From: Ignacio Tomas (-EXP) Date: Mon, 3 Feb 2020 03:05:57 +0000 (-0700) Subject: update documentation, part IX X-Git-Tag: v9.2.0-rc1~443^2~23 X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=7016b4ab2b1f681b48885e00dfed3925e5032778;p=dealii.git update documentation, part IX --- diff --git a/examples/step-69/step-69.cc b/examples/step-69/step-69.cc index 97edd6dee0..2071ec15d5 100644 --- a/examples/step-69/step-69.cc +++ b/examples/step-69/step-69.cc @@ -256,11 +256,27 @@ namespace Step69 // used rarely and with caution in situations such as this one, where we // actually know (due to benchmarking) that inlining the function in // question actually improves performance. + // + // Finally we note that: + // - This is the only class in this tutorial step that is tied to a + // particular "physics" or "hyperbolic conservation law" (in this + // case Euler's equations). All the other classes are primarily + // "discretization" classes, very much agnostic of the particular physics + // being solved. + // - This is a "pure static" class (the antithesis of a + // "pure virtual" class). It's just a convenient way to wrap-up a + // collection of related methods into a single object. Note that we will + // be able to invoke such methods without without creating an instance of + // the class. Similarly, we will not have to provide a constructor + // for this class. template class ProblemDescription { public: + + /* constexpr tells the compiler to evaluate "2 + dim" just once at compile + time rather than everytime problem_dimension is invoked. */ static constexpr unsigned int problem_dimension = 2 + dim; using rank1_type = Tensor<1, problem_dimension>; @@ -298,10 +314,18 @@ namespace Step69 // direction and a 1D primitive state (density, velocity, pressure) are // read from the parameter file. // - // Instead of implementing yet another setup() function we - // use a callback function parse_parameters_callback that - // can be hooked up to the corresponding signal - // ParameterAcceptor::parse_parameters_call_back. + // It would be desirable to initialize the class in a single shot: + // initialize/set the parameters and define the class members that + // depend on these default parameters. However, since we do not know the + // actual final values for the parameters, this would be sort of + // meaningless an unsafe in general (we would like to have mechanisms to + // check the consistency of the input parameters). Instead of defining + // another setup() method to be called (by-hand) after the + // call to ParameterAcceptor::initialize() we provide an + // "implementation" for the class member + // parse_parameters_call_back which is automatically called when + // invoking ParameterAcceptor::initialize() for every class + // that inherits from ParameterAceptor. template class InitialValues : public ParameterAcceptor @@ -314,6 +338,9 @@ namespace Step69 std::function &point, double t)> initial_state; private: + + /* Auxiliary void function to be hooked to the inherited class member + ParameterAcceptor::parse_parameters_call_back. */ void parse_parameters_callback(); Tensor<1, dim> initial_direction; @@ -327,8 +354,13 @@ namespace Step69 // that was introduced in the discussion above. The main method of the // TimeStep class is step(vector_type &U, double // t). That takes a reference to a state vector U and - // a time point t as arguments, updates the state vector in - // place and returns the chosen step-size $\tau$. + // a time point t as arguments, computes the updated solution, + // stores it in the vector temp, swaps its contents with the + // vector U, and returns the chosen step-size $\tau$. + // + // The other important method is prepare() which primarily sets + // the proper partition and sparsity pattern for the auxiliary vector + // temp and the matrix dij_matrix. // template @@ -1383,8 +1415,9 @@ namespace Step69 // in the context of Euler's equations using with ideal gas law. If we wanted // to re-purpose Step-69 for a different conservation law (say for instance // shallow water equations) the implementation of this entire class would - // have to change. But most of the other classes, in particular those - // defining loop structures, would remain unchanged. + // have to change (or wiped out in its entirety). But most of the other + // classes, in particular those defining loop structures, would remain + // unchanged. // // Now we define the implementation of the utility // functions momentum, @@ -1654,12 +1687,24 @@ namespace Step69 // @sect4{Class InitialValues implementation} - // Constructor for the class InitialValues. + // Constructor for the class InitialValues. We add some parameters with + // some default values. We also provide a non-empty an implementation + // for the class member parse_parameters_call_back. + // + // The class member parse_parameters_call_back (inherited + // ParameterAcceptor) has an empty implementation by default. + // This function will only be invoked for every class that is derived + // from ParameterAceptor after the call to ParameterAcceptor::initialize. In + // that regard, its use is appropriate for situations where the parameters + // have to be postprocessed (in some sense) or some consistency + // condition between the parameters has to be checked. template InitialValues::InitialValues(const std::string &subsection) : ParameterAcceptor(subsection) { + /* We wire-up InitialValues::parse_parameters_callback (declared + a few lines below) to ParameterAcceptor::parse_parameters_call_back */ ParameterAcceptor::parse_parameters_call_back.connect( std::bind(&InitialValues::parse_parameters_callback, this)); @@ -1677,7 +1722,19 @@ namespace Step69 "Initial 1d state (rho, u, p) of the uniform flow field"); } - // Placeholder here. + // So far the constructor of InitialValues has defined + // default values for the two private members initial_direction + // and initial_1d_state and added them to the parameter list. + // But we have not defined an implementation for the only public member that + // we really care about, which is initial_state (the + // function that we are going to call to actually evaluate the initial + // solution at the mesh nodes). + // + // As commented, we could have avoided using the method + // parse_parameters_call_back and define a class member + // setup() in order to define the implementation of + // initial_state. But this illustrates a different way to use + // inheritance of ParameterAceptor to our benefit. template void InitialValues::parse_parameters_callback() @@ -1689,6 +1746,9 @@ namespace Step69 static constexpr auto gamma = ProblemDescription::gamma; + /* Function that translates primitive 1d states in to conserved 2d states. + Note that we have some room for freedom to change the direction of the + flow. */ const auto from_1d_state = [=](const Tensor<1, 3, double> &state_1d) -> rank1_type { const auto &rho = state_1d[0]; @@ -1730,7 +1790,12 @@ namespace Step69 "relative CFL constant used for update"); } - // Placeholder here. + // In the class member prepare() we set the partition of the + // auxiliary vector temp (locally owned + ghosted layer) and + // set the sparsity pattern for dij_matrix (borrowed from + // offline_data, a pointer to the unique OfflineData instance). + // The vector temp will be used to store temporarily the + // solution update, to later swap its contents with the old vector. template void TimeStep::prepare() @@ -1875,12 +1940,12 @@ namespace Step69 // So far the matrix dij_matrix contains the off-diagonal // components. We still have to fill its diagonal entries defined as // $d_{ii}^n = - \sum_{j \in \mathcal{I}(i)\backslash \{i\}} d_{ij}^n$. We - // use parallel::apply_to_subranges for this purpose. While - // computing the $d_{ii}$'s we also record the largest admissible - // time-step, which is defined as + // use again parallel::apply_to_subranges for this purpose. + // While in the process of computing the $d_{ii}$'s we also record the + // largest admissible time-step, which is defined as // // \f[ \tau_n := c_{\text{cfl}}\,\min_{ - // i\in\mathcal{V}}\left(\frac{m_i}{-2\,d_{ii}^{n}}\right)\f] . + // i\in\mathcal{V}}\left(\frac{m_i}{-2\,d_{ii}^{n}}\right) \, . \f] // // Note that the operation $\min_{i \in \mathcal{V}}$ is intrinsically // global, it operates on all nodes: first we would have to first take the @@ -1896,7 +1961,7 @@ namespace Step69 // Utilities::MPI::min. /* We define tau_max as an atomic double in order to avoid any read/write - conflict between threads and initialize it as the largest possible + conflicts between threads and initialize it as the largest possible number that can be represented by the float-type double. */ std::atomic tau_max{std::numeric_limits::infinity()}; @@ -1935,7 +2000,7 @@ namespace Step69 current_tau_max > tau_max_on_subrange && !tau_max.compare_exchange_weak(current_tau_max, tau_max_on_subrange)) ; - }; /* End of definition of on_subranges */ + }; /* End of definition of the worker on_subranges */ /* Thread-parallel loop on locally owned rows */ parallel::apply_to_subranges(indices_relevant.begin(), @@ -2046,7 +2111,7 @@ namespace Step69 // \boldsymbol{\nu}_i$ // // which removes the normal component of $\mathbf{m}$. We note that - // conservation is not just a consequence of this operation but also a + // conservation is not just a consequence of this correction but also a // consequence of modification of the $\mathbf{c}_{ij}$ coefficients at the // boundary (see the third thread-parallel loop on nodes in // OfflineData::assemble()). @@ -2107,14 +2172,13 @@ namespace Step69 // @sect4{Class SchlierenPostprocessor implementation} - // Constructor of SchlierenPostprocessor. // Here - // - schlieren_beta: is an ad-hoc amplification factor in order to + // - schlieren_beta: is an ad-hoc positive amplification factor in order to // enhance/exaggerate contrast in the visualization. Its actual value is a // matter of taste. - // - schlieren_index: indicates which component of the state - // $[\rho, \mathbf{m},E]$ are we going to use in order generate the - // visualization. + // - schlieren_index: is a integer indicates which component of the + // state $[\rho, \mathbf{m},E]$ are we going to use in order generate + // the visualization. template SchlierenPostprocessor::SchlierenPostprocessor( @@ -2158,11 +2222,12 @@ namespace Step69 // We now discuss the implementation of the class member // SchlierenPostprocessor::compute_schlieren, which // basically takes a component of the state vector U and - // computes the Schlieren indicator for such component. We start by noting - // that the formula for the Schlieren indicator - // requires the "nodal gradients" $\nabla r_j$. However, nodal values of - // gradients are not defined for $\mathcal{C}^0$ finite - // element functions. More generally, pointwise values of gradients + // computes the Schlieren indicator for such component (the formula of the + // Schlieren indicator can be found just before the declaration of the class + // SchlierenPostprocessor). We start by noting + // that this formula requires the "nodal gradients" $\nabla r_j$. + // However, nodal values of gradients are not defined for $\mathcal{C}^0$ + // finite element functions. More generally, pointwise values of gradients // are not defined for $W^{1,p}(\Omega)$ functions (though weak // derivatives are). The simplest technique we can use to recover gradients // at nodes is weighted-averaging i.e. @@ -2188,7 +2253,7 @@ namespace Step69 // Using this last formula we can recover averaged nodal gradients without // resorting to any form of quadrature. This idea aligns quite well with // the whole spirit of edge-based schemes (or algebraic schemes) where - // we want to operate as directly/intimately on matrices and vectors as + // we want to operate on matrices and vectors as directly as // it could be possible avoiding by all means assembly of bilinear // forms, cell-loops, quadrature, or any other // intermediate construct/operation between the input arguments (the state @@ -2198,7 +2263,7 @@ namespace Step69 // The second thing to note is that we have to compute global minimum and // maximums $\max_j |\nabla r_j|$ and $\min_j |\nabla r_j|$. Following the // same ideas used to compute the time step size in the class member - // TimeStep::step : we define $\max_j |\nabla r_j|$ and + // TimeStep::step we define $\max_j |\nabla r_j|$ and // $\min_j |\nabla r_j|$ as atomic doubles in order to // resolve any conflicts between threads. As usual, we use // Utilities::MPI::max and Utilities::MPI::min to @@ -2210,7 +2275,8 @@ namespace Step69 // - The first loop computes $|\nabla r_i|$ for all $i \in \mathcal{V}$ in // the mesh, and the bounds $\max_j |\nabla r_j|$ and // $\min_j |\nabla r_j|$. - // - Second loop finally computes the Schlieren indicator using the formula + // - The second loop finally computes the Schlieren indicator using the + // formula // // \f[ \text{schlieren}[i] = e^{\beta \frac{ |\nabla r_i| // - \min_j |\nabla r_j| }{\max_j |\nabla r_j| - \min_j |\nabla r_j| } } @@ -2238,8 +2304,8 @@ namespace Step69 std::atomic r_i_max{0.}; std::atomic r_i_min{std::numeric_limits::infinity()}; - /* Implementation of the worker that computes the averaged gradient at each - node and the global max and mins of such gradients */ + /* Implementation of the first worker: computes the averaged gradient + at each node and the global max and mins of such gradients. */ { const auto on_subranges = [&](auto i1, const auto i2) { double r_i_max_on_subrange = 0.; @@ -2319,9 +2385,9 @@ namespace Step69 r_i_max.store(Utilities::MPI::max(r_i_max.load(), mpi_communicator)); r_i_min.store(Utilities::MPI::min(r_i_min.load(), mpi_communicator)); - /* So far we have computed the vector r_i and the scalars r_i_max and - r_i_min. Now we are in position of actually computing the Schlieren - indicator, so we define the worker for this task */ + /* Implementation of the second worker: we have the vector r_i and the + scalars r_i_max and r_i_min at our disposal. Now we are in position of + actually computing the Schlieren indicator. */ { const auto on_subranges = [&](auto i1, const auto i2) { @@ -2348,7 +2414,27 @@ namespace Step69 schlieren.update_ghost_values(); } - // @sect4{The Timeloop::run() function} + // @sect4{The Timeloop class implementation.} + + // Constructor of the class Timeloop. Note that this class wraps + // up pretty much all the other classes that we have discussed so far. + // More precisely the constructor has to initialize an instance of + // - Discretization + // - OfflineData + // - InitialValues + // - TimeStep + // - SchlierenPostprocessor + // + // Most of the functionality of the class + // Timeloop comes from the methods of those five classes. In + // itself, the class TimeLoop only requires the + // implementation of three new class members/methods: + // - TimeLoop::run . + // - TimeLoop::interpolate_initial_values + // - TimeLoop::output + // + // Note that in the construction we also add the boolean parameter + // "resume" which will be used to restart interrupted computations. template TimeLoop::TimeLoop(const MPI_Comm &mpi_comm) @@ -2390,7 +2476,10 @@ namespace Step69 add_parameter("resume", resume, "Resume an interrupted computation."); } - // Placeholder here. + // We define an auxiliary namespace to be used in the implementation of + // the class member TimeLoop::run(). It's only content + // is the void function print_head used to output + // messages in the terminal with a "nice" format. namespace { @@ -2421,14 +2510,25 @@ namespace Step69 } } // namespace - - // Implementation of the class member interpolate_initial_values - // . + // The class member TimeLoop::run() is one of only three + // class member we actually have to implement. We initialize the + // (global) parameter list, setup all the accessory classes (discretization, + // offline_data, time_step, and schlieren_postprocessor), interpolate the + // initial data, and run a forward-Euler time loop. + // + // We note here that the (unique) call to ParameterAcceptor::initialize + // initializes the global ParameterHandler with the + // parameters contained in the classes derived from ParameterAceptor. + // This function enters the subsection returned by get_section_name() for + // each derived class, and declares all parameters that were added using + // add_parameter() template void TimeLoop::run() { pcout << "Reading parameters and allocating objects... " << std::flush; + + /* Initialization of the global ParameterHandler. */ ParameterAcceptor::initialize("step-69.prm"); pcout << "done" << std::endl; @@ -2447,8 +2547,12 @@ namespace Step69 unsigned int output_cycle = 0; print_head(pcout, "interpolate initial values"); + /* The vector U and time_step.temp are the only ones in the entire code + storing the old and/or new state of the system. */ auto U = interpolate_initial_values(); + /* By default resume is false, but that could have changed after reading + the input file when calling ParameterAcceptor::initialize */ if (resume) { print_head(pcout, "restore interrupted computation"); @@ -2488,7 +2592,7 @@ namespace Step69 if (t > output_cycle * output_granularity) output(U, base_name + "-solution", t, output_cycle++, true); - } /* end of loop */ + } /* End of time loop */ if (output_thread.joinable()) output_thread.join(); @@ -2497,8 +2601,10 @@ namespace Step69 pcout << timer_output.str() << std::endl; } - // Implementation of the class member interpolate_initial_values - // . + // Implementation of the class member interpolate_initial_values. + // This function takes an initial time "t" as input argument in order to + // evaluate an analytic expression (a function of space and time) + // and returns a vector_type containing the initial values. template typename TimeLoop::vector_type @@ -2532,7 +2638,28 @@ namespace Step69 return U; } - // Implementation of the class member output . + // Implementation of the class member output. Most of the + // following lines of code are invested in the implementation of the + // output_worker in order to write the output. We note that: + // - Before calling the output_worker, we create a copy of + // U[i] (the vector we want to output). This copy is stored in + // output_vector. + // - the task output_worker is assigned to a thread + // - this task is later moved to the thread output_thread. + // + // Since output_vector and output_thread are class + // members of TimeLoop, their scope extends beyond that one of + // anything defined inside output_worker. This allows the + // output task to continue its execution even when we + // TimeLoop::output releases its control to the function + // that called it. This is how (ideally) writing to disk becomes a + // background process and not a locking method. + // + // The only penalty is the copy of the vector we want to output. This + // penalty could be minimized by defining a class member + // TimeLoop::prepare() in order to allocate a priori the space for + // output_vector as we did with the vector temp in + // TimeStep::prepare(). template void TimeLoop::output(const typename TimeLoop::vector_type &U, @@ -2544,6 +2671,8 @@ namespace Step69 pcout << "TimeLoop::output(t = " << t << ", checkpoint = " << checkpoint << ")" << std::endl; + /* We check if the thread is still running */ + /* If so, we wait to for it to join. */ if (output_thread.joinable()) { TimerOutput::Scope timer(computing_timer, "time_loop - stalled output"); @@ -2554,6 +2683,7 @@ namespace Step69 ProblemDescription::problem_dimension; const auto &component_names = ProblemDescription::component_names; + /* We make a copy the vector we want to output */ for (unsigned int i = 0; i < problem_dimension; ++i) { output_vector[i] = U[i]; @@ -2562,6 +2692,7 @@ namespace Step69 schlieren_postprocessor.compute_schlieren(output_vector); + /* We define the lambda function "output_worker" */ const auto output_worker = [this, name, t, cycle, checkpoint]() { constexpr auto problem_dimension = ProblemDescription::problem_dimension; @@ -2606,12 +2737,18 @@ namespace Step69 data_out.set_flags(flags); data_out.write_vtu_with_pvtu_record("", name, cycle, 6, mpi_communicator); - }; + /* There is no return statement, we don't need it this is a void-like + lambda expression */ + }; + + /* We launch the thread that executing the output and abandon the + function TimeLoop::output (returning the control to the + function that called it). */ output_thread = std::move(std::thread(output_worker)); - } + } -} // namespace Step69 +} /* End of namespace Step69 */ // @sect4{The main()}