[doc] updated doc for read_in_prj classes

[doc] documentation for the updated classes

[doc] documentation for new keywords

[doc] documentation for prj_com_property

DESCRIPTION

@@ -50,7 +50,7 @@ Imports:
     config,
     sticky,
     foreach
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 VignetteBuilder: knitr
 Depends: 
     R (>= 2.10)

NAMESPACE

@@ -28,6 +28,7 @@ export(prj_convergence_criterion)
 export(prj_curve)
 export(prj_deactivated_subdomain)
 export(prj_eigen)
+export(prj_exchangers)
 export(prj_flow_and_temperature_control)
 export(prj_fluid)
 export(prj_fracture_model)

R/prj_medium.R

@@ -595,6 +595,11 @@ new_prj_component <- function(name,
 #' @param reference_diffusion Optional: character
 #' @param activation_energy Optional: string | double
 #' @param reference_temperature Optional: numeric
+#' @param triple_temperature Optional: numeric
+#' @param triple_pressure Optional: numeric
+#' @param critical_temperature Optional: numeric
+#' @param critical_pressure Optional: numeric
+#' @param reference_pressure Optional: numeric
 #' @example man/examples/ex_prj_com_property.R
 #' @export
 prj_com_property <- function(name,

man/OGS6.Rd

@@ -37,6 +37,15 @@ 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$update_component`
+## ------------------------------------------------
+
+\dontrun{ogs6_obj$update_component(list(
+                   list("ogs6_obj$parameters[[1]]$value", 2.3),
+                   list("ogs6_obj$media[[1]]$properties[[2]]$value",
+                        1.0e-3)))}
+
 ## ------------------------------------------------
 ## Method `OGS6$get_status`
 ## ------------------------------------------------
@@ -113,6 +122,7 @@ ogs6_obj$get_status()
 \item \href{#method-add}{\code{OGS6$add()}}
 \item \href{#method-add_gml}{\code{OGS6$add_gml()}}
 \item \href{#method-add_vtu}{\code{OGS6$add_vtu()}}
+\item \href{#method-update_component}{\code{OGS6$update_component()}}
 \item \href{#method-get_status}{\code{OGS6$get_status()}}
 \item \href{#method-print}{\code{OGS6$print()}}
 \item \href{#method-print_log}{\code{OGS6$print_log()}}
@@ -235,6 +245,36 @@ ogs6_obj$add_vtu("this_works.vtu")
 
 }
 
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-update_component"></a>}}
+\if{latex}{\out{\hypertarget{method-update_component}{}}}
+\subsection{Method \code{update_component()}}{
+Update a component of the \code{OGS6} object.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6$update_component(cmpts)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{cmpts}}{list(sublist, length(sublist) == 2): The first element
+of a sublist is a character that calls an \code{OGS6} component, the
+second one is the corresponding value.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{ogs6_obj$update_component(list(
+                   list("ogs6_obj$parameters[[1]]$value", 2.3),
+                   list("ogs6_obj$media[[1]]$properties[[2]]$value",
+                        1.0e-3)))}
+}
+\if{html}{\out{</div>}}
+
+}
+
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-get_status"></a>}}

man/ogs6_generate_benchmark_script.Rd

@@ -9,7 +9,7 @@ ogs6_generate_benchmark_script(
   sim_path,
   ogs6_bin_path,
   script_path,
-  read_in_gml,
+  read_in_gml = FALSE,
   read_in_vtu = FALSE
 )
 }

man/ogs6_generate_benchmark_scripts.Rd

@@ -11,7 +11,8 @@ ogs6_generate_benchmark_scripts(
   read_in_gml,
   read_in_vtu = FALSE,
   starting_from_prj_path = "",
-  skip_prj_paths = character()
+  skip_prj_paths = character(),
+  only_prj_files = character()
 )
 }
 \arguments{
@@ -30,6 +31,8 @@ or read in too?}
 \item{starting_from_prj_path}{string: Optional: `.prj` path to start from}
 
 \item{skip_prj_paths}{character: Optional: `.prj` paths to skip}
+
+\item{only_prj_files}{character: Optional: `.prj` files to limit to.}
 }
 \description{
 This is a wrapper function for `ogs6_generate_benchmark_script()`.

man/prj_chemical_system.Rd

@@ -14,7 +14,9 @@ prj_chemical_system(
   rates = NULL,
   equilibrium_reactants = NULL,
   surface = NULL,
-  user_punch = NULL
+  user_punch = NULL,
+  linear_solver = NULL,
+  exchangers = NULL
 )
 }
 \arguments{
@@ -37,6 +39,10 @@ prj_chemical_system(
 \item{surface}{Optional:}
 
 \item{user_punch}{Optional:}
+
+\item{linear_solver}{Optional:}
+
+\item{exchangers}{Optional: prj_exchangers}
 }
 \description{
 tag: chemical_system

man/prj_com_property.Rd

@@ -4,7 +4,20 @@
 \alias{prj_com_property}
 \title{prj_com_property}
 \usage{
-prj_com_property(name, type, value = NULL, parameter_name = NULL)
+prj_com_property(
+  name,
+  type,
+  value = NULL,
+  parameter_name = NULL,
+  reference_diffusion = NULL,
+  activation_energy = NULL,
+  reference_temperature = NULL,
+  triple_temperature = NULL,
+  triple_pressure = NULL,
+  critical_temperature = NULL,
+  critical_pressure = NULL,
+  reference_pressure = NULL
+)
 }
 \arguments{
 \item{name}{string: Property name}
@@ -14,6 +27,22 @@ prj_com_property(name, type, value = NULL, parameter_name = NULL)
 \item{value}{Optional: string | double: ...}
 
 \item{parameter_name}{Optional:}
+
+\item{reference_diffusion}{Optional: character}
+
+\item{activation_energy}{Optional: string | double}
+
+\item{reference_temperature}{Optional: numeric}
+
+\item{triple_temperature}{Optional: numeric}
+
+\item{triple_pressure}{Optional: numeric}
+
+\item{critical_temperature}{Optional: numeric}
+
+\item{critical_pressure}{Optional: numeric}
+
+\item{reference_pressure}{Optional: numeric}
 }
 \description{
 tag: property

man/prj_exchangers.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_chemical_system.R
+\name{prj_exchangers}
+\alias{prj_exchangers}
+\title{prj_exchangers}
+\usage{
+prj_exchangers(exchange_site)
+}
+\arguments{
+\item{exchange_site}{list}
+}
+\description{
+tag: exchangers
+}

man/prj_output.Rd

@@ -14,7 +14,8 @@ prj_output(
   data_mode = NULL,
   output_iteration_results = NULL,
   meshes = NULL,
-  fixed_output_times = NULL
+  fixed_output_times = NULL,
+  hdf = NULL
 )
 }
 \arguments{
@@ -38,6 +39,8 @@ Either "true" or "false"}
 \item{meshes}{Optional: character: A vector of mesh names}
 
 \item{fixed_output_times}{Optional: string | numeric:}
+
+\item{hdf}{Optional: numeric}
 }
 \description{
 tag: output

man/prj_parameter.Rd

@@ -16,6 +16,8 @@ prj_parameter(
   mesh = NULL,
   time_series = NULL,
   use_local_coordinate_system = NULL,
+  range = NULL,
+  seed = NULL,
   ...
 )
 }
@@ -42,6 +44,10 @@ prj_parameter(
 
 \item{use_local_coordinate_system}{Optional: string, "true" | "false":}
 
+\item{range}{Optional: list}
+
+\item{seed}{Optional: number}
+
 \item{...}{Optional: for index_values and expression tags (since there can be
 multiple)}
 }

man/prj_phasefield_parameters.Rd

@@ -8,7 +8,7 @@ prj_phasefield_parameters(
   residual_stiffness,
   crack_resistance,
   crack_length_scale,
-  kinetic_coefficient,
+  kinetic_coefficient = NULL,
   history_field = NULL
 )
 }

man/prj_pr_property.Rd

@@ -27,8 +27,13 @@ prj_pr_property(
   intrinsic_permeability = NULL,
   initial_aperture = NULL,
   mean_frac_distance = NULL,
+  mean_frac_distances = NULL,
   threshold_strain = NULL,
+  threshold_strains = NULL,
   fracture_normal = NULL,
+  fracture_normals = NULL,
+  fracture_rotation_xy = NULL,
+  fracture_rotation_yz = NULL,
   reference_permeability = NULL,
   fitting_factor = NULL,
   cohesion = NULL,
@@ -88,10 +93,20 @@ prj_pr_property(
 
 \item{mean_frac_distance}{Optional:}
 
+\item{mean_frac_distances}{Optional: numeric vector}
+
 \item{threshold_strain}{Optional:}
 
+\item{threshold_strains}{Optional: numeric vector}
+
 \item{fracture_normal}{Optional:}
 
+\item{fracture_normals}{Optional: numeric vector}
+
+\item{fracture_rotation_xy}{Optional:}
+
+\item{fracture_rotation_yz}{Optional:}
+
 \item{reference_permeability}{Optional:}
 
 \item{fitting_factor}{Optional:}

man/prj_process.Rd

@@ -71,6 +71,14 @@ prj_process(
   pf_irrv = NULL,
   micro_porosity = NULL,
   explicit_hm_coupling_in_unsaturated_zone = NULL,
+  simplified_elasticity = NULL,
+  chemically_induced_porosity_change = NULL,
+  use_server_communication = NULL,
+  phasefield_model = NULL,
+  irreversible_threshold = NULL,
+  tabular_file = NULL,
+  temperature_field = NULL,
+  use_stokes_brinkman_form = NULL,
   ...
 )
 }
@@ -207,6 +215,22 @@ prj_process(
 
 \item{explicit_hm_coupling_in_unsaturated_zone}{Optional:}
 
+\item{simplified_elasticity}{Optional: character}
+
+\item{chemically_induced_porosity_change}{Optional: character}
+
+\item{use_server_communication}{Optional:}
+
+\item{phasefield_model}{Optional:}
+
+\item{irreversible_threshold}{Optional: numeric}
+
+\item{tabular_file}{Optional: character}
+
+\item{temperature_field}{Optional: character}
+
+\item{use_stokes_brinkman_form}{Optional: character}
+
 \item{...}{Optional: fracture_properties, constitutive_relation}
 }
 \description{