From: bangerth Date: Sat, 1 Mar 2008 13:45:53 +0000 (+0000) Subject: Add David Neckel's compressible Euler flow tutorial program. X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=4d9e9156a92082e9649c6fc6131edf2ad22dfa6f;p=dealii-svn.git Add David Neckel's compressible Euler flow tutorial program. git-svn-id: https://svn.dealii.org/trunk@15823 0785d39b-7218-0410-832d-ea1e28bc413d --- diff --git a/deal.II/examples/step-33/Makefile b/deal.II/examples/step-33/Makefile new file mode 100644 index 0000000000..2102793621 --- /dev/null +++ b/deal.II/examples/step-33/Makefile @@ -0,0 +1,154 @@ +# $Id: Makefile 14008 2006-10-17 04:05:33Z bangerth $ + + +# For the small projects Makefile, you basically need to fill in only +# four fields. +# +# The first is the name of the application. It is assumed that the +# application name is the same as the base file name of the single C++ +# file from which the application is generated. +target = $(basename $(shell echo step-*.cc)) + +# The second field determines whether you want to run your program in +# debug or optimized mode. The latter is significantly faster, but no +# run-time checking of parameters and internal states is performed, so +# you should set this value to `on' while you develop your program, +# and to `off' when running production computations. +debug-mode = on + + +# As third field, we need to give the path to the top-level deal.II +# directory. You need to adjust this to your needs. Since this path is +# probably the most often needed one in the Makefile internals, it is +# designated by a single-character variable, since that can be +# reference using $D only, i.e. without the parentheses that are +# required for most other parameters, as e.g. in $(target). +D = ../../ + + +# The last field specifies the names of data and other files that +# shall be deleted when calling `make clean'. Object and backup files, +# executables and the like are removed anyway. Here, we give a list of +# files in the various output formats that deal.II supports. +clean-up-files = *gmv *gnuplot *gpl *eps *pov + + + + +# +# +# Usually, you will not need to change something beyond this point. +# +# +# The next statement tell the `make' program where to find the +# deal.II top level directory and to include the file with the global +# settings +include $D/common/Make.global_options + + +# Since the whole project consists of only one file, we need not +# consider difficult dependencies. We only have to declare the +# libraries which we want to link to the object file, and there need +# to be two sets of libraries: one for the debug mode version of the +# application and one for the optimized mode. Here we have selected +# the versions for 2d. Note that the order in which the libraries are +# given here is important and that your applications won't link +# properly if they are given in another order. +# +# You may need to augment the lists of libraries when compiling your +# program for other dimensions, or when using third party libraries +libs.g = $(lib-deal2-2d.g) \ + $(lib-lac.g) \ + $(lib-base.g) +libs.o = $(lib-deal2-2d.o) \ + $(lib-lac.o) \ + $(lib-base.o) + + +# We now use the variable defined above which switch between debug and +# optimized mode to select the set of libraries to link with. Included +# in the list of libraries is the name of the object file which we +# will produce from the single C++ file. Note that by default we use +# the extension .g.o for object files compiled in debug mode and .o for +# object files in optimized mode (or whatever the local default on your +# system is instead of .o). +ifeq ($(debug-mode),on) + libraries = $(target).g.$(OBJEXT) $(libs.g) +else + libraries = $(target).$(OBJEXT) $(libs.o) +endif + + +# Now comes the first production rule: how to link the single object +# file produced from the single C++ file into the executable. Since +# this is the first rule in the Makefile, it is the one `make' selects +# if you call it without arguments. +$(target) : $(libraries) + @echo ============================ Linking $@ + @$(CXX) -o $@$(EXEEXT) $^ $(LIBS) $(LDFLAGS) + + +# To make running the application somewhat independent of the actual +# program name, we usually declare a rule `run' which simply runs the +# program. You can then run it by typing `make run'. This is also +# useful if you want to call the executable with arguments which do +# not change frequently. You may then want to add them to the +# following rule: +run: $(target) + @echo ============================ Running $< + @./$(target)$(EXEEXT) + + +# As a last rule to the `make' program, we define what to do when +# cleaning up a directory. This usually involves deleting object files +# and other automatically created files such as the executable itself, +# backup files, and data files. Since the latter are not usually quite +# diverse, you needed to declare them at the top of this file. +clean: + -rm -f *.$(OBJEXT) *~ Makefile.dep $(target)$(EXEEXT) $(clean-up-files) + + +# Since we have not yet stated how to make an object file from a C++ +# file, we should do so now. Since the many flags passed to the +# compiler are usually not of much interest, we suppress the actual +# command line using the `at' sign in the first column of the rules +# and write the string indicating what we do instead. +./%.g.$(OBJEXT) : + @echo ==============debug========= $( $@ \ + || (rm -f $@ ; false) + @if test -s $@ ; then : else rm $@ ; fi + + +# To make the dependencies known to `make', we finally have to include +# them: +include Makefile.dep + + diff --git a/deal.II/examples/step-33/doc/intro.dox b/deal.II/examples/step-33/doc/intro.dox new file mode 100644 index 0000000000..e720513c32 --- /dev/null +++ b/deal.II/examples/step-33/doc/intro.dox @@ -0,0 +1,152 @@ +

Introduction

+ +This program was written for fun by David Neckels (NCAR) while working +at Sandia (on the Wyoming Express bus to and from Corrales each day). +The main purpose was to better understand Euler flow. +The code solves the basic Euler equations of gas dynamics, by using a +fully implicit Newton iteration (inspired by Sandia's Aria code). The +code may be configured by an input deck to run different simulations +on different meshes, with differing boundary conditions. + +The program also uses the Trilinos linear solvers (Aztec/Amesos) and +an automatic differentiation package, Sacado. + +

Euler flow

+ +The equations for a compressible, inviscid gas (the Euler equations) are +a basic system of conservation laws, in spatial dimension $d$, +@f[ +\partial_t \mathbf{w} + \nabla \cdot \mathbf{F}(\mathbf{w}) = \mathbf{0}, +@f] +with $\mathbf{w}=(\rho,\rho v_1,\dots,\rho v_d, E)^{\top}$ for $v_i$ equal to the +flow velocity in spatial direction $i$, $\rho$ equal to the fluid density, and +$E$ the energy of the gas. The flux matrix (or system of flux functions) +are defined such that the entire system of equations are +@f{eqnarray*} + \partial_t \rho + \sum_{s=1}^d \frac{\partial(\rho v_s)}{\partial x_s} &=& 0 \\ + \partial_t (\rho v_i) + \sum_{s=1}^d \frac{\partial(\rho v_i v_s + \delta_{is} p)}{\partial x_s} &=& 0, i=1,\dots,d \\ + \partial_t E + \sum_{s=1}^d \frac{\partial((E+p)v_s)}{\partial x_s} &=& 0 \\ + p = (\gamma -1)(E-\frac{1}{2} \rho |v|^2). +@f} + +For air, $\gamma=1.4$. + +

Discretization

+ +We choose a finite element space $V_h$, and integrate our conservation law against +our (vector) test function $\mathbf{v} \in V_h$. We integrate by parts and approximate the +boundary flux with a numerical flux $\mathbf{H}$, +@f{eqnarray*} +\int_{\Omega} (\partial_t \mathbf{w}, \mathbf{v}) + (\nabla \cdot \mathbf{F}(\mathbf{w}), \mathbf{v}) & \approx & \\ +\int_{\Omega} (\partial_t \mathbf{w}, \mathbf{v}) + (\mathbf{F}(\mathbf{w}), \nabla \mathbf{v}) + h^{\eta}(\nabla \mathbf{w} , \nabla \mathbf{v}) + \int_{\partial \Omega} (\mathbf{H}(\mathbf{w}^+, \mathbf{w}^-, \mathbf{n}), \mathbf{v}^+), +@f} +where $+$ is the interior trace of a function, and $-$ represents the outer trace. +The diffusion term $h^{\eta}(\nabla \mathbf{w} , \nabla \mathbf{v})$ is introduced strictly for stability, + where $h$ is the mesh size and $\eta$ is a parameter prescribing how much diffusion to add. +Depending on the boundary condition, we prescribe the outer trace $\mathbf{w}^-$, + + +For more information, please consult Ralf Hartmann's thesis TODO:Ref. + + +Our full discretization is thus +@f{eqnarray*} +R(\mathbf{W}_{n+1}) = \\ +\int_{\Omega} (\frac{\mathbf{w}_{n+1} - \mathbf{w}_n}{\delta t}, \mathbf{v}) + \int_{\Omega} (\mathbf{F}(\tilde{\mathbf{w}}), \mathbf{v}) + h^{\eta}(\nabla \mathbf{w} , \nabla \mathbf{v}) + \int_{\partial \Omega} (\mathbf{H}(\tilde{\mathbf{w}^+}), \mathbf{w}^-((\tilde{\mathbf{w}^+})), \mathbf{n}), \mathbf{v}) & = & 0 +@f} +where $\tilde{\mathbf{w}} = \theta \mathbf{w}_{n+1} + (1-\theta) \mathbf{w}_n$ for $0 \leq \theta \leq 1$ and +$\mathbf{w}_i = \sum_k \mathbf{W}_i^k \mathbf{\phi}_k$. + +We choose the Lax-Friedrich's flux, +$\mathbf{H}(\mathbf{a},\mathbf{b},\mathbf{n}) = \frac{1}{2}(\mathbf{F}(\mathbf{a})\cdot \mathbf{n} + \mathbf{F}(\mathbf{b})\cdot \mathbf{n} + \alpha (\mathbf{a} - \mathbf{b}))$. + +We solve the nonlinear system by a Newton iteration, i.e. by iterating +@f{eqnarray*} +\partial R(\mathbf{W}^k) \delta \mathbf{W} & = & - R(\mathbf{W}^{k}) \\ +\mathbf{W}^{k+1} &=& \mathbf{W}^k + \delta \mathbf{W}, +@f} +until $|R(\mathbf{W}^k)|$ (the residual) is sufficiently small. + +

Auto-Differentiation

+ +Since computing the Jacobian $\partial R$ is a terrible beast, we use an automatic differentiation package, +Sacado, to do this. Sacado is a C++ type that supports basic arithmetic operators and functions +such as sqrt, sin, cos, pow, etc. One declares a collection Sacado type and then declares +some of this collection as degrees of freedom. These variables are used in an algorithm, and as the variables +are used, their sensitivities with respect to these degrees of freedom are continuously updated. +One can imagine that for the full Jacobian, this could be prohibitively expensive. However, we do +not use the Sacado type for the entire computation, but only element by element. The author has +used this approach side by side with a hand coded Jacobian for the Incompressible Navier-Stokes problem +and found the Sacado approach to be just as fast as using a hand coded Jacobian. Since using the +auto-differentiation requires only that one code the Residual $R(\mathbf{W})$, ensuring code correctness +and maintaining code becomes tremendously more simple. We show a very simple Sacado example: + +@code +#include + +typedef Sacado::Fad::DFad fad_double; + +main() { + + fad_double a,b,c; + + a.diff(0,2); // Set a to be dof 0, in a 2-dof system. + + b.diff(1,2); // Set b to be dof 1, in a 2-dof system. + + a = 1; b = 2; + + c = 2*a+cos(a*b); + + double *derivs = c.fastAccessDx(0); // Access derivatives + + std::cout << "dc/da = " << derivs[0] << ", dc/db=" << derivs[1] << std::endl; + +} +@endcode + +It should be noted that Sacado provides more auto-differentation capabilities than the small subset +that I use in this program. However, if one understands the example above, they will understand +how I use Sacado in this Euler flow program. + +

Trilinos solvers

+The program uses either the Aztec iterative solvers, or the Amesos direct solver, as provided by +the Trilinos package. This package is inherently designed to be used in a parallel program, however, +it may be used in serial just as easily, as is done here. The Epetra package is the basic +vector/matrix library upon which the solvers are built. This very powerful package can be used +to describe the parallel distribution of a vector, and to define sparse matrices that operate +on these vectors. Please view the commented code for more details on how these solvers are used +within the example. + +

Adaptivity

+The example uses an ad-hoc refinement indicator that shows some usefullness in shock-type problems, and +in the downhill flow example included. We refine according to the squared gradient of the density. +Hanging nodes are handled by using computing the numerical flux across cells that are of differing +refinement levels. In this way, the example combines the continuous and DG methodologies. + +Further, we enforce a maximum number of refinement levels to keep refinement under check. It is the +author's experience that adaptivity in a time dependent problem, refinement can easily lead the simulation to +a screeching halt if care is not taken. The amount of refinement is +limited in the example by letting the user specify the +maximum level of refinement that will be present anywhere in the mesh. In this way, refinement +tends not to slow the simulation to a halt. This, of course, is purely a heuristic strategy, and +if the author's advisor heard about it, the author would likely be exiled forever from the finite + element error estimation community. + +

Input Deck

+ +We use an input file deck to drive the simulation. In this way, we can alter the boundary conditions +and other important properties of the simulation without having to recompile. For more information on +the format, look at the results section, where we describe an example file in more detail. + + + + diff --git a/deal.II/examples/step-33/doc/results.dox b/deal.II/examples/step-33/doc/results.dox new file mode 100644 index 0000000000..4e4ad15b43 --- /dev/null +++ b/deal.II/examples/step-33/doc/results.dox @@ -0,0 +1,134 @@ +

Results

+ +We run the problem with the mesh slide.inp and the following input deck: +@verbatim +# Listing of Parameters +# --------------------- + +# The input grid +set mesh=slide.inp + +# Stabilization parameter +set diffusion power = 2.0 + +# Scaled value for gravity. Positive means gravity points down. +set gravity = 1.0 + +# Boundary conditions +# We may specify boundary conditions for up to MAX_BD boundaries. +# Your .inp file should have these boundaries designated. +# +subsection boundary_1 + set no penetration = true # reflective boundary condition +end + +subsection boundary_2 +# outflow boundary + #set w_3 = pressure + #set w_3 value = 1.5 - y +end + +subsection boundary_3 + set no penetration = true # reflective + #set w_3 = pressure + #set w_3 value = 1.0 +end +subsection boundary_4 + set no penetration = true #reflective +end + +# Initial Conditions +# We set the initial conditions of the conservative variables. These lines +# are passed to the expression parsing function. You should use x,y,z for +# the coordinate variables. +# +subsection initial condition + set w_0 value = 0 + set w_1 value = 0 + set w_2 value = 10*(x<-0.7)*(y> 0.3)*(y< 0.45) + (1-(x<-0.7)*(y> 0.3)*(y< 0.45))*1.0 + set w_3 value = (1.5-(1.0*1.0*y))/0.4 +end + +# Time stepping control +# +subsection time stepping + set final time = 10.0 # simulation end time + set time step = 0.02 # simulation time step +end + +subsection linear solver + set output = quiet + set method = gmres + set ilut fill = 1.5 + set ilut drop tolerance = 1e-6 + set ilut absolute tolerance = 1e-6 + set ilut relative tolerance = 1.0 +end + +# Output frequency. +# You may wish to set this > time step if you dont want output at every step +subsection output + set step = 0.01 +end + +# Refinement control +subsection refinement + set refinement = shock # none only other option + set shock value = 1.5 + set shock levels = 1 # how many levels of refinement to allow +end + +# Flux parameters +subsection flux + set stab = mesh + #set stab value = 1.0 +end +@endverbatim + +When we run the program, we get the following kind of output: +@code +T=3.14, Number of active cells: 2617 + Number of degrees of freedom: 11184 +NonLin Res: Lin Iter Lin Res +______________________________________ +* 1.684e-02 0007 1.84e-13 +* 4.414e-05 0006 3.82e-15 +* 1.750e-09 0006 1.56e-19 +* 6.831e-16 0000 1.56e-19 +max_df:124 +T=3.16, Number of active cells: 2626 + Number of degrees of freedom: 11220 +NonLin Res: Lin Iter Lin Res +______________________________________ +* 1.673e-02 0007 9.64e-14 +* 4.230e-05 0006 3.83e-15 +* 8.748e-10 0006 7.67e-20 +* 6.804e-16 0000 7.67e-20 +max_df:124 +T=3.18, Number of active cells: 2644 + Number of degrees of freedom: 11296 +NonLin Res: Lin Iter Lin Res +______________________________________ +* 1.674e-02 0007 9.29e-14 +* 3.306e-05 0007 8.07e-17 +* 4.660e-10 0006 4.05e-20 +* 6.898e-16 0000 4.05e-20 +max_df:128 +T=3.2, Number of active cells: 2647 + Number of degrees of freedom: 11312 +NonLin Res: Lin Iter Lin Res +______________________________________ +... +@endcode + +This output reports the progress of the Newton iterations and the time stepping. + +@image html step-33.slide.gif + +As we see, the heavy mass of fluid is drawn down the slope by gravity, where it collides +with the ski lodge and is flung into the air! Hopefully everyone escapes! + +@image html step-33.slide_adapt.gif + +The adaptivity follows and preceeds the flow pattern, based on this heuristic refinement scheme. + diff --git a/deal.II/examples/step-33/doc/step-33.slide.gif b/deal.II/examples/step-33/doc/step-33.slide.gif new file mode 100644 index 0000000000..1b35b6b886 Binary files /dev/null and b/deal.II/examples/step-33/doc/step-33.slide.gif differ diff --git a/deal.II/examples/step-33/doc/step-33.slide_adapt.gif b/deal.II/examples/step-33/doc/step-33.slide_adapt.gif new file mode 100644 index 0000000000..afefcac800 Binary files /dev/null and b/deal.II/examples/step-33/doc/step-33.slide_adapt.gif differ diff --git a/deal.II/examples/step-33/slide.inp b/deal.II/examples/step-33/slide.inp new file mode 100644 index 0000000000..66684bc8b6 --- /dev/null +++ b/deal.II/examples/step-33/slide.inp @@ -0,0 +1,3560 @@ +1731 1827 0 0 0 +195 -0.964976 0.485465 0.000000 +133 -0.970149 0.500000 0.000000 +67 -1.000000 0.500000 0.000000 +180 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21 +1814 4 line 21 22 +1815 4 line 22 23 +1816 4 line 23 24 +1817 4 line 24 25 +1818 4 line 25 26 +1819 4 line 26 27 +1820 4 line 27 28 +1821 4 line 28 29 +1822 4 line 29 30 +1823 4 line 30 31 +1824 4 line 31 32 +1825 4 line 32 33 +1826 4 line 33 9 + diff --git a/deal.II/examples/step-33/step-33.cc b/deal.II/examples/step-33/step-33.cc new file mode 100644 index 0000000000..bb2389e563 --- /dev/null +++ b/deal.II/examples/step-33/step-33.cc @@ -0,0 +1,2114 @@ +/* step-12.cc,v 1.33 2005/08/08 16:41:40 wolf Exp */ +/* Author: David Neckels, Boulder Colorado 2007 */ +/* step-12.cc,v 1.33 2005/08/08 16:41:40 wolf Exp */ +/* Version: Version-5-2-0 */ +/* */ +/* Copyright (C) 2001, 2002, 2003, 2004, 2005 by the deal.II authors */ +/* */ +/* This file is subject to QPL and may not be distributed */ +/* without copyright and license information. Please refer */ +/* to the file deal.II/doc/license.html for the text and */ +/* further information on this license. */ + + // This program solves the Euler equations + // of gas dynamics for a given configuration + // file. It uses a standard Galerkin approach + // with weakly applied boundary conditions. + + // @sect3{Include files} + + // Aztecoo require mpi (even though we run on only + // one processor in this example). +#include + + // Here we have the necessary TRILINOS includes. + // + // Epetra is the basic trilinos vector/matrix library. +#include +#include +#include +#include +#include + // Teuchos is a Trilinos utility library that is used + // to set parameters within the Aztec solver library. +#include "Teuchos_ParameterList.hpp" + // Aztec is the iterative solver library. +#include +#include +#define HAVE_IFPACK_TEUCHOS +#include + + // Amesos is a direct solver package within Trilinos. +#include + // Sacado is the automatic differentiation package, which + // is used to find the jacobian for a fully implicit Newton + // iteration. +#include + + // A standard set of dealii includes. Nothing special to + // comment on here. +#include +#include +#include +#include + +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +#include +#include +#include + +#include +#include +#include + +#include +#include +#include + // And this again is C++: +#include +#include +#include + + // Introduce the dealii library into the current namespace. +using namespace dealii; + + // We define a shorter name for the automatic differentiation + // type. +typedef Sacado::Fad::DFad fad_double; +typedef unsigned int UInt; + // The Epetra library requires a 'communicator', which describes + // the layout of a parallel (or serial) set of processors. +Epetra_MpiComm *Comm; + + //@sect3{Flux function definition} + // Here we define the flux function for this system of conservation + // laws. Note: it would be terribly difficult to use this example + // to solve some other system of conservation laws. + // + // We define the number of components in the system. Euler's has + // one entry for momenta in each spatial direction, plus the energy + // and density components. +#define N_COMP (2 + DIMENSION) + // Define a handle to the density and energy indices. We have arrange + // the momenta to be first, then density, and, lastly, energy. +#define DENS_IDX DIMENSION +#define ENERGY_IDX (DIMENSION+1) + + // The gas constant. This value is representative of air. +const double GAMMA = 1.4; + // We define the flux functions as one large matrix. Each row of this + // matrix represents a scalar conservation law for the component in + // that row. We template the numerical type of the flux function + // so that we may use the automatic differentiation type here. + // The flux functions are defined in terms of the + // conserved variables $\rho w_0, \dots, \rho w_{d-1}, \rho, E$, + // so they do not look exactly like the Euler equations one is + // used to seeing. We evaluate the flux at a single quadrature + // point. +template +void Flux(std::vector > &flux, + const Point &point, + const std::vector &W) +{ + + // Pressure is a dependent variable: $p = + // (\gamma - 1)(E-\frac{1}{2} \rho |v|^2)$. + number rho_normVsqr; + for (int d0 = 0; d0 < dim; d0++) rho_normVsqr += W[d0]*W[d0]; + // Since W are $\rho v$, we get a $\rho^2$ in the + // numerator, so dividing a $\rho$ out gives the desired $ \rho |v|^2$. + rho_normVsqr /= W[DENS_IDX]; + + number pressure = (GAMMA-1.0)*(W[ENERGY_IDX] - number(0.5)*(rho_normVsqr)); + + // We compute the momentum terms. We divide by the + // density here to get $v_i \rho v_j$ + for (int d = 0; d < dim; d++) { + for (int d1 = 0; d1 < dim; d1++) { + flux[d][d1] = W[d]*W[d1]/W[DENS_IDX]; + } + // The pressure contribution, along the diagonal: + flux[d][d] += pressure; + // Advection/conservation of density: + flux[DENS_IDX][d] = W[d]; + // And, lastly, conservation of energy. + flux[ENERGY_IDX][d] = W[d]/W[DENS_IDX]* + (W[ENERGY_IDX] + pressure); // energy + } +} + + // On the boundaries of the domain and across `hanging nodes` we use + // a numerical flux function to enforce boundary conditions. This routine + // is the basic Lax-Friedrich's flux with a stabilization parameter + // $\alpha$. +template +void LFNumFlux( + std::vector > &nflux, + const std::vector > &points, + const std::vector > &normals, + const std::vector > &Wplus, + const std::vector > &Wminus, + double alpha) +{ + int n_q_points = points.size(); + + // We evaluate the flux at each of the quadrature points. + for (int q = 0; q < n_q_points; q++) { + std::vector > iflux(N_COMP, + std::vector(dim, 0)); + std::vector > oflux(N_COMP, + std::vector(dim, 0)); + + Flux(iflux, points[q], Wplus[q]); + Flux(oflux, points[q], Wminus[q]); + + for (int di = 0; di < N_COMP; di++) { + nflux[q][di] = 0; + for (int d = 0; d < dim; d++) { + nflux[q][di] += 0.5*(iflux[di][d] + oflux[di][d])*normals[q](d); + } + nflux[q][di] += 0.5*alpha*(Wplus[q][di] - Wminus[q][di]); + } + } + +} + + // @sect3{Initial and side condition parsing} + // For the initial condition we use the expression parser function + // object. +template +class InitialCondition : public FunctionParser +{ + public: + InitialCondition (); + + // This function should be called after parsing, but before using + // the object. It formalizes the expressions and initializes the + // function parser with the appropriate expressions. + void Init(); + + // During parsing we call this function as the initial condition + // for one of the $\mathbf{w}$ variables is encountered. + + void set_ic(int _row, std::string &expr) { + expressions[_row] = expr; + } + + virtual void vector_value_list (const std::vector > &points, + std::vector > &value_list) const; + private: + std::vector expressions; +}; + +template +InitialCondition::InitialCondition () : + FunctionParser (N_COMP), + expressions(N_COMP, "0.0") +{} + + // Here we set up x,y,z as the variables that one should use in the input + // deck to describe their initial condition. +template +void InitialCondition::Init() { + std::map constants; + constants["M_PI"] = M_PI; + std::string variables = (dim == 2 ? "x,y" : "x,y,z"); + + FunctionParser::initialize(variables, expressions, constants); + +} + +template +void InitialCondition::vector_value_list (const std::vector > &points, + std::vector > &value_list) const +{ + const unsigned int n_points = points.size(); + + Assert (value_list.size() == n_points, + ExcDimensionMismatch (value_list.size(), n_points)); + + for (unsigned int p=0; p::vector_value (points[p], + value_list[p]); +} + + // As above, we use the expression function parser for boundary conditions. +template +class SideCondition : public FunctionParser +{ + public: + SideCondition (int ncomp); + ~SideCondition (); + + // As above. + void Init(); + // As above. + void set_coeff_row(int _row_n, std::string &expr); + + virtual void vector_value_list (const std::vector > &points, + std::vector > &value_list) const; + private: + std::vector expressions; +}; + +template +SideCondition::SideCondition (int ncomp) : + FunctionParser (ncomp), + expressions(ncomp, "0.0") +{ +} +template +void SideCondition::set_coeff_row (int _row_n, std::string &expr) +{ + expressions[_row_n] = expr; +} + +template +void SideCondition::Init() { + std::map constants; + constants["M_PI"] = M_PI; + std::string variables = (dim == 2 ? "x,y" : "x,y,z"); + + FunctionParser::initialize(variables, expressions, constants); + +} + +template +SideCondition::~SideCondition () +{ +} + +template +void SideCondition::vector_value_list (const std::vector > &points, + std::vector > &value_list) const +{ + const unsigned int n_points = points.size(); + + Assert (value_list.size() == n_points, + ExcDimensionMismatch (value_list.size(), n_points)); + + for (unsigned int p=0; p::vector_value (points[p], + value_list[p]); +} + //@sect3{Conservation Law class} + // Here we define a Conservation Law class that helps group + // operations and data for our Euler equations into a manageable + // entity. Functions will be described as their definitions appear. +template +class ConsLaw +{ + public: + ConsLaw (); + ~ConsLaw (); + + void run (); + void declare_parameters(); + void load_parameters(const char *); + + private: + void build_fe(); + void setup_system (); + void initialize_system (); + void assemble_system (double &res_norm); + void solve (Vector &solution, int &, double &); + void refine_grid (); + void output_results (const unsigned int cycle) const; + void initialize(); + void zero_matrix(); + void estimate(); + void postprocess(); + void compute_predictor(); + + Triangulation triangulation; + const MappingQ1 mapping; + + + FESystem *fe_ptr; + + DoFHandler dof_handler; + + SparsityPattern sparsity_pattern; + const QGauss quadrature; + const QGauss face_quadrature; + + // The actual solution to the Euler equation + Vector solution; + // The current value of the solution during the Newton iteration + Vector nlsolution; + // An estimate of the next time value; used for adaptivity and as a + // guess for the next Newton iteration. + Vector predictor; + // Values after post-processing (used to output the physical variables). + Vector ppsolution; + // The solution to the linear problem during the Newton iteration + Vector dsolution; + Vector right_hand_side; + + public: + + void assemble_cell_term(const FEValues& fe_v, + std::vector &dofs, + unsigned int cell_no + ); + + void assemble_face_term( + int face_no, + const FEFaceValuesBase& fe_v, + const FEFaceValuesBase& fe_v_neighbor, + std::vector &dofs, + std::vector &dofs_neighbor, + int boundary = -1 + ); + + unsigned int get_n_components() const { return N_COMP;} + + private: + // T = current time, dT = time step, TF = final time. + double T, dT, TF; + double face_diameter; + double cell_diameter; + // An object to handle parsing the input deck. + ParameterHandler prm; + // Name of the mesh to read in. + string mesh; + InitialCondition ic; + + // Enums for the various supported boundary conditions. + typedef enum {INFLOW_BC = 1, OUTFLOW_BC=2, NO_PENETRATION_BC=3, PRESSURE_BC=4} bc_type; + + // For each boundary we store a map from boundary # to the type + // of boundary condition. If the boundary condition is prescribed, + // we store a pointer to a function object that will hold the expression + // for that boundary condition. + typedef typename std::map, Function*> > bdry_map_type; + bdry_map_type bdry_map; + + void add_boundary(unsigned int bd, std::vector& flags, Function *bf); + + // An object to store parameter information about the Aztec solver. + typedef struct { + int LIN_OUTPUT; + typedef enum { GMRES = 0, DIRECT = 1} solver_type; + solver_type SOLVER; + typedef enum { QUIET = 0, VERBOSE = 1 } output_type; + output_type OUTPUT; + // Linear residual tolerance. + double RES; + int MAX_ITERS; + // We use the ILUT preconditioner. This is similar + // to the ILU. FILL is the number of extra entries + // to add when forming the ILU decomposition. + double ILUT_FILL; + // When forming the preconditioner, for certain problems + // bad conditioning (or just bad luck) can cause the + // preconditioner to be very poorly conditioned. Hence + // it can help to add diagonal perturbations to the + // original matrix and form the preconditioner for this + // slightly better matrix. ATOL is an absolute perturbation + // that is added to the diagonal before forming the + // prec, and RTOL is a scaling factor $rtol >= 1$. + double ILUT_ATOL; + double ILUT_RTOL; + // The ILUT will drop any values that have magnitude less + // than this value. This is a way to + // manage the amount of memory used by this preconditioner. + double ILUT_DROP; + } solver_params_type; + + solver_params_type solver_params; + + // Some refinement parameters. + typedef struct { + typedef enum { NONE = 0, FIXED_NUMBER = 1, SHOCK = 2} refine_type; + double high_frac; + double low_frac; + refine_type refine; + double high_frac_sav; + double max_cells; + double shock_val; + double shock_levels; + } refinement_params_type; + + refinement_params_type refinement_params; + + // The user can set the stabilization parameter $\alpha$ + // in the Lax-Friedrich's flux. + typedef struct { + typedef enum {CONSTANT=1,MESH=2} LF_stab_type; + LF_stab_type LF_stab; + double LF_stab_value; + } flux_params_type; + + flux_params_type flux_params; + + bool is_stationary; + + // Power for the mesh stabilization term. + double diffusion_power; + double gravity; + // If true, we output the squared gradient of the + // density instead of density. Using this one can + // create shock plots. + bool schlieren_plot; + // How often to create an output file. + double output_step; + + Epetra_CrsMatrix *Matrix; + Epetra_Map *Map; + Vector indicator; + + // Crank-Nicolson value + const double theta; + +}; + + + // Asign a row of the conservation law a specified + // boundary type and (possibly) function. +template +void ConsLaw::add_boundary(unsigned int bd, + std::vector &flags, Function *bf) { + + std::pair, Function *> entry(flags, bf); + bdry_map[bd] = entry; +} + + + // Apply the initialial condition. Simultaneously + // initialize the non-linear solution. +template +void ConsLaw::initialize() { + VectorTools::interpolate(dof_handler, + ic, solution); + VectorTools::interpolate(dof_handler, + ic, nlsolution); + +} + + // @sect3{Assembly} + // @sect4{Function: assemble_cell_term} + // + // Assembles the cell term, adding minus the residual + // to the right hand side, and adding in the Jacobian + // contributions. +template +void ConsLaw::assemble_cell_term( + const FEValues &fe_v, + std::vector &dofs, + unsigned int cell_no + ) +{ + // The residual for each row (i) will be accumulating + // into this fad variable. At the end of the assembly + // for this row, we will query for the sensitivities + // to this variable and add them into the Jacobian. + fad_double F_i; + int dofs_per_cell = fe_v.dofs_per_cell; + int n_q_points = fe_v.n_quadrature_points; + + // We will define the dofs on this cell in these fad variables. + std::vector DOF(dofs_per_cell); + + // Values of the conservative variables at the quadrature points. + std::vector > W (n_q_points, + std::vector(get_n_components())); + + // Values at the last time step of the conservative variables. + // Note that these do not use fad variables, since they do + // not depend on the 'variables to be sought'=DOFS. + std::vector > Wl (n_q_points, + std::vector(get_n_components())); + + // Here we will hold the averaged values of the conservative + // variables that we will linearize around (cn=Crank Nicholson). + std::vector > Wcn (n_q_points, + std::vector(get_n_components())); + + // Gradients of the current variables. It is a + // bit of a shame that we have to compute these; we almost don't. + // The nice thing about a simple conservation law is that the + // the flux doesn't generally involve any gradients. We do + // need these, however, for the diffusion stabilization. + std::vector > > Wgrads (n_q_points, + std::vector >(get_n_components(), + std::vector(dim))); + + + const std::vector &JxW = fe_v.get_JxW_values (); + + + // Here is the magical point where we declare a subset + // of the fad variables as degrees of freedom. All + // calculations that reference these variables (either + // directly or indirectly) will accumulate sensitivies + // with respect to these dofs. + for (int in = 0; in < dofs_per_cell; in++) { + DOF[in] = nlsolution(dofs[in]); + DOF[in].diff(in, dofs_per_cell); + } + + // Here we compute the shape function values and gradients + // at the quadrature points. Ideally, we could call into + // something like get_function_values, get_function_grads, + // but since we don't want to make the entire solution vector + // fad types, only the local cell variables, we explicitly + // code this loop; + for (int q = 0; q < n_q_points; q++) { + for (int di = 0; di < get_n_components(); di++) { + W[q][di] = 0; + Wl[q][di] = 0; + Wcn[q][di] = 0; + for (int d = 0; d < dim; d++) { + Wgrads[q][di][d] = 0; + } + } + for (int sf = 0; sf < dofs_per_cell; sf++) { + int di = fe_v.get_fe().system_to_component_index(sf).first; + W[q][di] += + DOF[sf]*fe_v.shape_value_component(sf, q, di); + Wl[q][di] += + solution(dofs[sf])*fe_v.shape_value_component(sf, q, di); + Wcn[q][di] += + (theta*DOF[sf]+(1-theta)*solution(dofs[sf]))*fe_v.shape_value_component(sf, q, di); + + for (int d = 0; d < dim; d++) { + Wgrads[q][di][d] += DOF[sf]* + fe_v.shape_grad_component(sf, q, di)[d]; + } // for d + + } + + } // for q + + // Gather the flux values for all components at + // all of the quadrature points. This also + // computes the matrix of sensitivities. Perhaps + // this could be done in a better way, since this + // could be a rather large object, but for now it + // seems to work just fine. + std::vector > > flux(n_q_points, + std::vector >(get_n_components(), + std::vector(dim, 0))); + + for (unsigned int q=0; q < n_q_points; ++q) { + Flux(flux[q], fe_v.get_quadrature_points()[q], Wcn[q]); + } + + // We now have all of the function values/grads/fluxes, + // so perform the assembly. We have an outer loop + // through the components of the system, and an + // inner loop over the quadrature points, where we + // accumulate contributions to the ith residual. + // + // We initialy sum all contributions of the residual + // in the positive sense, so that we don't need to + // negative the Jacobian entries. Then, when we sum + // into the right_hand_side vector, + // we negate this residual. + for (unsigned int i=0; iSumIntoGlobalValues(dofs[i], + dofs_per_cell, &values[0], reinterpret_cast(&dofs[0])); + + // Add minus the residual to the right hand side. + right_hand_side(dofs[i]) -= F_i.val(); + + } // for i +} + // @sect4{Function: assemble_face_term} + // These are either + // boundary terms or terms across differing + // levels of refinement. In the first case, + // fe_v==fe_v_neighbor and dofs==dofs_neighbor. + // The int boundary < 0 if not at a boundary, + // otherwise it is the boundary indicator. +template +void ConsLaw::assemble_face_term( + int face_no, + const FEFaceValuesBase& fe_v, + const FEFaceValuesBase& fe_v_neighbor, + std::vector &dofs, + std::vector &dofs_neighbor, + int boundary + ) +{ + fad_double F_i; + const unsigned int n_q_points = fe_v.n_quadrature_points; + const unsigned int dofs_per_cell = fe_v.get_fe().dofs_per_cell; + const unsigned int ndofs_per_cell = fe_v_neighbor.get_fe().dofs_per_cell; + Assert(dofs_per_cell == ndofs_per_cell, + ExcDimensionMismatch(dofs_per_cell, ndofs_per_cell)); + + // As above, the fad degrees of freedom + std::vector DOF(dofs_per_cell+ndofs_per_cell); + + // The conservative variables for this cell, + // and for + std::vector > Wplus (n_q_points, + std::vector(get_n_components())); + std::vector > Wminus (n_q_points, + std::vector(get_n_components())); + + + const std::vector &JxW = fe_v.get_JxW_values (); + const std::vector > &normals = fe_v.get_normal_vectors (); + + + // If we are at a boundary, then dofs_neighbor are + // the same as dofs, so we do not want to duplicate them. + // If there is a neighbor cell, then we want to include + // them. + int ndofs = (boundary < 0 ? dofs_per_cell + ndofs_per_cell : dofs_per_cell); + // Set the local DOFS. + for (int in = 0; in < dofs_per_cell; in++) { + DOF[in] = nlsolution(dofs[in]); + DOF[in].diff(in, ndofs); + } + // If present, set the neighbor dofs. + if (boundary < 0) + for (int in = 0; in < ndofs_per_cell; in++) { + DOF[in+dofs_per_cell] = nlsolution(dofs_neighbor[in]); + DOF[in+dofs_per_cell].diff(in+dofs_per_cell, ndofs); + } + + // Set the values of the local conservative variables. + // Initialize all variables to zero. + for (int q = 0; q < n_q_points; q++) { + for (int di = 0; di < get_n_components(); di++) { + Wplus[q][di] = 0; + Wminus[q][di] = 0; + } + for (int sf = 0; sf < dofs_per_cell; sf++) { + int di = fe_v.get_fe().system_to_component_index(sf).first; + Wplus[q][di] += + (theta*DOF[sf]+(1.0-theta)*solution(dofs[sf]))*fe_v.shape_value_component(sf, q, di); + } + + + // If there is a cell across, then initialize + // the exterior trace as a function of the other + // cell degrees of freedom. + if (boundary < 0) { + for (int sf = 0; sf < ndofs_per_cell; sf++) { + int di = fe_v_neighbor.get_fe().system_to_component_index(sf).first; + Wminus[q][di] += + (theta*DOF[sf+dofs_per_cell]+(1.0-theta)*solution(dofs_neighbor[sf]))* + fe_v_neighbor.shape_value_component(sf, q, di); + } + } + } // for q + + // If this is a boundary, then the values of $W^-$ will + // be either functions of $W^+$, or they will be prescribed. + // This switch sets them appropriately. Since we are + // using fad variables here, sensitivities will be updated + // appropriately. These sensitivities would be tremendously + // difficult to manage without fad!!! + if (boundary >= 0) { + // Get the boundary descriptor. + typename bdry_map_type::iterator bme = bdry_map.find(boundary); + assert(bme != bdry_map.end()); + + // Evaluate the function object. This is a bit + // tricky; a given boundary might have both prescribed + // and implicit values. If a particular component is not + // prescribed, the values evaluate to zero and are + // ignored, below. + std::vector > bvals(n_q_points, Vector(N_COMP)); + bme->second.second->vector_value_list(fe_v.get_quadrature_points(), bvals); + + // We loop the quadrature points, and we treat each + // component individualy. + for (int q = 0; q < n_q_points; q++) { + for (int di = 0; di < get_n_components(); di++) { + + // An inflow/dirichlet type of boundary condition + if (bme->second.first[di] == INFLOW_BC) { + Wminus[q][di] = bvals[q](di); + } else if (bme->second.first[di] == PRESSURE_BC) { + // A prescribed pressure boundary condition. This boundary + // condition is complicated by the fact that even though + // the pressure is prescribed, we really are setting + // the energy index here, which will depend on velocity + // and pressure. So even though this seems like a dirichlet + // type boundary condition, we get sensitivities of + // energy to velocity and density (unless these + // are also prescribed. + fad_double rho_vel_sqr = 0; + fad_double dens; + + dens = bme->second.first[DENS_IDX] == INFLOW_BC ? bvals[q](DENS_IDX) : + Wplus[q][DENS_IDX]; + + for (int d=0; d < dim; d++) { + if (bme->second.first[d] == INFLOW_BC) + rho_vel_sqr += bvals[q](d)*bvals[q](d); + else + rho_vel_sqr += Wplus[q][d]*Wplus[q][d]; + } + rho_vel_sqr /= dens; + // Finally set the energy value as determined by the + // prescribed pressure and the other variables. + Wminus[q][di] = bvals[q](di)/(GAMMA-1.0) + + 0.5*rho_vel_sqr; + + } else if (bme->second.first[di] == OUTFLOW_BC) { + // A free/outflow boundary, very simple. + Wminus[q][di] = Wplus[q][di]; + + } else { + // We must be at a no-penetration boundary. We + // prescribe the velocity (we are dealing with a + // particular component here so that the average + // of the velocities is orthogonal to the surface + // normal. This creates sensitivies of across + // the velocity components. + fad_double vdotn = 0; + for (int d = 0; d < dim; d++) { + vdotn += Wplus[q][d]*normals[q](d); + } + + Wminus[q][di] = Wplus[q][di] - 2.0*vdotn*normals[q](di); + } + } + } // for q + } // b>= 0 + + // Determine the Lax-Friedrich's stability parameter, + // and evaluate the numerical flux function at the quadrature points + std::vector > nflux(n_q_points, std::vector(get_n_components(), 0)); + double alpha = 1; + + switch(flux_params.LF_stab) { + case flux_params_type::CONSTANT: + alpha = flux_params.LF_stab_value; + break; + case flux_params_type::MESH: + alpha = face_diameter/(2.0*dT); + break; + } + + LFNumFlux(nflux, fe_v.get_quadrature_points(), normals, Wplus, Wminus, + alpha); + + // Now assemble the face term + for (unsigned int i=0; iSumIntoGlobalValues(dofs[i], + dofs_per_cell, &values[0], reinterpret_cast(&dofs[0])); + if (boundary < 0) { + Matrix->SumIntoGlobalValues(dofs[i], + dofs_per_cell, &values[dofs_per_cell], reinterpret_cast(&dofs_neighbor[0])); + } + + // And add into the residual + right_hand_side(dofs[i]) -= F_i.val(); + } + +} + // @sect4{Assembling the whole system} + // Now we put all of the assembly pieces together + // in a routine that dispatches the correct + // piece for each cell/face. We keep track of + // the norm of the resdual for the Newton iteration. +template +void ConsLaw::assemble_system (double &res_norm) +{ + FESystem &fe = *fe_ptr; + const unsigned int dofs_per_cell = dof_handler.get_fe().dofs_per_cell; + + // We track the dofs on this cell and (if necessary) + // the adjacent cell. + std::vector dofs (dofs_per_cell); + std::vector dofs_neighbor (dofs_per_cell); + + // First we create the + // ``UpdateFlags'' for the + // ``FEValues'' and the + // ``FEFaceValues'' objects. + UpdateFlags update_flags = update_values + | update_gradients + | update_q_points + | update_JxW_values; + + // Note, that on faces we do not + // need gradients but we need + // normal vectors. + UpdateFlags face_update_flags = update_values + | update_q_points + | update_JxW_values + | update_normal_vectors; + + // On the neighboring cell we only + // need the shape values. Given a + // specific face, the quadrature + // points and `JxW values' are the + // same as for the current cells, + // the normal vectors are known to + // be the negative of the normal + // vectors of the current cell. + UpdateFlags neighbor_face_update_flags = update_values; + + // Then we create the ``FEValues'' + // object. Note, that since version + // 3.2.0 of deal.II the constructor + // of this class takes a + // ``Mapping'' object as first + // argument. Although the + // constructor without ``Mapping'' + // argument is still supported it + // is recommended to use the new + // constructor. This reduces the + // effect of `hidden magic' (the + // old constructor implicitely + // assumes a ``MappingQ1'' mapping) + // and makes it easier to change + // the mapping object later. + FEValues fe_v ( + mapping, fe, quadrature, update_flags); + + // Similarly we create the + // ``FEFaceValues'' and + // ``FESubfaceValues'' objects for + // both, the current and the + // neighboring cell. Within the + // following nested loop over all + // cells and all faces of the cell + // they will be reinited to the + // current cell and the face (and + // subface) number. + FEFaceValues fe_v_face ( + mapping, fe, face_quadrature, face_update_flags); + FESubfaceValues fe_v_subface ( + mapping, fe, face_quadrature, face_update_flags); + FEFaceValues fe_v_face_neighbor ( + mapping, fe, face_quadrature, neighbor_face_update_flags); + FESubfaceValues fe_v_subface_neighbor ( + mapping, fe, face_quadrature, neighbor_face_update_flags); + + // Furthermore we need some cell + // iterators. + typename DoFHandler::active_cell_iterator + cell = dof_handler.begin_active(), + endc = dof_handler.end(); + + // Now we start the loop over all + // active cells. + int fdofs_per_cell = fe_v.dofs_per_cell; + int fn_q_points = face_quadrature.n_quadrature_points; + + unsigned int cell_no = 0; + for (;cell!=endc; ++cell, ++cell_no) + { + + // Now we reinit the ``FEValues'' + // object for the current cell + fe_v.reinit (cell); + + // Collect the local dofs and + // asssemble the cell term. + cell->get_dof_indices (dofs); + + cell_diameter = cell->diameter(); + + assemble_cell_term(fe_v, + dofs, + cell_no); + + // We use the DG style loop through faces + // to determine if we need to apply a + // 'hanging node' flux calculation or a boundary + // computation. + for (unsigned int face_no=0; face_no::faces_per_cell; ++face_no) + { + // First we set the face + // iterator + typename DoFHandler::face_iterator face=cell->face(face_no); + face_diameter = face->diameter(); + + if (face->at_boundary()) + { + // We reinit the + // ``FEFaceValues'' + // object to the + // current face + fe_v_face.reinit (cell, face_no); + + // and assemble the + // corresponding face + // terms. We send the same + // fe_v and dofs as described + // in the assembly routine. + assemble_face_term( + face_no, fe_v_face, + fe_v_face, + dofs, + dofs, + face->boundary_indicator()); + } + else + { + // Now we are not on + // the boundary of the + // domain, therefore + // there must exist a + // neighboring cell. + typename DoFHandler::cell_iterator neighbor= + cell->neighbor(face_no);; + + if (face->has_children()) + { + // case I: This cell refined compared to neighbor + + const unsigned int neighbor2= + cell->neighbor_of_neighbor(face_no); + + + // We loop over + // subfaces + for (unsigned int subface_no=0; + subface_no::subfaces_per_face; + ++subface_no) + { + typename DoFHandler::active_cell_iterator + neighbor_child + = cell->neighbor_child_on_subface (face_no, subface_no); + + face_diameter = neighbor_child->diameter(); // working on subface + + Assert (neighbor_child->face(neighbor2) == face->child(subface_no), + ExcInternalError()); + Assert (!neighbor_child->has_children(), ExcInternalError()); + + fe_v_subface.reinit (cell, face_no, subface_no); + fe_v_face_neighbor.reinit (neighbor_child, neighbor2); + neighbor_child->get_dof_indices (dofs_neighbor); + + // Assemble as if we are working with + // a DG element. + assemble_face_term( + face_no, fe_v_subface, + fe_v_face_neighbor, + dofs, + dofs_neighbor); + + } + // End of ``if + // (face->has_children())'' + } + else + { + // We have no children, but + // the neighbor cell may be refine + // compared to use + neighbor->get_dof_indices (dofs_neighbor); + if (neighbor->level() != cell->level()) + { + // case II: This is refined compared to neighbor + Assert(neighbor->level() < cell->level(), ExcInternalError()); + const std::pair faceno_subfaceno= + cell->neighbor_of_coarser_neighbor(face_no); + const unsigned int neighbor_face_no=faceno_subfaceno.first, + neighbor_subface_no=faceno_subfaceno.second; + + Assert (neighbor->neighbor_child_on_subface (neighbor_face_no, + neighbor_subface_no) + == cell, + ExcInternalError()); + + // Reinit the + // appropriate + // ``FEFaceValues'' + // and assemble + // the face + // terms. + fe_v_face.reinit (cell, face_no); + fe_v_subface_neighbor.reinit (neighbor, neighbor_face_no, + neighbor_subface_no); + + assemble_face_term( + face_no, fe_v_face, + fe_v_subface_neighbor, + dofs, + dofs_neighbor); + + } + + } + // End of ``face not at boundary'': + } + // End of loop over all faces: + } + + // End iteration through cells. + } + + // Notify Epetra that the matrix is done. + Matrix->FillComplete(); + + // Compute the nonlinear residual. + res_norm = right_hand_side.l2_norm(); + +} + + // Create a conservation law with some defaults. +template +ConsLaw::ConsLaw () + : + mapping (), + fe_ptr(NULL), + dof_handler (triangulation), + quadrature (2), + face_quadrature (2), + T(0), + dT(0.05), + TF(10), + Map(NULL), + Matrix(NULL), + is_stationary(false), + theta(0.5) +{} + + // At one time this example could work for both DG and + // continuous finite elements. The choice was made here. +template +void ConsLaw::build_fe() { + fe_ptr = new FESystem(FE_Q(1), N_COMP); +} + + // Bye bye Conservation law. +template +ConsLaw::~ConsLaw () +{ + dof_handler.clear (); + delete fe_ptr; +} + + // @sect3{Initialize System} + // Sizes all of the vectors and sets up the + // sparsity patter. This function is called at + // the very beginning of a simulation. The function + // setup_system repeats some of these + // chores and is called after adaptivity in leiu + // of this function. +template +void ConsLaw::initialize_system () +{ + // First we need to distribute the + // DoFs. + dof_handler.clear(); + dof_handler.distribute_dofs (*fe_ptr); + + // Size all of the fields. + solution.reinit (dof_handler.n_dofs()); + nlsolution.reinit (dof_handler.n_dofs()); + predictor.reinit (dof_handler.n_dofs()); + ppsolution.reinit (dof_handler.n_dofs()); + dsolution.reinit (dof_handler.n_dofs()); + right_hand_side.reinit (dof_handler.n_dofs()); + indicator.reinit(triangulation.n_active_cells()); +} + + // @sect3{Setup System} + // We call this function to build the sparsity + // and the matrix. +template +void ConsLaw::setup_system () +{ + + // The DoFs of a cell are coupled + // with all DoFs of all neighboring + // cells. Therefore the maximum + // number of matrix entries per row + // is needed when all neighbors of + // a cell are once more refined + // than the cell under + // consideration. + sparsity_pattern.reinit (dof_handler.n_dofs(), + dof_handler.n_dofs(), + (GeometryInfo::faces_per_cell + *GeometryInfo::subfaces_per_face+1)*fe_ptr->dofs_per_cell); + + // Since the continuous sparsity pattern is + // a subset of the DG one, and since we need + // the DG terms for handling hanging nodes, we use + // the flux pattern. + DoFTools::make_flux_sparsity_pattern (dof_handler, sparsity_pattern); + + sparsity_pattern.compress(); + + // Rebuild the map. In serial this doesn't do much, + // but is needed. In parallel, this would desribe + // the parallel dof layout. + if (Map) delete Map; + Map = new Epetra_Map(dof_handler.n_dofs(), 0, *Comm); + + // Epetra can build a more efficient matrix if + // one knows ahead of time the maxiumum number of + // columns in any row entry. We traverse the sparsity + // to discover this. + int cur_row = 0; + int cur_col = 0; + int max_df = -1; + for (SparsityPattern::iterator s_i = sparsity_pattern.begin(); + s_i != sparsity_pattern.end(); s_i++) { + if (s_i->row() != cur_row) { + cur_col = 0; + cur_row = s_i->row(); + } + cur_col++; + if (cur_col >= max_df) max_df = cur_col; + } + + if (cur_col >= max_df) max_df = cur_col; + std::cout << "max_df:" << max_df << std::endl; + + // Now we build the matrix, using the constructor + // that optimizes with the max_df variable. + if (Matrix) delete Matrix; + Matrix = new Epetra_CrsMatrix(Copy, *Map, max_df+1, true); + + // We add the sparsity pattern to the matrix by + // inserting zeros. + std::vector vals(max_df, 0); + std::vector row_indices(max_df); + + cur_row = 0; + cur_col = 0; + for (SparsityPattern::iterator s_i = sparsity_pattern.begin(); + s_i != sparsity_pattern.end(); s_i++) { + if (s_i->row() != cur_row) { + Matrix->InsertGlobalValues(cur_row, cur_col, &vals[0], &row_indices[0]); + cur_col = 0; + cur_row = s_i->row(); + } + row_indices[cur_col++] = s_i->column(); + } + // The last row. + Matrix->InsertGlobalValues(cur_row, cur_col, &vals[0], &row_indices[0]); + + // Epetra requires this function after building or + // filling a matrix. It typically does some parallel + // bookeeping; perhaps more. + Matrix->FillComplete(); + +} + + // @sect3{Solving the linear system} + // Actually solve the linear system, using either + // Aztec of Amesos. +template +void ConsLaw::solve (Vector &dsolution, int &niter, double &lin_residual) +{ + + // We must hand the solvers Epetra vectors. + // Luckily, they support the concept of a + // 'view', so we just send in a pointer to our + // dealii vectors. + Epetra_Vector x(View, *Map, dsolution.begin()); + Epetra_Vector b(View, *Map, right_hand_side.begin()); + + // The Direct option selects the Amesos solver. + if (solver_params.SOLVER == solver_params_type::DIRECT) { + + // Setup for solving with + // Amesos. + Epetra_LinearProblem prob; + prob.SetOperator(Matrix); + Amesos_BaseSolver *solver; + Amesos Factory; + + // Other solvers are available + // and may be selected by changing this + // string. + char *stype = "Amesos_Klu"; + + solver = Factory.Create(stype, prob); + + Assert (solver != NULL, ExcInternalError()); + + // There are two parts to the direct solve. + // As I understand, the symbolic part figures + // out the sparsity patterns, and then the + // numerical part actually performs Gaussian + // elimination or whatever the approach is. + if (solver_params.OUTPUT == solver_params_type::VERBOSE) + std::cout << "Starting Symbolic fact\n" << std::flush; + + solver->SymbolicFactorization(); + + if (solver_params.OUTPUT == solver_params_type::VERBOSE) + std::cout << "Starting Numeric fact\n" << std::flush; + + solver->NumericFactorization(); + + + // Define the linear problem by setting the + // right hand and left hand sides. + prob.SetRHS(&b); + prob.SetLHS(&x); + // And finally solve the problem. + if (solver_params.OUTPUT == solver_params_type::VERBOSE) + std::cout << "Starting solve\n" << std::flush; + solver->Solve(); + niter = 0; + lin_residual = 0; + + // We must free the solver that was created + // for us. + delete solver; + + } else if (solver_params.SOLVER == solver_params_type::GMRES) { + + // For the iterative solvers, we use Aztec. + AztecOO Solver; + + // Select the appropriate level of verbosity. + if (solver_params.OUTPUT == solver_params_type::QUIET) + Solver.SetAztecOption(AZ_output, AZ_none); + + if (solver_params.OUTPUT == solver_params_type::VERBOSE) + Solver.SetAztecOption(AZ_output, AZ_all); + + // Select gmres. Other solvers are available. + Solver.SetAztecOption(AZ_solver, AZ_gmres); + Solver.SetRHS(&b); + Solver.SetLHS(&x); + + // Set up the ILUT preconditioner. I do not know + // why, but we must pretend like we are in parallel + // using domain decomposition or the preconditioner + // refuses to activate. + Solver.SetAztecOption(AZ_precond, AZ_dom_decomp); + Solver.SetAztecOption(AZ_subdomain_solve, AZ_ilut); + Solver.SetAztecOption(AZ_overlap, 0); + Solver.SetAztecOption(AZ_reorder, 0); + + // ILUT parameters as described above. + Solver.SetAztecParam(AZ_drop, solver_params.ILUT_DROP); + Solver.SetAztecParam(AZ_ilut_fill, solver_params.ILUT_FILL); + Solver.SetAztecParam(AZ_athresh, solver_params.ILUT_ATOL); + Solver.SetAztecParam(AZ_rthresh, solver_params.ILUT_RTOL); + Solver.SetUserMatrix(Matrix); + + // Run the solver iteration. Collect the number + // of iterations and the residual. + Solver.Iterate(solver_params.MAX_ITERS, solver_params.RES); + niter = Solver.NumIters(); + lin_residual = Solver.TrueResidual(); + } +} + + // @sect3{Postprocessing and Output} + // Recover the physical variables from the conservative + // variables so that output will be (perhaps) more + // meaningfull. +template +void ConsLaw::postprocess() { + const unsigned int dofs_per_cell = dof_handler.get_fe().dofs_per_cell; + std::vector dofs (dofs_per_cell); + UpdateFlags update_flags = update_values + | update_gradients + | update_q_points + | update_JxW_values; + UpdateFlags update_flags1 = update_values + | update_gradients + | update_q_points + | update_JxW_values; + + QGauss quadrature_formula(4); + + const std::vector > &us = fe_ptr->base_element(0).get_unit_support_points(); + + + Quadrature unit_support(us); + + int n_q_points = quadrature_formula.n_quadrature_points; + int n_uq_points = unit_support.n_quadrature_points; + + FEValues fe_v ( + mapping, *fe_ptr, quadrature_formula, update_flags); + + FEValues fe_v_unit ( + mapping, *fe_ptr, unit_support, update_flags1); + + std::vector > U(n_uq_points, + Vector(get_n_components())); + std::vector > UU(n_q_points, + Vector(get_n_components())); + std::vector > > dU(n_uq_points, + std::vector >(get_n_components())); + + typename DoFHandler::active_cell_iterator + cell = dof_handler.begin_active(), + endc = dof_handler.end(); + + // Loop the cells + for (unsigned int cell_no=0; cell!=endc; ++cell, ++cell_no) { + cell->get_dof_indices (dofs); + fe_v_unit.reinit(cell); + fe_v.reinit(cell); + + fe_v_unit.get_function_values(solution, U); + fe_v_unit.get_function_grads(solution, dU); + fe_v.get_function_values(solution, UU); + + const std::vector &JxW = fe_v.get_JxW_values (); + + for (int q = 0; q < fe_v.get_fe().base_element(0).n_dofs_per_cell(); q++) { + unsigned int didx = fe_v.get_fe().component_to_system_index(DENS_IDX, q); + unsigned int eidx = fe_v.get_fe().component_to_system_index(ENERGY_IDX, q); + double rho_normVsqr = 0; + for (int d = 0; d < dim; d++) { + unsigned int vidx = fe_v.get_fe().component_to_system_index(d, q); + ppsolution(dofs[vidx]) = solution(dofs[vidx])/solution(dofs[didx]); + rho_normVsqr += solution(dofs[vidx])*solution(dofs[vidx]); + } + rho_normVsqr /= solution(dofs[didx]); + // Pressure + ppsolution(dofs[eidx]) = (GAMMA-1.0)*(solution(dofs[eidx]) - 0.5*rho_normVsqr); + + // Either output density or gradient squared of density, + // depending on what the user wants. + if (!schlieren_plot) { + ppsolution(dofs[didx]) = solution(dofs[didx]); + } else { + double ng = 0; + for (int i = 0; i < dim; i++) ng += dU[q][DENS_IDX][i]*dU[q][DENS_IDX][i]; + ng = std::sqrt(ng); + ppsolution(dofs[didx]) = ng; + } + } + + } // cell + +} + + // Loop and assign a value for refinement. We + // simply use the density squared, which selects + // shocks with some success. +template +void ConsLaw::estimate() { + + const unsigned int dofs_per_cell = dof_handler.get_fe().dofs_per_cell; + std::vector dofs (dofs_per_cell); + UpdateFlags update_flags = update_values + | update_gradients + | update_q_points + | update_JxW_values; + + QGauss quadrature_formula(1); + int n_q_points = quadrature_formula.n_quadrature_points; + + + FEValues fe_v ( + mapping, *fe_ptr, quadrature_formula, update_flags); + + std::vector > U(n_q_points, + Vector(get_n_components())); + std::vector > > dU(n_q_points, + std::vector >(get_n_components())); + + typename DoFHandler::active_cell_iterator + cell = dof_handler.begin_active(), + endc = dof_handler.end(); + for (unsigned int cell_no=0; cell!=endc; ++cell, ++cell_no) { + fe_v.reinit(cell); + + fe_v.get_function_values(predictor, U); + fe_v.get_function_grads(predictor, dU); + + indicator(cell_no) = 0; + for (int q = 0; q < n_q_points; q++) { + double ng = 0; + for (int d = 0; d < dim; d++) ng += dU[q][DENS_IDX][d]*dU[q][DENS_IDX][d]; + + indicator(cell_no) += std::log(1+std::sqrt(ng)); + + } + indicator(cell_no) /= n_q_points; + + } +} + +template +void ConsLaw::refine_grid () +{ + + SolutionTransfer soltrans(dof_handler); + + typename DoFHandler::active_cell_iterator + cell = dof_handler.begin_active(), + endc = dof_handler.end(); + + // Loop cells. If the indicator + // for the cell matches the refinement criterion, + // refine, else unrefine. The unrefinement has + // a slight hysterisis to avoid 'flashing' from refined + // to unrefined. + for (unsigned int cell_no=0; cell!=endc; ++cell, ++cell_no) { + cell->clear_coarsen_flag(); + cell->clear_refine_flag(); + if (cell->level() < refinement_params.shock_levels && + std::fabs(indicator(cell_no)) > refinement_params.shock_val ) { + cell->set_refine_flag(); + } else { + if (cell->level() > 0 && + std::fabs(indicator(cell_no)) < 0.75*refinement_params.shock_val) + cell->set_coarsen_flag(); + } + } + + // The following code prolongs the solution + // to the new grid and carries out the refinement. + std::vector > interp_in; + std::vector > interp_out; + + interp_in.push_back(solution); + interp_in.push_back(predictor); + + triangulation.prepare_coarsening_and_refinement(); + soltrans.prepare_for_coarsening_and_refinement(interp_in); + + triangulation.execute_coarsening_and_refinement (); + + dof_handler.clear(); + dof_handler.distribute_dofs (*fe_ptr); + + { + Vector new_solution(1); + Vector new_predictor(1); + + interp_out.push_back(new_solution); + interp_out.push_back(new_predictor); + interp_out[0].reinit(dof_handler.n_dofs()); + interp_out[1].reinit(dof_handler.n_dofs()); + } + + soltrans.interpolate(interp_in, interp_out); + + // Let the vector delete a very small vector + solution.reinit(1); + predictor.reinit(1); + solution.swap(interp_out[0]); + predictor.swap(interp_out[1]); + + // resize these vectors for the new grid. + nlsolution.reinit(dof_handler.n_dofs()); + ppsolution.reinit(dof_handler.n_dofs()); + nlsolution = solution; + dsolution.reinit (dof_handler.n_dofs()); + right_hand_side.reinit (dof_handler.n_dofs()); + + indicator.reinit(triangulation.n_active_cells()); + +} + +template +void ConsLaw::output_results (const unsigned int cycle) const +{ + char filename[512]; + std::sprintf(filename, "solution-%03d.vtk", cycle); + std::ofstream output (filename); + + DataOut data_out; + data_out.attach_dof_handler (dof_handler); + std::vector solution_names; + + // Rename the output with the physical variable + // names. Send the post-processed values. + solution_names.clear(); + for (int i = 0; i < dim; i++) { + char buf[512]; + std::sprintf(buf, "v_%d", i); + solution_names.push_back (buf); + } + solution_names.push_back("density"); + solution_names.push_back("pressure"); + data_out.add_data_vector (ppsolution, solution_names); + + data_out.add_data_vector (indicator, "error"); + data_out.build_patches (); + data_out.write_vtk (output); + + output.close(); +} + + // @sect3{Parsing the Input Deck} + // Declare the parameters for the + // input deck. We assume a certain + // maximum number of boundaries and process + // any boundary the user supplies up to + // that maximum number. We + // leave a detailed explanation of these + // parameters to our description of the input + // sample file. +const UInt MAX_BD = 10; +template +void ConsLaw::declare_parameters() { + + // Global scope parameters/ + prm.declare_entry("mesh", "grid.inp", + Patterns::Anything(), + "intput file"); + + prm.declare_entry("diffusion power", "2.0", + Patterns::Double(), + "power of mesh size for diffusion"); + + prm.declare_entry("gravity", "0.0", + Patterns::Double(), + "gravity forcing"); + + // Time stepping block + prm.enter_subsection("time stepping"); + prm.declare_entry("time step", "0.1", + Patterns::Double(), + "simulation time step"); + prm.declare_entry("final time", "10.0", + Patterns::Double(), + "simulation end time"); + prm.leave_subsection(); + + + // Declare the boundary parameters + for (int b = 0; b < MAX_BD; b++) { + char bd[512]; + std::sprintf(bd, "boundary_%d", b); + prm.enter_subsection(bd); + prm.declare_entry("no penetration", "false", + Patterns::Selection("true|false"), + ""); + // declare a slot for each of the conservative + // variables. + for (int di = 0; di < N_COMP; di++) { + char var[512]; + std::sprintf(var, "w_%d", di); + prm.declare_entry(var, "outflow", + Patterns::Selection( + "inflow|outflow|pressure"), + ""); + + // for dirichlet, a function in x,y,z + std::sprintf(var, "w_%d value", di); + prm.declare_entry(var, "0.0", + Patterns::Anything(), + "expression in x,y,z"); + } + + prm.leave_subsection(); + } + + // Initial condition block. + prm.enter_subsection("initial condition"); + for (int di = 0; di < N_COMP; di++) { + char var[512]; + std::sprintf(var, "w_%d", di); + + // for dirichlet, a function in x,y,z + std::sprintf(var, "w_%d value", di); + prm.declare_entry(var, "0.0", + Patterns::Anything(), + "expression in x,y,z"); + } + prm.leave_subsection(); + + // The linear solver block. + prm.enter_subsection("linear solver"); + prm.declare_entry("output", "quiet", + Patterns::Selection( + "quiet|verbose"), + ""); + prm.declare_entry("method", "gmres", + Patterns::Selection( + "gmres|direct"), + ""); + prm.declare_entry("residual", "1e-10", + Patterns::Double(), + "linear solver residual"); + prm.declare_entry("max iters", "300", + Patterns::Double(), + "maximum solver iterations"); + prm.declare_entry("ilut fill", "2", + Patterns::Double(), + "ilut preconditioner fill"); + prm.declare_entry("ilut absolute tolerance", "1e-9", + Patterns::Double(), + "ilut preconditioner tolerance"); + prm.declare_entry("ilut relative tolerance", "1.1", + Patterns::Double(), + "rel tol"); + prm.declare_entry("ilut drop tolerance", "1e-10", + Patterns::Double(), + "ilut drop tol"); + prm.leave_subsection(); + + + // A refinement controller block. + prm.enter_subsection("refinement"); + prm.declare_entry("refinement", "none", + Patterns::Selection( + "none|fixed number|shock"), + ""); + prm.declare_entry("refinement fraction", "0.1", + Patterns::Double(), + "Fraction of high refinement"); + prm.declare_entry("unrefinement fraction", "0.1", + Patterns::Double(), + "Fraction of low unrefinement"); + prm.declare_entry("max elements", "1000000", + Patterns::Double(), + "maximum number of elements"); + prm.declare_entry("shock value", "4.0", + Patterns::Double(), + "value for shock indicator"); + prm.declare_entry("shock levels", "3.0", + Patterns::Double(), + "number of shock refinement levels"); + prm.leave_subsection(); + + // Output control. + prm.enter_subsection("output"); + prm.declare_entry("density", "standard", + Patterns::Selection( + "standard|schlieren"), + ""); + prm.declare_entry("step", "-1", + Patterns::Double(), + "output once per this period"); + prm.leave_subsection(); + + // Flux control + prm.enter_subsection("flux"); + prm.declare_entry("stab", "alpha", + Patterns::Selection( + "alpha|constant|mesh"), + ""); + prm.declare_entry("stab value", "1", + Patterns::Double(), + "alpha stabilization"); + prm.leave_subsection(); + + +} + + // Code to actually parse an input file. This function + // matches the declarations above. +template +void ConsLaw::load_parameters(const char *infile){ + + prm.read_input(infile); + + // The global parameters. + mesh = prm.get("mesh"); + + diffusion_power = prm.get_double("diffusion power"); + + gravity = prm.get_double("gravity"); + + // The time stepping. + prm.enter_subsection("time stepping"); + dT = prm.get_double("time step"); + std::cout << "dT=" << dT << std::endl; + if (dT == 0) { + is_stationary = true; + dT = 1.0; + TF = 1.0; + std::cout << "Stationary mode" << std::endl; + } + TF = prm.get_double("final time"); + std::cout << "TF=" << TF << std::endl; + prm.leave_subsection(); + + // The boundary info + for (int b = 0; b < MAX_BD; b++) { + std::vector flags(N_COMP, OUTFLOW_BC); + + // Define a parser for every boundary, though it may be + // unused. + SideCondition *sd = new SideCondition(N_COMP); + char bd[512]; + std::sprintf(bd, "boundary_%d", b); + prm.enter_subsection(bd); + + const std::string &nopen = prm.get("no penetration"); + + // Determine how each component is handled. + for (int di = 0; di < N_COMP; di++) { + char var[512]; + std::sprintf(var, "w_%d", di); + std::string btype = prm.get(var); + std::sprintf(var, "w_%d value", di); + std::string var_value = prm.get(var); + + if (di < dim && nopen == "true") { + flags[di] = NO_PENETRATION_BC; + } else if (btype == "inflow") { + flags[di] = INFLOW_BC; + sd->set_coeff_row(di, var_value); + } else if (btype == "pressure") { + flags[di] = PRESSURE_BC; + sd->set_coeff_row(di, var_value); + } + } + prm.leave_subsection(); + + // Add the boundary condition to the law. + sd->Init(); + add_boundary(b, flags, sd); + } + + // Initial conditions. + prm.enter_subsection("initial condition"); + for (int di = 0; di < N_COMP; di++) { + char var[512]; + + std::sprintf(var, "w_%d value", di); + std::string var_value = prm.get(var); + ic.set_ic(di, var_value); + } + ic.Init(); + prm.leave_subsection(); + + // The linear solver. + prm.enter_subsection("linear solver"); + const std::string &op = prm.get("output"); + if (op == "verbose") solver_params.OUTPUT = solver_params_type::VERBOSE; + if (op == "quiet") solver_params.OUTPUT = solver_params_type::QUIET; + const std::string &sv = prm.get("method"); + if (sv == "direct") { + solver_params.SOLVER = solver_params_type::DIRECT; + } else if (sv == "gmres") { + solver_params.SOLVER = solver_params_type::GMRES; + } + + solver_params.RES = prm.get_double("residual"); + solver_params.MAX_ITERS = (int) prm.get_double("max iters"); + solver_params.ILUT_FILL = prm.get_double("ilut fill"); + solver_params.ILUT_ATOL = prm.get_double("ilut absolute tolerance"); + solver_params.ILUT_RTOL = prm.get_double("ilut relative tolerance"); + solver_params.ILUT_DROP = prm.get_double("ilut drop tolerance"); + solver_params.RES = prm.get_double("residual"); + prm.leave_subsection(); + + + // And refiement. + prm.enter_subsection("refinement"); + const std::string &ref = prm.get("refinement"); + if (ref == "none") { + refinement_params.refine = refinement_params_type::NONE; + } else if (ref == "fixed number") { + refinement_params.refine = refinement_params_type::FIXED_NUMBER; + } else if (ref == "shock") { + refinement_params.refine = refinement_params_type::SHOCK; + } else + refinement_params.high_frac = prm.get_double("refinement fraction"); + refinement_params.high_frac_sav = refinement_params.high_frac; + refinement_params.low_frac = prm.get_double("unrefinement fraction"); + refinement_params.max_cells = prm.get_double("max elements"); + refinement_params.shock_val = prm.get_double("shock value"); + refinement_params.shock_levels = prm.get_double("shock levels"); + prm.leave_subsection(); + + // Output control. + prm.enter_subsection("output"); + const std::string &dens = prm.get("density"); + schlieren_plot = dens == "schlieren" ? true : false; + output_step = prm.get_double("step"); + prm.leave_subsection(); + + // Flux control. + prm.enter_subsection("flux"); + const std::string &stab = prm.get("stab"); + if (stab == "constant") { + flux_params.LF_stab = flux_params_type::CONSTANT; + } else if (stab == "mesh ") { + flux_params.LF_stab = flux_params_type::MESH; + } + flux_params.LF_stab_value = prm.get_double("stab value"); + prm.leave_subsection(); + + +} + +template +void ConsLaw::zero_matrix() { + Matrix->PutScalar(0); Matrix->FillComplete(); +} + + // We use a predictor to try and make adaptivity + // work better. The idea is to try and refine ahead + // of a front, rather than stepping into a coarse + // set of elements and smearing the solution. This + // simple time extrapolator does the job. +template +void ConsLaw::compute_predictor() { + predictor = nlsolution; + predictor.sadd(3/2.0, -1/2.0, solution); +} + + // @sect3{Run the simulation} Contains the initialization, + // the time loop, and the inner Newton iteration. +template +void ConsLaw::run () +{ + + // Open and load the mesh. + GridIn grid_in; + grid_in.attach_triangulation(triangulation); + std::cout << "Opening mesh <" << mesh << ">" << std::endl; + std::ifstream input_file(mesh.c_str(), std::ios::in); + + Assert (infile, + ExcFileNotOpen()); + + grid_in.read_ucd(input_file); + input_file.close(); + + build_fe(); + + unsigned int nstep = 0; + + // Initialize fields and matrices. + initialize_system (); + setup_system(); + initialize(); + predictor = solution; + + // Initial refinement. We apply the ic, + // estimate, refine, and repeat until + // happy. + if (refinement_params.refine != refinement_params_type::NONE) + for (int i = 0; i < refinement_params.shock_levels; i++) { + estimate(); + refine_grid(); + setup_system(); + initialize(); + predictor = solution; + } + postprocess(); + output_results (nstep); + + // Determine when we will output next. + double next_output = T + output_step; + + // @sect4{Main time stepping loop} + predictor = solution; + while(T < TF) + { + std::cout << "T=" << T << ", "; + + + std::cout << " Number of active cells: " + << triangulation.n_active_cells() + << std::endl; + + + std::cout << " Number of degrees of freedom: " + << dof_handler.n_dofs() + << std::endl; + + bool nonlin_done = false; + double res_norm; + int lin_iter; + + // Print some relevant information during the + // Newton iteration. + std::cout << "NonLin Res: Lin Iter Lin Res" << std::endl; + std::cout << "______________________________________" << std::endl; + + int max_nonlin = 7; + int nonlin_iter = 0; + double lin_res; + + // @sect5{Newton iteration} + nlsolution = predictor; + while (!nonlin_done) { + lin_iter = 0; + zero_matrix(); + right_hand_side = 0; + assemble_system (res_norm); + // Flash a star to the screen so one can + // know when the assembly has stopped and the linear + // solution is starting. + std::cout << "* " << std::flush; + + // Test against a (hardcoded) nonlinear tolderance. + // Do not solve the linear system at the last step + // (since it would be a waste). + + if (fabs(res_norm) < 1e-10) { + nonlin_done = true; + } else { + // Solve the linear system and update with the + // delta. + dsolution = 0; + solve (dsolution, lin_iter, lin_res); + nlsolution.add(1.0, dsolution); + } + + // Print the residuals. + std::printf("%-16.3e %04d %-5.2e\n", + res_norm, lin_iter, lin_res); + + nonlin_iter++; + } + + // Various post convergence tasks. + compute_predictor(); + + solution = nlsolution; + + + estimate(); + + postprocess(); + + T += dT; + + // Output if it is time. + if (output_step < 0) { + output_results (++nstep); + } else if (T >= next_output) { + output_results (++nstep); + next_output += output_step; + } + + // Refine, if refinement is selected. + if (refinement_params.refine != refinement_params_type::NONE) { + refine_grid(); + setup_system(); + } + } +} + + // The following ``main'' function is + // similar to previous examples and + // need not to be commented on. +int main (int argc, char *argv[]) +{ + + MPI_Init(&argc, &argv); + Comm = new Epetra_MpiComm(MPI_COMM_WORLD); + + if (argc != 2) { + std::cout << "Usage:" << argv[0] << " infile" << std::endl; + std::exit(1); + } + try + { + ConsLaw cons; + cons.declare_parameters(); + cons.load_parameters(argv[1]); + cons.run (); + } + catch (std::exception &exc) + { + std::cerr << std::endl << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Exception on processing: " << std::endl + << exc.what() << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + return 1; + } + catch (...) + { + std::cerr << std::endl << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Unknown exception!" << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + return 1; + }; + + return 0; +} +