[doc] add protocol for update to support ogs642

doc/protocol_update_v6.4.2_Benchmarks.R

+packrat::packrat_mode(on=T)
+library(dplyr)
+devtools::load_all(".") # load current r2ogs6 version
+
+temppath <- "tmp/update_v6.4.2"
+
+# top level tags -----------------------------------------------------------
+# Both the old and new BM folders are supposed to be stored in the directory
+# now check for new top level tags
+old <- analyse_xml(path = paste0(temppath,"/Data_641"),
+                   pattern = "\\.prj$",
+                   xpath = "*",
+                   print_findings = TRUE)
+
+new <- analyse_xml(path = paste0(temppath,"/Data_642"),
+                    pattern = "\\.prj$",
+                    xpath = "*",
+                    print_findings = TRUE)
+
+ind <- names(new$both_sorted) %in% names(old$both_sorted)
+names(new$both_sorted)[!ind]
+# there are no new top-level tag, however, the include tag now appears at
+# top level with file as attribute
+# !!! A function to handle top-level includes have been introduced and tested
+
+
+# top-level/child tags-------------------------------------------------------
+keywords_lvl1 <- names(old$both_sorted)
+change_df <- tibble::tibble(parent = character(), child = character(), new = logical())
+
+# walk over every old level1 tag and check which child elements are found for
+# old and new benchmarks (v6.4.1 and v6.4.2)
+for (i in seq_along(keywords_lvl1)) {
+    old <- analyse_xml(path = paste0(temppath,"/Data_641"),
+                        pattern = "\\.prj$",
+                        xpath = paste0("//", keywords_lvl1[i]),
+                        print_findings = FALSE)$both_sorted %>% names
+
+    new <- analyse_xml(path = paste0(temppath,"/Data_642"),
+                         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 tag: ")
+        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 tag: ")
+        cat(keywords_lvl1[i])
+        cat("\n")
+        cat(rep("#", 10))
+        cat("\n")
+    }
+    rm(old, new)
+}
+# new child: compensate_non_equilibrium_initial_residuum
+# of tag: process_variable
+# # # # # # # # # # #
+# new child: energy_split_model softening_curve characteristic_length
+# coupling_scheme_parameter
+# of tag: process
+# # # # # # # # # # #
+#
+#
+# old child (not in new)
+# compensate_non_equilibrium_initial_residuum density_solid
+# latent_heat_evaporation
+# of tag: process
+# # # # # # # # # # #
+# new child: fixing_pe
+# of tag: solution
+# # # # # # # # # # #
+# new child: site_unit
+# of tag: surface
+# # # # # # # # # # #
+
+save(change_df, file = "tmp/update6.4.1_summary.rda")
+#load("update6.4.1_summary.rda")
+#print(change_df, n = 26)
+
+
+# work through list tag ----------------------------------------------------
+# insert every tag/child into analyse_xml, look at xml files and implement
+# changes in r2ogs6. At best, test if bm is read in correctly
+
+# of tag: process_variable -------------------------------------------------
+# new child: compensate_non_equilibrium_initial_residuum
+lvl2_process_var <- analyse_xml(path = paste0(temppath,"/Data_642"),
+            pattern = "\\.prj$",
+            xpath = "//OpenGeoSysProject/process_variables/process_variable",
+            print_findings = TRUE)
+
+analyse_xml(path = paste0(temppath,"/Data_642"),
+            pattern = "\\.prj$",
+            xpath = paste("//OpenGeoSysProject/process_variables/",
+                          "process_variable/",
+                          "compensate_non_equilibrium_initial_residuum"),
+            print_findings = TRUE)
+# child element was added to class prj_process_variable
+
+# test
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- "ThermoRichardsMechanics/TaskCDECOVALEX2023/Decovalex-0.prj"
+read_in_prj(test, paste0(temppath,"/Data_642/", bm))
+test$process_variables$displacement$compensate_non_equilibrium_initial_residuum
+# read of tag works!
+dir_make_overwrite(test$sim_path)
+run_benchmark(prj_path = paste0(temppath,"/Data_642/", bm),
+              sim_path = test$sim_path)
+# execution of bm returned zero exit status!
+
+# of tag: process -----------------------------------------------------
+# new child: energy_split_model
+lvl2_process <- analyse_xml(path = paste0(temppath,"/Data_642"),
+            pattern = "\\.prj$",
+            xpath = "//OpenGeoSysProject/processes/process",
+            print_findings = TRUE)
+
+analyse_xml(path = paste0(temppath,"/Data_642"),
+            pattern = "\\.prj$",
+            xpath = "//OpenGeoSysProject/processes/process/energy_split_model",
+            print_findings = TRUE)
+# child element was added to class prj_process
+# test
+rm(test)
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- "PhaseField/beam/AT1_iso_tensile.prj"
+read_in_prj(test, paste0(temppath,"/Data_642/", bm))
+test$processes$PhaseField$energy_split_model
+# read of tag works!
+dir_make_overwrite(test$sim_path)
+run_benchmark(prj_path = paste0(temppath,"/Data_642/", bm),
+              sim_path = test$sim_path)
+# bm does fail. OGS error message:
+# critical: /usr/local/ogs/src/MathLib/LinAlg/Eigen/
+# LinearSolverOptionsParser.h:49 parseNameAndOptions()
+# error: OGS was compiled with Eigen but the config section in the project file
+# seems to be invalid
+# This is an error in the ogs-singularity version and will not be handled here
+
+
+# child: softening_curve
+# of tag: process
+analyse_xml(path = paste0(temppath,"/Data_642"),
+            pattern = "\\.prj$",
+            xpath = "//OpenGeoSysProject/processes/process/softening_curve",
+            print_findings = TRUE)
+# child element was added to class prj_process
+# test
+rm(test)
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- "PhaseField/beam/bar_COHESIVE_exponential.prj"
+read_in_prj(test, paste0(temppath,"/Data_642/", bm))
+test$processes$PhaseField$softening_curve
+# read of tag works!
+dir_make_overwrite(test$sim_path)
+run_benchmark(prj_path = paste0(temppath,"/Data_642/", bm),
+              sim_path = test$sim_path)
+# bm does fail. OGS error message:
+# critical: /usr/local/ogs/src/MathLib/LinAlg/Eigen/
+# LinearSolverOptionsParser.h:49 parseNameAndOptions()
+# error: OGS was compiled with Eigen but the config section in the project file
+# seems to be invalid
+# This is an error in the ogs-singularity version and will not be handled here
+
+
+
+# child: characteristic_length
+# of tag: process
+analyse_xml(path = paste0(temppath,"/Data_642"),
+        pattern = "\\.prj$",
+        xpath = "//OpenGeoSysProject/processes/process/characteristic_length",
+        print_findings = TRUE)
+# child element was added to class prj_process
+# test
+rm(test)
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- "PhaseField/beam/bar_COHESIVE_exponential.prj"
+read_in_prj(test, paste0(temppath,"/Data_642/", bm))
+test$processes$PhaseField$characteristic_length
+# read of tag works!
+dir_make_overwrite(test$sim_path)
+run_benchmark(prj_path = paste0(temppath,"/Data_642/", bm),
+              sim_path = test$sim_path)
+# bm does fail. OGS error message:
+# critical: /usr/local/ogs/src/MathLib/LinAlg/Eigen/
+# LinearSolverOptionsParser.h:49 parseNameAndOptions()
+# error: OGS was compiled with Eigen but the config section in the project file
+# seems to be invalid
+# This is an error in the ogs-singularity version and will not be handled here
+
+
+#: child coupling_scheme_parameter
+# of tag: process
+analyse_xml(path = paste0(temppath,"/Data_642"),
+    pattern = "\\.prj$",
+    xpath = "//OpenGeoSysProject/processes/process/coupling_scheme_parameter",
+    print_findings = TRUE)
+# child element was added to class prj_process
+# test
+rm(test)
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- "HydroMechanics/StaggeredScheme/MandelCryer/MandelCryerStaggered.prj"
+read_in_prj(test, paste0(temppath,"/Data_642/", bm))
+test$processes$MandelCryer$coupling_scheme_parameter
+# read of tag works!
+dir_make_overwrite(test$sim_path)
+run_benchmark(prj_path = paste0(temppath,"/Data_642/", bm),
+              sim_path = test$sim_path)
+
+
+# old child (not in new)
+# compensate_non_equilibrium_initial_residuum
+# density_solid
+# latent_heat_evaporation
+# of tag: process
+analyse_xml(path = paste0(temppath,"/Data_642"),
+    pattern = "\\.prj$",
+    xpath = "//OpenGeoSysProject/processes/process/latent_heat_evaporation",
+    print_findings = TRUE)
+
+
+# of tag: chemical system/solution---------------------------------------------
+# new child: fixing_pe
+analyse_xml(path = paste0(temppath,"/Data_642"),
+            pattern = "\\.prj$",
+            xpath = "//chemical_system/solution",
+            print_findings = TRUE)
+# test
+rm(test)
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- "Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/RadionuclideSorption_fixed_pe.prj"
+read_in_prj(test, paste0(temppath,"/Data_642/", bm))
+test$chemical_system$solution$fixing_pe
+# read of tag works!
+dir_make_overwrite(test$sim_path)
+run_benchmark(prj_path = paste0(temppath,"/Data_642/", bm),
+              sim_path = test$sim_path)
+
+
+# new child: site_unit
+chem_srf <- analyse_xml(path = paste0(temppath,"/Data_642"),
+            pattern = "\\.prj$",
+            xpath = "//chemical_system/surface",
+            print_findings = TRUE)
+# !!! Need to create class for surface tag
+generate_constructor(chem_srf, print_result = TRUE)
+generate_helper(chem_srf, print_result = TRUE)
+# execute data_raw/xpaths_for_classes.R
+xpaths_for_classes[["prj_surface"]]
+# class created
+# test
+rm(test)
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- "Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/RadionuclideSorption_fixed_pe.prj"
+read_in_prj(test, paste0(temppath,"/Data_642/", bm))
+test$chemical_system$surface
+run_benchmark(prj_path = paste0(temppath,"/Data_642/", bm),
+              sim_path = test$sim_path)
+# works!
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