From 0ea1ddfda5d8227bf0aca85f94f7ce4849db577d Mon Sep 17 00:00:00 2001
From: aheinri5 <Anna@netzkritzler.de>
Date: Fri, 11 Dec 2020 12:11:13 +0100
Subject: [PATCH] [base] Removed unneeded files, updated NAMESPACE
---
.Rprofile | 3 -
NAMESPACE | 1 -
R/validate_gml.R | 167 -----------
..._input_example.R => flow_free_expansion.R} | 265 ++++++++----------
.../generate_benchmark_script_example.R | 4 +-
man/find_read_in_func_call.Rd | 19 --
man/get_grandchild_length_vector.Rd | 19 --
man/get_list_status.Rd | 21 --
man/input_add.r2ogs6_gml.Rd | 16 --
man/is_het_wrapper.Rd | 17 --
man/list_from_nodeset.Rd | 14 -
man/obj_is_defined.Rd | 21 --
man/read_in_timesteps_node.Rd | 14 -
man/validate_paths.Rd | 16 --
tests/testthat/test-validate_gml.R | 63 -----
15 files changed, 113 insertions(+), 547 deletions(-)
delete mode 100755 .Rprofile
delete mode 100644 R/validate_gml.R
rename inst/examples/{user_input_example.R => flow_free_expansion.R} (54%)
delete mode 100644 man/find_read_in_func_call.Rd
delete mode 100644 man/get_grandchild_length_vector.Rd
delete mode 100644 man/get_list_status.Rd
delete mode 100644 man/input_add.r2ogs6_gml.Rd
delete mode 100644 man/is_het_wrapper.Rd
delete mode 100644 man/list_from_nodeset.Rd
delete mode 100644 man/obj_is_defined.Rd
delete mode 100644 man/read_in_timesteps_node.Rd
delete mode 100644 man/validate_paths.Rd
delete mode 100644 tests/testthat/test-validate_gml.R
diff --git a/.Rprofile b/.Rprofile
deleted file mode 100755
index cae66ba..0000000
--- a/.Rprofile
+++ /dev/null
@@ -1,3 +0,0 @@
-#### -- Packrat Autoloader (version 0.5.0) -- ####
-source("packrat/init.R")
-#### -- End Packrat Autoloader -- ####
diff --git a/NAMESPACE b/NAMESPACE
index 4938f2c..d791f1d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -3,7 +3,6 @@
export(OGS6)
export(generate_benchmark_script)
export(generate_structured_mesh)
-export(input_add.r2ogs6_gml)
export(pick_vtu_file)
export(r2ogs6_borehole_heat_exchanger)
export(r2ogs6_boundary_condition)
diff --git a/R/validate_gml.R b/R/validate_gml.R
deleted file mode 100644
index 5d1b96b..0000000
--- a/R/validate_gml.R
+++ /dev/null
@@ -1,167 +0,0 @@
-#This script contains various functions to verify data for a .gml file (WIP)
-
-#'validate_r2ogs6_gml
-#'@description Validator for class r2ogs6_gml. Checks if the defined polylines
-#' and surfaces reference existing points.
-#'@param r2ogs6_gml A r2ogs6_gml class object
-validate_r2ogs6_gml <- function(r2ogs6_gml) {
-
- maximal_point_id <- length(r2ogs6_gml$points[[1]]) - 1
-
- #Check if polylines reference existing points
- for(i in seq_len(length(r2ogs6_gml$polylines))){
- for(j in seq_len(length(r2ogs6_gml$polylines[[i]][[2]]))){
- if(r2ogs6_gml$polylines[[i]][[2]][[j]] > maximal_point_id ||
- r2ogs6_gml$polylines[[i]][[2]][[j]] < 0){
- stop("Polyline references point ID which does not exist", call. = FALSE)
- }
- }
- }
-
- #Check if surfaces reference existing points
- for(i in seq_len(length(r2ogs6_gml$surfaces))){
- for(j in seq_len(length(r2ogs6_gml$surfaces[[i]][[2]]))){
- if(r2ogs6_gml$surfaces[[i]][[2]][[j]] > maximal_point_id ||
- r2ogs6_gml$surfaces[[i]][[2]][[j]] < 0 ||
- r2ogs6_gml$surfaces[[i]][[3]][[j]] > maximal_point_id ||
- r2ogs6_gml$surfaces[[i]][[3]][[j]] < 0){
- stop("Surface references point ID which does not exist", call. = FALSE)
- }
- }
- }
-
- return(invisible(r2ogs6_gml))
-}
-
-
-#'validate_points
-#'@description Checks if the input is a tibble, if this tibble has the right number of elements,
-#' if those elements are named correctly and if there are any overlapping points or duplicate point names
-#'@param points A tibble with 3 vectors named 'x', 'y' and 'z' (and an optional 'name' vector)
-validate_points <- function(points) {
-
- assertthat::assert_that(inherits(points, "tbl_df"))
-
- names <- names(points)
-
- if (!((length(points) == 4 && names[[1]] == "x" && names[[2]] == "y" &&
- names[[3]] == "z" && names[[4]] == "name") ||
- (length(points) == 3 && names[[1]] == "x" && names[[2]] == "y" &&
- names[[3]] == "z"))){
- stop(paste(points, " column names do not fit to 'x, y, z, (name)' "), call. = FALSE)
- }
-
- assertthat::assert_that(is.numeric(points$x))
- assertthat::assert_that(is.numeric(points$y))
- assertthat::assert_that(is.numeric(points$z))
-
- has_names <- (length(points) == 4)
-
- #Find overlapping points and duplicate names
- for(i in 1:(length(points[[1]])-1)){
- for(j in (i+1):length(points[[1]])){
- if(points[[1]][[i]] == points[[1]][[j]] &&
- points[[2]][[i]] == points[[2]][[j]] &&
- points[[3]][[i]] == points[[3]][[j]]){
- stop("Overlapping .gml points (with the same coordinates) detected", call. = FALSE)
- }
-
- if(has_names){
- if(points[[4]][[i]] == points[[4]][[j]] &&
- points[[4]][[i]] != ""){
- warning("Duplicate .gml point names detected", call. = FALSE)
- }
- }
- }
- }
-
- return(invisible(points))
-}
-
-
-#'validate_polylines
-#'@description Checks if the input is a list, if this list consists of other lists and
-#' if those child lists have the correct structure (length of 2, first element is a string named
-#' 'name', second element is a numeric vector)
-#'@param polylines A list consisting of other lists
-validate_polylines <- function(polylines) {
-
- assertthat::assert_that(is.list(polylines))
-
- for(i in 1:length(polylines)){
-
- assertthat::assert_that(is.list(polylines[[i]]))
- assertthat::assert_that(length(polylines[[i]]) == 2)
- assertthat::assert_that(names(polylines[[i]])[[1]] == "name")
- assertthat::assert_that(assertthat::is.string(polylines[[i]][[1]]))
- assertthat::assert_that(is.numeric(polylines[[i]][[2]]))
-
- #Check for duplicate points / polylines?
- }
-
- return(invisible(polylines))
-}
-
-
-#'validate_surfaces
-#'@description Checks if the input is a list, if this list consists of other lists and
-#' if those child lists have the correct structure (length of 3, first element is a string named
-#' 'name', second and third element are numeric vectors)
-#'@param surfaces A list consisting of other lists
-validate_surfaces <- function(surfaces) {
-
- assertthat::assert_that(is.list(surfaces))
-
- for(i in 1:length(surfaces)){
-
- assertthat::assert_that(is.list(surfaces[[i]]))
- assertthat::assert_that(length(surfaces[[i]]) == 3)
- assertthat::assert_that(names(surfaces[[i]])[[1]] == "name")
-
- assertthat::assert_that(is.numeric(surfaces[[i]][[2]]))
- assertthat::assert_that(length(surfaces[[i]][[2]]) == 3)
- assertthat::assert_that(is.numeric(surfaces[[i]][[3]]))
- assertthat::assert_that(length(surfaces[[i]][[3]]) == 3)
-
- validate_surface_elements(surfaces[[i]][[2]], surfaces[[i]][[3]])
-
- #Check for duplicate points / surfaces?
- }
-
- return(invisible(surfaces))
-}
-
-
-#'validate_surface_elements
-#'@description Helper function, checks if two numerical vectors of length 3 (two surface elements)
-#' each consist of 3 different elements and also have exactly 2 matching elements between them
-#' which means they describe a valid surface. You can think of the two vectors as two triangles,
-#' and the two triangles together form a square which is our surface.
-#'@param surface_element_1 A numerical vector of length 3
-#'@param surface_element_2 A numerical vector of length 3
-validate_surface_elements = function (surface_element_1, surface_element_2) {
-
- if(surface_element_1[[1]] == surface_element_1[[2]] ||
- surface_element_1[[1]] == surface_element_1[[3]] ||
- surface_element_1[[2]] == surface_element_1[[3]] ||
- surface_element_2[[1]] == surface_element_2[[2]] ||
- surface_element_2[[1]] == surface_element_2[[3]] ||
- surface_element_2[[2]] == surface_element_2[[3]]) {
- stop("A surface element must consist of 3 different points", call. = FALSE)
- }
-
- equal_count <- 0
-
- for(i in 1:length(surface_element_1)) {
- for(j in 1:length(surface_element_2)) {
- if(surface_element_1[[i]] == surface_element_2[[j]]) {
- equal_count <- equal_count + 1
- break
- }
- }
- }
-
- if(equal_count != 2) {
- stop("Invalid surface detected", call. = FALSE)
- }
-}
\ No newline at end of file
diff --git a/inst/examples/user_input_example.R b/inst/examples/flow_free_expansion.R
similarity index 54%
rename from inst/examples/user_input_example.R
rename to inst/examples/flow_free_expansion.R
index d596b91..94279bd 100644
--- a/inst/examples/user_input_example.R
+++ b/inst/examples/flow_free_expansion.R
@@ -1,10 +1,13 @@
+detach("package:r2ogs6", unload=TRUE)
library(r2ogs6)
ogs6_obj <- OGS6$new(
- sim_name = flow_free_expansion,
+ sim_name = "flow_free_expansion",
sim_id = 1,
sim_path = "D:\\OGS_Sim\\",
- ogs_bin_path = "D:\\Programme\\OpenGeoSys\\ogs-6.3.2-Windows-10.0.14393-x64-python-3.7.2-de-utils\\bin\\"
+ ogs_bin_path <- paste0("D:\\Programme\\OpenGeoSys\\",
+ "ogs-6.3.2-Windows-10.0.14393-x64-python-3.7.2-de-utils",
+ "\\bin\\")
)
@@ -70,17 +73,12 @@ ogs6_obj$add_gml(
)
+
ogs6_obj$add_process(
r2ogs6_process(
name = "HM",
type = "HYDRO_MECHANICS",
integration_order = 3,
- dimension = 3,
- constitutive_relation = list(
- type = "LinearElasticIsotropic",
- youngs_modulus = "E",
- poissons_ratio = "nu"
- ),
process_variables = list(displacement = "displacement",
pressure = "pressure"),
secondary_variables = list(
@@ -95,137 +93,108 @@ ogs6_obj$add_process(
secondary_variable = c(internal_name = "velocity", output_name = "velocity")
),
specific_body_force = c(0, 0, 0),
- coupling_scheme = NULL
+ constitutive_relation = list(
+ type = "LinearElasticIsotropic",
+ youngs_modulus = "E",
+ poissons_ratio = "nu"
+ ),
+ dimension = 3
)
)
ogs6_obj$add_medium(r2ogs6_medium(
phases = list(
- r2ogs6_medium_phase(
+ phase = r2ogs6_phase(
type = "Gas",
properties = list(
- r2ogs6_medium_property(
- name = "viscosity",
- type = "Constant",
- value = 1e-05,
- ... = NULL
- ),
- r2ogs6_medium_property(
- name = "density",
- type = "IdealGasLaw",
- value = NULL,
- ... = NULL
- ),
- r2ogs6_medium_property(
- name = "molar_mass",
- type = "Constant",
- value = 0.0289643977872068,
- ... = NULL
- )
+ property = r2ogs6_ph_property(name = "viscosity",
+ type = "Constant",
+ value = 1e-05),
+ property = r2ogs6_ph_property(name = "density",
+ type = "IdealGasLaw"),
+ property = r2ogs6_ph_property(name = "molar_mass",
+ type = "Constant",
+ value = 0.0289643977872068)
)
),
- r2ogs6_medium_phase(
+ phase = r2ogs6_phase(
type = "Solid",
properties = list(
- r2ogs6_medium_property(
- name = "porosity",
- type = "Constant",
- value = 0.3,
- ... = NULL
- ),
- r2ogs6_medium_property(
- name = "density",
- type = "Constant",
- value = 1430,
- ... = NULL
- ),
- r2ogs6_medium_property(
- name = "biot_coefficient",
- type = "Constant",
- value = 0.6,
- ... = NULL
- )
+ property = r2ogs6_ph_property(name = "porosity",
+ type = "Constant",
+ value = 0.3),
+ property = r2ogs6_ph_property(name = "density",
+ type = "Constant",
+ value = 1430),
+ property = r2ogs6_ph_property(name = "biot_coefficient",
+ type = "Constant",
+ value = 0.6)
)
)
),
properties = list(
- r2ogs6_medium_property(
- name = "reference_temperature",
- type = "Constant",
- value = 293.15,
- ... = NULL
- ),
- r2ogs6_medium_property(
- name = "permeability",
- type = "Constant",
- value = 1e-05,
- ... = NULL
- )
- ),
- id = NULL
+ property = r2ogs6_pr_property(name = "reference_temperature",
+ type = "Constant",
+ value = 293.15),
+ property = r2ogs6_pr_property(name = "permeability",
+ type = "Constant",
+ value = 1e-05)
+ )
))
-ogs6_obj$add_time_loop(
- r2ogs6_time_loop(
- processes = list(
- r2ogs6_tl_process(
- ref = "HM",
- nonlinear_solver = "basic_newton",
- convergence_criterion = list(
- type = "DeltaX",
- norm_type = "NORM2",
- reltol = "1e-8"
- ),
- time_discretization = list(type = "BackwardEuler"),
- time_stepping = list(
- type = "FixedTimeStepping",
- t_initial = 0,
- t_end = 10000,
- timesteps = list(pair = c(`repeat` = 1000, delta_t = 10))
- )
- )
- ),
- output = r2ogs6_tl_output(
- type = "VTK",
- prefix = "flow_free_expansion_pcs_{:process_id}",
- suffix = "_ts_{:timestep}_t_{:time}",
- timesteps = list(pair = c(
- `repeat` = 1, each_steps = 1000
- )),
- variables = list(
- variable = "displacement",
- variable = "pressure",
- variable = "sigma_xx",
- variable = "sigma_yy",
- variable = "sigma_zz",
- variable = "sigma_xy",
- variable = "epsilon_xx",
- variable = "epsilon_yy",
- variable = "epsilon_zz",
- variable = "epsilon_xy",
- variable = "velocity"
+ogs6_obj$add_time_loop(r2ogs6_time_loop(
+ processes = list(
+ process = r2ogs6_tl_process(
+ ref = "HM",
+ nonlinear_solver = "basic_newton",
+ convergence_criterion = r2ogs6_convergence_criterion(
+ type = "DeltaX",
+ norm_type = "NORM2",
+ reltol = "1e-8"
),
- compress_output = NULL
+ time_discretization = list(type = "BackwardEuler"),
+ time_stepping = r2ogs6_time_stepping(
+ type = "FixedTimeStepping",
+ t_initial = 0,
+ t_end = 10000,
+ timesteps = list(pair = list(1000,
+ delta_t = 10))
+ )
+ )
+ ),
+ output = r2ogs6_output(
+ type = "VTK",
+ prefix = "flow_free_expansion_pcs_{:process_id}",
+ variables = list(
+ variable = "displacement",
+ variable = "pressure",
+ variable = "sigma_xx",
+ variable = "sigma_yy",
+ variable = "sigma_zz",
+ variable = "sigma_xy",
+ variable = "epsilon_xx",
+ variable = "epsilon_yy",
+ variable = "epsilon_zz",
+ variable = "epsilon_xy",
+ variable = "velocity"
),
- global_processes_coupling = NULL
+ suffix = "_ts_{:timestep}_t_{:time}",
+ timesteps = list(pair = list(1,
+ each_steps = 1000))
)
-)
+))
-ogs6_obj$add_parameter(r2ogs6_parameter(
- name = "E",
- type = "Constant",
- values = 1e+10
-))
+ogs6_obj$add_parameter(r2ogs6_parameter(name = "E",
+ type = "Constant",
+ value = 1e+10))
-ogs6_obj$add_parameter(r2ogs6_parameter(
- name = "nu",
- type = "Constant",
- values = 0.3
-))
+ogs6_obj$add_parameter(r2ogs6_parameter(name = "nu",
+ type = "Constant",
+ value = 0.3))
ogs6_obj$add_parameter(r2ogs6_parameter(
@@ -249,18 +218,14 @@ ogs6_obj$add_parameter(r2ogs6_parameter(
))
-ogs6_obj$add_parameter(r2ogs6_parameter(
- name = "zero",
- type = "Constant",
- values = 0
-))
+ogs6_obj$add_parameter(r2ogs6_parameter(name = "zero",
+ type = "Constant",
+ value = 0))
-ogs6_obj$add_parameter(r2ogs6_parameter(
- name = "flux_in",
- type = "Constant",
- values = 1e-04
-))
+ogs6_obj$add_parameter(r2ogs6_parameter(name = "flux_in",
+ type = "Constant",
+ value = 1e-04))
ogs6_obj$add_process_variable(
@@ -270,53 +235,47 @@ ogs6_obj$add_process_variable(
order = 2,
initial_condition = "displacement0",
boundary_conditions = list(
- r2ogs6_boundary_condition(
+ boundary_condition = r2ogs6_boundary_condition(
type = "Dirichlet",
parameter = "zero",
- component = 1,
- mesh = NULL,
geometrical_set = "cube_1x1x1_geometry",
- geometry = "front"
+ geometry = "front",
+ component = 1
),
- r2ogs6_boundary_condition(
+ boundary_condition = r2ogs6_boundary_condition(
type = "Dirichlet",
parameter = "zero",
- component = 0,
- mesh = NULL,
geometrical_set = "cube_1x1x1_geometry",
- geometry = "left"
+ geometry = "left",
+ component = 0
),
- r2ogs6_boundary_condition(
+ boundary_condition = r2ogs6_boundary_condition(
type = "Dirichlet",
parameter = "zero",
- component = 2,
- mesh = NULL,
geometrical_set = "cube_1x1x1_geometry",
- geometry = "bottom"
+ geometry = "bottom",
+ component = 2
),
- r2ogs6_boundary_condition(
+ boundary_condition = r2ogs6_boundary_condition(
type = "Neumann",
parameter = "pressure_load",
- component = 1,
- mesh = NULL,
geometrical_set = "cube_1x1x1_geometry",
- geometry = "back"
+ geometry = "back",
+ component = 1
),
- r2ogs6_boundary_condition(
+ boundary_condition = r2ogs6_boundary_condition(
type = "Neumann",
parameter = "pressure_load",
- component = 0,
- mesh = NULL,
geometrical_set = "cube_1x1x1_geometry",
- geometry = "right"
+ geometry = "right",
+ component = 0
),
- r2ogs6_boundary_condition(
+ boundary_condition = r2ogs6_boundary_condition(
type = "Neumann",
parameter = "pressure_load",
- component = 2,
- mesh = NULL,
geometrical_set = "cube_1x1x1_geometry",
- geometry = "top"
+ geometry = "top",
+ component = 2
)
)
)
@@ -330,13 +289,12 @@ ogs6_obj$add_process_variable(
order = 1,
initial_condition = "pressure0",
boundary_conditions = list(
- r2ogs6_boundary_condition(
+ boundary_condition = r2ogs6_boundary_condition(
type = "Neumann",
parameter = "flux_in",
- component = 0,
- mesh = NULL,
geometrical_set = "cube_1x1x1_geometry",
- geometry = "left"
+ geometry = "left",
+ component = 0
)
)
)
@@ -356,14 +314,13 @@ ogs6_obj$add_nonlinear_solver(
ogs6_obj$add_linear_solver(
r2ogs6_linear_solver(
name = "general_linear_solver",
- eigen = list(
+ eigen = r2ogs6_eigen(
solver_type = "BiCGSTAB",
precon_type = "ILUT",
max_iteration_step = 10000,
error_tolerance = 1e-16
),
- lis = "-i bicgstab -p ilu -tol 1e-16 -maxiter 10000",
- petsc = NULL
+ lis = "-i bicgstab -p ilu -tol 1e-16 -maxiter 10000"
)
)
diff --git a/inst/examples/generate_benchmark_script_example.R b/inst/examples/generate_benchmark_script_example.R
index 6e651b7..f62848e 100644
--- a/inst/examples/generate_benchmark_script_example.R
+++ b/inst/examples/generate_benchmark_script_example.R
@@ -1,8 +1,8 @@
detach("package:r2ogs6", unload=TRUE)
library(r2ogs6)
-# As a user you will want to alter the paths since this will only work if the working directory
-# is r2ogs6, which is ok for developers but not for you (sorry!)
+# As a user you will want to alter the paths since this will only work if the
+# working directory is r2ogs6
#Define .prj path
prj_path <- paste0("inst/extdata/flow_free_expansion/flow_free_expansion.prj")
diff --git a/man/find_read_in_func_call.Rd b/man/find_read_in_func_call.Rd
deleted file mode 100644
index 4e903b4..0000000
--- a/man/find_read_in_func_call.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{find_read_in_func_call}
-\alias{find_read_in_func_call}
-\title{find_read_in_func_call}
-\usage{
-find_read_in_func_call(node_name)
-}
-\arguments{
-\item{node_name}{The name of an XML node}
-}
-\value{
-A ready-to-call string if a corresponding function was found, an
-empty string otherwise
-}
-\description{
-Checks if a custom read_in function was defined for nodes
-with the given name
-}
diff --git a/man/get_grandchild_length_vector.Rd b/man/get_grandchild_length_vector.Rd
deleted file mode 100644
index d36b7b8..0000000
--- a/man/get_grandchild_length_vector.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{get_grandchild_length_vector}
-\alias{get_grandchild_length_vector}
-\title{get_grandchild_length_vector}
-\usage{
-get_grandchild_length_vector(xml_node)
-}
-\arguments{
-\item{xml_node}{An XML node}
-}
-\value{
-A numeric vector containing the number of children of each child of
-xml_node
-}
-\description{
-Helper function to check the number of children of children of
-an XML node (i.e. grandchildren)
-}
diff --git a/man/get_list_status.Rd b/man/get_list_status.Rd
deleted file mode 100644
index 74f44f2..0000000
--- a/man/get_list_status.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_list_status}
-\alias{get_list_status}
-\title{get_list_status}
-\usage{
-get_list_status(flag, obj_list, element_type = "list element", is_opt = FALSE)
-}
-\arguments{
-\item{flag}{Boolean flag to keep track of missing components}
-
-\item{obj_list}{The specified list}
-
-\item{element_type}{Optional: What kind of elements are in the list?}
-
-\item{is_opt}{flag: Does the list need at least one element?}
-}
-\description{
-Helper function for get_status() to check if a list has at least
-one element.
-}
diff --git a/man/input_add.r2ogs6_gml.Rd b/man/input_add.r2ogs6_gml.Rd
deleted file mode 100644
index 5099cff..0000000
--- a/man/input_add.r2ogs6_gml.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gml.R
-\name{input_add.r2ogs6_gml}
-\alias{input_add.r2ogs6_gml}
-\title{input_add.r2ogs6_gml}
-\usage{
-input_add.r2ogs6_gml(x, ogs6_obj)
-}
-\arguments{
-\item{x}{A r2ogs6_gml class object}
-
-\item{ogs6_obj}{A OGS6 class object}
-}
-\description{
-Implementation of generic function input_add for S3 class r2ogs6_gml
-}
diff --git a/man/is_het_wrapper.Rd b/man/is_het_wrapper.Rd
deleted file mode 100644
index eca5e57..0000000
--- a/man/is_het_wrapper.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{is_het_wrapper}
-\alias{is_het_wrapper}
-\title{is_het_wrapper}
-\usage{
-is_het_wrapper(xml_node, subclasses_names = character())
-}
-\arguments{
-\item{xml_node}{An XML node (of class xml2::xml_node)}
-
-\item{subclasses_names}{Optional: A character vector containing the names of
-r2ogs6 subclasses (r2ogs6 classes without a method for input_add)}
-}
-\description{
-Tests if a node is a heterogenous wrapper
-}
diff --git a/man/list_from_nodeset.Rd b/man/list_from_nodeset.Rd
deleted file mode 100644
index 77175d5..0000000
--- a/man/list_from_nodeset.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{list_from_nodeset}
-\alias{list_from_nodeset}
-\title{list_from_nodeset}
-\usage{
-list_from_nodeset(xml_nodeset)
-}
-\arguments{
-\item{xml_nodeset}{An XML nodeset (of class xml2::xml_nodeset)}
-}
-\description{
-Creates a named vector from a nodeset
-}
diff --git a/man/obj_is_defined.Rd b/man/obj_is_defined.Rd
deleted file mode 100644
index 31e4fa1..0000000
--- a/man/obj_is_defined.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{obj_is_defined}
-\alias{obj_is_defined}
-\title{obj_is_defined}
-\usage{
-obj_is_defined(flag, obj, obj_type = "", is_opt = FALSE)
-}
-\arguments{
-\item{flag}{Boolean flag to keep track of missing components}
-
-\item{obj}{The specified object}
-
-\item{obj_type}{Optional: What kind of object is this?}
-
-\item{is_opt}{flag: Is the element optional i.e. can it be NULL?}
-}
-\description{
-Helper function for get_status() to check if an object was
-defined
-}
diff --git a/man/read_in_timesteps_node.Rd b/man/read_in_timesteps_node.Rd
deleted file mode 100644
index 6aee261..0000000
--- a/man/read_in_timesteps_node.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_prj.R
-\name{read_in_timesteps_node}
-\alias{read_in_timesteps_node}
-\title{read_in_timesteps_node}
-\usage{
-read_in_timesteps_node(timesteps_node)
-}
-\arguments{
-\item{timesteps_node}{The timesteps node}
-}
-\description{
-Reads in a timesteps node
-}
diff --git a/man/validate_paths.Rd b/man/validate_paths.Rd
deleted file mode 100644
index 1ad4c8f..0000000
--- a/man/validate_paths.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/sim_utils.R
-\name{validate_paths}
-\alias{validate_paths}
-\title{validate_paths}
-\usage{
-validate_paths(sim_path, ogs_bin_path)
-}
-\arguments{
-\item{sim_path}{The path where all relevant files for the simulation will be saved}
-
-\item{ogs_bin_path}{Path to OpenGeoSys6 /bin directory}
-}
-\description{
-Helper function to pull path validation out of already large class OGS6
-}
diff --git a/tests/testthat/test-validate_gml.R b/tests/testthat/test-validate_gml.R
deleted file mode 100644
index 59465b0..0000000
--- a/tests/testthat/test-validate_gml.R
+++ /dev/null
@@ -1,63 +0,0 @@
-test_that("validate_points function checks if input is a tibble with the right contents", {
-
- point_list <- list(x = c(0, 0), y = c(1, 1), z = c(0, 1))
-
- #Check class (should expect a tibble, not a list)
- expect_error(validate_points(point_list))
-
- point_tibble_inv_0 <- tibble::tibble(a = c(0, 0), b = c(1, 1), c = c(0, 1))
- point_tibble_inv_1 <- tibble::tibble(x = c(0, 0), y = c(1, 1), z = c(0))
- point_tibble_inv_2 <- tibble::tibble(x = c(0, 0), y = c(1, 1), z = c(0, 1), name = c("oh", "oh"))
-
- #Check column names
- expect_error(validate_points(point_tibble_inv_0))
-
- #Check if duplicate points and point names are detected
- expect_error(validate_points(point_tibble_inv_1))
- expect_warning(validate_points(point_tibble_inv_2))
-
- point_tibble_val <- tibble::tibble(x = c(0, 0), y = c(1, 1), z = c(0, 1), name = c("this", "works"))
- point_tibble_val_2 <- tibble::tibble(x = c(0, 0), y = c(1, 1), z = c(0, 1))
-
- expect_invisible(validate_points(point_tibble_val))
- expect_invisible(validate_points(point_tibble_val_2))
-})
-
-
-test_that("validate_polylines function checks if input is a list with the right contents", {
-
- polyline_tibble <- tibble::tibble(name = "tibble", polyline = c(c(1, 2)))
-
- #Check class (should expect a list, not a tibble)
- expect_error(validate_polylines(polyline_tibble))
-
- polyline_list_inv_0 <- list(name = "missing_polyline_list", c(1,2))
- polyline_list_inv_1 <- list(list(name = "wrong_length", c(0, 1, 2), c(1, 2)))
- polyline_list_inv_2 <- list(list(name = 42, c(1, 2)))
- polyline_list_inv_3 <- list(list(name = "wrong_points", c("this", "should", "fail")))
-
- expect_error(validate_polylines(polyline_list_inv_0))
- expect_error(validate_polylines(polyline_list_inv_1))
- expect_error(validate_polylines(polyline_list_inv_2))
- expect_error(validate_polylines(polyline_list_inv_3))
-
- polyline_list_val_0 <- list(list(name = "cool", c(1, 2)))
- polyline_list_val_1 <- list(list(name = "also cool", c(1, 2, 4, 5, 1)))
-
- expect_invisible(validate_polylines(polyline_list_val_0))
- expect_invisible(validate_polylines(polyline_list_val_1))
-
- #...(WIP)
-
-})
-
-
-test_that("validate_surfaces function checks if input is a list with the right contents", {
-
- surface_tibble <- tibble::tibble(name = "tibble", surface = c(c(0, 1, 2), c(1, 2, 3)))
-
- #Check class (should expect a list, not a tibble)
- expect_error(validate_surfaces(surface_tibble))
-
- #...(WIP)
-})
\ No newline at end of file
--
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