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Commit bb4d5e57 authored by Ruben Heinrich's avatar Ruben Heinrich
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[base] Updated R Version and packages

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4 merge requests!57 vtkdiff,!47 parameter,!37 process borehole heat exchanger,!2Basic import and export functionality
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.Rbuildignore
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...@@ -2,3 +2,4 @@ ...@@ -2,3 +2,4 @@
^\.Rproj\.user$ ^\.Rproj\.user$
^packrat/ ^packrat/
^\.Rprofile$ ^\.Rprofile$
^LICENSE.md
DESCRIPTION
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...@@ -15,8 +15,7 @@ Encoding: UTF-8 ...@@ -15,8 +15,7 @@ Encoding: UTF-8
LazyData: true LazyData: true
Suggests: Suggests:
testthat, testthat,
knitr, knitr
rmarkdown
Imports: Imports:
purrr, purrr,
magrittr, magrittr,
...@@ -31,6 +30,7 @@ Imports: ...@@ -31,6 +30,7 @@ Imports:
snakecase, snakecase,
rlist, rlist,
utils, utils,
qpdf qpdf,
rmarkdown
RoxygenNote: 7.1.1 RoxygenNote: 7.1.1
VignetteBuilder: knitr VignetteBuilder: knitr
NAMESPACE
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...@@ -11,6 +11,7 @@ S3method(input_add,r2ogs6_process_variable) ...@@ -11,6 +11,7 @@ S3method(input_add,r2ogs6_process_variable)
S3method(input_add,r2ogs6_time_loop) S3method(input_add,r2ogs6_time_loop)
S3method(input_add,r2ogs6_vtkdiff) S3method(input_add,r2ogs6_vtkdiff)
export(OGS6) export(OGS6)
export(generate_benchmark_script)
export(generate_structured_mesh) export(generate_structured_mesh)
export(input_add) export(input_add)
export(pick_vtu_file) export(pick_vtu_file)
...@@ -21,6 +22,7 @@ export(r2ogs6_linear_solver) ...@@ -21,6 +22,7 @@ export(r2ogs6_linear_solver)
export(r2ogs6_medium) export(r2ogs6_medium)
export(r2ogs6_medium_phase) export(r2ogs6_medium_phase)
export(r2ogs6_medium_property) export(r2ogs6_medium_property)
export(r2ogs6_mesh)
export(r2ogs6_nonlinear_solver) export(r2ogs6_nonlinear_solver)
export(r2ogs6_parameter) export(r2ogs6_parameter)
export(r2ogs6_process) export(r2ogs6_process)
......
R/gml_prefabs.R deleted 100644 → 0
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#This script contains some useful S3 classes for premade geometry
#'Constructor based on HydroMechanics/IdealGas/flow_free_expansion/cube_1x1x1.gml
new_r2ogs6_gml_cube_1x1x1 <- function() {
new_r2ogs6_gml(name = "cube_1x1x1_geometry",
#Cube points (will become second XML child under root)
points = tibble::tibble(x = c(0, 0, 0, 0, 1, 1, 1, 1),
y = c(0, 0, 1, 1, 0, 0, 1, 1),
z = c(0, 1, 1, 0, 0, 1, 1, 0),
name = c("origin", rep("", 7))),
#Cube polylines (will become third XML child under root)
polylines = list(list(name = "front_left", c(0, 1)),
list(name = "front_right", c(4, 5)),
list(name = "front_bottom", c(0, 4)),
list(name = "front_top", c(1, 5)),
list(name = "bottom_left", c(0, 3)),
list(name = "bottom_right", c(4, 7)),
list(name = "top_left", c(1, 2)),
list(name = "top_right", c(5, 6)),
list(name = "back_left", c(2, 3)),
list(name = "back_right", c(6, 7)),
list(name = "back_bottom", c(3, 7)),
list(name = "back_top", c(2, 6))),
#Cube surfaces (will become fourth XML child under root)
surfaces = list(list(name = "left", c(0, 1, 2), c(0, 3, 2)),
list(name = "right", c(4, 6, 5), c(4, 6, 7)),
list(name = "top", c(1, 2, 5), c(5, 2, 6)),
list(name = "bottom", c(0, 3, 4), c(4, 3, 7)),
list(name = "front", c(0, 1, 4), c(4, 1, 5)),
list(name = "back", c(2, 3, 6), c(6, 3, 7)))
)
}
#Another cube but without polylines
#'Constructor based on HydroMechanics/IdealGas/flow_no_strain/square_1x1.gml
new_r2ogs6_gml_square_1x1 <- function() {
new_r2ogs6_gml(
name = "square_1x1_geometry",
points = tibble::tibble(x = c(0, 0, 1, 1),
y = c(0, 1, 0, 1),
z = c(0, 0, 0, 0),
name = c("origin", rep("", 3))),
polylines = list(list(name = "left", c(0, 1)),
list(name = "right", c(2, 3)),
list(name = "bottom", c(0, 2)),
list(name = "top", c(1, 3)))
)
}
#'Constructor based on HydroMechanics/IdealGas/flow_pressure_boundary/quad_1x10.gml
new_r2ogs6_gml_quad_1x10 <- function() {
new_r2ogs6_gml(
name = "quad_1x10_geometry",
points = tibble::tibble(x = c(0, 0, 10, 10),
y = c(0, 1, 0, 1),
z = c(0, 0, 0, 0),
name = c("origin", rep("", 3))),
polylines = list(list(name = "left", c(0, 1)),
list(name = "right", c(2, 3)),
list(name = "bottom", c(0, 2)),
list(name = "top", c(1, 3)))
)
}
#'Constructor based on HydroMechanics/StaggeredScheme/InjectionProduction1D/bar.gml
new_r2ogs6_gml_bar <- function() {
new_r2ogs6_gml(
name = "bar",
points = tibble::tibble(x = c(0, 10, 10, 0),
y = c(0, 0, 150, 150),
z = c(0, 0, 0, 0),
name = c(rep("", 4))),
polylines = list(list(name = "left", c(0, 3)),
list(name = "right", c(1, 2)),
list(name = "bottom", c(0, 1)),
list(name = "top", c(2, 3)))
)
}
#'Constructor based on HydroMechanics/Verification/hm1_1Dbeam.gml
new_r2ogs6_gml_hm1_1Dbeam <- function() {
new_r2ogs6_gml(
name = "geometry",
points = tibble::tibble(x = c(1, 1, 1, 1, 0, 0, 0, 0),
y = c(0.10000000000000001, 0, 0, 0.10000000000000001,
0, 0, 0.10000000000000001, 0.10000000000000001),
z = c(0, 0, 0.10000000000000001, 0.10000000000000001,
0, 0.10000000000000001, 0, 0.10000000000000001),
name = c("POINT0", "POINT1", "POINT2", "POINT3",
"POINT4", "POINT7", "POINT8", "POINT22")),
polylines = list(list(name = "POLYLINE1", c(0, 1, 2, 3, 0)),
list(name = "POLYLINE2", c(4, 1, 2, 5, 4)),
list(name = "POLYLINE3", c(6, 0, 3, 7, 6)),
list(name = "POLYLINE4", c(4, 1, 0, 6, 4)),
list(name = "POLYLINE5", c(5, 2, 3, 7, 5)),
list(name = "POLYLINE6", c(4, 6, 7, 5, 4)),
list(name = "POLYLINE7", c(1, 0, 3, 2, 1))),
surfaces = list(list(name = "SURFACE1", c(0, 2, 1), c(2, 0, 3)),
list(name = "SURFACE2", c(4, 2, 1), c(2, 4, 5)),
list(name = "SURFACE3", c(6, 3, 0), c(3, 6, 7)),
list(name = "SURFACE4", c(4, 0, 1), c(0, 4, 6)),
list(name = "SURFACE5", c(5, 3, 2), c(3, 5, 7)),
list(name = "SURFACE6", c(4, 7, 6), c(7, 4, 5)),
list(name = "SURFACE7", c(1, 3, 0), c(3, 1, 2)))
)
}
#'Constructor based on HydroMechanics/Verification/hm1_2Dsquare.gml
new_r2ogs6_gml_hm1_2Dsquare <- function() {
new_r2ogs6_gml(
name = "geometry",
points = tibble::tibble(x = c(0, 1, 1, 0, 0, 0, 1, 1),
y = c(0, 0, 1, 1, 1, 0, 0, 1),
z = c(0, 0, 0, 0, 0.10000000000000001, 0.10000000000000001,
0.10000000000000001, 0.10000000000000001),
name = c("POINT0", "POINT1", "POINT2", "POINT3",
"POINT6", "POINT7", "POINT17", "POINT18")),
polylines = list(list(name = "POLYLINE1", c(0, 1, 2, 3, 0)),
list(name = "POLYLINE2", c(0, 3, 4, 5, 0)),
list(name = "POLYLINE3", c(0, 1, 6, 5, 0)),
list(name = "POLYLINE4", c(0, 1, 2, 3, 0)),
list(name = "POLYLINE5", c(5, 6, 7, 4, 5))),
surfaces = list(list(name = "SURFACE1", c(0, 2, 1), c(2, 0, 3)),
list(name = "SURFACE2", c(0, 4, 3), c(4, 0, 5)),
list(name = "SURFACE3", c(0, 6, 1), c(6, 0, 5)),
list(name = "SURFACE4", c(0, 2, 1), c(2, 0, 3)),
list(name = "SURFACE5", c(5, 7, 6), c(7, 5, 4)))
)
}
#'Constructor based on HydroMechanics/Verification/hm1_3Dcube.gml
new_r2ogs6_gml_hm1_3Dcube <- function() {
new_r2ogs6_gml(
name = "geometry",
points = tibble::tibble(x = c(0, 1, 1, 0, 1, 0, 0, 1),
y = c(0, 0, 1, 1, 0, 0, 1, 1),
z = c(0, 0, 0, 0, 1, 1, 1, 1),
name = c("POINT0", "POINT1", "POINT2", "POINT3",
"POINT6", "POINT7", "POINT15", "POINT14")),
polylines = list(list(name = "POLYLINE1", c(0, 1, 2, 3, 0)),
list(name = "POLYLINE2", c(0, 1, 4, 5, 0)),
list(name = "POLYLINE3", c(0, 3, 6, 5, 0)),
list(name = "POLYLINE4", c(5, 4, 7, 6, 5))),
surfaces = list(list(name = "SURFACE1", c(0, 2, 1), c(2, 0, 3)),
list(name = "SURFACE2", c(0, 4, 1), c(4, 0, 5)),
list(name = "SURFACE3", c(0, 6, 3), c(6, 0, 5)),
list(name = "SURFACE4", c(5, 7, 4), c(7, 5, 6)))
)
}
#'Constructor based on HydroMechanics/Verification/hm1_3Dgravity.gml
new_r2ogs6_gml_hm1_3Dgravity <- function() {
new_r2ogs6_gml(
name = "geometry",
points = tibble::tibble(x = c(0, 60, 60, 0, 0, 60, 60, 0),
y = c(0, 0, 30, 30, 0, 0, 30, 30),
z = c(30, 30, 30, 30, 0, 0, 0, 0),
name = c("POINT0", "POINT1", "POINT2", "POINT3",
"POINT4", "POINT5", "POINT6", "POINT7")),
polylines = list(list(name = "POLYLINE1", c(0, 1, 2, 3, 0)),
list(name = "POLYLINE2", c(4, 5, 6, 7, 4)),
list(name = "POLYLINE3", c(4, 5, 1, 0, 4)),
list(name = "POLYLINE4", c(7, 6, 2, 3, 7)),
list(name = "POLYLINE5", c(4, 7, 3, 0, 4)),
list(name = "POLYLINE6", c(5, 6, 2, 1, 5))),
surfaces = list(list(name = "SURFACE1", c(0, 2, 1), c(2, 0, 3)),
list(name = "SURFACE2", c(4, 6, 5), c(6, 4, 7)),
list(name = "SURFACE3", c(4, 1, 5), c(1, 4, 0)),
list(name = "SURFACE4", c(7, 2, 6), c(2, 7, 3)),
list(name = "SURFACE5", c(4, 3, 7), c(3, 4, 0)),
list(name = "SURFACE6", c(5, 2, 6), c(2, 5, 1)))
)
}
#.../hm2_1d1bt.gml (add the hm2-gml prefabs)
#'Constructor based on ogs6_benchmarks/Elliptic/circle_radius_1/circle_1_axi.gml
#'
#'
new_r2ogs6_gml_circle_1_axi <- function() {
new_r2ogs6_gml(
name = "geometry",
points = tibble::tibble(x = c(0, 1),
y = c(0, 0),
z = c(0, 0),
name = c("inner", "outer"))
)
}
man/make_call_from_parameters.Rd deleted 100644 → 0
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/read_in_utils.R
\name{make_call_from_parameters}
\alias{make_call_from_parameters}
\title{make_call_from_parameters}
\usage{
make_call_from_parameters(class_name, parameters)
}
\arguments{
\item{class_name}{Which class constructor should be called?}
\item{parameters}{A named list of parameters}
}
\description{
Helper function to construct a call from a class name and a
list of class parameters
}
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