From e6f3d9a9aac7f73412694f71b58cad9b7a6585db Mon Sep 17 00:00:00 2001
From: aheinri5 <Anna@netzkritzler.de>
Date: Mon, 18 Jan 2021 21:30:22 +0100
Subject: [PATCH] [base] Added .pvd parameter slot to OGS6 class
---
R/ogs6.R | 98 +++++++++++++++++++++++++++++++++++++-------------------
1 file changed, 65 insertions(+), 33 deletions(-)
diff --git a/R/ogs6.R b/R/ogs6.R
index 99c45c6..8d81ebc 100644
--- a/R/ogs6.R
+++ b/R/ogs6.R
@@ -59,13 +59,15 @@ OGS6 <- R6::R6Class("OGS6",
#' not of a proprietary `r2ogs6` class, `component_name` must be
#' supplied. E.g. If you're adding a `python_script` which is a string, you
#' would call `your_ogs6_obj$add("some_script.py", "python_script")`
+ #'@param component_name string: Optional: The name of the component to be
+ #' added
add = function(x,
component_name = ""){
assertthat::assert_that(assertthat::is.string(component_name))
# Assert that class name is in implemented classes for OGS6
- ogs6_components <- get_implemented_classes()
+ ogs6_components <- addable_prj_components()
x_class_name <- ""
x_of_r2ogs6_class <- FALSE
@@ -118,17 +120,17 @@ OGS6 <- R6::R6Class("OGS6",
add_gml = function(gml){
if(assertthat::is.string(gml)){
- check_file_extension(gml, "gml")
+ assertthat::assert_that(grepl("\\.gml$", gml))
private$.geometry <- gml
}else{
- assertthat::assert_that(class(gml) == "r2ogs6_gml")
+ assertthat::assert_that(inherits(gml, "OGS6_gml"))
private$.gml <- gml
if(!is.null(private$.geometry)){
warning(paste("OGS6 parameter 'geometry' now refers",
"to a different .gml object"), call. = FALSE)
}
- private$.geometry <- paste0(gml$name, ".gml")
+ private$.geometry <- paste0(self$sim_name, ".gml")
}
},
@@ -140,15 +142,13 @@ OGS6 <- R6::R6Class("OGS6",
add_vtu = function(path,
read_in_vtu = FALSE){
assertthat::assert_that(assertthat::is.string(path))
- assertthat::assert_that(grepl("\\.vtu$", path) ||
- grepl("\\.vtk$", path) ||
- grepl("\\.msh$", path))
+ assertthat::assert_that(grepl("\\.vtu$", path))
assertthat::assert_that(assertthat::is.flag(read_in_vtu))
self$meshes <- c(self$meshes, mesh = path)
if(read_in_vtu){
- private$.vtus <- c(private$.vtus, list(read_in_vtu(path)))
+ private$.vtus <- c(private$.vtus, list(OGS6_vtu$new(path)))
}
},
@@ -276,7 +276,7 @@ OGS6 <- R6::R6Class("OGS6",
assertthat::assert_that(assertthat::is.flag(print_status))
flag <- TRUE
- impl_classes <- get_implemented_classes()
+ impl_classes <- addable_prj_components()
status_strs <- character()
@@ -320,12 +320,12 @@ OGS6 <- R6::R6Class("OGS6",
#'Clears components from the OGS6 object
#'@param which character: The names of the components (all by default).
#' If you want to delete only some components, run
- #' names(get_implemented_classes()) for the available options.
- clear = function(which = names(get_implemented_classes())){
+ #' names(addable_prj_components()) for the available options.
+ clear = function(which = names(addable_prj_components())){
assertthat::assert_that(is.character(which))
- valid_input = names(get_implemented_classes())
+ valid_input = names(addable_prj_components())
null_it <- c("geometry", "time_loop")
@@ -439,7 +439,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.vtus
}else{
validate_wrapper_list(value,
- get_implemented_classes()[["vtus"]])
+ addable_prj_components()[["vtus"]])
private$.vtus <- value
}
},
@@ -462,7 +462,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.search_length_algorithm
}else{
assertthat::assert_that(
- get_implemented_classes()[["search_length_algorithm"]] %in%
+ addable_prj_components()[["search_length_algorithm"]] %in%
class(value))
private$.search_length_algorithm <- value
}
@@ -474,8 +474,26 @@ OGS6 <- R6::R6Class("OGS6",
if(missing(value)) {
private$.processes
}else{
- validate_wrapper_list(value,
- get_implemented_classes()[["processes"]])
+ # If there already is a process element
+ if(length(private$.processes) > 0){
+ if(addable_prj_components()[["processes"]] %in%
+ class(private$.processes[[1]])){
+ validate_wrapper_list(value,
+ addable_prj_components()[["processes"]])
+ }else{
+ assertthat::assert_that(assertthat::is.string(value))
+ value <- list(include = c(file = value))
+ }
+
+ }else{
+ if(assertthat::is.string(value)){
+ value <- list(include = c(file = value))
+ }else{
+ validate_wrapper_list(value,
+ addable_prj_components()[["processes"]])
+ }
+ }
+
private$.processes <- value
}
},
@@ -487,7 +505,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.time_loop
}else{
assertthat::assert_that(
- get_implemented_classes()[["time_loop"]] %in%
+ addable_prj_components()[["time_loop"]] %in%
class(value))
private$.time_loop <- value
}
@@ -500,7 +518,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.local_coordinate_system
}else{
assertthat::assert_that(
- get_implemented_classes()[["local_coordinate_system"]] %in%
+ addable_prj_components()[["local_coordinate_system"]] %in%
class(value))
private$.local_coordinate_system <- value
}
@@ -513,7 +531,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.media
}else{
validate_wrapper_list(value,
- get_implemented_classes()[["media"]])
+ addable_prj_components()[["media"]])
private$.media <- value
}
},
@@ -525,7 +543,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.parameters
}else{
validate_wrapper_list(value,
- get_implemented_classes()[["parameters"]])
+ addable_prj_components()[["parameters"]])
private$.parameters <- value
}
},
@@ -537,7 +555,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.curves
}else{
validate_wrapper_list(value,
- get_implemented_classes()[["curves"]])
+ addable_prj_components()[["curves"]])
private$.curves <- value
}
},
@@ -550,7 +568,7 @@ OGS6 <- R6::R6Class("OGS6",
}else{
validate_wrapper_list(
value,
- get_implemented_classes()[["process_variables"]])
+ addable_prj_components()[["process_variables"]])
private$.process_variables <- value
}
},
@@ -563,7 +581,7 @@ OGS6 <- R6::R6Class("OGS6",
}else{
validate_wrapper_list(
value,
- get_implemented_classes()[["nonlinear_solvers"]])
+ addable_prj_components()[["nonlinear_solvers"]])
private$.nonlinear_solvers <- value
}
},
@@ -575,7 +593,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.linear_solvers
}else{
validate_wrapper_list(value,
- get_implemented_classes()[["linear_solvers"]])
+ addable_prj_components()[["linear_solvers"]])
private$.linear_solvers <- value
}
},
@@ -587,7 +605,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.test_definition
}else{
validate_wrapper_list(value,
- get_implemented_classes()[["test_definition"]])
+ addable_prj_components()[["test_definition"]])
private$.test_definition <- value
}
},
@@ -599,15 +617,26 @@ OGS6 <- R6::R6Class("OGS6",
private$.insitu
}else{
assertthat::assert_that(
- get_implemented_classes()[["insitu"]] %in%
+ addable_prj_components()[["insitu"]] %in%
class(value))
private$.insitu <- value
}
+ },
+
+ #'@field pvd
+ #'Access to private parameter '.pvd'
+ pvd = function(value) {
+ if(missing(value)) {
+ private$.pvd
+ }else{
+ assertthat::assert_that(inherits(value, "OGS6_pvd"))
+ private$.pvd <- value
+ }
}
),
private = list(
- #general parameters
+ # general parameters
.sim_name = NULL,
.sim_id = NULL,
.sim_path = NULL,
@@ -615,18 +644,18 @@ OGS6 <- R6::R6Class("OGS6",
.logfile = NULL,
- #.gml parameters
+ # .gml object
.gml = NULL,
- #.vtu parameters
+ # .vtu objects
.vtus = NULL,
- #.prj parameters
+ # .prj parameters
- #.gml reference
+ # .gml reference
.geometry = NULL,
- #.vtu reference(s)
+ # .vtu reference(s)
.meshes = list(),
.python_script = NULL,
@@ -641,6 +670,9 @@ OGS6 <- R6::R6Class("OGS6",
.nonlinear_solvers = list(),
.linear_solvers = list(),
.test_definition = list(),
- .insitu = NULL
+ .insitu = NULL,
+
+ # .pvd object (output)
+ .pvd = NULL
)
)
--
GitLab