[docs] updated documentation for renamed classes

man/prj_kinetic_reactant.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_chemical_system.R
+\name{prj_kinetic_reactant}
+\alias{prj_kinetic_reactant}
+\title{prj_kinetic_reactant}
+\usage{
+prj_kinetic_reactant(
+  name,
+  initial_amount = NULL,
+  chemical_formula = NULL,
+  fix_amount = NULL
+)
+}
+\arguments{
+\item{name}{The component name}
+
+\item{initial_amount}{The initial amount of the component}
+
+\item{chemical_formula}{The chemical formula of the component}
+
+\item{fix_amount}{Should the amount be fixed or not?}
+}
+\description{
+S3 class describing .prj kinetic_reactant
+}
+\examples{
+prj_kinetic_reactant(name = "Productc",
+                        initial_amount = 1e-06)
+}

man/prj_linear_solver.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_linear_solver.R
+\name{prj_linear_solver}
+\alias{prj_linear_solver}
+\title{prj_linear_solver}
+\usage{
+prj_linear_solver(name, eigen = NULL, lis = NULL, petsc = NULL)
+}
+\arguments{
+\item{name}{string: The name of the linear solver}
+
+\item{eigen}{Optional: list: ...}
+
+\item{lis}{Optional: string: ...}
+
+\item{petsc}{Optional: character: ...}
+}
+\description{
+tag: linear_solver
+}
+\examples{
+prj_linear_solver(
+    name = "general_linear_solver",
+    eigen = prj_eigen(
+        solver_type = "BiCGSTAB",
+        precon_type = "ILUT",
+        max_iteration_step = 10000,
+        error_tolerance = 1e-16
+    ),
+    lis = "-i bicgstab -p ilu -tol 1e-16 -maxiter 10000"
+)
+}

man/prj_local_coordinate_system.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_local_coordinate_system.R
+\name{prj_local_coordinate_system}
+\alias{prj_local_coordinate_system}
+\title{prj_local_coordinate_system}
+\usage{
+prj_local_coordinate_system(
+  basis_vector_0,
+  basis_vector_1,
+  basis_vector_2 = NULL
+)
+}
+\arguments{
+\item{basis_vector_0}{string | double: A basis vector}
+
+\item{basis_vector_1}{string | double: A basis vector}
+
+\item{basis_vector_2}{Optional: string | double: A basis vector}
+}
+\description{
+tag: local_coordinate_system
+}
+\examples{
+prj_local_coordinate_system(basis_vector_0 = "e0",
+                               basis_vector_1 = "e1",
+                               basis_vector_2 = "e2")
+}

man/prj_material_property.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_material_property.R
+\name{prj_material_property}
+\alias{prj_material_property}
+\title{prj_material_property}
+\usage{
+prj_material_property(fluid, porous_medium)
+}
+\arguments{
+\item{fluid}{prj_fluid:}
+
+\item{porous_medium}{prj_porous_medium:}
+}
+\description{
+tag: material_property
+}
+\examples{
+prj_material_property(
+    fluid = prj_fluid(
+        liquid_density = list(type = "Constant",
+                              value = " 1.e3 "),
+        gas_density = list(type = "IdealGasLaw",
+                           molar_mass = " 0.002 "),
+        liquid_viscosity = list(type = "Constant",
+                                value = " 3.171e-11 "),
+        gas_viscosity = list(type = "Constant",
+                             value = " 2.8539e-13 ")
+    ),
+    porous_medium = list(
+        porous_medium = prj_porous_medium(
+            id = 0,
+            permeability = list(permeability_tensor_entries = "kappa1",
+                                type = "Constant"),
+            porosity = list(type = "Constant",
+                            porosity_parameter = "constant_porosity_parameter"),
+            storage = list(type = "Constant",
+                           value = " 0.0 "),
+            capillary_pressure = prj_capillary_pressure(
+                type = "vanGenuchten",
+                pd = 2e+06,
+                sr = 0.4,
+                smax = 1,
+                m = 0.3288590604,
+                pc_max = 2e+07,
+                has_regularized = "true"
+            ),
+            relative_permeability = list(
+                relative_permeability = prj_relative_permeability(
+                    type = "NonWettingPhaseVanGenuchten",
+                    sr = 0,
+                    smax = 0.6,
+                    m = 0.3288590604,
+                    krel_min = 0,
+                    id = "0"
+                )
+            )
+        )
+    )
+)
+}

man/prj_medium.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_medium.R
+\name{prj_medium}
+\alias{prj_medium}
+\title{prj_medium}
+\usage{
+prj_medium(phases = NULL, properties = NULL, id = NULL)
+}
+\arguments{
+\item{phases}{list, prj_phase: Optional: Medium phases}
+
+\item{properties}{list, prj_pr_property: Optional: Medium properties}
+
+\item{id}{string | double: Optional: ID corresponding to the MaterialIDs}
+}
+\description{
+tag: medium, a specific medium with optional id corresponding
+  to the MaterialIDs
+}
+\examples{
+prj_medium(
+    phases = list(
+        phase = prj_phase(
+            type = "Gas",
+            properties = list(
+                property = prj_ph_property(name = "viscosity",
+                                              type = "Constant",
+                                              value = 1e-05)
+            )
+        ),
+        phase = prj_phase(
+            type = "Solid",
+            properties = list(
+                property = prj_ph_property(name = "porosity",
+                                              type = "Constant",
+                                              value = 0.3)
+            )
+        )
+    ),
+    properties = list(
+        property = prj_pr_property(name = "reference_temperature",
+                                      type = "Constant",
+                                      value = 293.15)
+    )
+)
+}

man/prj_nonlinear_solver.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_nonlinear_solver.R
+\name{prj_nonlinear_solver}
+\alias{prj_nonlinear_solver}
+\title{prj_nonlinear_solver}
+\usage{
+prj_nonlinear_solver(name, type, max_iter, linear_solver, damping = NULL)
+}
+\arguments{
+\item{name}{string: Name}
+
+\item{type}{string: Type}
+
+\item{max_iter}{string | double: Maximal number of iterations}
+
+\item{linear_solver}{string: Name of corresponding linear_solver}
+
+\item{damping}{Optional: string | double: Damping}
+}
+\description{
+tag: nonlinear_solver
+}
+\examples{
+prj_nonlinear_solver(
+    name = "basic_newton",
+    type = "Newton",
+    max_iter = 50,
+    linear_solver = "general_linear_solver"
+)
+}

man/prj_output.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_time_loop.R
+\name{prj_output}
+\alias{prj_output}
+\title{prj_output}
+\usage{
+prj_output(
+  type,
+  prefix,
+  variables,
+  suffix = NULL,
+  timesteps = NULL,
+  compress_output = NULL,
+  data_mode = NULL,
+  output_iteration_results = NULL,
+  meshes = NULL,
+  fixed_output_times = NULL
+)
+}
+\arguments{
+\item{type}{string:}
+
+\item{prefix}{string:}
+
+\item{variables}{vector:}
+
+\item{suffix}{Optional: string:}
+
+\item{timesteps}{Optional:}
+
+\item{compress_output}{Optional: string: Should the output be compressed?
+Either "true" or "false"}
+
+\item{data_mode}{Optional: string:}
+
+\item{output_iteration_results}{Optional: string: Either "true" or "false"}
+
+\item{meshes}{Optional: character: A vector of mesh names}
+
+\item{fixed_output_times}{Optional: string | numeric:}
+}
+\description{
+tag: output
+}
+\examples{
+prj_output(
+    type = "VTK",
+    prefix = "flow_free_expansion",
+    variables = list(
+        variable = "displacement",
+        variable = "pressure"
+    ),
+    suffix = "_ts_{:timestep}_t_{:time}",
+    timesteps = list(pair = list(1,
+                                 each_steps = 1000))
+)
+}

man/prj_parameter.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_parameter.R
+\name{prj_parameter}
+\alias{prj_parameter}
+\title{prj_parameter}
+\usage{
+prj_parameter(
+  name,
+  type,
+  value = NULL,
+  values = NULL,
+  curve = NULL,
+  parameter = NULL,
+  group_id_property = NULL,
+  field_name = NULL,
+  mesh = NULL,
+  time_series = NULL,
+  use_local_coordinate_system = NULL,
+  ...
+)
+}
+\arguments{
+\item{name}{string:}
+
+\item{type}{string:}
+
+\item{value}{Optional: string | double: Parameter value}
+
+\item{values}{Optional: string | double: Parameter values}
+
+\item{curve}{Optional: string:}
+
+\item{parameter}{Optional: string:}
+
+\item{group_id_property}{Optional: string:}
+
+\item{field_name}{Optional: string:}
+
+\item{mesh}{Optional: string:}
+
+\item{time_series}{Optional: list:}
+
+\item{use_local_coordinate_system}{Optional: string, "true" | "false":}
+
+\item{...}{Optional: for index_values and expression tags (since there can be
+multiple)}
+}
+\description{
+tag: parameter
+}
+\examples{
+prj_parameter(name = "zero",
+                 type = "Constant",
+                 value = 0)
+
+prj_parameter(name = "flux_in",
+                 type = "Constant",
+                 value = 1e-04)
+}

man/prj_ph_property.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_medium.R
+\name{prj_ph_property}
+\alias{prj_ph_property}
+\title{prj_ph_property}
+\usage{
+prj_ph_property(
+  name,
+  type,
+  value = NULL,
+  reference_value = NULL,
+  initial_porosity = NULL,
+  minimal_porosity = NULL,
+  maximal_porosity = NULL,
+  parameter_name = NULL,
+  exponents = NULL,
+  offset = NULL,
+  exponent = NULL,
+  swelling_pressures = NULL,
+  lower_saturation_limit = NULL,
+  upper_saturation_limit = NULL,
+  intrinsic_permeabilities = NULL,
+  ...
+)
+}
+\arguments{
+\item{name}{string: Property name}
+
+\item{type}{string: Property type}
+
+\item{value}{Optional: string | double: ...}
+
+\item{reference_value}{Optional: string | double:}
+
+\item{initial_porosity}{Optional: string:}
+
+\item{minimal_porosity}{Optional: string | double:}
+
+\item{maximal_porosity}{Optional: string | double:}
+
+\item{parameter_name}{Optional: string:}
+
+\item{exponents}{Optional: string | numeric:}
+
+\item{offset}{Optional: string | double:}
+
+\item{exponent}{Optional: list:}
+
+\item{swelling_pressures}{Optional: string | numeric:}
+
+\item{lower_saturation_limit}{Optional: string | double:}
+
+\item{upper_saturation_limit}{Optional: string | double:}
+
+\item{intrinsic_permeabilities}{Optional: string | numeric:}
+
+\item{...}{independent_variable}
+}
+\description{
+tag: property
+}
+\examples{
+prj_ph_property(name = "porosity",
+                   type = "Constant",
+                   value = 0.3)
+}

man/prj_phase.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_medium.R
+\name{prj_phase}
+\alias{prj_phase}
+\title{prj_phase}
+\usage{
+prj_phase(type, properties = NULL, components = NULL)
+}
+\arguments{
+\item{type}{string: Phase type
+(get valid types with get_valid_phase_types())}
+
+\item{properties}{list, prj_pr_property: Properties}
+
+\item{components}{list, components}
+}
+\description{
+tag: phase, a coherent material with homogeneous properties
+}
+\examples{
+prj_phase(
+    type = "Solid",
+    properties = list(
+        property = prj_ph_property(name = "porosity",
+                                      type = "Constant",
+                                      value = 0.3)
+    )
+)
+}

man/prj_phase_component.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_chemical_system.R
+\name{prj_phase_component}
+\alias{prj_phase_component}
+\title{prj_phase_component}
+\usage{
+prj_phase_component(name, saturation_index, initial_amount = NULL)
+}
+\arguments{
+\item{name}{The component name}
+
+\item{saturation_index}{The saturation index of the component}
+
+\item{initial_amount}{optional: The initial amount of the component}
+}
+\description{
+S3 class describing .prj phase_component
+}
+\examples{
+prj_phase_component(
+    name = "Calcite",
+    saturation_index = 0,
+    initial_amount = 0.000207
+)
+}

man/prj_phasefield_parameters.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process.R
+\name{prj_phasefield_parameters}
+\alias{prj_phasefield_parameters}
+\title{prj_phasefield_parameters}
+\usage{
+prj_phasefield_parameters(
+  residual_stiffness,
+  crack_resistance,
+  crack_length_scale,
+  kinetic_coefficient,
+  history_field = NULL
+)
+}
+\arguments{
+\item{residual_stiffness}{string:}
+
+\item{crack_resistance}{string:}
+
+\item{crack_length_scale}{string:}
+
+\item{kinetic_coefficient}{string:}
+
+\item{history_field}{Optional: string:}
+}
+\description{
+tag: phasefield_parameters
+}
+\examples{
+prj_phasefield_parameters(
+    residual_stiffness = "k",
+    crack_resistance = "gc",
+    crack_length_scale = "ls",
+    kinetic_coefficient = "M",
+    history_field = "H"
+)
+}

man/prj_pipes.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_borehole_heat_exchanger.R
+\name{prj_pipes}
+\alias{prj_pipes}
+\title{prj_pipes}
+\usage{
+prj_pipes(
+  longitudinal_dispersion_length,
+  inlet = NULL,
+  outlet = NULL,
+  distance_between_pipes = NULL,
+  outer = NULL,
+  inner = NULL
+)
+}
+\arguments{
+\item{longitudinal_dispersion_length}{string | double:}
+
+\item{inlet}{Optional: list:}
+
+\item{outlet}{Optional: list:}
+
+\item{distance_between_pipes}{Optional: string | double:}
+
+\item{outer}{Optional: list:}
+
+\item{inner}{Optional: list:}
+}
+\description{
+tag: pipes
+}
+\examples{
+prj_pipes(
+    longitudinal_dispersion_length = 0.001,
+    inlet = list(
+        diameter = " 0.013665",
+        wall_thickness = "0.003035",
+        wall_thermal_conductivity = "0.39"
+    ),
+    outlet = list(
+        diameter = "0.013665",
+        wall_thickness = "0.003035",
+        wall_thermal_conductivity = "0.39"
+    ),
+    distance_between_pipes = 0.053
+)
+}

man/prj_porous_medium.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_porous_medium.R
+\name{prj_porous_medium}
+\alias{prj_porous_medium}
+\title{prj_porous_medium}
+\usage{
+prj_porous_medium(
+  id,
+  permeability,
+  porosity,
+  storage,
+  capillary_pressure,
+  relative_permeability
+)
+}
+\arguments{
+\item{id}{string | double:}
+
+\item{permeability}{list:}
+
+\item{porosity}{list:}
+
+\item{storage}{list:}
+
+\item{capillary_pressure}{prj_capillary_pressure:}
+
+\item{relative_permeability}{list:}
+}
+\description{
+tag: porous_medium
+}
+\examples{
+prj_porous_medium(
+    id = 0,
+    permeability = list(permeability_tensor_entries = "kappa1",
+                        type = "Constant"),
+    porosity = list(type = "Constant",
+                    porosity_parameter = "constant_porosity_parameter"),
+    storage = list(type = "Constant",
+                   value = " 0.0 "),
+    capillary_pressure = prj_capillary_pressure(
+        type = "vanGenuchten",
+        pd = 2e+06,
+        sr = 0.4,
+        smax = 1,
+        m = 0.3288590604,
+        pc_max = 2e+07,
+        has_regularized = "true"
+    ),
+    relative_permeability = list(
+        relative_permeability = prj_relative_permeability(
+            type = "NonWettingPhaseVanGenuchten",
+            sr = 0,
+            smax = 0.6,
+            m = 0.3288590604,
+            krel_min = 0,
+            id = "0"
+        )
+    )
+)
+}

man/prj_pr_property.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_medium.R
+\name{prj_pr_property}
+\alias{prj_pr_property}
+\title{prj_pr_property}
+\usage{
+prj_pr_property(
+  name,
+  type,
+  value = NULL,
+  parameter_name = NULL,
+  exponent = NULL,
+  residual_liquid_saturation = NULL,
+  residual_gas_saturation = NULL,
+  p_b = NULL,
+  independent_variable = NULL,
+  curve = NULL,
+  minimum_relative_permeability_liquid = NULL,
+  initial_permeability = NULL,
+  maximum_permeability = NULL,
+  lambda = NULL,
+  cutoff_value = NULL,
+  intrinsic_permeability = NULL,
+  initial_aperture = NULL,
+  mean_frac_distance = NULL,
+  threshold_strain = NULL,
+  fracture_normal = NULL,
+  reference_permeability = NULL,
+  fitting_factor = NULL,
+  cohesion = NULL,
+  friction_angle = NULL,
+  tensile_strength_parameter = NULL,
+  b1 = NULL,
+  b2 = NULL,
+  b3 = NULL,
+  minimum_permeability = NULL,
+  initial_porosity = NULL,
+  entry_pressure = NULL,
+  min_relative_permeability_liquid = NULL,
+  min_relative_permeability_gas = NULL
+)
+}
+\arguments{
+\item{name}{string:}
+
+\item{type}{string:}
+
+\item{value}{Optional:}
+
+\item{parameter_name}{Optional:}
+
+\item{exponent}{Optional:}
+
+\item{residual_liquid_saturation}{Optional:}
+
+\item{residual_gas_saturation}{Optional:}
+
+\item{p_b}{Optional:}
+
+\item{independent_variable}{Optional:}
+
+\item{curve}{Optional:}
+
+\item{minimum_relative_permeability_liquid}{Optional:}
+
+\item{initial_permeability}{Optional:}
+
+\item{maximum_permeability}{Optional:}
+
+\item{lambda}{Optional:}
+
+\item{cutoff_value}{Optional:}
+
+\item{intrinsic_permeability}{Optional:}
+
+\item{initial_aperture}{Optional:}
+
+\item{mean_frac_distance}{Optional:}
+
+\item{threshold_strain}{Optional:}
+
+\item{fracture_normal}{Optional:}
+
+\item{reference_permeability}{Optional:}
+
+\item{fitting_factor}{Optional:}
+
+\item{cohesion}{Optional:}
+
+\item{friction_angle}{Optional:}
+
+\item{tensile_strength_parameter}{Optional:}
+
+\item{b1}{Optional:}
+
+\item{b2}{Optional:}
+
+\item{b3}{Optional:}
+
+\item{minimum_permeability}{Optional:}
+
+\item{initial_porosity}{Optional:}
+
+\item{entry_pressure}{Optional:}
+
+\item{min_relative_permeability_liquid}{Optional:}
+
+\item{min_relative_permeability_gas}{Optional:}
+}
+\description{
+tag: property
+}
+\examples{
+prj_pr_property(name = "reference_temperature",
+                   type = "Constant",
+                   value = 293.15)
+}

man/prj_process.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process.R
+\name{prj_process}
+\alias{prj_process}
+\title{prj_process}
+\usage{
+prj_process(
+  name,
+  type,
+  integration_order,
+  process_variables,
+  secondary_variables = NULL,
+  specific_body_force = NULL,
+  solid_density = NULL,
+  dimension = NULL,
+  coupling_scheme = NULL,
+  reference_solid_density = NULL,
+  linear_thermal_expansion_coefficient = NULL,
+  specific_heat_capacity = NULL,
+  thermal_conductivity = NULL,
+  darcy_gravity = NULL,
+  reference_temperature = NULL,
+  fracture_model = NULL,
+  jacobian_assembler = NULL,
+  internal_length = NULL,
+  mass_lumping = NULL,
+  porosity = NULL,
+  calculatesurfaceflux = NULL,
+  intrinsic_permeability = NULL,
+  specific_storage = NULL,
+  fluid_viscosity = NULL,
+  biot_coefficient = NULL,
+  fluid_density = NULL,
+  initial_effective_stress = NULL,
+  initial_fracture_effective_stress = NULL,
+  phasefield_parameters = NULL,
+  deactivate_matrix_in_flow = NULL,
+  borehole_heat_exchangers = NULL,
+  temperature = NULL,
+  reactive_system = NULL,
+  fluid_specific_heat_source = NULL,
+  fluid_specific_isobaric_heat_capacity = NULL,
+  solid_hydraulic_permeability = NULL,
+  solid_specific_heat_source = NULL,
+  solid_heat_conductivity = NULL,
+  solid_specific_isobaric_heat_capacity = NULL,
+  tortuosity = NULL,
+  diffusion_coefficient = NULL,
+  solid_density_dry = NULL,
+  solid_density_initial = NULL,
+  characteristic_pressure = NULL,
+  characteristic_temperature = NULL,
+  characteristic_vapour_mass_fraction = NULL,
+  output_element_matrices = NULL,
+  material_property = NULL,
+  diffusion_coeff_component_b = NULL,
+  diffusion_coeff_component_a = NULL,
+  hydro_crack_scheme = NULL,
+  at_num = NULL,
+  initial_stress = NULL,
+  split_method = NULL,
+  reg_param = NULL,
+  thermal_parameters = NULL,
+  non_advective_form = NULL,
+  fluid = NULL,
+  porous_medium = NULL,
+  decay_rate = NULL,
+  fluid_reference_density = NULL,
+  retardation_factor = NULL,
+  solute_dispersivity_longitudinal = NULL,
+  solute_dispersivity_transverse = NULL,
+  molecular_diffusion_coefficient = NULL,
+  density_solid = NULL,
+  latent_heat_evaporation = NULL,
+  pf_irrv = NULL,
+  ...
+)
+}
+\arguments{
+\item{name}{string:}
+
+\item{type}{string:}
+
+\item{integration_order}{string | double:}
+
+\item{process_variables}{list, character:}
+
+\item{secondary_variables}{Optional:}
+
+\item{specific_body_force}{Optional:}
+
+\item{solid_density}{Optional:}
+
+\item{dimension}{Optional:}
+
+\item{coupling_scheme}{Optional:}
+
+\item{reference_solid_density}{Optional:}
+
+\item{linear_thermal_expansion_coefficient}{Optional:}
+
+\item{specific_heat_capacity}{Optional:}
+
+\item{thermal_conductivity}{Optional:}
+
+\item{darcy_gravity}{Optional:}
+
+\item{reference_temperature}{Optional:}
+
+\item{fracture_model}{Optional:}
+
+\item{jacobian_assembler}{Optional:}
+
+\item{internal_length}{Optional:}
+
+\item{mass_lumping}{Optional:}
+
+\item{porosity}{Optional:}
+
+\item{calculatesurfaceflux}{Optional:}
+
+\item{intrinsic_permeability}{Optional:}
+
+\item{specific_storage}{Optional:}
+
+\item{fluid_viscosity}{Optional:}
+
+\item{biot_coefficient}{Optional:}
+
+\item{fluid_density}{Optional:}
+
+\item{initial_effective_stress}{Optional:}
+
+\item{initial_fracture_effective_stress}{Optional:}
+
+\item{phasefield_parameters}{Optional:}
+
+\item{deactivate_matrix_in_flow}{Optional:}
+
+\item{borehole_heat_exchangers}{Optional:}
+
+\item{temperature}{Optional:}
+
+\item{reactive_system}{Optional:}
+
+\item{fluid_specific_heat_source}{Optional:}
+
+\item{fluid_specific_isobaric_heat_capacity}{Optional:}
+
+\item{solid_hydraulic_permeability}{Optional:}
+
+\item{solid_specific_heat_source}{Optional:}
+
+\item{solid_heat_conductivity}{Optional:}
+
+\item{solid_specific_isobaric_heat_capacity}{Optional:}
+
+\item{tortuosity}{Optional:}
+
+\item{diffusion_coefficient}{Optional:}
+
+\item{solid_density_dry}{Optional:}
+
+\item{solid_density_initial}{Optional:}
+
+\item{characteristic_pressure}{Optional:}
+
+\item{characteristic_temperature}{Optional:}
+
+\item{characteristic_vapour_mass_fraction}{Optional:}
+
+\item{output_element_matrices}{Optional:}
+
+\item{material_property}{Optional:}
+
+\item{diffusion_coeff_component_b}{Optional:}
+
+\item{diffusion_coeff_component_a}{Optional:}
+
+\item{hydro_crack_scheme}{Optional:}
+
+\item{at_num}{Optional:}
+
+\item{initial_stress}{Optional:}
+
+\item{split_method}{Optional:}
+
+\item{reg_param}{Optional:}
+
+\item{thermal_parameters}{Optional:}
+
+\item{non_advective_form}{Optional:}
+
+\item{fluid}{Optional:}
+
+\item{porous_medium}{Optional:}
+
+\item{decay_rate}{Optional:}
+
+\item{fluid_reference_density}{Optional:}
+
+\item{retardation_factor}{Optional:}
+
+\item{solute_dispersivity_longitudinal}{Optional:}
+
+\item{solute_dispersivity_transverse}{Optional:}
+
+\item{molecular_diffusion_coefficient}{Optional:}
+
+\item{density_solid}{Optional:}
+
+\item{latent_heat_evaporation}{Optional:}
+
+\item{pf_irrv}{Optional:}
+
+\item{...}{Optional: fracture_properties, constitutive_relation}
+}
+\description{
+tag: process (parent tag: processes)
+}
+\examples{
+prj_process(
+    name = "HM",
+    type = "HYDRO_MECHANICS",
+    integration_order = 3,
+    process_variables = list(displacement = "displacement",
+                             pressure = "pressure"),
+    secondary_variables = list(
+        secondary_variable = c(internal_name = "sigma_xx", output_name = "sigma_xx"),
+        secondary_variable = c(internal_name = "sigma_yy", output_name = "sigma_yy")
+    ),
+    specific_body_force = c(0, 0, 0),
+    dimension = 3,
+    constitutive_relation = prj_constitutive_relation(
+        type = "LinearElasticIsotropic",
+        youngs_modulus = "E",
+        poissons_ratio = "nu"
+    )
+)
+}

man/prj_process_variable.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process_variable.R
+\name{prj_process_variable}
+\alias{prj_process_variable}
+\title{prj_process_variable}
+\usage{
+prj_process_variable(
+  name,
+  components,
+  order,
+  initial_condition,
+  boundary_conditions = NULL,
+  source_terms = NULL,
+  mesh = NULL,
+  deactivated_subdomains = NULL
+)
+}
+\arguments{
+\item{name}{string: The name of the process variable}
+
+\item{components}{string | double:}
+
+\item{order}{string | double:}
+
+\item{initial_condition}{string:}
+
+\item{boundary_conditions}{list, prj_boundary_condition:}
+
+\item{source_terms}{Optional: list, prj_source_term:}
+
+\item{mesh}{Optional: string: list:}
+
+\item{deactivated_subdomains}{Optional: list, prj_deactivated_subdomain:}
+}
+\description{
+tag: process_variable
+}
+\examples{
+prj_process_variable(
+    name = "pressure",
+    components = 1,
+    order = 1,
+    initial_condition = "pressure0",
+    boundary_conditions = list(
+        boundary_condition = prj_boundary_condition(
+            type = "Neumann",
+            parameter = "flux_in",
+            geometrical_set = "cube_1x1x1_geometry",
+            geometry = "left",
+            component = 0
+        )
+    )
+)
+}

man/prj_rate.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_chemical_system.R
+\name{prj_rate}
+\alias{prj_rate}
+\title{prj_rate}
+\usage{
+prj_rate(kinetic_reactant, expression)
+}
+\arguments{
+\item{kinetic_reactant}{string: References a kinetic_reactant object}
+
+\item{expression}{character: Statements}
+}
+\description{
+S3 class describing .prj rate
+}
+\examples{
+prj_rate(
+    kinetic_reactant = "Productc",
+    expression = list(
+        statement = "Km = 10",
+        statement = "U = 1e-3",
+        statement =
+            "rate = U * TOT(\"Synthetica\") / (Km + TOT(\"Syntheticb\"))",
+        statement = "moles = - rate * TIME",
+        statement = "save moles"
+    )
+)
+}

man/prj_relative_permeability.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_porous_medium.R
+\name{prj_relative_permeability}
+\alias{prj_relative_permeability}
+\title{prj_relative_permeability}
+\usage{
+prj_relative_permeability(type, sr, smax, m, krel_min, id = NULL)
+}
+\arguments{
+\item{type}{string:}
+
+\item{sr}{string | number:}
+
+\item{smax}{string | number:}
+
+\item{m}{string | number:}
+
+\item{krel_min}{string | number:}
+
+\item{id}{string: Optional:}
+}
+\description{
+tag: relative_permeability
+}
+\examples{
+prj_relative_permeability(
+    type = "NonWettingPhaseVanGenuchten",
+    sr = 0,
+    smax = 0.6,
+    m = 0.3288590604,
+    krel_min = 0,
+    id = "0"
+)
+}

man/prj_search_length_algorithm.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_search_length_algorithm.R
+\name{prj_search_length_algorithm}
+\alias{prj_search_length_algorithm}
+\title{prj_search_length_algorithm}
+\usage{
+prj_search_length_algorithm(type, value = NULL)
+}
+\arguments{
+\item{type}{string: The type}
+
+\item{value}{string | double: The value}
+}
+\description{
+tag: search_length_algorithm
+}
+\examples{
+prj_search_length_algorithm(type = "fixed",
+                               value = 1e-06)
+}