From 9ea08faae6003c75db83052a2469af1542ed9d32 Mon Sep 17 00:00:00 2001
From: aheinri5 <Anna@netzkritzler.de>
Date: Tue, 16 Feb 2021 21:52:47 +0100
Subject: [PATCH] [docs] changed names in examples and raw data
---
data-raw/xpaths_for_classes.R | 19 +--
data/xpaths_for_classes.rda | Bin 1054 -> 1055 bytes
.../workflow_demos/flow_free_expansion.R | 132 +++++++++---------
.../generate_benchmark_script.R | 7 +-
.../workflow_demos/read_from_benchmark.R | 2 +-
5 files changed, 80 insertions(+), 80 deletions(-)
diff --git a/data-raw/xpaths_for_classes.R b/data-raw/xpaths_for_classes.R
index 20dca39..60f4862 100644
--- a/data-raw/xpaths_for_classes.R
+++ b/data-raw/xpaths_for_classes.R
@@ -1,23 +1,24 @@
# While having r2ogs6 loaded:
-#'get_xpaths_for_classes
-#'@description Creates a list of all `xpath` arguments of `r2ogs6` classes.
+#' get_xpaths_for_classes
+#' @description
+#' Creates a list of all `xpath` arguments of `prj` classes.
#' This is for efficiency as getting arguments from non-instantiated S3 classes
#' requires string parsing.
get_xpaths_for_classes <- function(){
ns_exports <- getNamespaceExports("r2ogs6")
- r2ogs6_class_constructor_names <-
- sort(ns_exports[grepl("^new_r2ogs6", ns_exports)])
- r2ogs6_class_helper_names <-
- sort(ns_exports[grepl("^r2ogs6", ns_exports)])
+ prj_class_constructor_names <-
+ sort(ns_exports[grepl("^new_prj_", ns_exports)])
+ prj_class_helper_names <-
+ sort(ns_exports[grepl("^prj_", ns_exports)])
xfc_list <- list()
- for(i in seq_len(length(r2ogs6_class_constructor_names))){
+ for(i in seq_len(length(prj_class_constructor_names))){
- cc <- r2ogs6_class_constructor_names[[i]]
+ cc <- prj_class_constructor_names[[i]]
cc_str <-
paste(utils::capture.output(dput(eval(parse(text = cc)))),
collapse="\n")
@@ -46,7 +47,7 @@ get_xpaths_for_classes <- function(){
list(xpath))
names(xfc_list)[[length(xfc_list)]] <-
- r2ogs6_class_helper_names[[i]]
+ prj_class_helper_names[[i]]
}
return(invisible(xfc_list))
diff --git a/data/xpaths_for_classes.rda b/data/xpaths_for_classes.rda
index 26ee951a0c92ada7ee5f5471c7a9e2f9ddd4f96b..03d04f8f8f88fa252cdf6898aead797c96224390 100644
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diff --git a/inst/examples/workflow_demos/flow_free_expansion.R b/inst/examples/workflow_demos/flow_free_expansion.R
index 15b68b1..5302406 100644
--- a/inst/examples/workflow_demos/flow_free_expansion.R
+++ b/inst/examples/workflow_demos/flow_free_expansion.R
@@ -1,6 +1,7 @@
+
library(r2ogs6)
#===== Set up simulation object =====
@@ -16,8 +17,7 @@ library(r2ogs6)
# Then we can create a simulation object.
ogs6_obj <- OGS6$new(sim_name = "flow_free_expansion",
- sim_id = 1,
- sim_path = "D:/OGS_Sim/")
+ sim_path = "D:/OGS_sims/")
ogs6_obj$add_gml(
@@ -90,13 +90,11 @@ ogs6_obj$add_gml(
)
)
-ogs6_obj$add_vtu(
- "D:/Programme/OpenGeoSys/ogs-master-Tests-Data/HydroMechanics/IdealGas/flow_free_expansion/cube_1x1x1_quad.vtu",
- FALSE
-)
+ogs6_obj$add_vtu("inst/extdata/benchmarks/flow_free_expansion/cube_1x1x1_quad.vtu",
+ FALSE)
ogs6_obj$add(
- r2ogs6_process(
+ prj_process(
name = "HM",
type = "HYDRO_MECHANICS",
integration_order = 3,
@@ -115,7 +113,7 @@ ogs6_obj$add(
),
specific_body_force = c(0, 0, 0),
dimension = 3,
- constitutive_relation = r2ogs6_constitutive_relation(
+ constitutive_relation = prj_constitutive_relation(
type = "LinearElasticIsotropic",
youngs_modulus = "E",
poissons_ratio = "nu"
@@ -125,48 +123,48 @@ ogs6_obj$add(
ogs6_obj$add(
- r2ogs6_process_variable(
+ prj_process_variable(
name = "displacement",
components = 3,
order = 2,
initial_condition = "displacement0",
boundary_conditions = list(
- boundary_condition = r2ogs6_boundary_condition(
+ boundary_condition = prj_boundary_condition(
type = "Dirichlet",
parameter = "zero",
geometrical_set = "cube_1x1x1_geometry",
geometry = "front",
component = 1
),
- boundary_condition = r2ogs6_boundary_condition(
+ boundary_condition = prj_boundary_condition(
type = "Dirichlet",
parameter = "zero",
geometrical_set = "cube_1x1x1_geometry",
geometry = "left",
component = 0
),
- boundary_condition = r2ogs6_boundary_condition(
+ boundary_condition = prj_boundary_condition(
type = "Dirichlet",
parameter = "zero",
geometrical_set = "cube_1x1x1_geometry",
geometry = "bottom",
component = 2
),
- boundary_condition = r2ogs6_boundary_condition(
+ boundary_condition = prj_boundary_condition(
type = "Neumann",
parameter = "pressure_load",
geometrical_set = "cube_1x1x1_geometry",
geometry = "back",
component = 1
),
- boundary_condition = r2ogs6_boundary_condition(
+ boundary_condition = prj_boundary_condition(
type = "Neumann",
parameter = "pressure_load",
geometrical_set = "cube_1x1x1_geometry",
geometry = "right",
component = 0
),
- boundary_condition = r2ogs6_boundary_condition(
+ boundary_condition = prj_boundary_condition(
type = "Neumann",
parameter = "pressure_load",
geometrical_set = "cube_1x1x1_geometry",
@@ -179,13 +177,13 @@ ogs6_obj$add(
ogs6_obj$add(
- r2ogs6_process_variable(
+ prj_process_variable(
name = "pressure",
components = 1,
order = 1,
initial_condition = "pressure0",
boundary_conditions = list(
- boundary_condition = r2ogs6_boundary_condition(
+ boundary_condition = prj_boundary_condition(
type = "Neumann",
parameter = "flux_in",
geometrical_set = "cube_1x1x1_geometry",
@@ -197,59 +195,59 @@ ogs6_obj$add(
)
-ogs6_obj$add(r2ogs6_medium(
+ogs6_obj$add(prj_medium(
phases = list(
- phase = r2ogs6_phase(
+ phase = prj_phase(
type = "Gas",
properties = list(
- 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)
+ property = prj_ph_property(name = "viscosity",
+ type = "Constant",
+ value = 1e-05),
+ property = prj_ph_property(name = "density",
+ type = "IdealGasLaw"),
+ property = prj_ph_property(name = "molar_mass",
+ type = "Constant",
+ value = 0.0289643977872068)
)
),
- phase = r2ogs6_phase(
+ phase = prj_phase(
type = "Solid",
properties = list(
- 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)
+ property = prj_ph_property(name = "porosity",
+ type = "Constant",
+ value = 0.3),
+ property = prj_ph_property(name = "density",
+ type = "Constant",
+ value = 1430),
+ property = prj_ph_property(name = "biot_coefficient",
+ type = "Constant",
+ value = 0.6)
)
)
),
properties = list(
- property = r2ogs6_pr_property(name = "reference_temperature",
- type = "Constant",
- value = 293.15),
- property = r2ogs6_pr_property(name = "permeability",
- type = "Constant",
- value = 1e-05)
+ property = prj_pr_property(name = "reference_temperature",
+ type = "Constant",
+ value = 293.15),
+ property = prj_pr_property(name = "permeability",
+ type = "Constant",
+ value = 1e-05)
)
))
-ogs6_obj$add(r2ogs6_time_loop(
+ogs6_obj$add(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,
@@ -258,7 +256,7 @@ ogs6_obj$add(r2ogs6_time_loop(
)
)
),
- output = r2ogs6_output(
+ output = prj_output(
type = "VTK",
prefix = "flow_free_expansion",
variables = list(
@@ -282,9 +280,9 @@ ogs6_obj$add(r2ogs6_time_loop(
ogs6_obj$add(
- r2ogs6_linear_solver(
+ prj_linear_solver(
name = "general_linear_solver",
- eigen = r2ogs6_eigen(
+ eigen = prj_eigen(
solver_type = "BiCGSTAB",
precon_type = "ILUT",
max_iteration_step = 10000,
@@ -296,7 +294,7 @@ ogs6_obj$add(
ogs6_obj$add(
- r2ogs6_nonlinear_solver(
+ prj_nonlinear_solver(
name = "basic_newton",
type = "Newton",
max_iter = 50,
@@ -305,45 +303,45 @@ ogs6_obj$add(
)
-ogs6_obj$add(r2ogs6_parameter(name = "E",
- type = "Constant",
- value = 1e+10))
+ogs6_obj$add(prj_parameter(name = "E",
+ type = "Constant",
+ value = 1e+10))
-ogs6_obj$add(r2ogs6_parameter(name = "nu",
- type = "Constant",
- value = 0.3))
+ogs6_obj$add(prj_parameter(name = "nu",
+ type = "Constant",
+ value = 0.3))
-ogs6_obj$add(r2ogs6_parameter(
+ogs6_obj$add(prj_parameter(
name = "displacement0",
type = "Constant",
values = c(0, 0, 0)
))
-ogs6_obj$add(r2ogs6_parameter(
+ogs6_obj$add(prj_parameter(
name = "pressure0",
type = "Constant",
values = 1e+05
))
-ogs6_obj$add(r2ogs6_parameter(
+ogs6_obj$add(prj_parameter(
name = "pressure_load",
type = "Constant",
values = -60000
))
-ogs6_obj$add(r2ogs6_parameter(name = "zero",
- type = "Constant",
- value = 0))
+ogs6_obj$add(prj_parameter(name = "zero",
+ type = "Constant",
+ value = 0))
-ogs6_obj$add(r2ogs6_parameter(name = "flux_in",
- type = "Constant",
- value = 1e-04))
+ogs6_obj$add(prj_parameter(name = "flux_in",
+ type = "Constant",
+ value = 1e-04))
-run_simulation(ogs6_obj)
+ogs6_run_simulation(ogs6_obj)
diff --git a/inst/examples/workflow_demos/generate_benchmark_script.R b/inst/examples/workflow_demos/generate_benchmark_script.R
index ce2c653..921333d 100644
--- a/inst/examples/workflow_demos/generate_benchmark_script.R
+++ b/inst/examples/workflow_demos/generate_benchmark_script.R
@@ -3,14 +3,15 @@ library(r2ogs6)
# Modify the prj_path depending on where you saved the benchmark file.
-prj_path <- "inst/extdata/flow_free_expansion/flow_free_expansion.prj"
+prj_path <-
+ "inst/extdata/benchmarks/flow_free_expansion/flow_free_expansion.prj"
# You can either define where to save the script explicitly...
script_path <- "some_directory/"
-generate_benchmark_script(prj_path, script_path)
+ogs6_generate_benchmark_script(prj_path, script_path)
# ... or you can leave the path out, then it will be saved in
@@ -19,5 +20,5 @@ generate_benchmark_script(prj_path, script_path)
# options("r2ogs6.default_script_path" = "your_path_here")
-generate_benchmark_script(prj_path)
+ogs6_generate_benchmark_script(prj_path)
diff --git a/inst/examples/workflow_demos/read_from_benchmark.R b/inst/examples/workflow_demos/read_from_benchmark.R
index 41f0047..b067d2a 100644
--- a/inst/examples/workflow_demos/read_from_benchmark.R
+++ b/inst/examples/workflow_demos/read_from_benchmark.R
@@ -30,4 +30,4 @@ read_in_prj(ogs6_obj, prj_path)
#===== Run simulation =====
-e <- ogs_run_simulation(ogs6_obj, write_logfile = FALSE)
+e <- ogs6_run_simulation(ogs6_obj, write_logfile = FALSE)
--
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