feat: add support for ignoring specified cells in simulation run

poet/include/PhreeqcRunner.hpp

@@ -50,6 +50,18 @@ public:
   void run(std::vector<std::vector<double>> &simulationInOut,
            const double time_step);
 
+  /**
+   * @brief Runs the simulation with the given input and output data.
+   *
+   * @param simulationInOut A reference to a 2D vector containing the simulation
+   * input and output data.
+   * @param time_step The time step for the simulation.
+   * @param to_ignore A vector of indices specifying which elements to ignore
+   * during the simulation.
+   */
+  void run(std::vector<std::vector<double>> &simulationInOut,
+           const double time_step, const std::vector<std::size_t> &to_ignore);
+
   /**
    * @brief Returns the number of engines currently stored.
    *

poet/src/Runner.cpp

@@ -1,9 +1,11 @@
 #include "PhreeqcEngine.hpp"
 #include "PhreeqcMatrix.hpp"
 #include "PhreeqcRunner.hpp"
+#include <algorithm>
 #include <cmath>
 #include <cstddef>
 #include <memory>
+#include <set>
 #include <vector>
 
 PhreeqcRunner::PhreeqcRunner(const PhreeqcMatrix &matrix) {
@@ -50,6 +52,32 @@ void PhreeqcRunner::run(std::vector<std::vector<double>> &simulationInOut,
 
     this->_engineStorage.at(pqc_id)->runCell(this->_buffer, time_step);
 
+    // Copy the buffer back to the output while ignoring the first element and
+    // NaNs
+    copy_from_buffer(this->_buffer, simulationInOut[i]);
+  }
+}
+
+void PhreeqcRunner::run(std::vector<std::vector<double>> &simulationInOut,
+                        const double time_step,
+                        const std::vector<std::size_t> &to_ignore) {
+  const std::set<std::size_t> to_ignore_set(to_ignore.begin(), to_ignore.end());
+
+  for (std::size_t i = 0; i < simulationInOut.size(); i++) {
+    if (to_ignore_set.find(i) != to_ignore_set.end()) {
+      continue;
+    }
+
+    const auto &current_inout = simulationInOut[i];
+    const auto pqc_id = static_cast<int>(current_inout[0]);
+
+    this->_buffer.clear();
+
+    // Copy the input to the buffer while ignoring the first element and NaNs
+    copy_to_buffer(this->_buffer, current_inout);
+
+    this->_engineStorage.at(pqc_id)->runCell(this->_buffer, time_step);
+
     // Copy the buffer back to the output while ignoring the first element and
     // NaNs
     copy_from_buffer(this->_buffer, simulationInOut[i]);

poet/test/testPhreeqcRunner.cpp

@@ -72,4 +72,26 @@ POET_TEST(PhreeqcRunnerUnknownID) {
   simulationInOut[0][0] = 1000;
 
   EXPECT_THROW(runner.run(simulationInOut, 100), std::out_of_range);
+}
+
+POET_TEST(PhreeqcRunnerSimulationWithIgnoredCells) {
+  PhreeqcMatrix pqc_mat(test_database, test_script);
+  const auto subsetted_pqc_mat = pqc_mat.subset({2, 3});
+  PhreeqcRunner runner(subsetted_pqc_mat);
+
+  const auto stl_mat = subsetted_pqc_mat.get();
+  const auto matrix_values = stl_mat.values;
+  const auto num_columns = stl_mat.names.size();
+
+  std::vector<double> second_line(matrix_values.begin() + num_columns,
+                                  matrix_values.end());
+  std::vector<std::vector<double>> simulationInOut;
+
+  simulationInOut.push_back(second_line);
+
+  EXPECT_NO_THROW(runner.run(simulationInOut, 10000, {0}));
+
+  for (std::size_t i = 0; i < num_columns; ++i) {
+    EXPECT_DOUBLE_EQ(simulationInOut[0][i], second_line[i]);
+  }
 }