[doc] update keywords log to ogs 6.4.4

doc/protocol_update_v6.4.4_keywords.R

+# !!!!! READ the developer guide before updateing r2ogs6 !!!!!!
+# https://gitlab.opengeosys.org/ogs/tools/r2ogs6/-/blob/master/vignettes/dev_workflow_vignette.Rmd
+library(dplyr)
+devtools::load_all(".") # load current r2ogs6 version
+
+temppath <- "tmp/update_v6.4.4"
+
+
+# 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_643"),
+                   pattern = "\\.prj$",
+                   xpath = "*",
+                   print_findings = TRUE)
+
+new <- analyse_xml(path = paste0(temppath,"/Data_644"),
+                    pattern = "\\.prj$",
+                    xpath = "*",
+                    print_findings = TRUE)
+
+ind <- names(new$both_sorted) %in% names(old$both_sorted)
+names(new$both_sorted)[!ind]
+# output: "submesh_residuum_output"
+# there are no new top-level tag
+
+# "submesh_residuum_output" is child tags of
+# time_loop
+
+
+
+# top-level/child tags-------------------------------------------------------
+keywords_lvl1 <- names(new$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 (v6.4.3 and v6.4.4)
+for (i in seq_along(keywords_lvl1)) {
+    old <- analyse_xml(path = paste0(temppath,"/Data_643"),
+                        pattern = "\\.prj$",
+                        xpath = paste0("//", keywords_lvl1[i]),
+                        print_findings = FALSE)$both_sorted %>% names
+
+    new <- analyse_xml(path = paste0(temppath,"/Data_644"),
+                         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: geometrical_sets
+# of tag: output
+# # # # # # # # # # #
+# new child: linear pressurized_crack_scheme subtype apply_body_force_for_deformation
+# of tag: process
+# # # # # # # # # # #
+# new child: type timesteps variables meshes prefix suffix
+# of tag: submesh_residuum_output
+# # # # # # # # # # #
+save(change_df, file = "tmp/update6.4.4_summary.rda")
+print(change_df)
+
+# > print(change_df)
+# # A tibble: 11 × 3
+#    parent                  child                            new
+#    <chr>                   <chr>                            <lgl>
+#  1 output                  geometrical_sets                 TRUE
+#  2 process                 linear                           TRUE
+#  3 process                 pressurized_crack_scheme         TRUE
+#  4 process                 subtype                          TRUE
+#  5 process                 apply_body_force_for_deformation TRUE
+#  6 submesh_residuum_output type                             TRUE
+#  7 submesh_residuum_output timesteps                        TRUE
+#  8 submesh_residuum_output variables                        TRUE
+#  9 submesh_residuum_output meshes                           TRUE
+# 10 submesh_residuum_output prefix                           TRUE
+# 11 submesh_residuum_output suffix                           TRUE
+
+
+# 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 -----------------------------------------------------
+lvl2_process <- analyse_xml(path = paste0(temppath,"/Data_644"),
+            pattern = "\\.prj$",
+            xpath = "//OpenGeoSysProject/processes/process",
+            print_findings = TRUE)
+
+# new child: linear
+analyse_xml(path = paste0(temppath,"/Data_644"),
+            pattern = "\\.prj$",
+            xpath = paste0("//OpenGeoSysProject/processes/process/",
+                           "linear"),
+            print_findings = TRUE)
+
+# child element was added to class prj_process
+# test
+rm(test)
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- paste0("Parabolic/LiquidFlow/SimpleSynthetics/PrimaryVariableConstraintDirichletBC/cuboid_1x1x1_hex_1000_Dirichlet_Dirichlet_1.prj")
+read_in_prj(test, paste0(temppath,"/Data_644/", bm))
+test$processes$LiquidFlow$linear
+# read of tag works!
+dir_make_overwrite(test$sim_path)
+run_benchmark(prj_path = paste0(temppath,"/Data_644/", bm),
+              sim_path = test$sim_path)
+# bm works!
+
+
+# new child: pressurized_crack_scheme
+analyse_xml(path = paste0(temppath,"/Data_644"),
+            pattern = "\\.prj$",
+            xpath = paste0("//OpenGeoSysProject/processes/process/",
+                           "pressurized_crack_scheme"),
+            print_findings = TRUE)
+
+# child element was added to class prj_process
+# test
+rm(test)
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- paste0("PhaseField/k_regime_HF/2D_bm_0p01.prj")
+read_in_prj(test, paste0(temppath,"/Data_644/", bm))
+test$processes$PhaseField$pressurized_crack_scheme
+# read of tag works!
+dir_make_overwrite(test$sim_path)
+run_benchmark(prj_path = paste0(temppath,"/Data_644/", bm),
+              sim_path = test$sim_path)
+# bm does not work due to problems with petsc solver on my machine
+
+
+# new child: subtype
+analyse_xml(path = paste0(temppath,"/Data_644"),
+            pattern = "\\.prj$",
+            xpath = paste0("//OpenGeoSysProject/processes/process/",
+                           "subtype"),
+            print_findings = TRUE)
+
+# child element was added to class prj_process
+# test
+rm(test)
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- paste0("ThermoRichardsMechanics/LinearMechanics/mechanics_linear.prj")
+read_in_prj(test, paste0(temppath,"/Data_644/", bm))
+test$processes$RM$subtype
+# read of tag works!
+dir_make_overwrite(test$sim_path)
+run_benchmark(prj_path = paste0(temppath,"/Data_644/", bm),
+              sim_path = test$sim_path)
+# bm works
+
+
+# new child: apply_body_force_for_deformation
+analyse_xml(path = paste0(temppath,"/Data_644"),
+            pattern = "\\.prj$",
+            xpath = paste0("//OpenGeoSysProject/processes/process/",
+                           "apply_body_force_for_deformation"),
+            print_findings = TRUE)
+
+# child element was added to class prj_process
+# test
+rm(test)
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- paste0("ThermoRichardsMechanics/BodyForce/square.prj")
+read_in_prj(test, paste0(temppath,"/Data_644/", bm))
+test$processes$BodyForceTest$apply_body_force_for_deformation
+# read of tag works!
+dir_make_overwrite(test$sim_path)
+run_benchmark(prj_path = paste0(temppath,"/Data_644/", bm),
+              sim_path = test$sim_path)
+# bm works
+
+
+# of tag: output -----------------------------------------------------
+lvl2_output <- analyse_xml(path = paste0(temppath,"/Data_644"),
+            pattern = "\\.prj$",
+            xpath = "//OpenGeoSysProject/time_loop/output",
+            print_findings = TRUE)
+
+# new child: apply_body_force_for_deformation
+analyse_xml(path = paste0(temppath,"/Data_644"),
+            pattern = "\\.prj$",
+            xpath = paste0("//OpenGeoSysProject/time_loop/output/",
+                           "geometrical_sets"),
+            print_findings = TRUE)
+# generate constructure
+geometrical_set_res <- analyse_xml(path = paste0(temppath,"/Data_644"),
+            pattern = "\\.prj$",
+            xpath = paste0("//OpenGeoSysProject/time_loop/output/",
+                           "geometrical_sets/geometrical_set"),
+            print_findings = TRUE)
+generate_constructor(params = geometrical_set_res,
+                     print_result = TRUE)
+
+generate_helper(params = geometrical_set_res,
+                print_result = TRUE)
+
+# child element was added to class prj_geometrical_set
+
+# test
+rm(test)
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- paste0("Elliptic/cube_1x1x1_SteadyStateDiffusion/cube_1e0_processed.prj")
+read_in_prj(test, paste0(temppath,"/Data_644/", bm))
+test$time_loop$output$geometrical_sets %>% length()
+# read of tag works!
+dir_make_overwrite(test$sim_path)
+run_benchmark(prj_path = paste0(temppath,"/Data_644/", bm),
+              sim_path = test$sim_path)
+# bm works
+
+
+# of tag: time_loop -----------------------------------------------------
+lvl2_submesh_residuum_output <- analyse_xml(
+                            path = paste0(temppath,"/Data_644"),
+                           pattern = "\\.prj$",
+                           xpath = "//OpenGeoSysProject/time_loop/submesh_residuum_output",
+                           print_findings = TRUE)
+
+# submesh_residuum_output is very similar to time_loop/output
+# https://doxygen.opengeosys.org/v6.4.4/d1/d94/ogs_file_param__prj__time_loop__submesh_residuum_output.html
+# thats why prj_submesh_residuum_output was set up similar to prj_output
+
+# test
+rm(test)
+test <- OGS6$new("test", sim_path = paste0(temppath, "/test"))
+bm <- paste0("ThermoRichardsMechanics/PointHeatSource/point_heat_source_2D.prj")
+read_in_prj(test, paste0(temppath,"/Data_644/", bm))
+test$time_loop$submesh_residuum_output
+# read of tag works!
+dir_make_overwrite(test$sim_path)
+run_benchmark(prj_path = paste0(temppath,"/Data_644/", bm),
+              sim_path = test$sim_path)
+# bm works
+
+
+# Now try to run all OGS v6.4.4 benchmarks!
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