transforming the states is working but not properly tested

Author: ZocoLini

example-files/nfkb_ess_serial_config.xml

@@ -0,0 +1,72 @@
+<xml>
+    <run>
+        <typebench>customized</typebench>
+        <id>0</id>
+        <log_scale>1</log_scale>
+        <output>0</output>
+        <verbose>1</verbose>
+        <local_search>1</local_search>
+        <stopping_criteria>
+            <maxevaluation>3e3</maxevaluation>
+            <maxtime>1e10</maxtime>
+            <vtr>0</vtr>
+        </stopping_criteria>
+    </run>
+    <method name="ScatterSearch">
+        <user_options>
+            <weight>default</weight>
+            <tolc>default</tolc>
+            <prob_bound>default</prob_bound>
+            <nstuck_solution>default</nstuck_solution>
+        </user_options>
+        <global_options>
+            <dim_ref>default</dim_ref>
+            <ndiverse>default</ndiverse>
+            <combination>default</combination>
+            <n_stuck>default</n_stuck>
+        </global_options>
+        <local_options>
+            <solver>nl2sol.dn2fb</solver>
+            <tol>0</tol>
+            <evalmax>9e3</evalmax>
+            <iterprint>0</iterprint>
+            <n1>1</n1>
+            <n2>10</n2>
+            <balance>0.25</balance>
+            <bestx>default</bestx>
+        </local_options>
+    </method>
+    <parallelization name="cooperative">
+        <!-- saCeSS options -->
+        <reception_threshold>1</reception_threshold>
+        <evals_threshold>1</evals_threshold>
+        <mult_num_sendSol>10</mult_num_sendSol>
+        <minimum_num_sendSol>20</minimum_num_sendSol>
+        <!-- CeSS option: migration time -->
+        <migration_max_time>10</migration_max_time>
+    </parallelization>
+
+    <problem>
+        <dim> 29 </dim>
+        <neq> 0 </neq>
+        <ineq> 0 </ineq>
+        <int_var> 0 </int_var>
+        <bin_var> 0 </bin_var>
+        <lb>
+            0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+            0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+            0, 0, 0, 0, 0, 0, 0, 0, 0
+        </lb>
+        <ub>
+            6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
+            6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
+            6, 6, 6, 6, 6, 6, 6, 6, 6
+        </ub>
+        <point>
+            1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+            1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+            1, 1, 1, 1, 1, 1, 1, 1, 1
+        </point>
+    </problem>
+
+</xml>

modules/cuqdyn-c/src/states_transformer.c

@@ -2,7 +2,9 @@
 // Created by borja on 12/06/25.
 //
 #include <nvector/nvector_serial.h>
+#include <stdio.h>
 #include <sunmatrix/sunmatrix_dense.h>
+#include <unistd.h>
 
 #include "config.h"
 #include "matlab.h"
@@ -20,26 +22,26 @@ SUNMatrix transform_states(SUNMatrix states)
 
     const int rows = SM_ROWS_D(states);
     const int cols = SM_COLUMNS_D(states);
-
+    
     SUNMatrix transformed_result = NewDenseMatrix(rows, conf->states_transformer.count + 1); // + 1 adds the time column
-
+    sunrealtype *output = malloc(conf->states_transformer.count * sizeof(sunrealtype));
+    
     for (int i = 0; i < rows; ++i)
     {
         N_Vector input = copy_matrix_row(states, i, 1, cols);
-        sunrealtype *output = malloc(conf->states_transformer.count * sizeof(sunrealtype));
 
         eval_states_transformer_expr(NV_DATA_S(input), output, get_cuqdyn_context());
 
         SM_ELEMENT_D(transformed_result, i, 0) = SM_ELEMENT_D(states, i, 0);
         for (int j = 0; j < conf->states_transformer.count; ++j)
         {
-            SM_ELEMENT_D(transformed_result, i, j + 1) = NV_Ith_S(input, j);
+            SM_ELEMENT_D(transformed_result, i, j + 1) = output[j];
         }
 
         N_VDestroy(input);
-        free(output);
     }
 
+    free(output);
     SUNMatDestroy(states);
     return transformed_result;
 }

modules/mexpreval/src/context.rs

@@ -372,14 +372,14 @@ impl From<CuqdynConfigRs> for CuqdynContext {
             }
         };
 
-        let obs_exprs = if let Some(states_transformer) = value.states_transformer.as_ref() {
-            states_transformer
+        let (obs_exprs, obs_exprs_count) = if let Some(states_transformer) = value.states_transformer.as_ref() {
+            (states_transformer
                 .expr
                 .iter()
                 .map(|a| CString::new(a.as_bytes()).unwrap())
-                .collect::<Vec<CString>>()
+                .collect::<Vec<CString>>(), states_transformer.count)
         } else {
-            vec![]
+            (vec![], 0)
         };
 
         let obs_exprs_c = obs_exprs
@@ -388,8 +388,8 @@ impl From<CuqdynConfigRs> for CuqdynContext {
             .collect::<Vec<*const c_char>>();
 
         let observables = StatesTransformerC {
-            count: obs_exprs.len() as i32,
-            exprs: if obs_exprs.len() >= 1 { obs_exprs_c.as_ptr() } else { std::ptr::null() },
+            count: obs_exprs_count,
+            exprs: if obs_exprs_count >= 1 { obs_exprs_c.as_ptr() } else { std::ptr::null() },
         };
 
         let c_config = CuqdynConfigC {