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Commit 0f453335 authored by Ruben Heinrich's avatar Ruben Heinrich
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[docs] updated documentation for renamed classes

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1 merge request!13Resolve "Rename ogs_ prefixes to ogs6_ and r2ogs6_prefixes to prj_"
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sim_utils.R
\name{ogs6_read_output_files}
\alias{ogs6_read_output_files}
\title{ogs6_read_output_files}
\usage{
ogs6_read_output_files(ogs6_obj)
}
\arguments{
\item{ogs6_obj}{OGS6: Simulation object}
}
\description{
Read in generated \code{.pvd} files and add it to ogs6_obj
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sim_utils.R
\name{ogs6_run_simulation}
\alias{ogs6_run_simulation}
\title{ogs6_run_simulation}
\usage{
ogs6_run_simulation(ogs6_obj, write_logfile = TRUE, ogs6_bin_path, verbose = F)
}
\arguments{
\item{ogs6_obj}{OGS6: Simulation object}
\item{write_logfile}{flag: Should output be written to a logfile? If
\code{FALSE}, output will be written to console. If \code{TRUE}, logfile
directory will be created in \code{ogs6$sim_path} directory}
\item{ogs6_bin_path}{string: Optional: OpenGeoSys 6 bin folder path. Defaults
to \code{options("r2ogs6.default_ogs6_bin_path")}}
\item{verbose}{flag}
}
\description{
Wrapper function that calls \code{ogs6_export_sim_files()},
\code{ogs6_call_ogs6()} and \code{ogs6_read_output_files()}.
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_borehole_heat_exchanger.R
\name{prj_borehole_heat_exchanger}
\alias{prj_borehole_heat_exchanger}
\title{prj_borehole_heat_exchanger}
\usage{
prj_borehole_heat_exchanger(
type,
flow_and_temperature_control,
borehole,
grout,
pipes,
refrigerant,
use_bhe_pipe_network = NULL
)
}
\arguments{
\item{type}{string:}
\item{flow_and_temperature_control}{prj_flow_and_temperature_control:}
\item{borehole}{list:}
\item{grout}{list:}
\item{pipes}{prj_pipes:}
\item{refrigerant}{list:}
\item{use_bhe_pipe_network}{Optional: string ("true" | "false"):}
}
\description{
tag: borehole_heat_exchanger
}
\examples{
prj_borehole_heat_exchanger(
type = "1U",
flow_and_temperature_control = prj_flow_and_temperature_control(
type = "TemperatureCurveConstantFlow",
flow_rate = 2e-04,
temperature_curve = "inflow_temperature"
),
borehole = list(length = "18.0",
diameter = "0.13"),
grout = list(
density = "2190.0",
porosity = "0.0",
heat_capacity = "1735.160",
thermal_conductivity = "0.806"
),
pipes = 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
),
refrigerant = list(
density = "992.92",
viscosity = "0.00067418",
specific_heat_capacity = "4068",
thermal_conductivity = "0.62863",
reference_temperature = "298.15"
)
)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_process_variable.R
\name{prj_boundary_condition}
\alias{prj_boundary_condition}
\title{prj_boundary_condition}
\usage{
prj_boundary_condition(
type,
parameter = NULL,
geometrical_set = NULL,
geometry = NULL,
component = NULL,
mesh = NULL,
alpha = NULL,
u_0 = NULL,
constraint_type = NULL,
constraining_process_variable = NULL,
constraint_threshold = NULL,
constraint_direction = NULL,
area_parameter = NULL,
bc_object = NULL,
flush_stdout = NULL,
property_name = NULL,
initial_value_parameter = NULL,
constant_name = NULL,
coefficient_current_variable_name = NULL,
coefficient_other_variable_name = NULL,
coefficient_mixed_variables_name = NULL,
threshold_parameter = NULL,
comparison_operator = NULL,
time_interval = NULL
)
}
\arguments{
\item{type}{string:}
\item{parameter}{string:}
\item{geometrical_set}{Optional: string:}
\item{geometry}{Optional: string:}
\item{component}{Optional: string | double:}
\item{mesh}{Optional: string:}
\item{alpha}{Optional: string:}
\item{u_0}{Optional: string:}
\item{constraint_type}{Optional: string:}
\item{constraining_process_variable}{Optional: string:}
\item{constraint_threshold}{Optional: string | double:}
\item{constraint_direction}{Optional: string:}
\item{area_parameter}{Optional: string:}
\item{bc_object}{Optional: string:}
\item{flush_stdout}{Optional: string:}
\item{property_name}{Optional: string:}
\item{initial_value_parameter}{Optional: string:}
\item{constant_name}{Optional: string:}
\item{coefficient_current_variable_name}{Optional: string:}
\item{coefficient_other_variable_name}{Optional: string:}
\item{coefficient_mixed_variables_name}{Optional: string:}
\item{threshold_parameter}{Optional: string:}
\item{comparison_operator}{Optional: string:}
\item{time_interval}{Optional: list of 2, character:}
}
\description{
tag: boundary_condition
}
\examples{
prj_boundary_condition(
type = "Neumann",
parameter = "flux_in",
geometrical_set = "cube_1x1x1_geometry",
geometry = "left",
component = 0
)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_porous_medium.R
\name{prj_capillary_pressure}
\alias{prj_capillary_pressure}
\title{prj_capillary_pressure}
\usage{
prj_capillary_pressure(
type,
pd = NULL,
sr = NULL,
smax = NULL,
m = NULL,
pc_max = NULL,
has_regularized = NULL,
curve = NULL
)
}
\arguments{
\item{type}{string:}
\item{pd}{Optional: string | double:}
\item{sr}{Optional: string | double:}
\item{smax}{Optional: string | double:}
\item{m}{Optional: string | double:}
\item{pc_max}{Optional: string | double:}
\item{has_regularized}{Optional: string, "true" | "false":}
\item{curve}{Optional: list:}
}
\description{
tag: capillary_pressure
}
\examples{
prj_capillary_pressure(
type = "vanGenuchten",
pd = 2e+06,
sr = 0.4,
smax = 1,
m = 0.3288590604,
pc_max = 2e+07,
has_regularized = "true"
)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_chemical_system.R
\name{prj_chemical_system}
\alias{prj_chemical_system}
\title{prj_chemical_system}
\usage{
prj_chemical_system(
chemical_solver,
database,
solution,
mesh = NULL,
knobs = NULL,
kinetic_reactants = NULL,
rates = NULL,
equilibrium_reactants = NULL,
surface = NULL,
user_punch = NULL
)
}
\arguments{
\item{chemical_solver}{string:}
\item{database}{string:}
\item{solution}{prj_solution:}
\item{mesh}{Optional: string:}
\item{knobs}{Optional: list:}
\item{kinetic_reactants}{Optional: list, prj_kinetic_reactant:}
\item{rates}{Optional: list, prj_rate:}
\item{equilibrium_reactants}{Optional: list, prj_phase_component:}
\item{surface}{Optional:}
\item{user_punch}{Optional:}
}
\description{
tag: chemical_system
}
\examples{
prj_chemical_system(
chemical_solver = "Phreeqc",
database = "PSINA_12_07_110615_DAV_s.dat",
solution = prj_solution(
temperature = 25,
pressure = 1,
pe = 4,
components = list(
component = "C(4)",
component = "Ca"
),
charge_balance = "pH"
),
mesh = "calcite_ReactiveDomain",
knobs = list(
max_iter = "100",
relative_convergence_tolerance = "1e-12",
tolerance = "1e-15",
step_size = "100",
scaling = "0"
),
equilibrium_reactants = list(
phase_component = prj_phase_component(
name = "Calcite",
saturation_index = 0,
initial_amount = 0.000207
)
)
)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_medium.R
\name{prj_com_property}
\alias{prj_com_property}
\title{prj_com_property}
\usage{
prj_com_property(name, type, value = NULL, parameter_name = NULL)
}
\arguments{
\item{name}{string: Property name}
\item{type}{string: Property type}
\item{value}{Optional: string | double: ...}
\item{parameter_name}{Optional:}
}
\description{
tag: property
}
\examples{
prj_com_property(name = "molecular_diffusion",
type = "Constant",
value = 2e-09)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_medium.R
\name{prj_component}
\alias{prj_component}
\title{prj_component}
\usage{
prj_component(name, properties)
}
\arguments{
\item{name}{string:}
\item{properties}{list, prj_com_property:}
}
\description{
tag: component
}
\examples{
prj_component(
name = "concentration",
properties = list(
property = prj_com_property(name = "molecular_diffusion",
type = "Constant",
value = 2e-09)
)
)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_process.R
\name{prj_constitutive_relation}
\alias{prj_constitutive_relation}
\title{prj_constitutive_relation}
\usage{
prj_constitutive_relation(
type,
id = NULL,
youngs_modulus = NULL,
poissons_ratio = NULL,
nonlinear_solver = NULL,
behaviour = NULL,
material_properties = NULL,
shear_modulus = NULL,
bulk_modulus = NULL,
kappa = NULL,
beta = NULL,
gamma = NULL,
hardening_modulus = NULL,
alpha = NULL,
delta = NULL,
eps = NULL,
m = NULL,
alphap = NULL,
deltap = NULL,
epsp = NULL,
mp = NULL,
betap = NULL,
gammap = NULL,
tangent_type = NULL,
damage_properties = NULL,
youngs_moduli = NULL,
shear_moduli = NULL,
poissons_ratios = NULL,
a = NULL,
n = NULL,
sigma0 = NULL,
q = NULL,
kelvin_shear_modulus = NULL,
kelvin_viscosity = NULL,
maxwell_shear_modulus = NULL,
maxwell_bulk_modulus = NULL,
maxwell_viscosity = NULL,
dependency_parameter_mk = NULL,
dependency_parameter_mvk = NULL,
dependency_parameter_mvm = NULL
)
}
\arguments{
\item{type}{string:}
\item{id}{Optional:}
\item{youngs_modulus}{Optional:}
\item{poissons_ratio}{Optional:}
\item{nonlinear_solver}{Optional:}
\item{behaviour}{Optional:}
\item{material_properties}{Optional:}
\item{shear_modulus}{Optional:}
\item{bulk_modulus}{Optional:}
\item{kappa}{Optional:}
\item{beta}{Optional:}
\item{gamma}{Optional:}
\item{hardening_modulus}{Optional:}
\item{alpha}{Optional:}
\item{delta}{Optional:}
\item{eps}{Optional:}
\item{m}{Optional:}
\item{alphap}{Optional:}
\item{deltap}{Optional:}
\item{epsp}{Optional:}
\item{mp}{Optional:}
\item{betap}{Optional:}
\item{gammap}{Optional:}
\item{tangent_type}{Optional:}
\item{damage_properties}{Optional:}
\item{youngs_moduli}{Optional:}
\item{shear_moduli}{Optional:}
\item{poissons_ratios}{Optional:}
\item{a}{Optional:}
\item{n}{Optional:}
\item{sigma0}{Optional:}
\item{q}{Optional:}
\item{kelvin_shear_modulus}{Optional:}
\item{kelvin_viscosity}{Optional:}
\item{maxwell_shear_modulus}{Optional:}
\item{maxwell_bulk_modulus}{Optional:}
\item{maxwell_viscosity}{Optional:}
\item{dependency_parameter_mk}{Optional:}
\item{dependency_parameter_mvk}{Optional:}
\item{dependency_parameter_mvm}{Optional:}
}
\description{
tag: constitutive_relation
}
\examples{
prj_constitutive_relation(
type = "LinearElasticIsotropic",
youngs_modulus = "E",
poissons_ratio = "nu"
)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_time_loop.R
\name{prj_convergence_criterion}
\alias{prj_convergence_criterion}
\title{prj_convergence_criterion}
\usage{
prj_convergence_criterion(
type,
norm_type,
abstol = NULL,
reltol = NULL,
abstols = NULL,
reltols = NULL
)
}
\arguments{
\item{type}{string: Type}
\item{norm_type}{string: ...}
\item{abstol}{string | double: Absolute tolerance}
\item{reltol}{string | double: Relative tolerance}
\item{abstols}{string | numeric: Absolute tolerances}
\item{reltols}{string | numeric: Relative tolerances}
}
\description{
tag: convergence_criterion
}
\examples{
prj_convergence_criterion(
type = "DeltaX",
norm_type = "INFINITY_N",
abstol = 1e-08,
reltol = 1e-10
)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_curve.R
\name{prj_curve}
\alias{prj_curve}
\title{prj_curve}
\usage{
prj_curve(name, coords, values)
}
\arguments{
\item{name}{string: Name of the curve}
\item{coords}{string | numeric: Coordinates at which the curve's values
are given}
\item{values}{string | numeric: Values of the curve at the given coordinates}
}
\description{
tag: curve, a curve
}
\examples{
prj_curve(name = "Dirichlet_temporal",
coords = "0 3",
values = "200 200")
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_process_variable.R
\name{prj_deactivated_subdomain}
\alias{prj_deactivated_subdomain}
\title{prj_deactivated_subdomain}
\usage{
prj_deactivated_subdomain(time_interval, material_ids)
}
\arguments{
\item{time_interval}{list, numeric:}
\item{material_ids}{string | double:}
}
\description{
tag: deactivated_subdomain
}
\examples{
prj_deactivated_subdomain(time_interval = list(start = "0",
end = "1"),
material_ids = 1)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_linear_solver.R
\name{prj_eigen}
\alias{prj_eigen}
\title{prj_eigen}
\usage{
prj_eigen(
solver_type,
precon_type = NULL,
max_iteration_step = NULL,
error_tolerance = NULL,
scaling = NULL,
restart = NULL
)
}
\arguments{
\item{solver_type}{string:}
\item{precon_type}{Optional: string:}
\item{max_iteration_step}{Optional: string | double: ...}
\item{error_tolerance}{Optional: string | double: ...}
\item{scaling}{Optional: string | double: ...}
\item{restart}{Optional: string | double: ...}
}
\description{
tag: eigen
}
\examples{
prj_eigen(
solver_type = "BiCGSTAB",
precon_type = "ILUT",
max_iteration_step = 10000,
error_tolerance = 1e-16
)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_borehole_heat_exchanger.R
\name{prj_flow_and_temperature_control}
\alias{prj_flow_and_temperature_control}
\title{prj_flow_and_temperature_control}
\usage{
prj_flow_and_temperature_control(
type,
flow_rate = NULL,
temperature_curve = NULL,
power = NULL,
power_curve = NULL,
flow_rate_curve = NULL
)
}
\arguments{
\item{type}{string:}
\item{flow_rate}{Optional: string | double:}
\item{temperature_curve}{Optional: string:}
\item{power}{Optional: string | double:}
\item{power_curve}{Optional: string:}
\item{flow_rate_curve}{Optional: string:}
}
\description{
tag: flow_and_temperature_control
}
\examples{
prj_flow_and_temperature_control(
type = "TemperatureCurveConstantFlow",
flow_rate = 2e-04,
temperature_curve = "inflow_temperature"
)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_material_property.R
\name{prj_fluid}
\alias{prj_fluid}
\title{prj_fluid}
\usage{
prj_fluid(
liquid_density,
gas_density,
liquid_viscosity,
gas_viscosity,
specific_heat_capacity_solid = NULL,
specific_heat_capacity_water = NULL,
specific_heat_capacity_air = NULL,
specific_heat_capacity_water_vapor = NULL,
thermal_conductivity_dry_solid = NULL,
thermal_conductivity_wet_solid = NULL
)
}
\arguments{
\item{liquid_density}{list:}
\item{gas_density}{list:}
\item{liquid_viscosity}{list:}
\item{gas_viscosity}{list:}
\item{specific_heat_capacity_solid}{Optional:}
\item{specific_heat_capacity_water}{Optional:}
\item{specific_heat_capacity_air}{Optional:}
\item{specific_heat_capacity_water_vapor}{Optional:}
\item{thermal_conductivity_dry_solid}{Optional:}
\item{thermal_conductivity_wet_solid}{Optional:}
}
\description{
tag: fluid
}
\examples{
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 ")
)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_process.R
\name{prj_fracture_model}
\alias{prj_fracture_model}
\title{prj_fracture_model}
\usage{
prj_fracture_model(
type,
normal_stiffness,
shear_stiffness,
penalty_aperture_cutoff,
tension_cutoff,
fracture_toughness = NULL,
peak_normal_traction = NULL,
friction_angle = NULL,
dilatancy_angle = NULL,
cohesion = NULL,
nonlinear_solver = NULL
)
}
\arguments{
\item{type}{string:}
\item{normal_stiffness}{string:}
\item{shear_stiffness}{string:}
\item{penalty_aperture_cutoff}{string | double:}
\item{tension_cutoff}{string | double:}
\item{fracture_toughness}{Optional: string:}
\item{peak_normal_traction}{Optional: string:}
\item{friction_angle}{Optional: string:}
\item{dilatancy_angle}{Optional: string:}
\item{cohesion}{Optional: string:}
\item{nonlinear_solver}{Optional: list:}
}
\description{
tag: fracture_model
}
\examples{
prj_fracture_model(type = "LinearElasticIsotropic",
normal_stiffness = "Kn",
shear_stiffness = "Ks",
penalty_aperture_cutoff = 1e-05,
tension_cutoff = 1)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_process.R
\name{prj_fracture_properties}
\alias{prj_fracture_properties}
\title{prj_fracture_properties}
\usage{
prj_fracture_properties(
material_id,
initial_aperture,
specific_storage = NULL,
biot_coefficient = NULL,
permeability_model = NULL
)
}
\arguments{
\item{material_id}{string | double:}
\item{initial_aperture}{string:}
\item{specific_storage}{Optional: string:}
\item{biot_coefficient}{Optional: string:}
\item{permeability_model}{Optional: list:}
}
\description{
tag: fracture_properties
}
\examples{
prj_fracture_properties(
material_id = 0,
initial_aperture = "aperture0",
specific_storage = "S_f",
biot_coefficient = "biot_f",
permeability_model = list(type = "CubicLaw")
)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_time_loop.R
\name{prj_global_process_coupling}
\alias{prj_global_process_coupling}
\title{prj_global_process_coupling}
\usage{
prj_global_process_coupling(max_iter, convergence_criteria)
}
\arguments{
\item{max_iter}{string | double: Maximal number of iterations}
\item{convergence_criteria}{list, prj_convergence_criterion:
Convergence criteria}
}
\description{
tag: global_process_coupling
}
\examples{
prj_global_process_coupling(
max_iter = 100,
convergence_criteria = list(
convergence_criterion = prj_convergence_criterion(
type = "DeltaX",
norm_type = "INFINITY_N",
abstol = 1e-08,
reltol = 1e-10
)
)
)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_insitu.R
\name{prj_insitu}
\alias{prj_insitu}
\title{prj_insitu}
\usage{
prj_insitu(scripts)
}
\arguments{
\item{scripts}{character: Script names}
}
\description{
tag: insitu
}
\examples{
prj_insitu(scripts = c(script = "square_1e1_neumann-insitu.py"))
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prj_process.R
\name{prj_jacobian_assembler}
\alias{prj_jacobian_assembler}
\title{prj_jacobian_assembler}
\usage{
prj_jacobian_assembler(
type,
component_magnitudes = NULL,
relative_epsilons = NULL
)
}
\arguments{
\item{type}{string:}
\item{component_magnitudes}{Optional: string | double:}
\item{relative_epsilons}{Optional: string | double:}
}
\description{
tag: jacobian_assembler
}
\examples{
prj_jacobian_assembler(
type = "CentralDifferences",
component_magnitudes = 1,
relative_epsilons = 1e-08
)
}
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