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Commit 9ea08faa authored by Ruben Heinrich's avatar Ruben Heinrich
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[docs] changed names in examples and raw data

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1 merge request!13Resolve "Rename ogs_ prefixes to ogs6_ and r2ogs6_prefixes to prj_"
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data-raw/xpaths_for_classes.R
+ 10
− 9
View file @ 9ea08faa
# 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))
......
data/xpaths_for_classes.rda
+ 0
− 0
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inst/examples/workflow_demos/flow_free_expansion.R
+ 65
− 67
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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)
inst/examples/workflow_demos/generate_benchmark_script.R
+ 4
− 3
View file @ 9ea08faa
......@@ -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)
inst/examples/workflow_demos/read_from_benchmark.R
+ 1
− 1
View file @ 9ea08faa
......@@ -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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