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Commit 63fda142 authored by phit0's avatar phit0
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[base] updated classes for rean_in_prj 

[base] update classes for ogs v6.4.1

[base] added class arguments for new keywords

[tests] skip benchmarks with *.xml project-files
parent 39f88d75
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3 merge requests!38Draft: standardize files references during prj import/export,!35Resolve "Manual CI job to run all benchmarks",!33Resolve "Update to OGSv6.4.1"
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R/prj_chemical_system.R
+ 39
− 4
View file @ 63fda142
......@@ -14,6 +14,8 @@
#' @param equilibrium_reactants Optional: list, prj_phase_component:
#' @param surface Optional:
#' @param user_punch Optional:
#' @param linear_solver Optional:
#' @param exchangers Optional: prj_exchangers
#' @example man/examples/ex_prj_chemical_system.R
#' @export
prj_chemical_system <- function(chemical_solver,
......@@ -25,7 +27,9 @@ prj_chemical_system <- function(chemical_solver,
rates = NULL,
equilibrium_reactants = NULL,
surface = NULL,
user_punch = NULL) {
user_punch = NULL,
linear_solver = NULL,
exchangers = NULL) {
# Add coercing utility here
......@@ -38,7 +42,9 @@ prj_chemical_system <- function(chemical_solver,
rates,
equilibrium_reactants,
surface,
user_punch)
user_punch,
linear_solver,
exchangers)
}
......@@ -51,13 +57,17 @@ new_prj_chemical_system <- function(chemical_solver,
rates = NULL,
equilibrium_reactants = NULL,
surface = NULL,
user_punch = NULL) {
user_punch = NULL,
linear_solver = NULL,
exchangers = NULL) {
are_strings(chemical_solver,
database)
assertthat::assert_that(class(solution) == "prj_solution")
assertthat::assert_that(is.null(exchangers) |
class(exchangers) == "prj_exchangers")
are_null_or_strings(mesh)
......@@ -95,6 +105,8 @@ new_prj_chemical_system <- function(chemical_solver,
equilibrium_reactants = equilibrium_reactants,
surface = surface,
user_punch = user_punch,
linear_solver = linear_solver,
exchangers = exchangers,
xpath = "chemical_system",
attr_names = c("chemical_solver"),
flatten_on_exp = character()
......@@ -141,7 +153,6 @@ new_prj_solution <- function(temperature,
pe,
components,
charge_balance = NULL) {
are_numbers(temperature,
pressure,
pe)
......@@ -301,3 +312,27 @@ new_prj_rate <- function(kinetic_reactant,
class = "prj_rate"
)
}
#'prj_exchangers
#'@description tag: exchangers
#'@param exchange_site list
#'@export
prj_exchangers <- function(exchange_site) {
# Add coercing utility here
new_prj_exchangers(exchange_site)
}
new_prj_exchangers <- function(exchange_site) {
assertthat::assert_that(is.list(exchange_site))
structure(list(exchange_site = exchange_site,
xpath = "chemical_system/exchangers",
attr_names = character(),
flatten_on_exp = character()
),
class = "prj_exchangers"
)
}
R/prj_medium.R
+ 96
− 11
View file @ 63fda142
......@@ -79,8 +79,13 @@ new_prj_medium <- function(phases = NULL,
#' @param intrinsic_permeability Optional:
#' @param initial_aperture Optional:
#' @param mean_frac_distance Optional:
#' @param mean_frac_distances Optional: numeric vector
#' @param threshold_strain Optional:
#' @param threshold_strains Optional: numeric vector
#' @param fracture_normal Optional:
#' @param fracture_normals Optional: numeric vector
#' @param fracture_rotation_xy Optional:
#' @param fracture_rotation_yz Optional:
#' @param reference_permeability Optional:
#' @param fitting_factor Optional:
#' @param cohesion Optional:
......@@ -117,8 +122,13 @@ prj_pr_property <- function(name,
intrinsic_permeability = NULL,
initial_aperture = NULL,
mean_frac_distance = NULL,
mean_frac_distances = NULL,
threshold_strain = NULL,
threshold_strains = NULL,
fracture_normal = NULL,
fracture_normals = NULL,
fracture_rotation_xy = NULL,
fracture_rotation_yz = NULL,
reference_permeability = NULL,
fitting_factor = NULL,
cohesion = NULL,
......@@ -174,8 +184,13 @@ prj_pr_property <- function(name,
intrinsic_permeability,
initial_aperture,
mean_frac_distance,
mean_frac_distances,
threshold_strain,
threshold_strains,
fracture_normal,
fracture_normals,
fracture_rotation_xy,
fracture_rotation_yz,
reference_permeability,
fitting_factor,
cohesion,
......@@ -213,8 +228,13 @@ new_prj_pr_property <- function(name,
intrinsic_permeability = NULL,
initial_aperture = NULL,
mean_frac_distance = NULL,
mean_frac_distances = NULL,
threshold_strain = NULL,
threshold_strains = NULL,
fracture_normal = NULL,
fracture_normals = NULL,
fracture_rotation_xy = NULL,
fracture_rotation_yz = NULL,
reference_permeability = NULL,
fitting_factor = NULL,
cohesion = NULL,
......@@ -277,8 +297,13 @@ new_prj_pr_property <- function(name,
intrinsic_permeability = intrinsic_permeability,
initial_aperture = initial_aperture,
mean_frac_distance = mean_frac_distance,
mean_frac_distances = mean_frac_distances,
threshold_strain = threshold_strain,
threshold_strains = threshold_strains,
fracture_normal = fracture_normal,
fracture_normals = fracture_normals,
fracture_rotation_xy = fracture_rotation_xy,
fracture_rotation_yz = fracture_rotation_yz,
reference_permeability = reference_permeability,
fitting_factor = fitting_factor,
cohesion = cohesion,
......@@ -414,7 +439,10 @@ prj_ph_property <- function(name,
...) {
#Coerce input
value <- coerce_string_to_numeric(value)
if (!is.list(value)) {
value <- coerce_string_to_numeric(value)
}
reference_value <- coerce_string_to_numeric(reference_value)
exponents <- coerce_string_to_numeric(exponents)
offset <- coerce_string_to_numeric(offset)
......@@ -457,7 +485,11 @@ new_prj_ph_property <- function(name,
are_strings(name,
type)
are_null_or_numeric(value)
if (is.list(value)) {
are_null_or_strings(value[[1]])
} else {
are_null_or_numeric(value)
}
are_null_or_numbers(
reference_value,
......@@ -560,34 +592,79 @@ new_prj_component <- function(name,
#' @param type string: Property type
#' @param value Optional: string | double: ...
#' @param parameter_name Optional:
#' @param reference_diffusion Optional: character
#' @param activation_energy Optional: string | double
#' @param reference_temperature Optional: numeric
#' @example man/examples/ex_prj_com_property.R
#' @export
prj_com_property <- function(name,
type,
value = NULL,
parameter_name = NULL) {
type,
value = NULL,
parameter_name = NULL,
reference_diffusion = NULL,
activation_energy = NULL,
reference_temperature = NULL,
triple_temperature = NULL,
triple_pressure = NULL,
critical_temperature = NULL,
critical_pressure = NULL,
reference_pressure= NULL) {
#Coerce input
value <- coerce_string_to_numeric(value)
activation_energy <- coerce_string_to_numeric(activation_energy)
reference_temperature <- coerce_string_to_numeric(reference_temperature)
triple_temperature <- coerce_string_to_numeric(triple_temperature)
triple_pressure <- coerce_string_to_numeric(triple_pressure)
critical_temperature <- coerce_string_to_numeric(critical_temperature)
critical_pressure <- coerce_string_to_numeric(critical_pressure)
reference_pressure <- coerce_string_to_numeric(reference_pressure)
new_prj_com_property(name,
type,
value,
parameter_name)
type,
value,
parameter_name,
reference_diffusion,
activation_energy,
reference_temperature,
triple_temperature,
triple_pressure,
critical_temperature,
critical_pressure,
reference_pressure
)
}
new_prj_com_property <- function(name,
type,
value = NULL,
parameter_name = NULL) {
type,
value = NULL,
parameter_name = NULL,
reference_diffusion = NULL,
activation_energy = NULL,
reference_temperature = NULL,
triple_temperature = NULL,
triple_pressure = NULL,
critical_temperature = NULL,
critical_pressure = NULL,
reference_pressure= NULL) {
assertthat::assert_that(assertthat::is.string(name))
assertthat::assert_that(assertthat::is.string(type))
are_null_or_numbers(value)
are_null_or_numeric(activation_energy)
are_null_or_numeric(reference_temperature)
are_null_or_numeric(triple_temperature)
are_null_or_numeric(triple_pressure)
are_null_or_numeric(critical_temperature)
are_null_or_numeric(critical_pressure)
are_null_or_numeric(reference_pressure)
are_null_or_strings(parameter_name)
are_null_or_strings(reference_diffusion)
structure(
list(
......@@ -595,6 +672,14 @@ new_prj_com_property <- function(name,
type = type,
value = value,
parameter_name = parameter_name,
reference_diffusion = reference_diffusion,
activation_energy = activation_energy,
reference_temperature = reference_temperature,
triple_temperature = triple_temperature,
triple_pressure = triple_pressure,
critical_temperature = critical_temperature,
critical_pressure = critical_pressure,
reference_pressure = reference_pressure,
xpath = paste0("media/medium/phases/phase/components/component/",
"properties/property"),
attr_names = character(),
......
R/prj_parameter.R
+ 17
− 2
View file @ 63fda142
......@@ -15,6 +15,8 @@
#' @param mesh Optional: string:
#' @param time_series Optional: list:
#' @param use_local_coordinate_system Optional: string, "true" | "false":
#' @param range Optional: list
#' @param seed Optional: number
#' @param ... Optional: for index_values and expression tags (since there can be
#' multiple)
#' @example man/examples/ex_prj_parameter.R
......@@ -30,6 +32,8 @@ prj_parameter <- function(name,
mesh = NULL,
time_series = NULL,
use_local_coordinate_system = NULL,
range = NULL,
seed = NULL,
...) {
#Coerce input
......@@ -41,6 +45,9 @@ prj_parameter <- function(name,
index_values <- ellipsis_list[names(ellipsis_list) == "index_values"]
expression <- ellipsis_list[names(ellipsis_list) == "expression"]
range <- coerce_string_to_numeric(range)
seed <- coerce_string_to_numeric(seed)
new_prj_parameter(name,
type,
value,
......@@ -53,7 +60,9 @@ prj_parameter <- function(name,
mesh,
expression,
time_series,
use_local_coordinate_system)
use_local_coordinate_system,
range,
seed)
}
......@@ -69,7 +78,9 @@ new_prj_parameter <- function(name,
mesh = NULL,
expression = NULL,
time_series = NULL,
use_local_coordinate_system = NULL) {
use_local_coordinate_system = NULL,
range = NULL,
seed = NULL) {
assertthat::assert_that(assertthat::is.string(name))
assertthat::assert_that(assertthat::is.string(type))
......@@ -104,6 +115,8 @@ new_prj_parameter <- function(name,
"parameter_name"))
}
}
are_null_or_numeric(range)
are_null_or_numbers(seed)
structure(list(name = name,
type = type,
......@@ -118,6 +131,8 @@ new_prj_parameter <- function(name,
expression = expression,
time_series = time_series,
use_local_coordinate_system = use_local_coordinate_system,
range = range,
seed = seed,
xpath = "parameters/parameter",
attr_names = character(),
flatten_on_exp = c("values"),
......
R/prj_process.R
+ 125
− 75
View file @ 63fda142
......@@ -70,6 +70,14 @@
#' @param pf_irrv Optional:
#' @param micro_porosity Optional:
#' @param explicit_hm_coupling_in_unsaturated_zone Optional:
#' @param simplified_elasticity Optional: character
#' @param chemically_induced_porosity_change Optional: character
#' @param use_server_communication Optional:
#' @param phasefield_model Optional:
#' @param irreversible_threshold Optional: numeric
#' @param tabular_file Optional: character
#' @param temperature_field Optional: character
#' @param use_stokes_brinkman_form Optional: character
#' @param ... Optional: fracture_properties, constitutive_relation
#' @example man/examples/ex_prj_process.R
#' @export
......@@ -137,8 +145,16 @@ prj_process <- function(name,
density_solid = NULL,
latent_heat_evaporation = NULL,
pf_irrv = NULL,
micro_porosity = NULL,
micro_porosity = NULL,
explicit_hm_coupling_in_unsaturated_zone = NULL,
simplified_elasticity = NULL,
chemically_induced_porosity_change = NULL,
use_server_communication = NULL,
phasefield_model = NULL,
irreversible_threshold = NULL,
tabular_file = NULL,
temperature_field = NULL,
use_stokes_brinkman_form = NULL,
...){
#Coerce input
......@@ -171,6 +187,7 @@ prj_process <- function(name,
split_method <- coerce_string_to_numeric(split_method)
reg_param <- coerce_string_to_numeric(reg_param)
pf_irrv <- coerce_string_to_numeric(pf_irrv)
irreversible_threshold <- coerce_string_to_numeric(irreversible_threshold)
ellipsis_list <- list(...)
......@@ -248,79 +265,95 @@ prj_process <- function(name,
latent_heat_evaporation,
pf_irrv,
micro_porosity,
explicit_hm_coupling_in_unsaturated_zone
explicit_hm_coupling_in_unsaturated_zone,
simplified_elasticity,
chemically_induced_porosity_change,
use_server_communication,
phasefield_model,
irreversible_threshold,
tabular_file,
temperature_field,
use_stokes_brinkman_form
)
}
new_prj_process <- function(name,
type,
integration_order,
process_variables,
secondary_variables = NULL,
specific_body_force = NULL,
constitutive_relation = NULL,
solid_density = NULL,
dimension = NULL,
coupling_scheme = NULL,
darcy_gravity = NULL,
reference_temperature = NULL,
fracture_model = NULL,
fracture_properties = NULL,
jacobian_assembler = NULL,
internal_length = NULL,
mass_lumping = NULL,
porosity = NULL,
calculatesurfaceflux = NULL,
intrinsic_permeability = NULL,
specific_storage = NULL,
fluid_viscosity = NULL,
biot_coefficient = NULL,
fluid_density = NULL,
initial_effective_stress = NULL,
initial_fracture_effective_stress = NULL,
phasefield_parameters = NULL,
deactivate_matrix_in_flow = NULL,
borehole_heat_exchangers = NULL,
temperature = NULL,
reactive_system = NULL,
fluid_specific_heat_source = NULL,
fluid_specific_isobaric_heat_capacity = NULL,
solid_hydraulic_permeability = NULL,
solid_specific_heat_source = NULL,
solid_heat_conductivity = NULL,
solid_specific_isobaric_heat_capacity = NULL,
tortuosity = NULL,
diffusion_coefficient = NULL,
solid_density_dry = NULL,
solid_density_initial = NULL,
characteristic_pressure = NULL,
characteristic_temperature = NULL,
characteristic_vapour_mass_fraction = NULL,
output_element_matrices = NULL,
material_property = NULL,
diffusion_coeff_component_b = NULL,
diffusion_coeff_component_a = NULL,
hydro_crack_scheme = NULL,
at_num = NULL,
initial_stress = NULL,
split_method = NULL,
reg_param = NULL,
thermal_parameters = NULL,
non_advective_form = NULL,
fluid = NULL,
porous_medium = NULL,
decay_rate = NULL,
fluid_reference_density = NULL,
retardation_factor = NULL,
solute_dispersivity_longitudinal = NULL,
solute_dispersivity_transverse = NULL,
molecular_diffusion_coefficient = NULL,
density_solid = NULL,
latent_heat_evaporation = NULL,
pf_irrv = NULL,
type,
integration_order,
process_variables,
secondary_variables = NULL,
specific_body_force = NULL,
constitutive_relation = NULL,
solid_density = NULL,
dimension = NULL,
coupling_scheme = NULL,
darcy_gravity = NULL,
reference_temperature = NULL,
fracture_model = NULL,
fracture_properties = NULL,
jacobian_assembler = NULL,
internal_length = NULL,
mass_lumping = NULL,
porosity = NULL,
calculatesurfaceflux = NULL,
intrinsic_permeability = NULL,
specific_storage = NULL,
fluid_viscosity = NULL,
biot_coefficient = NULL,
fluid_density = NULL,
initial_effective_stress = NULL,
initial_fracture_effective_stress = NULL,
phasefield_parameters = NULL,
deactivate_matrix_in_flow = NULL,
borehole_heat_exchangers = NULL,
temperature = NULL,
reactive_system = NULL,
fluid_specific_heat_source = NULL,
fluid_specific_isobaric_heat_capacity = NULL,
solid_hydraulic_permeability = NULL,
solid_specific_heat_source = NULL,
solid_heat_conductivity = NULL,
solid_specific_isobaric_heat_capacity = NULL,
tortuosity = NULL,
diffusion_coefficient = NULL,
solid_density_dry = NULL,
solid_density_initial = NULL,
characteristic_pressure = NULL,
characteristic_temperature = NULL,
characteristic_vapour_mass_fraction = NULL,
output_element_matrices = NULL,
material_property = NULL,
diffusion_coeff_component_b = NULL,
diffusion_coeff_component_a = NULL,
hydro_crack_scheme = NULL,
at_num = NULL,
initial_stress = NULL,
split_method = NULL,
reg_param = NULL,
thermal_parameters = NULL,
non_advective_form = NULL,
fluid = NULL,
porous_medium = NULL,
decay_rate = NULL,
fluid_reference_density = NULL,
retardation_factor = NULL,
solute_dispersivity_longitudinal = NULL,
solute_dispersivity_transverse = NULL,
molecular_diffusion_coefficient = NULL,
density_solid = NULL,
latent_heat_evaporation = NULL,
pf_irrv = NULL,
micro_porosity = NULL,
explicit_hm_coupling_in_unsaturated_zone = NULL) {
explicit_hm_coupling_in_unsaturated_zone = NULL,
simplified_elasticity = NULL,
chemically_induced_porosity_change = NULL,
use_server_communication = NULL,
phasefield_model = NULL,
irreversible_threshold = NULL,
tabular_file = NULL,
temperature_field = NULL,
use_stokes_brinkman_form = NULL) {
#Basic validation
assertthat::assert_that(assertthat::is.string(name))
......@@ -416,7 +449,13 @@ new_prj_process <- function(name,
porosity,
deactivate_matrix_in_flow,
output_element_matrices,
reference_temperature)
reference_temperature,
simplified_elasticity,
chemically_induced_porosity_change,
use_server_communication,
tabular_file,
temperature_field,
use_stokes_brinkman_form)
are_null_or_numbers(dimension,
......@@ -437,7 +476,8 @@ new_prj_process <- function(name,
at_num,
split_method,
reg_param,
pf_irrv)
pf_irrv,
irreversible_threshold)
if(!is.null(mass_lumping)){
mass_lumping <- stringr::str_remove_all(mass_lumping, "[:space:]*")
......@@ -521,6 +561,15 @@ new_prj_process <- function(name,
micro_porosity = micro_porosity,
explicit_hm_coupling_in_unsaturated_zone =
explicit_hm_coupling_in_unsaturated_zone,
simplified_elasticity = simplified_elasticity,
chemically_induced_porosity_change =
chemically_induced_porosity_change,
use_server_communication = use_server_communication,
phasefield_model = phasefield_model,
irreversible_threshold = irreversible_threshold,
tabular_file = tabular_file,
temperature_field = temperature_field,
use_stokes_brinkman_form = use_stokes_brinkman_form,
xpath = "processes/process",
attr_names = c("secondary_variable"),
flatten_on_exp = c("specific_body_force"),
......@@ -985,7 +1034,7 @@ new_prj_jacobian_assembler <- function(type,
prj_phasefield_parameters <- function(residual_stiffness,
crack_resistance,
crack_length_scale,
kinetic_coefficient,
kinetic_coefficient = NULL,
history_field = NULL) {
# Add coercing utility here
......@@ -1001,15 +1050,15 @@ prj_phasefield_parameters <- function(residual_stiffness,
new_prj_phasefield_parameters <- function(residual_stiffness,
crack_resistance,
crack_length_scale,
kinetic_coefficient,
kinetic_coefficient = NULL,
history_field = NULL) {
are_strings(residual_stiffness,
crack_resistance,
crack_length_scale,
kinetic_coefficient)
crack_length_scale)
are_null_or_strings(history_field)
are_null_or_strings(kinetic_coefficient,
history_field)
structure(list(residual_stiffness = residual_stiffness,
crack_resistance = crack_resistance,
......@@ -1094,6 +1143,7 @@ validate_process_variables <- function(process_variables){
"gas_pressure",
"capillary_pressure",
"liquid_pressure",
"liquid_velocity",
"overall_mass_density")
for(i in seq_len(length(process_variables))){
......
R/prj_time_loop.R
+ 8
− 3
View file @ 63fda142
......@@ -141,6 +141,7 @@ new_prj_tl_process <- function(ref,
#' @param output_iteration_results Optional: string: Either "true" or "false"
#' @param meshes Optional: character: A vector of mesh names
#' @param fixed_output_times Optional: string | numeric:
#' @param hdf Optional: numeric
#' @example man/examples/ex_prj_output.R
#' @export
prj_output <- function(type,
......@@ -152,7 +153,8 @@ prj_output <- function(type,
data_mode = NULL,
output_iteration_results = NULL,
meshes = NULL,
fixed_output_times = NULL) {
fixed_output_times = NULL,
hdf = NULL) {
#Coerce input
fixed_output_times <- coerce_string_to_numeric(fixed_output_times)
......@@ -170,7 +172,8 @@ prj_output <- function(type,
data_mode,
output_iteration_results,
meshes,
fixed_output_times)
fixed_output_times,
hdf)
}
......@@ -183,7 +186,8 @@ new_prj_output <- function(type,
data_mode = NULL,
output_iteration_results = NULL,
meshes = NULL,
fixed_output_times = NULL) {
fixed_output_times = NULL,
hdf = NULL) {
assertthat::assert_that(assertthat::is.string(type))
assertthat::assert_that(assertthat::is.string(prefix))
......@@ -218,6 +222,7 @@ new_prj_output <- function(type,
output_iteration_results = output_iteration_results,
meshes = meshes,
fixed_output_times = fixed_output_times,
hdf = hdf,
xpath = "time_loop/output",
attr_names = character(),
flatten_on_exp = c("fixed_output_times")
......
R/sim_utils.R
+ 1
− 1
View file @ 63fda142
......@@ -374,7 +374,7 @@ run_all_benchmarks <- function(path,
# Filter nonexisting files from prj_paths
nonexisting_prj_paths <- prj_paths[!file.exists(prj_paths)]
nonexisting_prj_paths <- prj_paths[!file.exists(unlist(prj_paths))]
prj_paths <- prj_paths[!prj_paths %in% nonexisting_prj_paths]
......
data/xpaths_for_classes.rda
+ 0
− 0
View file @ 63fda142
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