Merge remote-tracking branch 'origin/main'

# Conflicts:
#	README.md

examples/charge_sensing.py

@@ -15,14 +15,17 @@
     coulomb_peak_width=0.05, T=100
 )
 
+model.gate_voltage_composer.virtual_gate_matrix = np.array([
+    [1, -0.0, 0],
+    [-0.0, 1, 0],
+    [-0.06, -0.05, 0],
+])
 
 # defining the min and max values for the dot voltage sweep
 vx_min, vx_max = -2, 2
 vy_min, vy_max = -2, 2
 # using the dot voltage composer to create the dot voltage array for the 2d sweep
-vg = model.gate_voltage_composer.do2d(1, vy_min, vx_max, 100, 2, vy_min, vy_max, 100)
-
-z, n = model.do2d_open(1, vy_min, vx_max, 100, 2, vy_min, vy_max, 100)
+vg = model.gate_voltage_composer.do2d('vP1', vy_min, vx_max, 100, 'vP2', vy_min, vy_max, 100)
 
 # centering the voltage sweep on the [0, 1] - [1, 0] interdot charge transition on the side of a charge sensor coulomb peak
 vg += model.optimal_Vg([0.5, 0.5, 0.6])

examples/triple_dot.py

@@ -46,7 +46,7 @@
 vx_min, vx_max = -10, 10
 vy_min, vy_max = -10, 10
 # using the dot voltage composer to create the dot voltage array for the 2d sweep
-vg = voltage_composer.do2d(1, vy_min, vx_max, 400, 3, vy_min, vy_max, 400)
+vg = model.gate_voltage_composer.do2d('vP1', vy_min, vx_max, 400, 'vP3', vy_min, vy_max, 400)
 
 # creating the figure and axes
 fig, axes = plt.subplots(2, 2, sharex=True, sharey=True)

qarray/DotArrays/ChargeSensedDotArray.py

@@ -117,7 +117,7 @@ def __post_init__(self):
         if self.algorithm in ['thresholded', 'default']:
             check_and_warn_user(self)
 
-        self.gate_voltage_composer = GateVoltageComposer(n_gate=self.n_gate, n_dot=self.n_dot)
+        self.gate_voltage_composer = GateVoltageComposer(n_gate=self.n_gate, n_dot=self.n_dot, n_sensor=self.n_sensor)
         self.gate_voltage_composer.virtual_gate_matrix = -np.linalg.pinv(self.cdd_inv @ self.cgd)
         self.gate_voltage_composer.virtual_gate_origin = np.zeros(self.n_gate)
 

qarray/DotArrays/GateVoltageComposer.py

@@ -20,10 +20,10 @@ class GateVoltageComposer:
     """
     n_gate: int  # the number of gates
     n_dot: int | None = None
+    n_sensor: int | None = 0
     virtual_gate_origin: np.ndarray | None = None  # the origin to consider virtual gates from
     virtual_gate_matrix: np.ndarray | None = None  # a matrix of virtual gates to be used for the dot array
 
-
     def _check_gate(self, gate: int):
         assert isinstance(gate, int), 'gate must be an int'
         assert gate in range(1, self.n_gate + 1), f'gate must be in the range 1 to {self.n_gate}'
@@ -149,7 +149,7 @@ def meshgrid_virtual(self, dots: List[int | str], arrays: List[np.ndarray]) -> n
         sizes = [array.size for array in arrays]
 
         # initialising the voltage array
-        Vd = np.zeros(shape=sizes + [self.n_dot])
+        Vd = np.zeros(shape=sizes + [self.n_dot + self.n_sensor])
 
         # creating the meshgrid
         V = np.meshgrid(*arrays)