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// $Id: point_value_history.h 30036 2013-07-18 16:55:32Z maier $
//
// Copyright (C) 2009 - 2013 by the deal.II authors
//
// This file is part of the deal.II library.
//
// The deal.II library is free software; you can use it, redistribute
// it, and/or modify it under the terms of the GNU Lesser General
// Public License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
// The full text of the license can be found in the file LICENSE at
// the top level of the deal.II distribution.
//
// ---------------------------------------------------------------------
#ifndef __dealii__point_value_history_h
#define __dealii__point_value_history_h
#include <deal.II/base/point.h>
#include <deal.II/base/smartpointer.h>
#include <deal.II/base/utilities.h>
#include <deal.II/base/exceptions.h>
#include <deal.II/base/quadrature_lib.h>
#include <deal.II/lac/vector.h>
#include <deal.II/grid/grid_tools.h>
#include <deal.II/dofs/dof_accessor.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/fe/fe_q.h>
#include <deal.II/fe/mapping.h>
#include <deal.II/fe/mapping_q1.h>
#include <deal.II/fe/fe_values.h>
#include <deal.II/fe/component_mask.h>
#include <deal.II/numerics/data_postprocessor.h>
#include <vector>
#include <iostream>
#include <fstream>
#include <sstream>
#include <string>
#include <map>
DEAL_II_NAMESPACE_OPEN
namespace internal
{
namespace PointValueHistory
{
template <int dim> class PointGeometryData;
}
}
namespace internal
{
namespace PointValueHistory
{
/**
* A class that stores the data needed
* to reference the support points
* closest to one requested point.
*/
template <int dim>
class PointGeometryData
{
public:
PointGeometryData(const Point <dim> &new_requested_location, const std::vector <Point <dim> > &new_locations,
const std::vector <types::global_dof_index> &new_sol_indices);
Point <dim> requested_location;
std::vector <Point <dim> > support_point_locations;
std::vector <types::global_dof_index> solution_indices;
};
}
}
/**
* PointValueHistory tackles the overhead of plotting time (or any other
* iterative process) graphs of solution values at specific points on the
* mesh. The user specifies the points which the solution should be monitored
* at ahead of time, as well as giving each solution vector that they want to
* record a mnemonic name. Then, for each step the user calls one of the three
* available "evaluate field" methods to store the data from each time step,
* and the class extracts data for the requested
* points to store it. Finally, once the computation is finished, the user can
* request output files to be generated; these files are in Gnuplot format but
* are basically just regular text and can easily be imported into other
* programs well, for example into spreadsheets.
*
* The user can store extra variables which do not relate to mesh location
* specifying n_independent_variables. The class then expects
* a std::vector of size n_independent_variables to be added during each step
* using the method @p push_back_independent. This may be used for example for
* recording external input, logging solver performance data such as time
* taken to solve the step and solver steps before convergence, saving
* norms calculated, or simply saving the time, number of time step, or number
* of nonlinear iteration along with the data evaluated from the mesh.
*
* The three "evaluate field" methods each have different strengths and
* weaknesses making each suitable for different contexts:
* <ol>
* <li>Firstly, the @p evaluate_field version that does not take a @p DataPostprocessor object
* selects the nearest support point (see @ref GlossSupport "this entry in the glossary")
* to a given point to
* extract data from. This makes the code that needs to be run at each time step very short,
* since looping over the mesh to extract the needed dof_index can be done
* just once at the start. However, this method is not suitable for
* FiniteElement objects that do not assign dofs to actual mesh locations
* (i.e. FEs without @ref GlossSupport "support points") or if adaptive mesh refinement is used.
* The reason for the latter restriction is that the location of the closest
* support point to a given point may change upon mesh refinement.
* The class will throw an exception if any change to the triangulation is made
* (Although the nearest support point could be re-computed upon mesh refinement,
* the location of the support point will most likely change slightly, making the interpretation
* of the data difficult, hence this is not implemented currently.)
*
* <li> Secondly, @p evaluate_field_at_requested_location calls @p
* VectorTools::point_value to compute values at the specific point requested.
* This method is valid for any FE that is supported by @p VectorTools::point_value.
* Specifically, this method can be called by codes using adaptive mesh refinement.
*
* <li>Finally, the class offers a function @p evaluate_field that takes a
* @p DataPostprocessor object. This method allows the deal.II
* data postprocessor to be used to compute new quantities from the
* solution on the fly. The values are located at the nearest quadrature
* point to the requested point. If the mesh is refined between calls, this
* point will change, so care must be taken when using this method in
* code using adaptive refinement, but as the output will be meaningful (in
* the sense that the quadrature point selected is guaranteed to remain in the
* same vicinity, the class does not prevent the use of this method in adaptive
* codes. The class provides warnings in the output files if the mesh has changed.
* Note that one can reduce the error this procedure introduces by providing
* a quadrature formula that has more points, at the expense of performing more
* work since then the closest quadrature points is nearer to the point at which
* the evaluation is really supposed to happen. (As a sidenote: Why not do the
* evaluation at the requested point right away? The reason for this is that it
* would require setting up a new quadrature point object on each cell that has
* only a single point corresponding to the reference coordinates of the point you
* really want; then initializing a FEValues object with it; then evaluating the
* solution at this point; then handing the result to the DataPostprocessor object.
* This sequence of things is expensive -- which is the reason why
* VectorTools::point_value() is expensive. Using the same quadrature formula
* on each cell on which we want to evaluate the solution and only having to
* initialize a FEValue object once is a much cheaper alternative, albeit of
* course at the expense of getting only an approximate result.)
* </ol>
*
* When recording a new mnemonic name, the user must supply a
* component_mask (see @ref GlossComponentMask "this glossary entry")
* to indicate the @ref GlossComponent "(vector) components"
* to be extracted from the given input. If the user simply wants to extract
* all the components, the mask need not be explicitly supplied to the @p
* add_field_name method and the default value of the parameter is sufficient.
* If the @p evaluate_field with a @p DataPostprocessor object is used, the
* component_mask is interpreted as the mask of the @p DataPostprocessor
* return vector. The size of this mask can be different to that of the FE
* space, but must be provided when the @p add_field_name method is
* called. One variant of the @p add_field_name method allows an unsigned int
* input to construct a suitable mask, if all values from the @p
* DataPostprocessor are desired.
*
* The class automatically generates names for the data stored based on the mnemonics
* supplied. The methods @p add_component_names and @p add_independent_names allow
* the user to provide lists of names to use instead if desired.
*
* Following is a little code snippet that shows a common usage of this class:
*
* @code
* #include <deal.II/numerics/point_value_history.h>
* //....
*
* //... code to setup Triangulation, perform any refinement necessary
* // and setup DoFHandler, sizing solution Vectors etc
*
* // call the constructor
* unsigned int n_inputs = 1; // just one independent value, which happens to be an input
* PointValueHistory<dim> node_monitor(dof_handler, n_inputs);
*
* // setup fields and points required
* node_monitor.add_field_name("Solution");
* std::vector <Point <dim> > point_vector(2);
* point_vector[0] = Point <dim>(0, 0);
* point_vector[1] = Point <dim>(0.25, 0);
* node_monitor.add_points(point_vector); // multiple points at once
* node_monitor.add_point(Point<dim>(1, 0.2)); // add a single point
* node_monitor.close(); // close the class once the setup is complete
* node_monitor.status(std::cout); // print out status to check if desired
*
* // ... more code ...
*
* // ... in an iterative loop ...
* // double time, vector <double> with size 1 input_value,
* // and Vector <double> solution calculated in the loop
* node_monitor.start_new_dataset(time);
* node_monitor.push_back_independent(input_value);
* node_monitor.evaluate_field("Solution", solution);
*
* // ... end of iterative loop ...
*
* node_monitor.write_gnuplot("node"); // write out data files
*
* @endcode
*/
template <int dim>
class PointValueHistory
{
public:
/**
* Provide a stripped down instance of
* the class which does not support
* adding points or mesh data. This may
* be used for example for recording
* external input or logging solver
* performance data.
*/
PointValueHistory (const unsigned int n_independent_variables = 0);
/**
* Constructor linking the class to a
* specific @p DoFHandler. This
* class reads specific data from the @p
* DoFHandler and stores it internally
* for quick access (in particular dof
* indices of closest neighbors to
* requested points) the class is fairly
* intolerant to changes to the @p
* DoFHandler if data at support points
* is required. Mesh refinement and @p
* DoFRenumbering methods should be
* performed before the @p add_points
* method is called and adaptive grid
* refinement is only supported by some
* methods.
*
* The user can store extra variables
* which do not relate to mesh location
* by specifying the number required
* using n_independent_variables and
* making calls to @p
* push_back_independent as needed. This
* may be used for example for recording
* external input or logging solver
* performance data.
*/
PointValueHistory (const DoFHandler<dim> &dof_handler,
const unsigned int n_independent_variables = 0);
/**
* Copy constructor. This constructor can
* be safely called with a @p
* PointValueHistory object that contains
* data, but this could be expensive and
* should be avoided.
*/
PointValueHistory (const PointValueHistory &point_value_history);
/**
* Assignment operator. This
* assignment operator can be safely
* called once the class is closed and
* data added, but this is provided
* primarily to allow a @p
* PointValueHistory object declared in a
* class to be reinitialized later in the
* class. Using the assignment operator
* when the object contains data could be
* expensive.
*/
PointValueHistory &operator=(const PointValueHistory &point_value_history);
/**
Deconstructor.
*/
~PointValueHistory ();
/**
* Add a single point to the class. The
* support points (one per component) in
* the mesh that are closest to that
* point are found and their details stored
* for use when @p evaluate_field is
* called. If more than one point is
* required rather use the @p add_points
* method since this minimizes iterations
* over the mesh.
*/
void add_point(const Point <dim> &location);
/**
* Add multiple points to the class. The
* support points (one per component) in
* the mesh that are closest to that
* point is found and their details stored
* for use when @p evaluate_field is
* called. If more than one point is
* required, rather call this method as it
* is more efficient than the add_point
* method since it minimizes iterations
* over the mesh. The points are added to
* the internal database in the order
* they appear in the list and there is
* always a one to one correspondence
* between the requested point and the
* added point, even if a point is
* requested multiple times.
*/
void add_points (const std::vector <Point <dim> > &locations);
/**
* Put another mnemonic string (and hence
* @p VECTOR) into the class. This method
* adds storage space for variables equal
* to the number of true values in
* component_mask.
* This also adds extra entries for points
* that are already in the class, so
* @p add_field_name and @p add_points can
* be called in any order.
*/
void add_field_name(const std::string &vector_name,
const ComponentMask &component_mask = ComponentMask());
/**
* Put another mnemonic string (and hence
* @p VECTOR) into the class. This method
* adds storage space for n_components
* variables.
* This also adds extra entries for points
* that are already in the class, so
* @p add_field_name and @p add_points can
* be called in any order.
* This method generates a std::vector
* 0, ..., n_components-1 and calls the
* previous function.
*/
void add_field_name(const std::string &vector_name,
const unsigned int n_components);
/**
* Provide optional names for each component
* of a field. These names will be used
* instead of names generated from the
* field name, if supplied.
*/
void add_component_names(const std::string &vector_name,
const std::vector <std::string> &component_names);
/**
* Provide optional names for the
* independent values. These names will
* be used instead of "Indep_...", if
* supplied.
*/
void add_independent_names(const std::vector <std::string> &independent_names);
/**
* Extract values at the stored points
* from the VECTOR supplied and add them
* to the new dataset in vector_name.
* The component mask supplied when the
* field was added is used to select
* components to extract.
* If a @p DoFHandler is used, one (and only
* one) evaluate_field method
* must be called for each dataset (time
* step, iteration, etc) for each
* vector_name, otherwise a @p
* ExcDataLostSync error can occur.
*/
template <class VECTOR>
void evaluate_field(const std::string &name,
const VECTOR &solution);
/**
* Compute values using a @p DataPostprocessor object
* with the @p VECTOR supplied and add them
* to the new dataset in vector_name.
* The component_mask supplied when the
* field was added is used to select
* components to extract from the @p DataPostprocessor
* return vector.
* This method takes a vector of field names to
* process and is preferred if many fields use the
* same @p DataPostprocessor object as each cell
* is only located once.
* The quadrature object supplied is used for all
* components of a vector field.
* Although this method will not throw an exception
* if the mesh has changed. (No internal data structures
* are invalidated as the quadrature points are repicked
* each time the function is called.) Nevertheless
* the user must be aware that if the mesh changes the
* point selected will also vary slightly, making
* interpretation of the data more difficult.
* If a @p DoFHandler is used, one (and only
* one) evaluate_field method
* must be called for each dataset (time
* step, iteration, etc) for each
* vector_name, otherwise a @p
* ExcDataLostSync error can occur.
*/
template <class VECTOR>
void evaluate_field(const std::vector <std::string> &names,
const VECTOR &solution,
const DataPostprocessor<dim> &data_postprocessor,
const Quadrature<dim> &quadrature);
/**
* Construct a std::vector <std::string>
* containing only vector_name and
* call the above function. The above function
* is more efficient if multiple fields
* use the same @p DataPostprocessor object.
*/
template <class VECTOR>
void evaluate_field(const std::string &name,
const VECTOR &solution,
const DataPostprocessor<dim> &data_postprocessor,
const Quadrature<dim> &quadrature);
/**
* Extract values at the points actually
* requested from the VECTOR supplied and
* add them to the new dataset in vector_name.
* Unlike the other evaluate_field methods
* this method does not care if the dof_handler
* has been modified because it uses calls to
* @p VectorTools::point_value to extract there
* data. Therefore, if only this method is used,
* the class is fully compatible with
* adaptive refinement.
* The component_mask supplied when the
* field was added is used to select
* components to extract. If
* a @p DoFHandler is used, one (and only
* one) evaluate_field method
* must be called for each dataset (time
* step, iteration, etc) for each
* vector_name, otherwise a @p
* ExcDataLostSync error can occur.
*/
template <class VECTOR>
void evaluate_field_at_requested_location(const std::string &name,
const VECTOR &solution);
/**
* Add the key for the current dataset to
* the dataset. Although calling this
* method first is sensible, the order in
* which this method, @p evaluate_field
* and @p push_back_independent is not
* important. It is however important
* that all the data for a give dataset
* is added to each dataset and that it
* is added before a new data set is
* started. This prevents a @p
* ExcDataLostSync.
*/
void start_new_dataset (const double key);
/**
* If independent values have been set
* up, this method stores these
* values. This should only be called
* once per dataset, and if independent
* values are used it must be called for
* every dataset. A @p ExcDataLostSync
* exception can be thrown if this method
* is not called.
*/
void push_back_independent (const std::vector <double> &independent_values);
/**
* Write out a series of .gpl files named
* base_name + "-00.gpl", base_name +
* "-01.gpl" etc. The data file gives
* info about where the support points
* selected and interpreting the data.
* If @p n_indep != 0 an additional file
* base_name + "_indep.gpl" containing
* key and independent data. The file
* name agrees with the order the points
* were added to the class.
* The names of the data columns can
* be supplied using the functions
* @p add_component_names and
* @p add_independent_names.
* The support point information is only
* meaningful if the dof_handler has not
* been changed. Therefore, if adaptive
* mesh refinement has been used the
* support point data should not be used.
* The optional parameter
* postprocessor_locations is used to
* add the postprocessor locations to the
* output files. If this is desired, the
* data should be obtained from a call to
* get_postprocessor_locations while the
* dof_handler is usable. The default
* parameter is an empty vector of strings,
* and will suppress postprocessor
* locations output.
*/
void write_gnuplot (const std::string &base_name,
const std::vector <Point <dim> > postprocessor_locations = std::vector <Point <dim> > ());
/**
* Return a @p Vector with the indices of
* selected points flagged with a 1. This
* method is mainly for testing and
* verifying that the class is working
* correctly. By passing this vector to a
* DataOut object, the user can verify
* that the positions returned by @p
* PointValueHistory< dim >::get_points
* agree with the positions that @p
* DataOut interprets from the @p Vector
* returned. The code snippet below
* demonstrates how this could be done:
* @code
* // Make a DataOut object and attach the dof_handler
* DataOut<dim> data_out;
* data_out.attach_dof_handler(dof_handler);
*
* // Call the mark_locations method to get the vector with indices flagged
* Vector<double> support_point_locations = node_monitor.mark_locations();
*
* // Add the vector to the data_out object and write out a file in the usual way
* data_out.add_data_vector(support_point_locations, "Monitor_Locations");
* data_out.build_patches(2);
* std::ofstream output("locations.gpl");
* data_out.write_gnuplot(output);
* @endcode
*/
Vector<double> mark_support_locations();
/**
* Depreciated:
*
* This function only exists for backward
* compatibility as this is the interface
* provided by previous versions of the library.
* The function mark_support_locations replaces
* it and reflects the fact that the locations
* marked are actually the support points.
*
* @deprecated
*/
Vector<double> mark_locations() DEAL_II_DEPRECATED;
/**
* Stores the actual location of each
* support point selected by the @p
* add_point(s) method. This can be used
* to compare with the point requested,
* for example by using the @p
* Point<dim>::distance function. For
* convenience, location is resized to
* the correct number of points by the
* method.
*/
void get_support_locations (std::vector <std::vector<Point <dim> > > &locations);
/**
* Depreciated:
*
* This function only exists for backward
* compatibility as this is the interface
* provided by previous versions of the library.
* The function get_support_locations replaces
* it and reflects the fact that the points
* returned are actually the support points.
*/
void get_points (std::vector <std::vector<Point <dim> > > &locations);
/**
* Stores the actual location of the
* points used by the data_postprocessor.
* This can be used to compare with the
* points requested, for example by using
* the @p Point<dim>::distance function.
* Unlike the support_locations, these
* locations are computed every time the
* evaluate_field method is called with a
* postprocessor. This method uses the
* same algorithm so can will find the
* same points.
* For convenience, location is resized
* to the correct number of points by the
* method.
*/
void get_postprocessor_locations (const Quadrature<dim> &quadrature,
std::vector<Point <dim> > &locations);
/**
* Once datasets have been added to the
* class, requests to add additional
* points will make the data
* interpretation unclear. The boolean @p
* closed defines a state of the class
* and ensures this does not
* happen. Additional points or vectors
* can only be added while the class is
* not closed, and the class must be
* closed before datasets can be added or
* written to file. @p
* PointValueHistory::get_points and @p
* PointValueHistory::status do not
* require the class to be closed. If a
* method that requires a class to be
* open or close is called while in the
* wrong state a @p ExcInvalidState
* exception is thrown.
*/
void close();
/**
* Delete the lock this object has to the
* @p DoFHandler used the last time the
* class was created. This method should
* not normally need to be called, but
* can be useful to ensure that the @p
* DoFHandler is released before it goes
* out of scope if the @p
* PointValueHistory class might live
* longer than it. Once this method has
* been called, the majority of methods
* will throw a @p ExcInvalidState
* exception, so if used this method
* should be the last call to the class.
*/
void clear();
/**
* Print useful debugging information
* about the class, include details about
* which support points were selected for
* each point and sizes of the data
* stored.
*/
void status(std::ostream &out);
/**
* Check the internal data sizes to test
* for a loss of data sync. This is often
* used in @p Assert statements with the
* @p ExcDataLostSync exception. If @p strict
* is @p false this method returns
* @p true if all sizes are within 1 of
* each other (needed to allow data to be
* added), with @p strict = @p true they
* must be exactly equal.
*/
bool deep_check (const bool strict);
/**
* A call has been made to @p
* push_back_independent when no
* independent values were requested.
*/
DeclException0(ExcNoIndependent);
/**
* This error is thrown to indicate that
* the data sets appear to be out of
* sync. The class requires that the
* number of dataset keys is the same as
* the number of independent values sets
* and mesh linked value sets. The number
* of each of these is allowed to differ
* by one to allow new values to be added
* with out restricting the order the
* user choses to do so. Special cases
* of no @p DoFHandler and no independent
* values should not trigger this error.
*/
DeclException0(ExcDataLostSync);
/**
* A method which requires access to a @p
* DoFHandler to be meaningful has been
* called when @p have_dof_handler is
* false (most likely due to default
* constructor being called). Only
* independent variables may be logged
* with no DoFHandler.
*/
DeclException0(ExcDoFHandlerRequired);
/**
* The triangulation indicated that mesh
* has been refined in some way. This suggests
* that the internal dof indices stored
* are no longer meaningful.
*/
DeclException0(ExcDoFHandlerChanged);
private:
/**
* Stores keys, values on the abscissa.
* This will often be time, but possibly
* time step, iteration etc.
*/
std::vector <double> dataset_key;
/**
* Values that do not depend on grid
* location.
*/
std::vector <std::vector <double> > independent_values;
/**
* Saves a vector listing component
* names associated with a independent_values.
* This will be an empty vector
* if the user does not supplies names.
*/
std::vector<std::string> indep_names;
/**
* Saves data for each mnemonic entry.
* data_store: mnemonic ->
* [point_0_components point_1_components
* ... point_n-1_components][key]
* This format facilitates scalar mnemonics
* in a vector space, because scalar mnemonics
* will only have one component per point.
* Vector components are strictly
* FE.n_components () long.
*/
std::map <std::string, std::vector <std::vector <double> > > data_store;
/**
* Saves a component mask
* for each mnemonic.
*/
std::map <std::string, ComponentMask> component_mask;
/**
* Saves a vector listing component
* names associated with a mnemonic.
* This will be an empty vector
* if the user does not supplies names.
*/
std::map <std::string, std::vector<std::string> > component_names_map;
/**
* Saves the location and other mesh info
* about support points.
*/
std::vector <internal::PointValueHistory::PointGeometryData <dim> >
point_geometry_data;
/**
* Used to enforce @p closed state for some
* methods.
*/
bool closed;
/**
* Used to enforce @p !cleared state for
* some methods.
*/
bool cleared;
/**
* A smart pointer to the dof_handler
* supplied to the constructor. This can be
* released by calling @p clear().
*/
SmartPointer<const DoFHandler<dim>,PointValueHistory<dim> > dof_handler;
/**
* Variable to check if the triangulation
* has changed. If it has changed, certain
* data is out of date (especially the
* PointGeometryData::solution_indices.
*/
bool triangulation_changed;
/**
* A boolean to record whether the class was
* initialized with a DoFHandler or not.
*/
bool have_dof_handler;
/**
* Used to detect signals from the Triangulation.
*/
boost::signals2::connection tria_listener;
/**
* Stores the number of independent
* variables requested.
*/
unsigned int n_indep;
/**
* A function that will be triggered
* through signals whenever the
* triangulation is modified.
*
* It is currently used to check
* if the triangulation has changed,
* invalidating precomputed values.
*/
void tria_change_listener ();
};
DEAL_II_NAMESPACE_CLOSE
#endif /* __dealii__point_value_history_h */
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