testGolemRunner + example

poet/test/run_kin_cor_end2.pqi

@@ -0,0 +1,98 @@
+SOLUTION 1 
+ units   mol/kgw
+ pH    6.653
+ pe    -3.167
+ water  1
+ temp  17
+ Na   1e-15
+ Cl   1e-15 charge
+ Ca   1e-15
+ C    1e-15
+ Fe   4.386e-9
+ S    8.772e-9
+ Al   5.031e-7
+ Si   5.031e-7
+
+PURE  1
+Pyrite  0.0  2.5e-4
+
+KINETICS 1
+Kaolinite
+  -m       1.5e-4 
+  -parms   0.6 100000
+
+SOLUTION 2
+units   mol/kgw
+pH     6.921 
+pe    -1.258
+water  1
+temp  17
+Na   1e-15
+Cl   1e-15 charge
+Ca   1e-15
+C    1e-15
+Fe   1e-15
+S    1e-15
+Al   1e-15
+Si   7.963e-5
+
+PURE  2
+Pyrite  0.0  2.1e-4
+
+KINETICS  2
+Quartz
+  -m         2.2e-4
+  -parms     0.01  1
+
+SOLUTION 3
+units   mol/kgw
+pH     9.963
+pe    -6.769 
+temp 17
+Na   1e-15
+Cl   1e-15 
+Ca   1.345e-4
+C    1.345e-4
+Fe   1.433e-8
+S    2.866e-8
+Al   2.692e-5
+Si   2.692e-5
+
+PURE  3
+Pyrite         0 2e-4
+Calcite        0 1e-4
+
+KINETICS  3
+Kaolinite
+  -m          1.4e-3
+  -parms      0.6 1000
+Siderite
+  -m          1.2e-12
+  -parms      1.2 10
+
+SOLUTION  4 
+units	mol/kgw
+temp	17
+pH      5.576
+pe      4      O2(g) -1
+Cl      0.0003 charge
+Na      0.0003
+C       1e-15 CO2(g) -3.38
+Ca	1e-15
+Fe      1e-15
+S       1e-15
+Al      1e-15
+Si      1e-15
+
+SOLUTION  5
+units	mol/kgw
+temp	35
+pH      7
+pe      4 
+Cl      0.003 charge
+Na      0.003
+C(4)    2.333e-3
+
+RUN_CELLS
+ -cells 1 2 3 4 5
+END

poet/test/testGolemRunner.cpp

@@ -1,4 +1,4 @@
-//  Time-stamp: "Last modified 2024-12-02 17:37:08 delucia"
+//  Time-stamp: "Last modified 2025-07-28 12:23:47 delucia"
 #include <iostream>
 #include <iomanip>
 #include <linux/limits.h>
@@ -99,12 +99,6 @@ int main(int argc, char *argv[]) {
     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 
 
@@ -117,39 +111,28 @@ int main(int argc, char *argv[]) {
     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()));
-	}
+    for (std::size_t index = 0; index < n; ++index) {
+	simulationInOut.push_back(std::vector<double>(
+        matrix_values.begin() + num_columns*index, matrix_values.begin() + num_columns*(index +1)));
     }
 
     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";
+	
+	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";
     }