Flow123d
master-f44eb46
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#include <balance.hh>
Classes | |
class | Quantity |
Public Types | |
enum | OutputFormat { legacy , txt , gnuplot } |
Public Member Functions | |
Balance (const std::string &file_prefix, const Mesh *mesh) | |
~Balance () | |
void | init_from_input (const Input::Record &in_rec, TimeGovernor &tg) |
void | units (const UnitSI &unit) |
Setter for units of conserved quantities. More... | |
bool | cumulative () const |
Getter for cumulative_. More... | |
unsigned int | add_quantity (const string &name) |
std::vector< unsigned int > | add_quantities (const std::vector< string > &names) |
void | allocate (const std::shared_ptr< DOFHandlerMultiDim > &dh, unsigned int max_dofs_per_boundary) |
void | allocate (unsigned int n_loc_dofs, unsigned int max_dofs_per_boundary) |
bool | is_current () |
Returns true if the current time step is marked for the balance output. More... | |
void | start_mass_assembly (unsigned int quantity_idx) |
void | start_mass_assembly (std::vector< unsigned int > q_idx_vec) |
Variant of the start_mass_assembly() method for a set of quantities. More... | |
void | start_flux_assembly (unsigned int quantity_idx) |
void | start_flux_assembly (std::vector< unsigned int > q_idx_vec) |
Variant of the start_flux_assembly() method for a set of quantities. More... | |
void | start_source_assembly (unsigned int quantity_idx) |
void | start_source_assembly (std::vector< unsigned int > q_idx_vec) |
Variant of the start_source_assembly() method for a set of quantities. More... | |
void | add_mass_values (unsigned int quantity_idx, const DHCellAccessor &dh_cell, const LocDofVec &loc_dof_indices, const std::vector< double > &mat_values, double vec_value) |
void | add_flux_values (unsigned int quantity_idx, const DHCellSide &side, const LocDofVec &loc_dof_indices, const std::vector< double > &mat_values, double vec_value) |
void | add_source_values (unsigned int quantity_idx, unsigned int region_idx, const LocDofVec &loc_dof_indices, const std::vector< double > &mult_mat_values, const std::vector< double > &add_mat_values) |
void | finish_mass_assembly (unsigned int quantity_idx) |
This method must be called after assembling the matrix for computing mass. More... | |
void | finish_mass_assembly (std::vector< unsigned int > q_idx_vec) |
Variant of the finish_mass_assembly() method for a set of quantities. More... | |
void | finish_flux_assembly (unsigned int quantity_idx) |
This method must be called after assembling the matrix and vector for computing flux. More... | |
void | finish_flux_assembly (std::vector< unsigned int > q_idx_vec) |
Variant of the finish_flux_assembly() method for a set of quantities. More... | |
void | finish_source_assembly (unsigned int quantity_idx) |
This method must be called after assembling the matrix and vectors for computing source. More... | |
void | finish_source_assembly (std::vector< unsigned int > q_idx_vec) |
Variant of the finish_source_assembly() method for a set of quantities. More... | |
void | calculate_cumulative (unsigned int quantity_idx, const Vec &solution) |
void | calculate_mass (unsigned int quantity_idx, const Vec &solution, vector< double > &output_array) |
void | calculate_instant (unsigned int quantity_idx, const Vec &solution) |
void | add_cumulative_source (unsigned int quantity_idx, double source) |
void | output () |
Perform output to file for given time instant. More... | |
Static Public Member Functions | |
static const Input::Type::Record & | get_input_type () |
Main balance input record type. More... | |
static const Input::Type::Selection & | get_format_selection_input_type () |
Input selection for file format. More... | |
static void | set_yaml_output () |
Set global variable to output balance files into YAML format (in addition to the table format). More... | |
Private Member Functions | |
void | lazy_initialize () |
void | output_legacy (double time) |
Perform output in old format (for compatibility) More... | |
void | output_csv (double time, char delimiter, const std::string &comment_string, unsigned int repeat=0) |
Perform output in csv format. More... | |
void | output_yaml (double time) |
Perform output in yaml format. More... | |
std::string | csv_zero_vals (unsigned int cnt, char delimiter) |
Return part of output represented by zero values. Count of zero values is given by cnt parameter. More... | |
void | format_csv_output_header (char delimiter, const std::string &comment_string) |
Print output header. More... | |
std::string | format_csv_val (std::string val, char delimiter, bool initial=false) |
Format string value of csv output. Wrap string into quotes and if delimiter is space, align text to column. More... | |
std::string | format_csv_val (double val, char delimiter, bool initial=false) |
Format double value of csv output. If delimiter is space, align text to column. More... | |
LongIdx | get_boundary_edge_uid (SideIter side) |
Private Attributes | |
unsigned int | n_loc_dofs_par_ |
Allocation parameters. Set by the allocate method used in the lazy_initialize. More... | |
unsigned int | n_loc_dofs_seq_ |
unsigned int | max_dofs_per_boundary_ |
std::string | file_prefix_ |
Save prefix passed in in constructor. More... | |
FilePath | balance_output_file_ |
File path for output_ stream. More... | |
std::ofstream | output_ |
Handle for file for output in given OutputFormat of balance and total fluxes over individual regions and region sets. More... | |
std::ofstream | output_yaml_ |
OutputFormat | output_format_ |
Format of output file. More... | |
std::vector< Quantity > | quantities_ |
Names of conserved quantities. More... | |
const Mesh * | mesh_ |
UnitSI | units_ |
Units of conserved quantities. More... | |
Mat * | region_mass_matrix_ |
Matrices for calculation of mass (n_dofs x n_bulk_regions). More... | |
Mat * | be_flux_matrix_ |
Matrices for calculation of flux (n_boundary_edges x n_dofs). More... | |
Mat * | region_source_matrix_ |
Matrices for calculation of source (n_dofs x n_bulk_regions). More... | |
Mat * | region_source_rhs_ |
Matrices for calculation of signed source (n_dofs x n_bulk_regions). More... | |
Vec * | be_flux_vec_ |
Vectors for calculation of flux (n_boundary_edges). More... | |
Vec * | region_mass_vec_ |
Vectors for calculation of mass (n_bulk_regions). More... | |
std::unordered_map< LongIdx, unsigned int > | be_id_map_ |
std::vector< unsigned int > | be_regions_ |
Maps local boundary edge to its region boundary index. More... | |
int | be_offset_ |
Offset for local part of vector of boundary edges. More... | |
std::vector< std::vector< double > > | fluxes_ |
std::vector< std::vector< double > > | fluxes_in_ |
std::vector< std::vector< double > > | fluxes_out_ |
std::vector< std::vector< double > > | masses_ |
std::vector< std::vector< double > > | sources_in_ |
std::vector< std::vector< double > > | sources_out_ |
std::vector< double > | sum_fluxes_ |
std::vector< double > | sum_fluxes_in_ |
std::vector< double > | sum_fluxes_out_ |
std::vector< double > | sum_masses_ |
std::vector< double > | sum_sources_ |
std::vector< double > | sum_sources_in_ |
std::vector< double > | sum_sources_out_ |
std::vector< double > | initial_mass_ |
std::vector< double > | integrated_sources_ |
std::vector< double > | integrated_fluxes_ |
std::vector< double > | increment_fluxes_ |
std::vector< double > | increment_sources_ |
double | last_time_ |
time of last calculated balance More... | |
TimeMark::Type | balance_output_type_ |
TimeMark type for balance output of particular equation. More... | |
TimeMark::Type | output_mark_type_ |
TimeMark type for output of particular equation. More... | |
bool | initial_ |
true before calculating the mass at initial time, otherwise false More... | |
bool | cumulative_ |
if true then cumulative balance is computed More... | |
bool | allocation_done_ |
true before allocating necessary internal structures (Petsc matrices etc.) More... | |
bool | balance_on_ |
If the balance is on. Balance is off in the case of no balance output time marks. More... | |
bool | add_output_times_ |
Add output time marks to balance output time marks. More... | |
int | rank_ |
MPI rank. More... | |
unsigned int | output_line_counter_ |
hold count of line printed into output_ More... | |
bool | output_yaml_header_ |
marks whether YAML output has printed header More... | |
Input::Record | input_record_ |
Record for current balance. More... | |
const TimeGovernor * | time_ |
Static Private Attributes | |
static const unsigned int | output_column_width = 20 |
Size of column in output (used if delimiter is space) More... | |
static bool | do_yaml_output_ = true |
Design of balance class - serves as storage and writer. Equations themselves call methods of Balance that add/modify mass, source and flux of various quantities and generate output.
One instance of Balance can handle several conservative quantities of the same type (e.g. mass of several substances or their phases).
The mass, flux and source are calculated as follows:
m(q,r) = ( M'(q) * solution + mv(q) )[r] f(q,r) = -( R' * ( F(q) * solution + fv(q) ) )[r] s(q,r) = ( S'(q) * solution + sv(q) )[r]
where M' stands for matrix transpose,
m(q,r)...mass of q-th substance in region r f(q,r)...incoming flux of q-th substance in region r s(q,r)...source of q-th substance in region r
and
M(q)...region_mass_matrix_ n_dofs x n_bulk_regions F(q)...be_flux_matrix_ n_boundary_edges x n_dofs S(q)...region_source_matrix_ n_dofs x n_bulk_regions SV(q)..region_source_rhs_ n_dofs x n_bulk_regions
mv(q)..region_mass_vec_ n_bulk_regions fv(q)..be_flux_vec_ n_boundary_edges sv(q)..region_source_vec_ n_bulk_regions R......region_be_matrix_ n_boundary_edges x n_boundary_regions
Remark: Matrix F and the vector fv are such that F*solution+fv produces outcoming fluxes per boundary edge. However we write to output incoming flux due to users' convention and consistently with input interface.
Note that it holds:
sv(q) = column sum of SV(q)
Except for that, we also provide information on positive/negative flux and source:
fp(q,r) = ( R' * EFP(q) )[r], EFP(q)[e] = max{ 0, ( F(q) * solution + fv(q) )[e] } fn(q,r) = ( R' * EFN(q) )[r], EFN(q)[e] = min{ 0, ( F(q) * solution + fv(q) )[e] } sp(q,r) = sum_{i in DOFS } max{ 0, ( S(q)[i,r] * solution[i] + SV(q)[i,r] ) } sn(q,r) = sum_{i in DOFS } min{ 0, ( S(q)[i,r] * solution[i] + SV(q)[i,r] ) }
where
fp(q,r)...positive (inward) flux of q-th quantity in region r fn(q,r)...negative (outward) flux of q-th quantity in region r sp(q,r)...positive source (spring) of q-th quantity in region r sn(q,r)...negative source (sink) of q-th quantity in region r
Remark: The matrix R is needed only for calculation of signed fluxes. The reason is that to determine sign, we decompose flux to sum of local contributions per each boundary element and check its sign. It is not possible to decompose flux using shape functions, since their normal derivatives may have any sign.
Output values (if not relevant, zero is supplied):
#time bulk_region quantity 0 0 0 mass source source_in source_out 0 0 0 #time boundary_region quantity flux flux_in flux_out 0 0 0 0 0 0 0 #time ALL quantity flux flux_in flux_out mass source source_in source_out integrated_flux integrated_source error
error = current_mass - (initial_mass + integrated_source - integrated_flux)
Definition at line 119 of file balance.hh.
Possible formats of output file.
Enumerator | |
---|---|
legacy | legacy |
txt | csv |
gnuplot | gnuplot |
Definition at line 146 of file balance.hh.
Balance::Balance | ( | const std::string & | file_prefix, |
const Mesh * | mesh | ||
) |
Constructor.
file_prefix | Prefix of output file name. |
mesh | Mesh. |
Definition at line 89 of file balance.cc.
Balance::~Balance | ( | ) |
Destructor.
Definition at line 106 of file balance.cc.
void Balance::add_cumulative_source | ( | unsigned int | quantity_idx, |
double | source | ||
) |
Adds provided values to the cumulative sources.
quantity_idx | Index of quantity. |
sources | Sources per region. |
dt | Actual time step. |
Definition at line 542 of file balance.cc.
void Balance::add_flux_values | ( | unsigned int | quantity_idx, |
const DHCellSide & | side, | ||
const LocDofVec & | loc_dof_indices, | ||
const std::vector< double > & | mat_values, | ||
double | vec_value | ||
) |
Adds elements into matrix for computing (outgoing) flux. The flux matrix F is in format [n_boundary_edges x n_dofs] for each quantity. The flux vector fv is in format [n_boundary_edges] for each quantity. See class Balance
description above for details.
quantity_idx | Index of quantity. |
side | DHCellSide iterator. |
loc_dof_indices | Local dof indices (to the solution vector) to be added. |
mat_values | Values to be added into matrix F. |
vec_value | Value to be added into vector fv. |
Definition at line 479 of file balance.cc.
void Balance::add_mass_values | ( | unsigned int | quantity_idx, |
const DHCellAccessor & | dh_cell, | ||
const LocDofVec & | loc_dof_indices, | ||
const std::vector< double > & | mat_values, | ||
double | vec_value | ||
) |
Adds elements into matrix for computing mass. The mass matrix M is in format [n_dofs x n_bulk_regions] for each quantity. The mass vector mv is in format [n_bulk_regions] for each quantity. The region mass is later computed using transpose multiplication (M'*u + mv)[r]. See class Balance
description above for details.
quantity_idx | Index of quantity. |
dh_cell | Dofhandler cell accessor. |
loc_dof_indices | Local dof indices (to the solution vector) to be added. |
mat_values | Values to be added into matrix M. |
vec_value | Value to be added into vector mv. |
Definition at line 448 of file balance.cc.
std::vector< unsigned int > Balance::add_quantities | ( | const std::vector< string > & | names | ) |
Define a set of conservative quantities.
names | List of quantities' names. |
Definition at line 176 of file balance.cc.
unsigned int Balance::add_quantity | ( | const string & | name | ) |
Define a single conservative quantity.
name | Name of the quantity. |
Definition at line 165 of file balance.cc.
void Balance::add_source_values | ( | unsigned int | quantity_idx, |
unsigned int | region_idx, | ||
const LocDofVec & | loc_dof_indices, | ||
const std::vector< double > & | mult_mat_values, | ||
const std::vector< double > & | add_mat_values | ||
) |
Adds elements into matrix and vector for computing source. The source region matrix S is in format [n_dofs x n_bulk_regions] for each quantity (multiplies solution). The source region rhs matrix SV is in format [n_dofs x n_bulk_regions] for each quantity (addition). The region source is then computed as (S'(q) * solution + sv(q))[r], while sv(q) being column sum of SV(q). The source term for a specific region and quantity is then
quantity_idx | Index of quantity. |
region_idx | Index of bulk region. |
loc_dof_indices | Local dof indices (to the solution vector) to be added. |
mult_mat_values | Values to be added into matrix S. |
add_mat_values | Values to be added into matrix SV. |
Definition at line 513 of file balance.cc.
void Balance::allocate | ( | const std::shared_ptr< DOFHandlerMultiDim > & | dh, |
unsigned int | max_dofs_per_boundary | ||
) |
Allocates matrices and vectors for balance based on DofHandler.
dh | DofHandler of the corresponding linear system (and solution). |
max_dofs_per_boundary | Number of dofs contributing to one boundary edge. |
Definition at line 194 of file balance.cc.
void Balance::allocate | ( | unsigned int | n_loc_dofs, |
unsigned int | max_dofs_per_boundary | ||
) |
Allocates matrices and vectors for balance.
n_loc_dofs | Number of solution dofs on the local process. |
max_dofs_per_boundary | Number of dofs contributing to one boundary edge. |
Definition at line 185 of file balance.cc.
void Balance::calculate_cumulative | ( | unsigned int | quantity_idx, |
const Vec & | solution | ||
) |
Updates cumulative quantities for balance. This method can be called in substeps even if no output is generated. It calculates the sum of source and sum of (incoming) flux over time interval.
quantity_idx | Index of quantity. |
solution | Solution vector. |
Definition at line 552 of file balance.cc.
void Balance::calculate_instant | ( | unsigned int | quantity_idx, |
const Vec & | solution | ||
) |
Calculates actual mass, incoming flux and source.
quantity_idx | Index of quantity. |
solution | Solution vector. |
Definition at line 636 of file balance.cc.
void Balance::calculate_mass | ( | unsigned int | quantity_idx, |
const Vec & | solution, | ||
vector< double > & | output_array | ||
) |
Calculates actual mass and save it to given vector.
quantity_idx | Index of quantity. |
solution | Solution vector. |
output_array | Vector of output masses per region. |
Definition at line 611 of file balance.cc.
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Return part of output represented by zero values. Count of zero values is given by cnt parameter.
Definition at line 1002 of file balance.cc.
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Getter for cumulative_.
Definition at line 190 of file balance.hh.
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Variant of the finish_flux_assembly() method for a set of quantities.
Definition at line 334 of file balance.hh.
void Balance::finish_flux_assembly | ( | unsigned int | quantity_idx | ) |
This method must be called after assembling the matrix and vector for computing flux.
Definition at line 425 of file balance.cc.
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Variant of the finish_mass_assembly() method for a set of quantities.
Definition at line 324 of file balance.hh.
void Balance::finish_mass_assembly | ( | unsigned int | quantity_idx | ) |
This method must be called after assembling the matrix for computing mass.
Definition at line 414 of file balance.cc.
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Variant of the finish_source_assembly() method for a set of quantities.
Definition at line 344 of file balance.hh.
void Balance::finish_source_assembly | ( | unsigned int | quantity_idx | ) |
This method must be called after assembling the matrix and vectors for computing source.
Definition at line 436 of file balance.cc.
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Print output header.
Definition at line 1096 of file balance.cc.
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Format double value of csv output. If delimiter is space, align text to column.
Definition at line 1141 of file balance.cc.
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Format string value of csv output. Wrap string into quotes and if delimiter is space, align text to column.
Definition at line 1124 of file balance.cc.
Computes unique id of local boundary edge from local element index and element side index
side | is a side of locally owned element |
Definition at line 426 of file balance.hh.
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Input selection for file format.
Definition at line 42 of file balance.cc.
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Main balance input record type.
Definition at line 53 of file balance.cc.
void Balance::init_from_input | ( | const Input::Record & | in_rec, |
TimeGovernor & | tg | ||
) |
Initialize the balance object according to the input. The balance output time marks are set according to the already existing output time marks of the same equation. So, this method must be called after Output::
in_rec | Input record of balance. |
tg | TimeGovernor of the equation. We need just equation mark type. |
Definition at line 132 of file balance.cc.
bool Balance::is_current | ( | ) |
Returns true if the current time step is marked for the balance output.
Definition at line 376 of file balance.cc.
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Postponed allocation and initialization to allow calling setters in arbitrary order. In particular we need to perform adding of output times after the output time marks are set. On the other hand we need to read the input before we make the allocation.
The initialization is done during the first call of any start_*_assembly method.
Definition at line 205 of file balance.cc.
void Balance::output | ( | ) |
Perform output to file for given time instant.
Definition at line 713 of file balance.cc.
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Perform output in csv format.
Definition at line 1010 of file balance.cc.
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Perform output in old format (for compatibility)
Definition at line 856 of file balance.cc.
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Perform output in yaml format.
Definition at line 1154 of file balance.cc.
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Set global variable to output balance files into YAML format (in addition to the table format).
Definition at line 66 of file balance.cc.
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Variant of the start_flux_assembly() method for a set of quantities.
Definition at line 246 of file balance.hh.
void Balance::start_flux_assembly | ( | unsigned int | quantity_idx | ) |
This method must be called before assembling the matrix and vector for fluxes. It actually erases the matrix and vector.
Definition at line 396 of file balance.cc.
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Variant of the start_mass_assembly() method for a set of quantities.
Definition at line 233 of file balance.hh.
void Balance::start_mass_assembly | ( | unsigned int | quantity_idx | ) |
This method must be called before assembling the matrix for computing mass. It actually erases the matrix.
Definition at line 387 of file balance.cc.
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Variant of the start_source_assembly() method for a set of quantities.
Definition at line 259 of file balance.hh.
void Balance::start_source_assembly | ( | unsigned int | quantity_idx | ) |
This method must be called before assembling the matrix and vectors for sources. It actually erases the matrix and vectors.
Definition at line 405 of file balance.cc.
void Balance::units | ( | const UnitSI & | unit | ) |
Setter for units of conserved quantities.
Definition at line 157 of file balance.cc.
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Add output time marks to balance output time marks.
Definition at line 542 of file balance.hh.
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true before allocating necessary internal structures (Petsc matrices etc.)
Definition at line 536 of file balance.hh.
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If the balance is on. Balance is off in the case of no balance output time marks.
Definition at line 539 of file balance.hh.
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File path for output_ stream.
Definition at line 443 of file balance.hh.
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TimeMark type for balance output of particular equation.
Definition at line 524 of file balance.hh.
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Matrices for calculation of flux (n_boundary_edges x n_dofs).
Definition at line 467 of file balance.hh.
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Vectors for calculation of flux (n_boundary_edges).
Definition at line 476 of file balance.hh.
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Maps unique identifier of (local bulk element idx, side idx) returned by get_boundary_edge_uid(side)
to local boundary edge. Example usage: be_id = be_id_map_[get_boundary_edge_uid(side)]
Definition at line 486 of file balance.hh.
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Offset for local part of vector of boundary edges.
Definition at line 492 of file balance.hh.
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Maps local boundary edge to its region boundary index.
Definition at line 489 of file balance.hh.
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if true then cumulative balance is computed
Definition at line 533 of file balance.hh.
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Definition at line 431 of file balance.hh.
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Save prefix passed in in constructor.
Definition at line 440 of file balance.hh.
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Definition at line 497 of file balance.hh.
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Definition at line 498 of file balance.hh.
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Definition at line 499 of file balance.hh.
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Definition at line 517 of file balance.hh.
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Definition at line 518 of file balance.hh.
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true before calculating the mass at initial time, otherwise false
Definition at line 530 of file balance.hh.
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Definition at line 512 of file balance.hh.
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Record for current balance.
Definition at line 555 of file balance.hh.
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Definition at line 516 of file balance.hh.
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Definition at line 515 of file balance.hh.
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time of last calculated balance
Definition at line 521 of file balance.hh.
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Definition at line 500 of file balance.hh.
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Definition at line 436 of file balance.hh.
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Definition at line 457 of file balance.hh.
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Allocation parameters. Set by the allocate method used in the lazy_initialize.
Definition at line 434 of file balance.hh.
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Definition at line 435 of file balance.hh.
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Handle for file for output in given OutputFormat of balance and total fluxes over individual regions and region sets.
Definition at line 446 of file balance.hh.
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Size of column in output (used if delimiter is space)
Definition at line 391 of file balance.hh.
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Format of output file.
Definition at line 452 of file balance.hh.
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hold count of line printed into output_
Definition at line 549 of file balance.hh.
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TimeMark type for output of particular equation.
Definition at line 527 of file balance.hh.
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Definition at line 449 of file balance.hh.
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marks whether YAML output has printed header
Definition at line 552 of file balance.hh.
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Names of conserved quantities.
Definition at line 455 of file balance.hh.
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MPI rank.
Definition at line 546 of file balance.hh.
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Matrices for calculation of mass (n_dofs x n_bulk_regions).
Definition at line 464 of file balance.hh.
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Vectors for calculation of mass (n_bulk_regions).
Definition at line 479 of file balance.hh.
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Matrices for calculation of source (n_dofs x n_bulk_regions).
Definition at line 470 of file balance.hh.
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Matrices for calculation of signed source (n_dofs x n_bulk_regions).
Definition at line 473 of file balance.hh.
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Definition at line 501 of file balance.hh.
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Definition at line 502 of file balance.hh.
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Definition at line 505 of file balance.hh.
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Definition at line 506 of file balance.hh.
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Definition at line 507 of file balance.hh.
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Definition at line 508 of file balance.hh.
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Definition at line 509 of file balance.hh.
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Definition at line 510 of file balance.hh.
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Definition at line 511 of file balance.hh.
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Definition at line 557 of file balance.hh.
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Units of conserved quantities.
Definition at line 460 of file balance.hh.