From f76af0ab81c4c976246b2f3049d502acaaa95cf1 Mon Sep 17 00:00:00 2001
From: aheinri5 <Anna@netzkritzler.de>
Date: Sat, 16 Jan 2021 22:02:14 +0100
Subject: [PATCH] [docs] updated documentation
---
man/OGS6.Rd | 19 ++++---
man/OGS6_vtu.Rd | 21 +++++++
man/addable_prj_components.Rd | 19 +++++++
man/coerce_string_to_numeric.Rd | 10 +---
man/decode_appended_data.Rd | 20 +++++++
man/generate_all_benchmark_scripts.Rd | 16 +++---
man/generate_benchmark_script.Rd | 8 +--
man/get_class_args.Rd | 17 ++++++
man/get_valid_vtu_categories.Rd | 14 +++++
man/get_vtu_data_arrays_from_file.Rd | 25 +++++++++
man/node_to_object.Rd | 29 ++++++++++
man/node_to_r2ogs6_class_object.Rd | 23 ++++++++
man/order_parameters.Rd | 3 +
man/r2ogs6_phase.Rd | 2 +-
man/r2ogs6_pr_property.Rd | 80 ++++++++++++++++++---------
man/read_in_output.Rd | 2 +-
man/read_in_prj.Rd | 9 ++-
man/read_in_pvd.Rd | 17 ++++++
man/read_in_vtu.Rd | 3 +-
19 files changed, 278 insertions(+), 59 deletions(-)
create mode 100644 man/addable_prj_components.Rd
create mode 100644 man/decode_appended_data.Rd
create mode 100644 man/get_class_args.Rd
create mode 100644 man/get_valid_vtu_categories.Rd
create mode 100644 man/get_vtu_data_arrays_from_file.Rd
create mode 100644 man/node_to_object.Rd
create mode 100644 man/node_to_r2ogs6_class_object.Rd
create mode 100644 man/read_in_pvd.Rd
diff --git a/man/OGS6.Rd b/man/OGS6.Rd
index ce0bb93..1e4eb53 100644
--- a/man/OGS6.Rd
+++ b/man/OGS6.Rd
@@ -59,7 +59,7 @@ Constructor for the OGS6 base class
\subsection{Public methods}{
\itemize{
\item \href{#method-new}{\code{OGS6$new()}}
-\item \href{#method-add_component}{\code{OGS6$add_component()}}
+\item \href{#method-add}{\code{OGS6$add()}}
\item \href{#method-add_gml}{\code{OGS6$add_gml()}}
\item \href{#method-add_vtu}{\code{OGS6$add_vtu()}}
\item \href{#method-add_python_script}{\code{OGS6$add_python_script()}}
@@ -109,18 +109,21 @@ validated. Unless you're a dev, please don't touch.}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_component"></a>}}
-\if{latex}{\out{\hypertarget{method-add_component}{}}}
-\subsection{Method \code{add_component()}}{
+\if{html}{\out{<a id="method-add"></a>}}
+\if{latex}{\out{\hypertarget{method-add}{}}}
+\subsection{Method \code{add()}}{
Adds a simulation component (WIP)
\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_component(x)}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{OGS6$add(x, component_name = "")}\if{html}{\out{</div>}}
}
\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
-\item{\code{x}}{OGS6_*: An object of a class listed in get_implemented_classes()}
+\item{\code{x}}{An object of any class listed in addable_components(). If `x` is
+not of a proprietary `r2ogs6` class, `component_name` must be
+supplied. E.g. If you're adding a `python_script` which is a string, you
+would call `your_ogs6_obj$add("some_script.py", "python_script")`}
}
\if{html}{\out{</div>}}
}
@@ -419,7 +422,7 @@ Prints logfile to console (if it exists)
\subsection{Method \code{clear()}}{
Clears components from the OGS6 object
\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$clear(which = names(get_implemented_classes()))}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{OGS6$clear(which = names(addable_prj_components()))}\if{html}{\out{</div>}}
}
\subsection{Arguments}{
@@ -427,7 +430,7 @@ Clears components from the OGS6 object
\describe{
\item{\code{which}}{character: The names of the components (all by default).
If you want to delete only some components, run
-names(get_implemented_classes()) for the available options.}
+names(addable_prj_components()) for the available options.}
}
\if{html}{\out{</div>}}
}
diff --git a/man/OGS6_vtu.Rd b/man/OGS6_vtu.Rd
index ee7efcf..bbf865e 100644
--- a/man/OGS6_vtu.Rd
+++ b/man/OGS6_vtu.Rd
@@ -35,6 +35,7 @@ Constructor for the OGS6_vtu base class
\subsection{Public methods}{
\itemize{
\item \href{#method-new}{\code{OGS6_vtu$new()}}
+\item \href{#method-get_data_arrays}{\code{OGS6_vtu$get_data_arrays()}}
\item \href{#method-clone}{\code{OGS6_vtu$clone()}}
}
}
@@ -76,6 +77,26 @@ Creates new OGS6_vtu object
}
}
\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_data_arrays"></a>}}
+\if{latex}{\out{\hypertarget{method-get_data_arrays}{}}}
+\subsection{Method \code{get_data_arrays()}}{
+Gets specified DataArrays
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_vtu$get_data_arrays(Names = character(), categories = character())}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{Names}}{character: Optional: Select `DataArray` by `Name`}
+
+\item{\code{categories}}{character: Optional: One or more of
+`get_valid_vtu_categories()`}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-clone"></a>}}
\if{latex}{\out{\hypertarget{method-clone}{}}}
\subsection{Method \code{clone()}}{
diff --git a/man/addable_prj_components.Rd b/man/addable_prj_components.Rd
new file mode 100644
index 0000000..7845a80
--- /dev/null
+++ b/man/addable_prj_components.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{addable_prj_components}
+\alias{addable_prj_components}
+\title{addable_prj_components}
+\usage{
+addable_prj_components()
+}
+\value{
+character: Named vector of `OGS6` top level .prj components (names)
+along with their respective class names (values)
+}
+\description{
+Returns all possible `OGS6` top level .prj components (names)
+along with their respective class names (values).
+Change this if you implement new `OGS6` .prj components or delete old ones!
+If you implement a new components, you add the following to the `class_names`
+vector: `name_of_prj_component = "name_of_your_class"`
+}
diff --git a/man/coerce_string_to_numeric.Rd b/man/coerce_string_to_numeric.Rd
index 93de4e7..33eee9b 100644
--- a/man/coerce_string_to_numeric.Rd
+++ b/man/coerce_string_to_numeric.Rd
@@ -4,21 +4,15 @@
\alias{coerce_string_to_numeric}
\title{coerce_string_to_numeric}
\usage{
-coerce_string_to_numeric(obj, split = FALSE)
+coerce_string_to_numeric(obj)
}
\arguments{
\item{obj}{An object to check}
-
-\item{split}{flag: Should object be split at ' ' (whitespace) if it is a
-string?}
}
\value{
The object as a numeric type (if 'obj' was a string, else the
unchanged 'obj')
}
\description{
-If an object is of type string, coerces it to a numeric type:
-A double if 'split' is FALSE as per default, a numeric vector otherwise.
-If 'split' is set to true the string will be split at ' ' (whitespace)
-characters.
+If an object is of type string, coerces it to a numeric type
}
diff --git a/man/decode_appended_data.Rd b/man/decode_appended_data.Rd
new file mode 100644
index 0000000..5b47001
--- /dev/null
+++ b/man/decode_appended_data.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_in_vtu.R
+\name{decode_appended_data}
+\alias{decode_appended_data}
+\title{decode_appended_data}
+\usage{
+decode_appended_data(appended_data, compressor = "")
+}
+\arguments{
+\item{appended_data}{character: AppendedData}
+
+\item{compressor}{string: Optional: How the data was compressed, this is the
+`compressor` attribute of *VTKFile*}
+}
+\value{
+list: DataArrays with `data` element which is the decoded data
+}
+\description{
+Decodes AppendedData
+}
diff --git a/man/generate_all_benchmark_scripts.Rd b/man/generate_all_benchmark_scripts.Rd
index 0f1bf40..eebd7e2 100644
--- a/man/generate_all_benchmark_scripts.Rd
+++ b/man/generate_all_benchmark_scripts.Rd
@@ -8,10 +8,10 @@ generate_all_benchmark_scripts(
path,
sim_path,
scripts_path,
- starting_from_prj_path = "",
- skip_prj_paths = character(),
+ read_in_gmls,
read_in_vtus = FALSE,
- read_in_gmls = TRUE
+ starting_from_prj_path = "",
+ skip_prj_paths = character()
)
}
\arguments{
@@ -21,15 +21,15 @@ generate_all_benchmark_scripts(
\item{scripts_path}{string: Path where benchmark scripts will be saved}
-\item{starting_from_prj_path}{string: Optional:}
-
-\item{skip_prj_paths}{character: Optional: .prj paths to skip}
+\item{read_in_gmls}{flag: Optional: Should .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_gmls}{flag: Optional: Should .gml 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}
}
\description{
Wrapper function to generate benchmark scripts from all .prj
diff --git a/man/generate_benchmark_script.Rd b/man/generate_benchmark_script.Rd
index 03126b3..cdd5d1d 100644
--- a/man/generate_benchmark_script.Rd
+++ b/man/generate_benchmark_script.Rd
@@ -9,8 +9,8 @@ generate_benchmark_script(
sim_path,
ogs_bin_path,
script_path,
- read_in_vtu = FALSE,
- read_in_gml = TRUE
+ read_in_gml,
+ read_in_vtu = FALSE
)
}
\arguments{
@@ -22,10 +22,10 @@ generate_benchmark_script(
\item{script_path}{string: Path where benchmark script will be saved}
-\item{read_in_vtu}{flag: Optional: Should .vtu file(s) just be copied or read
+\item{read_in_gml}{flag: Optional: Should .gml file just be copied or read
in too?}
-\item{read_in_gml}{flag: Optional: Should .gml file just be copied or read
+\item{read_in_vtu}{flag: Optional: Should .vtu file(s) just be copied or read
in too?}
}
\description{
diff --git a/man/get_class_args.Rd b/man/get_class_args.Rd
new file mode 100644
index 0000000..82debcb
--- /dev/null
+++ b/man/get_class_args.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_in_utils.R
+\name{get_class_args}
+\alias{get_class_args}
+\title{get_class_args}
+\usage{
+get_class_args(class_name)
+}
+\arguments{
+\item{class_name}{string: The name of a class}
+}
+\value{
+character: Named vector of class arguments
+}
+\description{
+Gets class arguments
+}
diff --git a/man/get_valid_vtu_categories.Rd b/man/get_valid_vtu_categories.Rd
new file mode 100644
index 0000000..9cda300
--- /dev/null
+++ b/man/get_valid_vtu_categories.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{get_valid_vtu_categories}
+\alias{get_valid_vtu_categories}
+\title{get_valid_vtu_categories}
+\usage{
+get_valid_vtu_categories()
+}
+\value{
+character: `OGS6_vtu` categories
+}
+\description{
+Returns all valid `OGS6_vtu` categories.
+}
diff --git a/man/get_vtu_data_arrays_from_file.Rd b/man/get_vtu_data_arrays_from_file.Rd
new file mode 100644
index 0000000..f812aaa
--- /dev/null
+++ b/man/get_vtu_data_arrays_from_file.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_in_vtu.R
+\name{get_vtu_data_arrays_from_file}
+\alias{get_vtu_data_arrays_from_file}
+\title{get_vtu_data_arrays_from_file}
+\usage{
+get_vtu_data_arrays_from_file(
+ vtu_path,
+ Names = character(),
+ categories = character()
+)
+}
+\arguments{
+\item{vtu_path}{string: .vtu file path}
+
+\item{Names}{character: Optional: Select `DataArray` elements by `Name`
+attribute}
+
+\item{categories}{character: Optional: One or more of `FieldData`, `PointData`,
+`CellData`, `Points` or `Cells`. If left empty, will get `DataArray`
+elements from whole XML document.}
+}
+\description{
+Reads DataArray elements from a .vtu file
+}
diff --git a/man/node_to_object.Rd b/man/node_to_object.Rd
new file mode 100644
index 0000000..4538056
--- /dev/null
+++ b/man/node_to_object.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_in_utils.R
+\name{node_to_object}
+\alias{node_to_object}
+\title{node_to_object}
+\usage{
+node_to_object(xml_node, xpath_expr = "", subclasses_names = character())
+}
+\arguments{
+\item{xml_node}{xml2::xml_node: XML node}
+
+\item{xpath_expr}{string: Optional: XPath expression (for subclass
+differentiation)}
+
+\item{subclasses_names}{character: Optional: Names of `r2ogs6` subclasses
+(`r2ogs6` classes without a OGS6$add method)}
+}
+\description{
+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
+}
diff --git a/man/node_to_r2ogs6_class_object.Rd b/man/node_to_r2ogs6_class_object.Rd
new file mode 100644
index 0000000..51a782e
--- /dev/null
+++ b/man/node_to_r2ogs6_class_object.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_in_utils.R
+\name{node_to_r2ogs6_class_object}
+\alias{node_to_r2ogs6_class_object}
+\title{node_to_r2ogs6_class_object}
+\usage{
+node_to_r2ogs6_class_object(
+ xml_node,
+ xpath_expr,
+ subclasses_names = character()
+)
+}
+\arguments{
+\item{xml_node}{xml2::xml_node: XML node}
+
+\item{xpath_expr}{string: XPath expression (for subclass differentiation)}
+
+\item{subclasses_names}{character: Optional: Names of r2ogs6 subclasses
+(r2ogs6 classes without a method for input_add)}
+}
+\description{
+Takes an XML node and turns it into a class object
+}
diff --git a/man/order_parameters.Rd b/man/order_parameters.Rd
index e6fb230..8d18945 100644
--- a/man/order_parameters.Rd
+++ b/man/order_parameters.Rd
@@ -11,6 +11,9 @@ order_parameters(parameters, class_name)
\item{class_name}{string: The name of a class}
}
+\value{
+list: Parameters ordered by argument order of class
+}
\description{
Orders a list of parameters corresponding to the argument order
of a class
diff --git a/man/r2ogs6_phase.Rd b/man/r2ogs6_phase.Rd
index a88c61c..af754f8 100644
--- a/man/r2ogs6_phase.Rd
+++ b/man/r2ogs6_phase.Rd
@@ -4,7 +4,7 @@
\alias{r2ogs6_phase}
\title{r2ogs6_phase}
\usage{
-r2ogs6_phase(type, properties, components = NULL)
+r2ogs6_phase(type, properties = NULL, components = NULL)
}
\arguments{
\item{type}{string: Phase type
diff --git a/man/r2ogs6_pr_property.Rd b/man/r2ogs6_pr_property.Rd
index 285a52d..5028f3f 100644
--- a/man/r2ogs6_pr_property.Rd
+++ b/man/r2ogs6_pr_property.Rd
@@ -16,67 +16,97 @@ r2ogs6_pr_property(
independent_variable = NULL,
curve = NULL,
minimum_relative_permeability_liquid = NULL,
+ initial_permeability = NULL,
+ maximum_permeability = NULL,
lambda = NULL,
cutoff_value = NULL,
- initial_permeability = NULL,
+ intrinsic_permeability = NULL,
+ initial_aperture = NULL,
+ mean_frac_distance = NULL,
+ threshold_strain = NULL,
+ fracture_normal = NULL,
reference_permeability = NULL,
fitting_factor = NULL,
cohesion = NULL,
friction_angle = NULL,
- maximum_permeability = NULL,
tensile_strength_parameter = NULL,
+ b1 = NULL,
+ b2 = NULL,
+ b3 = NULL,
+ minimum_permeability = NULL,
+ initial_porosity = NULL,
entry_pressure = NULL,
min_relative_permeability_liquid = NULL,
min_relative_permeability_gas = NULL
)
}
\arguments{
-\item{name}{string: Property name}
+\item{name}{string:}
-\item{type}{string: Property type}
+\item{type}{string:}
-\item{value}{Optional: string | double: ...}
+\item{value}{Optional:}
-\item{parameter_name}{Optional: string:}
+\item{parameter_name}{Optional:}
-\item{exponent}{Optional: string | double:}
+\item{exponent}{Optional:}
-\item{residual_liquid_saturation}{Optional: string | double:}
+\item{residual_liquid_saturation}{Optional:}
-\item{residual_gas_saturation}{Optional: string | double:}
+\item{residual_gas_saturation}{Optional:}
-\item{p_b}{Optional: string | double: string | double:}
+\item{p_b}{Optional:}
-\item{independent_variable}{Optional: string}
+\item{independent_variable}{Optional:}
-\item{curve}{Optional: string:}
+\item{curve}{Optional:}
\item{minimum_relative_permeability_liquid}{Optional:}
-\item{lambda}{Optional: string | double:}
+\item{initial_permeability}{Optional:}
+
+\item{maximum_permeability}{Optional:}
+
+\item{lambda}{Optional:}
+
+\item{cutoff_value}{Optional:}
+
+\item{intrinsic_permeability}{Optional:}
+
+\item{initial_aperture}{Optional:}
+
+\item{mean_frac_distance}{Optional:}
+
+\item{threshold_strain}{Optional:}
+
+\item{fracture_normal}{Optional:}
+
+\item{reference_permeability}{Optional:}
+
+\item{fitting_factor}{Optional:}
-\item{cutoff_value}{Optional: string | double:}
+\item{cohesion}{Optional:}
-\item{initial_permeability}{Optional: string:}
+\item{friction_angle}{Optional:}
-\item{reference_permeability}{Optional: string | double:}
+\item{tensile_strength_parameter}{Optional:}
-\item{fitting_factor}{Optional: string | double:}
+\item{b1}{Optional:}
-\item{cohesion}{Optional: string | double:}
+\item{b2}{Optional:}
-\item{friction_angle}{Optional: string | double:}
+\item{b3}{Optional:}
-\item{maximum_permeability}{Optional: string | double:}
+\item{minimum_permeability}{Optional:}
-\item{tensile_strength_parameter}{Optional: string | double:}
+\item{initial_porosity}{Optional:}
-\item{entry_pressure}{Optional: string | double:}
+\item{entry_pressure}{Optional:}
-\item{min_relative_permeability_liquid}{Optional: string | double:}
+\item{min_relative_permeability_liquid}{Optional:}
-\item{min_relative_permeability_gas}{Optional: string | double:}
+\item{min_relative_permeability_gas}{Optional:}
}
\description{
-tag: property, a constitutive property
+tag: property
}
diff --git a/man/read_in_output.Rd b/man/read_in_output.Rd
index e4f6637..17d3f0e 100644
--- a/man/read_in_output.Rd
+++ b/man/read_in_output.Rd
@@ -7,7 +7,7 @@
read_in_output(ogs6_obj)
}
\arguments{
-\item{ogs6_obj}{A OGS6 class object}
+\item{ogs6_obj}{OGS6: Simulation object}
}
\description{
After a OGS6 simulation was run, reads in the generated .vtu
diff --git a/man/read_in_prj.Rd b/man/read_in_prj.Rd
index f4fb4f8..9633b09 100644
--- a/man/read_in_prj.Rd
+++ b/man/read_in_prj.Rd
@@ -4,16 +4,19 @@
\alias{read_in_prj}
\title{read_in_prj}
\usage{
-read_in_prj(ogs6_obj, prj_path, read_in_vtu = FALSE, read_in_gml = TRUE)
+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{read_in_vtu}{flag: Should .vtu file just be copied or read in too?}
+\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 <= the
+number of lines in `options("r2ogs6.max_lines_gml")`, the .gml will be read
+in. Else, only the geometry reference will be saved.}
-\item{read_in_gml}{flag: Should .gml file just be copied or read in too?}
+\item{read_in_vtu}{flag: Should .vtu file just be copied or read in too?}
}
\description{
Wrapper function to read in a whole .prj file
diff --git a/man/read_in_pvd.Rd b/man/read_in_pvd.Rd
new file mode 100644
index 0000000..4f17da0
--- /dev/null
+++ b/man/read_in_pvd.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_in_vtu.R
+\name{read_in_pvd}
+\alias{read_in_pvd}
+\title{read_in_pvd}
+\usage{
+read_in_pvd(pvd_path)
+}
+\arguments{
+\item{pvd_path}{string: Path to .pvd file that should be read in}
+}
+\value{
+character: Vector containing .vtu paths
+}
+\description{
+Function to read in a .pvd file
+}
diff --git a/man/read_in_vtu.Rd b/man/read_in_vtu.Rd
index 929b7bd..1f2df67 100644
--- a/man/read_in_vtu.Rd
+++ b/man/read_in_vtu.Rd
@@ -13,5 +13,6 @@ read_in_vtu(vtu_path)
OGS6_vtu: Mesh object
}
\description{
-Wrapper function to read in a whole .vtu file
+Wrapper function to read in a whole .vtu file as a OGS6_vtu
+class object
}
--
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