Fixed commit

poet/test/barite_het.pqi

@@ -23,12 +23,11 @@ RUN_CELLS
 COPY solution 1 2-3
 
 ## Here a 5x2 domain:
-
-       |---+---+---+---+---|
-    -> | 2 | 2 | 2 | 2 | 2 |
-     4 |---+---+---+---+---|
-    -> | 3 | 3 | 3 | 3 | 3 |
-       |---+---+---+---+---|
+##    |---+---+---+---+---|
+## -> | 2 | 2 | 2 | 2 | 2 |
+##  4 |---+---+---+---+---|
+## -> | 3 | 3 | 3 | 3 | 3 |
+##    |---+---+---+---+---|
 
 ## East boundary: "injection" of solution 4. North, W, S boundaries: closed
 
@@ -77,4 +76,4 @@ END
 ## KINETICS 3.
 
 RUN_CELLS
- -cells 2-4
+ -cells 2-4

poet/test/testGolemRunner.cpp

@@ -0,0 +1,161 @@
+//  Time-stamp: "Last modified 2024-12-02 17:37:08 delucia"
+#include <iostream>
+#include <iomanip>
+#include <linux/limits.h>
+#include <sstream>
+#include <fstream>
+#include <algorithm>
+#include <iterator>
+#include <vector>
+#include <string>
+#include <memory>
+#include <cmath>
+
+#include "PhreeqcMatrix.hpp"
+#include "PhreeqcEngine.hpp"
+#include "PhreeqcRunner.hpp"
+
+
+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();
+}
+
+// pretty print a vector, standard implementation from stackoverflow 
+template<typename T>
+std::ostream & operator<<(std::ostream & os, std::vector<T> vec)
+{
+    os << "{ ";
+    std::copy(vec.begin(), vec.end(), std::ostream_iterator<T>(os, ", "));
+    os << " }";
+    return os;
+}
+
+
+int main(int argc, char *argv[]) {
+    
+    if (argc < 3) {
+	std::cout << "::" << argv[0] << ": two args needed, script and database\n";
+	return 1;
+    }
+
+
+    ////// INITIALISATION
+    // read Script and Database and put it in a std::string
+    auto script = readFile(argv[1]);
+    auto db     = readFile(argv[2]);
+
+    // Create the matrix directly from database and init script
+    PhreeqcMatrix pqc_mat(db, script);
+    
+    // How many different SOLUTIONS ("CELLS") are defined in the script?
+    const auto ids = pqc_mat.getIds();
+    
+    int n = ids.size();
+    
+    std::cout << ":: Found " << n << " distinct PHREEQC problems \n";
+    std::cout << ids << "\n";
+
+    const auto solutes  = pqc_mat.getSolutionNames();
+    std::cout << ":: These are the common solutes across all the " << n << " problems: \n";
+    std::cout << solutes << "\n";
+    
+    // iterate on the ids (THEY start at 1!!)
+    for (const auto & i : ids) {
+	auto pphases  = pqc_mat.getEquilibriumNames(i);
+	if (!pphases.empty()) {
+	    std::cout << ":: Equilibrium phases [" << (int) i <<  "]: \n";
+	    std::cout << pphases << "\n";
+	}
+	
+	auto kinetics = pqc_mat.getKineticsNames(i);
+	if (!kinetics.empty()) {
+	    std::cout << ":: Kinetics [" << i <<  "]: \n";
+	    std::cout << kinetics << "\n";
+	}
+    }
+
+    // The exported data type holds the matrix in a "STL format" with
+    // a "header" of names and their accompanying values. The values
+    // are stored in a row-major order per default.
+    auto exported_mat = pqc_mat.get();
+    // Get the total number of solutes
+    const int len = exported_mat.names.size();
+    // Get the values as reference to modify them in place
+    std::vector<double> &cell_values = exported_mat.values;
+
+    std::cout << ":: Values in the PhreeqcMatrix: \n";
+
+    // std::cout << exported_mat.names  << "\n";
+    // std::cout << cell_values << "\n";
+    // END INIT
+
+
+    
+    //// Phreeqc RUN through the new Runner class 
+
+    // optional SUBSET the matrix (i.e., the unique ids defined in
+    // golem map as input)
+    // const auto subsetted_pqc_mat = pqc_mat.subset({1, 2});
+    PhreeqcRunner runner(pqc_mat);
+
+    const auto stl_mat = pqc_mat.get();
+    const auto matrix_values = stl_mat.values;
+    const auto num_columns = stl_mat.names.size();
+    const auto spec_names = stl_mat.names;
+
+    // container to pass in/out
+    std::vector<std::vector<double>> simulationInOut;
+
+    // grid cells
+    const std::size_t num_cells = 10;
+    const std::size_t half_cells = 5;
+
+    // copy the values to the InOut vector. We replicate cell 1 
+    for (std::size_t index = 0; index < num_cells; ++index) {
+	if (index < half_cells) {
+	    simulationInOut.push_back(std::vector<double>(
+            matrix_values.begin(), matrix_values.begin() + num_columns));
+	} else {
+	    simulationInOut.push_back(std::vector<double>(
+            matrix_values.begin() + num_columns, matrix_values.end()));
+	}
+    }
+
+    const double timestep = 100.;
+
+    // compute 1 timestep
+    runner.run(simulationInOut, timestep);
+
+    for (std::size_t cell_index = 0; cell_index < simulationInOut.size(); ++cell_index) {
+	const bool is_first_half = cell_index < half_cells;
+	if (is_first_half) {
+	    std::cout << "Grid element: " << cell_index << " \n";
+	    for (std::size_t spec = 0; spec < num_columns; ++spec) {
+		std::cout << ":" << spec_names[spec] << "=" << simulationInOut[cell_index][spec];
+	    }
+	    std::cout << "\n";
+	}
+    }
+
+    
+    return 0;
+}
+
+// Oneliner for rz-vm278 relative to iphreeqc/poet/test!!
+
+// g++ testGolemRunner.cpp -o testG -Wall -I../../poet/include -I../../src -I../../src/phreeqcpp -I../../src/phreeqcpp/common -I../../src/phreeqcpp/PhreeqcKeywords -lIPhreeqc -lIPhreeqcPOET -L../../bbuild/ -L../../bbuild/poet