diff --git a/R/ogs6.R b/R/ogs6.R
index 6d8a5c74e9178446b345f70c175564504710c431..c05732b0c3def4dab910aa1ca85a33ea874bb4cd 100644
--- a/R/ogs6.R
+++ b/R/ogs6.R
@@ -2,17 +2,19 @@
#===== OGS6 =====
-#'OGS6
-#'@description Constructor for the OGS6 base class
-#'@export
+#' OGS6
+#' @description Constructor for the \code{OGS6} base class
+#' @export
OGS6 <- R6::R6Class("OGS6",
public = list(
- #'@description
- #'Creates new OGS6 object
- #'@param sim_name string: Simulation name
- #'@param sim_path string: Path where all files for the simulation will be
- #' saved
+ #' @description
+ #' Creates new OGS6 object
+ #' @param sim_name string: Simulation name
+ #' @param sim_path string: Path where all files for the simulation will be
+ #' saved
+ #' @examples
+ #' ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
initialize = function(sim_name,
sim_path) {
@@ -30,9 +32,12 @@ OGS6 <- R6::R6Class("OGS6",
#===== Adding components =====
- #'@description
- #'Adds a .prj simulation component
- #'@param x An object of any .prj `r2ogs6` class
+ #' @description
+ #' Adds a .prj simulation component
+ #' @param x An object of any .prj `r2ogs6` class
+ #' @examples
+ #' ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
+ #' ogs6_obj$add(r2ogs6_parameter$new(name = "foo", type = "bar"))
add = function(x){
# Assert that class name is in implemented .prj classes for OGS6
@@ -66,11 +71,15 @@ OGS6 <- R6::R6Class("OGS6",
invisible(self)
},
- #'@description
- #'Adds a reference to a .gml file and optionally, a OGS6_gml object
- #'@param gml string | r2ogs6_gml: Either a path to a file with extension
- #' .gml or a r2ogs6_gml object.
- #@examples
+ #' @description
+ #' Adds a reference to a file with ending .gml and optionally, a
+ #' \code{OGS6_gml} object
+ #' @param gml string | OGS6_gml: Either a path to a file with extension
+ #' .gml or a OGS6_gml object.
+ #' @examples
+ #' ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
+ #' ogs6_obj$add_gml("this_works.gml")
+ #' \dontrun{ogs6_obj$add_gml("this_doesnt.oops")}
add_gml = function(gml){
if(assertthat::is.string(gml)){
@@ -85,11 +94,16 @@ OGS6 <- R6::R6Class("OGS6",
invisible(self)
},
- #'@description
- #'Adds a reference to a .vtu file and optionally, a OGS6_vtu object
- #'@param path string:
- #'@param read_in_vtu flag: Optional: Should .vtu file just be copied or
- #' read in too?
+ #' @description
+ #' Adds a reference to a \code{.vtu} file and optionally, a \code{OGS6_vtu}
+ #' object
+ #' @param path string: A path
+ #' @param read_in_vtu flag: Optional: Should \code{.vtu} file just be
+ #' copied or read in too?
+ #' @examples
+ #' ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
+ #' ogs6_obj$add_vtu("this_works.vtu")
+ #' \dontrun{ogs6_obj$add_vtu("this_doesnt.oops")}
add_vtu = function(path,
read_in_vtu = FALSE){
assertthat::assert_that(assertthat::is.string(path))
@@ -109,10 +123,13 @@ OGS6 <- R6::R6Class("OGS6",
#===== Utility =====
- #'@description
- #'Checks if the OGS6 object has all necessary parameters for
+ #' @description
+ #' Checks if the \code{OGS6} object has all necessary parameters for
#' starting a simulation
- #'@param print_status flag: Should the status be printed to the console?
+ #' @param print_status flag: Should the status be printed to the console?
+ #' @examples
+ #' ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
+ #' ogs6_obj$get_status()
get_status = function(print_status = TRUE){
assertthat::assert_that(assertthat::is.flag(print_status))
@@ -166,8 +183,8 @@ OGS6 <- R6::R6Class("OGS6",
return(invisible(flag))
},
- #'@description
- #'Overrides default printing behaviour
+ #' @description
+ #' Overrides default printing behaviour
print = function(){
cat("OGS6\n")
cat("simulation name: ", self$sim_name, "\n", sep = "")
@@ -197,8 +214,8 @@ OGS6 <- R6::R6Class("OGS6",
invisible(self)
},
- #'print_log
- #'@description Prints logfile to console (if it exists)
+ #' print_log
+ #' @description Prints logfile to console (if it exists)
print_log = function(){
if(!is.null(self$logfile)){
writeLines(readLines(self$logfile))
@@ -209,11 +226,11 @@ OGS6 <- R6::R6Class("OGS6",
invisible(self)
},
- #'@description
- #'Clears components from the OGS6 object
- #'@param which character: The names of the components (all by default).
+ #' @description
+ #' Clears components from the \code{OGS6} object
+ #' @param which character: The names of the components (all by default).
#' If you want to delete only some components, run
- #' names(prj_top_level_classes()) for the available options.
+ #' \code{names(prj_top_level_classes())} for the available options.
clear = function(which){
if(missing(which)){
@@ -254,8 +271,8 @@ OGS6 <- R6::R6Class("OGS6",
active = list(
- #'@field sim_name
- #'Simulation name. `value` must be string
+ #' @field sim_name
+ #' Simulation name. \code{value} must be string
sim_name = function(value) {
if(missing(value)) {
private$.sim_name
@@ -265,8 +282,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field sim_path
- #'Simulation path. `value` must be string
+ #' @field sim_path
+ #' Simulation path. \code{value} must be string
sim_path = function(value) {
if(missing(value)) {
private$.sim_path
@@ -275,8 +292,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field logfile
- #'Logfile path. `value` must be string
+ #' @field logfile
+ #' Logfile path. \code{value} must be string
logfile = function(value) {
if(missing(value)) {
private$.logfile
@@ -286,14 +303,14 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field gml
- #'.gml. read-only
+ #' @field gml
+ #' \code{.gml}. read-only
gml = function() {
private$.gml
},
- #'@field geometry
- #'.prj `geometry` tag. `value` must be string
+ #' @field geometry
+ #' \code{.prj} \code{geometry} tag. \code{value} must be string
geometry = function(value) {
if(missing(value)) {
private$.geometry
@@ -303,8 +320,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field meshes
- #'.prj `meshes` tag. `value` must be list of strings
+ #' @field meshes
+ #' \code{.prj} \code{meshes} tag. \code{value} must be list of strings
meshes = function(value) {
if(missing(value)) {
private$.meshes
@@ -317,8 +334,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field vtus
- #'.vtus. `value` must be list of `OGS_vtu` objects
+ #' @field vtus
+ #' \code{.vtu}s. \code{value} must be list of \code{OGS6_vtu} objects
vtus = function(value) {
if(missing(value)) {
private$.vtus
@@ -329,8 +346,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field python_script
- #'.prj `python_script` tag. `value` must be string
+ #' @field python_script
+ #' \code{.prj} \code{python_script} tag. \code{value} must be string
python_script = function(value) {
if(missing(value)) {
private$.python_script
@@ -340,9 +357,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field search_length_algorithm
- #'.prj `search_length_algorithm` tag. `value` must be
- #' `r2ogs6_search_length_algorithm` object
+ #' @field search_length_algorithm
+ #' \code{.prj} \code{search_length_algorithm} tag. \code{value} must be
+ #' \code{r2ogs6_search_length_algorithm} object
search_length_algorithm = function(value) {
if(missing(value)) {
private$.search_length_algorithm
@@ -354,8 +371,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field processes
- #'.prj `processes` tag. `value` must be list of `r2ogs6_process` objects
+ #' @field processes
+ #' \code{.prj} \code{processes} tag. \code{value} must be list of
+ #' \code{r2ogs6_process} objects
processes = function(value) {
if(missing(value)) {
private$.processes
@@ -384,8 +402,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field time_loop
- #'.prj `time_loop` tag. `value` must be `r2ogs6_time_loop` object
+ #' @field time_loop
+ #' \code{.prj} \code{time_loop} tag. \code{value} must be
+ #' \code{r2ogs6_time_loop} object
time_loop = function(value) {
if(missing(value)) {
private$.time_loop
@@ -397,9 +416,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field local_coordinate_system
- #'.prj `local_coordinate_system` tag. `value` must be
- #' `r2ogs6_local_coordinate_system` object
+ #' @field local_coordinate_system
+ #' \code{.prj} \code{local_coordinate_system} tag. \code{value} must be
+ #' \code{r2ogs6_local_coordinate_system} object
local_coordinate_system = function(value) {
if(missing(value)) {
private$.local_coordinate_system
@@ -411,8 +430,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field media
- #'.prj `media` tag. `value` must be list of `r2ogs6_medium` objects
+ #' @field media
+ #' \code{.prj} \code{media} tag. \code{value} must be list of
+ #' \code{r2ogs6_medium} objects
media = function(value) {
if(missing(value)) {
private$.media
@@ -423,9 +443,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field parameters
- #'.prj `parameters` tag. `value` must be list of `r2ogs6_parameter`
- #' objects
+ #' @field parameters
+ #' \code{.prj} \code{parameters} tag. \code{value} must be list of
+ #' \code{r2ogs6_parameter} objects
parameters = function(value) {
if(missing(value)) {
private$.parameters
@@ -436,9 +456,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field chemical_system
- #'.prj `chemical_system` tag. `value` must be `r2ogs6_chemical_system`
- #' object
+ #' @field chemical_system
+ #' \code{.prj} \code{chemical_system} tag. \code{value} must be
+ #' \code{r2ogs6_chemical_system} object
chemical_system = function(value) {
if(missing(value)) {
private$.chemical_system
@@ -450,8 +470,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field curves
- #'.prj `curves` tag. `value` must be list of `r2ogs6_curve` objects
+ #' @field curves
+ #' \code{.prj} \code{curves} tag. \code{value} must be list of
+ #' \code{r2ogs6_curve} objects
curves = function(value) {
if(missing(value)) {
private$.curves
@@ -462,9 +483,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field process_variables
- #'.prj `process_variables` tag. `value` must be list of
- #' `r2ogs6_process_variable` objects
+ #' @field process_variables
+ #' \code{.prj} \code{process_variables} tag. \code{value} must be list of
+ #' \code{r2ogs6_process_variable} objects
process_variables = function(value) {
if(missing(value)) {
private$.process_variables
@@ -476,9 +497,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field nonlinear_solvers
- #'.prj `nonlinear_solvers` tag. `value` must be list of
- #' `r2ogs6_nonlinear_solver` objects
+ #' @field nonlinear_solvers
+ #' \code{.prj} \code{nonlinear_solvers} tag. \code{value} must be list of
+ #' \code{r2ogs6_nonlinear_solver} objects
nonlinear_solvers = function(value) {
if(missing(value)) {
private$.nonlinear_solvers
@@ -490,9 +511,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field linear_solvers
- #'.prj `linear_solvers` tag. `value` must be list of
- #' `r2ogs6_linear_solver` objects
+ #' @field linear_solvers
+ #' \code{.prj} \code{linear_solvers} tag. \code{value} must be list of
+ #' \code{r2ogs6_linear_solver} objects
linear_solvers = function(value) {
if(missing(value)) {
private$.linear_solvers
@@ -503,9 +524,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field test_definition
- #'.prj `test_definition` tag. `value` must be list of `r2ogs6_vtkdiff`
- #' objects
+ #' @field test_definition
+ #' \code{.prj} \code{test_definition} tag. \code{value} must be list of
+ #' \code{r2ogs6_vtkdiff} objects
test_definition = function(value) {
if(missing(value)) {
private$.test_definition
@@ -516,8 +537,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field insitu
- #'.prj `insitu` tag. `value` must be `r2ogs6_insitu` object
+ #' @field insitu
+ #' \code{.prj} \code{insitu} tag. \code{value} must be
+ #' \code{r2ogs6_insitu} object
insitu = function(value) {
if(missing(value)) {
private$.insitu
@@ -529,8 +551,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@field pvds
- #'.pvds. `value` must be list of `OGS6_pvd` objects
+ #' @field pvds
+ #' \code{.pvd}s. \code{value} must be list of \code{OGS6_pvd} objects
pvds = function(value) {
if(missing(value)) {
private$.pvds
diff --git a/R/ogs6_gml.R b/R/ogs6_gml.R
index 6d6ce74011e8e6d27c0a94a25d78b82e56a3e797..1dd40a99dd11150e24945914286266f713c4cd5f 100644
--- a/R/ogs6_gml.R
+++ b/R/ogs6_gml.R
@@ -2,21 +2,40 @@
#===== OGS6_gml =====
-#'OGS6_gml
-#'@description Constructor for the OGS6_gml base class
-#'@export
+#' OGS6_gml
+#' @description Constructor for the OGS6_gml base class
+#' @examples
+#' OGS6_gml$new(
+#' name = "cube_1x1x1_geometry",
+#' points = tibble::tibble(
+#' x = c(0, 0, 0, 0),
+#' y = c(0, 0, 1, 1),
+#' z = c(0, 1, 1, 0),
+#' name = c("origin", "", "", "")
+#' ),
+#' polylines = list(polyline = list("front_left",
+#' c(
+#' pnt = 0, pnt = 1
+#' ))),
+#' surfaces = list(surface = list(
+#' name = "left",
+#' element = c(p1 = 0, p2 = 1, p3 = 2),
+#' element = c(p1 = 0, p2 = 3, p3 = 2)
+#' ))
+#' )
+#' @export
OGS6_gml <- R6::R6Class(
"OGS6_gml",
public = list(
- #'@description
- #'Creates new OGS6_gml object
- #'@param gml_path string: Optional: Path to .gml file
- #'@param name string: Geometry name
- #'@param points tibble: Must have 3 vectors named 'x', 'y' and 'z', may
- #' have optional 'name' vector
- #'@param polylines list(list("foo", c(1, 2))):
- #'@param surfaces list(list("foo", c(1, 2, 3), c(2, 3, 4))):
+ #' @description
+ #' Creates new OGS6_gml object
+ #' @param gml_path string: Optional: Path to .gml file
+ #' @param name string: Geometry name
+ #' @param points tibble: Must have 3 vectors named 'x', 'y' and 'z', may
+ #' have optional 'name' vector
+ #' @param polylines list(list("foo", c(1, 2))):
+ #' @param surfaces list(list("foo", c(1, 2, 3), c(2, 3, 4)))
initialize = function(gml_path = NULL,
name = NULL,
points = NULL,
diff --git a/R/prj_borehole_heat_exchanger.R b/R/prj_borehole_heat_exchanger.R
index 0fb58882726198e55e52d29d93fd9da23a17987a..f833e0f697982c04db12cab45ed52272f2be882e 100644
--- a/R/prj_borehole_heat_exchanger.R
+++ b/R/prj_borehole_heat_exchanger.R
@@ -2,16 +2,17 @@
#===== r2ogs6_borehole_heat_exchanger =====
-#'r2ogs6_borehole_heat_exchanger
-#'@description tag: borehole_heat_exchanger
-#'@param type string:
-#'@param flow_and_temperature_control r2ogs6_flow_and_temperature_control:
-#'@param borehole list:
-#'@param grout list:
-#'@param pipes r2ogs6_pipes:
-#'@param refrigerant list:
-#'@param use_bhe_pipe_network Optional: string ("true" | "false"):
-#'@export
+#' r2ogs6_borehole_heat_exchanger
+#' @description tag: borehole_heat_exchanger
+#' @param type string:
+#' @param flow_and_temperature_control r2ogs6_flow_and_temperature_control:
+#' @param borehole list:
+#' @param grout list:
+#' @param pipes r2ogs6_pipes:
+#' @param refrigerant list:
+#' @param use_bhe_pipe_network Optional: string ("true" | "false"):
+#' @example man/examples/ex_prj_borehole_heat_exchanger.R
+#' @export
r2ogs6_borehole_heat_exchanger <- function(type,
flow_and_temperature_control,
borehole,
@@ -81,15 +82,16 @@ new_r2ogs6_borehole_heat_exchanger <- function(type,
#===== r2ogs6_flow_and_temperature_control =====
-#'r2ogs6_flow_and_temperature_control
-#'@description tag: flow_and_temperature_control
-#'@param type string:
-#'@param flow_rate Optional: string | double:
-#'@param temperature_curve Optional: string:
-#'@param power Optional: string | double:
-#'@param power_curve Optional: string:
-#'@param flow_rate_curve Optional: string:
-#'@export
+#' r2ogs6_flow_and_temperature_control
+#' @description tag: flow_and_temperature_control
+#' @param type string:
+#' @param flow_rate Optional: string | double:
+#' @param temperature_curve Optional: string:
+#' @param power Optional: string | double:
+#' @param power_curve Optional: string:
+#' @param flow_rate_curve Optional: string:
+#' @example man/examples/ex_prj_flow_and_temperature_control.R
+#' @export
r2ogs6_flow_and_temperature_control <- function(type,
flow_rate = NULL,
temperature_curve = NULL,
@@ -146,15 +148,16 @@ new_r2ogs6_flow_and_temperature_control <- function(type,
#===== r2ogs6_pipes =====
-#'r2ogs6_pipes
-#'@description tag: pipes
-#'@param longitudinal_dispersion_length string | double:
-#'@param inlet Optional: list:
-#'@param outlet Optional: list:
-#'@param distance_between_pipes Optional: string | double:
-#'@param outer Optional: list:
-#'@param inner Optional: list:
-#'@export
+#' r2ogs6_pipes
+#' @description tag: pipes
+#' @param longitudinal_dispersion_length string | double:
+#' @param inlet Optional: list:
+#' @param outlet Optional: list:
+#' @param distance_between_pipes Optional: string | double:
+#' @param outer Optional: list:
+#' @param inner Optional: list:
+#' @example man/examples/ex_prj_pipes.R
+#' @export
r2ogs6_pipes <- function(longitudinal_dispersion_length,
inlet = NULL,
outlet = NULL,
@@ -213,4 +216,4 @@ new_r2ogs6_pipes <- function(longitudinal_dispersion_length,
),
class = "r2ogs6_pipes"
)
-}
\ No newline at end of file
+}
diff --git a/R/prj_chemical_system.R b/R/prj_chemical_system.R
index eb16116b1f38724ecb1fc06d7f9d25fac3e32278..66b455d45d519c1e725291e9c9d348830c6a8a3d 100644
--- a/R/prj_chemical_system.R
+++ b/R/prj_chemical_system.R
@@ -2,19 +2,20 @@
#===== r2ogs6_chemical_system =====
-#'r2ogs6_chemical_system
-#'@description tag: chemical_system
-#'@param chemical_solver string:
-#'@param database string:
-#'@param solution r2ogs6_solution:
-#'@param mesh Optional: string:
-#'@param knobs Optional: list:
-#'@param kinetic_reactants Optional: list, r2ogs6_kinetic_reactant:
-#'@param rates Optional: list, r2ogs6_rate:
-#'@param equilibrium_reactants Optional: list, r2ogs6_phase_component:
-#'@param surface Optional:
-#'@param user_punch Optional:
-#'@export
+#' r2ogs6_chemical_system
+#' @description tag: chemical_system
+#' @param chemical_solver string:
+#' @param database string:
+#' @param solution r2ogs6_solution:
+#' @param mesh Optional: string:
+#' @param knobs Optional: list:
+#' @param kinetic_reactants Optional: list, r2ogs6_kinetic_reactant:
+#' @param rates Optional: list, r2ogs6_rate:
+#' @param equilibrium_reactants Optional: list, r2ogs6_phase_component:
+#' @param surface Optional:
+#' @param user_punch Optional:
+#' @example man/examples/ex_prj_chemical_system.R
+#' @export
r2ogs6_chemical_system <- function(chemical_solver,
database,
solution,
@@ -106,14 +107,15 @@ new_r2ogs6_chemical_system <- function(chemical_solver,
#===== r2ogs6_solution =====
-#'r2ogs6_solution
-#'@description tag: solution
-#'@param temperature string | double: Temperature
-#'@param pressure string | double: Pressure
-#'@param pe string | double: pe
-#'@param components list: Components
-#'@param charge_balance Optional: string: Charge balance
-#'@export
+#' r2ogs6_solution
+#' @description tag: solution
+#' @param temperature string | double: Temperature
+#' @param pressure string | double: Pressure
+#' @param pe string | double: pe
+#' @param components list: Components
+#' @param charge_balance Optional: string: Charge balance
+#' @example man/examples/ex_prj_solution.R
+#' @export
r2ogs6_solution <- function(temperature,
pressure,
pe,
@@ -168,12 +170,13 @@ new_r2ogs6_solution <- function(temperature,
#===== r2ogs6_phase_component =====
-#'r2ogs6_phase_component
-#'@description S3 class describing .prj phase_component
-#'@param name The component name
-#'@param saturation_index The saturation index of the component
-#'@param initial_amount optional: The initial amount of the component
-#'@export
+#' r2ogs6_phase_component
+#' @description S3 class describing .prj phase_component
+#' @param name The component name
+#' @param saturation_index The saturation index of the component
+#' @param initial_amount optional: The initial amount of the component
+#' @example man/examples/ex_prj_phase_component.R
+#' @export
r2ogs6_phase_component <- function(name,
saturation_index,
initial_amount = NULL) {
@@ -214,17 +217,18 @@ new_r2ogs6_phase_component <- function(name,
#===== r2ogs6_kinetic_reactant =====
-#'r2ogs6_kinetic_reactant
-#'@description S3 class describing .prj kinetic_reactant
-#'@param name The component name
-#'@param initial_amount The initial amount of the component
-#'@param chemical_formula The chemical formula of the component
-#'@param fix_amount Should the amount be fixed or not?
-#'@export
+#' r2ogs6_kinetic_reactant
+#' @description S3 class describing .prj kinetic_reactant
+#' @param name The component name
+#' @param initial_amount The initial amount of the component
+#' @param chemical_formula The chemical formula of the component
+#' @param fix_amount Should the amount be fixed or not?
+#' @example man/examples/ex_prj_kinetic_reactant.R
+#' @export
r2ogs6_kinetic_reactant <- function(name,
- initial_amount = NULL,
- chemical_formula = NULL,
- fix_amount = NULL) {
+ initial_amount = NULL,
+ chemical_formula = NULL,
+ fix_amount = NULL) {
#Coerce input
initial_amount <- coerce_string_to_numeric(initial_amount)
@@ -264,11 +268,12 @@ new_r2ogs6_kinetic_reactant <- function(name,
#===== r2ogs6_rate =====
-#'r2ogs6_rate
-#'@description S3 class describing .prj rate
-#'@param kinetic_reactant string: References a kinetic_reactant object
-#'@param expression character: Statements
-#'@export
+#' r2ogs6_rate
+#' @description S3 class describing .prj rate
+#' @param kinetic_reactant string: References a kinetic_reactant object
+#' @param expression character: Statements
+#' @example man/examples/ex_prj_rate.R
+#' @export
r2ogs6_rate <- function(kinetic_reactant,
expression) {
diff --git a/R/prj_curve.R b/R/prj_curve.R
index 274c63bfe0d2a0d59b62f2587df1f9f4e148305b..a6d06a73d477f860651d533f9ce20967d88a2f3b 100644
--- a/R/prj_curve.R
+++ b/R/prj_curve.R
@@ -2,13 +2,14 @@
#===== r2ogs6_curve =====
-#'r2ogs6_curve
-#'@description tag: curve, a curve
-#'@param name string: Name of the curve
-#'@param coords string | numeric: Coordinates at which the curve's values
-#' are given
-#'@param values string | numeric: Values of the curve at the given coordinates
-#'@export
+#' r2ogs6_curve
+#' @description tag: curve, a curve
+#' @param name string: Name of the curve
+#' @param coords string | numeric: Coordinates at which the curve's values
+#' are given
+#' @param values string | numeric: Values of the curve at the given coordinates
+#' @example man/examples/ex_prj_curve.R
+#' @export
r2ogs6_curve <- function(name, coords, values){
#Coerce input
diff --git a/R/prj_insitu.R b/R/prj_insitu.R
index 8309023e3a6ef96b8e3d62ac26468111bde73085..c97f53544769314d88079bf290cdea0ede56002c 100644
--- a/R/prj_insitu.R
+++ b/R/prj_insitu.R
@@ -2,10 +2,11 @@
#===== r2ogs6_insitu =====
-#'r2ogs6_insitu
-#'@description tag: insitu
-#'@param scripts character: Script names
-#'@export
+#' r2ogs6_insitu
+#' @description tag: insitu
+#' @param scripts character: Script names
+#' @example man/examples/ex_prj_insitu.R
+#' @export
r2ogs6_insitu <- function(scripts) {
#Make this more user friendly
diff --git a/R/prj_linear_solver.R b/R/prj_linear_solver.R
index fdde0e88752c15a77a4127f48640251daf0d5a90..801b4ef4670de884269ca625a347c31193913d90 100644
--- a/R/prj_linear_solver.R
+++ b/R/prj_linear_solver.R
@@ -2,13 +2,14 @@
#===== r2ogs6_linear_solver =====
-#'r2ogs6_linear_solver
-#'@description tag: linear_solver
-#'@param name string: The name of the linear solver
-#'@param eigen Optional: list: ...
-#'@param lis Optional: string: ...
-#'@param petsc Optional: character: ...
-#'@export
+#' r2ogs6_linear_solver
+#' @description tag: linear_solver
+#' @param name string: The name of the linear solver
+#' @param eigen Optional: list: ...
+#' @param lis Optional: string: ...
+#' @param petsc Optional: character: ...
+#' @example man/examples/ex_prj_linear_solver.R
+#' @export
r2ogs6_linear_solver <- function(name,
eigen = NULL,
lis = NULL,
@@ -60,15 +61,16 @@ new_r2ogs6_linear_solver <- function(name,
#===== r2ogs6_eigen =====
-#'r2ogs6_eigen
-#'@description tag: eigen
-#'@param solver_type string:
-#'@param precon_type Optional: string:
-#'@param max_iteration_step Optional: string | double: ...
-#'@param error_tolerance Optional: string | double: ...
-#'@param scaling Optional: string | double: ...
-#'@param restart Optional: string | double: ...
-#'@export
+#' r2ogs6_eigen
+#' @description tag: eigen
+#' @param solver_type string:
+#' @param precon_type Optional: string:
+#' @param max_iteration_step Optional: string | double: ...
+#' @param error_tolerance Optional: string | double: ...
+#' @param scaling Optional: string | double: ...
+#' @param restart Optional: string | double: ...
+#' @example man/examples/ex_prj_eigen.R
+#' @export
r2ogs6_eigen <- function(solver_type,
precon_type = NULL,
max_iteration_step = NULL,
diff --git a/R/prj_local_coordinate_system.R b/R/prj_local_coordinate_system.R
index 2e558fc47992f8f8281056242efce83ff1bbfd60..fd2d5952f7d01b068268b26976200d7c7cbddebb 100644
--- a/R/prj_local_coordinate_system.R
+++ b/R/prj_local_coordinate_system.R
@@ -1,10 +1,11 @@
-#'r2ogs6_local_coordinate_system
-#'@description tag: local_coordinate_system
-#'@param basis_vector_0 string | double: A basis vector
-#'@param basis_vector_1 string | double: A basis vector
-#'@param basis_vector_2 Optional: string | double: A basis vector
-#'@export
+#' r2ogs6_local_coordinate_system
+#' @description tag: local_coordinate_system
+#' @param basis_vector_0 string | double: A basis vector
+#' @param basis_vector_1 string | double: A basis vector
+#' @param basis_vector_2 Optional: string | double: A basis vector
+#' @example man/examples/ex_prj_local_coordinate_system.R
+#' @export
r2ogs6_local_coordinate_system <- function(basis_vector_0,
basis_vector_1,
basis_vector_2 = NULL) {
@@ -35,4 +36,4 @@ new_r2ogs6_local_coordinate_system <- function(basis_vector_0,
),
class = "r2ogs6_local_coordinate_system"
)
-}
\ No newline at end of file
+}
diff --git a/R/prj_material_property.R b/R/prj_material_property.R
index 57873a995c3cb8afb31ac3df9df56e49a53c8acb..b3336252450f2fad14d6bb99e0ba949cbbb0d25f 100644
--- a/R/prj_material_property.R
+++ b/R/prj_material_property.R
@@ -2,11 +2,12 @@
#===== r2ogs6_material_property =====
-#'r2ogs6_material_property
-#'@description tag: material_property
-#'@param fluid r2ogs6_fluid:
-#'@param porous_medium r2ogs6_porous_medium:
-#'@export
+#' r2ogs6_material_property
+#' @description tag: material_property
+#' @param fluid r2ogs6_fluid:
+#' @param porous_medium r2ogs6_porous_medium:
+#' @example man/examples/ex_prj_material_property.R
+#' @export
r2ogs6_material_property <- function(fluid,
porous_medium) {
@@ -38,19 +39,20 @@ new_r2ogs6_material_property <- function(fluid,
#===== r2ogs6_fluid =====
-#'r2ogs6_fluid
-#'@description tag: fluid
-#'@param liquid_density list:
-#'@param gas_density list:
-#'@param liquid_viscosity list:
-#'@param gas_viscosity list:
-#'@param specific_heat_capacity_solid Optional:
-#'@param specific_heat_capacity_water Optional:
-#'@param specific_heat_capacity_air Optional:
-#'@param specific_heat_capacity_water_vapor Optional:
-#'@param thermal_conductivity_dry_solid Optional:
-#'@param thermal_conductivity_wet_solid Optional:
-#'@export
+#' r2ogs6_fluid
+#' @description tag: fluid
+#' @param liquid_density list:
+#' @param gas_density list:
+#' @param liquid_viscosity list:
+#' @param gas_viscosity list:
+#' @param specific_heat_capacity_solid Optional:
+#' @param specific_heat_capacity_water Optional:
+#' @param specific_heat_capacity_air Optional:
+#' @param specific_heat_capacity_water_vapor Optional:
+#' @param thermal_conductivity_dry_solid Optional:
+#' @param thermal_conductivity_wet_solid Optional:
+#' @example man/examples/ex_prj_fluid.R
+#' @export
r2ogs6_fluid <- function(liquid_density,
gas_density,
liquid_viscosity,
diff --git a/R/prj_medium.R b/R/prj_medium.R
index 4530511a1ba1a79d403efd877be53f8b3e52f2da..524fe18f6dcc36a82e8a84076f1327d83b9ef06c 100644
--- a/R/prj_medium.R
+++ b/R/prj_medium.R
@@ -2,13 +2,14 @@
#===== r2ogs6_medium =====
-#'r2ogs6_medium
-#'@description tag: medium, a specific medium with optional id corresponding
-#' to the MaterialIDs
-#'@param phases list, r2ogs6_phase: Optional: Medium phases
-#'@param properties list, r2ogs6_pr_property: Optional: Medium properties
-#'@param id string | double: Optional: ID corresponding to the MaterialIDs
-#'@export
+#' r2ogs6_medium
+#' @description tag: medium, a specific medium with optional id corresponding
+#' to the MaterialIDs
+#' @param phases list, r2ogs6_phase: Optional: Medium phases
+#' @param properties list, r2ogs6_pr_property: Optional: Medium properties
+#' @param id string | double: Optional: ID corresponding to the MaterialIDs
+#' @example man/examples/ex_prj_medium.R
+#' @export
r2ogs6_medium <- function(phases = NULL,
properties = NULL,
id = NULL) {
@@ -54,42 +55,43 @@ new_r2ogs6_medium <- function(phases = NULL,
#===== r2ogs6_pr_property =====
-#'r2ogs6_pr_property
-#'@description tag: property
-#'@param name string:
-#'@param type string:
-#'@param value Optional:
-#'@param parameter_name Optional:
-#'@param exponent Optional:
-#'@param residual_liquid_saturation Optional:
-#'@param residual_gas_saturation Optional:
-#'@param p_b Optional:
-#'@param independent_variable Optional:
-#'@param curve Optional:
-#'@param minimum_relative_permeability_liquid Optional:
-#'@param initial_permeability Optional:
-#'@param maximum_permeability Optional:
-#'@param lambda Optional:
-#'@param cutoff_value Optional:
-#'@param intrinsic_permeability Optional:
-#'@param initial_aperture Optional:
-#'@param mean_frac_distance Optional:
-#'@param threshold_strain Optional:
-#'@param fracture_normal Optional:
-#'@param reference_permeability Optional:
-#'@param fitting_factor Optional:
-#'@param cohesion Optional:
-#'@param friction_angle Optional:
-#'@param tensile_strength_parameter Optional:
-#'@param b1 Optional:
-#'@param b2 Optional:
-#'@param b3 Optional:
-#'@param minimum_permeability Optional:
-#'@param initial_porosity Optional:
-#'@param entry_pressure Optional:
-#'@param min_relative_permeability_liquid Optional:
-#'@param min_relative_permeability_gas Optional:
-#'@export
+#' r2ogs6_pr_property
+#' @description tag: property
+#' @param name string:
+#' @param type string:
+#' @param value Optional:
+#' @param parameter_name Optional:
+#' @param exponent Optional:
+#' @param residual_liquid_saturation Optional:
+#' @param residual_gas_saturation Optional:
+#' @param p_b Optional:
+#' @param independent_variable Optional:
+#' @param curve Optional:
+#' @param minimum_relative_permeability_liquid Optional:
+#' @param initial_permeability Optional:
+#' @param maximum_permeability Optional:
+#' @param lambda Optional:
+#' @param cutoff_value Optional:
+#' @param intrinsic_permeability Optional:
+#' @param initial_aperture Optional:
+#' @param mean_frac_distance Optional:
+#' @param threshold_strain Optional:
+#' @param fracture_normal Optional:
+#' @param reference_permeability Optional:
+#' @param fitting_factor Optional:
+#' @param cohesion Optional:
+#' @param friction_angle Optional:
+#' @param tensile_strength_parameter Optional:
+#' @param b1 Optional:
+#' @param b2 Optional:
+#' @param b3 Optional:
+#' @param minimum_permeability Optional:
+#' @param initial_porosity Optional:
+#' @param entry_pressure Optional:
+#' @param min_relative_permeability_liquid Optional:
+#' @param min_relative_permeability_gas Optional:
+#' @example man/examples/ex_prj_pr_property.R
+#' @export
r2ogs6_pr_property <- function(name,
type,
value = NULL,
@@ -292,12 +294,12 @@ new_r2ogs6_pr_property <- function(name,
}
-#'ogs_get_medium_property
-#'@description Returns a medium property based on the property name
-#'@param medium r2ogs6_medium
-#'@param name string: The property name
-#'@return r2ogs6_pr_property
-#'@export
+#' ogs_get_medium_property
+#' @description Returns a medium property based on the property name
+#' @param medium r2ogs6_medium
+#' @param name string: The property name
+#' @return r2ogs6_pr_property
+#' @export
ogs_get_medium_property <- function(medium, name){
assertthat::assert_that(class(medium) == "r2ogs6_medium")
@@ -313,13 +315,14 @@ ogs_get_medium_property <- function(medium, name){
#===== r2ogs6_phase =====
-#'r2ogs6_phase
-#'@description tag: phase, a coherent material with homogeneous properties
-#'@param type string: Phase type
-#' (get valid types with get_valid_phase_types())
-#'@param properties list, r2ogs6_pr_property: Properties
-#'@param components list, components
-#'@export
+#' r2ogs6_phase
+#' @description tag: phase, a coherent material with homogeneous properties
+#' @param type string: Phase type
+#' (get valid types with get_valid_phase_types())
+#' @param properties list, r2ogs6_pr_property: Properties
+#' @param components list, components
+#' @example man/examples/ex_prj_phase.R
+#' @export
r2ogs6_phase <- function(type,
properties = NULL,
components = NULL){
@@ -375,25 +378,26 @@ get_valid_phase_types <- function(){
#===== r2ogs6_ph_property =====
-#'r2ogs6_ph_property
-#'@description tag: property
-#'@param name string: Property name
-#'@param type string: Property type
-#'@param value Optional: string | double: ...
-#'@param reference_value Optional: string | double:
-#'@param initial_porosity Optional: string:
-#'@param minimal_porosity Optional: string | double:
-#'@param maximal_porosity Optional: string | double:
-#'@param parameter_name Optional: string:
-#'@param exponents Optional: string | numeric:
-#'@param offset Optional: string | double:
-#'@param exponent Optional: list:
-#'@param swelling_pressures Optional: string | numeric:
-#'@param lower_saturation_limit Optional: string | double:
-#'@param upper_saturation_limit Optional: string | double:
-#'@param intrinsic_permeabilities Optional: string | numeric:
-#'@param ... independent_variable
-#'@export
+#' r2ogs6_ph_property
+#' @description tag: property
+#' @param name string: Property name
+#' @param type string: Property type
+#' @param value Optional: string | double: ...
+#' @param reference_value Optional: string | double:
+#' @param initial_porosity Optional: string:
+#' @param minimal_porosity Optional: string | double:
+#' @param maximal_porosity Optional: string | double:
+#' @param parameter_name Optional: string:
+#' @param exponents Optional: string | numeric:
+#' @param offset Optional: string | double:
+#' @param exponent Optional: list:
+#' @param swelling_pressures Optional: string | numeric:
+#' @param lower_saturation_limit Optional: string | double:
+#' @param upper_saturation_limit Optional: string | double:
+#' @param intrinsic_permeabilities Optional: string | numeric:
+#' @param ... independent_variable
+#' @example man/examples/ex_prj_ph_property.R
+#' @export
r2ogs6_ph_property <- function(name,
type,
value = NULL,
@@ -537,11 +541,12 @@ new_r2ogs6_ph_property <- function(name,
#===== r2ogs6_component =====
-#'r2ogs6_component
-#'@description tag: component
-#'@param name string:
-#'@param properties list, r2ogs6_com_property:
-#'@export
+#' r2ogs6_component
+#' @description tag: component
+#' @param name string:
+#' @param properties list, r2ogs6_com_property:
+#' @example man/examples/ex_prj_component.R
+#' @export
r2ogs6_component <- function(name,
properties){
@@ -577,13 +582,14 @@ new_r2ogs6_component <- function(name,
#===== r2ogs6_com_property =====
-#'r2ogs6_com_property
-#'@description tag: property
-#'@param name string: Property name
-#'@param type string: Property type
-#'@param value Optional: string | double: ...
-#'@param parameter_name Optional:
-#'@export
+#' r2ogs6_com_property
+#' @description tag: property
+#' @param name string: Property name
+#' @param type string: Property type
+#' @param value Optional: string | double: ...
+#' @param parameter_name Optional:
+#' @example man/examples/ex_prj_com_property.R
+#' @export
r2ogs6_com_property <- function(name,
type,
value = NULL,
diff --git a/R/prj_nonlinear_solver.R b/R/prj_nonlinear_solver.R
index 7f137b8a8d503354965fbd54e076d253a8621ded..a5107372f7ebea26df70f6018790dad4cd594150 100644
--- a/R/prj_nonlinear_solver.R
+++ b/R/prj_nonlinear_solver.R
@@ -2,14 +2,15 @@
#===== r2ogs6_nonlinear_solver =====
-#'r2ogs6_nonlinear_solver
-#'@description tag: nonlinear_solver
-#'@param name string: Name
-#'@param type string: Type
-#'@param max_iter string | double: Maximal number of iterations
-#'@param linear_solver string: Name of corresponding linear_solver
-#'@param damping Optional: string | double: Damping
-#'@export
+#' r2ogs6_nonlinear_solver
+#' @description tag: nonlinear_solver
+#' @param name string: Name
+#' @param type string: Type
+#' @param max_iter string | double: Maximal number of iterations
+#' @param linear_solver string: Name of corresponding linear_solver
+#' @param damping Optional: string | double: Damping
+#' @example man/examples/ex_prj_nonlinear_solver.R
+#' @export
r2ogs6_nonlinear_solver <- function(name,
type,
max_iter,
diff --git a/R/prj_parameter.R b/R/prj_parameter.R
index 19f2729902fcb81ddade088a6f89e0ae46a5e24f..af27cbecf9edc354656db581f127ec22d2fcd415 100644
--- a/R/prj_parameter.R
+++ b/R/prj_parameter.R
@@ -2,22 +2,23 @@
#===== r2ogs6_parameter =====
-#'r2ogs6_parameter
-#'@description tag: parameter
-#'@param name string:
-#'@param type string:
-#'@param value Optional: string | double: Parameter value
-#'@param values Optional: string | double: Parameter values
-#'@param curve Optional: string:
-#'@param parameter Optional: string:
-#'@param group_id_property Optional: string:
-#'@param field_name Optional: string:
-#'@param mesh Optional: string:
-#'@param time_series Optional: list:
-#'@param use_local_coordinate_system Optional: string, "true" | "false":
-#'@param ... Optional: for index_values and expression tags (since there can be
+#' r2ogs6_parameter
+#' @description tag: parameter
+#' @param name string:
+#' @param type string:
+#' @param value Optional: string | double: Parameter value
+#' @param values Optional: string | double: Parameter values
+#' @param curve Optional: string:
+#' @param parameter Optional: string:
+#' @param group_id_property Optional: string:
+#' @param field_name Optional: string:
+#' @param mesh Optional: string:
+#' @param time_series Optional: list:
+#' @param use_local_coordinate_system Optional: string, "true" | "false":
+#' @param ... Optional: for index_values and expression tags (since there can be
#' multiple)
-#'@export
+#' @example man/examples/ex_prj_parameter.R
+#' @export
r2ogs6_parameter <- function(name,
type,
value = NULL,
diff --git a/R/prj_porous_medium.R b/R/prj_porous_medium.R
index ad05b5ce4ff00dd8f9906200263ffb74b7c05bf7..9f66b13ba839b9395d11720c47c4e7a5418b9529 100644
--- a/R/prj_porous_medium.R
+++ b/R/prj_porous_medium.R
@@ -2,15 +2,16 @@
#===== r2ogs6_porous_medium =====
-#'r2ogs6_porous_medium
-#'@description tag: porous_medium
-#'@param id string | double:
-#'@param permeability list:
-#'@param porosity list:
-#'@param storage list:
-#'@param capillary_pressure r2ogs6_capillary_pressure:
-#'@param relative_permeability list:
-#'@export
+#' r2ogs6_porous_medium
+#' @description tag: porous_medium
+#' @param id string | double:
+#' @param permeability list:
+#' @param porosity list:
+#' @param storage list:
+#' @param capillary_pressure r2ogs6_capillary_pressure:
+#' @param relative_permeability list:
+#' @example man/examples/ex_prj_porous_medium.R
+#' @export
r2ogs6_porous_medium <- function(id,
permeability,
porosity,
@@ -80,17 +81,18 @@ new_r2ogs6_porous_medium <- function(id,
#===== r2ogs6_capillary_pressure =====
-#'r2ogs6_capillary_pressure
-#'@description tag: capillary_pressure
-#'@param type string:
-#'@param pd Optional: string | double:
-#'@param sr Optional: string | double:
-#'@param smax Optional: string | double:
-#'@param m Optional: string | double:
-#'@param pc_max Optional: string | double:
-#'@param has_regularized Optional: string, "true" | "false":
-#'@param curve Optional: list:
-#'@export
+#' r2ogs6_capillary_pressure
+#' @description tag: capillary_pressure
+#' @param type string:
+#' @param pd Optional: string | double:
+#' @param sr Optional: string | double:
+#' @param smax Optional: string | double:
+#' @param m Optional: string | double:
+#' @param pc_max Optional: string | double:
+#' @param has_regularized Optional: string, "true" | "false":
+#' @param curve Optional: list:
+#' @example man/examples/ex_prj_capillary_pressure.R
+#' @export
r2ogs6_capillary_pressure <- function(type,
pd = NULL,
sr = NULL,
@@ -177,14 +179,16 @@ new_r2ogs6_capillary_pressure <- function(type,
#===== r2ogs6_relative_permeability =====
-#'r2ogs6_relative_permeability
-#'@description tag: relative_permeability
-#'@param type string:
-#'@param sr string | number:
-#'@param smax string | number:
-#'@param m string | number:
-#'@param krel_min string | number:
-#'@param id string: Optional:
+#' r2ogs6_relative_permeability
+#' @description tag: relative_permeability
+#' @param type string:
+#' @param sr string | number:
+#' @param smax string | number:
+#' @param m string | number:
+#' @param krel_min string | number:
+#' @param id string: Optional:
+#' @example man/examples/ex_prj_relative_permeability.R
+#' @export
r2ogs6_relative_permeability <- function(type,
sr,
smax,
diff --git a/R/prj_process.R b/R/prj_process.R
index 3a624ab7eff3dc9ee44ec9dc10b40e7f4b03cfd0..fb6573ef183e6cb14c7026bba2028ce637ddd489 100644
--- a/R/prj_process.R
+++ b/R/prj_process.R
@@ -2,78 +2,79 @@
#===== r2ogs6_process =====
-#'r2ogs6_process
-#'@description tag: process (parent tag: processes)
-#'@param name string:
-#'@param type string:
-#'@param integration_order string | double:
-#'@param process_variables list, character:
-#'@param secondary_variables Optional:
-#'@param specific_body_force Optional:
-#'@param solid_density Optional:
-#'@param dimension Optional:
-#'@param coupling_scheme Optional:
-#'@param reference_solid_density Optional:
-#'@param linear_thermal_expansion_coefficient Optional:
-#'@param specific_heat_capacity Optional:
-#'@param thermal_conductivity Optional:
-#'@param darcy_gravity Optional:
-#'@param reference_temperature Optional:
-#'@param fracture_model Optional:
-#'@param jacobian_assembler Optional:
-#'@param internal_length Optional:
-#'@param mass_lumping Optional:
-#'@param porosity Optional:
-#'@param calculatesurfaceflux Optional:
-#'@param intrinsic_permeability Optional:
-#'@param specific_storage Optional:
-#'@param fluid_viscosity Optional:
-#'@param biot_coefficient Optional:
-#'@param fluid_density Optional:
-#'@param initial_effective_stress Optional:
-#'@param initial_fracture_effective_stress Optional:
-#'@param phasefield_parameters Optional:
-#'@param deactivate_matrix_in_flow Optional:
-#'@param borehole_heat_exchangers Optional:
-#'@param temperature Optional:
-#'@param reactive_system Optional:
-#'@param fluid_specific_heat_source Optional:
-#'@param fluid_specific_isobaric_heat_capacity Optional:
-#'@param solid_hydraulic_permeability Optional:
-#'@param solid_specific_heat_source Optional:
-#'@param solid_heat_conductivity Optional:
-#'@param solid_specific_isobaric_heat_capacity Optional:
-#'@param tortuosity Optional:
-#'@param diffusion_coefficient Optional:
-#'@param solid_density_dry Optional:
-#'@param solid_density_initial Optional:
-#'@param characteristic_pressure Optional:
-#'@param characteristic_temperature Optional:
-#'@param characteristic_vapour_mass_fraction Optional:
-#'@param output_element_matrices Optional:
-#'@param material_property Optional:
-#'@param diffusion_coeff_component_b Optional:
-#'@param diffusion_coeff_component_a Optional:
-#'@param hydro_crack_scheme Optional:
-#'@param at_num Optional:
-#'@param initial_stress Optional:
-#'@param split_method Optional:
-#'@param reg_param Optional:
-#'@param thermal_parameters Optional:
-#'@param non_advective_form Optional:
-#'@param fluid Optional:
-#'@param porous_medium Optional:
-#'@param decay_rate Optional:
-#'@param fluid_reference_density Optional:
-#'@param retardation_factor Optional:
-#'@param solute_dispersivity_longitudinal Optional:
-#'@param solute_dispersivity_transverse Optional:
-#'@param molecular_diffusion_coefficient Optional:
-#'@param density_solid Optional:
-#'@param latent_heat_evaporation Optional:
-#'@param pf_irrv Optional:
-#'@param ... Optional: fracture_properties, constitutive_relation
-#'@export
+#' r2ogs6_process
+#' @description tag: process (parent tag: processes)
+#' @param name string:
+#' @param type string:
+#' @param integration_order string | double:
+#' @param process_variables list, character:
+#' @param secondary_variables Optional:
+#' @param specific_body_force Optional:
+#' @param solid_density Optional:
+#' @param dimension Optional:
+#' @param coupling_scheme Optional:
+#' @param reference_solid_density Optional:
+#' @param linear_thermal_expansion_coefficient Optional:
+#' @param specific_heat_capacity Optional:
+#' @param thermal_conductivity Optional:
+#' @param darcy_gravity Optional:
+#' @param reference_temperature Optional:
+#' @param fracture_model Optional:
+#' @param jacobian_assembler Optional:
+#' @param internal_length Optional:
+#' @param mass_lumping Optional:
+#' @param porosity Optional:
+#' @param calculatesurfaceflux Optional:
+#' @param intrinsic_permeability Optional:
+#' @param specific_storage Optional:
+#' @param fluid_viscosity Optional:
+#' @param biot_coefficient Optional:
+#' @param fluid_density Optional:
+#' @param initial_effective_stress Optional:
+#' @param initial_fracture_effective_stress Optional:
+#' @param phasefield_parameters Optional:
+#' @param deactivate_matrix_in_flow Optional:
+#' @param borehole_heat_exchangers Optional:
+#' @param temperature Optional:
+#' @param reactive_system Optional:
+#' @param fluid_specific_heat_source Optional:
+#' @param fluid_specific_isobaric_heat_capacity Optional:
+#' @param solid_hydraulic_permeability Optional:
+#' @param solid_specific_heat_source Optional:
+#' @param solid_heat_conductivity Optional:
+#' @param solid_specific_isobaric_heat_capacity Optional:
+#' @param tortuosity Optional:
+#' @param diffusion_coefficient Optional:
+#' @param solid_density_dry Optional:
+#' @param solid_density_initial Optional:
+#' @param characteristic_pressure Optional:
+#' @param characteristic_temperature Optional:
+#' @param characteristic_vapour_mass_fraction Optional:
+#' @param output_element_matrices Optional:
+#' @param material_property Optional:
+#' @param diffusion_coeff_component_b Optional:
+#' @param diffusion_coeff_component_a Optional:
+#' @param hydro_crack_scheme Optional:
+#' @param at_num Optional:
+#' @param initial_stress Optional:
+#' @param split_method Optional:
+#' @param reg_param Optional:
+#' @param thermal_parameters Optional:
+#' @param non_advective_form Optional:
+#' @param fluid Optional:
+#' @param porous_medium Optional:
+#' @param decay_rate Optional:
+#' @param fluid_reference_density Optional:
+#' @param retardation_factor Optional:
+#' @param solute_dispersivity_longitudinal Optional:
+#' @param solute_dispersivity_transverse Optional:
+#' @param molecular_diffusion_coefficient Optional:
+#' @param density_solid Optional:
+#' @param latent_heat_evaporation Optional:
+#' @param pf_irrv Optional:
+#' @param ... Optional: fracture_properties, constitutive_relation
+#' @example man/examples/ex_prj_process.R
+#' @export
r2ogs6_process <- function(name,
type,
integration_order,
@@ -545,48 +546,50 @@ new_r2ogs6_process <- function(name,
#===== r2ogs6_constitutive_relation =====
-#'r2ogs6_constitutive_relation
-#'@description tag: constitutive_relation
-#'@param type string:
-#'@param id Optional:
-#'@param youngs_modulus Optional:
-#'@param poissons_ratio Optional:
-#'@param nonlinear_solver Optional:
-#'@param behaviour Optional:
-#'@param material_properties Optional:
-#'@param shear_modulus Optional:
-#'@param bulk_modulus Optional:
-#'@param kappa Optional:
-#'@param beta Optional:
-#'@param gamma Optional:
-#'@param hardening_modulus Optional:
-#'@param alpha Optional:
-#'@param delta Optional:
-#'@param eps Optional:
-#'@param m Optional:
-#'@param alphap Optional:
-#'@param deltap Optional:
-#'@param epsp Optional:
-#'@param mp Optional:
-#'@param betap Optional:
-#'@param gammap Optional:
-#'@param tangent_type Optional:
-#'@param damage_properties Optional:
-#'@param youngs_moduli Optional:
-#'@param shear_moduli Optional:
-#'@param poissons_ratios Optional:
-#'@param a Optional:
-#'@param n Optional:
-#'@param sigma0 Optional:
-#'@param q Optional:
-#'@param kelvin_shear_modulus Optional:
-#'@param kelvin_viscosity Optional:
-#'@param maxwell_shear_modulus Optional:
-#'@param maxwell_bulk_modulus Optional:
-#'@param maxwell_viscosity Optional:
-#'@param dependency_parameter_mk Optional:
-#'@param dependency_parameter_mvk Optional:
-#'@param dependency_parameter_mvm Optional:
+#' r2ogs6_constitutive_relation
+#' @description tag: constitutive_relation
+#' @param type string:
+#' @param id Optional:
+#' @param youngs_modulus Optional:
+#' @param poissons_ratio Optional:
+#' @param nonlinear_solver Optional:
+#' @param behaviour Optional:
+#' @param material_properties Optional:
+#' @param shear_modulus Optional:
+#' @param bulk_modulus Optional:
+#' @param kappa Optional:
+#' @param beta Optional:
+#' @param gamma Optional:
+#' @param hardening_modulus Optional:
+#' @param alpha Optional:
+#' @param delta Optional:
+#' @param eps Optional:
+#' @param m Optional:
+#' @param alphap Optional:
+#' @param deltap Optional:
+#' @param epsp Optional:
+#' @param mp Optional:
+#' @param betap Optional:
+#' @param gammap Optional:
+#' @param tangent_type Optional:
+#' @param damage_properties Optional:
+#' @param youngs_moduli Optional:
+#' @param shear_moduli Optional:
+#' @param poissons_ratios Optional:
+#' @param a Optional:
+#' @param n Optional:
+#' @param sigma0 Optional:
+#' @param q Optional:
+#' @param kelvin_shear_modulus Optional:
+#' @param kelvin_viscosity Optional:
+#' @param maxwell_shear_modulus Optional:
+#' @param maxwell_bulk_modulus Optional:
+#' @param maxwell_viscosity Optional:
+#' @param dependency_parameter_mk Optional:
+#' @param dependency_parameter_mvk Optional:
+#' @param dependency_parameter_mvm Optional:
+#' @example man/examples/ex_prj_constitutive_relation.R
+#' @export
r2ogs6_constitutive_relation <- function(type,
id = NULL,
youngs_modulus = NULL,
@@ -765,20 +768,21 @@ new_r2ogs6_constitutive_relation <- function(type,
#===== r2ogs6_fracture_model =====
-#'r2ogs6_fracture_model
-#'@description tag: fracture_model
-#'@param type string:
-#'@param normal_stiffness string:
-#'@param shear_stiffness string:
-#'@param penalty_aperture_cutoff string | double:
-#'@param tension_cutoff string | double:
-#'@param fracture_toughness Optional: string:
-#'@param peak_normal_traction Optional: string:
-#'@param friction_angle Optional: string:
-#'@param dilatancy_angle Optional: string:
-#'@param cohesion Optional: string:
-#'@param nonlinear_solver Optional: list:
-#'@export
+#' r2ogs6_fracture_model
+#' @description tag: fracture_model
+#' @param type string:
+#' @param normal_stiffness string:
+#' @param shear_stiffness string:
+#' @param penalty_aperture_cutoff string | double:
+#' @param tension_cutoff string | double:
+#' @param fracture_toughness Optional: string:
+#' @param peak_normal_traction Optional: string:
+#' @param friction_angle Optional: string:
+#' @param dilatancy_angle Optional: string:
+#' @param cohesion Optional: string:
+#' @param nonlinear_solver Optional: list:
+#' @example man/examples/ex_prj_fracture_model.R
+#' @export
r2ogs6_fracture_model <- function(type,
normal_stiffness,
shear_stiffness,
@@ -863,14 +867,15 @@ new_r2ogs6_fracture_model <- function(type,
#===== r2ogs6_fracture_properties =====
-#'r2ogs6_fracture_properties
-#'@description tag: fracture_properties
-#'@param material_id string | double:
-#'@param initial_aperture string:
-#'@param specific_storage Optional: string:
-#'@param biot_coefficient Optional: string:
-#'@param permeability_model Optional: list:
-#'@export
+#' r2ogs6_fracture_properties
+#' @description tag: fracture_properties
+#' @param material_id string | double:
+#' @param initial_aperture string:
+#' @param specific_storage Optional: string:
+#' @param biot_coefficient Optional: string:
+#' @param permeability_model Optional: list:
+#' @example man/examples/ex_prj_fracture_properties.R
+#' @export
r2ogs6_fracture_properties <- function(material_id,
initial_aperture,
specific_storage = NULL,
@@ -937,12 +942,13 @@ new_r2ogs6_fracture_properties <- function(material_id,
#===== r2ogs6_jacobian_assembler =====
-#'r2ogs6_jacobian_assembler
-#'@description tag: jacobian_assembler
-#'@param type string:
-#'@param component_magnitudes Optional: string | double:
-#'@param relative_epsilons Optional: string | double:
-#'@export
+#' r2ogs6_jacobian_assembler
+#' @description tag: jacobian_assembler
+#' @param type string:
+#' @param component_magnitudes Optional: string | double:
+#' @param relative_epsilons Optional: string | double:
+#' @example man/examples/ex_prj_jacobian_assembler.R
+#' @export
r2ogs6_jacobian_assembler <- function(type,
component_magnitudes = NULL,
relative_epsilons = NULL) {
@@ -981,14 +987,15 @@ new_r2ogs6_jacobian_assembler <- function(type,
#===== r2ogs6_phasefield_parameters =====
-#'r2ogs6_phasefield_parameters
-#'@description tag: phasefield_parameters
-#'@param residual_stiffness string:
-#'@param crack_resistance string:
-#'@param crack_length_scale string:
-#'@param kinetic_coefficient string:
-#'@param history_field Optional: string:
-#'@export
+#' r2ogs6_phasefield_parameters
+#' @description tag: phasefield_parameters
+#' @param residual_stiffness string:
+#' @param crack_resistance string:
+#' @param crack_length_scale string:
+#' @param kinetic_coefficient string:
+#' @param history_field Optional: string:
+#' @example man/examples/ex_prj_phasefield_parameters.R
+#' @export
r2ogs6_phasefield_parameters <- function(residual_stiffness,
crack_resistance,
crack_length_scale,
diff --git a/R/prj_process_variable.R b/R/prj_process_variable.R
index e4b95c118e6707f742ef2db32d6a4e74d5d476c4..30213a4513e42b5a57a2e21d6162d5ae19a8bf96 100644
--- a/R/prj_process_variable.R
+++ b/R/prj_process_variable.R
@@ -2,17 +2,18 @@
#===== r2ogs6_process_variable =====
-#'r2ogs6_process_variable
-#'@description tag: process_variable
-#'@param name string: The name of the process variable
-#'@param components string | double:
-#'@param order string | double:
-#'@param initial_condition string:
-#'@param boundary_conditions list, r2ogs6_boundary_condition:
-#'@param source_terms Optional: list, r2ogs6_source_term:
-#'@param mesh Optional: string: list:
-#'@param deactivated_subdomains Optional: list, r2ogs6_deactivated_subdomain:
-#'@export
+#' r2ogs6_process_variable
+#' @description tag: process_variable
+#' @param name string: The name of the process variable
+#' @param components string | double:
+#' @param order string | double:
+#' @param initial_condition string:
+#' @param boundary_conditions list, r2ogs6_boundary_condition:
+#' @param source_terms Optional: list, r2ogs6_source_term:
+#' @param mesh Optional: string: list:
+#' @param deactivated_subdomains Optional: list, r2ogs6_deactivated_subdomain:
+#' @example man/examples/ex_prj_process_variable.R
+#' @export
r2ogs6_process_variable <- function(name,
components,
order,
@@ -92,33 +93,34 @@ new_r2ogs6_process_variable <- function(name,
#===== r2ogs6_boundary_condition =====
-#'r2ogs6_boundary_condition
-#'@description tag: boundary_condition
-#'@param type string:
-#'@param parameter string:
-#'@param geometrical_set Optional: string:
-#'@param geometry Optional: string:
-#'@param component Optional: string | double:
-#'@param mesh Optional: string:
-#'@param alpha Optional: string:
-#'@param u_0 Optional: string:
-#'@param constraint_type Optional: string:
-#'@param constraining_process_variable Optional: string:
-#'@param constraint_threshold Optional: string | double:
-#'@param constraint_direction Optional: string:
-#'@param area_parameter Optional: string:
-#'@param bc_object Optional: string:
-#'@param flush_stdout Optional: string:
-#'@param property_name Optional: string:
-#'@param initial_value_parameter Optional: string:
-#'@param constant_name Optional: string:
-#'@param coefficient_current_variable_name Optional: string:
-#'@param coefficient_other_variable_name Optional: string:
-#'@param coefficient_mixed_variables_name Optional: string:
-#'@param threshold_parameter Optional: string:
-#'@param comparison_operator Optional: string:
-#'@param time_interval Optional: list of 2, character:
-#'@export
+#' r2ogs6_boundary_condition
+#' @description tag: boundary_condition
+#' @param type string:
+#' @param parameter string:
+#' @param geometrical_set Optional: string:
+#' @param geometry Optional: string:
+#' @param component Optional: string | double:
+#' @param mesh Optional: string:
+#' @param alpha Optional: string:
+#' @param u_0 Optional: string:
+#' @param constraint_type Optional: string:
+#' @param constraining_process_variable Optional: string:
+#' @param constraint_threshold Optional: string | double:
+#' @param constraint_direction Optional: string:
+#' @param area_parameter Optional: string:
+#' @param bc_object Optional: string:
+#' @param flush_stdout Optional: string:
+#' @param property_name Optional: string:
+#' @param initial_value_parameter Optional: string:
+#' @param constant_name Optional: string:
+#' @param coefficient_current_variable_name Optional: string:
+#' @param coefficient_other_variable_name Optional: string:
+#' @param coefficient_mixed_variables_name Optional: string:
+#' @param threshold_parameter Optional: string:
+#' @param comparison_operator Optional: string:
+#' @param time_interval Optional: list of 2, character:
+#' @example man/examples/ex_prj_boundary_condition.R
+#' @export
r2ogs6_boundary_condition <- function(type,
parameter = NULL,
geometrical_set = NULL,
@@ -275,15 +277,16 @@ new_r2ogs6_boundary_condition <- function(type,
#===== r2ogs6_source_term =====
-#'r2ogs6_source_term
-#'@description tag: source_term
-#'@param type string:
-#'@param parameter Optional: string:
-#'@param geometrical_set Optional: string:
-#'@param geometry Optional: string:
-#'@param mesh Optional: string:
-#'@param source_term_object Optional: string:
-#'@export
+#' r2ogs6_source_term
+#' @description tag: source_term
+#' @param type string:
+#' @param parameter Optional: string:
+#' @param geometrical_set Optional: string:
+#' @param geometry Optional: string:
+#' @param mesh Optional: string:
+#' @param source_term_object Optional: string:
+#' @example man/examples/ex_prj_source_term.R
+#' @export
r2ogs6_source_term <- function(type,
parameter = NULL,
geometrical_set = NULL,
@@ -312,10 +315,10 @@ new_r2ogs6_source_term <- function(type,
assertthat::assert_that(assertthat::is.string(type))
are_null_or_strings(parameter,
- geometrical_set,
- geometry,
- mesh,
- source_term_object)
+ geometrical_set,
+ geometry,
+ mesh,
+ source_term_object)
structure(list(type = type,
parameter = parameter,
@@ -336,11 +339,12 @@ new_r2ogs6_source_term <- function(type,
#===== r2ogs6_deactivated_subdomain =====
-#'r2ogs6_deactivated_subdomain
-#'@description tag: deactivated_subdomain
-#'@param time_interval list, numeric:
-#'@param material_ids string | double:
-#'@export
+#' r2ogs6_deactivated_subdomain
+#' @description tag: deactivated_subdomain
+#' @param time_interval list, numeric:
+#' @param material_ids string | double:
+#' @example man/examples/ex_prj_deactivated_subdomain.R
+#' @export
r2ogs6_deactivated_subdomain <- function(time_interval,
material_ids){
diff --git a/R/prj_search_length_algorithm.R b/R/prj_search_length_algorithm.R
index 7e98dc421b8fb031826156240bb5d7c46975b87b..967952d5334f8b82488adc13c399b288c1121bab 100644
--- a/R/prj_search_length_algorithm.R
+++ b/R/prj_search_length_algorithm.R
@@ -2,11 +2,12 @@
#===== r2ogs6_search_length_algorithm =====
-#'r2ogs6_search_length_algorithm
-#'@description tag: search_length_algorithm
-#'@param type string: The type
-#'@param value string | double: The value
-#'@export
+#' r2ogs6_search_length_algorithm
+#' @description tag: search_length_algorithm
+#' @param type string: The type
+#' @param value string | double: The value
+#' @example man/examples/ex_prj_search_length_algorithm.R
+#' @export
r2ogs6_search_length_algorithm <- function(type,
value = NULL) {
diff --git a/R/prj_time_loop.R b/R/prj_time_loop.R
index 3d8d08ddd557da280fa624c3d0f0d374cdecfd0f..e056cf16375e47e9c033ed821558c01bae5dffaa 100644
--- a/R/prj_time_loop.R
+++ b/R/prj_time_loop.R
@@ -2,12 +2,13 @@
#===== r2ogs6_time_loop =====
-#'r2ogs6_time_loop
-#'@description tag: time_loop
-#'@param processes list, r2ogs6_tl_process:
-#'@param output r2ogs6_output:
-#'@param global_process_coupling Optional: r2ogs6_global_process_coupling:
-#'@export
+#' r2ogs6_time_loop
+#' @description tag: time_loop
+#' @param processes list, r2ogs6_tl_process:
+#' @param output r2ogs6_output:
+#' @param global_process_coupling Optional: r2ogs6_global_process_coupling:
+#' @example man/examples/ex_prj_time_loop.R
+#' @export
r2ogs6_time_loop <- function(processes,
output,
global_process_coupling = NULL) {
@@ -48,16 +49,17 @@ new_r2ogs6_time_loop <- function(processes,
#===== r2ogs6_tl_process =====
-#'r2ogs6_tl_process
-#'@description tag: process (parent: time_loop, NOT processes!)
-#'@param ref string: References a r2ogs6_process object by name
-#'@param nonlinear_solver string:
-#'@param convergence_criterion r2ogs6_convergence_criterion:
-#'@param time_discretization vector:
-#'@param time_stepping r2ogs6_time_stepping:
-#'@param compensate_non_equilibrium_initial_residuum string: Optional: Either
-#'"true" or "false"
-#'@export
+#' r2ogs6_tl_process
+#' @description tag: process (parent: time_loop, NOT processes!)
+#' @param ref string: References a r2ogs6_process object by name
+#' @param nonlinear_solver string:
+#' @param convergence_criterion r2ogs6_convergence_criterion:
+#' @param time_discretization vector:
+#' @param time_stepping r2ogs6_time_stepping:
+#' @param compensate_non_equilibrium_initial_residuum string: Optional: Either
+#' "true" or "false"
+#' @example man/examples/ex_prj_tl_process.R
+#' @export
r2ogs6_tl_process <- function(ref,
nonlinear_solver,
convergence_criterion,
@@ -126,30 +128,31 @@ new_r2ogs6_tl_process <- function(ref,
#===== r2ogs6_output =====
-#'r2ogs6_output
-#'@description tag: output
-#'@param type string:
-#'@param prefix string:
-#'@param variables vector:
-#'@param suffix Optional: string:
-#'@param timesteps Optional:
-#'@param compress_output Optional: string: Should the output be compressed?
-#' Either "true" or "false"
-#'@param data_mode Optional: string:
-#'@param output_iteration_results Optional: string: Either "true" or "false"
-#'@param meshes Optional: character: A vector of mesh names
-#'@param fixed_output_times Optional: string | numeric:
-#'@export
+#' r2ogs6_output
+#' @description tag: output
+#' @param type string:
+#' @param prefix string:
+#' @param variables vector:
+#' @param suffix Optional: string:
+#' @param timesteps Optional:
+#' @param compress_output Optional: string: Should the output be compressed?
+#' Either "true" or "false"
+#' @param data_mode Optional: string:
+#' @param output_iteration_results Optional: string: Either "true" or "false"
+#' @param meshes Optional: character: A vector of mesh names
+#' @param fixed_output_times Optional: string | numeric:
+#' @example man/examples/ex_prj_output.R
+#' @export
r2ogs6_output <- function(type,
- prefix,
- variables,
- suffix = NULL,
- timesteps = NULL,
- compress_output = NULL,
- data_mode = NULL,
- output_iteration_results = NULL,
- meshes = NULL,
- fixed_output_times = NULL) {
+ prefix,
+ variables,
+ suffix = NULL,
+ timesteps = NULL,
+ compress_output = NULL,
+ data_mode = NULL,
+ output_iteration_results = NULL,
+ meshes = NULL,
+ fixed_output_times = NULL) {
#Coerce input
fixed_output_times <- coerce_string_to_numeric(fixed_output_times)
@@ -227,12 +230,13 @@ new_r2ogs6_output <- function(type,
#===== r2ogs6_global_process_coupling =====
-#'r2ogs6_global_process_coupling
-#'@description tag: global_process_coupling
-#'@param max_iter string | double: Maximal number of iterations
-#'@param convergence_criteria list, r2ogs6_convergence_criterion:
-#' Convergence criteria
-#'@export
+#' r2ogs6_global_process_coupling
+#' @description tag: global_process_coupling
+#' @param max_iter string | double: Maximal number of iterations
+#' @param convergence_criteria list, r2ogs6_convergence_criterion:
+#' Convergence criteria
+#' @example man/examples/ex_prj_global_process_coupling.R
+#' @export
r2ogs6_global_process_coupling <- function(max_iter,
convergence_criteria) {
@@ -268,15 +272,16 @@ new_r2ogs6_global_process_coupling <- function(max_iter,
#===== r2ogs6_convergence_criterion =====
-#'r2ogs6_convergence_criterion
-#'@description tag: convergence_criterion
-#'@param type string: Type
-#'@param norm_type string: ...
-#'@param abstol string | double: Absolute tolerance
-#'@param reltol string | double: Relative tolerance
-#'@param abstols string | numeric: Absolute tolerances
-#'@param reltols string | numeric: Relative tolerances
-#'@export
+#' r2ogs6_convergence_criterion
+#' @description tag: convergence_criterion
+#' @param type string: Type
+#' @param norm_type string: ...
+#' @param abstol string | double: Absolute tolerance
+#' @param reltol string | double: Relative tolerance
+#' @param abstols string | numeric: Absolute tolerances
+#' @param reltols string | numeric: Relative tolerances
+#' @example man/examples/ex_prj_convergence_criterion.R
+#' @export
r2ogs6_convergence_criterion <- function(type,
norm_type,
abstol = NULL,
@@ -336,24 +341,25 @@ new_r2ogs6_convergence_criterion <- function(type,
#===== r2ogs6_time_stepping =====
-#'r2ogs6_time_stepping
-#'@description tag: time_stepping
-#'@param type string:
-#'@param t_initial Optional: string | double:
-#'@param t_end Optional: string | double:
-#'@param timesteps Optional: list:
-#'@param initial_dt Optional: string | double:
-#'@param minimum_dt Optional: string | double:
-#'@param maximum_dt Optional: string | double:
-#'@param number_iterations Optional: string | numeric:
-#'@param multiplier Optional: string | numeric:
-#'@param dt_guess Optional: string | double:
-#'@param dt_min Optional: string | double:
-#'@param dt_max Optional: string | double:
-#'@param rel_dt_min Optional: string | double:
-#'@param rel_dt_max Optional: string | double:
-#'@param tol Optional: string | double:
-#'@export
+#' r2ogs6_time_stepping
+#' @description tag: time_stepping
+#' @param type string:
+#' @param t_initial Optional: string | double:
+#' @param t_end Optional: string | double:
+#' @param timesteps Optional: list:
+#' @param initial_dt Optional: string | double:
+#' @param minimum_dt Optional: string | double:
+#' @param maximum_dt Optional: string | double:
+#' @param number_iterations Optional: string | numeric:
+#' @param multiplier Optional: string | numeric:
+#' @param dt_guess Optional: string | double:
+#' @param dt_min Optional: string | double:
+#' @param dt_max Optional: string | double:
+#' @param rel_dt_min Optional: string | double:
+#' @param rel_dt_max Optional: string | double:
+#' @param tol Optional: string | double:
+#' @example man/examples/ex_prj_time_stepping.R
+#' @export
r2ogs6_time_stepping <- function(type,
t_initial = NULL,
t_end = NULL,
@@ -423,16 +429,16 @@ new_r2ogs6_time_stepping <- function(type,
are_strings(type)
are_null_or_numbers(t_initial,
- t_end,
- initial_dt,
- minimum_dt,
- maximum_dt,
- dt_guess,
- dt_min,
- dt_max,
- rel_dt_min,
- rel_dt_max,
- tol)
+ t_end,
+ initial_dt,
+ minimum_dt,
+ maximum_dt,
+ dt_guess,
+ dt_min,
+ dt_max,
+ rel_dt_min,
+ rel_dt_max,
+ tol)
are_null_or_numeric(number_iterations,
multiplier)
diff --git a/R/prj_vtkdiff.R b/R/prj_vtkdiff.R
index 8ab67b727189ed4d59e4f7842c154700821bb103..da33947ae80546f2a450f822031db5255eb13bbf 100644
--- a/R/prj_vtkdiff.R
+++ b/R/prj_vtkdiff.R
@@ -2,15 +2,16 @@
#===== r2ogs6_vtkdiff =====
-#'r2ogs6_vtkdiff
-#'@description tag: vtkdiff
+#' r2ogs6_vtkdiff
+#' @description tag: vtkdiff
#'
-#'@param field string: ...
-#'@param absolute_tolerance string | double: Absolute tolerance
-#'@param relative_tolerance string | double: Relative tolerance
-#'@param file string: Optional: File
-#'@param regex string: Optional: A regular expression
-#'@export
+#' @param field string: ...
+#' @param absolute_tolerance string | double: Absolute tolerance
+#' @param relative_tolerance string | double: Relative tolerance
+#' @param file string: Optional: File
+#' @param regex string: Optional: A regular expression
+#' @example man/examples/ex_prj_vtkdiff.R
+#' @export
r2ogs6_vtkdiff <- function(field,
absolute_tolerance,
relative_tolerance,
@@ -38,10 +39,10 @@ new_r2ogs6_vtkdiff <- function(field,
assertthat::assert_that(assertthat::is.string(field))
are_numbers(absolute_tolerance,
- relative_tolerance)
+ relative_tolerance)
are_null_or_strings(file,
- regex)
+ regex)
structure(
list(field = field,
diff --git a/R/scrape_benchmarks.R b/R/scrape_benchmarks.R
deleted file mode 100644
index b8c55d890f05d3542c440eb1128c2abead3835ba..0000000000000000000000000000000000000000
--- a/R/scrape_benchmarks.R
+++ /dev/null
@@ -1,56 +0,0 @@
-
-#===== download_benchmark =====
-
-
-#'download_benchmark
-#'@description Downloads a single benchmark (consisting of one .prj file and
-#' either one .gml and one .vtu file or multiple .vtu files)
-#'@param prj_url string: URL of a .prj file
-#'@param path string: Path the benchmark files should be saved to
-download_benchmark <- function(prj_url, path) {
-
- assertthat::assert_that(assertthat::is.string(prj_url))
-
- path <- as_dir_path(path)
-
- prj_dest_file <- paste0(path, basename(prj_url))
- file.create(prj_dest_file)
-
- prj_dir <- paste0(dirname(prj_url), "/")
-
- #Download the .prj file
- tmp <- tempfile()
- curl::curl_download(prj_url, tmp)
- prj_doc <- validate_read_in_xml(tmp)
- xml2::write_xml(prj_doc, prj_dest_file)
-
- gml_ref_node <- xml2::xml_find_first(prj_doc, "//geometry")
-
- #Get name of geometry file (if any)
- if (class(gml_ref_node) != "xml_missing") {
- geo_url <- paste0(prj_dir, xml2::xml_text(gml_ref_node))
-
- gml_dest_file <- paste0(path, basename(geo_url))
- file.create(gml_dest_file)
- curl::curl_download(geo_url, gml_dest_file)
-
- vtu_ref_node <- xml2::xml_find_first(prj_doc, "//mesh")
- vtu_url <- paste0(prj_dir, xml2::xml_text(vtu_ref_node))
-
- vtu_dest_file <- paste0(path, basename(vtu_url))
- file.create(vtu_dest_file)
- curl::curl_download(vtu_url, vtu_dest_file)
- }else{
- vtu_ref_nodes <- xml2::xml_find_all(prj_doc, "//meshes/*")
-
- for (i in seq_len(length(vtu_ref_nodes))) {
- vtu_url <- paste0(prj_dir, xml2::xml_text(vtu_ref_nodes[[i]]))
-
- vtu_dest_file <- paste0(path, basename(vtu_url))
- file.create(vtu_dest_file)
- curl::curl_download(vtu_url, vtu_dest_file)
- }
- }
-
- return(invisible(prj_dest_file))
-}
diff --git a/R/utils.R b/R/utils.R
index c4d4d4e634736839604cca12e132897cc28d992a..43f2a6a3f90fa3c07f363a8f2bd47ca57d4c3f7c 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -2,10 +2,12 @@
#===== Implementation utility =====
-#'get_class_from_xpath
-#'@description Gets r2ogs6 class name from an xpath-like expression
-#'@param xpath string: An xpath expression. Works for path-like xpaths only
-#'@return string: The class name.
+#' get_class_from_xpath
+#' @description Gets r2ogs6 class name from an xpath-like expression
+#' @param xpath string: An xpath expression. Works for path-like xpaths only
+#' @return string: The class name.
+#' @examples
+#' get_class_from_xpath("processes/process")
get_class_from_xpath <- function(xpath){
assertthat::assert_that(assertthat::is.string(xpath))
@@ -21,14 +23,16 @@ get_class_from_xpath <- function(xpath){
}
}
- return(invisible(NULL))
+ return(NULL)
}
-#'get_tag_from_class
-#'@description Utility function, returns the tag name of a r2ogs6 class
-#'@param class_name string: The name of a r2ogs6 class
-#'@return string: The tag name corresponding to `class_name`
+#' get_tag_from_class
+#' @description Utility function, returns the tag name of a r2ogs6 class
+#' @param class_name string: The name of a r2ogs6 class
+#' @return string: The tag name corresponding to \code{class_name}
+#' @examples
+#' get_tag_from_class("r2ogs6_process")
get_tag_from_class <- function(class_name) {
assertthat::assert_that(assertthat::is.string(class_name))
@@ -39,14 +43,16 @@ get_tag_from_class <- function(class_name) {
split_xpath <- unlist(strsplit(xpath[[1]], "/", fixed = TRUE))
tag_name <- split_xpath[[length(split_xpath)]]
- return(invisible(tag_name))
+ return(tag_name)
}
-#'get_tag_from_xpath
-#'@description Gets the XML tag name from an xpath expression
-#'@param xpath string: An xpath expression. Works for path-like xpaths only
-#'@return string: The XML tag name.
+#' get_tag_from_xpath
+#' @description Gets the XML tag name from an xpath expression
+#' @param xpath string: An xpath expression. Works for path-like xpaths only
+#' @return string: The XML tag name
+#' @examples
+#' get_tag_from_xpath("processes/process")
get_tag_from_xpath <- function(xpath){
xpath_split <- unlist(strsplit(xpath, "/", fixed = TRUE))
@@ -56,9 +62,9 @@ get_tag_from_xpath <- function(xpath){
}
-#'prj_top_level_tags
-#'@description Gets top level .prj tags along with info if they are required.
-#'@return list: List of lists.
+#' prj_top_level_tags
+#' @description Gets top level .prj tags along with info if they are required.
+#' @return list: List of lists.
prj_top_level_tags <- function(){
prj_reduxml <- system.file("extdata/xml_redux/", "prj_redu.xml",
@@ -75,10 +81,11 @@ prj_top_level_tags <- function(){
}
-#'prj_top_level_classes
-#'@description Returns named character vector of `OGS6` top level .prj tags
-#' (names) represented by r2ogs6 classes along with their class names (values).
-#'@return character
+#' prj_top_level_classes
+#' @description Returns named character vector of \code{OGS6} top level
+#' \code{.prj} tags (names) represented by \code{r2ogs6} classes along with their
+#' class names (values).
+#' @return character
prj_top_level_classes <- function(){
xpaths_for_classes <- xpaths_for_classes
@@ -117,10 +124,12 @@ prj_top_level_classes <- function(){
#===== Coercion utility =====
-#'coerce_string_to_numeric
-#'@description If an object is of type string, coerces it to a numeric type
-#'@param obj object: Any object
-#'@return numeric if 'obj' was a string, else unchanged 'obj'
+#' coerce_string_to_numeric
+#' @description If an object is of type string, coerces it to a numeric type
+#' @param obj object: Any object
+#' @return numeric if \code{obj} was a string, else unchanged \code{obj}
+#' @examples
+#' coerce_string_to_numeric("12 54 2 \n 2")
coerce_string_to_numeric <- function(obj){
if(assertthat::is.string(obj)){
@@ -132,13 +141,12 @@ coerce_string_to_numeric <- function(obj){
}
-
-#'coerce_names
-#'@description Validator function for a parameter vector
-#'@param vector vector: Vector of parameters
-#'@param names character: How the vector elements will be named as
+#' coerce_names
+#' @description Validator function for a parameter vector
+#' @param vector vector: Vector of parameters
+#' @param names character: How the vector elements will be named as
#' per default
-#'@return vector: Named vector where the names correspond to `names`
+#' @return vector: Named vector where the names correspond to \code{names}
coerce_names <- function(vector, names) {
assertthat::assert_that(is.vector(vector))
@@ -166,10 +174,10 @@ coerce_names <- function(vector, names) {
}
-#'is_null_or_coerce_names
-#'@description Validator function for a parameter list or vector or NULL
-#'@param obj A list (or vector) of parameters
-#'@param names How the list elements will be named as per default
+#' is_null_or_coerce_names
+#' @description Validator function for a parameter list or vector or \code{NULL}
+#' @param obj A list (or vector) of parameters
+#' @param names How the list elements will be named as per default
is_null_or_coerce_names <- function(obj, names){
if(!is.null(obj)){
@@ -180,10 +188,10 @@ is_null_or_coerce_names <- function(obj, names){
}
-#'clean_imported_list
-#'@description Cleans an imported list because sometimes strings containing
+#' clean_imported_list
+#' @description Cleans an imported list because sometimes strings containing
#' only newline characters and spaces get imported in
-#'@param list list: A list
+#' @param list list: A list
clean_imported_list <- function(list){
assertthat::assert_that(is.list(list))
@@ -203,9 +211,9 @@ clean_imported_list <- function(list){
}
-#'as_dir_path
-#'@description Checks if a given path ends on '/'
-#'@param path string: A path
+#' as_dir_path
+#' @description Checks if a given path ends on \code{/}
+#' @param path string: A path
as_dir_path <- function(path){
assertthat::assert_that(assertthat::is.string(path))
@@ -222,12 +230,13 @@ as_dir_path <- function(path){
}
-#'filter_invalid_xml
-#'@description Filters invalid XML paths out of a vector
-#'@param paths character: Vector of (maybe-)XML paths
-#'@param encoding string: Optional: XML encoding. Defaults to ISO-8859-1
-#'@param print_messages flag: Optional: Print error messages? Defaults to TRUE
-#'@return character: Vector of invalid XML paths
+#' filter_invalid_xml
+#' @description Filters invalid XML paths out of a vector
+#' @param paths character: Vector of (maybe-)XML paths
+#' @param encoding string: Optional: XML encoding. Defaults to ISO-8859-1
+#' @param print_messages flag: Optional: Print error messages? Defaults to
+#' \code{TRUE}
+#' @return character: Vector of invalid XML paths
filter_invalid_xml <- function(paths,
encoding = "ISO-8859-1",
print_messages = TRUE){
@@ -258,9 +267,9 @@ filter_invalid_xml <- function(paths,
#===== Validation utility =====
-#'are_numbers
-#'@description Checks if objects are numbers
-#'@param ... Ellipsis
+#' are_numbers
+#' @description Checks if objects are numbers
+#' @param ... Ellipsis
are_numbers <- function(...){
lapply(list(...), function(x){
@@ -271,9 +280,9 @@ are_numbers <- function(...){
}
-#'are_null_or_numbers
-#'@description Checks if objects are either NULL or numbers
-#'@param ... Ellipsis
+#' are_null_or_numbers
+#' @description Checks if objects are either \code{NULL} or numbers
+#' @param ... Ellipsis
are_null_or_numbers <- function(...){
lapply(list(...), function(x){
@@ -286,9 +295,9 @@ are_null_or_numbers <- function(...){
}
-#'are_numeric
-#'@description Checks if objects are numeric
-#'@param ... Ellipsis
+#' are_numeric
+#' @description Checks if objects are numeric
+#' @param ... Ellipsis
are_numeric <- function(...){
lapply(list(...), function(x){
@@ -299,9 +308,9 @@ are_numeric <- function(...){
}
-#'are_null_or_numeric
-#'@description Checks if objects are either NULL or numeric
-#'@param ... Ellipsis
+#' are_null_or_numeric
+#' @description Checks if objects are either \code{NULL} or numeric
+#' @param ... Ellipsis
are_null_or_numeric <- function(...){
lapply(list(...), function(x){
@@ -314,9 +323,9 @@ are_null_or_numeric <- function(...){
}
-#'are_strings
-#'@description Checks if objects are strings
-#'@param ... Ellipsis
+#' are_strings
+#' @description Checks if objects are strings
+#' @param ... Ellipsis
are_strings <- function(...){
lapply(list(...), function(x){
@@ -327,9 +336,9 @@ are_strings <- function(...){
}
-#'are_null_or_strings
-#'@description Checks if objects are either NULL or strings
-#'@param ... Ellipsis
+#' are_null_or_strings
+#' @description Checks if objects are either \code{NULL} or strings
+#' @param ... Ellipsis
are_null_or_strings <- function(...){
lapply(list(...), function(x){
@@ -342,9 +351,9 @@ are_null_or_strings <- function(...){
}
-#'are_string_flags
-#'@description Checks if objects are strings reading either "true" or "false"
-#'@param ... Ellipsis
+#' are_string_flags
+#' @description Checks if objects are strings reading either "true" or "false"
+#' @param ... Ellipsis
are_string_flags <- function(...){
lapply(list(...), function(x){
@@ -356,10 +365,10 @@ are_string_flags <- function(...){
}
-#'are_null_or_string_flags
-#'@description Checks if objects are either NULL or strings reading either
-#' "true" or "false"
-#'@param ... Ellipsis
+#' are_null_or_string_flags
+#' @description Checks if objects are either \code{NULL} or strings reading
+#' either "true" or "false"
+#' @param ... Ellipsis
are_null_or_string_flags <- function(...){
lapply(list(...), function(x){
@@ -372,11 +381,11 @@ are_null_or_string_flags <- function(...){
}
-#'is_wrapper_list
-#'@description Checks if a list consists only of elements of class
-#' `element_class`
-#'@param list list: List to check
-#'@param element_class string: Class each element of `list` should have
+#' is_wrapper_list
+#' @description Checks if a list consists only of elements of class
+#' \code{element_class}
+#' @param list list: List to check
+#' @param element_class string: Class each element of \code{list} should have
is_wrapper_list <- function(list, element_class) {
assertthat::assert_that(is.list(list))
@@ -389,11 +398,11 @@ is_wrapper_list <- function(list, element_class) {
}
-#'is_null_or_wrapper_list
-#'@description Checks if an object is either NULL or a list of elements
-#' of class `element_class`
-#'@param obj list | NULL: Object to check
-#'@param element_class string: Class each element of `obj` should have
+#' is_null_or_wrapper_list
+#' @description Checks if an object is either \code{NULL} or a list of elements
+#' of class \code{element_class}
+#' @param obj list | NULL: Object to check
+#' @param element_class string: Class each element of \code{obj} should have
is_null_or_wrapper_list <- function(obj, element_class) {
if(!is.null(obj)){
@@ -408,11 +417,11 @@ is_null_or_wrapper_list <- function(obj, element_class) {
}
-#'is_null_or_has_class
-#'@description Checks if an object is either null or a class object of class
-#' 'class_name'
-#'@param obj The object to check
-#'@param class_name The name of the expected class
+#' is_null_or_has_class
+#' @description Checks if an object is either \code{NULL} or a class object of
+#' class \code{class_name}
+#' @param obj The object to check
+#' @param class_name The name of the expected class
is_null_or_has_class <- function(obj, class_name){
if(!is.null(obj)){
diff --git a/man/OGS6.Rd b/man/OGS6.Rd
index 3e941a8979bbf59ee88ecfab338dd36a4dde30f9..14948b8edccd1d32959a84fecca7130cd1a07700 100644
--- a/man/OGS6.Rd
+++ b/man/OGS6.Rd
@@ -4,62 +4,105 @@
\alias{OGS6}
\title{OGS6}
\description{
-Constructor for the OGS6 base class
+Constructor for the \code{OGS6} base class
+}
+\examples{
+
+## ------------------------------------------------
+## Method `OGS6$new`
+## ------------------------------------------------
+
+ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
+
+## ------------------------------------------------
+## Method `OGS6$add`
+## ------------------------------------------------
+
+ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
+ogs6_obj$add(r2ogs6_parameter$new(name = "foo", type = "bar"))
+
+## ------------------------------------------------
+## Method `OGS6$add_gml`
+## ------------------------------------------------
+
+ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
+ogs6_obj$add_gml("this_works.gml")
+\dontrun{ogs6_obj$add_gml("this_doesnt.oops")}
+
+## ------------------------------------------------
+## Method `OGS6$add_vtu`
+## ------------------------------------------------
+
+ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
+ogs6_obj$add_vtu("this_works.vtu")
+\dontrun{ogs6_obj$add_vtu("this_doesnt.oops")}
+
+## ------------------------------------------------
+## Method `OGS6$get_status`
+## ------------------------------------------------
+
+ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
+ogs6_obj$get_status()
}
\section{Active bindings}{
\if{html}{\out{<div class="r6-active-bindings">}}
\describe{
-\item{\code{sim_name}}{Simulation name. `value` must be string}
+\item{\code{sim_name}}{Simulation name. \code{value} must be string}
-\item{\code{sim_path}}{Simulation path. `value` must be string}
+\item{\code{sim_path}}{Simulation path. \code{value} must be string}
-\item{\code{logfile}}{Logfile path. `value` must be string}
+\item{\code{logfile}}{Logfile path. \code{value} must be string}
-\item{\code{gml}}{.gml. read-only}
+\item{\code{gml}}{\code{.gml}. read-only}
-\item{\code{geometry}}{.prj `geometry` tag. `value` must be string}
+\item{\code{geometry}}{\code{.prj} \code{geometry} tag. \code{value} must be string}
-\item{\code{meshes}}{.prj `meshes` tag. `value` must be list of strings}
+\item{\code{meshes}}{\code{.prj} \code{meshes} tag. \code{value} must be list of strings}
-\item{\code{vtus}}{.vtus. `value` must be list of `OGS_vtu` objects}
+\item{\code{vtus}}{\code{.vtu}s. \code{value} must be list of \code{OGS6_vtu} objects}
-\item{\code{python_script}}{.prj `python_script` tag. `value` must be string}
+\item{\code{python_script}}{\code{.prj} \code{python_script} tag. \code{value} must be string}
-\item{\code{search_length_algorithm}}{.prj `search_length_algorithm` tag. `value` must be
-`r2ogs6_search_length_algorithm` object}
+\item{\code{search_length_algorithm}}{\code{.prj} \code{search_length_algorithm} tag. \code{value} must be
+\code{r2ogs6_search_length_algorithm} object}
-\item{\code{processes}}{.prj `processes` tag. `value` must be list of `r2ogs6_process` objects}
+\item{\code{processes}}{\code{.prj} \code{processes} tag. \code{value} must be list of
+\code{r2ogs6_process} objects}
-\item{\code{time_loop}}{.prj `time_loop` tag. `value` must be `r2ogs6_time_loop` object}
+\item{\code{time_loop}}{\code{.prj} \code{time_loop} tag. \code{value} must be
+\code{r2ogs6_time_loop} object}
-\item{\code{local_coordinate_system}}{.prj `local_coordinate_system` tag. `value` must be
-`r2ogs6_local_coordinate_system` object}
+\item{\code{local_coordinate_system}}{\code{.prj} \code{local_coordinate_system} tag. \code{value} must be
+\code{r2ogs6_local_coordinate_system} object}
-\item{\code{media}}{.prj `media` tag. `value` must be list of `r2ogs6_medium` objects}
+\item{\code{media}}{\code{.prj} \code{media} tag. \code{value} must be list of
+\code{r2ogs6_medium} objects}
-\item{\code{parameters}}{.prj `parameters` tag. `value` must be list of `r2ogs6_parameter`
-objects}
+\item{\code{parameters}}{\code{.prj} \code{parameters} tag. \code{value} must be list of
+\code{r2ogs6_parameter} objects}
-\item{\code{chemical_system}}{.prj `chemical_system` tag. `value` must be `r2ogs6_chemical_system`
-object}
+\item{\code{chemical_system}}{\code{.prj} \code{chemical_system} tag. \code{value} must be
+\code{r2ogs6_chemical_system} object}
-\item{\code{curves}}{.prj `curves` tag. `value` must be list of `r2ogs6_curve` objects}
+\item{\code{curves}}{\code{.prj} \code{curves} tag. \code{value} must be list of
+\code{r2ogs6_curve} objects}
-\item{\code{process_variables}}{.prj `process_variables` tag. `value` must be list of
-`r2ogs6_process_variable` objects}
+\item{\code{process_variables}}{\code{.prj} \code{process_variables} tag. \code{value} must be list of
+\code{r2ogs6_process_variable} objects}
-\item{\code{nonlinear_solvers}}{.prj `nonlinear_solvers` tag. `value` must be list of
-`r2ogs6_nonlinear_solver` objects}
+\item{\code{nonlinear_solvers}}{\code{.prj} \code{nonlinear_solvers} tag. \code{value} must be list of
+\code{r2ogs6_nonlinear_solver} objects}
-\item{\code{linear_solvers}}{.prj `linear_solvers` tag. `value` must be list of
-`r2ogs6_linear_solver` objects}
+\item{\code{linear_solvers}}{\code{.prj} \code{linear_solvers} tag. \code{value} must be list of
+\code{r2ogs6_linear_solver} objects}
-\item{\code{test_definition}}{.prj `test_definition` tag. `value` must be list of `r2ogs6_vtkdiff`
-objects}
+\item{\code{test_definition}}{\code{.prj} \code{test_definition} tag. \code{value} must be list of
+\code{r2ogs6_vtkdiff} objects}
-\item{\code{insitu}}{.prj `insitu` tag. `value` must be `r2ogs6_insitu` object}
+\item{\code{insitu}}{\code{.prj} \code{insitu} tag. \code{value} must be
+\code{r2ogs6_insitu} object}
-\item{\code{pvds}}{.pvds. `value` must be list of `OGS6_pvd` objects}
+\item{\code{pvds}}{\code{.pvd}s. \code{value} must be list of \code{OGS6_pvd} objects}
}
\if{html}{\out{</div>}}
}
@@ -96,6 +139,14 @@ saved}
}
\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")
+}
+\if{html}{\out{</div>}}
+
+}
+
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-add"></a>}}
@@ -113,12 +164,22 @@ Adds a .prj simulation component
}
\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$new(name = "foo", type = "bar"))
+}
+\if{html}{\out{</div>}}
+
+}
+
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-add_gml"></a>}}
\if{latex}{\out{\hypertarget{method-add_gml}{}}}
\subsection{Method \code{add_gml()}}{
-Adds a reference to a .gml file and optionally, a OGS6_gml object
+Adds a reference to a file with ending .gml and optionally, a
+\code{OGS6_gml} object
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_gml(gml)}\if{html}{\out{</div>}}
}
@@ -126,17 +187,28 @@ Adds a reference to a .gml file and optionally, a OGS6_gml object
\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
-\item{\code{gml}}{string | r2ogs6_gml: Either a path to a file with extension
-.gml or a r2ogs6_gml object.}
+\item{\code{gml}}{string | OGS6_gml: Either a path to a file with extension
+.gml or a OGS6_gml object.}
}
\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_gml("this_works.gml")
+\dontrun{ogs6_obj$add_gml("this_doesnt.oops")}
+}
+\if{html}{\out{</div>}}
+
+}
+
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-add_vtu"></a>}}
\if{latex}{\out{\hypertarget{method-add_vtu}{}}}
\subsection{Method \code{add_vtu()}}{
-Adds a reference to a .vtu file and optionally, a OGS6_vtu object
+Adds a reference to a \code{.vtu} file and optionally, a \code{OGS6_vtu}
+object
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_vtu(path, read_in_vtu = FALSE)}\if{html}{\out{</div>}}
}
@@ -144,19 +216,29 @@ Adds a reference to a .vtu file and optionally, a OGS6_vtu object
\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
-\item{\code{path}}{string:}
+\item{\code{path}}{string: A path}
-\item{\code{read_in_vtu}}{flag: Optional: Should .vtu file just be copied or
-read in too?}
+\item{\code{read_in_vtu}}{flag: Optional: Should \code{.vtu} file just be
+copied or read in too?}
+}
+\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_vtu("this_works.vtu")
+\dontrun{ogs6_obj$add_vtu("this_doesnt.oops")}
}
\if{html}{\out{</div>}}
+
}
+
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-get_status"></a>}}
\if{latex}{\out{\hypertarget{method-get_status}{}}}
\subsection{Method \code{get_status()}}{
-Checks if the OGS6 object has all necessary parameters for
+Checks if the \code{OGS6} object has all necessary parameters for
starting a simulation
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6$get_status(print_status = TRUE)}\if{html}{\out{</div>}}
@@ -169,6 +251,15 @@ starting a simulation
}
\if{html}{\out{</div>}}
}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
+ogs6_obj$get_status()
+}
+\if{html}{\out{</div>}}
+
+}
+
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-print"></a>}}
@@ -195,7 +286,7 @@ Prints logfile to console (if it exists)
\if{html}{\out{<a id="method-clear"></a>}}
\if{latex}{\out{\hypertarget{method-clear}{}}}
\subsection{Method \code{clear()}}{
-Clears components from the OGS6 object
+Clears components from the \code{OGS6} object
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6$clear(which)}\if{html}{\out{</div>}}
}
@@ -205,7 +296,7 @@ Clears components from the OGS6 object
\describe{
\item{\code{which}}{character: The names of the components (all by default).
If you want to delete only some components, run
-names(prj_top_level_classes()) for the available options.}
+\code{names(prj_top_level_classes())} for the available options.}
}
\if{html}{\out{</div>}}
}
diff --git a/man/OGS6_Ensemble.Rd b/man/OGS6_Ensemble.Rd
index 2d42dac93d22a4bef90de32320a082fd9c6f3594..15b77c315aac1960b0f9aee64c19a7c7dc09be63 100644
--- a/man/OGS6_Ensemble.Rd
+++ b/man/OGS6_Ensemble.Rd
@@ -27,7 +27,7 @@ Constructor for the OGS6_Ensemble base class
\item \href{#method-new}{\code{OGS6_Ensemble$new()}}
\item \href{#method-print}{\code{OGS6_Ensemble$print()}}
\item \href{#method-run_simulation}{\code{OGS6_Ensemble$run_simulation()}}
-\item \href{#method-relevant_parameter_at}{\code{OGS6_Ensemble$relevant_parameter_at()}}
+\item \href{#method-get_point_data}{\code{OGS6_Ensemble$get_point_data()}}
\item \href{#method-clone}{\code{OGS6_Ensemble$clone()}}
}
}
@@ -94,22 +94,38 @@ This is implementented via the 'parallel' package.}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-relevant_parameter_at"></a>}}
-\if{latex}{\out{\hypertarget{method-relevant_parameter_at}{}}}
-\subsection{Method \code{relevant_parameter_at()}}{
-If the ensemble was created in sequential_mode, this will get the
-name of the value vector that was being iterated over at the given
-`index` during ensemble creation. I. e. if the ensemble was created
-with the value vectors `a = c(1, 2, 3)` and `b = c("foo", "bar")`,
-an `index` of 4 would return `"b"`
+\if{html}{\out{<a id="method-get_point_data"></a>}}
+\if{latex}{\out{\hypertarget{method-get_point_data}{}}}
+\subsection{Method \code{get_point_data()}}{
+Wrapper for `OGS6_pvd$get_point_data()` Returns combined dataframe
+with extra `name` and / or `perc` column depending on if
+`sequential_mode` and / or `percentages_mode` were used.
\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$relevant_parameter_at(index)}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$get_point_data(
+ pvd_id = 1,
+ point_ids,
+ keys,
+ start_at_timestep,
+ end_at_timestep
+)}\if{html}{\out{</div>}}
}
\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
-\item{\code{index}}{number: Index}
+\item{\code{pvd_id}}{number: Optional: Which .pvd to consider in OGS6$pvds.
+Defaults to 1.}
+
+\item{\code{point_ids}}{numeric: Optional: Point IDs. Defaults to all.}
+
+\item{\code{keys}}{character: Optional: `Name` attributes of `DataArray`
+elements. Defaults to all.}
+
+\item{\code{start_at_timestep}}{number: Optional: Timestep to start at.
+Defaults to first timestep.}
+
+\item{\code{end_at_timestep}}{number: Optional: Timestep to end at. Defaults
+to last timestep.}
}
\if{html}{\out{</div>}}
}
diff --git a/man/OGS6_gml.Rd b/man/OGS6_gml.Rd
index c7f4e63d323ad621c93f9fc69b7a2efdc2c89293..48aad92508f8439a3ce953d3e51b7147e639198d 100644
--- a/man/OGS6_gml.Rd
+++ b/man/OGS6_gml.Rd
@@ -6,6 +6,26 @@
\description{
Constructor for the OGS6_gml base class
}
+\examples{
+OGS6_gml$new(
+ name = "cube_1x1x1_geometry",
+ points = tibble::tibble(
+ x = c(0, 0, 0, 0),
+ y = c(0, 0, 1, 1),
+ z = c(0, 1, 1, 0),
+ name = c("origin", "", "", "")
+ ),
+ polylines = list(polyline = list("front_left",
+ c(
+ pnt = 0, pnt = 1
+ ))),
+ surfaces = list(surface = list(
+ name = "left",
+ element = c(p1 = 0, p2 = 1, p3 = 2),
+ element = c(p1 = 0, p2 = 3, p3 = 2)
+ ))
+)
+}
\section{Active bindings}{
\if{html}{\out{<div class="r6-active-bindings">}}
\describe{
@@ -62,7 +82,7 @@ have optional 'name' vector}
\item{\code{polylines}}{list(list("foo", c(1, 2))):}
-\item{\code{surfaces}}{list(list("foo", c(1, 2, 3), c(2, 3, 4))):}
+\item{\code{surfaces}}{list(list("foo", c(1, 2, 3), c(2, 3, 4)))}
}
\if{html}{\out{</div>}}
}
diff --git a/man/are_null_or_numbers.Rd b/man/are_null_or_numbers.Rd
index bfa1f97512acce88d821d94f50b2cc2f88fd7573..a646d8c38c459e29f8024965596693c5749d96d1 100644
--- a/man/are_null_or_numbers.Rd
+++ b/man/are_null_or_numbers.Rd
@@ -10,5 +10,5 @@ are_null_or_numbers(...)
\item{...}{Ellipsis}
}
\description{
-Checks if objects are either NULL or numbers
+Checks if objects are either \code{NULL} or numbers
}
diff --git a/man/are_null_or_numeric.Rd b/man/are_null_or_numeric.Rd
index 088882791d709636769dd4f1d33bcb61729e516a..d6f3c7b7e0a3f9fc36d79d17343f747b4020b60f 100644
--- a/man/are_null_or_numeric.Rd
+++ b/man/are_null_or_numeric.Rd
@@ -10,5 +10,5 @@ are_null_or_numeric(...)
\item{...}{Ellipsis}
}
\description{
-Checks if objects are either NULL or numeric
+Checks if objects are either \code{NULL} or numeric
}
diff --git a/man/are_null_or_string_flags.Rd b/man/are_null_or_string_flags.Rd
index a719b10fedb113c2e1e378b213647f79befe4afd..31b05fdeef2f14a2fdec1b9f5c0908a02931ccb2 100644
--- a/man/are_null_or_string_flags.Rd
+++ b/man/are_null_or_string_flags.Rd
@@ -10,6 +10,6 @@ are_null_or_string_flags(...)
\item{...}{Ellipsis}
}
\description{
-Checks if objects are either NULL or strings reading either
-"true" or "false"
+Checks if objects are either \code{NULL} or strings reading
+either "true" or "false"
}
diff --git a/man/are_null_or_strings.Rd b/man/are_null_or_strings.Rd
index 533510897c125c7c8333c9ed38054034f76912cc..c9c67f0df76c7a298fa01d1eb72530094be6df54 100644
--- a/man/are_null_or_strings.Rd
+++ b/man/are_null_or_strings.Rd
@@ -10,5 +10,5 @@ are_null_or_strings(...)
\item{...}{Ellipsis}
}
\description{
-Checks if objects are either NULL or strings
+Checks if objects are either \code{NULL} or strings
}
diff --git a/man/as_dir_path.Rd b/man/as_dir_path.Rd
index d6adefeea91300910a65bb9307bc1bc03b4a8b6e..47b0dc6ed94582cc19e38593865b065fca955df1 100644
--- a/man/as_dir_path.Rd
+++ b/man/as_dir_path.Rd
@@ -10,5 +10,5 @@ as_dir_path(path)
\item{path}{string: A path}
}
\description{
-Checks if a given path ends on '/'
+Checks if a given path ends on \code{/}
}
diff --git a/man/build_redux_doc.Rd b/man/build_redux_doc.Rd
index 24e0d59f10137c7bb705f5387bb05fae128fdfd7..85e005c088c3eec2f9ad7a86291511eed47db4f4 100644
--- a/man/build_redux_doc.Rd
+++ b/man/build_redux_doc.Rd
@@ -7,15 +7,16 @@
build_redux_doc(path, pattern, xpath, export_path)
}
\arguments{
-\item{path}{string: See ?analyse_xml}
+\item{path}{string: See \code{?analyse_xml}}
-\item{pattern}{string: See ?analyse_xml}
+\item{pattern}{string: See \code{?analyse_xml}}
-\item{xpath}{string: See ?analyse_xml}
+\item{xpath}{string: See \code{?analyse_xml}}
\item{export_path}{string: Path to export the XML document to}
}
\description{
-Builds an XML document based on the findings of analyse_xml.
-Calls recursive function `build_redux_tree` internally.
+Builds an XML document based on the findings of
+\code{analyse_xml()}. Calls recursive function \code{build_redux_tree()}
+internally.
}
diff --git a/man/build_redux_tree.Rd b/man/build_redux_tree.Rd
index 9de941080512ca774b5c37712fabcb3cf9b283e3..11f2cc7ecc0d692234617cb7530f8903431596f9 100644
--- a/man/build_redux_tree.Rd
+++ b/man/build_redux_tree.Rd
@@ -7,15 +7,15 @@
build_redux_tree(path, pattern, xpath, required)
}
\arguments{
-\item{path}{string: See ?analyse_xml}
+\item{path}{string: See \code{?analyse_xml}}
-\item{pattern}{string: See ?analyse_xml}
+\item{pattern}{string: See \code{?analyse_xml}}
-\item{xpath}{string: See ?analyse_xml}
+\item{xpath}{string: See \code{?analyse_xml}}
\item{required}{flag: Recursion utility}
}
\description{
-Builds an XML tree based on the findings of analyse_xml.
-This is a recursive function. Handle with care.
+Builds an XML tree based on the findings of
+\code{analyse_xml()}. This is a recursive function.
}
diff --git a/man/coerce_names.Rd b/man/coerce_names.Rd
index ea12331dc11a8c1c6a6cd0cab5713a788201e6f1..be60541341a4930832171abc851ac402db62b686 100644
--- a/man/coerce_names.Rd
+++ b/man/coerce_names.Rd
@@ -13,7 +13,7 @@ coerce_names(vector, names)
per default}
}
\value{
-vector: Named vector where the names correspond to `names`
+vector: Named vector where the names correspond to \code{names}
}
\description{
Validator function for a parameter vector
diff --git a/man/coerce_string_to_numeric.Rd b/man/coerce_string_to_numeric.Rd
index b3f45c507054291514e27471301ab9579608a90d..4061da8a4305c77485bf9295d927195a3545f2c4 100644
--- a/man/coerce_string_to_numeric.Rd
+++ b/man/coerce_string_to_numeric.Rd
@@ -10,8 +10,11 @@ coerce_string_to_numeric(obj)
\item{obj}{object: Any object}
}
\value{
-numeric if 'obj' was a string, else unchanged 'obj'
+numeric if \code{obj} was a string, else unchanged \code{obj}
}
\description{
If an object is of type string, coerces it to a numeric type
}
+\examples{
+ coerce_string_to_numeric("12 54 2 \n 2")
+}
diff --git a/man/construct_add_call.Rd b/man/construct_add_call.Rd
index fb98e19e309c5b7cb4f88e0492a2e7bab7a63690..3753914b929358ba876859776d1eac2790b9320b 100644
--- a/man/construct_add_call.Rd
+++ b/man/construct_add_call.Rd
@@ -7,17 +7,17 @@
construct_add_call(object, nested_call = FALSE)
}
\arguments{
-\item{object}{An object (numeric, character, list, NULL, OGS6 or r2ogs6 class
-object)}
+\item{object}{An object (numeric, character, list, NULL, \code{OGS6} or
+\code{r2ogs6} class object)}
\item{nested_call}{Optional: For recursion purposes, you should leave this as
it is.}
}
\value{
-A string representing the code with which the component would be added
-to an OGS6 object
+A string representing the code with which the component would be
+added to an \code{OGS6} object
}
\description{
-Constructs a call based on an OGS6 component. This is a
+Constructs a call based on an \code{OGS6} component. This is a
recursive function, handle with care.
}
diff --git a/man/download_benchmark.Rd b/man/download_benchmark.Rd
deleted file mode 100644
index f7b6eb03e2c5bdb1d581b8833dc5b8420cc578d9..0000000000000000000000000000000000000000
--- a/man/download_benchmark.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/scrape_benchmarks.R
-\name{download_benchmark}
-\alias{download_benchmark}
-\title{download_benchmark}
-\usage{
-download_benchmark(prj_url, path)
-}
-\arguments{
-\item{prj_url}{string: URL of a .prj file}
-
-\item{path}{string: Path the benchmark files should be saved to}
-}
-\description{
-Downloads a single benchmark (consisting of one .prj file and
-either one .gml and one .vtu file or multiple .vtu files)
-}
diff --git a/man/examples/ex_prj_borehole_heat_exchanger.R b/man/examples/ex_prj_borehole_heat_exchanger.R
new file mode 100644
index 0000000000000000000000000000000000000000..45959518076908b46ff8f1a9d9637d044dc9e15e
--- /dev/null
+++ b/man/examples/ex_prj_borehole_heat_exchanger.R
@@ -0,0 +1,37 @@
+r2ogs6_borehole_heat_exchanger(
+ type = "1U",
+ flow_and_temperature_control = r2ogs6_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 = r2ogs6_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"
+ )
+)
diff --git a/man/examples/ex_prj_boundary_condition.R b/man/examples/ex_prj_boundary_condition.R
new file mode 100644
index 0000000000000000000000000000000000000000..f64d1c2911125d43f473b3f7bf0662a27dc9a1a1
--- /dev/null
+++ b/man/examples/ex_prj_boundary_condition.R
@@ -0,0 +1,7 @@
+r2ogs6_boundary_condition(
+ type = "Neumann",
+ parameter = "flux_in",
+ geometrical_set = "cube_1x1x1_geometry",
+ geometry = "left",
+ component = 0
+)
diff --git a/man/examples/ex_prj_capillary_pressure.R b/man/examples/ex_prj_capillary_pressure.R
new file mode 100644
index 0000000000000000000000000000000000000000..0e4a0a013f6317a92c3a5d7c595b4bd3710d8bff
--- /dev/null
+++ b/man/examples/ex_prj_capillary_pressure.R
@@ -0,0 +1,9 @@
+r2ogs6_capillary_pressure(
+ type = "vanGenuchten",
+ pd = 2e+06,
+ sr = 0.4,
+ smax = 1,
+ m = 0.3288590604,
+ pc_max = 2e+07,
+ has_regularized = "true"
+)
diff --git a/man/examples/ex_prj_chemical_system.R b/man/examples/ex_prj_chemical_system.R
new file mode 100644
index 0000000000000000000000000000000000000000..72427ae876ae5d25ac15a33cd97adf346a35b4d7
--- /dev/null
+++ b/man/examples/ex_prj_chemical_system.R
@@ -0,0 +1,29 @@
+r2ogs6_chemical_system(
+ chemical_solver = "Phreeqc",
+ database = "PSINA_12_07_110615_DAV_s.dat",
+ solution = r2ogs6_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 = r2ogs6_phase_component(
+ name = "Calcite",
+ saturation_index = 0,
+ initial_amount = 0.000207
+ )
+ )
+)
diff --git a/man/examples/ex_prj_com_property.R b/man/examples/ex_prj_com_property.R
new file mode 100644
index 0000000000000000000000000000000000000000..31b57e34249fdbc64b38de94f983647db03c0a10
--- /dev/null
+++ b/man/examples/ex_prj_com_property.R
@@ -0,0 +1,3 @@
+r2ogs6_com_property(name = "molecular_diffusion",
+ type = "Constant",
+ value = 2e-09)
diff --git a/man/examples/ex_prj_component.R b/man/examples/ex_prj_component.R
new file mode 100644
index 0000000000000000000000000000000000000000..ee35ed0d491717f970cb333e50515288df2c7d15
--- /dev/null
+++ b/man/examples/ex_prj_component.R
@@ -0,0 +1,8 @@
+r2ogs6_component(
+ name = "concentration",
+ properties = list(
+ property = r2ogs6_com_property(name = "molecular_diffusion",
+ type = "Constant",
+ value = 2e-09)
+ )
+)
diff --git a/man/examples/ex_prj_constitutive_relation.R b/man/examples/ex_prj_constitutive_relation.R
new file mode 100644
index 0000000000000000000000000000000000000000..206d6fa19b40f0241c0f39fa6233057bdcb357dd
--- /dev/null
+++ b/man/examples/ex_prj_constitutive_relation.R
@@ -0,0 +1,5 @@
+r2ogs6_constitutive_relation(
+ type = "LinearElasticIsotropic",
+ youngs_modulus = "E",
+ poissons_ratio = "nu"
+)
diff --git a/man/examples/ex_prj_convergence_criterion.R b/man/examples/ex_prj_convergence_criterion.R
new file mode 100644
index 0000000000000000000000000000000000000000..f34fbdd975c14ab910946782d7320250dc935f55
--- /dev/null
+++ b/man/examples/ex_prj_convergence_criterion.R
@@ -0,0 +1,6 @@
+r2ogs6_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "INFINITY_N",
+ abstol = 1e-08,
+ reltol = 1e-10
+)
diff --git a/man/examples/ex_prj_curve.R b/man/examples/ex_prj_curve.R
new file mode 100644
index 0000000000000000000000000000000000000000..26f166a2b96458dca2d015d58669a67bb663ce0d
--- /dev/null
+++ b/man/examples/ex_prj_curve.R
@@ -0,0 +1,3 @@
+r2ogs6_curve(name = "Dirichlet_temporal",
+ coords = "0 3",
+ values = "200 200")
\ No newline at end of file
diff --git a/man/examples/ex_prj_deactivated_subdomain.R b/man/examples/ex_prj_deactivated_subdomain.R
new file mode 100644
index 0000000000000000000000000000000000000000..e67be0a5eb0bc5d7ecad069bd281d8a9eef63ea2
--- /dev/null
+++ b/man/examples/ex_prj_deactivated_subdomain.R
@@ -0,0 +1,3 @@
+r2ogs6_deactivated_subdomain(time_interval = list(start = "0",
+ end = "1"),
+ material_ids = 1)
diff --git a/man/examples/ex_prj_eigen.R b/man/examples/ex_prj_eigen.R
new file mode 100644
index 0000000000000000000000000000000000000000..29aa95b4c5f9d1fa44f2676670c7274a2b567757
--- /dev/null
+++ b/man/examples/ex_prj_eigen.R
@@ -0,0 +1,6 @@
+r2ogs6_eigen(
+ solver_type = "BiCGSTAB",
+ precon_type = "ILUT",
+ max_iteration_step = 10000,
+ error_tolerance = 1e-16
+)
\ No newline at end of file
diff --git a/man/examples/ex_prj_flow_and_temperature_control.R b/man/examples/ex_prj_flow_and_temperature_control.R
new file mode 100644
index 0000000000000000000000000000000000000000..ee98437ff302fcc8421438aa3d275f0a33910757
--- /dev/null
+++ b/man/examples/ex_prj_flow_and_temperature_control.R
@@ -0,0 +1,5 @@
+r2ogs6_flow_and_temperature_control(
+ type = "TemperatureCurveConstantFlow",
+ flow_rate = 2e-04,
+ temperature_curve = "inflow_temperature"
+)
diff --git a/man/examples/ex_prj_fluid.R b/man/examples/ex_prj_fluid.R
new file mode 100644
index 0000000000000000000000000000000000000000..4805e549e7a52b4e7c9482fcc71b19c37e792499
--- /dev/null
+++ b/man/examples/ex_prj_fluid.R
@@ -0,0 +1,10 @@
+r2ogs6_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 ")
+)
diff --git a/man/examples/ex_prj_fracture_model.R b/man/examples/ex_prj_fracture_model.R
new file mode 100644
index 0000000000000000000000000000000000000000..2e6c88c4d5bdc29212d15824d8a32791f962bf76
--- /dev/null
+++ b/man/examples/ex_prj_fracture_model.R
@@ -0,0 +1,5 @@
+r2ogs6_fracture_model(type = "LinearElasticIsotropic",
+ normal_stiffness = "Kn",
+ shear_stiffness = "Ks",
+ penalty_aperture_cutoff = 1e-05,
+ tension_cutoff = 1)
diff --git a/man/examples/ex_prj_fracture_properties.R b/man/examples/ex_prj_fracture_properties.R
new file mode 100644
index 0000000000000000000000000000000000000000..9c8c9a997cb521e48efc7e898d9c10efba3fc41a
--- /dev/null
+++ b/man/examples/ex_prj_fracture_properties.R
@@ -0,0 +1,7 @@
+r2ogs6_fracture_properties(
+ material_id = 0,
+ initial_aperture = "aperture0",
+ specific_storage = "S_f",
+ biot_coefficient = "biot_f",
+ permeability_model = list(type = "CubicLaw")
+)
diff --git a/man/examples/ex_prj_global_process_coupling.R b/man/examples/ex_prj_global_process_coupling.R
new file mode 100644
index 0000000000000000000000000000000000000000..9ae65ef077912bae289dab2701e861b178113521
--- /dev/null
+++ b/man/examples/ex_prj_global_process_coupling.R
@@ -0,0 +1,11 @@
+r2ogs6_global_process_coupling(
+ max_iter = 100,
+ convergence_criteria = list(
+ convergence_criterion = r2ogs6_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "INFINITY_N",
+ abstol = 1e-08,
+ reltol = 1e-10
+ )
+ )
+)
diff --git a/man/examples/ex_prj_insitu.R b/man/examples/ex_prj_insitu.R
new file mode 100644
index 0000000000000000000000000000000000000000..83ac5fdb0c212572ecf9ca9be5a04d8207eebd5e
--- /dev/null
+++ b/man/examples/ex_prj_insitu.R
@@ -0,0 +1 @@
+r2ogs6_insitu(scripts = c(script = "square_1e1_neumann-insitu.py"))
diff --git a/man/examples/ex_prj_jacobian_assembler.R b/man/examples/ex_prj_jacobian_assembler.R
new file mode 100644
index 0000000000000000000000000000000000000000..a1b80a22a26d39b08db3031a609e0edc567ce2e4
--- /dev/null
+++ b/man/examples/ex_prj_jacobian_assembler.R
@@ -0,0 +1,5 @@
+r2ogs6_jacobian_assembler(
+ type = "CentralDifferences",
+ component_magnitudes = 1,
+ relative_epsilons = 1e-08
+)
diff --git a/man/examples/ex_prj_kinetic_reactant.R b/man/examples/ex_prj_kinetic_reactant.R
new file mode 100644
index 0000000000000000000000000000000000000000..0a8e9cd30103b46e29a4f16350eaa3074069d9bc
--- /dev/null
+++ b/man/examples/ex_prj_kinetic_reactant.R
@@ -0,0 +1,2 @@
+r2ogs6_kinetic_reactant(name = "Productc",
+ initial_amount = 1e-06)
diff --git a/man/examples/ex_prj_linear_solver.R b/man/examples/ex_prj_linear_solver.R
new file mode 100644
index 0000000000000000000000000000000000000000..e02ee09c7dbd415b4af72bc6b694248eaf0b54a7
--- /dev/null
+++ b/man/examples/ex_prj_linear_solver.R
@@ -0,0 +1,10 @@
+r2ogs6_linear_solver(
+ name = "general_linear_solver",
+ eigen = r2ogs6_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"
+)
\ No newline at end of file
diff --git a/man/examples/ex_prj_local_coordinate_system.R b/man/examples/ex_prj_local_coordinate_system.R
new file mode 100644
index 0000000000000000000000000000000000000000..b2bb3f68c87275258d54834c40bafae1bca56116
--- /dev/null
+++ b/man/examples/ex_prj_local_coordinate_system.R
@@ -0,0 +1,3 @@
+r2ogs6_local_coordinate_system(basis_vector_0 = "e0",
+ basis_vector_1 = "e1",
+ basis_vector_2 = "e2")
diff --git a/man/examples/ex_prj_material_property.R b/man/examples/ex_prj_material_property.R
new file mode 100644
index 0000000000000000000000000000000000000000..744ea511f8df219232bc8c76b6b3b173277a714a
--- /dev/null
+++ b/man/examples/ex_prj_material_property.R
@@ -0,0 +1,42 @@
+r2ogs6_material_property(
+ fluid = r2ogs6_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 = r2ogs6_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 = r2ogs6_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 = r2ogs6_relative_permeability(
+ type = "NonWettingPhaseVanGenuchten",
+ sr = 0,
+ smax = 0.6,
+ m = 0.3288590604,
+ krel_min = 0,
+ id = "0"
+ )
+ )
+ )
+ )
+)
diff --git a/man/examples/ex_prj_medium.R b/man/examples/ex_prj_medium.R
new file mode 100644
index 0000000000000000000000000000000000000000..46f3444a3f04b6fe373c823d8d817f53503c7e75
--- /dev/null
+++ b/man/examples/ex_prj_medium.R
@@ -0,0 +1,25 @@
+r2ogs6_medium(
+ phases = list(
+ phase = r2ogs6_phase(
+ type = "Gas",
+ properties = list(
+ property = r2ogs6_ph_property(name = "viscosity",
+ type = "Constant",
+ value = 1e-05)
+ )
+ ),
+ phase = r2ogs6_phase(
+ type = "Solid",
+ properties = list(
+ property = r2ogs6_ph_property(name = "porosity",
+ type = "Constant",
+ value = 0.3)
+ )
+ )
+ ),
+ properties = list(
+ property = r2ogs6_pr_property(name = "reference_temperature",
+ type = "Constant",
+ value = 293.15)
+ )
+)
diff --git a/man/examples/ex_prj_nonlinear_solver.R b/man/examples/ex_prj_nonlinear_solver.R
new file mode 100644
index 0000000000000000000000000000000000000000..2e1e62a917b821eeca3675961df20638beaa5058
--- /dev/null
+++ b/man/examples/ex_prj_nonlinear_solver.R
@@ -0,0 +1,6 @@
+r2ogs6_nonlinear_solver(
+ name = "basic_newton",
+ type = "Newton",
+ max_iter = 50,
+ linear_solver = "general_linear_solver"
+)
\ No newline at end of file
diff --git a/man/examples/ex_prj_output.R b/man/examples/ex_prj_output.R
new file mode 100644
index 0000000000000000000000000000000000000000..ff4d8ec45e33a694708c65de7427e33fff8a9046
--- /dev/null
+++ b/man/examples/ex_prj_output.R
@@ -0,0 +1,11 @@
+r2ogs6_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))
+)
diff --git a/man/examples/ex_prj_parameter.R b/man/examples/ex_prj_parameter.R
new file mode 100644
index 0000000000000000000000000000000000000000..52659945e893eec6834869d62647c4f6c1017f8d
--- /dev/null
+++ b/man/examples/ex_prj_parameter.R
@@ -0,0 +1,7 @@
+r2ogs6_parameter(name = "zero",
+ type = "Constant",
+ value = 0)
+
+r2ogs6_parameter(name = "flux_in",
+ type = "Constant",
+ value = 1e-04)
\ No newline at end of file
diff --git a/man/examples/ex_prj_ph_property.R b/man/examples/ex_prj_ph_property.R
new file mode 100644
index 0000000000000000000000000000000000000000..a400332ba57e51e55f724470397b3db74f9a1913
--- /dev/null
+++ b/man/examples/ex_prj_ph_property.R
@@ -0,0 +1,3 @@
+r2ogs6_ph_property(name = "porosity",
+ type = "Constant",
+ value = 0.3)
diff --git a/man/examples/ex_prj_phase.R b/man/examples/ex_prj_phase.R
new file mode 100644
index 0000000000000000000000000000000000000000..9e5bebbc7a0f66420cc785e5a9f2de486de7fd8c
--- /dev/null
+++ b/man/examples/ex_prj_phase.R
@@ -0,0 +1,8 @@
+r2ogs6_phase(
+ type = "Solid",
+ properties = list(
+ property = r2ogs6_ph_property(name = "porosity",
+ type = "Constant",
+ value = 0.3)
+ )
+)
diff --git a/man/examples/ex_prj_phase_component.R b/man/examples/ex_prj_phase_component.R
new file mode 100644
index 0000000000000000000000000000000000000000..6177a8be4a35f0a3e51b7e6cca28fec2b54abafd
--- /dev/null
+++ b/man/examples/ex_prj_phase_component.R
@@ -0,0 +1,5 @@
+r2ogs6_phase_component(
+ name = "Calcite",
+ saturation_index = 0,
+ initial_amount = 0.000207
+)
diff --git a/man/examples/ex_prj_phasefield_parameters.R b/man/examples/ex_prj_phasefield_parameters.R
new file mode 100644
index 0000000000000000000000000000000000000000..d70227d357aafba77471441397f86ddbfba57a4c
--- /dev/null
+++ b/man/examples/ex_prj_phasefield_parameters.R
@@ -0,0 +1,7 @@
+r2ogs6_phasefield_parameters(
+ residual_stiffness = "k",
+ crack_resistance = "gc",
+ crack_length_scale = "ls",
+ kinetic_coefficient = "M",
+ history_field = "H"
+)
diff --git a/man/examples/ex_prj_pipes.R b/man/examples/ex_prj_pipes.R
new file mode 100644
index 0000000000000000000000000000000000000000..ae6fd21d6d98b27dd374edbca09c70de865b604f
--- /dev/null
+++ b/man/examples/ex_prj_pipes.R
@@ -0,0 +1,14 @@
+r2ogs6_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
+)
diff --git a/man/examples/ex_prj_porous_medium.R b/man/examples/ex_prj_porous_medium.R
new file mode 100644
index 0000000000000000000000000000000000000000..0adf4d7efb9ab1684085c8fa9bf56cbec5a384a6
--- /dev/null
+++ b/man/examples/ex_prj_porous_medium.R
@@ -0,0 +1,28 @@
+r2ogs6_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 = r2ogs6_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 = r2ogs6_relative_permeability(
+ type = "NonWettingPhaseVanGenuchten",
+ sr = 0,
+ smax = 0.6,
+ m = 0.3288590604,
+ krel_min = 0,
+ id = "0"
+ )
+ )
+)
diff --git a/man/examples/ex_prj_pr_property.R b/man/examples/ex_prj_pr_property.R
new file mode 100644
index 0000000000000000000000000000000000000000..341bc10b7b27dff7642dcd930691fd1701525dd3
--- /dev/null
+++ b/man/examples/ex_prj_pr_property.R
@@ -0,0 +1,3 @@
+r2ogs6_pr_property(name = "reference_temperature",
+ type = "Constant",
+ value = 293.15)
diff --git a/man/examples/ex_prj_process.R b/man/examples/ex_prj_process.R
new file mode 100644
index 0000000000000000000000000000000000000000..c615361d4799583b27a73c34a4934fe901731336
--- /dev/null
+++ b/man/examples/ex_prj_process.R
@@ -0,0 +1,18 @@
+r2ogs6_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 = r2ogs6_constitutive_relation(
+ type = "LinearElasticIsotropic",
+ youngs_modulus = "E",
+ poissons_ratio = "nu"
+ )
+)
diff --git a/man/examples/ex_prj_process_variable.R b/man/examples/ex_prj_process_variable.R
new file mode 100644
index 0000000000000000000000000000000000000000..8aecaeab0000ca22092ebee7b3e6f08afb0f7fa0
--- /dev/null
+++ b/man/examples/ex_prj_process_variable.R
@@ -0,0 +1,15 @@
+r2ogs6_process_variable(
+ name = "pressure",
+ components = 1,
+ order = 1,
+ initial_condition = "pressure0",
+ boundary_conditions = list(
+ boundary_condition = r2ogs6_boundary_condition(
+ type = "Neumann",
+ parameter = "flux_in",
+ geometrical_set = "cube_1x1x1_geometry",
+ geometry = "left",
+ component = 0
+ )
+ )
+)
diff --git a/man/examples/ex_prj_rate.R b/man/examples/ex_prj_rate.R
new file mode 100644
index 0000000000000000000000000000000000000000..d9d9fcfc79e176891c34fe2e7a635037e2a83087
--- /dev/null
+++ b/man/examples/ex_prj_rate.R
@@ -0,0 +1,11 @@
+r2ogs6_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"
+ )
+)
diff --git a/man/examples/ex_prj_relative_permeability.R b/man/examples/ex_prj_relative_permeability.R
new file mode 100644
index 0000000000000000000000000000000000000000..535363602e599523636a53cdc238091ce58b0542
--- /dev/null
+++ b/man/examples/ex_prj_relative_permeability.R
@@ -0,0 +1,8 @@
+r2ogs6_relative_permeability(
+ type = "NonWettingPhaseVanGenuchten",
+ sr = 0,
+ smax = 0.6,
+ m = 0.3288590604,
+ krel_min = 0,
+ id = "0"
+)
diff --git a/man/examples/ex_prj_search_length_algorithm.R b/man/examples/ex_prj_search_length_algorithm.R
new file mode 100644
index 0000000000000000000000000000000000000000..971cec498e8d8854028b1bac54d5927c41d921a6
--- /dev/null
+++ b/man/examples/ex_prj_search_length_algorithm.R
@@ -0,0 +1,2 @@
+r2ogs6_search_length_algorithm(type = "fixed",
+ value = 1e-06)
diff --git a/man/examples/ex_prj_solution.R b/man/examples/ex_prj_solution.R
new file mode 100644
index 0000000000000000000000000000000000000000..58076b732f4c74a440eb0e90d991e20b750cc31c
--- /dev/null
+++ b/man/examples/ex_prj_solution.R
@@ -0,0 +1,10 @@
+r2ogs6_solution(
+ temperature = 25,
+ pressure = 1,
+ pe = 4,
+ components = list(
+ component = "C(4)",
+ component = "Ca"
+ ),
+ charge_balance = "pH"
+)
diff --git a/man/examples/ex_prj_source_term.R b/man/examples/ex_prj_source_term.R
new file mode 100644
index 0000000000000000000000000000000000000000..3113b8432f818c9499969f23ea4752424be26502
--- /dev/null
+++ b/man/examples/ex_prj_source_term.R
@@ -0,0 +1,6 @@
+r2ogs6_source_term(
+ type = "Nodal",
+ parameter = "sourceterm_heat_transfer_coefficient",
+ geometrical_set = "geometry",
+ geometry = "po0"
+)
diff --git a/man/examples/ex_prj_time_loop.R b/man/examples/ex_prj_time_loop.R
new file mode 100644
index 0000000000000000000000000000000000000000..8befb8e732c69fcb18bb37d1c6c1ce005041a563
--- /dev/null
+++ b/man/examples/ex_prj_time_loop.R
@@ -0,0 +1,32 @@
+r2ogs6_time_loop(
+ processes = list(
+ process = r2ogs6_tl_process(
+ ref = "HM",
+ nonlinear_solver = "basic_newton",
+ convergence_criterion = r2ogs6_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "NORM2",
+ reltol = 1e-08
+ ),
+ time_discretization = list(type = "BackwardEuler"),
+ time_stepping = r2ogs6_time_stepping(
+ type = "FixedTimeStepping",
+ t_initial = 0,
+ t_end = 10000,
+ timesteps = list(pair = list(1000,
+ delta_t = 10))
+ )
+ )
+ ),
+ output = r2ogs6_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))
+ )
+)
diff --git a/man/examples/ex_prj_time_stepping.R b/man/examples/ex_prj_time_stepping.R
new file mode 100644
index 0000000000000000000000000000000000000000..5c9a10f5f4275c46a4c95e1538b6e02b769fdae6
--- /dev/null
+++ b/man/examples/ex_prj_time_stepping.R
@@ -0,0 +1,7 @@
+r2ogs6_time_stepping(
+ type = "FixedTimeStepping",
+ t_initial = 0,
+ t_end = 10000,
+ timesteps = list(pair = list(1000,
+ delta_t = 10))
+)
diff --git a/man/examples/ex_prj_tl_process.R b/man/examples/ex_prj_tl_process.R
new file mode 100644
index 0000000000000000000000000000000000000000..5a9cf5e7ed8db6c213dc48835178767e384c64e3
--- /dev/null
+++ b/man/examples/ex_prj_tl_process.R
@@ -0,0 +1,17 @@
+r2ogs6_tl_process(
+ ref = "HM",
+ nonlinear_solver = "basic_newton",
+ convergence_criterion = r2ogs6_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "NORM2",
+ reltol = 1e-08
+ ),
+ time_discretization = list(type = "BackwardEuler"),
+ time_stepping = r2ogs6_time_stepping(
+ type = "FixedTimeStepping",
+ t_initial = 0,
+ t_end = 10000,
+ timesteps = list(pair = list(1000,
+ delta_t = 10))
+ )
+)
diff --git a/man/examples/ex_prj_vtkdiff.R b/man/examples/ex_prj_vtkdiff.R
new file mode 100644
index 0000000000000000000000000000000000000000..8029098348a17a6916cacc1cc5c74992a633043c
--- /dev/null
+++ b/man/examples/ex_prj_vtkdiff.R
@@ -0,0 +1,4 @@
+r2ogs6_vtkdiff(field = "displacement",
+ absolute_tolerance = 1e-15,
+ relative_tolerance = 0,
+ regex = "gravity_pcs_0_ts_.*_t_.*.vtu")
\ No newline at end of file
diff --git a/man/export_prj.Rd b/man/export_prj.Rd
index e2f5e24dfbbabe5633547506f522523efe45831b..6aabeb8da266cb9dc9b090a39dbecf7cea647a48 100644
--- a/man/export_prj.Rd
+++ b/man/export_prj.Rd
@@ -10,6 +10,6 @@ export_prj(ogs6_obj)
\item{ogs6_obj}{OGS6: Simulation object}
}
\description{
-Wrapper function to create a .prj XML document based on the user
-input data
+Wrapper function to create a \code{.prj} XML document based on
+the user input data
}
diff --git a/man/filter_invalid_xml.Rd b/man/filter_invalid_xml.Rd
index ab07c1bba15cf3335cc9519b81b9f0dcf8fcf99a..512b64458afecef2f05bac5407aced522c20ca1c 100644
--- a/man/filter_invalid_xml.Rd
+++ b/man/filter_invalid_xml.Rd
@@ -11,7 +11,8 @@ filter_invalid_xml(paths, encoding = "ISO-8859-1", print_messages = TRUE)
\item{encoding}{string: Optional: XML encoding. Defaults to ISO-8859-1}
-\item{print_messages}{flag: Optional: Print error messages? Defaults to TRUE}
+\item{print_messages}{flag: Optional: Print error messages? Defaults to
+\code{TRUE}}
}
\value{
character: Vector of invalid XML paths
diff --git a/man/generate_R6.Rd b/man/generate_R6.Rd
index 7bbb5ab1fc4dcf4493a8929e0fbf7c8fb58859ad..664e8232b49d006d0eaa744d1cabc95340fc9a86 100644
--- a/man/generate_R6.Rd
+++ b/man/generate_R6.Rd
@@ -7,7 +7,7 @@
generate_R6(params, prefix = "", print_result = TRUE)
}
\arguments{
-\item{params}{list: (Return value of analyse_xml())}
+\item{params}{list: (Return value of \code{analyse_xml()})}
\item{prefix}{Optional: For subclasses whose represented elements have
the same tag name as an element for which a class was already specified,
diff --git a/man/generate_add_method.Rd b/man/generate_add_method.Rd
index ab1868717f88951b7393a7ec926fbf7ce64438f6..9957c8e1f195b87069276ba371ed5c60eb5eb903 100644
--- a/man/generate_add_method.Rd
+++ b/man/generate_add_method.Rd
@@ -14,6 +14,6 @@ object}
represented by the class object}
}
\description{
-Helper function to generate an R6 add_* method for a
+Helper function to generate an R6 \code{add_*} method for a
r2ogs6 class object
}
diff --git a/man/generate_all_benchmark_scripts.Rd b/man/generate_all_benchmark_scripts.Rd
index eebd7e23f3f0e1a626de9f0f3d94580c42222c2f..3832caf0aadc4f3b15b19e5db9e067e3709fe7e0 100644
--- a/man/generate_all_benchmark_scripts.Rd
+++ b/man/generate_all_benchmark_scripts.Rd
@@ -21,17 +21,17 @@ generate_all_benchmark_scripts(
\item{scripts_path}{string: Path where benchmark scripts will be saved}
-\item{read_in_gmls}{flag: Optional: Should .gml files just be copied or read
-in too?}
+\item{read_in_gmls}{flag: Optional: Should \code{.gml} files just be copied
+or read in too?}
-\item{read_in_vtus}{flag: Optional: Should .vtu files just be copied or read
-in too?}
+\item{read_in_vtus}{flag: Optional: Should \code{.vtu} files just be copied
+or read in too?}
\item{starting_from_prj_path}{string: Optional:}
-\item{skip_prj_paths}{character: Optional: .prj paths to skip}
+\item{skip_prj_paths}{character: Optional: \code{.prj} paths to skip}
}
\description{
-Wrapper function to generate benchmark scripts from all .prj
-files in a directory
+Wrapper function to generate benchmark scripts from all
+\code{.prj} files in a directory
}
diff --git a/man/generate_benchmark_script.Rd b/man/generate_benchmark_script.Rd
index cdd5d1da7a9dae69389a23e3471d8d8c903ca81b..0df3411c426c51addcc24b22e71635b85754cd78 100644
--- a/man/generate_benchmark_script.Rd
+++ b/man/generate_benchmark_script.Rd
@@ -14,7 +14,7 @@ generate_benchmark_script(
)
}
\arguments{
-\item{prj_path}{string: .prj file the script will be based on}
+\item{prj_path}{string: \code{.prj} file the script will be based on}
\item{sim_path}{string: Path where all simulation files will be saved}
@@ -22,12 +22,12 @@ generate_benchmark_script(
\item{script_path}{string: Path where benchmark script will be saved}
-\item{read_in_gml}{flag: Optional: Should .gml file just be copied or read
-in too?}
+\item{read_in_gml}{flag: Optional: Should \code{.gml} file just be copied or
+read in too?}
-\item{read_in_vtu}{flag: Optional: Should .vtu file(s) just be copied or read
-in too?}
+\item{read_in_vtu}{flag: Optional: Should \code{.vtu} file(s) just be copied
+or read in too?}
}
\description{
-Generates a benchmark script from an existing .prj file.
+Generates a benchmark script from an existing \code{.prj} file.
}
diff --git a/man/generate_constructor.Rd b/man/generate_constructor.Rd
index 91b0b083442e2fa6b1740a84b4b52a144f23d108..e4709eba899f055184af40317b1ec6da1cb6a239 100644
--- a/man/generate_constructor.Rd
+++ b/man/generate_constructor.Rd
@@ -7,7 +7,7 @@
generate_constructor(params, prefix = "", print_result = FALSE)
}
\arguments{
-\item{params}{list: (Return value of analyse_xml())}
+\item{params}{list: (Return value of \code{analyse_xml()})}
\item{prefix}{Optional: For subclasses whose represented elements have
the same tag name as an element for which a class was already specified,
diff --git a/man/generate_helper.Rd b/man/generate_helper.Rd
index 8775ffe9b1a978a9ec2204f07a298bb686973654..92a6b422c229e57ef453cb2d24e5a2af0bc9c021 100644
--- a/man/generate_helper.Rd
+++ b/man/generate_helper.Rd
@@ -7,7 +7,7 @@
generate_helper(params, prefix = "", print_result = FALSE)
}
\arguments{
-\item{params}{list: (Return value of analyse_xml())}
+\item{params}{list: (Return value of \code{analyse_xml()})}
\item{prefix}{Optional: For subclasses whose represented elements have
the same tag name as an element for which a class was already specified,
diff --git a/man/get_class_from_xpath.Rd b/man/get_class_from_xpath.Rd
index 94377ed30b0ef91edd087c8a6050271cabf898ea..c064a55df381e43d94dfa61ae370864a402ee5d8 100644
--- a/man/get_class_from_xpath.Rd
+++ b/man/get_class_from_xpath.Rd
@@ -15,3 +15,6 @@ string: The class name.
\description{
Gets r2ogs6 class name from an xpath-like expression
}
+\examples{
+ get_class_from_xpath("processes/process")
+}
diff --git a/man/get_tag_from_class.Rd b/man/get_tag_from_class.Rd
index 04e0ba72925eeed1eed06682d7bf0aeb1667c7ee..6e4c93d72a23a62161434ef1dabf58b533d94ac9 100644
--- a/man/get_tag_from_class.Rd
+++ b/man/get_tag_from_class.Rd
@@ -10,8 +10,11 @@ get_tag_from_class(class_name)
\item{class_name}{string: The name of a r2ogs6 class}
}
\value{
-string: The tag name corresponding to `class_name`
+string: The tag name corresponding to \code{class_name}
}
\description{
Utility function, returns the tag name of a r2ogs6 class
}
+\examples{
+ get_tag_from_class("r2ogs6_process")
+}
diff --git a/man/get_tag_from_xpath.Rd b/man/get_tag_from_xpath.Rd
index bac95f3a7e7ae2a8e5195894115753a6d43172da..116a8885697ac7bc9b364533db0bcb78dd084689 100644
--- a/man/get_tag_from_xpath.Rd
+++ b/man/get_tag_from_xpath.Rd
@@ -10,8 +10,11 @@ get_tag_from_xpath(xpath)
\item{xpath}{string: An xpath expression. Works for path-like xpaths only}
}
\value{
-string: The XML tag name.
+string: The XML tag name
}
\description{
Gets the XML tag name from an xpath expression
}
+\examples{
+ get_tag_from_xpath("processes/process")
+}
diff --git a/man/is_null_or_coerce_names.Rd b/man/is_null_or_coerce_names.Rd
index 641c6e5f7119b9630ae3c4ecd6cd279c2da150b3..8b49faf8895e77f2e6031c5d7cf53258855635da 100644
--- a/man/is_null_or_coerce_names.Rd
+++ b/man/is_null_or_coerce_names.Rd
@@ -12,5 +12,5 @@ is_null_or_coerce_names(obj, names)
\item{names}{How the list elements will be named as per default}
}
\description{
-Validator function for a parameter list or vector or NULL
+Validator function for a parameter list or vector or \code{NULL}
}
diff --git a/man/is_null_or_has_class.Rd b/man/is_null_or_has_class.Rd
index d0de551bdb4c1ecd3ab85f4780b8da52f49913e0..42fc9c114e745f265697bc2fb8c7b1a3e840ca14 100644
--- a/man/is_null_or_has_class.Rd
+++ b/man/is_null_or_has_class.Rd
@@ -12,6 +12,6 @@ is_null_or_has_class(obj, class_name)
\item{class_name}{The name of the expected class}
}
\description{
-Checks if an object is either null or a class object of class
-'class_name'
+Checks if an object is either \code{NULL} or a class object of
+class \code{class_name}
}
diff --git a/man/is_null_or_wrapper_list.Rd b/man/is_null_or_wrapper_list.Rd
index a8e3f9bdf12304f1da20a632ec22a20f1e33d479..9c76eddf56a80ed99c153bea7b16c6cbfc9fef22 100644
--- a/man/is_null_or_wrapper_list.Rd
+++ b/man/is_null_or_wrapper_list.Rd
@@ -9,9 +9,9 @@ is_null_or_wrapper_list(obj, element_class)
\arguments{
\item{obj}{list | NULL: Object to check}
-\item{element_class}{string: Class each element of `obj` should have}
+\item{element_class}{string: Class each element of \code{obj} should have}
}
\description{
-Checks if an object is either NULL or a list of elements
-of class `element_class`
+Checks if an object is either \code{NULL} or a list of elements
+of class \code{element_class}
}
diff --git a/man/is_wrapper_list.Rd b/man/is_wrapper_list.Rd
index 5dbacdfed1884fadbe10560f77dd76c8591e0e6a..379ef3e83f77996962b0295484e523e1b3222391 100644
--- a/man/is_wrapper_list.Rd
+++ b/man/is_wrapper_list.Rd
@@ -9,9 +9,9 @@ is_wrapper_list(list, element_class)
\arguments{
\item{list}{list: List to check}
-\item{element_class}{string: Class each element of `list` should have}
+\item{element_class}{string: Class each element of \code{list} should have}
}
\description{
Checks if a list consists only of elements of class
-`element_class`
+\code{element_class}
}
diff --git a/man/node_to_object.Rd b/man/node_to_object.Rd
index fc6da47d8bdb5b47c5ec4135e23661d7dd5e77dd..141f78e8077e4fff783d600999cf0f7f8e03c63f 100644
--- a/man/node_to_object.Rd
+++ b/man/node_to_object.Rd
@@ -16,10 +16,6 @@ Returns representation of an XML node. This is a recursive
function.
ASSUMPTIONS:
1) Leaf nodes will never be r2ogs6_* objects
-2) If there are multiple occurrences of r2ogs6_* class (and subclass)
-elements on the same level, they have a wrapper node as their parent
-(e.g. <processes>, <properties>) which will contain ONLY elements of this
-type
-3) Wrapper nodes are represented as lists
-4) Parent nodes whose children have no children are represented as lists
+2) Wrapper nodes are represented as lists
+3) Parent nodes whose children have no children are represented as lists
}
diff --git a/man/ogs_call_ogs6.Rd b/man/ogs_call_ogs6.Rd
index 931bceca1a1d4c46a9fb63ad62cd122e641ef939..ceff868bc2f2779fa2b833bbd9d6032efb489f4a 100644
--- a/man/ogs_call_ogs6.Rd
+++ b/man/ogs_call_ogs6.Rd
@@ -9,12 +9,12 @@ ogs_call_ogs6(ogs6_obj, write_logfile = TRUE, ogs_bin_path, verbose = F)
\arguments{
\item{ogs6_obj}{OGS6: Simulation object}
-\item{write_logfile}{flag: Should output be written to a logfile? If `FALSE`,
-output will be written to console. If `TRUE`, logfile directory will be
-created in `ogs6$sim_path` directory}
+\item{write_logfile}{flag: Should output be written to a logfile? If
+\code{FALSE}, output will be written to console. If \code{TRUE}, logfile
+directory will be created in \code{ogs6$sim_path} directory}
\item{ogs_bin_path}{string: Optional: OpenGeoSys 6 bin folder path. Defaults
-to `options("r2ogs6.default_ogs_bin_path")`}
+to \code{options("r2ogs6.default_ogs_bin_path")}}
\item{verbose}{flag}
}
diff --git a/man/ogs_export_sim_files.Rd b/man/ogs_export_sim_files.Rd
index bdc0eb89a5ea5bec4b87726da11993d7e76ff6c7..6ec05b68c17fa0e45bc5faa68e1afad438dac6bf 100644
--- a/man/ogs_export_sim_files.Rd
+++ b/man/ogs_export_sim_files.Rd
@@ -9,10 +9,10 @@ ogs_export_sim_files(ogs6_obj, test_mode = FALSE)
\arguments{
\item{ogs6_obj}{OGS6: Simulation object}
-\item{test_mode}{flag: If `TRUE`, Will not check status of `ogs6_obj` before
-exporting files. Defaults to `FALSE`}
+\item{test_mode}{flag: If \code{TRUE}, Will not check status of
+\code{ogs6_obj} before exporting files. Defaults to \code{FALSE}}
}
\description{
-Creates `ogs6_obj$sim_path` directory if it does not exist yet
+Creates \code{ogs6$sim_path} directory if it does not exist yet
and exports and / or copies all simulation files to it.
}
diff --git a/man/ogs_read_output_files.Rd b/man/ogs_read_output_files.Rd
index 151d4ab30f072fb54ff04fbf8f43d0bc61457069..75216493fa3bc9614fd5a7c9a4f2827afab1d5bb 100644
--- a/man/ogs_read_output_files.Rd
+++ b/man/ogs_read_output_files.Rd
@@ -10,5 +10,5 @@ ogs_read_output_files(ogs6_obj)
\item{ogs6_obj}{OGS6: Simulation object}
}
\description{
-Read in generated .pvd files and add it to ogs6_obj
+Read in generated \code{.pvd} files and add it to ogs6_obj
}
diff --git a/man/ogs_run_simulation.Rd b/man/ogs_run_simulation.Rd
index 1070ff5e363a5a6753311c3cde10a527e93ab94f..0cb1b045cbf57d59d49330b98b988617a2ccab13 100644
--- a/man/ogs_run_simulation.Rd
+++ b/man/ogs_run_simulation.Rd
@@ -9,16 +9,16 @@ ogs_run_simulation(ogs6_obj, write_logfile = TRUE, ogs_bin_path, verbose = F)
\arguments{
\item{ogs6_obj}{OGS6: Simulation object}
-\item{write_logfile}{flag: Should output be written to a logfile? If `FALSE`,
-output will be written to console. If `TRUE`, logfile directory will be
-created in `ogs6$sim_path` directory}
+\item{write_logfile}{flag: Should output be written to a logfile? If
+\code{FALSE}, output will be written to console. If \code{TRUE}, logfile
+directory will be created in \code{ogs6$sim_path} directory}
\item{ogs_bin_path}{string: Optional: OpenGeoSys 6 bin folder path. Defaults
-to `options("r2ogs6.default_ogs_bin_path")`}
+to \code{options("r2ogs6.default_ogs_bin_path")}}
\item{verbose}{flag}
}
\description{
-Wrapper function that calls `ogs_export_sim_files`,
-`ogs_call_ogs6` and `ogs_read_output_files`.
+Wrapper function that calls \code{ogs_export_sim_files()},
+\code{ogs_call_ogs6()} and \code{ogs_read_output_files()}.
}
diff --git a/man/prj_top_level_classes.Rd b/man/prj_top_level_classes.Rd
index 8906060f6e5a3687b8649b21f6400c6d404094e2..e9e47962ceb633962bf1c1dd41f6b4f501965b2e 100644
--- a/man/prj_top_level_classes.Rd
+++ b/man/prj_top_level_classes.Rd
@@ -10,6 +10,7 @@ prj_top_level_classes()
character
}
\description{
-Returns named character vector of `OGS6` top level .prj tags
-(names) represented by r2ogs6 classes along with their class names (values).
+Returns named character vector of \code{OGS6} top level
+\code{.prj} tags (names) represented by \code{r2ogs6} classes along with their
+class names (values).
}
diff --git a/man/r2ogs6_borehole_heat_exchanger.Rd b/man/r2ogs6_borehole_heat_exchanger.Rd
index e99ad45f73d0072dddcf3569cbd565a0293efa04..a24919a58edde00b2df99af11cb1942a0f8360c4 100644
--- a/man/r2ogs6_borehole_heat_exchanger.Rd
+++ b/man/r2ogs6_borehole_heat_exchanger.Rd
@@ -32,3 +32,42 @@ r2ogs6_borehole_heat_exchanger(
\description{
tag: borehole_heat_exchanger
}
+\examples{
+r2ogs6_borehole_heat_exchanger(
+ type = "1U",
+ flow_and_temperature_control = r2ogs6_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 = r2ogs6_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"
+ )
+)
+}
diff --git a/man/r2ogs6_boundary_condition.Rd b/man/r2ogs6_boundary_condition.Rd
index bf52d28d98476af984e61ac6b8e44616e3261685..16b90a1a91736cabdeec78e77ba4692fba7adc70 100644
--- a/man/r2ogs6_boundary_condition.Rd
+++ b/man/r2ogs6_boundary_condition.Rd
@@ -83,3 +83,12 @@ r2ogs6_boundary_condition(
\description{
tag: boundary_condition
}
+\examples{
+r2ogs6_boundary_condition(
+ type = "Neumann",
+ parameter = "flux_in",
+ geometrical_set = "cube_1x1x1_geometry",
+ geometry = "left",
+ component = 0
+)
+}
diff --git a/man/r2ogs6_capillary_pressure.Rd b/man/r2ogs6_capillary_pressure.Rd
index b3db5d7ac5451aff36dd047113c26370825f4ab6..e8d53cbb4334322ee5bf17182147f6abf3492bfd 100644
--- a/man/r2ogs6_capillary_pressure.Rd
+++ b/man/r2ogs6_capillary_pressure.Rd
@@ -35,3 +35,14 @@ r2ogs6_capillary_pressure(
\description{
tag: capillary_pressure
}
+\examples{
+r2ogs6_capillary_pressure(
+ type = "vanGenuchten",
+ pd = 2e+06,
+ sr = 0.4,
+ smax = 1,
+ m = 0.3288590604,
+ pc_max = 2e+07,
+ has_regularized = "true"
+)
+}
diff --git a/man/r2ogs6_chemical_system.Rd b/man/r2ogs6_chemical_system.Rd
index c1b1f207e4a70b0d072065489d58411791655e72..65a0a5836379445fa3120e7fd8ca383c351438d7 100644
--- a/man/r2ogs6_chemical_system.Rd
+++ b/man/r2ogs6_chemical_system.Rd
@@ -41,3 +41,34 @@ r2ogs6_chemical_system(
\description{
tag: chemical_system
}
+\examples{
+r2ogs6_chemical_system(
+ chemical_solver = "Phreeqc",
+ database = "PSINA_12_07_110615_DAV_s.dat",
+ solution = r2ogs6_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 = r2ogs6_phase_component(
+ name = "Calcite",
+ saturation_index = 0,
+ initial_amount = 0.000207
+ )
+ )
+)
+}
diff --git a/man/r2ogs6_com_property.Rd b/man/r2ogs6_com_property.Rd
index 541e266d50456232437008766e8251cfab8f4224..b5b8bb2acb80ecd9e58b0ef56b02fe7507f105d0 100644
--- a/man/r2ogs6_com_property.Rd
+++ b/man/r2ogs6_com_property.Rd
@@ -18,3 +18,8 @@ r2ogs6_com_property(name, type, value = NULL, parameter_name = NULL)
\description{
tag: property
}
+\examples{
+r2ogs6_com_property(name = "molecular_diffusion",
+ type = "Constant",
+ value = 2e-09)
+}
diff --git a/man/r2ogs6_component.Rd b/man/r2ogs6_component.Rd
index 41ab4aa3886c5ee4814e16c6c23f60c18edde325..208d019f18ae0b30221c79648fbb559d8a24de68 100644
--- a/man/r2ogs6_component.Rd
+++ b/man/r2ogs6_component.Rd
@@ -14,3 +14,13 @@ r2ogs6_component(name, properties)
\description{
tag: component
}
+\examples{
+r2ogs6_component(
+ name = "concentration",
+ properties = list(
+ property = r2ogs6_com_property(name = "molecular_diffusion",
+ type = "Constant",
+ value = 2e-09)
+ )
+)
+}
diff --git a/man/r2ogs6_constitutive_relation.Rd b/man/r2ogs6_constitutive_relation.Rd
index 3c04d628ee562352cfd82f2ad9f27cd2fc95c6df..3b52baf17a339bbf9159cfeee5fa268cefb8777d 100644
--- a/man/r2ogs6_constitutive_relation.Rd
+++ b/man/r2ogs6_constitutive_relation.Rd
@@ -131,3 +131,10 @@ r2ogs6_constitutive_relation(
\description{
tag: constitutive_relation
}
+\examples{
+r2ogs6_constitutive_relation(
+ type = "LinearElasticIsotropic",
+ youngs_modulus = "E",
+ poissons_ratio = "nu"
+)
+}
diff --git a/man/r2ogs6_convergence_criterion.Rd b/man/r2ogs6_convergence_criterion.Rd
index cf8c9c4442bc8d9af5fae7ebdbdfd2603455e294..73c28e416d5d4a2ebaf39650e08d1132f595b000 100644
--- a/man/r2ogs6_convergence_criterion.Rd
+++ b/man/r2ogs6_convergence_criterion.Rd
@@ -29,3 +29,11 @@ r2ogs6_convergence_criterion(
\description{
tag: convergence_criterion
}
+\examples{
+r2ogs6_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "INFINITY_N",
+ abstol = 1e-08,
+ reltol = 1e-10
+)
+}
diff --git a/man/r2ogs6_curve.Rd b/man/r2ogs6_curve.Rd
index 88aeb1629f7e9290e8351ccb745819dbd98426a6..043c1fc9a9886172cf09363ee33230c68d188309 100644
--- a/man/r2ogs6_curve.Rd
+++ b/man/r2ogs6_curve.Rd
@@ -17,3 +17,8 @@ are given}
\description{
tag: curve, a curve
}
+\examples{
+r2ogs6_curve(name = "Dirichlet_temporal",
+ coords = "0 3",
+ values = "200 200")
+}
diff --git a/man/r2ogs6_deactivated_subdomain.Rd b/man/r2ogs6_deactivated_subdomain.Rd
index b6c0efb483edd588abe52e7c62f121cc59e8d215..a48e1c191d3235f4935ab7c8419992c5e160cba3 100644
--- a/man/r2ogs6_deactivated_subdomain.Rd
+++ b/man/r2ogs6_deactivated_subdomain.Rd
@@ -14,3 +14,8 @@ r2ogs6_deactivated_subdomain(time_interval, material_ids)
\description{
tag: deactivated_subdomain
}
+\examples{
+r2ogs6_deactivated_subdomain(time_interval = list(start = "0",
+ end = "1"),
+ material_ids = 1)
+}
diff --git a/man/r2ogs6_eigen.Rd b/man/r2ogs6_eigen.Rd
index 90380224d58be177508435459fca030603fd2df0..6d58152d09b91158c4f5542fbb37bf4a97824756 100644
--- a/man/r2ogs6_eigen.Rd
+++ b/man/r2ogs6_eigen.Rd
@@ -29,3 +29,11 @@ r2ogs6_eigen(
\description{
tag: eigen
}
+\examples{
+r2ogs6_eigen(
+ solver_type = "BiCGSTAB",
+ precon_type = "ILUT",
+ max_iteration_step = 10000,
+ error_tolerance = 1e-16
+)
+}
diff --git a/man/r2ogs6_flow_and_temperature_control.Rd b/man/r2ogs6_flow_and_temperature_control.Rd
index 0bf6abb1e8d1ebab7fb7ebded815b581b2b38209..bca6a61454533051b1cf48eafd0573324e31ef7e 100644
--- a/man/r2ogs6_flow_and_temperature_control.Rd
+++ b/man/r2ogs6_flow_and_temperature_control.Rd
@@ -29,3 +29,10 @@ r2ogs6_flow_and_temperature_control(
\description{
tag: flow_and_temperature_control
}
+\examples{
+r2ogs6_flow_and_temperature_control(
+ type = "TemperatureCurveConstantFlow",
+ flow_rate = 2e-04,
+ temperature_curve = "inflow_temperature"
+)
+}
diff --git a/man/r2ogs6_fluid.Rd b/man/r2ogs6_fluid.Rd
index beb2f7c53da00d6cb0bad1e427fa9da69f3e0337..154918d538a90f5aca4cb6c336f17be8501b0fbe 100644
--- a/man/r2ogs6_fluid.Rd
+++ b/man/r2ogs6_fluid.Rd
@@ -41,3 +41,15 @@ r2ogs6_fluid(
\description{
tag: fluid
}
+\examples{
+r2ogs6_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 ")
+)
+}
diff --git a/man/r2ogs6_fracture_model.Rd b/man/r2ogs6_fracture_model.Rd
index 8c8e4cc166447a0ddcf7999a7eb8444b61fd20e5..020b30842a44bdccb341cb4ce982f82884be8ef5 100644
--- a/man/r2ogs6_fracture_model.Rd
+++ b/man/r2ogs6_fracture_model.Rd
@@ -44,3 +44,10 @@ r2ogs6_fracture_model(
\description{
tag: fracture_model
}
+\examples{
+r2ogs6_fracture_model(type = "LinearElasticIsotropic",
+ normal_stiffness = "Kn",
+ shear_stiffness = "Ks",
+ penalty_aperture_cutoff = 1e-05,
+ tension_cutoff = 1)
+}
diff --git a/man/r2ogs6_fracture_properties.Rd b/man/r2ogs6_fracture_properties.Rd
index 8f737b9cd0b7bb0442bc52cffc1a400878c72ead..913b822eed8895ebf39154de2b3cfe65a5dda4ee 100644
--- a/man/r2ogs6_fracture_properties.Rd
+++ b/man/r2ogs6_fracture_properties.Rd
@@ -26,3 +26,12 @@ r2ogs6_fracture_properties(
\description{
tag: fracture_properties
}
+\examples{
+r2ogs6_fracture_properties(
+ material_id = 0,
+ initial_aperture = "aperture0",
+ specific_storage = "S_f",
+ biot_coefficient = "biot_f",
+ permeability_model = list(type = "CubicLaw")
+)
+}
diff --git a/man/r2ogs6_global_process_coupling.Rd b/man/r2ogs6_global_process_coupling.Rd
index 44e2d961bbc28c4b90b4d6797006c754a9455e4e..aa4343cc924bb0923cb89fed6a64c3c3f38810ca 100644
--- a/man/r2ogs6_global_process_coupling.Rd
+++ b/man/r2ogs6_global_process_coupling.Rd
@@ -15,3 +15,16 @@ Convergence criteria}
\description{
tag: global_process_coupling
}
+\examples{
+r2ogs6_global_process_coupling(
+ max_iter = 100,
+ convergence_criteria = list(
+ convergence_criterion = r2ogs6_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "INFINITY_N",
+ abstol = 1e-08,
+ reltol = 1e-10
+ )
+ )
+)
+}
diff --git a/man/r2ogs6_insitu.Rd b/man/r2ogs6_insitu.Rd
index f8a5a50618544ed6231fd2fdaf53084d5548066e..37e60376713f4d902c0ad1e3f2925de58f974eae 100644
--- a/man/r2ogs6_insitu.Rd
+++ b/man/r2ogs6_insitu.Rd
@@ -12,3 +12,6 @@ r2ogs6_insitu(scripts)
\description{
tag: insitu
}
+\examples{
+r2ogs6_insitu(scripts = c(script = "square_1e1_neumann-insitu.py"))
+}
diff --git a/man/r2ogs6_jacobian_assembler.Rd b/man/r2ogs6_jacobian_assembler.Rd
index 9d8b15bdec521edee1095fde9d4fec52106de0c4..5c582422215e5dffe844b77a0d576e62a5bf212e 100644
--- a/man/r2ogs6_jacobian_assembler.Rd
+++ b/man/r2ogs6_jacobian_assembler.Rd
@@ -20,3 +20,10 @@ r2ogs6_jacobian_assembler(
\description{
tag: jacobian_assembler
}
+\examples{
+r2ogs6_jacobian_assembler(
+ type = "CentralDifferences",
+ component_magnitudes = 1,
+ relative_epsilons = 1e-08
+)
+}
diff --git a/man/r2ogs6_kinetic_reactant.Rd b/man/r2ogs6_kinetic_reactant.Rd
index e41d39b5dcdecd0198783592e67f43726da5aa53..522694029905a4add88955c19de785ec5cf89d20 100644
--- a/man/r2ogs6_kinetic_reactant.Rd
+++ b/man/r2ogs6_kinetic_reactant.Rd
@@ -23,3 +23,7 @@ r2ogs6_kinetic_reactant(
\description{
S3 class describing .prj kinetic_reactant
}
+\examples{
+r2ogs6_kinetic_reactant(name = "Productc",
+ initial_amount = 1e-06)
+}
diff --git a/man/r2ogs6_linear_solver.Rd b/man/r2ogs6_linear_solver.Rd
index 0b0182f40c682c8e2699c7d9addb8d1a5f21d15f..f1695c2a452f111014bfc852a270b53ebbc2cdd1 100644
--- a/man/r2ogs6_linear_solver.Rd
+++ b/man/r2ogs6_linear_solver.Rd
@@ -18,3 +18,15 @@ r2ogs6_linear_solver(name, eigen = NULL, lis = NULL, petsc = NULL)
\description{
tag: linear_solver
}
+\examples{
+r2ogs6_linear_solver(
+ name = "general_linear_solver",
+ eigen = r2ogs6_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"
+)
+}
diff --git a/man/r2ogs6_local_coordinate_system.Rd b/man/r2ogs6_local_coordinate_system.Rd
index 2e5ca5b3170ba8cd251a12a53fc2c143bf0d742d..11609bb6e2512fcac0cc3d5ed0f8cac1a4d320ac 100644
--- a/man/r2ogs6_local_coordinate_system.Rd
+++ b/man/r2ogs6_local_coordinate_system.Rd
@@ -20,3 +20,8 @@ r2ogs6_local_coordinate_system(
\description{
tag: local_coordinate_system
}
+\examples{
+r2ogs6_local_coordinate_system(basis_vector_0 = "e0",
+ basis_vector_1 = "e1",
+ basis_vector_2 = "e2")
+}
diff --git a/man/r2ogs6_material_property.Rd b/man/r2ogs6_material_property.Rd
index 448f556fd5065165c3c899f2844447d95fec7984..880c17d2dfc26402c8cf2d640ed145ab3b42a604 100644
--- a/man/r2ogs6_material_property.Rd
+++ b/man/r2ogs6_material_property.Rd
@@ -14,3 +14,47 @@ r2ogs6_material_property(fluid, porous_medium)
\description{
tag: material_property
}
+\examples{
+r2ogs6_material_property(
+ fluid = r2ogs6_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 = r2ogs6_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 = r2ogs6_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 = r2ogs6_relative_permeability(
+ type = "NonWettingPhaseVanGenuchten",
+ sr = 0,
+ smax = 0.6,
+ m = 0.3288590604,
+ krel_min = 0,
+ id = "0"
+ )
+ )
+ )
+ )
+)
+}
diff --git a/man/r2ogs6_medium.Rd b/man/r2ogs6_medium.Rd
index a4431cf95440c5a39082a97e37f769b874dd4c22..84917d079f811457a85ea1ac1f53b5700b95ee81 100644
--- a/man/r2ogs6_medium.Rd
+++ b/man/r2ogs6_medium.Rd
@@ -15,5 +15,32 @@ r2ogs6_medium(phases = NULL, properties = NULL, id = NULL)
}
\description{
tag: medium, a specific medium with optional id corresponding
-to the MaterialIDs
+ to the MaterialIDs
+}
+\examples{
+r2ogs6_medium(
+ phases = list(
+ phase = r2ogs6_phase(
+ type = "Gas",
+ properties = list(
+ property = r2ogs6_ph_property(name = "viscosity",
+ type = "Constant",
+ value = 1e-05)
+ )
+ ),
+ phase = r2ogs6_phase(
+ type = "Solid",
+ properties = list(
+ property = r2ogs6_ph_property(name = "porosity",
+ type = "Constant",
+ value = 0.3)
+ )
+ )
+ ),
+ properties = list(
+ property = r2ogs6_pr_property(name = "reference_temperature",
+ type = "Constant",
+ value = 293.15)
+ )
+)
}
diff --git a/man/r2ogs6_nonlinear_solver.Rd b/man/r2ogs6_nonlinear_solver.Rd
index 862972c15c2e1d878384a622a7c1cb22ee06e08b..e127818f2398ee76d06eb0cd27849c21947f53ff 100644
--- a/man/r2ogs6_nonlinear_solver.Rd
+++ b/man/r2ogs6_nonlinear_solver.Rd
@@ -20,3 +20,11 @@ r2ogs6_nonlinear_solver(name, type, max_iter, linear_solver, damping = NULL)
\description{
tag: nonlinear_solver
}
+\examples{
+r2ogs6_nonlinear_solver(
+ name = "basic_newton",
+ type = "Newton",
+ max_iter = 50,
+ linear_solver = "general_linear_solver"
+)
+}
diff --git a/man/r2ogs6_output.Rd b/man/r2ogs6_output.Rd
index 78e5f50ac0d998cd516d2770b1c2175371e24871..e9e5cced99053680d90c950412bb1f08a25255ec 100644
--- a/man/r2ogs6_output.Rd
+++ b/man/r2ogs6_output.Rd
@@ -42,3 +42,16 @@ Either "true" or "false"}
\description{
tag: output
}
+\examples{
+r2ogs6_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))
+)
+}
diff --git a/man/r2ogs6_parameter.Rd b/man/r2ogs6_parameter.Rd
index 2b33b1bafe1f5ec0b14eca3f3ba56bbbc5b4b2e7..a7d96c6a078fe8542da2d6de2f3ecf602939ea96 100644
--- a/man/r2ogs6_parameter.Rd
+++ b/man/r2ogs6_parameter.Rd
@@ -48,3 +48,12 @@ multiple)}
\description{
tag: parameter
}
+\examples{
+r2ogs6_parameter(name = "zero",
+ type = "Constant",
+ value = 0)
+
+r2ogs6_parameter(name = "flux_in",
+ type = "Constant",
+ value = 1e-04)
+}
diff --git a/man/r2ogs6_ph_property.Rd b/man/r2ogs6_ph_property.Rd
index afe8dc0924a6bfac7da23c75553a93cbc13fe7e6..f334fff1c0280166f6370b00ec77a129ee0c17ce 100644
--- a/man/r2ogs6_ph_property.Rd
+++ b/man/r2ogs6_ph_property.Rd
@@ -59,3 +59,8 @@ r2ogs6_ph_property(
\description{
tag: property
}
+\examples{
+r2ogs6_ph_property(name = "porosity",
+ type = "Constant",
+ value = 0.3)
+}
diff --git a/man/r2ogs6_phase.Rd b/man/r2ogs6_phase.Rd
index af754f8466ad5a54c5dd582b4dca491af49e4672..304d45c5bf0b2d0fd75786b304d260c4f9c3ace5 100644
--- a/man/r2ogs6_phase.Rd
+++ b/man/r2ogs6_phase.Rd
@@ -17,3 +17,13 @@ r2ogs6_phase(type, properties = NULL, components = NULL)
\description{
tag: phase, a coherent material with homogeneous properties
}
+\examples{
+r2ogs6_phase(
+ type = "Solid",
+ properties = list(
+ property = r2ogs6_ph_property(name = "porosity",
+ type = "Constant",
+ value = 0.3)
+ )
+)
+}
diff --git a/man/r2ogs6_phase_component.Rd b/man/r2ogs6_phase_component.Rd
index bbb3570617365f2ba0e19d6374c8421db3283c52..2ae1eb33fabf01ac5bf4e42496ef550896833d47 100644
--- a/man/r2ogs6_phase_component.Rd
+++ b/man/r2ogs6_phase_component.Rd
@@ -16,3 +16,10 @@ r2ogs6_phase_component(name, saturation_index, initial_amount = NULL)
\description{
S3 class describing .prj phase_component
}
+\examples{
+r2ogs6_phase_component(
+ name = "Calcite",
+ saturation_index = 0,
+ initial_amount = 0.000207
+)
+}
diff --git a/man/r2ogs6_phasefield_parameters.Rd b/man/r2ogs6_phasefield_parameters.Rd
index eca7f7903cbf00c512532c1dd18dcacbcf01cc58..2b8fae79d6c74880e3e353c5aaa530bffbe10ec4 100644
--- a/man/r2ogs6_phasefield_parameters.Rd
+++ b/man/r2ogs6_phasefield_parameters.Rd
@@ -26,3 +26,12 @@ r2ogs6_phasefield_parameters(
\description{
tag: phasefield_parameters
}
+\examples{
+r2ogs6_phasefield_parameters(
+ residual_stiffness = "k",
+ crack_resistance = "gc",
+ crack_length_scale = "ls",
+ kinetic_coefficient = "M",
+ history_field = "H"
+)
+}
diff --git a/man/r2ogs6_pipes.Rd b/man/r2ogs6_pipes.Rd
index 0964723926959a7742192bd7cc7462fa8e537317..d03d055bf895a0f88c1bd0fce1b029eb5336f1a3 100644
--- a/man/r2ogs6_pipes.Rd
+++ b/man/r2ogs6_pipes.Rd
@@ -29,3 +29,19 @@ r2ogs6_pipes(
\description{
tag: pipes
}
+\examples{
+r2ogs6_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
+)
+}
diff --git a/man/r2ogs6_porous_medium.Rd b/man/r2ogs6_porous_medium.Rd
index 742d823cd8b30631b0c4e0ab3e7b90675061a5fa..fba9e7ff8fefc57806a2e47e018835f283cb5711 100644
--- a/man/r2ogs6_porous_medium.Rd
+++ b/man/r2ogs6_porous_medium.Rd
@@ -29,3 +29,33 @@ r2ogs6_porous_medium(
\description{
tag: porous_medium
}
+\examples{
+r2ogs6_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 = r2ogs6_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 = r2ogs6_relative_permeability(
+ type = "NonWettingPhaseVanGenuchten",
+ sr = 0,
+ smax = 0.6,
+ m = 0.3288590604,
+ krel_min = 0,
+ id = "0"
+ )
+ )
+)
+}
diff --git a/man/r2ogs6_pr_property.Rd b/man/r2ogs6_pr_property.Rd
index 5028f3fbf977565b610e7b2b3ba8c9c6ae21e916..c77c01496f7e7391bee1679f94f5a4a49e4cfc2d 100644
--- a/man/r2ogs6_pr_property.Rd
+++ b/man/r2ogs6_pr_property.Rd
@@ -110,3 +110,8 @@ r2ogs6_pr_property(
\description{
tag: property
}
+\examples{
+r2ogs6_pr_property(name = "reference_temperature",
+ type = "Constant",
+ value = 293.15)
+}
diff --git a/man/r2ogs6_process.Rd b/man/r2ogs6_process.Rd
index f1e926b5b1155c7855afd025ef5b66e95f00496d..f338095a882d4306c8af2dad5006ddedc115e265 100644
--- a/man/r2ogs6_process.Rd
+++ b/man/r2ogs6_process.Rd
@@ -218,3 +218,23 @@ r2ogs6_process(
\description{
tag: process (parent tag: processes)
}
+\examples{
+r2ogs6_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 = r2ogs6_constitutive_relation(
+ type = "LinearElasticIsotropic",
+ youngs_modulus = "E",
+ poissons_ratio = "nu"
+ )
+)
+}
diff --git a/man/r2ogs6_process_variable.Rd b/man/r2ogs6_process_variable.Rd
index b4b12e99acf781b8774c648d75b5046fee0a8389..112984c3159cc4a39568bdb4bb39a94c0c84c3ee 100644
--- a/man/r2ogs6_process_variable.Rd
+++ b/man/r2ogs6_process_variable.Rd
@@ -35,3 +35,20 @@ r2ogs6_process_variable(
\description{
tag: process_variable
}
+\examples{
+r2ogs6_process_variable(
+ name = "pressure",
+ components = 1,
+ order = 1,
+ initial_condition = "pressure0",
+ boundary_conditions = list(
+ boundary_condition = r2ogs6_boundary_condition(
+ type = "Neumann",
+ parameter = "flux_in",
+ geometrical_set = "cube_1x1x1_geometry",
+ geometry = "left",
+ component = 0
+ )
+ )
+)
+}
diff --git a/man/r2ogs6_rate.Rd b/man/r2ogs6_rate.Rd
index 7c7b9eab0722b5f03c3ff98134580b98d5ae3fe3..c534c779bec86f15e8d2bef25aa35b10b3fbf24e 100644
--- a/man/r2ogs6_rate.Rd
+++ b/man/r2ogs6_rate.Rd
@@ -14,3 +14,16 @@ r2ogs6_rate(kinetic_reactant, expression)
\description{
S3 class describing .prj rate
}
+\examples{
+r2ogs6_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"
+ )
+)
+}
diff --git a/man/r2ogs6_relative_permeability.Rd b/man/r2ogs6_relative_permeability.Rd
index cd82b1c0ae93424d9c8f93bead5b3541fc7fc20a..1db4fb619207925d2a16127e28386b2326dffb66 100644
--- a/man/r2ogs6_relative_permeability.Rd
+++ b/man/r2ogs6_relative_permeability.Rd
@@ -22,3 +22,13 @@ r2ogs6_relative_permeability(type, sr, smax, m, krel_min, id = NULL)
\description{
tag: relative_permeability
}
+\examples{
+r2ogs6_relative_permeability(
+ type = "NonWettingPhaseVanGenuchten",
+ sr = 0,
+ smax = 0.6,
+ m = 0.3288590604,
+ krel_min = 0,
+ id = "0"
+)
+}
diff --git a/man/r2ogs6_search_length_algorithm.Rd b/man/r2ogs6_search_length_algorithm.Rd
index 07745676ac0b200a8c6b7cd1ac9b468ffa68ca0b..42fd636c5e68b34ef91b51691f99db5f10f55cf3 100644
--- a/man/r2ogs6_search_length_algorithm.Rd
+++ b/man/r2ogs6_search_length_algorithm.Rd
@@ -14,3 +14,7 @@ r2ogs6_search_length_algorithm(type, value = NULL)
\description{
tag: search_length_algorithm
}
+\examples{
+r2ogs6_search_length_algorithm(type = "fixed",
+ value = 1e-06)
+}
diff --git a/man/r2ogs6_solution.Rd b/man/r2ogs6_solution.Rd
index 0d9fe49c5ddb22a61ed0e0963fe50b20caf82899..42e87bd688abff9ea5ebba8bd3a38bcff8471844 100644
--- a/man/r2ogs6_solution.Rd
+++ b/man/r2ogs6_solution.Rd
@@ -20,3 +20,15 @@ r2ogs6_solution(temperature, pressure, pe, components, charge_balance = NULL)
\description{
tag: solution
}
+\examples{
+r2ogs6_solution(
+ temperature = 25,
+ pressure = 1,
+ pe = 4,
+ components = list(
+ component = "C(4)",
+ component = "Ca"
+ ),
+ charge_balance = "pH"
+)
+}
diff --git a/man/r2ogs6_source_term.Rd b/man/r2ogs6_source_term.Rd
index 57f5b7d126d86ed585a99f06dd4b2c21ed850258..cc7be19f0b09863c2806b03e66e16136faf2d824 100644
--- a/man/r2ogs6_source_term.Rd
+++ b/man/r2ogs6_source_term.Rd
@@ -29,3 +29,11 @@ r2ogs6_source_term(
\description{
tag: source_term
}
+\examples{
+r2ogs6_source_term(
+ type = "Nodal",
+ parameter = "sourceterm_heat_transfer_coefficient",
+ geometrical_set = "geometry",
+ geometry = "po0"
+)
+}
diff --git a/man/r2ogs6_time_loop.Rd b/man/r2ogs6_time_loop.Rd
index a61f6d1fd973a4ea125fd53b8f5ad048b2874302..7c2c3dd37b1ad0e7f8a1a9375589a949a978dfc4 100644
--- a/man/r2ogs6_time_loop.Rd
+++ b/man/r2ogs6_time_loop.Rd
@@ -16,3 +16,37 @@ r2ogs6_time_loop(processes, output, global_process_coupling = NULL)
\description{
tag: time_loop
}
+\examples{
+r2ogs6_time_loop(
+ processes = list(
+ process = r2ogs6_tl_process(
+ ref = "HM",
+ nonlinear_solver = "basic_newton",
+ convergence_criterion = r2ogs6_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "NORM2",
+ reltol = 1e-08
+ ),
+ time_discretization = list(type = "BackwardEuler"),
+ time_stepping = r2ogs6_time_stepping(
+ type = "FixedTimeStepping",
+ t_initial = 0,
+ t_end = 10000,
+ timesteps = list(pair = list(1000,
+ delta_t = 10))
+ )
+ )
+ ),
+ output = r2ogs6_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))
+ )
+)
+}
diff --git a/man/r2ogs6_time_stepping.Rd b/man/r2ogs6_time_stepping.Rd
index 4d1a4f07fcf13f8cbcf7e69b29d1dc1817d076a6..28f8b259bb0717a0459abea91e7f1e5dbcffc8ab 100644
--- a/man/r2ogs6_time_stepping.Rd
+++ b/man/r2ogs6_time_stepping.Rd
@@ -56,3 +56,12 @@ r2ogs6_time_stepping(
\description{
tag: time_stepping
}
+\examples{
+r2ogs6_time_stepping(
+ type = "FixedTimeStepping",
+ t_initial = 0,
+ t_end = 10000,
+ timesteps = list(pair = list(1000,
+ delta_t = 10))
+)
+}
diff --git a/man/r2ogs6_tl_process.Rd b/man/r2ogs6_tl_process.Rd
index e4e8fb500bf0a8a860ecb9a987310e2d4e996400..c43bb4cfa88ae1fa6a0832a4fcf923ccb27dc743 100644
--- a/man/r2ogs6_tl_process.Rd
+++ b/man/r2ogs6_tl_process.Rd
@@ -30,3 +30,22 @@ r2ogs6_tl_process(
\description{
tag: process (parent: time_loop, NOT processes!)
}
+\examples{
+r2ogs6_tl_process(
+ ref = "HM",
+ nonlinear_solver = "basic_newton",
+ convergence_criterion = r2ogs6_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "NORM2",
+ reltol = 1e-08
+ ),
+ time_discretization = list(type = "BackwardEuler"),
+ time_stepping = r2ogs6_time_stepping(
+ type = "FixedTimeStepping",
+ t_initial = 0,
+ t_end = 10000,
+ timesteps = list(pair = list(1000,
+ delta_t = 10))
+ )
+)
+}
diff --git a/man/r2ogs6_vtkdiff.Rd b/man/r2ogs6_vtkdiff.Rd
index 0ab8165d3aaadbf3506e681d9a20d19c3c041557..534a35b4ec4965b75ecf342f428fab214b4f6228 100644
--- a/man/r2ogs6_vtkdiff.Rd
+++ b/man/r2ogs6_vtkdiff.Rd
@@ -26,3 +26,9 @@ r2ogs6_vtkdiff(
\description{
tag: vtkdiff
}
+\examples{
+r2ogs6_vtkdiff(field = "displacement",
+ absolute_tolerance = 1e-15,
+ relative_tolerance = 0,
+ regex = "gravity_pcs_0_ts_.*_t_.*.vtu")
+}
diff --git a/man/read_in_points.Rd b/man/read_in_points.Rd
index e0956b9ccb297636f9404e61780cb1b704cf399e..2b486cf2cf37efbdf536f7142640b60ba31ebc1b 100644
--- a/man/read_in_points.Rd
+++ b/man/read_in_points.Rd
@@ -7,8 +7,8 @@
read_in_points(xml_doc)
}
\arguments{
-\item{xml_doc}{A parsed XML document (of class 'xml2::xml_document')}
+\item{xml_doc}{A parsed XML document (of class \code{xml2::xml_document})}
}
\description{
-Reads points from a .gml file
+Reads points from a \code{.gml} file
}
diff --git a/man/read_in_polylines.Rd b/man/read_in_polylines.Rd
index 242ac2a1d728666c394b8247f55a3b895d7d89c1..69b60ffc3521c4ab8310c698dc0ce63578e77489 100644
--- a/man/read_in_polylines.Rd
+++ b/man/read_in_polylines.Rd
@@ -7,8 +7,8 @@
read_in_polylines(xml_doc)
}
\arguments{
-\item{xml_doc}{A parsed XML document (of class 'xml2::xml_document')}
+\item{xml_doc}{A parsed XML document (of class \code{xml2::xml_document})}
}
\description{
-Reads polylines from a .gml file
+Reads polylines from a \code{.gml} file
}
diff --git a/man/read_in_prj.Rd b/man/read_in_prj.Rd
index 3d5b8bc49334b1a7d87c4bedb9cd544e3d8087ec..314aada86924e6393e009a32e60871d3528d0caa 100644
--- a/man/read_in_prj.Rd
+++ b/man/read_in_prj.Rd
@@ -9,15 +9,16 @@ read_in_prj(ogs6_obj, prj_path, read_in_gml, read_in_vtu = FALSE)
\arguments{
\item{ogs6_obj}{OGS6: Simulation object}
-\item{prj_path}{string: Path to the project file that should be read in}
+\item{prj_path}{string: Path to the \code{.prj} file that should be read in}
-\item{read_in_gml}{flag: Optional: Should .gml file just be copied or read in
-too? If this parameter is missing and the .gml file contains <=
-`options("r2ogs6.max_lines_gml")`, the .gml will be read in. Else, only the
-geometry reference will be saved.}
+\item{read_in_gml}{flag: Optional: Should \code{.gml} file just be copied or
+read in too? If this parameter is missing and the \code{.gml} file contains
+<= \code{options("r2ogs6.max_lines_gml")}, the \code{.gml} will be read in.
+Else, only the geometry reference will be saved.}
-\item{read_in_vtu}{flag: Should .vtu file just be copied or read in too?}
+\item{read_in_vtu}{flag: Should \code{.vtu} file just be copied or read in
+too?}
}
\description{
-Wrapper function to read in a whole .prj file
+Wrapper function to read in a whole \code{.prj} file
}
diff --git a/man/read_in_surfaces.Rd b/man/read_in_surfaces.Rd
index f197240d1f0d7cdbf3142a1b1aae83b5144725d3..ded5155738587b478b3c9f14a54a20fcc870fdcc 100644
--- a/man/read_in_surfaces.Rd
+++ b/man/read_in_surfaces.Rd
@@ -7,8 +7,8 @@
read_in_surfaces(xml_doc)
}
\arguments{
-\item{xml_doc}{A parsed XML document (of class 'xml2::xml_document')}
+\item{xml_doc}{A parsed XML document (of class \code{xml2::xml_document})}
}
\description{
-Reads surfaces from a .gml file
+Reads surfaces from a \code{.gml} file
}
diff --git a/man/run_all_benchmarks.Rd b/man/run_all_benchmarks.Rd
index e69498cecab2e1f1c68ba416604d5e6f0ed24b8c..caac9a41641ce18d3bb57882a5cd8dfcd28f460a 100644
--- a/man/run_all_benchmarks.Rd
+++ b/man/run_all_benchmarks.Rd
@@ -23,7 +23,7 @@ which contains relevant Tests.cmake files}
\item{sim_path}{string: Path where simulation files will be saved}
-\item{starting_from_prj_path}{string: .prj path to start from}
+\item{starting_from_prj_path}{string: \code{.prj} path to start from}
\item{print_results}{flag: Print results in the end?}
}
diff --git a/man/validate_read_in_xml.Rd b/man/validate_read_in_xml.Rd
index 6177cf85e9b9b6fae0eb47bc43d446b4944638f8..c97deee00c15d2e2fc3886b7d052f38eff18c3ac 100644
--- a/man/validate_read_in_xml.Rd
+++ b/man/validate_read_in_xml.Rd
@@ -10,7 +10,8 @@ validate_read_in_xml(path)
\item{path}{string: A file to be parsed as XML}
}
\value{
-The parsed XML file (as class object of type xml2::xml_document)
+The parsed XML file (as class object of type
+\code{xml2::xml_document})
}
\description{
Utility function, tries parsing the provided file as an XML