back into nonlinear solver AutoPtr nonlinear_solver = petsc_solver; This does not seem to work and gives me an error. Is there a better way to do it than to override the nonlinear_solver? Thanks, Subramanya "But memory eventually fades. Turbulences damp out, internal strains yield to plastic flow, concentration inhomogeneities diffuse to uniformity. Systems tend to subside to very simple states,independent of their specific history." Herbert Callen . Thermodynamics and an Introduction to Thermostatics.  Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb _______________________________________________ Libmeshusers mailing list Libmeshusers@... https://lists.sourceforge.net/lists/listinfo/libmeshusers 
From: Subramanya Gautam Sadasiva <ssadasiv@pu...>  20130222 19:22:52

Hi, I want to use the petsc_dm solver without passing usepetscdm at the command line. I did this in the constructor of my class that derives from nonlinearimplicitsystem . AutoPtr<PetscNonlinearSolver<Number> > petsc_solver = AutoPtr<PetscNonlinearSolver<Number> > (new PetscNonlinearSolver<Number> (*this)); // Attach the R & J calculation object petsc_solver>residual_object = this; petsc_solver>jacobian_object = this; // Attach the bounds calculation object petsc_solver>bounds_object = this; // Get a petsc error . this is an alias for a integer PetscErrorCode ierr; petsc_solver>PetscNonlinearSolver<Number>::init(); // The prefix is ch_solve_. I need to figure out how to // put it into the documentation ierr = SNESSetOptionsPrefix(petsc_solver>_snes,"ch_solve_"); // Set from options file for the solve ierr = SNESSetFromOptions(petsc_solver>_snes); // Now put petsc solver back into nonlinear solver AutoPtr nonlinear_solver = petsc_solver; This does not seem to work and gives me an error. Is there a better way to do it than to override the nonlinear_solver? Thanks, Subramanya "But memory eventually fades. Turbulences damp out, internal strains yield to plastic flow, concentration inhomogeneities diffuse to uniformity. Systems tend to subside to very simple states,independent of their specific history." Herbert Callen . Thermodynamics and an Introduction to Thermostatics. 
From: Manav Bhatia <bhatiamanav@gm...>  20130222 04:51:45

On Feb 21, 2013, at 3:25 PM, Roy Stogner <roystgnr@...> wrote: >> >> Additionally, within the existing framework, how does one account for >> *nonlinear* systems that have a mass matrix >> >> [M] du/dt = f(u) > > Right now, we allow you to request an "elem_fixed_solution" that can > be used for either loworder time integration of nonlinear mass > matrices or for nonlinear stabilization in test functions. We're > actually planning a (backwardsincompatible, unfortunately) change in > this API, to make it less unnecessarily confusing and to allow for > higherorder time integration of nonlinear mass matrices and/or for > nonlinear mass matrices with nonlinear stabilization in test > functions. If you'd like, I could probably push that change up higher > on my todo list. Upon further study, it seems like the elem_fixed_solution stores the element solution in situations where the elem_solution may contain the velocity or delta solution. Is this correct? Manav 
From: Manav Bhatia <bhatiamanav@gm...>  20130222 04:44:27

On Feb 21, 2013, at 3:25 PM, Roy Stogner <roystgnr@...> wrote: > >> Additionally, within the existing framework, how does one account for >> *nonlinear* systems that have a mass matrix >> >> [M] du/dt = f(u) > > Right now, we allow you to request an "elem_fixed_solution" that can > be used for either loworder time integration of nonlinear mass > matrices or for nonlinear stabilization in test functions. We're > actually planning a (backwardsincompatible, unfortunately) change in > this API, to make it less unnecessarily confusing and to allow for > higherorder time integration of nonlinear mass matrices and/or for > nonlinear mass matrices with nonlinear stabilization in test > functions. If you'd like, I could probably push that change up higher > on my todo list. > OK, I think I may have started to understand this a little better now (although still a little confused). Please correct me as you see fit. I see that the method mass_residual is used in the classes Euler_Solver and Euler2_Solver. What is throwing me off is that the class documentation of Euler2_Solver says: * Euler solves u' = f(theta*u_new + (1theta)*u_old), * Euler2 solves u' = theta*f(u_new) + (1theta)*f(u_old) which seems to imply that no mass matrix is accounted for. Are the u and f(u) here the solution after discretization, or before discretization? My current guess is that the u' in these equations should actually be replaced with the product [M] u' , like one would encounter postdiscretization. What is your assessment? Also, while going through the code, I came across the following in euler_solver.C (lines 124129) // We do a trick here to avoid using a non1 // elem_solution_derivative: context.elem_jacobian *= 1.0; jacobian_computed = _system.mass_residual(jacobian_computed, context) && jacobian_computed; context.elem_jacobian *= 1.0; What is the need to multiply the elem_jacobian by 1.0 both before and after the function call? Wouldn't the call to mass_residual overwrite the elem_jacobian anyways? Thanks, Manav 