From 0f45333502001f0f21c283109cc89bf67dd20dbc Mon Sep 17 00:00:00 2001
From: aheinri5 <Anna@netzkritzler.de>
Date: Tue, 16 Feb 2021 21:50:07 +0100
Subject: [PATCH] [docs] updated documentation for renamed classes
---
man/OGS6.Rd | 32 +--
man/OGS6_Chain.Rd | 12 +-
man/OGS6_Ensemble.Rd | 2 +-
man/OGS6_pvd.Rd | 7 +-
man/OGS6_vtu.Rd | 44 ++--
man/examples/ex_prj_borehole_heat_exchanger.R | 6 +-
man/examples/ex_prj_boundary_condition.R | 2 +-
man/examples/ex_prj_capillary_pressure.R | 2 +-
man/examples/ex_prj_chemical_system.R | 6 +-
man/examples/ex_prj_com_property.R | 2 +-
man/examples/ex_prj_component.R | 4 +-
man/examples/ex_prj_constitutive_relation.R | 2 +-
man/examples/ex_prj_convergence_criterion.R | 2 +-
man/examples/ex_prj_curve.R | 2 +-
man/examples/ex_prj_deactivated_subdomain.R | 2 +-
man/examples/ex_prj_eigen.R | 2 +-
.../ex_prj_flow_and_temperature_control.R | 2 +-
man/examples/ex_prj_fluid.R | 2 +-
man/examples/ex_prj_fracture_model.R | 2 +-
man/examples/ex_prj_fracture_properties.R | 2 +-
man/examples/ex_prj_global_process_coupling.R | 4 +-
man/examples/ex_prj_insitu.R | 2 +-
man/examples/ex_prj_jacobian_assembler.R | 2 +-
man/examples/ex_prj_kinetic_reactant.R | 2 +-
man/examples/ex_prj_linear_solver.R | 4 +-
man/examples/ex_prj_local_coordinate_system.R | 2 +-
man/examples/ex_prj_material_property.R | 10 +-
man/examples/ex_prj_medium.R | 12 +-
man/examples/ex_prj_nonlinear_solver.R | 2 +-
man/examples/ex_prj_output.R | 2 +-
man/examples/ex_prj_parameter.R | 4 +-
man/examples/ex_prj_ph_property.R | 2 +-
man/examples/ex_prj_phase.R | 4 +-
man/examples/ex_prj_phase_component.R | 2 +-
man/examples/ex_prj_phasefield_parameters.R | 2 +-
man/examples/ex_prj_pipes.R | 2 +-
man/examples/ex_prj_porous_medium.R | 6 +-
man/examples/ex_prj_pr_property.R | 2 +-
man/examples/ex_prj_process.R | 4 +-
man/examples/ex_prj_process_variable.R | 4 +-
man/examples/ex_prj_rate.R | 2 +-
man/examples/ex_prj_relative_permeability.R | 2 +-
man/examples/ex_prj_search_length_algorithm.R | 2 +-
man/examples/ex_prj_solution.R | 2 +-
man/examples/ex_prj_source_term.R | 2 +-
man/examples/ex_prj_time_loop.R | 10 +-
man/examples/ex_prj_time_stepping.R | 2 +-
man/examples/ex_prj_tl_process.R | 6 +-
man/examples/ex_prj_vtkdiff.R | 2 +-
man/get_benchmark_paths.Rd | 4 +-
man/get_prj_top_level_tags.Rd | 14 +
man/get_tag_from_class.Rd | 2 +-
man/node_to_object.Rd | 2 +-
man/node_to_prj_class_object.Rd | 16 ++
man/ogs6_call_ogs6.Rd | 23 ++
man/ogs6_export_sim_files.Rd | 18 ++
man/ogs6_generate_benchmark_script.Rd | 33 +++
man/ogs6_generate_structured_mesh.Rd | 22 ++
man/ogs6_get_combinations.Rd | 14 +
man/ogs6_get_medium_property.Rd | 19 ++
man/ogs6_read_output_files.Rd | 14 +
man/ogs6_run_simulation.Rd | 24 ++
man/prj_borehole_heat_exchanger.Rd | 73 ++++++
man/prj_boundary_condition.Rd | 94 +++++++
man/prj_capillary_pressure.Rd | 48 ++++
man/prj_chemical_system.Rd | 74 ++++++
man/prj_com_property.Rd | 25 ++
man/prj_component.Rd | 26 ++
man/prj_constitutive_relation.Rd | 140 ++++++++++
man/prj_convergence_criterion.Rd | 39 +++
man/prj_curve.Rd | 24 ++
man/prj_deactivated_subdomain.Rd | 21 ++
man/prj_eigen.Rd | 39 +++
man/prj_flow_and_temperature_control.Rd | 38 +++
man/prj_fluid.Rd | 55 ++++
man/prj_fracture_model.Rd | 53 ++++
man/prj_fracture_properties.Rd | 37 +++
man/prj_global_process_coupling.Rd | 30 +++
man/prj_insitu.Rd | 17 ++
man/prj_jacobian_assembler.Rd | 29 +++
man/prj_kinetic_reactant.Rd | 29 +++
man/prj_linear_solver.Rd | 32 +++
man/prj_local_coordinate_system.Rd | 27 ++
man/prj_material_property.Rd | 60 +++++
man/prj_medium.Rd | 46 ++++
man/prj_nonlinear_solver.Rd | 30 +++
man/prj_output.Rd | 57 +++++
man/prj_parameter.Rd | 59 +++++
man/prj_ph_property.Rd | 66 +++++
man/prj_phase.Rd | 29 +++
man/prj_phase_component.Rd | 25 ++
man/prj_phasefield_parameters.Rd | 37 +++
man/prj_pipes.Rd | 47 ++++
man/prj_porous_medium.Rd | 61 +++++
man/prj_pr_property.Rd | 117 +++++++++
man/prj_process.Rd | 240 ++++++++++++++++++
man/prj_process_variable.Rd | 54 ++++
man/prj_rate.Rd | 29 +++
man/prj_relative_permeability.Rd | 34 +++
man/prj_search_length_algorithm.Rd | 20 ++
man/prj_solution.Rd | 34 +++
man/prj_source_term.Rd | 39 +++
man/prj_time_loop.Rd | 52 ++++
man/prj_time_stepping.Rd | 67 +++++
man/prj_tl_process.Rd | 51 ++++
man/prj_vtkdiff.Rd | 34 +++
man/run_all_benchmarks.Rd | 10 +-
man/run_benchmark.Rd | 4 +-
108 files changed, 2568 insertions(+), 130 deletions(-)
create mode 100644 man/get_prj_top_level_tags.Rd
create mode 100644 man/node_to_prj_class_object.Rd
create mode 100644 man/ogs6_call_ogs6.Rd
create mode 100644 man/ogs6_export_sim_files.Rd
create mode 100644 man/ogs6_generate_benchmark_script.Rd
create mode 100644 man/ogs6_generate_structured_mesh.Rd
create mode 100644 man/ogs6_get_combinations.Rd
create mode 100644 man/ogs6_get_medium_property.Rd
create mode 100644 man/ogs6_read_output_files.Rd
create mode 100644 man/ogs6_run_simulation.Rd
create mode 100644 man/prj_borehole_heat_exchanger.Rd
create mode 100644 man/prj_boundary_condition.Rd
create mode 100644 man/prj_capillary_pressure.Rd
create mode 100644 man/prj_chemical_system.Rd
create mode 100644 man/prj_com_property.Rd
create mode 100644 man/prj_component.Rd
create mode 100644 man/prj_constitutive_relation.Rd
create mode 100644 man/prj_convergence_criterion.Rd
create mode 100644 man/prj_curve.Rd
create mode 100644 man/prj_deactivated_subdomain.Rd
create mode 100644 man/prj_eigen.Rd
create mode 100644 man/prj_flow_and_temperature_control.Rd
create mode 100644 man/prj_fluid.Rd
create mode 100644 man/prj_fracture_model.Rd
create mode 100644 man/prj_fracture_properties.Rd
create mode 100644 man/prj_global_process_coupling.Rd
create mode 100644 man/prj_insitu.Rd
create mode 100644 man/prj_jacobian_assembler.Rd
create mode 100644 man/prj_kinetic_reactant.Rd
create mode 100644 man/prj_linear_solver.Rd
create mode 100644 man/prj_local_coordinate_system.Rd
create mode 100644 man/prj_material_property.Rd
create mode 100644 man/prj_medium.Rd
create mode 100644 man/prj_nonlinear_solver.Rd
create mode 100644 man/prj_output.Rd
create mode 100644 man/prj_parameter.Rd
create mode 100644 man/prj_ph_property.Rd
create mode 100644 man/prj_phase.Rd
create mode 100644 man/prj_phase_component.Rd
create mode 100644 man/prj_phasefield_parameters.Rd
create mode 100644 man/prj_pipes.Rd
create mode 100644 man/prj_porous_medium.Rd
create mode 100644 man/prj_pr_property.Rd
create mode 100644 man/prj_process.Rd
create mode 100644 man/prj_process_variable.Rd
create mode 100644 man/prj_rate.Rd
create mode 100644 man/prj_relative_permeability.Rd
create mode 100644 man/prj_search_length_algorithm.Rd
create mode 100644 man/prj_solution.Rd
create mode 100644 man/prj_source_term.Rd
create mode 100644 man/prj_time_loop.Rd
create mode 100644 man/prj_time_stepping.Rd
create mode 100644 man/prj_tl_process.Rd
create mode 100644 man/prj_vtkdiff.Rd
diff --git a/man/OGS6.Rd b/man/OGS6.Rd
index 14948b8..02a07ae 100644
--- a/man/OGS6.Rd
+++ b/man/OGS6.Rd
@@ -19,7 +19,7 @@ ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
## ------------------------------------------------
ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
-ogs6_obj$add(r2ogs6_parameter$new(name = "foo", type = "bar"))
+ogs6_obj$add(prj_parameter$new(name = "foo", type = "bar"))
## ------------------------------------------------
## Method `OGS6$add_gml`
@@ -64,43 +64,43 @@ ogs6_obj$get_status()
\item{\code{python_script}}{\code{.prj} \code{python_script} tag. \code{value} must be string}
\item{\code{search_length_algorithm}}{\code{.prj} \code{search_length_algorithm} tag. \code{value} must be
-\code{r2ogs6_search_length_algorithm} object}
+\code{prj_search_length_algorithm} object}
\item{\code{processes}}{\code{.prj} \code{processes} tag. \code{value} must be list of
-\code{r2ogs6_process} objects}
+\code{prj_process} objects}
\item{\code{time_loop}}{\code{.prj} \code{time_loop} tag. \code{value} must be
-\code{r2ogs6_time_loop} object}
+\code{prj_time_loop} object}
\item{\code{local_coordinate_system}}{\code{.prj} \code{local_coordinate_system} tag. \code{value} must be
-\code{r2ogs6_local_coordinate_system} object}
+\code{prj_local_coordinate_system} object}
\item{\code{media}}{\code{.prj} \code{media} tag. \code{value} must be list of
-\code{r2ogs6_medium} objects}
+\code{prj_medium} objects}
\item{\code{parameters}}{\code{.prj} \code{parameters} tag. \code{value} must be list of
-\code{r2ogs6_parameter} objects}
+\code{prj_parameter} objects}
\item{\code{chemical_system}}{\code{.prj} \code{chemical_system} tag. \code{value} must be
-\code{r2ogs6_chemical_system} object}
+\code{prj_chemical_system} object}
\item{\code{curves}}{\code{.prj} \code{curves} tag. \code{value} must be list of
-\code{r2ogs6_curve} objects}
+\code{prj_curve} objects}
\item{\code{process_variables}}{\code{.prj} \code{process_variables} tag. \code{value} must be list of
-\code{r2ogs6_process_variable} objects}
+\code{prj_process_variable} objects}
\item{\code{nonlinear_solvers}}{\code{.prj} \code{nonlinear_solvers} tag. \code{value} must be list of
-\code{r2ogs6_nonlinear_solver} objects}
+\code{prj_nonlinear_solver} objects}
\item{\code{linear_solvers}}{\code{.prj} \code{linear_solvers} tag. \code{value} must be list of
-\code{r2ogs6_linear_solver} objects}
+\code{prj_linear_solver} objects}
\item{\code{test_definition}}{\code{.prj} \code{test_definition} tag. \code{value} must be list of
-\code{r2ogs6_vtkdiff} objects}
+\code{prj_vtkdiff} objects}
\item{\code{insitu}}{\code{.prj} \code{insitu} tag. \code{value} must be
-\code{r2ogs6_insitu} object}
+\code{prj_insitu} object}
\item{\code{pvds}}{\code{.pvd}s. \code{value} must be list of \code{OGS6_pvd} objects}
}
@@ -160,14 +160,14 @@ Adds a .prj simulation component
\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
-\item{\code{x}}{An object of any .prj `r2ogs6` class}
+\item{\code{x}}{An object of any .prj `prj` class}
}
\if{html}{\out{</div>}}
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
\preformatted{ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
-ogs6_obj$add(r2ogs6_parameter$new(name = "foo", type = "bar"))
+ogs6_obj$add(prj_parameter$new(name = "foo", type = "bar"))
}
\if{html}{\out{</div>}}
diff --git a/man/OGS6_Chain.Rd b/man/OGS6_Chain.Rd
index 27266e5..ce8ffed 100644
--- a/man/OGS6_Chain.Rd
+++ b/man/OGS6_Chain.Rd
@@ -10,7 +10,7 @@ Constructor for the OGS6_Chain base class
\subsection{Public methods}{
\itemize{
\item \href{#method-new}{\code{OGS6_Chain$new()}}
-\item \href{#method-ogs_run_simulation}{\code{OGS6_Chain$ogs_run_simulation()}}
+\item \href{#method-ogs6_run_simulation}{\code{OGS6_Chain$ogs6_run_simulation()}}
\item \href{#method-print_log}{\code{OGS6_Chain$print_log()}}
\item \href{#method-clone}{\code{OGS6_Chain$clone()}}
}
@@ -35,13 +35,13 @@ Creates new OGS6_Chain object
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-ogs_run_simulation"></a>}}
-\if{latex}{\out{\hypertarget{method-ogs_run_simulation}{}}}
-\subsection{Method \code{ogs_run_simulation()}}{
-Runs the simulation. This calls r2ogs6::ogs_run_simulation() internally.
+\if{html}{\out{<a id="method-ogs6_run_simulation"></a>}}
+\if{latex}{\out{\hypertarget{method-ogs6_run_simulation}{}}}
+\subsection{Method \code{ogs6_run_simulation()}}{
+Runs the simulation. This calls r2ogs6::ogs6_run_simulation() internally.
For chains, output will be written to logfiles.
\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6_Chain$ogs_run_simulation()}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_Chain$ogs6_run_simulation()}\if{html}{\out{</div>}}
}
}
diff --git a/man/OGS6_Ensemble.Rd b/man/OGS6_Ensemble.Rd
index 15b77c3..746a402 100644
--- a/man/OGS6_Ensemble.Rd
+++ b/man/OGS6_Ensemble.Rd
@@ -76,7 +76,7 @@ Overrides default printing behaviour
\if{html}{\out{<a id="method-run_simulation"></a>}}
\if{latex}{\out{\hypertarget{method-run_simulation}{}}}
\subsection{Method \code{run_simulation()}}{
-Runs the simulation. This calls r2ogs6::ogs_run_simulation()
+Runs the simulation. This calls r2ogs6::ogs6_run_simulation()
internally. For ensembles, output will always be written to logfiles.
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$run_simulation(parallel = FALSE, verbose = F)}\if{html}{\out{</div>}}
diff --git a/man/OGS6_pvd.Rd b/man/OGS6_pvd.Rd
index 182a0a5..9427f76 100644
--- a/man/OGS6_pvd.Rd
+++ b/man/OGS6_pvd.Rd
@@ -15,13 +15,14 @@ Constructor for the OGS6_pvd base class
\item{\code{vtu_paths}}{Getter for `datasets` `file`}
-\item{\code{abs_vtu_paths}}{Gets absolute .vtu paths, e.g. `dirname(pvd_path)` + `datasets` `file`}
+\item{\code{abs_vtu_paths}}{Gets absolute .vtu paths, e.g. `dirname(pvd_path)` + `datasets`
+`file`}
\item{\code{last_timestep}}{Gets last timestep}
-\item{\code{timesteps}}{Gets timesteps from private parameter '.datasets'}
+\item{\code{timesteps}}{Gets timesteps from private parameter `datasets`}
-\item{\code{OGS6_vtus}}{Getter for private parameter '.OGS6_vtus'}
+\item{\code{OGS6_vtus}}{Getter for private parameter `.OGS6_vtus`}
}
\if{html}{\out{</div>}}
}
diff --git a/man/OGS6_vtu.Rd b/man/OGS6_vtu.Rd
index 4cebb21..fb9077c 100644
--- a/man/OGS6_vtu.Rd
+++ b/man/OGS6_vtu.Rd
@@ -4,32 +4,32 @@
\alias{OGS6_vtu}
\title{OGS6_vtu}
\description{
-Constructor for the OGS6_vtu base class
+Constructor for the `OGS6_vtu` base class
}
\section{Active bindings}{
\if{html}{\out{<div class="r6-active-bindings">}}
\describe{
-\item{\code{vtu_path}}{Getter for private parameter '.vtu_path'}
+\item{\code{vtu_path}}{Getter for private parameter `.vtu_path`}
-\item{\code{number_of_points}}{Getter for NumberOfPoints parameter of '.vtkUnstructuredGrid'}
+\item{\code{number_of_points}}{Getter for NumberOfPoints parameter of `.vtkUnstructuredGrid`}
-\item{\code{number_of_cells}}{Getter for NumberOfCells parameter of '.vtkUnstructuredGrid'}
+\item{\code{number_of_cells}}{Getter for NumberOfCells parameter of `.vtkUnstructuredGrid`}
-\item{\code{points}}{Getter for Points parameter of '.dsa_vtkUnstructuredGrid'}
+\item{\code{points}}{Getter for Points parameter of `.dsa_vtkUnstructuredGrid`}
-\item{\code{cells}}{Getter for Cells parameter of '.dsa_vtkUnstructuredGrid'}
+\item{\code{cells}}{Getter for Cells parameter of `.dsa_vtkUnstructuredGrid`}
-\item{\code{field_data}}{Getter for FieldData parameter of '.dsa_vtkUnstructuredGrid'}
+\item{\code{field_data}}{Getter for FieldData parameter of `.dsa_vtkUnstructuredGrid`}
-\item{\code{point_data}}{Getter for PointData parameter of '.dsa_vtkUnstructuredGrid'}
+\item{\code{point_data}}{Getter for PointData parameter of `.dsa_vtkUnstructuredGrid`}
-\item{\code{cell_data}}{Getter for CellData parameter of '.dsa_vtkUnstructuredGrid'}
+\item{\code{cell_data}}{Getter for CellData parameter of `.dsa_vtkUnstructuredGrid`}
-\item{\code{vtkPointLocator}}{Getter for private parameter '.vtkPointLocator'}
+\item{\code{vtkPointLocator}}{Getter for private parameter `.vtkPointLocator`}
-\item{\code{vtkUnstructuredGrid}}{Access to private parameter '.vtkUnstructuredGrid'}
+\item{\code{vtkUnstructuredGrid}}{Access to private parameter `.vtkUnstructuredGrid`}
-\item{\code{dsa_vtkUnstructuredGrid}}{Getter for private parameter '.dsa_vtkUnstructuredGrid'}
+\item{\code{dsa_vtkUnstructuredGrid}}{Getter for private parameter `.dsa_vtkUnstructuredGrid`}
}
\if{html}{\out{</div>}}
}
@@ -50,7 +50,7 @@ Constructor for the OGS6_vtu base class
\if{html}{\out{<a id="method-new"></a>}}
\if{latex}{\out{\hypertarget{method-new}{}}}
\subsection{Method \code{new()}}{
-Creates new OGS6_vtu object
+Creates new OGS6_vtu object.
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6_vtu$new(vtu_path)}\if{html}{\out{</div>}}
}
@@ -67,7 +67,7 @@ Creates new OGS6_vtu object
\if{html}{\out{<a id="method-print"></a>}}
\if{latex}{\out{\hypertarget{method-print}{}}}
\subsection{Method \code{print()}}{
-Overrides default printing behaviour
+Overrides default printing behaviour.
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6_vtu$print()}\if{html}{\out{</div>}}
}
@@ -86,13 +86,14 @@ Gets FieldData.
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{keys}}{character: Optional: `Name` attributes of `DataArray`
-elements, defaults to all in `FieldData`}
+elements, defaults to all in `FieldData`.}
}
\if{html}{\out{</div>}}
}
\subsection{Returns}{
-list: List of format list(value_a = 1, value_b = 2), where the
-names reference the `Name` attributes of the `DataArray` elements
+A list of format list(value_a = 1, value_b = 2), where
+the names reference the `Name` attributes of the `DataArray`
+elements.
}
}
\if{html}{\out{<hr>}}
@@ -112,8 +113,9 @@ Gets coordinates of specific points by their IDs.
\if{html}{\out{</div>}}
}
\subsection{Returns}{
-If `point_ids` is a number, a coordinate array. If `point_ids`
-is a numeric vector with length > 1, a list of coordinate arrays.
+If `point_ids` is a number, a coordinate array. If
+point_ids` is a numeric vector with length > 1, a list of coordinate
+arrays.
}
}
\if{html}{\out{<hr>}}
@@ -157,7 +159,7 @@ elements, defaults to all in `PointData`}
\if{html}{\out{</div>}}
}
\subsection{Returns}{
-tibble: Tibble where each row represents a point.
+A tibble::tibble where each row represents a point.
}
}
\if{html}{\out{<hr>}}
@@ -180,7 +182,7 @@ elements, defaults to all in `CellData`}
\if{html}{\out{</div>}}
}
\subsection{Returns}{
-tibble: Tibble where each row represents a cell.
+A tibble::tibble where each row represents a cell.
}
}
\if{html}{\out{<hr>}}
diff --git a/man/examples/ex_prj_borehole_heat_exchanger.R b/man/examples/ex_prj_borehole_heat_exchanger.R
index 4595951..8972a9a 100644
--- a/man/examples/ex_prj_borehole_heat_exchanger.R
+++ b/man/examples/ex_prj_borehole_heat_exchanger.R
@@ -1,6 +1,6 @@
-r2ogs6_borehole_heat_exchanger(
+prj_borehole_heat_exchanger(
type = "1U",
- flow_and_temperature_control = r2ogs6_flow_and_temperature_control(
+ flow_and_temperature_control = prj_flow_and_temperature_control(
type = "TemperatureCurveConstantFlow",
flow_rate = 2e-04,
temperature_curve = "inflow_temperature"
@@ -13,7 +13,7 @@ r2ogs6_borehole_heat_exchanger(
heat_capacity = "1735.160",
thermal_conductivity = "0.806"
),
- pipes = r2ogs6_pipes(
+ pipes = prj_pipes(
longitudinal_dispersion_length = 0.001,
inlet = list(
diameter = " 0.013665",
diff --git a/man/examples/ex_prj_boundary_condition.R b/man/examples/ex_prj_boundary_condition.R
index f64d1c2..314556f 100644
--- a/man/examples/ex_prj_boundary_condition.R
+++ b/man/examples/ex_prj_boundary_condition.R
@@ -1,4 +1,4 @@
-r2ogs6_boundary_condition(
+prj_boundary_condition(
type = "Neumann",
parameter = "flux_in",
geometrical_set = "cube_1x1x1_geometry",
diff --git a/man/examples/ex_prj_capillary_pressure.R b/man/examples/ex_prj_capillary_pressure.R
index 0e4a0a0..b676262 100644
--- a/man/examples/ex_prj_capillary_pressure.R
+++ b/man/examples/ex_prj_capillary_pressure.R
@@ -1,4 +1,4 @@
-r2ogs6_capillary_pressure(
+prj_capillary_pressure(
type = "vanGenuchten",
pd = 2e+06,
sr = 0.4,
diff --git a/man/examples/ex_prj_chemical_system.R b/man/examples/ex_prj_chemical_system.R
index 72427ae..68cfe7d 100644
--- a/man/examples/ex_prj_chemical_system.R
+++ b/man/examples/ex_prj_chemical_system.R
@@ -1,7 +1,7 @@
-r2ogs6_chemical_system(
+prj_chemical_system(
chemical_solver = "Phreeqc",
database = "PSINA_12_07_110615_DAV_s.dat",
- solution = r2ogs6_solution(
+ solution = prj_solution(
temperature = 25,
pressure = 1,
pe = 4,
@@ -20,7 +20,7 @@ r2ogs6_chemical_system(
scaling = "0"
),
equilibrium_reactants = list(
- phase_component = r2ogs6_phase_component(
+ phase_component = prj_phase_component(
name = "Calcite",
saturation_index = 0,
initial_amount = 0.000207
diff --git a/man/examples/ex_prj_com_property.R b/man/examples/ex_prj_com_property.R
index 31b57e3..3bfa006 100644
--- a/man/examples/ex_prj_com_property.R
+++ b/man/examples/ex_prj_com_property.R
@@ -1,3 +1,3 @@
-r2ogs6_com_property(name = "molecular_diffusion",
+prj_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
index ee35ed0..49a2987 100644
--- a/man/examples/ex_prj_component.R
+++ b/man/examples/ex_prj_component.R
@@ -1,7 +1,7 @@
-r2ogs6_component(
+prj_component(
name = "concentration",
properties = list(
- property = r2ogs6_com_property(name = "molecular_diffusion",
+ property = prj_com_property(name = "molecular_diffusion",
type = "Constant",
value = 2e-09)
)
diff --git a/man/examples/ex_prj_constitutive_relation.R b/man/examples/ex_prj_constitutive_relation.R
index 206d6fa..95148a2 100644
--- a/man/examples/ex_prj_constitutive_relation.R
+++ b/man/examples/ex_prj_constitutive_relation.R
@@ -1,4 +1,4 @@
-r2ogs6_constitutive_relation(
+prj_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
index f34fbdd..8993abf 100644
--- a/man/examples/ex_prj_convergence_criterion.R
+++ b/man/examples/ex_prj_convergence_criterion.R
@@ -1,4 +1,4 @@
-r2ogs6_convergence_criterion(
+prj_convergence_criterion(
type = "DeltaX",
norm_type = "INFINITY_N",
abstol = 1e-08,
diff --git a/man/examples/ex_prj_curve.R b/man/examples/ex_prj_curve.R
index 26f166a..92c1d7e 100644
--- a/man/examples/ex_prj_curve.R
+++ b/man/examples/ex_prj_curve.R
@@ -1,3 +1,3 @@
-r2ogs6_curve(name = "Dirichlet_temporal",
+prj_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
index e67be0a..b47d693 100644
--- a/man/examples/ex_prj_deactivated_subdomain.R
+++ b/man/examples/ex_prj_deactivated_subdomain.R
@@ -1,3 +1,3 @@
-r2ogs6_deactivated_subdomain(time_interval = list(start = "0",
+prj_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
index 29aa95b..ce08189 100644
--- a/man/examples/ex_prj_eigen.R
+++ b/man/examples/ex_prj_eigen.R
@@ -1,4 +1,4 @@
-r2ogs6_eigen(
+prj_eigen(
solver_type = "BiCGSTAB",
precon_type = "ILUT",
max_iteration_step = 10000,
diff --git a/man/examples/ex_prj_flow_and_temperature_control.R b/man/examples/ex_prj_flow_and_temperature_control.R
index ee98437..b1d9e60 100644
--- a/man/examples/ex_prj_flow_and_temperature_control.R
+++ b/man/examples/ex_prj_flow_and_temperature_control.R
@@ -1,4 +1,4 @@
-r2ogs6_flow_and_temperature_control(
+prj_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
index 4805e54..a044263 100644
--- a/man/examples/ex_prj_fluid.R
+++ b/man/examples/ex_prj_fluid.R
@@ -1,4 +1,4 @@
-r2ogs6_fluid(
+prj_fluid(
liquid_density = list(type = "Constant",
value = " 1.e3 "),
gas_density = list(type = "IdealGasLaw",
diff --git a/man/examples/ex_prj_fracture_model.R b/man/examples/ex_prj_fracture_model.R
index 2e6c88c..3e1eb54 100644
--- a/man/examples/ex_prj_fracture_model.R
+++ b/man/examples/ex_prj_fracture_model.R
@@ -1,4 +1,4 @@
-r2ogs6_fracture_model(type = "LinearElasticIsotropic",
+prj_fracture_model(type = "LinearElasticIsotropic",
normal_stiffness = "Kn",
shear_stiffness = "Ks",
penalty_aperture_cutoff = 1e-05,
diff --git a/man/examples/ex_prj_fracture_properties.R b/man/examples/ex_prj_fracture_properties.R
index 9c8c9a9..eb40a43 100644
--- a/man/examples/ex_prj_fracture_properties.R
+++ b/man/examples/ex_prj_fracture_properties.R
@@ -1,4 +1,4 @@
-r2ogs6_fracture_properties(
+prj_fracture_properties(
material_id = 0,
initial_aperture = "aperture0",
specific_storage = "S_f",
diff --git a/man/examples/ex_prj_global_process_coupling.R b/man/examples/ex_prj_global_process_coupling.R
index 9ae65ef..f917a55 100644
--- a/man/examples/ex_prj_global_process_coupling.R
+++ b/man/examples/ex_prj_global_process_coupling.R
@@ -1,7 +1,7 @@
-r2ogs6_global_process_coupling(
+prj_global_process_coupling(
max_iter = 100,
convergence_criteria = list(
- convergence_criterion = r2ogs6_convergence_criterion(
+ convergence_criterion = prj_convergence_criterion(
type = "DeltaX",
norm_type = "INFINITY_N",
abstol = 1e-08,
diff --git a/man/examples/ex_prj_insitu.R b/man/examples/ex_prj_insitu.R
index 83ac5fd..d2c4430 100644
--- a/man/examples/ex_prj_insitu.R
+++ b/man/examples/ex_prj_insitu.R
@@ -1 +1 @@
-r2ogs6_insitu(scripts = c(script = "square_1e1_neumann-insitu.py"))
+prj_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
index a1b80a2..0e068f0 100644
--- a/man/examples/ex_prj_jacobian_assembler.R
+++ b/man/examples/ex_prj_jacobian_assembler.R
@@ -1,4 +1,4 @@
-r2ogs6_jacobian_assembler(
+prj_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
index 0a8e9cd..666fd91 100644
--- a/man/examples/ex_prj_kinetic_reactant.R
+++ b/man/examples/ex_prj_kinetic_reactant.R
@@ -1,2 +1,2 @@
-r2ogs6_kinetic_reactant(name = "Productc",
+prj_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
index e02ee09..42dceae 100644
--- a/man/examples/ex_prj_linear_solver.R
+++ b/man/examples/ex_prj_linear_solver.R
@@ -1,6 +1,6 @@
-r2ogs6_linear_solver(
+prj_linear_solver(
name = "general_linear_solver",
- eigen = r2ogs6_eigen(
+ eigen = prj_eigen(
solver_type = "BiCGSTAB",
precon_type = "ILUT",
max_iteration_step = 10000,
diff --git a/man/examples/ex_prj_local_coordinate_system.R b/man/examples/ex_prj_local_coordinate_system.R
index b2bb3f6..c64d86e 100644
--- a/man/examples/ex_prj_local_coordinate_system.R
+++ b/man/examples/ex_prj_local_coordinate_system.R
@@ -1,3 +1,3 @@
-r2ogs6_local_coordinate_system(basis_vector_0 = "e0",
+prj_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
index 744ea51..932d67b 100644
--- a/man/examples/ex_prj_material_property.R
+++ b/man/examples/ex_prj_material_property.R
@@ -1,5 +1,5 @@
-r2ogs6_material_property(
- fluid = r2ogs6_fluid(
+prj_material_property(
+ fluid = prj_fluid(
liquid_density = list(type = "Constant",
value = " 1.e3 "),
gas_density = list(type = "IdealGasLaw",
@@ -10,7 +10,7 @@ r2ogs6_material_property(
value = " 2.8539e-13 ")
),
porous_medium = list(
- porous_medium = r2ogs6_porous_medium(
+ porous_medium = prj_porous_medium(
id = 0,
permeability = list(permeability_tensor_entries = "kappa1",
type = "Constant"),
@@ -18,7 +18,7 @@ r2ogs6_material_property(
porosity_parameter = "constant_porosity_parameter"),
storage = list(type = "Constant",
value = " 0.0 "),
- capillary_pressure = r2ogs6_capillary_pressure(
+ capillary_pressure = prj_capillary_pressure(
type = "vanGenuchten",
pd = 2e+06,
sr = 0.4,
@@ -28,7 +28,7 @@ r2ogs6_material_property(
has_regularized = "true"
),
relative_permeability = list(
- relative_permeability = r2ogs6_relative_permeability(
+ relative_permeability = prj_relative_permeability(
type = "NonWettingPhaseVanGenuchten",
sr = 0,
smax = 0.6,
diff --git a/man/examples/ex_prj_medium.R b/man/examples/ex_prj_medium.R
index 46f3444..40bae6b 100644
--- a/man/examples/ex_prj_medium.R
+++ b/man/examples/ex_prj_medium.R
@@ -1,24 +1,24 @@
-r2ogs6_medium(
+prj_medium(
phases = list(
- phase = r2ogs6_phase(
+ phase = prj_phase(
type = "Gas",
properties = list(
- property = r2ogs6_ph_property(name = "viscosity",
+ property = prj_ph_property(name = "viscosity",
type = "Constant",
value = 1e-05)
)
),
- phase = r2ogs6_phase(
+ phase = prj_phase(
type = "Solid",
properties = list(
- property = r2ogs6_ph_property(name = "porosity",
+ property = prj_ph_property(name = "porosity",
type = "Constant",
value = 0.3)
)
)
),
properties = list(
- property = r2ogs6_pr_property(name = "reference_temperature",
+ property = prj_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
index 2e1e62a..1e21e74 100644
--- a/man/examples/ex_prj_nonlinear_solver.R
+++ b/man/examples/ex_prj_nonlinear_solver.R
@@ -1,4 +1,4 @@
-r2ogs6_nonlinear_solver(
+prj_nonlinear_solver(
name = "basic_newton",
type = "Newton",
max_iter = 50,
diff --git a/man/examples/ex_prj_output.R b/man/examples/ex_prj_output.R
index ff4d8ec..fca911b 100644
--- a/man/examples/ex_prj_output.R
+++ b/man/examples/ex_prj_output.R
@@ -1,4 +1,4 @@
-r2ogs6_output(
+prj_output(
type = "VTK",
prefix = "flow_free_expansion",
variables = list(
diff --git a/man/examples/ex_prj_parameter.R b/man/examples/ex_prj_parameter.R
index 5265994..131671e 100644
--- a/man/examples/ex_prj_parameter.R
+++ b/man/examples/ex_prj_parameter.R
@@ -1,7 +1,7 @@
-r2ogs6_parameter(name = "zero",
+prj_parameter(name = "zero",
type = "Constant",
value = 0)
-r2ogs6_parameter(name = "flux_in",
+prj_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
index a400332..c3db218 100644
--- a/man/examples/ex_prj_ph_property.R
+++ b/man/examples/ex_prj_ph_property.R
@@ -1,3 +1,3 @@
-r2ogs6_ph_property(name = "porosity",
+prj_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
index 9e5bebb..c91af32 100644
--- a/man/examples/ex_prj_phase.R
+++ b/man/examples/ex_prj_phase.R
@@ -1,7 +1,7 @@
-r2ogs6_phase(
+prj_phase(
type = "Solid",
properties = list(
- property = r2ogs6_ph_property(name = "porosity",
+ property = prj_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
index 6177a8b..57f1b8c 100644
--- a/man/examples/ex_prj_phase_component.R
+++ b/man/examples/ex_prj_phase_component.R
@@ -1,4 +1,4 @@
-r2ogs6_phase_component(
+prj_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
index d70227d..7f1857c 100644
--- a/man/examples/ex_prj_phasefield_parameters.R
+++ b/man/examples/ex_prj_phasefield_parameters.R
@@ -1,4 +1,4 @@
-r2ogs6_phasefield_parameters(
+prj_phasefield_parameters(
residual_stiffness = "k",
crack_resistance = "gc",
crack_length_scale = "ls",
diff --git a/man/examples/ex_prj_pipes.R b/man/examples/ex_prj_pipes.R
index ae6fd21..6f5baf7 100644
--- a/man/examples/ex_prj_pipes.R
+++ b/man/examples/ex_prj_pipes.R
@@ -1,4 +1,4 @@
-r2ogs6_pipes(
+prj_pipes(
longitudinal_dispersion_length = 0.001,
inlet = list(
diameter = " 0.013665",
diff --git a/man/examples/ex_prj_porous_medium.R b/man/examples/ex_prj_porous_medium.R
index 0adf4d7..2a1abc3 100644
--- a/man/examples/ex_prj_porous_medium.R
+++ b/man/examples/ex_prj_porous_medium.R
@@ -1,4 +1,4 @@
-r2ogs6_porous_medium(
+prj_porous_medium(
id = 0,
permeability = list(permeability_tensor_entries = "kappa1",
type = "Constant"),
@@ -6,7 +6,7 @@ r2ogs6_porous_medium(
porosity_parameter = "constant_porosity_parameter"),
storage = list(type = "Constant",
value = " 0.0 "),
- capillary_pressure = r2ogs6_capillary_pressure(
+ capillary_pressure = prj_capillary_pressure(
type = "vanGenuchten",
pd = 2e+06,
sr = 0.4,
@@ -16,7 +16,7 @@ r2ogs6_porous_medium(
has_regularized = "true"
),
relative_permeability = list(
- relative_permeability = r2ogs6_relative_permeability(
+ relative_permeability = prj_relative_permeability(
type = "NonWettingPhaseVanGenuchten",
sr = 0,
smax = 0.6,
diff --git a/man/examples/ex_prj_pr_property.R b/man/examples/ex_prj_pr_property.R
index 341bc10..fa64494 100644
--- a/man/examples/ex_prj_pr_property.R
+++ b/man/examples/ex_prj_pr_property.R
@@ -1,3 +1,3 @@
-r2ogs6_pr_property(name = "reference_temperature",
+prj_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
index c615361..e8d5481 100644
--- a/man/examples/ex_prj_process.R
+++ b/man/examples/ex_prj_process.R
@@ -1,4 +1,4 @@
-r2ogs6_process(
+prj_process(
name = "HM",
type = "HYDRO_MECHANICS",
integration_order = 3,
@@ -10,7 +10,7 @@ r2ogs6_process(
),
specific_body_force = c(0, 0, 0),
dimension = 3,
- constitutive_relation = r2ogs6_constitutive_relation(
+ constitutive_relation = prj_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
index 8aecaea..e27da5f 100644
--- a/man/examples/ex_prj_process_variable.R
+++ b/man/examples/ex_prj_process_variable.R
@@ -1,10 +1,10 @@
-r2ogs6_process_variable(
+prj_process_variable(
name = "pressure",
components = 1,
order = 1,
initial_condition = "pressure0",
boundary_conditions = list(
- boundary_condition = r2ogs6_boundary_condition(
+ boundary_condition = prj_boundary_condition(
type = "Neumann",
parameter = "flux_in",
geometrical_set = "cube_1x1x1_geometry",
diff --git a/man/examples/ex_prj_rate.R b/man/examples/ex_prj_rate.R
index d9d9fcf..7f9fa12 100644
--- a/man/examples/ex_prj_rate.R
+++ b/man/examples/ex_prj_rate.R
@@ -1,4 +1,4 @@
-r2ogs6_rate(
+prj_rate(
kinetic_reactant = "Productc",
expression = list(
statement = "Km = 10",
diff --git a/man/examples/ex_prj_relative_permeability.R b/man/examples/ex_prj_relative_permeability.R
index 5353636..cf9fff6 100644
--- a/man/examples/ex_prj_relative_permeability.R
+++ b/man/examples/ex_prj_relative_permeability.R
@@ -1,4 +1,4 @@
-r2ogs6_relative_permeability(
+prj_relative_permeability(
type = "NonWettingPhaseVanGenuchten",
sr = 0,
smax = 0.6,
diff --git a/man/examples/ex_prj_search_length_algorithm.R b/man/examples/ex_prj_search_length_algorithm.R
index 971cec4..1cae9de 100644
--- a/man/examples/ex_prj_search_length_algorithm.R
+++ b/man/examples/ex_prj_search_length_algorithm.R
@@ -1,2 +1,2 @@
-r2ogs6_search_length_algorithm(type = "fixed",
+prj_search_length_algorithm(type = "fixed",
value = 1e-06)
diff --git a/man/examples/ex_prj_solution.R b/man/examples/ex_prj_solution.R
index 58076b7..1f4e8fd 100644
--- a/man/examples/ex_prj_solution.R
+++ b/man/examples/ex_prj_solution.R
@@ -1,4 +1,4 @@
-r2ogs6_solution(
+prj_solution(
temperature = 25,
pressure = 1,
pe = 4,
diff --git a/man/examples/ex_prj_source_term.R b/man/examples/ex_prj_source_term.R
index 3113b84..fdc8e2c 100644
--- a/man/examples/ex_prj_source_term.R
+++ b/man/examples/ex_prj_source_term.R
@@ -1,4 +1,4 @@
-r2ogs6_source_term(
+prj_source_term(
type = "Nodal",
parameter = "sourceterm_heat_transfer_coefficient",
geometrical_set = "geometry",
diff --git a/man/examples/ex_prj_time_loop.R b/man/examples/ex_prj_time_loop.R
index 8befb8e..35cbcfb 100644
--- a/man/examples/ex_prj_time_loop.R
+++ b/man/examples/ex_prj_time_loop.R
@@ -1,15 +1,15 @@
-r2ogs6_time_loop(
+prj_time_loop(
processes = list(
- process = r2ogs6_tl_process(
+ process = prj_tl_process(
ref = "HM",
nonlinear_solver = "basic_newton",
- convergence_criterion = r2ogs6_convergence_criterion(
+ convergence_criterion = prj_convergence_criterion(
type = "DeltaX",
norm_type = "NORM2",
reltol = 1e-08
),
time_discretization = list(type = "BackwardEuler"),
- time_stepping = r2ogs6_time_stepping(
+ time_stepping = prj_time_stepping(
type = "FixedTimeStepping",
t_initial = 0,
t_end = 10000,
@@ -18,7 +18,7 @@ r2ogs6_time_loop(
)
)
),
- output = r2ogs6_output(
+ output = prj_output(
type = "VTK",
prefix = "flow_free_expansion",
variables = list(
diff --git a/man/examples/ex_prj_time_stepping.R b/man/examples/ex_prj_time_stepping.R
index 5c9a10f..084a5ea 100644
--- a/man/examples/ex_prj_time_stepping.R
+++ b/man/examples/ex_prj_time_stepping.R
@@ -1,4 +1,4 @@
-r2ogs6_time_stepping(
+prj_time_stepping(
type = "FixedTimeStepping",
t_initial = 0,
t_end = 10000,
diff --git a/man/examples/ex_prj_tl_process.R b/man/examples/ex_prj_tl_process.R
index 5a9cf5e..0e78559 100644
--- a/man/examples/ex_prj_tl_process.R
+++ b/man/examples/ex_prj_tl_process.R
@@ -1,13 +1,13 @@
-r2ogs6_tl_process(
+prj_tl_process(
ref = "HM",
nonlinear_solver = "basic_newton",
- convergence_criterion = r2ogs6_convergence_criterion(
+ convergence_criterion = prj_convergence_criterion(
type = "DeltaX",
norm_type = "NORM2",
reltol = 1e-08
),
time_discretization = list(type = "BackwardEuler"),
- time_stepping = r2ogs6_time_stepping(
+ time_stepping = prj_time_stepping(
type = "FixedTimeStepping",
t_initial = 0,
t_end = 10000,
diff --git a/man/examples/ex_prj_vtkdiff.R b/man/examples/ex_prj_vtkdiff.R
index 8029098..9d3c05f 100644
--- a/man/examples/ex_prj_vtkdiff.R
+++ b/man/examples/ex_prj_vtkdiff.R
@@ -1,4 +1,4 @@
-r2ogs6_vtkdiff(field = "displacement",
+prj_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/get_benchmark_paths.Rd b/man/get_benchmark_paths.Rd
index af0609c..112419d 100644
--- a/man/get_benchmark_paths.Rd
+++ b/man/get_benchmark_paths.Rd
@@ -4,10 +4,10 @@
\alias{get_benchmark_paths}
\title{get_benchmark_paths}
\usage{
-get_benchmark_paths(ogs_processlib_path)
+get_benchmark_paths(ogs6_processlib_path)
}
\arguments{
-\item{ogs_processlib_path}{string: Path to OpenGeoSys 6 ProcessLib folder
+\item{ogs6_processlib_path}{string: Path to OpenGeoSys 6 ProcessLib folder
which contains relevant Tests.cmake files}
}
\description{
diff --git a/man/get_prj_top_level_tags.Rd b/man/get_prj_top_level_tags.Rd
new file mode 100644
index 0000000..4c8ea40
--- /dev/null
+++ b/man/get_prj_top_level_tags.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{get_prj_top_level_tags}
+\alias{get_prj_top_level_tags}
+\title{get_prj_top_level_tags}
+\usage{
+get_prj_top_level_tags()
+}
+\value{
+list: List of lists.
+}
+\description{
+Gets top level .prj tags along with info if they are required.
+}
diff --git a/man/get_tag_from_class.Rd b/man/get_tag_from_class.Rd
index 6e4c93d..e546c8a 100644
--- a/man/get_tag_from_class.Rd
+++ b/man/get_tag_from_class.Rd
@@ -16,5 +16,5 @@ string: The tag name corresponding to \code{class_name}
Utility function, returns the tag name of a r2ogs6 class
}
\examples{
- get_tag_from_class("r2ogs6_process")
+ get_tag_from_class("prj_process")
}
diff --git a/man/node_to_object.Rd b/man/node_to_object.Rd
index 141f78e..3a44763 100644
--- a/man/node_to_object.Rd
+++ b/man/node_to_object.Rd
@@ -15,7 +15,7 @@ node_to_object(xml_node, xpath = "")
Returns representation of an XML node. This is a recursive
function.
ASSUMPTIONS:
-1) Leaf nodes will never be r2ogs6_* objects
+1) Leaf nodes will never be prj_* objects
2) Wrapper nodes are represented as lists
3) Parent nodes whose children have no children are represented as lists
}
diff --git a/man/node_to_prj_class_object.Rd b/man/node_to_prj_class_object.Rd
new file mode 100644
index 0000000..3e92a99
--- /dev/null
+++ b/man/node_to_prj_class_object.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_in_utils.R
+\name{node_to_prj_class_object}
+\alias{node_to_prj_class_object}
+\title{node_to_prj_class_object}
+\usage{
+node_to_prj_class_object(xml_node, xpath)
+}
+\arguments{
+\item{xml_node}{xml2::xml_node: XML node}
+
+\item{xpath}{string: XPath expression (for subclass differentiation)}
+}
+\description{
+Takes an XML node and turns it into a class object
+}
diff --git a/man/ogs6_call_ogs6.Rd b/man/ogs6_call_ogs6.Rd
new file mode 100644
index 0000000..ab4c915
--- /dev/null
+++ b/man/ogs6_call_ogs6.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sim_utils.R
+\name{ogs6_call_ogs6}
+\alias{ogs6_call_ogs6}
+\title{ogs6_call_ogs6}
+\usage{
+ogs6_call_ogs6(ogs6_obj, write_logfile = TRUE, ogs6_bin_path, verbose = F)
+}
+\arguments{
+\item{ogs6_obj}{OGS6: Simulation object}
+
+\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{ogs6_bin_path}{string: Optional: OpenGeoSys 6 bin folder path. Defaults
+to \code{options("r2ogs6.default_ogs6_bin_path")}}
+
+\item{verbose}{flag}
+}
+\description{
+Makes system call to OpenGeoSys 6 and retrieves exit code.
+}
diff --git a/man/ogs6_export_sim_files.Rd b/man/ogs6_export_sim_files.Rd
new file mode 100644
index 0000000..28d6294
--- /dev/null
+++ b/man/ogs6_export_sim_files.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sim_utils.R
+\name{ogs6_export_sim_files}
+\alias{ogs6_export_sim_files}
+\title{ogs6_export_sim_files}
+\usage{
+ogs6_export_sim_files(ogs6_obj, test_mode = FALSE)
+}
+\arguments{
+\item{ogs6_obj}{OGS6: Simulation object}
+
+\item{test_mode}{flag: If \code{TRUE}, Will not check status of
+\code{ogs6_obj} before exporting files. Defaults to \code{FALSE}}
+}
+\description{
+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/ogs6_generate_benchmark_script.Rd b/man/ogs6_generate_benchmark_script.Rd
new file mode 100644
index 0000000..1f2ea5d
--- /dev/null
+++ b/man/ogs6_generate_benchmark_script.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_benchmark_script.R
+\name{ogs6_generate_benchmark_script}
+\alias{ogs6_generate_benchmark_script}
+\title{ogs6_generate_benchmark_script}
+\usage{
+ogs6_generate_benchmark_script(
+ prj_path,
+ sim_path,
+ ogs6_bin_path,
+ script_path,
+ read_in_gml,
+ read_in_vtu = FALSE
+)
+}
+\arguments{
+\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}
+
+\item{ogs6_bin_path}{string: OpenGeoSys bin folder path}
+
+\item{script_path}{string: Path where benchmark script will be saved}
+
+\item{read_in_gml}{flag: Optional: Should \code{.gml} file 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 \code{.prj} file.
+}
diff --git a/man/ogs6_generate_structured_mesh.Rd b/man/ogs6_generate_structured_mesh.Rd
new file mode 100644
index 0000000..40166ce
--- /dev/null
+++ b/man/ogs6_generate_structured_mesh.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ogs6_vtu.R
+\name{ogs6_generate_structured_mesh}
+\alias{ogs6_generate_structured_mesh}
+\title{ogs6_generate_structured_mesh}
+\usage{
+ogs6_generate_structured_mesh(args_str, ogs6_bin_path)
+}
+\arguments{
+\item{args_str}{string: The arguments the script will be called with}
+
+\item{ogs6_bin_path}{string: Optional: Path to OpenGeoSys6 bin folder.
+Defaults to options("r2ogs6.default_ogs6_bin_path")}
+}
+\value{
+string: .vtu file path
+}
+\description{
+Wrapper function to call generateStructuredMesh.exe
+ (VTK mesh generator). For full documentation see
+ https://www.opengeosys.org/docs/tools/meshing/structured-mesh-generation/
+}
diff --git a/man/ogs6_get_combinations.Rd b/man/ogs6_get_combinations.Rd
new file mode 100644
index 0000000..bec1b93
--- /dev/null
+++ b/man/ogs6_get_combinations.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ogs6_ensemble.R
+\name{ogs6_get_combinations}
+\alias{ogs6_get_combinations}
+\title{ogs6_get_combinations}
+\usage{
+ogs6_get_combinations(...)
+}
+\arguments{
+\item{...}{vector:}
+}
+\description{
+Gets possible combinations from supplied vectors
+}
diff --git a/man/ogs6_get_medium_property.Rd b/man/ogs6_get_medium_property.Rd
new file mode 100644
index 0000000..e7793a6
--- /dev/null
+++ b/man/ogs6_get_medium_property.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_medium.R
+\name{ogs6_get_medium_property}
+\alias{ogs6_get_medium_property}
+\title{ogs6_get_medium_property}
+\usage{
+ogs6_get_medium_property(medium, name)
+}
+\arguments{
+\item{medium}{prj_medium}
+
+\item{name}{string: The property name}
+}
+\value{
+prj_pr_property
+}
+\description{
+Returns a medium property based on the property name
+}
diff --git a/man/ogs6_read_output_files.Rd b/man/ogs6_read_output_files.Rd
new file mode 100644
index 0000000..9386a0d
--- /dev/null
+++ b/man/ogs6_read_output_files.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sim_utils.R
+\name{ogs6_read_output_files}
+\alias{ogs6_read_output_files}
+\title{ogs6_read_output_files}
+\usage{
+ogs6_read_output_files(ogs6_obj)
+}
+\arguments{
+\item{ogs6_obj}{OGS6: Simulation object}
+}
+\description{
+Read in generated \code{.pvd} files and add it to ogs6_obj
+}
diff --git a/man/ogs6_run_simulation.Rd b/man/ogs6_run_simulation.Rd
new file mode 100644
index 0000000..d7ec431
--- /dev/null
+++ b/man/ogs6_run_simulation.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sim_utils.R
+\name{ogs6_run_simulation}
+\alias{ogs6_run_simulation}
+\title{ogs6_run_simulation}
+\usage{
+ogs6_run_simulation(ogs6_obj, write_logfile = TRUE, ogs6_bin_path, verbose = F)
+}
+\arguments{
+\item{ogs6_obj}{OGS6: Simulation object}
+
+\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{ogs6_bin_path}{string: Optional: OpenGeoSys 6 bin folder path. Defaults
+to \code{options("r2ogs6.default_ogs6_bin_path")}}
+
+\item{verbose}{flag}
+}
+\description{
+Wrapper function that calls \code{ogs6_export_sim_files()},
+ \code{ogs6_call_ogs6()} and \code{ogs6_read_output_files()}.
+}
diff --git a/man/prj_borehole_heat_exchanger.Rd b/man/prj_borehole_heat_exchanger.Rd
new file mode 100644
index 0000000..3d13a0a
--- /dev/null
+++ b/man/prj_borehole_heat_exchanger.Rd
@@ -0,0 +1,73 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_borehole_heat_exchanger.R
+\name{prj_borehole_heat_exchanger}
+\alias{prj_borehole_heat_exchanger}
+\title{prj_borehole_heat_exchanger}
+\usage{
+prj_borehole_heat_exchanger(
+ type,
+ flow_and_temperature_control,
+ borehole,
+ grout,
+ pipes,
+ refrigerant,
+ use_bhe_pipe_network = NULL
+)
+}
+\arguments{
+\item{type}{string:}
+
+\item{flow_and_temperature_control}{prj_flow_and_temperature_control:}
+
+\item{borehole}{list:}
+
+\item{grout}{list:}
+
+\item{pipes}{prj_pipes:}
+
+\item{refrigerant}{list:}
+
+\item{use_bhe_pipe_network}{Optional: string ("true" | "false"):}
+}
+\description{
+tag: borehole_heat_exchanger
+}
+\examples{
+prj_borehole_heat_exchanger(
+ type = "1U",
+ flow_and_temperature_control = prj_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 = prj_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/prj_boundary_condition.Rd b/man/prj_boundary_condition.Rd
new file mode 100644
index 0000000..a60e5a1
--- /dev/null
+++ b/man/prj_boundary_condition.Rd
@@ -0,0 +1,94 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process_variable.R
+\name{prj_boundary_condition}
+\alias{prj_boundary_condition}
+\title{prj_boundary_condition}
+\usage{
+prj_boundary_condition(
+ type,
+ parameter = NULL,
+ geometrical_set = NULL,
+ geometry = NULL,
+ component = NULL,
+ mesh = NULL,
+ alpha = NULL,
+ u_0 = NULL,
+ constraint_type = NULL,
+ constraining_process_variable = NULL,
+ constraint_threshold = NULL,
+ constraint_direction = NULL,
+ area_parameter = NULL,
+ bc_object = NULL,
+ flush_stdout = NULL,
+ property_name = NULL,
+ initial_value_parameter = NULL,
+ constant_name = NULL,
+ coefficient_current_variable_name = NULL,
+ coefficient_other_variable_name = NULL,
+ coefficient_mixed_variables_name = NULL,
+ threshold_parameter = NULL,
+ comparison_operator = NULL,
+ time_interval = NULL
+)
+}
+\arguments{
+\item{type}{string:}
+
+\item{parameter}{string:}
+
+\item{geometrical_set}{Optional: string:}
+
+\item{geometry}{Optional: string:}
+
+\item{component}{Optional: string | double:}
+
+\item{mesh}{Optional: string:}
+
+\item{alpha}{Optional: string:}
+
+\item{u_0}{Optional: string:}
+
+\item{constraint_type}{Optional: string:}
+
+\item{constraining_process_variable}{Optional: string:}
+
+\item{constraint_threshold}{Optional: string | double:}
+
+\item{constraint_direction}{Optional: string:}
+
+\item{area_parameter}{Optional: string:}
+
+\item{bc_object}{Optional: string:}
+
+\item{flush_stdout}{Optional: string:}
+
+\item{property_name}{Optional: string:}
+
+\item{initial_value_parameter}{Optional: string:}
+
+\item{constant_name}{Optional: string:}
+
+\item{coefficient_current_variable_name}{Optional: string:}
+
+\item{coefficient_other_variable_name}{Optional: string:}
+
+\item{coefficient_mixed_variables_name}{Optional: string:}
+
+\item{threshold_parameter}{Optional: string:}
+
+\item{comparison_operator}{Optional: string:}
+
+\item{time_interval}{Optional: list of 2, character:}
+}
+\description{
+tag: boundary_condition
+}
+\examples{
+prj_boundary_condition(
+ type = "Neumann",
+ parameter = "flux_in",
+ geometrical_set = "cube_1x1x1_geometry",
+ geometry = "left",
+ component = 0
+)
+}
diff --git a/man/prj_capillary_pressure.Rd b/man/prj_capillary_pressure.Rd
new file mode 100644
index 0000000..4a8618b
--- /dev/null
+++ b/man/prj_capillary_pressure.Rd
@@ -0,0 +1,48 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_porous_medium.R
+\name{prj_capillary_pressure}
+\alias{prj_capillary_pressure}
+\title{prj_capillary_pressure}
+\usage{
+prj_capillary_pressure(
+ type,
+ pd = NULL,
+ sr = NULL,
+ smax = NULL,
+ m = NULL,
+ pc_max = NULL,
+ has_regularized = NULL,
+ curve = NULL
+)
+}
+\arguments{
+\item{type}{string:}
+
+\item{pd}{Optional: string | double:}
+
+\item{sr}{Optional: string | double:}
+
+\item{smax}{Optional: string | double:}
+
+\item{m}{Optional: string | double:}
+
+\item{pc_max}{Optional: string | double:}
+
+\item{has_regularized}{Optional: string, "true" | "false":}
+
+\item{curve}{Optional: list:}
+}
+\description{
+tag: capillary_pressure
+}
+\examples{
+prj_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/prj_chemical_system.Rd b/man/prj_chemical_system.Rd
new file mode 100644
index 0000000..bbd563b
--- /dev/null
+++ b/man/prj_chemical_system.Rd
@@ -0,0 +1,74 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_chemical_system.R
+\name{prj_chemical_system}
+\alias{prj_chemical_system}
+\title{prj_chemical_system}
+\usage{
+prj_chemical_system(
+ chemical_solver,
+ database,
+ solution,
+ mesh = NULL,
+ knobs = NULL,
+ kinetic_reactants = NULL,
+ rates = NULL,
+ equilibrium_reactants = NULL,
+ surface = NULL,
+ user_punch = NULL
+)
+}
+\arguments{
+\item{chemical_solver}{string:}
+
+\item{database}{string:}
+
+\item{solution}{prj_solution:}
+
+\item{mesh}{Optional: string:}
+
+\item{knobs}{Optional: list:}
+
+\item{kinetic_reactants}{Optional: list, prj_kinetic_reactant:}
+
+\item{rates}{Optional: list, prj_rate:}
+
+\item{equilibrium_reactants}{Optional: list, prj_phase_component:}
+
+\item{surface}{Optional:}
+
+\item{user_punch}{Optional:}
+}
+\description{
+tag: chemical_system
+}
+\examples{
+prj_chemical_system(
+ chemical_solver = "Phreeqc",
+ database = "PSINA_12_07_110615_DAV_s.dat",
+ solution = prj_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 = prj_phase_component(
+ name = "Calcite",
+ saturation_index = 0,
+ initial_amount = 0.000207
+ )
+ )
+)
+}
diff --git a/man/prj_com_property.Rd b/man/prj_com_property.Rd
new file mode 100644
index 0000000..d21bb8e
--- /dev/null
+++ b/man/prj_com_property.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_medium.R
+\name{prj_com_property}
+\alias{prj_com_property}
+\title{prj_com_property}
+\usage{
+prj_com_property(name, type, value = NULL, parameter_name = NULL)
+}
+\arguments{
+\item{name}{string: Property name}
+
+\item{type}{string: Property type}
+
+\item{value}{Optional: string | double: ...}
+
+\item{parameter_name}{Optional:}
+}
+\description{
+tag: property
+}
+\examples{
+prj_com_property(name = "molecular_diffusion",
+ type = "Constant",
+ value = 2e-09)
+}
diff --git a/man/prj_component.Rd b/man/prj_component.Rd
new file mode 100644
index 0000000..727376b
--- /dev/null
+++ b/man/prj_component.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_medium.R
+\name{prj_component}
+\alias{prj_component}
+\title{prj_component}
+\usage{
+prj_component(name, properties)
+}
+\arguments{
+\item{name}{string:}
+
+\item{properties}{list, prj_com_property:}
+}
+\description{
+tag: component
+}
+\examples{
+prj_component(
+ name = "concentration",
+ properties = list(
+ property = prj_com_property(name = "molecular_diffusion",
+ type = "Constant",
+ value = 2e-09)
+ )
+)
+}
diff --git a/man/prj_constitutive_relation.Rd b/man/prj_constitutive_relation.Rd
new file mode 100644
index 0000000..81b3af4
--- /dev/null
+++ b/man/prj_constitutive_relation.Rd
@@ -0,0 +1,140 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process.R
+\name{prj_constitutive_relation}
+\alias{prj_constitutive_relation}
+\title{prj_constitutive_relation}
+\usage{
+prj_constitutive_relation(
+ type,
+ id = NULL,
+ youngs_modulus = NULL,
+ poissons_ratio = NULL,
+ nonlinear_solver = NULL,
+ behaviour = NULL,
+ material_properties = NULL,
+ shear_modulus = NULL,
+ bulk_modulus = NULL,
+ kappa = NULL,
+ beta = NULL,
+ gamma = NULL,
+ hardening_modulus = NULL,
+ alpha = NULL,
+ delta = NULL,
+ eps = NULL,
+ m = NULL,
+ alphap = NULL,
+ deltap = NULL,
+ epsp = NULL,
+ mp = NULL,
+ betap = NULL,
+ gammap = NULL,
+ tangent_type = NULL,
+ damage_properties = NULL,
+ youngs_moduli = NULL,
+ shear_moduli = NULL,
+ poissons_ratios = NULL,
+ a = NULL,
+ n = NULL,
+ sigma0 = NULL,
+ q = NULL,
+ kelvin_shear_modulus = NULL,
+ kelvin_viscosity = NULL,
+ maxwell_shear_modulus = NULL,
+ maxwell_bulk_modulus = NULL,
+ maxwell_viscosity = NULL,
+ dependency_parameter_mk = NULL,
+ dependency_parameter_mvk = NULL,
+ dependency_parameter_mvm = NULL
+)
+}
+\arguments{
+\item{type}{string:}
+
+\item{id}{Optional:}
+
+\item{youngs_modulus}{Optional:}
+
+\item{poissons_ratio}{Optional:}
+
+\item{nonlinear_solver}{Optional:}
+
+\item{behaviour}{Optional:}
+
+\item{material_properties}{Optional:}
+
+\item{shear_modulus}{Optional:}
+
+\item{bulk_modulus}{Optional:}
+
+\item{kappa}{Optional:}
+
+\item{beta}{Optional:}
+
+\item{gamma}{Optional:}
+
+\item{hardening_modulus}{Optional:}
+
+\item{alpha}{Optional:}
+
+\item{delta}{Optional:}
+
+\item{eps}{Optional:}
+
+\item{m}{Optional:}
+
+\item{alphap}{Optional:}
+
+\item{deltap}{Optional:}
+
+\item{epsp}{Optional:}
+
+\item{mp}{Optional:}
+
+\item{betap}{Optional:}
+
+\item{gammap}{Optional:}
+
+\item{tangent_type}{Optional:}
+
+\item{damage_properties}{Optional:}
+
+\item{youngs_moduli}{Optional:}
+
+\item{shear_moduli}{Optional:}
+
+\item{poissons_ratios}{Optional:}
+
+\item{a}{Optional:}
+
+\item{n}{Optional:}
+
+\item{sigma0}{Optional:}
+
+\item{q}{Optional:}
+
+\item{kelvin_shear_modulus}{Optional:}
+
+\item{kelvin_viscosity}{Optional:}
+
+\item{maxwell_shear_modulus}{Optional:}
+
+\item{maxwell_bulk_modulus}{Optional:}
+
+\item{maxwell_viscosity}{Optional:}
+
+\item{dependency_parameter_mk}{Optional:}
+
+\item{dependency_parameter_mvk}{Optional:}
+
+\item{dependency_parameter_mvm}{Optional:}
+}
+\description{
+tag: constitutive_relation
+}
+\examples{
+prj_constitutive_relation(
+ type = "LinearElasticIsotropic",
+ youngs_modulus = "E",
+ poissons_ratio = "nu"
+)
+}
diff --git a/man/prj_convergence_criterion.Rd b/man/prj_convergence_criterion.Rd
new file mode 100644
index 0000000..eae2911
--- /dev/null
+++ b/man/prj_convergence_criterion.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_time_loop.R
+\name{prj_convergence_criterion}
+\alias{prj_convergence_criterion}
+\title{prj_convergence_criterion}
+\usage{
+prj_convergence_criterion(
+ type,
+ norm_type,
+ abstol = NULL,
+ reltol = NULL,
+ abstols = NULL,
+ reltols = NULL
+)
+}
+\arguments{
+\item{type}{string: Type}
+
+\item{norm_type}{string: ...}
+
+\item{abstol}{string | double: Absolute tolerance}
+
+\item{reltol}{string | double: Relative tolerance}
+
+\item{abstols}{string | numeric: Absolute tolerances}
+
+\item{reltols}{string | numeric: Relative tolerances}
+}
+\description{
+tag: convergence_criterion
+}
+\examples{
+prj_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "INFINITY_N",
+ abstol = 1e-08,
+ reltol = 1e-10
+)
+}
diff --git a/man/prj_curve.Rd b/man/prj_curve.Rd
new file mode 100644
index 0000000..aaf6f88
--- /dev/null
+++ b/man/prj_curve.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_curve.R
+\name{prj_curve}
+\alias{prj_curve}
+\title{prj_curve}
+\usage{
+prj_curve(name, coords, values)
+}
+\arguments{
+\item{name}{string: Name of the curve}
+
+\item{coords}{string | numeric: Coordinates at which the curve's values
+are given}
+
+\item{values}{string | numeric: Values of the curve at the given coordinates}
+}
+\description{
+tag: curve, a curve
+}
+\examples{
+prj_curve(name = "Dirichlet_temporal",
+ coords = "0 3",
+ values = "200 200")
+}
diff --git a/man/prj_deactivated_subdomain.Rd b/man/prj_deactivated_subdomain.Rd
new file mode 100644
index 0000000..6442863
--- /dev/null
+++ b/man/prj_deactivated_subdomain.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process_variable.R
+\name{prj_deactivated_subdomain}
+\alias{prj_deactivated_subdomain}
+\title{prj_deactivated_subdomain}
+\usage{
+prj_deactivated_subdomain(time_interval, material_ids)
+}
+\arguments{
+\item{time_interval}{list, numeric:}
+
+\item{material_ids}{string | double:}
+}
+\description{
+tag: deactivated_subdomain
+}
+\examples{
+prj_deactivated_subdomain(time_interval = list(start = "0",
+ end = "1"),
+ material_ids = 1)
+}
diff --git a/man/prj_eigen.Rd b/man/prj_eigen.Rd
new file mode 100644
index 0000000..da17edf
--- /dev/null
+++ b/man/prj_eigen.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_linear_solver.R
+\name{prj_eigen}
+\alias{prj_eigen}
+\title{prj_eigen}
+\usage{
+prj_eigen(
+ solver_type,
+ precon_type = NULL,
+ max_iteration_step = NULL,
+ error_tolerance = NULL,
+ scaling = NULL,
+ restart = NULL
+)
+}
+\arguments{
+\item{solver_type}{string:}
+
+\item{precon_type}{Optional: string:}
+
+\item{max_iteration_step}{Optional: string | double: ...}
+
+\item{error_tolerance}{Optional: string | double: ...}
+
+\item{scaling}{Optional: string | double: ...}
+
+\item{restart}{Optional: string | double: ...}
+}
+\description{
+tag: eigen
+}
+\examples{
+prj_eigen(
+ solver_type = "BiCGSTAB",
+ precon_type = "ILUT",
+ max_iteration_step = 10000,
+ error_tolerance = 1e-16
+)
+}
diff --git a/man/prj_flow_and_temperature_control.Rd b/man/prj_flow_and_temperature_control.Rd
new file mode 100644
index 0000000..36d24e5
--- /dev/null
+++ b/man/prj_flow_and_temperature_control.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_borehole_heat_exchanger.R
+\name{prj_flow_and_temperature_control}
+\alias{prj_flow_and_temperature_control}
+\title{prj_flow_and_temperature_control}
+\usage{
+prj_flow_and_temperature_control(
+ type,
+ flow_rate = NULL,
+ temperature_curve = NULL,
+ power = NULL,
+ power_curve = NULL,
+ flow_rate_curve = NULL
+)
+}
+\arguments{
+\item{type}{string:}
+
+\item{flow_rate}{Optional: string | double:}
+
+\item{temperature_curve}{Optional: string:}
+
+\item{power}{Optional: string | double:}
+
+\item{power_curve}{Optional: string:}
+
+\item{flow_rate_curve}{Optional: string:}
+}
+\description{
+tag: flow_and_temperature_control
+}
+\examples{
+prj_flow_and_temperature_control(
+ type = "TemperatureCurveConstantFlow",
+ flow_rate = 2e-04,
+ temperature_curve = "inflow_temperature"
+)
+}
diff --git a/man/prj_fluid.Rd b/man/prj_fluid.Rd
new file mode 100644
index 0000000..c04b57d
--- /dev/null
+++ b/man/prj_fluid.Rd
@@ -0,0 +1,55 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_material_property.R
+\name{prj_fluid}
+\alias{prj_fluid}
+\title{prj_fluid}
+\usage{
+prj_fluid(
+ liquid_density,
+ gas_density,
+ liquid_viscosity,
+ gas_viscosity,
+ specific_heat_capacity_solid = NULL,
+ specific_heat_capacity_water = NULL,
+ specific_heat_capacity_air = NULL,
+ specific_heat_capacity_water_vapor = NULL,
+ thermal_conductivity_dry_solid = NULL,
+ thermal_conductivity_wet_solid = NULL
+)
+}
+\arguments{
+\item{liquid_density}{list:}
+
+\item{gas_density}{list:}
+
+\item{liquid_viscosity}{list:}
+
+\item{gas_viscosity}{list:}
+
+\item{specific_heat_capacity_solid}{Optional:}
+
+\item{specific_heat_capacity_water}{Optional:}
+
+\item{specific_heat_capacity_air}{Optional:}
+
+\item{specific_heat_capacity_water_vapor}{Optional:}
+
+\item{thermal_conductivity_dry_solid}{Optional:}
+
+\item{thermal_conductivity_wet_solid}{Optional:}
+}
+\description{
+tag: fluid
+}
+\examples{
+prj_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/prj_fracture_model.Rd b/man/prj_fracture_model.Rd
new file mode 100644
index 0000000..8b2819c
--- /dev/null
+++ b/man/prj_fracture_model.Rd
@@ -0,0 +1,53 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process.R
+\name{prj_fracture_model}
+\alias{prj_fracture_model}
+\title{prj_fracture_model}
+\usage{
+prj_fracture_model(
+ type,
+ normal_stiffness,
+ shear_stiffness,
+ penalty_aperture_cutoff,
+ tension_cutoff,
+ fracture_toughness = NULL,
+ peak_normal_traction = NULL,
+ friction_angle = NULL,
+ dilatancy_angle = NULL,
+ cohesion = NULL,
+ nonlinear_solver = NULL
+)
+}
+\arguments{
+\item{type}{string:}
+
+\item{normal_stiffness}{string:}
+
+\item{shear_stiffness}{string:}
+
+\item{penalty_aperture_cutoff}{string | double:}
+
+\item{tension_cutoff}{string | double:}
+
+\item{fracture_toughness}{Optional: string:}
+
+\item{peak_normal_traction}{Optional: string:}
+
+\item{friction_angle}{Optional: string:}
+
+\item{dilatancy_angle}{Optional: string:}
+
+\item{cohesion}{Optional: string:}
+
+\item{nonlinear_solver}{Optional: list:}
+}
+\description{
+tag: fracture_model
+}
+\examples{
+prj_fracture_model(type = "LinearElasticIsotropic",
+ normal_stiffness = "Kn",
+ shear_stiffness = "Ks",
+ penalty_aperture_cutoff = 1e-05,
+ tension_cutoff = 1)
+}
diff --git a/man/prj_fracture_properties.Rd b/man/prj_fracture_properties.Rd
new file mode 100644
index 0000000..17c7cb8
--- /dev/null
+++ b/man/prj_fracture_properties.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process.R
+\name{prj_fracture_properties}
+\alias{prj_fracture_properties}
+\title{prj_fracture_properties}
+\usage{
+prj_fracture_properties(
+ material_id,
+ initial_aperture,
+ specific_storage = NULL,
+ biot_coefficient = NULL,
+ permeability_model = NULL
+)
+}
+\arguments{
+\item{material_id}{string | double:}
+
+\item{initial_aperture}{string:}
+
+\item{specific_storage}{Optional: string:}
+
+\item{biot_coefficient}{Optional: string:}
+
+\item{permeability_model}{Optional: list:}
+}
+\description{
+tag: fracture_properties
+}
+\examples{
+prj_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/prj_global_process_coupling.Rd b/man/prj_global_process_coupling.Rd
new file mode 100644
index 0000000..f496725
--- /dev/null
+++ b/man/prj_global_process_coupling.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_time_loop.R
+\name{prj_global_process_coupling}
+\alias{prj_global_process_coupling}
+\title{prj_global_process_coupling}
+\usage{
+prj_global_process_coupling(max_iter, convergence_criteria)
+}
+\arguments{
+\item{max_iter}{string | double: Maximal number of iterations}
+
+\item{convergence_criteria}{list, prj_convergence_criterion:
+Convergence criteria}
+}
+\description{
+tag: global_process_coupling
+}
+\examples{
+prj_global_process_coupling(
+ max_iter = 100,
+ convergence_criteria = list(
+ convergence_criterion = prj_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "INFINITY_N",
+ abstol = 1e-08,
+ reltol = 1e-10
+ )
+ )
+)
+}
diff --git a/man/prj_insitu.Rd b/man/prj_insitu.Rd
new file mode 100644
index 0000000..7cfd068
--- /dev/null
+++ b/man/prj_insitu.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_insitu.R
+\name{prj_insitu}
+\alias{prj_insitu}
+\title{prj_insitu}
+\usage{
+prj_insitu(scripts)
+}
+\arguments{
+\item{scripts}{character: Script names}
+}
+\description{
+tag: insitu
+}
+\examples{
+prj_insitu(scripts = c(script = "square_1e1_neumann-insitu.py"))
+}
diff --git a/man/prj_jacobian_assembler.Rd b/man/prj_jacobian_assembler.Rd
new file mode 100644
index 0000000..bffd4bd
--- /dev/null
+++ b/man/prj_jacobian_assembler.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process.R
+\name{prj_jacobian_assembler}
+\alias{prj_jacobian_assembler}
+\title{prj_jacobian_assembler}
+\usage{
+prj_jacobian_assembler(
+ type,
+ component_magnitudes = NULL,
+ relative_epsilons = NULL
+)
+}
+\arguments{
+\item{type}{string:}
+
+\item{component_magnitudes}{Optional: string | double:}
+
+\item{relative_epsilons}{Optional: string | double:}
+}
+\description{
+tag: jacobian_assembler
+}
+\examples{
+prj_jacobian_assembler(
+ type = "CentralDifferences",
+ component_magnitudes = 1,
+ relative_epsilons = 1e-08
+)
+}
diff --git a/man/prj_kinetic_reactant.Rd b/man/prj_kinetic_reactant.Rd
new file mode 100644
index 0000000..958dbc2
--- /dev/null
+++ b/man/prj_kinetic_reactant.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_chemical_system.R
+\name{prj_kinetic_reactant}
+\alias{prj_kinetic_reactant}
+\title{prj_kinetic_reactant}
+\usage{
+prj_kinetic_reactant(
+ name,
+ initial_amount = NULL,
+ chemical_formula = NULL,
+ fix_amount = NULL
+)
+}
+\arguments{
+\item{name}{The component name}
+
+\item{initial_amount}{The initial amount of the component}
+
+\item{chemical_formula}{The chemical formula of the component}
+
+\item{fix_amount}{Should the amount be fixed or not?}
+}
+\description{
+S3 class describing .prj kinetic_reactant
+}
+\examples{
+prj_kinetic_reactant(name = "Productc",
+ initial_amount = 1e-06)
+}
diff --git a/man/prj_linear_solver.Rd b/man/prj_linear_solver.Rd
new file mode 100644
index 0000000..13f2c3d
--- /dev/null
+++ b/man/prj_linear_solver.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_linear_solver.R
+\name{prj_linear_solver}
+\alias{prj_linear_solver}
+\title{prj_linear_solver}
+\usage{
+prj_linear_solver(name, eigen = NULL, lis = NULL, petsc = NULL)
+}
+\arguments{
+\item{name}{string: The name of the linear solver}
+
+\item{eigen}{Optional: list: ...}
+
+\item{lis}{Optional: string: ...}
+
+\item{petsc}{Optional: character: ...}
+}
+\description{
+tag: linear_solver
+}
+\examples{
+prj_linear_solver(
+ name = "general_linear_solver",
+ eigen = prj_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/prj_local_coordinate_system.Rd b/man/prj_local_coordinate_system.Rd
new file mode 100644
index 0000000..3c21341
--- /dev/null
+++ b/man/prj_local_coordinate_system.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_local_coordinate_system.R
+\name{prj_local_coordinate_system}
+\alias{prj_local_coordinate_system}
+\title{prj_local_coordinate_system}
+\usage{
+prj_local_coordinate_system(
+ basis_vector_0,
+ basis_vector_1,
+ basis_vector_2 = NULL
+)
+}
+\arguments{
+\item{basis_vector_0}{string | double: A basis vector}
+
+\item{basis_vector_1}{string | double: A basis vector}
+
+\item{basis_vector_2}{Optional: string | double: A basis vector}
+}
+\description{
+tag: local_coordinate_system
+}
+\examples{
+prj_local_coordinate_system(basis_vector_0 = "e0",
+ basis_vector_1 = "e1",
+ basis_vector_2 = "e2")
+}
diff --git a/man/prj_material_property.Rd b/man/prj_material_property.Rd
new file mode 100644
index 0000000..e1c9bf9
--- /dev/null
+++ b/man/prj_material_property.Rd
@@ -0,0 +1,60 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_material_property.R
+\name{prj_material_property}
+\alias{prj_material_property}
+\title{prj_material_property}
+\usage{
+prj_material_property(fluid, porous_medium)
+}
+\arguments{
+\item{fluid}{prj_fluid:}
+
+\item{porous_medium}{prj_porous_medium:}
+}
+\description{
+tag: material_property
+}
+\examples{
+prj_material_property(
+ fluid = prj_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 = prj_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 = prj_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 = prj_relative_permeability(
+ type = "NonWettingPhaseVanGenuchten",
+ sr = 0,
+ smax = 0.6,
+ m = 0.3288590604,
+ krel_min = 0,
+ id = "0"
+ )
+ )
+ )
+ )
+)
+}
diff --git a/man/prj_medium.Rd b/man/prj_medium.Rd
new file mode 100644
index 0000000..9783a4c
--- /dev/null
+++ b/man/prj_medium.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_medium.R
+\name{prj_medium}
+\alias{prj_medium}
+\title{prj_medium}
+\usage{
+prj_medium(phases = NULL, properties = NULL, id = NULL)
+}
+\arguments{
+\item{phases}{list, prj_phase: Optional: Medium phases}
+
+\item{properties}{list, prj_pr_property: Optional: Medium properties}
+
+\item{id}{string | double: Optional: ID corresponding to the MaterialIDs}
+}
+\description{
+tag: medium, a specific medium with optional id corresponding
+ to the MaterialIDs
+}
+\examples{
+prj_medium(
+ phases = list(
+ phase = prj_phase(
+ type = "Gas",
+ properties = list(
+ property = prj_ph_property(name = "viscosity",
+ type = "Constant",
+ value = 1e-05)
+ )
+ ),
+ phase = prj_phase(
+ type = "Solid",
+ properties = list(
+ property = prj_ph_property(name = "porosity",
+ type = "Constant",
+ value = 0.3)
+ )
+ )
+ ),
+ properties = list(
+ property = prj_pr_property(name = "reference_temperature",
+ type = "Constant",
+ value = 293.15)
+ )
+)
+}
diff --git a/man/prj_nonlinear_solver.Rd b/man/prj_nonlinear_solver.Rd
new file mode 100644
index 0000000..83390f5
--- /dev/null
+++ b/man/prj_nonlinear_solver.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_nonlinear_solver.R
+\name{prj_nonlinear_solver}
+\alias{prj_nonlinear_solver}
+\title{prj_nonlinear_solver}
+\usage{
+prj_nonlinear_solver(name, type, max_iter, linear_solver, damping = NULL)
+}
+\arguments{
+\item{name}{string: Name}
+
+\item{type}{string: Type}
+
+\item{max_iter}{string | double: Maximal number of iterations}
+
+\item{linear_solver}{string: Name of corresponding linear_solver}
+
+\item{damping}{Optional: string | double: Damping}
+}
+\description{
+tag: nonlinear_solver
+}
+\examples{
+prj_nonlinear_solver(
+ name = "basic_newton",
+ type = "Newton",
+ max_iter = 50,
+ linear_solver = "general_linear_solver"
+)
+}
diff --git a/man/prj_output.Rd b/man/prj_output.Rd
new file mode 100644
index 0000000..a74c78a
--- /dev/null
+++ b/man/prj_output.Rd
@@ -0,0 +1,57 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_time_loop.R
+\name{prj_output}
+\alias{prj_output}
+\title{prj_output}
+\usage{
+prj_output(
+ type,
+ prefix,
+ variables,
+ suffix = NULL,
+ timesteps = NULL,
+ compress_output = NULL,
+ data_mode = NULL,
+ output_iteration_results = NULL,
+ meshes = NULL,
+ fixed_output_times = NULL
+)
+}
+\arguments{
+\item{type}{string:}
+
+\item{prefix}{string:}
+
+\item{variables}{vector:}
+
+\item{suffix}{Optional: string:}
+
+\item{timesteps}{Optional:}
+
+\item{compress_output}{Optional: string: Should the output be compressed?
+Either "true" or "false"}
+
+\item{data_mode}{Optional: string:}
+
+\item{output_iteration_results}{Optional: string: Either "true" or "false"}
+
+\item{meshes}{Optional: character: A vector of mesh names}
+
+\item{fixed_output_times}{Optional: string | numeric:}
+}
+\description{
+tag: output
+}
+\examples{
+prj_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/prj_parameter.Rd b/man/prj_parameter.Rd
new file mode 100644
index 0000000..3cd5611
--- /dev/null
+++ b/man/prj_parameter.Rd
@@ -0,0 +1,59 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_parameter.R
+\name{prj_parameter}
+\alias{prj_parameter}
+\title{prj_parameter}
+\usage{
+prj_parameter(
+ name,
+ type,
+ value = NULL,
+ values = NULL,
+ curve = NULL,
+ parameter = NULL,
+ group_id_property = NULL,
+ field_name = NULL,
+ mesh = NULL,
+ time_series = NULL,
+ use_local_coordinate_system = NULL,
+ ...
+)
+}
+\arguments{
+\item{name}{string:}
+
+\item{type}{string:}
+
+\item{value}{Optional: string | double: Parameter value}
+
+\item{values}{Optional: string | double: Parameter values}
+
+\item{curve}{Optional: string:}
+
+\item{parameter}{Optional: string:}
+
+\item{group_id_property}{Optional: string:}
+
+\item{field_name}{Optional: string:}
+
+\item{mesh}{Optional: string:}
+
+\item{time_series}{Optional: list:}
+
+\item{use_local_coordinate_system}{Optional: string, "true" | "false":}
+
+\item{...}{Optional: for index_values and expression tags (since there can be
+multiple)}
+}
+\description{
+tag: parameter
+}
+\examples{
+prj_parameter(name = "zero",
+ type = "Constant",
+ value = 0)
+
+prj_parameter(name = "flux_in",
+ type = "Constant",
+ value = 1e-04)
+}
diff --git a/man/prj_ph_property.Rd b/man/prj_ph_property.Rd
new file mode 100644
index 0000000..4377a6c
--- /dev/null
+++ b/man/prj_ph_property.Rd
@@ -0,0 +1,66 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_medium.R
+\name{prj_ph_property}
+\alias{prj_ph_property}
+\title{prj_ph_property}
+\usage{
+prj_ph_property(
+ name,
+ type,
+ value = NULL,
+ reference_value = NULL,
+ initial_porosity = NULL,
+ minimal_porosity = NULL,
+ maximal_porosity = NULL,
+ parameter_name = NULL,
+ exponents = NULL,
+ offset = NULL,
+ exponent = NULL,
+ swelling_pressures = NULL,
+ lower_saturation_limit = NULL,
+ upper_saturation_limit = NULL,
+ intrinsic_permeabilities = NULL,
+ ...
+)
+}
+\arguments{
+\item{name}{string: Property name}
+
+\item{type}{string: Property type}
+
+\item{value}{Optional: string | double: ...}
+
+\item{reference_value}{Optional: string | double:}
+
+\item{initial_porosity}{Optional: string:}
+
+\item{minimal_porosity}{Optional: string | double:}
+
+\item{maximal_porosity}{Optional: string | double:}
+
+\item{parameter_name}{Optional: string:}
+
+\item{exponents}{Optional: string | numeric:}
+
+\item{offset}{Optional: string | double:}
+
+\item{exponent}{Optional: list:}
+
+\item{swelling_pressures}{Optional: string | numeric:}
+
+\item{lower_saturation_limit}{Optional: string | double:}
+
+\item{upper_saturation_limit}{Optional: string | double:}
+
+\item{intrinsic_permeabilities}{Optional: string | numeric:}
+
+\item{...}{independent_variable}
+}
+\description{
+tag: property
+}
+\examples{
+prj_ph_property(name = "porosity",
+ type = "Constant",
+ value = 0.3)
+}
diff --git a/man/prj_phase.Rd b/man/prj_phase.Rd
new file mode 100644
index 0000000..7406df3
--- /dev/null
+++ b/man/prj_phase.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_medium.R
+\name{prj_phase}
+\alias{prj_phase}
+\title{prj_phase}
+\usage{
+prj_phase(type, properties = NULL, components = NULL)
+}
+\arguments{
+\item{type}{string: Phase type
+(get valid types with get_valid_phase_types())}
+
+\item{properties}{list, prj_pr_property: Properties}
+
+\item{components}{list, components}
+}
+\description{
+tag: phase, a coherent material with homogeneous properties
+}
+\examples{
+prj_phase(
+ type = "Solid",
+ properties = list(
+ property = prj_ph_property(name = "porosity",
+ type = "Constant",
+ value = 0.3)
+ )
+)
+}
diff --git a/man/prj_phase_component.Rd b/man/prj_phase_component.Rd
new file mode 100644
index 0000000..5306014
--- /dev/null
+++ b/man/prj_phase_component.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_chemical_system.R
+\name{prj_phase_component}
+\alias{prj_phase_component}
+\title{prj_phase_component}
+\usage{
+prj_phase_component(name, saturation_index, initial_amount = NULL)
+}
+\arguments{
+\item{name}{The component name}
+
+\item{saturation_index}{The saturation index of the component}
+
+\item{initial_amount}{optional: The initial amount of the component}
+}
+\description{
+S3 class describing .prj phase_component
+}
+\examples{
+prj_phase_component(
+ name = "Calcite",
+ saturation_index = 0,
+ initial_amount = 0.000207
+)
+}
diff --git a/man/prj_phasefield_parameters.Rd b/man/prj_phasefield_parameters.Rd
new file mode 100644
index 0000000..f98d927
--- /dev/null
+++ b/man/prj_phasefield_parameters.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process.R
+\name{prj_phasefield_parameters}
+\alias{prj_phasefield_parameters}
+\title{prj_phasefield_parameters}
+\usage{
+prj_phasefield_parameters(
+ residual_stiffness,
+ crack_resistance,
+ crack_length_scale,
+ kinetic_coefficient,
+ history_field = NULL
+)
+}
+\arguments{
+\item{residual_stiffness}{string:}
+
+\item{crack_resistance}{string:}
+
+\item{crack_length_scale}{string:}
+
+\item{kinetic_coefficient}{string:}
+
+\item{history_field}{Optional: string:}
+}
+\description{
+tag: phasefield_parameters
+}
+\examples{
+prj_phasefield_parameters(
+ residual_stiffness = "k",
+ crack_resistance = "gc",
+ crack_length_scale = "ls",
+ kinetic_coefficient = "M",
+ history_field = "H"
+)
+}
diff --git a/man/prj_pipes.Rd b/man/prj_pipes.Rd
new file mode 100644
index 0000000..c9d4287
--- /dev/null
+++ b/man/prj_pipes.Rd
@@ -0,0 +1,47 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_borehole_heat_exchanger.R
+\name{prj_pipes}
+\alias{prj_pipes}
+\title{prj_pipes}
+\usage{
+prj_pipes(
+ longitudinal_dispersion_length,
+ inlet = NULL,
+ outlet = NULL,
+ distance_between_pipes = NULL,
+ outer = NULL,
+ inner = NULL
+)
+}
+\arguments{
+\item{longitudinal_dispersion_length}{string | double:}
+
+\item{inlet}{Optional: list:}
+
+\item{outlet}{Optional: list:}
+
+\item{distance_between_pipes}{Optional: string | double:}
+
+\item{outer}{Optional: list:}
+
+\item{inner}{Optional: list:}
+}
+\description{
+tag: pipes
+}
+\examples{
+prj_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/prj_porous_medium.Rd b/man/prj_porous_medium.Rd
new file mode 100644
index 0000000..bd632cd
--- /dev/null
+++ b/man/prj_porous_medium.Rd
@@ -0,0 +1,61 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_porous_medium.R
+\name{prj_porous_medium}
+\alias{prj_porous_medium}
+\title{prj_porous_medium}
+\usage{
+prj_porous_medium(
+ id,
+ permeability,
+ porosity,
+ storage,
+ capillary_pressure,
+ relative_permeability
+)
+}
+\arguments{
+\item{id}{string | double:}
+
+\item{permeability}{list:}
+
+\item{porosity}{list:}
+
+\item{storage}{list:}
+
+\item{capillary_pressure}{prj_capillary_pressure:}
+
+\item{relative_permeability}{list:}
+}
+\description{
+tag: porous_medium
+}
+\examples{
+prj_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 = prj_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 = prj_relative_permeability(
+ type = "NonWettingPhaseVanGenuchten",
+ sr = 0,
+ smax = 0.6,
+ m = 0.3288590604,
+ krel_min = 0,
+ id = "0"
+ )
+ )
+)
+}
diff --git a/man/prj_pr_property.Rd b/man/prj_pr_property.Rd
new file mode 100644
index 0000000..c45abbf
--- /dev/null
+++ b/man/prj_pr_property.Rd
@@ -0,0 +1,117 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_medium.R
+\name{prj_pr_property}
+\alias{prj_pr_property}
+\title{prj_pr_property}
+\usage{
+prj_pr_property(
+ name,
+ type,
+ value = NULL,
+ parameter_name = NULL,
+ exponent = NULL,
+ residual_liquid_saturation = NULL,
+ residual_gas_saturation = NULL,
+ p_b = NULL,
+ independent_variable = NULL,
+ curve = NULL,
+ minimum_relative_permeability_liquid = NULL,
+ initial_permeability = NULL,
+ maximum_permeability = NULL,
+ lambda = NULL,
+ cutoff_value = 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,
+ 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:}
+
+\item{type}{string:}
+
+\item{value}{Optional:}
+
+\item{parameter_name}{Optional:}
+
+\item{exponent}{Optional:}
+
+\item{residual_liquid_saturation}{Optional:}
+
+\item{residual_gas_saturation}{Optional:}
+
+\item{p_b}{Optional:}
+
+\item{independent_variable}{Optional:}
+
+\item{curve}{Optional:}
+
+\item{minimum_relative_permeability_liquid}{Optional:}
+
+\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{cohesion}{Optional:}
+
+\item{friction_angle}{Optional:}
+
+\item{tensile_strength_parameter}{Optional:}
+
+\item{b1}{Optional:}
+
+\item{b2}{Optional:}
+
+\item{b3}{Optional:}
+
+\item{minimum_permeability}{Optional:}
+
+\item{initial_porosity}{Optional:}
+
+\item{entry_pressure}{Optional:}
+
+\item{min_relative_permeability_liquid}{Optional:}
+
+\item{min_relative_permeability_gas}{Optional:}
+}
+\description{
+tag: property
+}
+\examples{
+prj_pr_property(name = "reference_temperature",
+ type = "Constant",
+ value = 293.15)
+}
diff --git a/man/prj_process.Rd b/man/prj_process.Rd
new file mode 100644
index 0000000..19de933
--- /dev/null
+++ b/man/prj_process.Rd
@@ -0,0 +1,240 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process.R
+\name{prj_process}
+\alias{prj_process}
+\title{prj_process}
+\usage{
+prj_process(
+ name,
+ type,
+ integration_order,
+ process_variables,
+ secondary_variables = NULL,
+ specific_body_force = NULL,
+ solid_density = NULL,
+ dimension = NULL,
+ coupling_scheme = NULL,
+ reference_solid_density = NULL,
+ linear_thermal_expansion_coefficient = NULL,
+ specific_heat_capacity = NULL,
+ thermal_conductivity = NULL,
+ darcy_gravity = NULL,
+ reference_temperature = NULL,
+ fracture_model = NULL,
+ jacobian_assembler = NULL,
+ internal_length = NULL,
+ mass_lumping = NULL,
+ porosity = NULL,
+ calculatesurfaceflux = NULL,
+ intrinsic_permeability = NULL,
+ specific_storage = NULL,
+ fluid_viscosity = NULL,
+ biot_coefficient = NULL,
+ fluid_density = NULL,
+ initial_effective_stress = NULL,
+ initial_fracture_effective_stress = NULL,
+ phasefield_parameters = NULL,
+ deactivate_matrix_in_flow = NULL,
+ borehole_heat_exchangers = NULL,
+ temperature = NULL,
+ reactive_system = NULL,
+ fluid_specific_heat_source = NULL,
+ fluid_specific_isobaric_heat_capacity = NULL,
+ solid_hydraulic_permeability = NULL,
+ solid_specific_heat_source = NULL,
+ solid_heat_conductivity = NULL,
+ solid_specific_isobaric_heat_capacity = NULL,
+ tortuosity = NULL,
+ diffusion_coefficient = NULL,
+ solid_density_dry = NULL,
+ solid_density_initial = NULL,
+ characteristic_pressure = NULL,
+ characteristic_temperature = NULL,
+ characteristic_vapour_mass_fraction = NULL,
+ output_element_matrices = NULL,
+ material_property = NULL,
+ diffusion_coeff_component_b = NULL,
+ diffusion_coeff_component_a = NULL,
+ hydro_crack_scheme = NULL,
+ at_num = NULL,
+ initial_stress = NULL,
+ split_method = NULL,
+ reg_param = NULL,
+ thermal_parameters = NULL,
+ non_advective_form = NULL,
+ fluid = NULL,
+ porous_medium = NULL,
+ decay_rate = NULL,
+ fluid_reference_density = NULL,
+ retardation_factor = NULL,
+ solute_dispersivity_longitudinal = NULL,
+ solute_dispersivity_transverse = NULL,
+ molecular_diffusion_coefficient = NULL,
+ density_solid = NULL,
+ latent_heat_evaporation = NULL,
+ pf_irrv = NULL,
+ ...
+)
+}
+\arguments{
+\item{name}{string:}
+
+\item{type}{string:}
+
+\item{integration_order}{string | double:}
+
+\item{process_variables}{list, character:}
+
+\item{secondary_variables}{Optional:}
+
+\item{specific_body_force}{Optional:}
+
+\item{solid_density}{Optional:}
+
+\item{dimension}{Optional:}
+
+\item{coupling_scheme}{Optional:}
+
+\item{reference_solid_density}{Optional:}
+
+\item{linear_thermal_expansion_coefficient}{Optional:}
+
+\item{specific_heat_capacity}{Optional:}
+
+\item{thermal_conductivity}{Optional:}
+
+\item{darcy_gravity}{Optional:}
+
+\item{reference_temperature}{Optional:}
+
+\item{fracture_model}{Optional:}
+
+\item{jacobian_assembler}{Optional:}
+
+\item{internal_length}{Optional:}
+
+\item{mass_lumping}{Optional:}
+
+\item{porosity}{Optional:}
+
+\item{calculatesurfaceflux}{Optional:}
+
+\item{intrinsic_permeability}{Optional:}
+
+\item{specific_storage}{Optional:}
+
+\item{fluid_viscosity}{Optional:}
+
+\item{biot_coefficient}{Optional:}
+
+\item{fluid_density}{Optional:}
+
+\item{initial_effective_stress}{Optional:}
+
+\item{initial_fracture_effective_stress}{Optional:}
+
+\item{phasefield_parameters}{Optional:}
+
+\item{deactivate_matrix_in_flow}{Optional:}
+
+\item{borehole_heat_exchangers}{Optional:}
+
+\item{temperature}{Optional:}
+
+\item{reactive_system}{Optional:}
+
+\item{fluid_specific_heat_source}{Optional:}
+
+\item{fluid_specific_isobaric_heat_capacity}{Optional:}
+
+\item{solid_hydraulic_permeability}{Optional:}
+
+\item{solid_specific_heat_source}{Optional:}
+
+\item{solid_heat_conductivity}{Optional:}
+
+\item{solid_specific_isobaric_heat_capacity}{Optional:}
+
+\item{tortuosity}{Optional:}
+
+\item{diffusion_coefficient}{Optional:}
+
+\item{solid_density_dry}{Optional:}
+
+\item{solid_density_initial}{Optional:}
+
+\item{characteristic_pressure}{Optional:}
+
+\item{characteristic_temperature}{Optional:}
+
+\item{characteristic_vapour_mass_fraction}{Optional:}
+
+\item{output_element_matrices}{Optional:}
+
+\item{material_property}{Optional:}
+
+\item{diffusion_coeff_component_b}{Optional:}
+
+\item{diffusion_coeff_component_a}{Optional:}
+
+\item{hydro_crack_scheme}{Optional:}
+
+\item{at_num}{Optional:}
+
+\item{initial_stress}{Optional:}
+
+\item{split_method}{Optional:}
+
+\item{reg_param}{Optional:}
+
+\item{thermal_parameters}{Optional:}
+
+\item{non_advective_form}{Optional:}
+
+\item{fluid}{Optional:}
+
+\item{porous_medium}{Optional:}
+
+\item{decay_rate}{Optional:}
+
+\item{fluid_reference_density}{Optional:}
+
+\item{retardation_factor}{Optional:}
+
+\item{solute_dispersivity_longitudinal}{Optional:}
+
+\item{solute_dispersivity_transverse}{Optional:}
+
+\item{molecular_diffusion_coefficient}{Optional:}
+
+\item{density_solid}{Optional:}
+
+\item{latent_heat_evaporation}{Optional:}
+
+\item{pf_irrv}{Optional:}
+
+\item{...}{Optional: fracture_properties, constitutive_relation}
+}
+\description{
+tag: process (parent tag: processes)
+}
+\examples{
+prj_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 = prj_constitutive_relation(
+ type = "LinearElasticIsotropic",
+ youngs_modulus = "E",
+ poissons_ratio = "nu"
+ )
+)
+}
diff --git a/man/prj_process_variable.Rd b/man/prj_process_variable.Rd
new file mode 100644
index 0000000..b3c7764
--- /dev/null
+++ b/man/prj_process_variable.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process_variable.R
+\name{prj_process_variable}
+\alias{prj_process_variable}
+\title{prj_process_variable}
+\usage{
+prj_process_variable(
+ name,
+ components,
+ order,
+ initial_condition,
+ boundary_conditions = NULL,
+ source_terms = NULL,
+ mesh = NULL,
+ deactivated_subdomains = NULL
+)
+}
+\arguments{
+\item{name}{string: The name of the process variable}
+
+\item{components}{string | double:}
+
+\item{order}{string | double:}
+
+\item{initial_condition}{string:}
+
+\item{boundary_conditions}{list, prj_boundary_condition:}
+
+\item{source_terms}{Optional: list, prj_source_term:}
+
+\item{mesh}{Optional: string: list:}
+
+\item{deactivated_subdomains}{Optional: list, prj_deactivated_subdomain:}
+}
+\description{
+tag: process_variable
+}
+\examples{
+prj_process_variable(
+ name = "pressure",
+ components = 1,
+ order = 1,
+ initial_condition = "pressure0",
+ boundary_conditions = list(
+ boundary_condition = prj_boundary_condition(
+ type = "Neumann",
+ parameter = "flux_in",
+ geometrical_set = "cube_1x1x1_geometry",
+ geometry = "left",
+ component = 0
+ )
+ )
+)
+}
diff --git a/man/prj_rate.Rd b/man/prj_rate.Rd
new file mode 100644
index 0000000..b86c2d1
--- /dev/null
+++ b/man/prj_rate.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_chemical_system.R
+\name{prj_rate}
+\alias{prj_rate}
+\title{prj_rate}
+\usage{
+prj_rate(kinetic_reactant, expression)
+}
+\arguments{
+\item{kinetic_reactant}{string: References a kinetic_reactant object}
+
+\item{expression}{character: Statements}
+}
+\description{
+S3 class describing .prj rate
+}
+\examples{
+prj_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/prj_relative_permeability.Rd b/man/prj_relative_permeability.Rd
new file mode 100644
index 0000000..c4b1bef
--- /dev/null
+++ b/man/prj_relative_permeability.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_porous_medium.R
+\name{prj_relative_permeability}
+\alias{prj_relative_permeability}
+\title{prj_relative_permeability}
+\usage{
+prj_relative_permeability(type, sr, smax, m, krel_min, id = NULL)
+}
+\arguments{
+\item{type}{string:}
+
+\item{sr}{string | number:}
+
+\item{smax}{string | number:}
+
+\item{m}{string | number:}
+
+\item{krel_min}{string | number:}
+
+\item{id}{string: Optional:}
+}
+\description{
+tag: relative_permeability
+}
+\examples{
+prj_relative_permeability(
+ type = "NonWettingPhaseVanGenuchten",
+ sr = 0,
+ smax = 0.6,
+ m = 0.3288590604,
+ krel_min = 0,
+ id = "0"
+)
+}
diff --git a/man/prj_search_length_algorithm.Rd b/man/prj_search_length_algorithm.Rd
new file mode 100644
index 0000000..517a604
--- /dev/null
+++ b/man/prj_search_length_algorithm.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_search_length_algorithm.R
+\name{prj_search_length_algorithm}
+\alias{prj_search_length_algorithm}
+\title{prj_search_length_algorithm}
+\usage{
+prj_search_length_algorithm(type, value = NULL)
+}
+\arguments{
+\item{type}{string: The type}
+
+\item{value}{string | double: The value}
+}
+\description{
+tag: search_length_algorithm
+}
+\examples{
+prj_search_length_algorithm(type = "fixed",
+ value = 1e-06)
+}
diff --git a/man/prj_solution.Rd b/man/prj_solution.Rd
new file mode 100644
index 0000000..dd7a195
--- /dev/null
+++ b/man/prj_solution.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_chemical_system.R
+\name{prj_solution}
+\alias{prj_solution}
+\title{prj_solution}
+\usage{
+prj_solution(temperature, pressure, pe, components, charge_balance = NULL)
+}
+\arguments{
+\item{temperature}{string | double: Temperature}
+
+\item{pressure}{string | double: Pressure}
+
+\item{pe}{string | double: pe}
+
+\item{components}{list: Components}
+
+\item{charge_balance}{Optional: string: Charge balance}
+}
+\description{
+tag: solution
+}
+\examples{
+prj_solution(
+ temperature = 25,
+ pressure = 1,
+ pe = 4,
+ components = list(
+ component = "C(4)",
+ component = "Ca"
+ ),
+ charge_balance = "pH"
+)
+}
diff --git a/man/prj_source_term.Rd b/man/prj_source_term.Rd
new file mode 100644
index 0000000..bfdf35f
--- /dev/null
+++ b/man/prj_source_term.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_process_variable.R
+\name{prj_source_term}
+\alias{prj_source_term}
+\title{prj_source_term}
+\usage{
+prj_source_term(
+ type,
+ parameter = NULL,
+ geometrical_set = NULL,
+ geometry = NULL,
+ mesh = NULL,
+ source_term_object = NULL
+)
+}
+\arguments{
+\item{type}{string:}
+
+\item{parameter}{Optional: string:}
+
+\item{geometrical_set}{Optional: string:}
+
+\item{geometry}{Optional: string:}
+
+\item{mesh}{Optional: string:}
+
+\item{source_term_object}{Optional: string:}
+}
+\description{
+tag: source_term
+}
+\examples{
+prj_source_term(
+ type = "Nodal",
+ parameter = "sourceterm_heat_transfer_coefficient",
+ geometrical_set = "geometry",
+ geometry = "po0"
+)
+}
diff --git a/man/prj_time_loop.Rd b/man/prj_time_loop.Rd
new file mode 100644
index 0000000..ef4f307
--- /dev/null
+++ b/man/prj_time_loop.Rd
@@ -0,0 +1,52 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_time_loop.R
+\name{prj_time_loop}
+\alias{prj_time_loop}
+\title{prj_time_loop}
+\usage{
+prj_time_loop(processes, output, global_process_coupling = NULL)
+}
+\arguments{
+\item{processes}{list, prj_tl_process:}
+
+\item{output}{prj_output:}
+
+\item{global_process_coupling}{Optional: prj_global_process_coupling:}
+}
+\description{
+tag: time_loop
+}
+\examples{
+prj_time_loop(
+ processes = list(
+ process = prj_tl_process(
+ ref = "HM",
+ nonlinear_solver = "basic_newton",
+ convergence_criterion = prj_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "NORM2",
+ reltol = 1e-08
+ ),
+ time_discretization = list(type = "BackwardEuler"),
+ time_stepping = prj_time_stepping(
+ type = "FixedTimeStepping",
+ t_initial = 0,
+ t_end = 10000,
+ timesteps = list(pair = list(1000,
+ delta_t = 10))
+ )
+ )
+ ),
+ output = prj_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/prj_time_stepping.Rd b/man/prj_time_stepping.Rd
new file mode 100644
index 0000000..c03ffdb
--- /dev/null
+++ b/man/prj_time_stepping.Rd
@@ -0,0 +1,67 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_time_loop.R
+\name{prj_time_stepping}
+\alias{prj_time_stepping}
+\title{prj_time_stepping}
+\usage{
+prj_time_stepping(
+ type,
+ t_initial = NULL,
+ t_end = NULL,
+ timesteps = NULL,
+ initial_dt = NULL,
+ minimum_dt = NULL,
+ maximum_dt = NULL,
+ number_iterations = NULL,
+ multiplier = NULL,
+ dt_guess = NULL,
+ dt_min = NULL,
+ dt_max = NULL,
+ rel_dt_min = NULL,
+ rel_dt_max = NULL,
+ tol = NULL
+)
+}
+\arguments{
+\item{type}{string:}
+
+\item{t_initial}{Optional: string | double:}
+
+\item{t_end}{Optional: string | double:}
+
+\item{timesteps}{Optional: list:}
+
+\item{initial_dt}{Optional: string | double:}
+
+\item{minimum_dt}{Optional: string | double:}
+
+\item{maximum_dt}{Optional: string | double:}
+
+\item{number_iterations}{Optional: string | numeric:}
+
+\item{multiplier}{Optional: string | numeric:}
+
+\item{dt_guess}{Optional: string | double:}
+
+\item{dt_min}{Optional: string | double:}
+
+\item{dt_max}{Optional: string | double:}
+
+\item{rel_dt_min}{Optional: string | double:}
+
+\item{rel_dt_max}{Optional: string | double:}
+
+\item{tol}{Optional: string | double:}
+}
+\description{
+tag: time_stepping
+}
+\examples{
+prj_time_stepping(
+ type = "FixedTimeStepping",
+ t_initial = 0,
+ t_end = 10000,
+ timesteps = list(pair = list(1000,
+ delta_t = 10))
+)
+}
diff --git a/man/prj_tl_process.Rd b/man/prj_tl_process.Rd
new file mode 100644
index 0000000..586aa90
--- /dev/null
+++ b/man/prj_tl_process.Rd
@@ -0,0 +1,51 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_time_loop.R
+\name{prj_tl_process}
+\alias{prj_tl_process}
+\title{prj_tl_process}
+\usage{
+prj_tl_process(
+ ref,
+ nonlinear_solver,
+ convergence_criterion,
+ time_discretization,
+ time_stepping,
+ compensate_non_equilibrium_initial_residuum = NULL
+)
+}
+\arguments{
+\item{ref}{string: References a prj_process object by name}
+
+\item{nonlinear_solver}{string:}
+
+\item{convergence_criterion}{prj_convergence_criterion:}
+
+\item{time_discretization}{vector:}
+
+\item{time_stepping}{prj_time_stepping:}
+
+\item{compensate_non_equilibrium_initial_residuum}{string: Optional: Either
+"true" or "false"}
+}
+\description{
+tag: process (parent: time_loop, NOT processes!)
+}
+\examples{
+prj_tl_process(
+ ref = "HM",
+ nonlinear_solver = "basic_newton",
+ convergence_criterion = prj_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "NORM2",
+ reltol = 1e-08
+ ),
+ time_discretization = list(type = "BackwardEuler"),
+ time_stepping = prj_time_stepping(
+ type = "FixedTimeStepping",
+ t_initial = 0,
+ t_end = 10000,
+ timesteps = list(pair = list(1000,
+ delta_t = 10))
+ )
+)
+}
diff --git a/man/prj_vtkdiff.Rd b/man/prj_vtkdiff.Rd
new file mode 100644
index 0000000..252f975
--- /dev/null
+++ b/man/prj_vtkdiff.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prj_vtkdiff.R
+\name{prj_vtkdiff}
+\alias{prj_vtkdiff}
+\title{prj_vtkdiff}
+\usage{
+prj_vtkdiff(
+ field,
+ absolute_tolerance,
+ relative_tolerance,
+ file = NULL,
+ regex = NULL
+)
+}
+\arguments{
+\item{field}{string: ...}
+
+\item{absolute_tolerance}{string | double: Absolute tolerance}
+
+\item{relative_tolerance}{string | double: Relative tolerance}
+
+\item{file}{string: Optional: File}
+
+\item{regex}{string: Optional: A regular expression}
+}
+\description{
+tag: vtkdiff
+}
+\examples{
+prj_vtkdiff(field = "displacement",
+ absolute_tolerance = 1e-15,
+ relative_tolerance = 0,
+ regex = "gravity_pcs_0_ts_.*_t_.*.vtu")
+}
diff --git a/man/run_all_benchmarks.Rd b/man/run_all_benchmarks.Rd
index caac9a4..67d157b 100644
--- a/man/run_all_benchmarks.Rd
+++ b/man/run_all_benchmarks.Rd
@@ -6,8 +6,8 @@
\usage{
run_all_benchmarks(
path,
- ogs_processlib_path,
- ogs_bin_path,
+ ogs6_processlib_path,
+ ogs6_bin_path,
sim_path,
starting_from_prj_path = "",
print_results = TRUE
@@ -16,10 +16,10 @@ run_all_benchmarks(
\arguments{
\item{path}{string: Path to benchmark folder}
-\item{ogs_processlib_path}{string: Path to OpenGeoSys 6 ProcessLib folder
+\item{ogs6_processlib_path}{string: Path to OpenGeoSys 6 ProcessLib folder
which contains relevant Tests.cmake files}
-\item{ogs_bin_path}{string:}
+\item{ogs6_bin_path}{string:}
\item{sim_path}{string: Path where simulation files will be saved}
@@ -29,5 +29,5 @@ which contains relevant Tests.cmake files}
}
\description{
Utility function, for quick benchmark runs. Calls
-run_benchmark internally.
+ run_benchmark internally.
}
diff --git a/man/run_benchmark.Rd b/man/run_benchmark.Rd
index 06c0d44..c05e535 100644
--- a/man/run_benchmark.Rd
+++ b/man/run_benchmark.Rd
@@ -4,12 +4,12 @@
\alias{run_benchmark}
\title{run_benchmark}
\usage{
-run_benchmark(prj_path, ogs_bin_path, sim_path)
+run_benchmark(prj_path, ogs6_bin_path, sim_path)
}
\arguments{
\item{prj_path}{string:}
-\item{ogs_bin_path}{string:}
+\item{ogs6_bin_path}{string:}
\item{sim_path}{string: Path where simulation files will be saved}
}
--
GitLab