Add 'app' directory from golem branch

CMakeLists.txt

@@ -393,6 +393,7 @@ if (BUILD_CLR_LIBS)
 endif()
 
 add_subdirectory(poet)
+add_subdirectory(app)
 
 include (CTest)
 

app/CMakeLists.txt

@@ -0,0 +1,25 @@
+## Time-stamp: "Last modified 2024-08-26 17:42:18 delucia"
+
+add_executable(ipqMain 
+    ipqMain.cpp
+  )
+add_executable(ipqEngine 
+    ipqEngine.cpp
+  )
+
+# add_library(IPhreeqcPOET ${PQC_POET_SRC})
+##target_link_libraries(IPhreeqcPOET PUBLIC IPhreeqc)
+
+target_include_directories(IPhreeqcPOET PUBLIC
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+    $<INSTALL_INTERFACE:include>
+    PRIVATE src)
+
+
+target_link_libraries(ipqMain 
+    IPhreeqcPOET
+)
+
+target_link_libraries(ipqEngine 
+    IPhreeqcPOET
+)

app/ipqEngine.cpp

@@ -0,0 +1,122 @@
+#include <algorithm>
+#include <cstddef>
+#include <cstdio>
+#include <iomanip>
+#include <linux/limits.h>
+#include <stdlib.h>
+#include <string>
+#include <unistd.h>
+#include <vector>
+#include <wordexp.h>
+
+#include "POETInit.hpp"
+#include "PhreeqcEngine.hpp"
+#include "PhreeqcInit.hpp"
+
+static std::string readFile(const std::string &path) {
+  std::string string_rpath(PATH_MAX, '\0');
+
+  if (realpath(path.c_str(), string_rpath.data()) == nullptr) {
+    throw std::runtime_error("Failed to resolve the realpath to file " + path);
+  }
+
+  std::ifstream file(string_rpath);
+
+  if (!file.is_open()) {
+    throw std::runtime_error("Failed to open file: " + path);
+  }
+
+  std::stringstream buffer;
+  buffer << file.rdbuf();
+
+  return buffer.str();
+}
+
+void printVectorsAsTable(const std::vector<std::string> &names,
+                         const std::vector<double> &values) {
+  if (names.size() != values.size()) {
+    std::cerr << "Error: Vectors are not of the same length." << std::endl;
+    return;
+  }
+
+  std::cout << std::left << std::setw(20) << "Name" << std::setw(20) << "Value"
+            << std::endl;
+  std::cout << std::string(40, '-') << std::endl;
+
+  for (std::size_t i = 0; i < names.size(); ++i) {
+    std::cout << std::left << std::setw(20) << names[i] << std::setw(20)
+              << values[i] << std::endl;
+  }
+}
+
+template <class T> void printVector(const std::vector<T> &vec) {
+  for (const auto &elem : vec) {
+    std::cout << elem << " ";
+  }
+  std::cout << std::endl;
+}
+
+int main(int argc, char *argv[]) {
+
+  if (argc < 3) {
+    std::cout << "Two args needed, PHREEQC script and database" << std::endl;
+    return 1;
+  }
+
+  const std::string &script = argv[1];
+  const std::string &database = argv[2];
+  wordexp_t exp_result;
+
+  std::cout << "Reading script from file " << script << " using database "
+            << database << std::endl;
+
+  // expand the script and database path
+  const std::string read_script = readFile(script);
+  const std::string read_database = readFile(database);
+
+  // initialize the module instance "ipqcmod"
+  PhreeqcInit ipqcmod(read_database, read_script);
+
+  // allocate tabular data
+  PhreeqcInit::PhreeqcMat pqc_mat = ipqcmod.getPhreeqcMat();
+
+  // for (std::size_t i = 0; i < nrows; ++i) {
+  auto pure_names = ipqcmod.getEquilibriumNames(pqc_mat.ids[0]);
+  auto totals_names = ipqcmod.getSolutionNames(pqc_mat.ids[0]);
+
+  POETConfig MyConfig;
+  MyConfig.database = read_database;
+  MyConfig.input_script = read_script;
+  MyConfig.cell = POETInitCell{
+      // H, O and charge need to be removed. I'm not sure why I did it this way.
+      std::vector<std::string>(totals_names.begin() + 3, totals_names.end()),
+      {},
+      {},
+      {},
+      pure_names,
+      {},
+      {}};
+
+  std::vector<std::string> full_names = {"ID"};
+  full_names.insert(full_names.end(), pqc_mat.names.begin(),
+                    pqc_mat.names.end());
+
+  PhreeqcEngine MyEngine(MyConfig);
+  std::vector<double> NewInp = pqc_mat.values[0];
+  NewInp.insert(NewInp.begin(), 1);
+
+  std::cout << "Before running the cell:\n";
+  printVectorsAsTable(full_names, NewInp);
+
+  // std::for_each(NewInp.begin()+3, NewInp.end(),
+  //               [](double a) { return a * 0.8;});
+
+  NewInp[7] += 0.2; // Cl
+  NewInp[9] += 0.2; // Na
+  MyEngine.runCell(NewInp, 200);
+
+  std::cout << "\n\nAfter running the cell:\n";
+  printVectorsAsTable(full_names, NewInp);
+
+  return 0;
+}

app/ipqMain.cpp

@@ -0,0 +1,92 @@
+//  Time-stamp: "Last modified 2024-08-27 09:00:18 delucia"
+#include <cstddef>
+#include <linux/limits.h>
+#include <stdlib.h>
+#include <string>
+#include <unistd.h>
+#include <vector>
+#include <wordexp.h>
+
+#include "POETInit.hpp"
+#include "PhreeqcEngine.hpp"
+#include "PhreeqcInit.hpp"
+
+static std::string readFile(const std::string &path) {
+  std::string string_rpath(PATH_MAX, '\0');
+
+  if (realpath(path.c_str(), string_rpath.data()) == nullptr) {
+    throw std::runtime_error("Failed to resolve the realpath to file " + path);
+  }
+
+  std::ifstream file(string_rpath);
+
+  if (!file.is_open()) {
+    throw std::runtime_error("Failed to open file: " + path);
+  }
+
+  std::stringstream buffer;
+  buffer << file.rdbuf();
+
+  return buffer.str();
+}
+
+int main(int argc, char *argv[]) {
+
+  const std::string &script = argv[1];
+  const std::string &database = argv[2];
+  // wordexp_t exp_result;
+
+  std::cout << "Reading script from file " << script << " using database "
+            << database << std::endl;
+
+  // expand the script and database path
+  const std::string read_script = readFile(script);
+  const std::string read_database = readFile(database);
+
+  // initialize the module instance "ipqcmod"
+  PhreeqcInit ipqcmod(read_database, read_script);
+
+  // allocate tabular data
+  PhreeqcInit::PhreeqcMat pqc_mat = ipqcmod.getPhreeqcMat();
+
+  const std::size_t ncols = pqc_mat.names.size();
+  const std::size_t nrows = pqc_mat.values.size();
+
+  std::cout << "Script contains " << nrows << " rows and " << ncols
+            << " columns" << std::endl;
+
+  // pqc_mat.names.insert(pqc_mat.names.begin(), "ID");
+
+  // Rcpp::NumericMatrix mat(nrows, ncols + 1);
+
+  std::cout << std::endl << "Number of CELLS/SOLUTIONS: " << nrows << std::endl;
+
+  for (std::size_t i = 0; i < nrows; ++i) {
+    auto pure_names = ipqcmod.getEquilibriumNames(pqc_mat.ids[i]);
+    auto totals_names = ipqcmod.getSolutionNames(pqc_mat.ids[i]);
+
+    std::cout << std::endl << "SOL " << pqc_mat.ids[i] << " - Pure phases : ";
+    for (std::size_t j = 0; j < pure_names.size(); j++) {
+      std::cout << pure_names[j] << ", ";
+    }
+
+    std::cout << std::endl << "SOL " << pqc_mat.ids[i] << " - Total concs: ";
+    for (std::size_t j = 0; j < totals_names.size(); j++) {
+      std::cout << totals_names[j] << ", ";
+    }
+    std::cout << std::endl;
+  }
+
+  // alternatively, use the pqc_mat object
+  std::cout << std::endl << "Total pqc_mat: " << std::endl;
+  for (std::size_t i = 0; i < nrows; ++i) {
+    std::cout << "ID: " << pqc_mat.ids[i] << " - ";
+    for (std::size_t j = 0; j < ncols; ++j) {
+      std::cout << pqc_mat.names[j] << ": " << pqc_mat.values[i][j] << ", ";
+    }
+    std::cout << std::endl;
+  }
+  std::cout << std::endl;
+
+  return 0;
+}

app/testEngine.pqi

@@ -0,0 +1,13 @@
+SOLUTION 1
+units mol/kgw
+temp 25
+Ca 0.1
+Mg 0.1
+Cl 0.5 charge
+Na 0.1
+PURE 1
+Calcite  0.0 1
+Dolomite 0.0 0
+## RUN_CELLS
+##  -cells 1
+END