From 14ccd507fca09d834ddb7d68d09f227d6a4e09dd Mon Sep 17 00:00:00 2001
From: phit0 <philipp.schad@stud.uni-goettingen.de>
Date: Wed, 10 Nov 2021 17:48:45 +0100
Subject: [PATCH] [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 | 2 +-
NAMESPACE | 1 +
R/prj_medium.R | 5 ++++
man/OGS6.Rd | 40 ++++++++++++++++++++++++++
man/ogs6_generate_benchmark_script.Rd | 2 +-
man/ogs6_generate_benchmark_scripts.Rd | 5 +++-
man/prj_chemical_system.Rd | 8 +++++-
man/prj_com_property.Rd | 31 +++++++++++++++++++-
man/prj_exchangers.Rd | 14 +++++++++
man/prj_output.Rd | 5 +++-
man/prj_parameter.Rd | 6 ++++
man/prj_phasefield_parameters.Rd | 2 +-
man/prj_pr_property.Rd | 15 ++++++++++
man/prj_process.Rd | 24 ++++++++++++++++
14 files changed, 153 insertions(+), 7 deletions(-)
create mode 100644 man/prj_exchangers.Rd
diff --git a/DESCRIPTION b/DESCRIPTION
index d3125fa..302d905 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -50,7 +50,7 @@ Imports:
config,
sticky,
foreach
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
VignetteBuilder: knitr
Depends:
R (>= 2.10)
diff --git a/NAMESPACE b/NAMESPACE
index 07c78ed..38dad9c 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/prj_medium.R b/R/prj_medium.R
index ba96631..861da57 100644
--- a/R/prj_medium.R
+++ b/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,
diff --git a/man/OGS6.Rd b/man/OGS6.Rd
index 8ef7607..5f82fad 100644
--- a/man/OGS6.Rd
+++ b/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>}}
diff --git a/man/ogs6_generate_benchmark_script.Rd b/man/ogs6_generate_benchmark_script.Rd
index afc6767..7602e46 100644
--- a/man/ogs6_generate_benchmark_script.Rd
+++ b/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
)
}
diff --git a/man/ogs6_generate_benchmark_scripts.Rd b/man/ogs6_generate_benchmark_scripts.Rd
index c6eaee7..7455aa1 100644
--- a/man/ogs6_generate_benchmark_scripts.Rd
+++ b/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()`.
diff --git a/man/prj_chemical_system.Rd b/man/prj_chemical_system.Rd
index bbd563b..865f1a5 100644
--- a/man/prj_chemical_system.Rd
+++ b/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
diff --git a/man/prj_com_property.Rd b/man/prj_com_property.Rd
index d21bb8e..c355051 100644
--- a/man/prj_com_property.Rd
+++ b/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
diff --git a/man/prj_exchangers.Rd b/man/prj_exchangers.Rd
new file mode 100644
index 0000000..18d2150
--- /dev/null
+++ b/man/prj_exchangers.Rd
@@ -0,0 +1,14 @@
+% 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
+}
diff --git a/man/prj_output.Rd b/man/prj_output.Rd
index a74c78a..355d401 100644
--- a/man/prj_output.Rd
+++ b/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
diff --git a/man/prj_parameter.Rd b/man/prj_parameter.Rd
index 3cd5611..0d5aff6 100644
--- a/man/prj_parameter.Rd
+++ b/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)}
}
diff --git a/man/prj_phasefield_parameters.Rd b/man/prj_phasefield_parameters.Rd
index f98d927..1159809 100644
--- a/man/prj_phasefield_parameters.Rd
+++ b/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
)
}
diff --git a/man/prj_pr_property.Rd b/man/prj_pr_property.Rd
index a5908fd..0b04929 100644
--- a/man/prj_pr_property.Rd
+++ b/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:}
diff --git a/man/prj_process.Rd b/man/prj_process.Rd
index ee0b7fe..376276e 100644
--- a/man/prj_process.Rd
+++ b/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{
--
GitLab