Root
Root record of JSON input for Flow123d.
- String (generic)
flow123d_version
obligatoryVersion of Flow123d for which the input file was created.Flow123d only warn about version incompatibility. However, external tools may use this information to provide conversion of the input file to the structure required by another version of Flow123d.
- Bool (generic)
pause_after_run
value at declaration = FalseIf true, the program will wait for key press before it terminates.
Coupling_Base
The root record of description of particular the problem to solve.
Record with data for a general sequential coupling.
Coupling_Sequential
Record with data for a general sequential coupling.
- String (generic)
description
optionalShort description of the solved problem.
Is displayed in the main log, and possibly in other text output files.- ABSTRACTAdvectionProcess
solute_equation
optionalTransport of soluted substances, depends on the velocity field from a Flow equation.
- ABSTRACTAdvectionProcess
heat_equation
optionalHeat transfer, depends on the velocity field from a Flow equation.
Mesh
Record with mesh related data.
- file nameinput
mesh_file
obligatoryInput file with mesh description.
- RECORDPartition
Parameters of mesh partitioning algorithms.
- Bool (generic)
print_regions
value at declaration = TrueIf true, print table of all used regions.
Region
Abstract record for Region.
Elementary region declared by ID.Allows to create new region with given id and labelor specify existing region by id which will be renamed.
Gives a new name to an elementary regionwith original name (in the mesh file) given by
mesh_label.
Elementary region declared by a list of elements. The new region is assigned to the list of elements spefied by the key
element_list
.Defines region (set) as a union of given two or more regions. Regions can be given by names or IDs or both ways together.
Defines region (set) as a difference of given pair of regions.
Defines region (set) as an intersection of given two or more regions.
From_Id
Elementary region declared by ID.Allows to create new region with given id and labelor specify existing region by id which will be renamed.
- String (generic)
name
obligatoryLabel (name) of the region. Has to be unique in one mesh.
- Integer [0, INT]
id
obligatoryThe ID of the region to which you assign label.
- Integer [0, INT]
dim
optionalThe dim of the region to which you assign label. Value is taken into account only if new region is created.
From_Label
Gives a new name to an elementary regionwith original name (in the mesh file) given by mesh_label.
- String (generic)
name
obligatoryNew label (name) of the region. Has to be unique in one mesh.
- String (generic)
mesh_label
obligatoryThe mesh_label is e.g. physical volume name in GMSH format.
From_Elements
Elementary region declared by a list of elements. The new region is assigned to the list of elements spefied by the keyelement_list
.
- String (generic)
name
obligatoryLabel (name) of the region. Has to be unique in one mesh.
- Integer [0, INT]
id
optionalThe ID of the region. If unset a unique ID will be generated automatically.
- Array [1, UINT]
- of INTEGER
element_list
obligatoryList of IDs of elements.
Union
Defines region (set) as a union of given two or more regions. Regions can be given by names or IDs or both ways together.
- String (generic)
name
obligatoryLabel (name) of the region. Has to be unique in one mesh.
- Array [0, UINT]
- of INTEGER
region_ids
optionalList of region ID numbers that has to be added to the region set.
- Array [0, UINT]
- of STRING
regions
optionalDefines region as a union of given pair of regions.
Difference
Defines region (set) as a difference of given pair of regions.
- String (generic)
name
obligatoryLabel (name) of the region. Has to be unique in one mesh.
- Array [2, 2]
- of STRING
regions
obligatoryList of exactly two regions given by their names.
Intersection
Defines region (set) as an intersection of given two or more regions.
- String (generic)
name
obligatoryLabel (name) of the region. Has to be unique in one mesh.
- Array [2, UINT]
- of STRING
regions
obligatoryList of two or more regions given by their names.
Partition
Setting for various types of mesh partitioning.
- SELECTIONGraphType
Algorithm for generating graph and its weights from a multidimensional mesh.
PartTool
Select the partitioning tool to use.
Use PETSc interface to various partitioning tools.
Use direct interface to Metis.
GraphType
Different algorithms to make the sparse graph with weighted edges
from the multidimensional mesh. Main difference is dealing with
neighborings of elements of different dimension.
Add edge for any pair of neighboring elements.
Same as before and assign higher weight to cuts of lower dimension in order to make them stick to one face.
Add edge for any pair of neighboring elements of same dimension (bad for matrix multiply).
TimeGovernor
Setting of the simulation time. (can be specific to one equation)
- Double (-inf, +inf)
start_time
value at declaration = 0.0Start time of the simulation.
- Double (-inf, +inf)
end_time
value at declaration = 5e+17End time of the simulation. Default value is more then age of universe in seconds.
- Double [0, +inf)
init_dt
value at declaration = 0.0Initial guess for the time step.
Only useful for equations that use adaptive time stepping.If set to 0.0, the time step is determined in fully autonomous way if the equation supports it.- Double [0, +inf)
min_dt
value at read time = Machine precision.Soft lower limit for the time step. Equation using adaptive time stepping can notsuggest smaller time step, but actual time step could be smaller in order to match prescribed input or output times.
- Double [0, +inf)
max_dt
value at read time = Whole time of the simulation if specified, infinity else.Hard upper limit for the time step. Actual length of the time step is also limitedby input and output times.
DarcyFlow
Darcy flow model. Abstraction of various porous media flow models.
Mixed-Hybrid solver for STEADY saturated Darcy flow.
Lumped Mixed-Hybrid solver for unsteady saturated Darcy flow.
Flow_Darcy_MH
Mixed-Hybrid solver for STEADY saturated Darcy flow.
- Array [3, 3]
- of DOUBLE
gravity
value at declaration = [0, 0, -1]Vector of the gravity force. Dimensionless.
- instance of RECORD
- generic typeEquationOutput
- parameter output_field_selection = Flow_Darcy_MH:OutputFields
Parameters of output from MH module.
- RECORDTimeGovernor
Time governor setting for the unsteady Darcy flow model.
- Integer [0, 2]
n_schurs
value at declaration = 2Number of Schur complements to perform when solving MH system.
- SELECTIONMH_MortarMethod
Method for coupling Darcy flow between dimensions.
Flow_Darcy_MH_Data
Record to set fields of the equation.
The fields are set only on the domain specified by one of the keys: 'region', 'rid'
and after the time given by the key 'time'. The field setting can be overridden by
any Flow_Darcy_MH_Data record that comes later in the boundary data array.
- Array [1, UINT]
- of STRING
region
optionalLabels of the regions where to set fields.
- Integer [0, INT]
rid
optionalID of the region where to set fields.
- Double [0, +inf)
time
value at declaration = 0.0Apply field setting in this record after this time.
These times have to form an increasing sequence.- instance of ABSTRACT
- generic typeField_R3_to_R[3,3]
- parameter element_input_type = DOUBLE
anisotropy
optionalAnisotropy of the conductivity tensor. {$[-]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
cross_section
optionalComplement dimension parameter (cross section for 1D, thickness for 2D). {$[m^{3-d}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
conductivity
optionalIsotropic conductivity scalar. {$[ms^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
sigma
optionalTransition coefficient between dimensions. {$[-]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
water_source_density
optionalWater source density. {$[s^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = Flow_Darcy_BC_Type
bc_type
optionalBoundary condition type, possible values: {$[-]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_pressure
optionalPrescribed pressure value on the boundary. Used for all values of 'bc_type' except for 'none' and 'seepage'. See documentation of 'bc_type' for exact meaning of 'bc_pressure' in individual boundary condition types. {$[m]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_flux
optionalIncoming water boundary flux. Used for bc_types : 'total_flux', 'seepage', 'river'. {$[m^{4-d}s^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_robin_sigma
optionalConductivity coefficient in the 'total_flux' or the 'river' boundary condition type. {$[m^{3-d}s^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_switch_pressure
optionalCritical switch pressure for 'seepage' and 'river' boundary conditions. {$[m]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
init_pressure
optionalInitial condition for pressure {$[m]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
storativity
optionalStorativity. {$[m^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_piezo_head
optionalBoundary piezometric head for BC types: dirichlet, robin, and river.
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_switch_piezo_head
optionalBoundary switch piezometric head for BC types: seepage, river.
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
init_piezo_head
optionalInitial condition for the pressure given as the piezometric head.
Field_R3_to_R[3,3]
Abstract for all time-space functions.
R3_to_R[3,3] Field given by a Python script.
R3_to_R[3,3] Field constant in space.
R3_to_R[3,3] Field given by runtime interpreted formula.
R3_to_R[3,3] Field piecewise constant on mesh elements.
R3_to_R[3,3] Field interpolated from external mesh data and piecewise constant on mesh elements.
R3_to_R[3,3] Field time-dependent function in space.
element_input_type
FieldPython
R3_to_R[3,3] Field given by a Python script.
- String (generic)
script_string
value at read time = Obligatory if 'script_file' is not given.Python script given as in place string
- file nameinput
script_file
value at read time = Obligatory if 'script_striong' is not given.Python script given as external file
- String (generic)
function
obligatoryFunction in the given script that returns tuple containing components of the return type.
For NxM tensor values: tensor(row,col) = tuple( M*row + col ).
Unit
Specify unit of an input value. Evaluation of the unit formula results into a coeficient and a unit in terms of powers of base SI units. The unit must match expected SI unit of the value, while the value provided on the input is multiplied by the coefficient before further processing. The unit formula have a form:
<UnitExpr>;<Variable>=<Number>*<UnitExpr>;...,
where <Variable>
is a variable name and <UnitExpr>
is a units expression which consists of products and divisions of terms.
A term has a form: <Base>^<N>
, where <N>
is an integer exponent and <Base>
is either a base SI unit, a derived unit, or a variable defined in the same unit formula. Example, unit for the pressure head:
MPa/rho/g_; rho = 990*kg*m^-3; g_ = 9.8*m*s^-2
- String (generic)
unit_formula
obligatoryDefinition of unit.
FieldConstant
R3_to_R[3,3] Field constant in space.
- Array [1, UINT]
- of ARRAY
value
obligatoryValue of the constant field. For vector values, you can use scalar value to enter constant vector. For square {$N\times N$}-matrix values, you can use: - vector of size {$N$} to enter diagonal matrix
- vector of size {$\frac12N(N+1)$} to enter symmetric matrix (upper triangle, row by row)
- scalar to enter multiple of the unit matrix.
element_input_type
FieldFormula
R3_to_R[3,3] Field given by runtime interpreted formula.
- Array [1, UINT]
- of ARRAY
value
obligatoryString, array of strings, or matrix of strings with formulas for individual entries of scalar, vector, or tensor value respectively.
For vector values, you can use just one string to enter homogeneous vector.
For square {$N\times N$}-matrix values, you can use:- array of strings of size {$N$} to enter diagonal matrix
- array of strings of size {$\frac12N(N+1)$} to enter symmetric matrix (upper triangle, row by row)
- just one string to enter (spatially variable) multiple of the unit matrix.
Formula can contain variablesx,y,z,t
and usual operators and functions.
FieldElementwise
R3_to_R[3,3] Field piecewise constant on mesh elements.
- file nameinput
gmsh_file
obligatoryInput file with ASCII GMSH file format.
- String (generic)
field_name
obligatoryThe values of the Field are read from the
$ElementData
section with field name given by this key.
FieldInterpolatedP0
R3_to_R[3,3] Field interpolated from external mesh data and piecewise constant on mesh elements.
- file nameinput
gmsh_file
obligatoryInput file with ASCII GMSH file format.
- String (generic)
field_name
obligatoryThe values of the Field are read from the
$ElementData
section with field name given by this key.
FieldTimeFunction
R3_to_R[3,3] Field time-dependent function in space.
element_input_type
TableFunction
Allow set variable series initialization of Fields.
element_input_type
IndependentValue
Value of Field for independent variable.
- Double [0, +inf)
t
obligatoryIndependent variable of stamp.
- Array [1, UINT]
- of ARRAY
value
obligatoryValue of the field in given stamp.
element_input_type
Field_R3_to_R
Abstract for all time-space functions.
R3_to_R Field given by a Python script.
R3_to_R Field constant in space.
R3_to_R Field given by runtime interpreted formula.
R3_to_R Field piecewise constant on mesh elements.
R3_to_R Field interpolated from external mesh data and piecewise constant on mesh elements.
R3_to_R Field time-dependent function in space.
element_input_type
FieldPython
R3_to_R Field given by a Python script.
- String (generic)
script_string
value at read time = Obligatory if 'script_file' is not given.Python script given as in place string
- file nameinput
script_file
value at read time = Obligatory if 'script_striong' is not given.Python script given as external file
- String (generic)
function
obligatoryFunction in the given script that returns tuple containing components of the return type.
For NxM tensor values: tensor(row,col) = tuple( M*row + col ).
FieldConstant
value
obligatoryValue of the constant field. For vector values, you can use scalar value to enter constant vector. For square {$N\times N$}-matrix values, you can use: - vector of size {$N$} to enter diagonal matrix
- vector of size {$\frac12N(N+1)$} to enter symmetric matrix (upper triangle, row by row)
- scalar to enter multiple of the unit matrix.
element_input_type
FieldFormula
R3_to_R Field given by runtime interpreted formula.
- String (generic)
value
obligatoryString, array of strings, or matrix of strings with formulas for individual entries of scalar, vector, or tensor value respectively.
For vector values, you can use just one string to enter homogeneous vector.
For square {$N\times N$}-matrix values, you can use:- array of strings of size {$N$} to enter diagonal matrix
- array of strings of size {$\frac12N(N+1)$} to enter symmetric matrix (upper triangle, row by row)
- just one string to enter (spatially variable) multiple of the unit matrix.
Formula can contain variablesx,y,z,t
and usual operators and functions.
FieldElementwise
R3_to_R Field piecewise constant on mesh elements.
- file nameinput
gmsh_file
obligatoryInput file with ASCII GMSH file format.
- String (generic)
field_name
obligatoryThe values of the Field are read from the
$ElementData
section with field name given by this key.
FieldInterpolatedP0
R3_to_R Field interpolated from external mesh data and piecewise constant on mesh elements.
- file nameinput
gmsh_file
obligatoryInput file with ASCII GMSH file format.
- String (generic)
field_name
obligatoryThe values of the Field are read from the
$ElementData
section with field name given by this key.
FieldTimeFunction
R3_to_R Field time-dependent function in space.
element_input_type
TableFunction
Allow set variable series initialization of Fields.
element_input_type
IndependentValue
Value of Field for independent variable.
- Double [0, +inf)
t
obligatoryIndependent variable of stamp.
value
obligatoryValue of the field in given stamp.
element_input_type
Flow_Darcy_BC_Type
Homogeneous Neumann boundary condition. Zero flux
Dirichlet boundary condition. Specify the pressure head through the ''bc_pressure'' field or the piezometric head through the ''bc_piezo_head'' field.
Flux boundary condition (combines Neumann and Robin type). Water inflow equal to {$ \delta_d(q_d^N + \sigma_d (h_d^R - h_d) )$}. Specify the water inflow by the 'bc_flux' field, the transition coefficient by 'bc_robin_sigma' and the reference pressure head or pieozmetric head through ''bc_pressure'' or ''bc_piezo_head'' respectively.
Seepage face boundary condition. Pressure and inflow bounded from above. Boundary with potential seepage flow is described by the pair of inequalities: {$h_d \le h_d^D$} and {$ -\boldsymbol q_d\cdot\boldsymbol n \le \delta q_d^N$}, where the equality holds in at least one of them. Caution. Setting {$q_d^N$} strictly negative may lead to an ill posed problem since a positive outflow is enforced. Parameters {$h_d^D$} and {$q_d^N$} are given by fields
bc_switch_pressure
(orbc_switch_piezo_head
) andbc_flux
respectively.River boundary condition. For the water level above the bedrock, {$H_d > H_d^S$}, the Robin boundary condition is used with the inflow given by: { $ \delta_d(q_d^N + \sigma_d(H_d^D - H_d) )$}. For the water level under the bedrock, constant infiltration is used: { $ \delta_d(q_d^N + \sigma_d(H_d^D - H_d^S) )$}. Parameters:
bc_pressure
,bc_switch_pressure
,bc_sigma,
bc_flux``.
NonlinearSolver
Parameters to a non-linear solver.
- Double [0, +inf)
tolerance
value at declaration = 1e-06Residual tolerance.
- Integer [0, INT]
min_it
value at declaration = 1Minimum number of iterations (linear solves) to use. This is usefull if the convergence criteria does not characterize your goal well enough so it converges prematurely possibly without the single linear solve.If greater then 'max_it' the value is set to 'max_it'.
- Integer [0, INT]
max_it
value at declaration = 100Maximum number of iterations (linear solves) of the non-linear solver.
- Bool (generic)
converge_on_stagnation
value at declaration = FalseIf a stagnation of the nonlinear solver is detected the solver stops. A divergence is reported by default forcing the end of the simulation. Setting this flag to 'true', the solverends with convergence success on stagnation, but report warning about it.
LinSys
Linear solver setting.
Interface to PETSc solvers. Convergence criteria is:
norm( res_n ) < max( norm( res_0 ) * r_tol, a_tol )
where res_i is the residuum vector after i-th iteration of the solver and res_0 is an estimate of the norm of initial residual. If the initial guess of the solution is provided (usually only for transient equations) the residual of this estimate is used, otherwise the norm of preconditioned RHS is used. The default norm is L2 norm of preconditioned residual: {$ P^{-1}(Ax-b)$}, usage of other norm may be prescribed using the 'option' key. See also PETSc documentation for KSPSetNormType.Solver setting.
Petsc
Interface to PETSc solvers. Convergence criteria is:
norm( res_n ) < max( norm( res_0 ) * r_tol, a_tol )
where res_i is the residuum vector after i-th iteration of the solver and res_0 is an estimate of the norm of initial residual. If the initial guess of the solution is provided (usually only for transient equations) the residual of this estimate is used, otherwise the norm of preconditioned RHS is used. The default norm is L2 norm of preconditioned residual: {$ P^{-1}(Ax-b)$}, usage of other norm may be prescribed using the 'option' key. See also PETSc documentation for KSPSetNormType.
- Double [0, 1]
r_tol
value at read time = Defalut value set by nonlinear solver or equation. If not we use value 1.0e-7.Relative residual tolerance, (to initial error).
- Double [0, +inf)
a_tol
value at read time = Defalut value set by nonlinear solver or equation. If not we use value 1.0e-11.Absolute residual tolerance.
- Integer [0, INT]
max_it
value at read time = Defalut value set by nonlinear solver or equation. If not we use value 1000.Maximum number of outer iterations of the linear solver.
- String (generic)
options
value at declaration =Options passed to PETSC before creating KSP instead of default setting.
Bddc
Solver setting.
- Double [0, 1]
r_tol
value at read time = Defalut value set by nonlinear solver or equation. If not we use value 1.0e-7.Relative residual tolerance, (to initial error).
- Integer [0, INT]
max_it
value at read time = Defalut value set by nonlinear solver or equation. If not we use value 1000.Maximum number of outer iterations of the linear solver.
- Integer [0, INT]
max_nondecr_it
value at declaration = 30Maximum number of iterations of the linear solver with non-decreasing residual.
- Integer [0, INT]
number_of_levels
value at declaration = 2Number of levels in the multilevel method (=2 for the standard BDDC).
- Bool (generic)
use_adaptive_bddc
value at declaration = FalseUse adaptive selection of constraints in BDDCML.
- Integer [0, 2]
bddcml_verbosity_level
value at declaration = 0Level of verbosity of the BDDCML library:
- 0 - no output
- 1 - mild output
- 2 - detailed output.
OutputStream
Configuration of the spatial output of a single balance equation.
- file nameoutput
file
value at read time = Name of the equation associated with the output stream.File path to the connected output file.
- Integer [0, INT]
precision
value at declaration = 17The number of decimal digits used in output of floating point values.\ Default is about 17 decimal digits which is enough to keep double values exect after write-read cycle.
OutputTime
Format of output stream and possible parameters.
Parameters of vtk output format.
Parameters of gmsh output format.
vtk
Parameters of vtk output format.
- SELECTIONVTK variant (ascii or binary)
Variant of output stream file format.
VTK variant (ascii or binary)
ASCII variant of VTK file format
Uncompressed appended binary XML VTK format without usage of base64 encoding of appended data.
Appended binary XML VTK format without usage of base64 encoding of appended data. Compressed with ZLib.
gmsh
Parameters of gmsh output format.
TimeGrid
Equally spaced grid of time points.
- Double [0, +inf)
begin
value at read time = The initial time of the associated equation.The start time of the grid.
- Double [0, +inf)
step
optionalThe step of the grid. If not specified, the grid consists only of the start time.
- Double [0, +inf)
end
value at read time = The end time of the simulation.The time greater or equal to the last time in the grid.
OutputMesh
Parameters of the refined output mesh.
- Integer [1, 20]
max_level
value at declaration = 3Maximal level of refinement of the output mesh.
- Bool (generic)
refine_by_error
value at declaration = FalseSet true for using error_control_field. Set false for global uniform refinement to max_level.
- String (generic)
error_control_field
optionalName of an output field, according to which the output mesh will be refined. The field must be a SCALAR one.
ObservePoint
Specification of the observation point. The actual observe element and the observe point on it is determined as follows:
- Find an initial element containing the initial point. If no such element exists we report the error.
- Use BFS starting from the inital element to find the 'observe element'. The observe element is the closest element 3. Find the closest projection of the inital point on the observe element and snap this projection according to the 'snap_dim'.
- String (generic)
name
value at read time = Default name have the form 'obs_<id>', where 'id' is the rank of the point on the input.Optional point name. Has to be unique. Any string that is valid YAML key in record without any quoting can be used howeverusing just alpha-numerical characters and underscore instead of the space is recommended.
- Array [3, 3]
- of DOUBLE
point
obligatoryInitial point for the observe point search.
- Integer [0, 4]
snap_dim
value at declaration = 4The dimension of the sub-element to which center we snap. For value 4 no snapping is done. For values 0 up to 3 the element containing the initial point is found and then the observepoint is snapped to the nearest center of the sub-element of the given dimension. E.g. for dimension 2 we snap to the nearest center of the face of the initial element.
- String (generic)
snap_region
value at declaration = ALLThe region of the initial element for snapping. Without snapping we make a projection to the initial element.
- Integer [0, INT]
n_search_levels
value at declaration = 1Maximum number of levels of the breadth first search used to find the observe element from the initial element. Value zero means to search only the initial element itself.
EquationOutput
Output of the equation's fields.The output is done through the output stream of the associated balance law equation.The stream defines output format for the full space information in selected times and observe points for the full time information. The key 'fields' select the fields for the full spatial output.The set of output times may be specified per field otherwise common time set 'times' is used. If even this is not providedthe time set of the output_stream is used. The initial time of the equation is automatically added to the time set of every selected field. The end time of the equation is automatically added to the common output time set.
- Bool (generic)
add_input_times
value at declaration = FalseAdd all input time points of the equation, mentioned in the 'input_fields' list, also as the output points.
- Array [0, UINT]
- of FieldOutputSetting
Array of output fields and their individual output settings.
- Array [0, UINT]
- of PARAMETER
observe_fields
value at declaration = []Array of the fields evaluated in the observe points of the associated output stream.
output_field_selection
FieldOutputSetting
Setting of the field output. The field name, output times, output interpolation (future).
field
obligatoryThe field name (from selection).
output_field_selection
Flow_Darcy_MH:OutputFields
Selection of output fields for the Flow_Darcy_MH model.
{$[m]$} Input field:
{$[m]$} Input field:
{$[m]$} Input field:
{$[ms^{-1}]$} Input field:
{$[-]$} Input field:
{$[-]$} Input field:
{$[-]$} Input field: Anisotropy of the conductivity tensor.
{$[m^{3-d}]$} Input field: Complement dimension parameter (cross section for 1D, thickness for 2D).
{$[ms^{-1}]$} Input field: Isotropic conductivity scalar.
{$[-]$} Input field: Transition coefficient between dimensions.
{$[s^{-1}]$} Input field: Water source density.
{$[m]$} Input field: Initial condition for pressure
{$[m^{-1}]$} Input field: Storativity.
{$[m]$} Input field:
{$[ms^{-1}]$} Input field:
{$[s^{-1}]$} Input field:
Output_DarcyMHSpecific
Specific Darcy flow MH output.
- Bool (generic)
compute_errors
value at declaration = FalseSPECIAL PURPOSE. Computing errors pro non-compatible coupling.
- file nameoutput
raw_flow_output
optionalOutput file with raw data form MH module.
Balance
Balance of a conservative quantity, boundary fluxes and sources.
- Bool (generic)
add_output_times
value at declaration = TrueAdd all output times of the balanced equation to the balance output times set. Note that this is not the time set of the output stream.
- Bool (generic)
cumulative
value at declaration = FalseCompute cumulative balance over time. If true, then balance is calculated at each computational time step, which can slow down the program.
- file nameoutput
file
value at read time = File name generated from the balanced quantity: <quantity_name>_balance.*File name for output of balance.
Balance_output_format
Format of output file for balance.
Legacy format used by previous program versions.
Excel format with tab delimiter.
Format compatible with GnuPlot datafile with fixed column width.
MH_MortarMethod
Mortar space: P0 on elements of lower dimension.
Mortar space: P0 on elements of lower dimension.
Mortar space: P1 on intersections, using non-conforming pressures.
Flow_Richards_LMH
Lumped Mixed-Hybrid solver for unsteady saturated Darcy flow.
- Array [3, 3]
- of DOUBLE
gravity
value at declaration = [0, 0, -1]Vector of the gravity force. Dimensionless.
- instance of RECORD
- generic typeEquationOutput
- parameter output_field_selection = Flow_Darcy_MH:OutputFields
Parameters of output from MH module.
- RECORDTimeGovernor
Time governor setting for the unsteady Darcy flow model.
- Integer [0, 2]
n_schurs
value at declaration = 2Number of Schur complements to perform when solving MH system.
- SELECTIONMH_MortarMethod
Method for coupling Darcy flow between dimensions.
RichardsLMH_Data
Record to set fields of the equation.
The fields are set only on the domain specified by one of the keys: 'region', 'rid'
and after the time given by the key 'time'. The field setting can be overridden by
any RichardsLMH_Data record that comes later in the boundary data array.
- Array [1, UINT]
- of STRING
region
optionalLabels of the regions where to set fields.
- Integer [0, INT]
rid
optionalID of the region where to set fields.
- Double [0, +inf)
time
value at declaration = 0.0Apply field setting in this record after this time.
These times have to form an increasing sequence.- instance of ABSTRACT
- generic typeField_R3_to_R[3,3]
- parameter element_input_type = DOUBLE
anisotropy
optionalAnisotropy of the conductivity tensor. {$[-]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
cross_section
optionalComplement dimension parameter (cross section for 1D, thickness for 2D). {$[m^{3-d}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
conductivity
optionalIsotropic conductivity scalar. {$[ms^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
sigma
optionalTransition coefficient between dimensions. {$[-]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
water_source_density
optionalWater source density. {$[s^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = Flow_Darcy_BC_Type
bc_type
optionalBoundary condition type, possible values: {$[-]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_pressure
optionalPrescribed pressure value on the boundary. Used for all values of 'bc_type' except for 'none' and 'seepage'. See documentation of 'bc_type' for exact meaning of 'bc_pressure' in individual boundary condition types. {$[m]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_flux
optionalIncoming water boundary flux. Used for bc_types : 'total_flux', 'seepage', 'river'. {$[m^{4-d}s^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_robin_sigma
optionalConductivity coefficient in the 'total_flux' or the 'river' boundary condition type. {$[m^{3-d}s^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_switch_pressure
optionalCritical switch pressure for 'seepage' and 'river' boundary conditions. {$[m]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
init_pressure
optionalInitial condition for pressure {$[m]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
storativity
optionalStorativity. {$[m^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
water_content_saturated
optionalSaturated water content {$ \theta_s $}.
relative volume of the water in a reference volume of a saturated porous media.
{$[-]$}- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
water_content_residual
optionalResidual water content {$ \theta_r $}.
Relative volume of the water in a reference volume of an ideally dry porous media.
{$[-]$}- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
genuchten_p_head_scale
optionalThe van Genuchten pressure head scaling parameter {$ \alpha $}.
The parameter of the van Genuchten's model to scale the pressure head.
Related to the inverse of the air entry pressure, i.e. the pressure where the relative water content starts to decrease below 1.
{$[m^{-1}]$}- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
genuchten_n_exponent
optionalThe van Genuchten exponent parameter {$ n $}. {$[-]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_piezo_head
optionalBoundary piezometric head for BC types: dirichlet, robin, and river.
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_switch_piezo_head
optionalBoundary switch piezometric head for BC types: seepage, river.
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
init_piezo_head
optionalInitial condition for the pressure given as the piezometric head.
SoilModel
Setting for the soil model.
- SELECTIONSoil_Model_Type
Selection of the globally applied soil model. In future we replace this key by a field for selection of the model.That will allow usage of different soil model in a single simulation.
- Double [0, 1]
cut_fraction
value at declaration = 0.999Fraction of the water content where we cut and rescale the curve.
Soil_Model_Type
Van Genuchten soil model with cutting near zero.
Irmay model for conductivity, Van Genuchten model for the water content. Suitable for bentonite.
AdvectionProcess
Abstract advection process. In particular: transport of substances or heat transfer.
Transport by convection and/or diffusion
coupled with reaction and adsorption model (ODE per element)
via operator splitting.DG solver for heat transfer.
Coupling_OperatorSplitting
Transport by convection and/or diffusion
coupled with reaction and adsorption model (ODE per element)
via operator splitting.
Substance
Chemical substance.
- String (generic)
name
obligatoryName of the substance.
- Double [0, +inf)
molar_mass
value at declaration = 1Molar mass of the substance [kg/mol].
Solute
Transport of soluted substances.
Explicit in time finite volume method for advection only solute transport.
DG solver for solute transport.
Solute_Advection_FV
Explicit in time finite volume method for advection only solute transport.
- instance of RECORD
- generic typeEquationOutput
- parameter output_field_selection = Solute_Advection_FV:OutputFields
Setting of the fields output.
Solute_Advection_FV:Data
Record to set fields of the equation.
The fields are set only on the domain specified by one of the keys: 'region', 'rid'
and after the time given by the key 'time'. The field setting can be overridden by
any Solute_Advection_FV:Data record that comes later in the boundary data array.
- Array [1, UINT]
- of STRING
region
optionalLabels of the regions where to set fields.
- Integer [0, INT]
rid
optionalID of the region where to set fields.
- Double [0, +inf)
time
value at declaration = 0.0Apply field setting in this record after this time.
These times have to form an increasing sequence.- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
porosity
optionalMobile porosity {$[-]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
sources_density
optionalDensity of concentration sources. {$[m^{-3}kgs^{-1}]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
sources_sigma
optionalConcentration flux. {$[s^{-1}]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
sources_conc
optionalConcentration sources threshold. {$[m^{-3}kg]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_conc
optionalBoundary conditions for concentrations. {$[m^{-3}kg]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
init_conc
optionalInitial concentrations. {$[m^{-3}kg]$}
Solute_Advection_FV:OutputFields
Selection of output fields for the Solute_Advection_FV model.
{$[-]$} Input field: Mobile porosity
{$[-]$} Input field: INTERNAL - water content passed from unsaturated Darcy
{$[m^{-3}kgs^{-1}]$} Input field: Density of concentration sources.
{$[s^{-1}]$} Input field: Concentration flux.
{$[m^{-3}kg]$} Input field: Concentration sources threshold.
{$[m^{-3}kg]$} Input field: Initial concentrations.
{$[m^{-3}kg]$}
{$[-]$} Input field:
{$[-]$} Input field:
Solute_AdvectionDiffusion_DG
DG solver for solute transport.
- Double [0, +inf)
solvent_density
value at declaration = 1.0Density of the solvent [ {$kg.m^(-3)$} ].
- Array [0, UINT]
- of Solute_AdvectionDiffusion_DG:Data
input_fields
obligatoryInput fields of the equation.
- SELECTIONDG_variant
Variant of interior penalty discontinuous Galerkin method.
- Integer [0, 3]
dg_order
value at declaration = 1Polynomial order for finite element in DG method (order 0 is suitable if there is no diffusion/dispersion).
- instance of RECORD
- generic typeEquationOutput
- parameter output_field_selection = Solute_AdvectionDiffusion_DG:OutputFields
Setting of the field output.
Solute_AdvectionDiffusion_DG:Data
Record to set fields of the equation.
The fields are set only on the domain specified by one of the keys: 'region', 'rid'
and after the time given by the key 'time'. The field setting can be overridden by
any Solute_AdvectionDiffusion_DG:Data record that comes later in the boundary data array.
- Array [1, UINT]
- of STRING
region
optionalLabels of the regions where to set fields.
- Integer [0, INT]
rid
optionalID of the region where to set fields.
- Double [0, +inf)
time
value at declaration = 0.0Apply field setting in this record after this time.
These times have to form an increasing sequence.- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
porosity
optionalMobile porosity {$[-]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
sources_density
optionalDensity of concentration sources. {$[m^{-3}kgs^{-1}]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
sources_sigma
optionalConcentration flux. {$[s^{-1}]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
sources_conc
optionalConcentration sources threshold. {$[m^{-3}kg]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = Solute_AdvectionDiffusion_BC_Type
bc_type
optionalType of boundary condition. {$[-]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_conc
optionalDirichlet boundary condition (for each substance). {$[m^{-3}kg]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_flux
optionalFlux in Neumann boundary condition. {$[m^{1-d}kgs^{-1}]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_robin_sigma
optionalConductivity coefficient in Robin boundary condition. {$[m^{4-d}s^{-1}]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
init_conc
optionalInitial concentrations. {$[m^{-3}kg]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
disp_l
optionalLongitudal dispersivity in the liquid (for each substance). {$[m]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
disp_t
optionalTransversal dispersivity in the liquid (for each substance). {$[m]$}
- Array [1, UINT]
- generic typeField_R3_to_R[3,3]
- parameter element_input_type = DOUBLE
diff_m
optionalMolecular diffusivity in the liquid (for each substance). {$[m^{2}s^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
rock_density
optionalRock matrix density. {$[m^{-3}kg]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
sorption_coefficient
optionalCoefficient of linear sorption. {$[m^{3}kg^{-1}]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
fracture_sigma
optionalCoefficient of diffusive transfer through fractures (for each substance). {$[-]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
dg_penalty
optionalPenalty parameter influencing the discontinuity of the solution (for each substance). Its default value 1 is sufficient in most cases. Higher value diminishes the inter-element jumps. {$[-]$}
Solute_AdvectionDiffusion_BC_Type
Types of boundary conditions for advection-diffusion solute transport model.
Default transport boundary condition.
On water inflow {$(q_w \le 0)$}, total flux is given by the reference concentration 'bc_conc'. On water outflow we prescribe zero diffusive flux, i.e. the mass flows out only due to advection.Dirichlet boundary condition {$ c = c_D $}.
The prescribed concentration {$c_D$} is specified by the field 'bc_conc'.Total mass flux boundary condition.
The prescribed total incoming flux can have the general form {$\delta(f_N+\sigma_R(c_R-c) )$}, where the absolute flux {$f_N$} is specified by the field 'bc_flux', the transition parameter {$\sigma_R$} by 'bc_robin_sigma', and the reference concentration {$c_R$} by 'bc_conc'.Diffusive flux boundary condition.
The prescribed incoming mass flux due to diffusion can have the general form {$\delta(f_N+\sigma_R(c_R-c) )$}, where the absolute flux {$f_N$} is specified by the field 'bc_flux', the transition parameter {$\sigma_R$} by 'bc_robin_sigma', and the reference concentration {$c_R$} by 'bc_conc'.
DG_variant
Type of penalty term.
non-symmetric weighted interior penalty DG method
incomplete weighted interior penalty DG method
symmetric weighted interior penalty DG method
Solute_AdvectionDiffusion_DG:OutputFields
Selection of output fields for the Solute_AdvectionDiffusion_DG model.
{$[-]$} Input field: Mobile porosity
{$[-]$} Input field: INTERNAL - water content passed from unsaturated Darcy
{$[m^{-3}kgs^{-1}]$} Input field: Density of concentration sources.
{$[s^{-1}]$} Input field: Concentration flux.
{$[m^{-3}kg]$} Input field: Concentration sources threshold.
{$[m^{-3}kg]$} Input field: Initial concentrations.
{$[m]$} Input field: Longitudal dispersivity in the liquid (for each substance).
{$[m]$} Input field: Transversal dispersivity in the liquid (for each substance).
{$[m^{2}s^{-1}]$} Input field: Molecular diffusivity in the liquid (for each substance).
{$[m^{-3}kg]$} Input field: Rock matrix density.
{$[m^{3}kg^{-1}]$} Input field: Coefficient of linear sorption.
{$[m^{-3}kg]$}
{$[-]$} Input field: Coefficient of diffusive transfer through fractures (for each substance).
{$[-]$} Input field: Penalty parameter influencing the discontinuity of the solution (for each substance). Its default value 1 is sufficient in most cases. Higher value diminishes the inter-element jumps.
{$[-]$} Input field:
{$[-]$} Input field:
ReactionTerm
Abstract equation for a reaction term (dual porosity, sorption, reactions). Can be part of coupling with a transport equation via. operator splitting.
A model of first order chemical reactions (decompositions of a reactant into products).
A model of a radioactive decay and possibly of a decay chain.
Sorption model in the reaction term of transport.
Dual porosity model in transport problems.
Provides computing the concentration of substances in mobile and immobile zone.
FirstOrderReaction
A model of first order chemical reactions (decompositions of a reactant into products).
- RECORDPadeApproximant
Numerical solver for the system of first order ordinary differential equations coming from the model.
Reaction
Describes a single first order chemical reaction.
- Array [1, UINT]
- of FirstOrderReactionReactant
reactants
obligatoryAn array of reactants. Do not use array, reactions with only one reactant (decays) are implemented at the moment!
- Double [0, +inf)
reaction_rate
obligatoryThe reaction rate coefficient of the first order reaction.
FirstOrderReactionReactant
A record describing a reactant of a reaction.
- String (generic)
name
obligatoryThe name of the reactant.
FirstOrderReactionProduct
A record describing a product of a reaction.
- String (generic)
name
obligatoryThe name of the product.
- Double [0, +inf)
branching_ratio
value at declaration = 1.0The branching ratio of the product when there are more products.
The value must be positive. Further, the branching ratios of all products are normalized in order to sum to one.
The default value 1.0, should only be used in the case of single product.
PadeApproximant
Record with an information about pade approximant parameters.Note that stable method is guaranteed only if d-n=1 or d-n=2, where d=degree of denominator and n=degree of nominator. In those cases the Pade approximant corresponds to an implicit Runge-Kutta method which is both A- and L-stable. The default values n=2, d=3 yield relatively good precision while keeping the order moderately low.
- Integer [1, INT]
pade_nominator_degree
value at declaration = 1Polynomial degree of the nominator of Pade approximant.
- Integer [1, INT]
pade_denominator_degree
value at declaration = 3Polynomial degree of the denominator of Pade approximant
RadioactiveDecay
A model of a radioactive decay and possibly of a decay chain.
- RECORDPadeApproximant
Numerical solver for the system of first order ordinary differential equations coming from the model.
Decay
A model of a radioactive decay.
- String (generic)
radionuclide
obligatoryThe name of the parent radionuclide.
- Double [0, +inf)
half_life
obligatoryThe half life of the parent radionuclide in seconds.
- Array [1, UINT]
- of RadioactiveDecayProduct
products
obligatoryAn array of the decay products (daughters).
RadioactiveDecayProduct
A record describing a product of a radioactive decay.
- String (generic)
name
obligatoryThe name of the product.
- Double [0, +inf)
energy
value at declaration = 0.0Not used at the moment! The released energy in MeV from the decay of the radionuclide into the product.
- Double [0, +inf)
branching_ratio
value at declaration = 1.0The branching ratio of the product when there is more than one.Considering only one product, the default ratio 1.0 is used.Its value must be positive. Further, the branching ratios of all products are normalizedby their sum, so the sum then gives 1.0 (this also resolves possible rounding errors).
Sorption
Sorption model in the reaction term of transport.
- Array [1, UINT]
- of STRING
substances
obligatoryNames of the substances that take part in the sorption model.
- Double [0, +inf)
solvent_density
value at declaration = 1.0Density of the solvent.
- Integer [1, INT]
substeps
value at declaration = 1000Number of equidistant substeps, molar mass and isotherm intersections
- Array [0, UINT]
- of DOUBLE
solubility
optionalSpecifies solubility limits of all the sorbing species.
- Array [0, UINT]
- of DOUBLE
table_limits
optionalSpecifies highest aqueous concentration in interpolation table.
- Array [0, UINT]
- of Sorption:Data
input_fields
obligatoryContaines region specific data necessary to construct isotherms.
- instance of RECORD
- generic typeEquationOutput
- parameter output_field_selection = Sorption:OutputFields
Setting of the fields output.
Sorption:Data
Record to set fields of the equation.
The fields are set only on the domain specified by one of the keys: 'region', 'rid'
and after the time given by the key 'time'. The field setting can be overridden by
any Sorption:Data record that comes later in the boundary data array.
- Array [1, UINT]
- of STRING
region
optionalLabels of the regions where to set fields.
- Integer [0, INT]
rid
optionalID of the region where to set fields.
- Double [0, +inf)
time
value at declaration = 0.0Apply field setting in this record after this time.
These times have to form an increasing sequence.- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
rock_density
optionalRock matrix density. {$[m^{-3}kg]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = SorptionType
sorption_type
optionalConsidered sorption is described by selected isotherm. If porosity on an element is equal or even higher than 1.0 (meaning no sorbing surface), then type 'none' will be selected automatically. {$[-]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
distribution_coefficient
optionalMultiplication parameters (k, omega) in either Langmuir c_s = omega * (alphac_a)/(1- alphac_a) or in linear c_s = k * c_a isothermal description. {$[m^{3}kg^{-1}]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
isotherm_other
optionalSecond parameters (alpha, ...) defining isotherm c_s = omega * (alphac_a)/(1- alphac_a). {$[-]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
init_conc_solid
optionalInitial solid concentration of substances. Vector, one value for every substance. {$[kg^{-1}mol]$}
SorptionType
No sorption considered.
Linear isotherm runs the concentration exchange between liquid and solid.
Langmuir isotherm runs the concentration exchange between liquid and solid.
Freundlich isotherm runs the concentration exchange between liquid and solid.
GenericReaction
Abstract equation for a reaction of species in single compartment (e.g. mobile solid).It can be part of: direct operator splitting coupling, dual porosity model, any sorption.
A model of first order chemical reactions (decompositions of a reactant into products).
A model of a radioactive decay and possibly of a decay chain.
Sorption:OutputFields
Selection of output fields for the Sorption model.
{$[m^{-3}kg]$} Input field: Rock matrix density.
{$[-]$} Input field: Considered sorption is described by selected isotherm. If porosity on an element is equal or even higher than 1.0 (meaning no sorbing surface), then type 'none' will be selected automatically.
{$[m^{3}kg^{-1}]$} Input field: Multiplication parameters (k, omega) in either Langmuir c_s = omega * (alphac_a)/(1- alphac_a) or in linear c_s = k * c_a isothermal description.
{$[-]$} Input field: Second parameters (alpha, ...) defining isotherm c_s = omega * (alphac_a)/(1- alphac_a).
{$[kg^{-1}mol]$} Input field: Initial solid concentration of substances. Vector, one value for every substance.
{$[-]$}
DualPorosity
Dual porosity model in transport problems.
Provides computing the concentration of substances in mobile and immobile zone.
- Array [0, UINT]
- of DualPorosity:Data
input_fields
obligatoryContaines region specific data necessary to construct dual porosity model.
- Double [0, +inf)
scheme_tolerance
value at declaration = 0.001Tolerance according to which the explicit Euler scheme is used or not.Set 0.0 to use analytic formula only (can be slower).
- instance of RECORD
- generic typeEquationOutput
- parameter output_field_selection = DualPorosity:OutputFields
Setting of the fields output.
DualPorosity:Data
Record to set fields of the equation.
The fields are set only on the domain specified by one of the keys: 'region', 'rid'
and after the time given by the key 'time'. The field setting can be overridden by
any DualPorosity:Data record that comes later in the boundary data array.
- Array [1, UINT]
- of STRING
region
optionalLabels of the regions where to set fields.
- Integer [0, INT]
rid
optionalID of the region where to set fields.
- Double [0, +inf)
time
value at declaration = 0.0Apply field setting in this record after this time.
These times have to form an increasing sequence.- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
diffusion_rate_immobile
optionalDiffusion coefficient of non-equilibrium linear exchange between mobile and immobile zone. {$[s^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
porosity_immobile
optionalPorosity of the immobile zone. {$[-]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
init_conc_immobile
optionalInitial concentration of substances in the immobile zone. {$[m^{-3}kg]$}
ReactionTermMobile
Abstract equation for a reaction term of the MOBILE pores (sorption, reactions). Is part of dual porosity model.
A model of first order chemical reactions (decompositions of a reactant into products).
A model of a radioactive decay and possibly of a decay chain.
Sorption model in the mobile zone, following the dual porosity model.
SorptionMobile
Sorption model in the mobile zone, following the dual porosity model.
- Array [1, UINT]
- of STRING
substances
obligatoryNames of the substances that take part in the sorption model.
- Double [0, +inf)
solvent_density
value at declaration = 1.0Density of the solvent.
- Integer [1, INT]
substeps
value at declaration = 1000Number of equidistant substeps, molar mass and isotherm intersections
- Array [0, UINT]
- of DOUBLE
solubility
optionalSpecifies solubility limits of all the sorbing species.
- Array [0, UINT]
- of DOUBLE
table_limits
optionalSpecifies highest aqueous concentration in interpolation table.
- Array [0, UINT]
- of Sorption:Data
input_fields
obligatoryContaines region specific data necessary to construct isotherms.
- instance of RECORD
- generic typeEquationOutput
- parameter output_field_selection = SorptionMobile:OutputFields
Setting of the fields output.
SorptionMobile:OutputFields
Selection of output fields for the SorptionMobile model.
{$[m^{-3}kg]$} Input field: Rock matrix density.
{$[-]$} Input field: Considered sorption is described by selected isotherm. If porosity on an element is equal or even higher than 1.0 (meaning no sorbing surface), then type 'none' will be selected automatically.
{$[m^{3}kg^{-1}]$} Input field: Multiplication parameters (k, omega) in either Langmuir c_s = omega * (alphac_a)/(1- alphac_a) or in linear c_s = k * c_a isothermal description.
{$[-]$} Input field: Second parameters (alpha, ...) defining isotherm c_s = omega * (alphac_a)/(1- alphac_a).
{$[kg^{-1}mol]$} Input field: Initial solid concentration of substances. Vector, one value for every substance.
{$[-]$}
ReactionTermImmobile
Abstract equation for a reaction term of the IMMOBILE pores (sorption, reactions). Is part of dual porosity model.
A model of first order chemical reactions (decompositions of a reactant into products).
A model of a radioactive decay and possibly of a decay chain.
Sorption model in the immobile zone, following the dual porosity model.
SorptionImmobile
Sorption model in the immobile zone, following the dual porosity model.
- Array [1, UINT]
- of STRING
substances
obligatoryNames of the substances that take part in the sorption model.
- Double [0, +inf)
solvent_density
value at declaration = 1.0Density of the solvent.
- Integer [1, INT]
substeps
value at declaration = 1000Number of equidistant substeps, molar mass and isotherm intersections
- Array [0, UINT]
- of DOUBLE
solubility
optionalSpecifies solubility limits of all the sorbing species.
- Array [0, UINT]
- of DOUBLE
table_limits
optionalSpecifies highest aqueous concentration in interpolation table.
- Array [0, UINT]
- of Sorption:Data
input_fields
obligatoryContaines region specific data necessary to construct isotherms.
- instance of RECORD
- generic typeEquationOutput
- parameter output_field_selection = SorptionImmobile:OutputFields
Setting of the fields output.
SorptionImmobile:OutputFields
Selection of output fields for the SorptionImmobile model.
{$[m^{-3}kg]$} Input field: Rock matrix density.
{$[-]$} Input field: Considered sorption is described by selected isotherm. If porosity on an element is equal or even higher than 1.0 (meaning no sorbing surface), then type 'none' will be selected automatically.
{$[m^{3}kg^{-1}]$} Input field: Multiplication parameters (k, omega) in either Langmuir c_s = omega * (alphac_a)/(1- alphac_a) or in linear c_s = k * c_a isothermal description.
{$[-]$} Input field: Second parameters (alpha, ...) defining isotherm c_s = omega * (alphac_a)/(1- alphac_a).
{$[kg^{-1}mol]$} Input field: Initial solid concentration of substances. Vector, one value for every substance.
{$[-]$}
DualPorosity:OutputFields
Selection of output fields for the DualPorosity model.
{$[s^{-1}]$} Input field: Diffusion coefficient of non-equilibrium linear exchange between mobile and immobile zone.
{$[-]$} Input field: Porosity of the immobile zone.
{$[m^{-3}kg]$} Input field: Initial concentration of substances in the immobile zone.
{$[m^{-3}kg]$}
Heat_AdvectionDiffusion_DG
DG solver for heat transfer.
- Array [0, UINT]
- of Heat_AdvectionDiffusion_DG:Data
input_fields
obligatoryInput fields of the equation.
- SELECTIONDG_variant
Variant of interior penalty discontinuous Galerkin method.
- Integer [0, 3]
dg_order
value at declaration = 1Polynomial order for finite element in DG method (order 0 is suitable if there is no diffusion/dispersion).
- instance of RECORD
- generic typeEquationOutput
- parameter output_field_selection = Heat_AdvectionDiffusion_DG:OutputFields
Setting of the field output.
Heat_AdvectionDiffusion_DG:Data
Record to set fields of the equation.
The fields are set only on the domain specified by one of the keys: 'region', 'rid'
and after the time given by the key 'time'. The field setting can be overridden by
any Heat_AdvectionDiffusion_DG:Data record that comes later in the boundary data array.
- Array [1, UINT]
- of STRING
region
optionalLabels of the regions where to set fields.
- Integer [0, INT]
rid
optionalID of the region where to set fields.
- Double [0, +inf)
time
value at declaration = 0.0Apply field setting in this record after this time.
These times have to form an increasing sequence.- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = Heat_BC_Type
bc_type
optionalType of boundary condition. {$[-]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_temperature
optionalBoundary value of temperature. {$[K]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_flux
optionalFlux in Neumann boundary condition. {$[m^{1-d}kgs^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
bc_robin_sigma
optionalConductivity coefficient in Robin boundary condition. {$[m^{4-d}s^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
init_temperature
optionalInitial temperature. {$[K]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
porosity
optionalPorosity. {$[-]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
fluid_density
optionalDensity of fluid. {$[m^{-3}kg]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
fluid_heat_capacity
optionalHeat capacity of fluid. {$[m^{2}s^{-2}K^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
fluid_heat_conductivity
optionalHeat conductivity of fluid. {$[mkgs^{-3}K^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
solid_density
optionalDensity of solid (rock). {$[m^{-3}kg]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
solid_heat_capacity
optionalHeat capacity of solid (rock). {$[m^{2}s^{-2}K^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
solid_heat_conductivity
optionalHeat conductivity of solid (rock). {$[mkgs^{-3}K^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
disp_l
optionalLongitudal heat dispersivity in fluid. {$[m]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
disp_t
optionalTransversal heat dispersivity in fluid. {$[m]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
fluid_thermal_source
optionalDensity of thermal source in fluid. {$[m^{-1}kgs^{-3}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
solid_thermal_source
optionalDensity of thermal source in solid. {$[m^{-1}kgs^{-3}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
fluid_heat_exchange_rate
optionalHeat exchange rate of source in fluid. {$[s^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
solid_heat_exchange_rate
optionalHeat exchange rate of source in solid. {$[s^{-1}]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
fluid_ref_temperature
optionalReference temperature of source in fluid. {$[K]$}
- instance of ABSTRACT
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
solid_ref_temperature
optionalReference temperature in solid. {$[K]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
fracture_sigma
optionalCoefficient of diffusive transfer through fractures (for each substance). {$[-]$}
- Array [1, UINT]
- generic typeField_R3_to_R
- parameter element_input_type = DOUBLE
dg_penalty
optionalPenalty parameter influencing the discontinuity of the solution (for each substance). Its default value 1 is sufficient in most cases. Higher value diminishes the inter-element jumps. {$[-]$}
Heat_BC_Type
Types of boundary conditions for heat transfer model.
Default heat transfer boundary condition.
On water inflow {$(q_w \le 0)$}, total energy flux is given by the reference temperature 'bc_temperature'. On water outflow we prescribe zero diffusive flux, i.e. the energy flows out only due to advection.Dirichlet boundary condition {$T = T_D $}.
The prescribed temperature {$T_D$} is specified by the field 'bc_temperature'.Total energy flux boundary condition.
The prescribed incoming total flux can have the general form {$\delta(f_N+\sigma_R(T_R-T) )$}, where the absolute flux {$f_N$} is specified by the field 'bc_flux', the transition parameter {$\sigma_R$} by 'bc_robin_sigma', and the reference temperature {$T_R$} by 'bc_temperature'.Diffusive flux boundary condition.
The prescribed incoming energy flux due to diffusion can have the general form {$\delta(f_N+\sigma_R(T_R-T) )$}, where the absolute flux {$f_N$} is specified by the field 'bc_flux', the transition parameter {$\sigma_R$} by 'bc_robin_sigma', and the reference temperature {$T_R$} by 'bc_temperature'.
Heat_AdvectionDiffusion_DG:OutputFields
Selection of output fields for the Heat_AdvectionDiffusion_DG model.
{$[K]$} Input field: Initial temperature.
{$[-]$} Input field: Porosity.
{$[-]$} Input field:
{$[m^{-3}kg]$} Input field: Density of fluid.
{$[m^{2}s^{-2}K^{-1}]$} Input field: Heat capacity of fluid.
{$[mkgs^{-3}K^{-1}]$} Input field: Heat conductivity of fluid.
{$[m^{-3}kg]$} Input field: Density of solid (rock).
{$[m^{2}s^{-2}K^{-1}]$} Input field: Heat capacity of solid (rock).
{$[mkgs^{-3}K^{-1}]$} Input field: Heat conductivity of solid (rock).
{$[m]$} Input field: Longitudal heat dispersivity in fluid.
{$[m]$} Input field: Transversal heat dispersivity in fluid.
{$[m^{-1}kgs^{-3}]$} Input field: Density of thermal source in fluid.
{$[m^{-1}kgs^{-3}]$} Input field: Density of thermal source in solid.
{$[s^{-1}]$} Input field: Heat exchange rate of source in fluid.
{$[s^{-1}]$} Input field: Heat exchange rate of source in solid.
{$[K]$} Input field: Reference temperature of source in fluid.
{$[K]$} Input field: Reference temperature in solid.
{$[K]$}
{$[-]$} Input field: Coefficient of diffusive transfer through fractures (for each substance).
{$[-]$} Input field: Penalty parameter influencing the discontinuity of the solution (for each substance). Its default value 1 is sufficient in most cases. Higher value diminishes the inter-element jumps.
{$[-]$} Input field:
{$[-]$} Input field: