[docs] updated documentation for renamed classes

man/OGS6.Rd

@@ -19,7 +19,7 @@ ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
 ## ------------------------------------------------
 
 ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
-ogs6_obj$add(r2ogs6_parameter$new(name = "foo", type = "bar"))
+ogs6_obj$add(prj_parameter$new(name = "foo", type = "bar"))
 
 ## ------------------------------------------------
 ## Method `OGS6$add_gml`
@@ -64,43 +64,43 @@ ogs6_obj$get_status()
 \item{\code{python_script}}{\code{.prj} \code{python_script} tag. \code{value} must be string}
 
 \item{\code{search_length_algorithm}}{\code{.prj} \code{search_length_algorithm} tag. \code{value} must be
-\code{r2ogs6_search_length_algorithm} object}
+\code{prj_search_length_algorithm} object}
 
 \item{\code{processes}}{\code{.prj} \code{processes} tag. \code{value} must be list of
-\code{r2ogs6_process} objects}
+\code{prj_process} objects}
 
 \item{\code{time_loop}}{\code{.prj} \code{time_loop} tag. \code{value} must be
-\code{r2ogs6_time_loop} object}
+\code{prj_time_loop} object}
 
 \item{\code{local_coordinate_system}}{\code{.prj} \code{local_coordinate_system} tag. \code{value} must be
-\code{r2ogs6_local_coordinate_system} object}
+\code{prj_local_coordinate_system} object}
 
 \item{\code{media}}{\code{.prj} \code{media} tag. \code{value} must be list of
-\code{r2ogs6_medium} objects}
+\code{prj_medium} objects}
 
 \item{\code{parameters}}{\code{.prj} \code{parameters} tag. \code{value} must be list of
-\code{r2ogs6_parameter} objects}
+\code{prj_parameter} objects}
 
 \item{\code{chemical_system}}{\code{.prj} \code{chemical_system} tag. \code{value} must be
-\code{r2ogs6_chemical_system} object}
+\code{prj_chemical_system} object}
 
 \item{\code{curves}}{\code{.prj} \code{curves} tag. \code{value} must be list of
-\code{r2ogs6_curve} objects}
+\code{prj_curve} objects}
 
 \item{\code{process_variables}}{\code{.prj} \code{process_variables} tag. \code{value} must be list of
-\code{r2ogs6_process_variable} objects}
+\code{prj_process_variable} objects}
 
 \item{\code{nonlinear_solvers}}{\code{.prj} \code{nonlinear_solvers} tag. \code{value} must be list of
-\code{r2ogs6_nonlinear_solver} objects}
+\code{prj_nonlinear_solver} objects}
 
 \item{\code{linear_solvers}}{\code{.prj} \code{linear_solvers} tag. \code{value} must be list of
-\code{r2ogs6_linear_solver} objects}
+\code{prj_linear_solver} objects}
 
 \item{\code{test_definition}}{\code{.prj} \code{test_definition} tag. \code{value} must be list of
-\code{r2ogs6_vtkdiff} objects}
+\code{prj_vtkdiff} objects}
 
 \item{\code{insitu}}{\code{.prj} \code{insitu} tag. \code{value} must be
-\code{r2ogs6_insitu} object}
+\code{prj_insitu} object}
 
 \item{\code{pvds}}{\code{.pvd}s. \code{value} must be list of \code{OGS6_pvd} objects}
 }
@@ -160,14 +160,14 @@ Adds a .prj simulation component
 \subsection{Arguments}{
 \if{html}{\out{<div class="arguments">}}
 \describe{
-\item{\code{x}}{An object of any .prj `r2ogs6` class}
+\item{\code{x}}{An object of any .prj `prj` class}
 }
 \if{html}{\out{</div>}}
 }
 \subsection{Examples}{
 \if{html}{\out{<div class="r example copy">}}
 \preformatted{ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
-ogs6_obj$add(r2ogs6_parameter$new(name = "foo", type = "bar"))
+ogs6_obj$add(prj_parameter$new(name = "foo", type = "bar"))
 }
 \if{html}{\out{</div>}}
 

man/OGS6_Chain.Rd

@@ -10,7 +10,7 @@ Constructor for the OGS6_Chain base class
 \subsection{Public methods}{
 \itemize{
 \item \href{#method-new}{\code{OGS6_Chain$new()}}
-\item \href{#method-ogs_run_simulation}{\code{OGS6_Chain$ogs_run_simulation()}}
+\item \href{#method-ogs6_run_simulation}{\code{OGS6_Chain$ogs6_run_simulation()}}
 \item \href{#method-print_log}{\code{OGS6_Chain$print_log()}}
 \item \href{#method-clone}{\code{OGS6_Chain$clone()}}
 }
@@ -35,13 +35,13 @@ Creates new OGS6_Chain object
 }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-ogs_run_simulation"></a>}}
-\if{latex}{\out{\hypertarget{method-ogs_run_simulation}{}}}
-\subsection{Method \code{ogs_run_simulation()}}{
-Runs the simulation. This calls r2ogs6::ogs_run_simulation() internally.
+\if{html}{\out{<a id="method-ogs6_run_simulation"></a>}}
+\if{latex}{\out{\hypertarget{method-ogs6_run_simulation}{}}}
+\subsection{Method \code{ogs6_run_simulation()}}{
+Runs the simulation. This calls r2ogs6::ogs6_run_simulation() internally.
 For chains, output will be written to logfiles.
 \subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6_Chain$ogs_run_simulation()}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_Chain$ogs6_run_simulation()}\if{html}{\out{</div>}}
 }
 
 }

man/OGS6_Ensemble.Rd

@@ -76,7 +76,7 @@ Overrides default printing behaviour
 \if{html}{\out{<a id="method-run_simulation"></a>}}
 \if{latex}{\out{\hypertarget{method-run_simulation}{}}}
 \subsection{Method \code{run_simulation()}}{
-Runs the simulation. This calls r2ogs6::ogs_run_simulation()
+Runs the simulation. This calls r2ogs6::ogs6_run_simulation()
 internally. For ensembles, output will always be written to logfiles.
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$run_simulation(parallel = FALSE, verbose = F)}\if{html}{\out{</div>}}

man/OGS6_pvd.Rd

@@ -15,13 +15,14 @@ Constructor for the OGS6_pvd base class
 
 \item{\code{vtu_paths}}{Getter for `datasets` `file`}
 
-\item{\code{abs_vtu_paths}}{Gets absolute .vtu paths, e.g. `dirname(pvd_path)` + `datasets` `file`}
+\item{\code{abs_vtu_paths}}{Gets absolute .vtu paths, e.g. `dirname(pvd_path)` + `datasets`
+`file`}
 
 \item{\code{last_timestep}}{Gets last timestep}
 
-\item{\code{timesteps}}{Gets timesteps from private parameter '.datasets'}
+\item{\code{timesteps}}{Gets timesteps from private parameter `datasets`}
 
-\item{\code{OGS6_vtus}}{Getter for private parameter '.OGS6_vtus'}
+\item{\code{OGS6_vtus}}{Getter for private parameter `.OGS6_vtus`}
 }
 \if{html}{\out{</div>}}
 }

man/OGS6_vtu.Rd

@@ -4,32 +4,32 @@
 \alias{OGS6_vtu}
 \title{OGS6_vtu}
 \description{
-Constructor for the OGS6_vtu base class
+Constructor for the `OGS6_vtu` base class
 }
 \section{Active bindings}{
 \if{html}{\out{<div class="r6-active-bindings">}}
 \describe{
-\item{\code{vtu_path}}{Getter for private parameter '.vtu_path'}
+\item{\code{vtu_path}}{Getter for private parameter `.vtu_path`}
 
-\item{\code{number_of_points}}{Getter for NumberOfPoints parameter of '.vtkUnstructuredGrid'}
+\item{\code{number_of_points}}{Getter for NumberOfPoints parameter of `.vtkUnstructuredGrid`}
 
-\item{\code{number_of_cells}}{Getter for NumberOfCells parameter of '.vtkUnstructuredGrid'}
+\item{\code{number_of_cells}}{Getter for NumberOfCells parameter of `.vtkUnstructuredGrid`}
 
-\item{\code{points}}{Getter for Points parameter of '.dsa_vtkUnstructuredGrid'}
+\item{\code{points}}{Getter for Points parameter of `.dsa_vtkUnstructuredGrid`}
 
-\item{\code{cells}}{Getter for Cells parameter of '.dsa_vtkUnstructuredGrid'}
+\item{\code{cells}}{Getter for Cells parameter of `.dsa_vtkUnstructuredGrid`}
 
-\item{\code{field_data}}{Getter for FieldData parameter of '.dsa_vtkUnstructuredGrid'}
+\item{\code{field_data}}{Getter for FieldData parameter of `.dsa_vtkUnstructuredGrid`}
 
-\item{\code{point_data}}{Getter for PointData parameter of '.dsa_vtkUnstructuredGrid'}
+\item{\code{point_data}}{Getter for PointData parameter of `.dsa_vtkUnstructuredGrid`}
 
-\item{\code{cell_data}}{Getter for CellData parameter of '.dsa_vtkUnstructuredGrid'}
+\item{\code{cell_data}}{Getter for CellData parameter of `.dsa_vtkUnstructuredGrid`}
 
-\item{\code{vtkPointLocator}}{Getter for private parameter '.vtkPointLocator'}
+\item{\code{vtkPointLocator}}{Getter for private parameter `.vtkPointLocator`}
 
-\item{\code{vtkUnstructuredGrid}}{Access to private parameter '.vtkUnstructuredGrid'}
+\item{\code{vtkUnstructuredGrid}}{Access to private parameter `.vtkUnstructuredGrid`}
 
-\item{\code{dsa_vtkUnstructuredGrid}}{Getter for private parameter '.dsa_vtkUnstructuredGrid'}
+\item{\code{dsa_vtkUnstructuredGrid}}{Getter for private parameter `.dsa_vtkUnstructuredGrid`}
 }
 \if{html}{\out{</div>}}
 }
@@ -50,7 +50,7 @@ Constructor for the OGS6_vtu base class
 \if{html}{\out{<a id="method-new"></a>}}
 \if{latex}{\out{\hypertarget{method-new}{}}}
 \subsection{Method \code{new()}}{
-Creates new OGS6_vtu object
+Creates new OGS6_vtu object.
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{OGS6_vtu$new(vtu_path)}\if{html}{\out{</div>}}
 }
@@ -67,7 +67,7 @@ Creates new OGS6_vtu object
 \if{html}{\out{<a id="method-print"></a>}}
 \if{latex}{\out{\hypertarget{method-print}{}}}
 \subsection{Method \code{print()}}{
-Overrides default printing behaviour
+Overrides default printing behaviour.
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{OGS6_vtu$print()}\if{html}{\out{</div>}}
 }
@@ -86,13 +86,14 @@ Gets FieldData.
 \if{html}{\out{<div class="arguments">}}
 \describe{
 \item{\code{keys}}{character: Optional: `Name` attributes of `DataArray`
-elements, defaults to all in `FieldData`}
+elements, defaults to all in `FieldData`.}
 }
 \if{html}{\out{</div>}}
 }
 \subsection{Returns}{
-list: List of format list(value_a = 1, value_b = 2), where the
-names reference the `Name` attributes of the `DataArray` elements
+A list of format list(value_a = 1, value_b = 2), where
+the names reference the `Name` attributes of the `DataArray`
+elements.
 }
 }
 \if{html}{\out{<hr>}}
@@ -112,8 +113,9 @@ Gets coordinates of specific points by their IDs.
 \if{html}{\out{</div>}}
 }
 \subsection{Returns}{
-If `point_ids` is a number, a coordinate array. If `point_ids`
-is a numeric vector with length > 1, a list of coordinate arrays.
+If `point_ids` is a number, a coordinate array. If
+point_ids` is a numeric vector with length > 1, a list of coordinate
+arrays.
 }
 }
 \if{html}{\out{<hr>}}
@@ -157,7 +159,7 @@ elements, defaults to all in `PointData`}
 \if{html}{\out{</div>}}
 }
 \subsection{Returns}{
-tibble: Tibble where each row represents a point.
+A tibble::tibble where each row represents a point.
 }
 }
 \if{html}{\out{<hr>}}
@@ -180,7 +182,7 @@ elements, defaults to all in `CellData`}
 \if{html}{\out{</div>}}
 }
 \subsection{Returns}{
-tibble: Tibble where each row represents a cell.
+A tibble::tibble where each row represents a cell.
 }
 }
 \if{html}{\out{<hr>}}

man/examples/ex_prj_borehole_heat_exchanger.R

-r2ogs6_borehole_heat_exchanger(
+prj_borehole_heat_exchanger(
     type = "1U",
-    flow_and_temperature_control = r2ogs6_flow_and_temperature_control(
+    flow_and_temperature_control = prj_flow_and_temperature_control(
         type = "TemperatureCurveConstantFlow",
         flow_rate = 2e-04,
         temperature_curve = "inflow_temperature"
@@ -13,7 +13,7 @@ r2ogs6_borehole_heat_exchanger(
         heat_capacity = "1735.160",
         thermal_conductivity = "0.806"
     ),
-    pipes = r2ogs6_pipes(
+    pipes = prj_pipes(
         longitudinal_dispersion_length = 0.001,
         inlet = list(
             diameter = " 0.013665",

man/examples/ex_prj_boundary_condition.R

-r2ogs6_boundary_condition(
+prj_boundary_condition(
     type = "Neumann",
     parameter = "flux_in",
     geometrical_set = "cube_1x1x1_geometry",

man/examples/ex_prj_capillary_pressure.R

-r2ogs6_capillary_pressure(
+prj_capillary_pressure(
     type = "vanGenuchten",
     pd = 2e+06,
     sr = 0.4,

man/examples/ex_prj_chemical_system.R

-r2ogs6_chemical_system(
+prj_chemical_system(
     chemical_solver = "Phreeqc",
     database = "PSINA_12_07_110615_DAV_s.dat",
-    solution = r2ogs6_solution(
+    solution = prj_solution(
         temperature = 25,
         pressure = 1,
         pe = 4,
@@ -20,7 +20,7 @@ r2ogs6_chemical_system(
         scaling = "0"
     ),
     equilibrium_reactants = list(
-        phase_component = r2ogs6_phase_component(
+        phase_component = prj_phase_component(
             name = "Calcite",
             saturation_index = 0,
             initial_amount = 0.000207

man/examples/ex_prj_com_property.R

-r2ogs6_com_property(name = "molecular_diffusion",
+prj_com_property(name = "molecular_diffusion",
                     type = "Constant",
                     value = 2e-09)

man/examples/ex_prj_component.R

-r2ogs6_component(
+prj_component(
     name = "concentration",
     properties = list(
-        property = r2ogs6_com_property(name = "molecular_diffusion",
+        property = prj_com_property(name = "molecular_diffusion",
                                        type = "Constant",
                                        value = 2e-09)
     )

man/examples/ex_prj_constitutive_relation.R

-r2ogs6_constitutive_relation(
+prj_constitutive_relation(
     type = "LinearElasticIsotropic",
     youngs_modulus = "E",
     poissons_ratio = "nu"

man/examples/ex_prj_convergence_criterion.R

-r2ogs6_convergence_criterion(
+prj_convergence_criterion(
     type = "DeltaX",
     norm_type = "INFINITY_N",
     abstol = 1e-08,

man/examples/ex_prj_curve.R

-r2ogs6_curve(name = "Dirichlet_temporal",
+prj_curve(name = "Dirichlet_temporal",
              coords = "0 3",
              values = "200 200")
\ No newline at end of file

man/examples/ex_prj_deactivated_subdomain.R

-r2ogs6_deactivated_subdomain(time_interval = list(start = "0",
+prj_deactivated_subdomain(time_interval = list(start = "0",
                                                   end = "1"),
                              material_ids = 1)

man/examples/ex_prj_eigen.R

-r2ogs6_eigen(
+prj_eigen(
     solver_type = "BiCGSTAB",
     precon_type = "ILUT",
     max_iteration_step = 10000,

man/examples/ex_prj_flow_and_temperature_control.R

-r2ogs6_flow_and_temperature_control(
+prj_flow_and_temperature_control(
     type = "TemperatureCurveConstantFlow",
     flow_rate = 2e-04,
     temperature_curve = "inflow_temperature"

man/examples/ex_prj_fluid.R

-r2ogs6_fluid(
+prj_fluid(
     liquid_density = list(type = "Constant",
                           value = " 1.e3 "),
     gas_density = list(type = "IdealGasLaw",

man/examples/ex_prj_fracture_model.R

-r2ogs6_fracture_model(type = "LinearElasticIsotropic",
+prj_fracture_model(type = "LinearElasticIsotropic",
                       normal_stiffness = "Kn",
                       shear_stiffness = "Ks",
                       penalty_aperture_cutoff = 1e-05,

man/examples/ex_prj_fracture_properties.R

-r2ogs6_fracture_properties(
+prj_fracture_properties(
     material_id = 0,
     initial_aperture = "aperture0",
     specific_storage = "S_f",