fixing stuff and adding comments

CMake/FindRRuntime.cmake

@@ -1,3 +1,4 @@
+## Time-stamp: "Last modified 2024-06-13 10:25:44 delucia"
 # prepare R environment (Rcpp + RInside)
 find_program(R_EXE "R")
 

CMake/POET_Scripts.cmake

@@ -13,7 +13,7 @@ macro(get_POET_version)
       WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
       OUTPUT_VARIABLE POET_GIT_VERSION
       OUTPUT_STRIP_TRAILING_WHITESPACE)
-    if(NOT POET_GIT_BRANCH STREQUAL "master")
+    if(NOT POET_GIT_BRANCH STREQUAL "main")
       set(POET_VERSION "${POET_GIT_BRANCH}/${POET_GIT_VERSION}")
     else()
       set(POET_VERSION "${POET_GIT_VERSION}")
@@ -21,7 +21,7 @@ macro(get_POET_version)
   elseif(EXISTS ${PROJECT_SOURCE_DIR}/.svn)
     file(STRINGS .gitversion POET_VERSION)
   else()
-    set(POET_VERSION "0.1")
+    set(POET_VERSION "not_versioned")
   endif()
 
   message(STATUS "Configuring POET version ${POET_VERSION}")

CMakeLists.txt

@@ -41,4 +41,4 @@ endif()
 
 option(BUILD_DOC "Build documentation with doxygen" OFF)
 
-add_subdirectory(docs)
+add_subdirectory(docs)

R_lib/init_r_lib.R

@@ -1,15 +1,33 @@
-pqc_to_grid <- function(pqc_in, grid) {
+### Copyright (C) 2018-2024 Marco De Lucia, Max Luebke (GFZ Potsdam, University of Potsdam)
+###
+### POET is free software; you can redistribute it and/or modify it under the
+### terms of the GNU General Public License as published by the Free Software
+### Foundation; either version 2 of the License, or (at your option) any later
+### version.
+###
+### POET is distributed in the hope that it will be useful, but WITHOUT ANY
+### WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+### A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+###
+### You should have received a copy of the GNU General Public License along with
+### this program; if not, write to the Free Software Foundation, Inc., 51
+### Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+##' @param pqc_mat matrix, containing IDs and PHREEQC outputs 
+##' @param grid matrix, zonation referring to pqc_mat$ID 
+##' @return a data.frame
+pqc_to_grid <- function(pqc_mat, grid) {
     # Convert the input DataFrame to a matrix
-    pqc_in <- as.matrix(pqc_in)
+    pqc_mat <- as.matrix(pqc_mat)
 
     # Flatten the matrix into a vector
-    id_vector <- as.numeric(t(grid))
+    id_vector <- as.integer(t(grid))
 
     # Find the matching rows in the matrix
-    row_indices <- match(id_vector, pqc_in[, "ID"])
+    row_indices <- match(id_vector, pqc_mat[, "ID"])
 
-    # Extract the matching rows from pqc_in to size of grid matrix
-    result_mat <- pqc_in[row_indices, ]
+    # Extract the matching rows from pqc_mat to size of grid matrix
+    result_mat <- pqc_mat[row_indices, ]
 
     # Convert the result matrix to a data frame
     res_df <- as.data.frame(result_mat)
@@ -23,6 +41,12 @@ pqc_to_grid <- function(pqc_in, grid) {
     return(res_df)
 }
 
+
+##' @param pqc_mat matrix, 
+##' @param transport_spec column name of species in pqc_mat
+##' @param id
+##' @title 
+##' @return 
 resolve_pqc_bound <- function(pqc_mat, transport_spec, id) {
     df <- as.data.frame(pqc_mat, check.names = FALSE)
     value <- df[df$ID == id, transport_spec]
@@ -34,6 +58,10 @@ resolve_pqc_bound <- function(pqc_mat, transport_spec, id) {
     return(value)
 }
 
+##' @title 
+##' @param init_grid 
+##' @param new_names 
+##' @return 
 add_missing_transport_species <- function(init_grid, new_names) {
     # add 'ID' to new_names front, as it is not a transport species but required
     new_names <- c("ID", new_names)

R_lib/kin_r_library.R

@@ -1,5 +1,3 @@
-## Time-stamp: "Last modified 2024-06-11 14:26:33 delucia"
-
 ### Copyright (C) 2018-2023 Marco De Lucia, Max Luebke (GFZ Potsdam)
 ###
 ### POET is free software; you can redistribute it and/or modify it under the

src/Init/DiffusionInit.cpp

@@ -1,3 +1,6 @@
+//  Time-stamp: "Last modified 2024-06-13 11:30:34 delucia"
+
+
 #include <algorithm>
 #include <tug/Boundary.hpp>
 // leave above Rcpp includes, as eigen seem to have problems with a preceding
@@ -146,7 +149,7 @@ InitialList::resolveBoundaries(const Rcpp::List &boundaries_list,
         extend_initial_grid(this->initial_grid, this->transport_names);
   }
 
-  for (const auto &species : this->transport_names) {
+  for (const auto &species_name : this->transport_names) {
     Rcpp::List spec_list;
 
     for (const auto &side : tug_side_mapping) {
@@ -163,8 +166,8 @@ InitialList::resolveBoundaries(const Rcpp::List &boundaries_list,
       if (boundaries_list.containsElementNamed(side.second.c_str())) {
         const Rcpp::List mapping = boundaries_list[side.second];
 
-        const Rcpp::NumericVector cells = mapping["cell"];
-        const Rcpp::NumericVector values = mapping["sol_id"];
+        const Rcpp::IntegerVector cells  = mapping["cell"];   // MDL 2024-06-13 
+        const Rcpp::IntegerVector values = mapping["sol_id"]; // MDL 
         const Rcpp::CharacterVector type_str = mapping["type"];
 
         if (cells.size() != values.size()) {
@@ -180,7 +183,7 @@ InitialList::resolveBoundaries(const Rcpp::List &boundaries_list,
           } else if (type_str[i] == "constant") {
             c_type[c_id] = tug::BC_TYPE_CONSTANT;
             c_value[c_id] = Rcpp::as<TugType>(
-                resolve_R(this->phreeqc_mat, Rcpp::wrap(species), values[i]));
+                resolve_R(this->phreeqc_mat, Rcpp::wrap(species_name), values[i]));
           } else {
             throw std::runtime_error("Unknown boundary type");
           }
@@ -191,7 +194,7 @@ InitialList::resolveBoundaries(const Rcpp::List &boundaries_list,
           Rcpp::Named("type") = c_type, Rcpp::Named("value") = c_value);
     }
 
-    bound_list[species] = spec_list;
+    bound_list[species_name] = spec_list;
 
     if (inner_boundaries.size() > 0) {
       const Rcpp::NumericVector &inner_row_vec = inner_boundaries["row"];
@@ -212,10 +215,10 @@ InitialList::resolveBoundaries(const Rcpp::List &boundaries_list,
         rows.push_back(inner_row_vec[i] - 1);
         cols.push_back(inner_col_vec[i] - 1);
         c_value.push_back(Rcpp::as<TugType>(resolve_R(
-            this->phreeqc_mat, Rcpp::wrap(species), inner_pqc_id_vec[i])));
+            this->phreeqc_mat, Rcpp::wrap(species_name), inner_pqc_id_vec[i])));
       }
 
-      inner_bound[species] =
+      inner_bound[species_name] =
           Rcpp::List::create(Rcpp::Named("row") = Rcpp::wrap(rows),
                              Rcpp::Named("col") = Rcpp::wrap(cols),
                              Rcpp::Named("value") = Rcpp::wrap(c_value));
@@ -403,4 +406,4 @@ InitialList::DiffusionInit InitialList::getDiffusionInit() const {
   return diff_init;
 }
 
-} // namespace poet
+} // namespace poet