diff --git a/.gitignore b/.gitignore
index df2d07740829d355a6fc57d6e09e60e1586a6472..cf10005fdb8f40c7826b536e5ba6ea690bcf62bd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,7 +6,6 @@ config.yml
packrat/lib*/
inst/doc
inst/extdata/test_tempdirs
-doc
Meta
tmp
packrat/src/
diff --git a/doc/protocol_update_v6.4.1_Benchmarks.R b/doc/protocol_update_v6.4.1_Benchmarks.R
new file mode 100644
index 0000000000000000000000000000000000000000..654bc032bb83111cd2313ca116efce87dacad483
--- /dev/null
+++ b/doc/protocol_update_v6.4.1_Benchmarks.R
@@ -0,0 +1,318 @@
+
+library(dplyr)
+devtools::load_all(".") # load current r2ogs6 version
+
+# level1 ------------------------------------------------------------------
+# Both the old and new BM folders are supposed to be stored in the directory
+# above the current wd
+
+old <- analyse_xml(path = "../ogs-6.4.0-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "*",
+ print_findings = TRUE)
+
+new <- analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "*",
+ print_findings = TRUE)
+
+ind <- names(new$both_sorted) %in% names(old$both_sorted)
+names(new$both_sorted)[!ind] # new keyword!
+lvl1 <- analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//chemical_system/exchangers",
+ print_findings = TRUE)
+# actually, this was included as a new subclass of "chemical_system" later
+# level2 ------------------------------------------------------------------
+
+keywords_lvl1 <- names(old$both_sorted)
+change_df <- tibble::tibble(parent = character(), child = character(), new = logical())
+
+# walk over every old level1 keyword and check which child elements are found for
+# old and new benchmarks (v6.4.0 and v6.4.1)
+for (i in seq_along(keywords_lvl1)) {
+ old <- analyse_xml(path = "../ogs-6.4.0-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = paste0("//", keywords_lvl1[i]),
+ print_findings = FALSE)$both_sorted %>% names
+
+ new <- analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = paste0("//", keywords_lvl1[i]),
+ print_findings = FALSE)$both_sorted %>% names
+
+ if (any(!new %in% old)) {
+ change_df <- rbind(change_df,
+ tibble::tibble(parent = keywords_lvl1[i],
+ child = new[!new %in% old],
+ new = TRUE))
+ cat("new child: ")
+ cat(new[!new %in% old])
+ cat("\nof keyword: ")
+ cat(keywords_lvl1[i])
+ cat("\n")
+ cat(rep("#", 10))
+ cat("\n")
+ }
+ if (any(!old %in% new)) {
+ change_df <- rbind(change_df,
+ tibble::tibble(parent = keywords_lvl1[i],
+ child = old[!old %in% new],
+ new = FALSE))
+ cat("\n\n old child (not in new)\n")
+ cat(old[!old %in% new])
+ cat("\n of keyword: ")
+ cat(keywords_lvl1[i])
+ cat("\n")
+ cat(rep("#", 10))
+ cat("\n")
+ }
+}
+save(change_df, file = "tmp/update6.4.1_summary.rda")
+#load("update6.4.1_summary.rda")
+print(change_df, n = 26)
+
+
+# work through list -------------------------------------------------------
+# insert every keyword/child into analyse_xml, look at xml files and implement
+# changes in r2ogs6. At best, test if bm is read in correctly
+lvl2_hdf <- analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//time_loop/output/hdf",
+ print_findings = TRUE)
+# inserted as argument in prj_time_loop.R
+test <- OGS6$new("test", sim_path = "tmp")
+read_in_prj(test, "../ogs-6.4.1-Tests-Data/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3_2files.prj")
+test$time_loop$output$hdf
+
+analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//parameter/range",
+ print_findings = TRUE)
+analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//parameter/seed",
+ print_findings = TRUE)
+# inserted in prj_parameter.R
+test <- OGS6$new("test", sim_path = "tmp")
+read_in_prj(test, "../ogs-6.4.1-Tests-Data/Tests/Data/HydroMechanics/OrthotropicEmbeddedFracturePermeability/disc_with_hole_quasiisotropic.prj")
+test$parameters[[1]]$range
+test$parameters[[1]]$seed
+
+
+lvl2_process <- analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//OpenGeoSysProject/processes/process",
+ print_findings = TRUE)
+# simlified_elasticity
+analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//OpenGeoSysProject/processes/process/simplified_elasticity",
+ print_findings = TRUE)
+
+# test:
+test <- OGS6$new("test", sim_path = "tmp")
+read_in_prj(test, "../ogs-6.4.1-Tests-Data/Tests/Data/ThermoRichardsFlow/SimplifiedMechanics/TRhyd_saturated.prj")
+test$processes[[1]]$simplified_elasticity
+# check!
+
+# chemically_induced_porosity_change
+analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//OpenGeoSysProject/processes/process/chemically_induced_porosity_change",
+ print_findings = TRUE)
+
+analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//chemical_system/linear_solver",
+ print_findings = TRUE)
+# added liner solver in prj_chemical_system.R
+
+# test:
+test <- OGS6$new("test", sim_path = "tmp")
+read_in_prj(test, "../ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/EquilibriumPhase/calcitePorosityChange.prj")
+read_in_prj(test, "../ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/CationExchange/exchange.prj")
+test$chemical_system$linear_solver
+test$processes[[1]]$chemically_induced_porosity_change
+
+chem_ex <- analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//chemical_system/exchangers",
+ print_findings = TRUE)
+generate_constructor(chem_ex, print_result = TRUE)
+generate_helper(chem_ex, print_result = TRUE)
+#added prj_exchange class
+# run script in data-raw
+# devtools::document()
+xpaths_for_classes[["prj_exchangers"]]
+xpaths_for_classes[["prj_solution"]]
+
+analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//process/use_server_communication",
+ print_findings = TRUE)
+read_in_prj(test, "../ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/T/3D_3BHEs_array_SimX/3bhes_1U.prj")
+read_in_prj(test, "../ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/T/3D_Beier_sandbox_SimX/beier_sandbox.prj")
+# added argument to prj_process.R
+
+print(change_df, n = 26)
+analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//process/phasefield_model",
+ print_findings = TRUE)
+
+test <- OGS6$new("test", sim_path = "tmp")
+read_in_prj(test, "../ogs-6.4.1-Tests-Data/Tests/Data/PhaseField/beam/AT1_iso_tensile.prj")
+test$processes[[1]]$phasefield_model
+
+analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//process/irreversible_threshold",
+ print_findings = TRUE)
+test$processes[[1]]$irreversible_threshold
+# added as argument
+
+analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//process/tabular_file",
+ print_findings = TRUE)
+test <- OGS6$new("test", sim_path = "tmp")
+read_in_prj(test, "../ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/LookupTable/RadionuclideSorption.prj")
+test$processes[[1]]$tabular_file
+
+
+analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//process/temperature_field",
+ print_findings = TRUE)
+test <- OGS6$new("test", sim_path = "tmp")
+read_in_prj(test, "../ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/ComponentTransport/ThermalDiffusion/TemperatureField_transport.prj")
+test$media[[1]]$phases$phase$components[[1]]$properties[[1]]$reference_temperature
+test$media[[1]]$phases$phase$components[[1]]$properties[[1]]$activation_energy
+
+analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//process/use_stokes_brinkman_form",
+ print_findings = TRUE)
+test <- OGS6$new("test", sim_path = "tmp")
+read_in_prj(test, "../ogs-6.4.1-Tests-Data/Tests/Data/StokesFlow/2DPlanarPermeableFracture/2DPlanarPermeableFracture.prj")
+test$processes[[1]]$use_stokes_brinkman_form
+# added as argument
+
+analyse_xml(path = "../ogs-6.4.1-Tests-Data",
+ pattern = "\\.prj$",
+ xpath = "//value/expression",
+ print_findings = TRUE)
+test <- OGS6$new("test", sim_path = "tmp")
+read_in_prj(test, "../ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/ComponentTransport/SimpleSynthetics/DiffusionAndStorageAndAdvection.prj")
+test$media[[1]]$phases$phase$properties$property$value
+
+
+# run benchmarks ----------------------------------------------------------
+options("r2ogs6.default_ogs6_bin_path" = "/usr/local/bin/ogs6.4.1.sif")
+options("r2ogs6.default_ogs6_processlib_path" = "../ogs-6.4.1-ProcessLib/ProcessLib")
+
+run_all_benchmarks("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/",
+ sim_path = "tmp/"
+ )
+
+
+# debug errors from benchmarks --------------------------------------------
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/T/t1_1Dsource/t1_1Dsource.prj",
+ sim_path = "tmp")
+# some benchmarks with *. mesh instead of vtu
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/HydroMechanics/OrthotropicEmbeddedFracturePermeability/x_strain_y_flow.prj",
+ sim_path = "tmp")
+validate_read_in_xml("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/HydroMechanics/OrthotropicEmbeddedFracturePermeability/x_strain_y_flow.prj")
+
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Elliptic/cube_1x1x1_SteadyStateDiffusion/cube_1e0.xml",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Elliptic/cube_1x1x1_SteadyStateDiffusion/cube_1e0.prj",
+ sim_path = "tmp")
+# wrong file ending *.xml from Tests.cmake (fixed)
+
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/TH2M/TH_unsaturated/heatpipe_radial_static_gas/heatpipe_radial_static_gas.prj",
+ sim_path = "tmp/")
+# triple_temperature
+# triple_pressure
+# critical_temperature
+# critical_pressure
+# reference_pressure
+
+## all inserted as arguments
+
+file.exists(
+"/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Elliptic/line_1_SteadyStateDiffusion/line_1e0.prj",
+"/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Elliptic/line_1_SteadyStateDiffusion/line_1e0_neumann.prj",
+"/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Elliptic/line_1_SteadyStateDiffusion/line_1e0_robin_right_picard.prj",
+"/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Elliptic/line_1_SteadyStateDiffusion/line_1e0_robin_left_picard.prj",
+"/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Elliptic/line_1_SteadyStateDiffusion/line_1e0_time_dep_dirichlet.prj",
+"/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Elliptic/line_1_SteadyStateDiffusion/line_1e0_time_dep_neumann.prj"
+) # k then
+
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/T/t1_1Dsource/t1_1Dsource.prj",
+ sim_path = "tmp")
+
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/T/t1_1Dsteady/t1_1Dsteady.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/T/t2_1D1bt/t2_1D1bt.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/T/t2_1D2bt/t2_1D2bt.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/HydroMechanics/OrthotropicEmbeddedFracturePermeability/x_strain_y_flow.prj",
+ sim_path = "tmp")
+
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/HydroMechanics/OrthotropicEmbeddedFracturePermeability/y_strain_z_flow.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/HydroMechanics/OrthotropicEmbeddedFracturePermeability/z_strain_x_flow.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/HydroMechanics/OrthotropicEmbeddedFracturePermeability/disc_with_hole_anisotropic.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/HydroMechanics/OrthotropicEmbeddedFracturePermeability/disc_with_hole_anisotropic_rotated.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/HydroMechanics/OrthotropicEmbeddedFracturePermeability/disc_with_hole_quasiisotropic.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/LiquidFlow/Verification/h1_1Dsource/h1_1Dsource.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/LiquidFlow/Verification/h1_1Dsteady/h1_1Dsteady.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/LiquidFlow/Verification/h1_3Dhydstat/h1_3Dhydstat.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/LiquidFlow/Verification/h2_1D1bt/h2_1D1bt.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/LiquidFlow/Verification/h2_1D2bt/h2_1D2bt.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Elliptic/cube_1x1x1_SteadyStateDiffusion/cube_1e0.xml",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/EllipticPETSc/quad_20x10_GroundWaterFlow.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/TES/1D/tes-1D-zeolite-discharge-small.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/TES/1D/tes-1D-zeolite-discharge-large.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/Parabolic/TES/1D/tes-1D-zeolite-discharge-small-newton.prj",
+ sim_path = "tmp")
+
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/TH2M/THM/slab/THM_1d_dirichlet.prj",
+ sim_path = "tmp")
+# source terms field of prj file is empty
+
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/TH2M/THM/slab/THM_1d_dirichlet_newton.xml",
+ sim_path = "tmp")
+
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/TH2M/TH_unsaturated/heatpipe_radial_static_gas/heatpipe_radial_static_gas.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/TH2M/TH_unsaturated/heatpipe_slab_static_gas/heatpipe_slab_static_gas.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/TH2M/TH2/heatpipe_radial/heatpipe_radial.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/TH2M/TH2/heatpipe_slab/heatpipe_slab.prj",
+ sim_path = "tmp")
+run_benchmark("/home/phit0/Public/ogs-6.4.1-Tests-Data/Tests/Data/ThermoRichardsFlow/SimplifiedMechanics/TaskCDECOVALEX2023/Decovalex-0-TRF.prj",
+ sim_path = "tmp")
+
+
+
+
+
+