[Fix] Simulation with state preparation errors fixed (#354)

* Fixing bug related to simulation with state preparation errors

* Updating the noisy simulations notebook

pulser/simulation/simulation.py

@@ -642,19 +642,18 @@ def _build_basis_and_op_matrices(self) -> None:
                 self.basis[proj[0]] * self.basis[proj[1]].dag()
             )
 
-    def _construct_hamiltonian(self, update_and_extract: bool = True) -> None:
+    def _construct_hamiltonian(self, update: bool = True) -> None:
         """Constructs the hamiltonian from the Sequence.
 
         Also builds qutip.Qobjs related to the Sequence if not built already,
         and refreshes potential noise parameters by drawing new at random.
 
         Args:
-            update_and_extract(bool=True): Whether to update the noise
-                parameters and extract the samples from the sequence.
+            update(bool=True): Whether to update the noise parameters.
         """
-        if update_and_extract:
+        if update:
             self._update_noise()
-            self._extract_samples()
+        self._extract_samples()
         if not hasattr(self, "basis_name"):
             self._build_basis_and_op_matrices()
 
@@ -976,7 +975,7 @@ def _run_solver() -> CoherentResults:
             else:
                 reps = 1
             # At each run, new random noise: new Hamiltonian
-            self._construct_hamiltonian(update_and_extract=update_ham)
+            self._construct_hamiltonian(update=update_ham)
             # Get CoherentResults instance from sequence with added noise:
             cleanres_noisyseq = _run_solver()
             # Extract statistics at eval time: