Add t_init parameter to model

blobmodel/geometry.py

@@ -17,6 +17,7 @@ def __init__(
         Ly: float,
         dt: float,
         T: float,
+        t_init: float,
         periodic_y: bool,
     ) -> None:
         """
@@ -36,6 +37,8 @@ def __init__(
             Time step.
         T : float
             Time length.
+        t_init : float
+            Initial time
         periodic_y : bool
             Flag indicating whether periodicity is allowed in the y-direction.
         """
@@ -45,6 +48,7 @@ def __init__(
         self.Ly = Ly
         self.dt = dt
         self.T = T
+        self.t_init = t_init
         self.periodic_y = periodic_y
 
         # calculate x, y and t coordinates
@@ -53,7 +57,7 @@ def __init__(
             self.y: NDArray[Literal[64], Any] = np.array([0])
         else:
             self.y = np.arange(0, self.Ly, self.Ly / self.Ny)
-        self.t: NDArray[Literal[64], Any] = np.arange(0, self.T, self.dt)
+        self.t: NDArray[Literal[64], Any] = np.arange(t_init, self.T + t_init, self.dt)
         self.x_matrix, self.y_matrix, self.t_matrix = np.meshgrid(
             self.x, self.y, self.t
         )
@@ -69,5 +73,5 @@ def __str__(self) -> str:
         """
         return (
             f"Geometry parameters:  Nx:{self.Nx},  Ny:{self.Ny}, Lx:{self.Lx}, Ly:{self.Ly}, "
-            + f"dt:{self.dt}, T:{self.T}, y-periodicity:{self.periodic_y}"
+            + f"dt:{self.dt}, T:{self.T}, t_init:{self.t_init}, y-periodicity:{self.periodic_y}"
         )

blobmodel/model.py

@@ -28,6 +28,7 @@ def __init__(
         num_blobs: int = 1000,
         t_drain: Union[float, NDArray, int] = 10,
         blob_factory: BlobFactory = DefaultBlobFactory(),
+        t_init: float = 0,
         labels: str = "off",
         label_border: float = 0.75,
         one_dimensional: bool = False,
@@ -63,6 +64,8 @@ def __init__(
             of length Nx.
         blob_factory : BlobFactory, optional
             BlobFactory instance for setting blob parameter distributions.
+        t_init : float, optional
+            Initial time for simulation, default 0.
         labels : str, optional
             Blob label setting. Possible values: "off", "same", "individual".
             "off": no blob labels returned
@@ -108,6 +111,7 @@ def __init__(
             Ly=Ly,
             dt=dt,
             T=T,
+            t_init=t_init,
             periodic_y=periodic_y,
         )
         self.blob_shape = (

blobmodel/plotting.py

@@ -14,7 +14,7 @@ def show_model(
     interval: int = 100,
     gif_name: Union[str, None] = None,
     fps: int = 10,
-    initial_time: float = 0
+    initial_time: float = 0,
 ) -> None:
     """
     Creates an animation that shows the evolution of a specific variable over time.

examples/blob_tilting.py

@@ -18,16 +18,14 @@
     vx_parameter=vx,
     wx_parameter=wx,
     wy_parameter=wy,
-    blob_alignment=True  # Blobs are aligned
+    blob_alignment=True,  # Blobs are aligned
 )
 
 # blob tilting
 theta = np.pi / 4
 # Using a lambda function to set the tilt angle theta, allows us to set a distribution for tilt angles if desired.
 # In this case we use a degenerate distribution.
-bf.set_theta_setter(
-    lambda: theta
-)
+bf.set_theta_setter(lambda: theta)
 
 # create data
 bm = Model(
@@ -42,7 +40,14 @@
     num_blobs=100,
     t_drain=1e10,
     blob_factory=bf,
+    t_init=10,
 )
 ds = bm.make_realization(speed_up=True, error=1e-2)
 # show animation and save as gif
-show_model(dataset=ds, interval=100, gif_name="blob_alignment_true.gif", fps=10, initial_time=10)
+show_model(
+    dataset=ds,
+    interval=100,
+    gif_name="blob_alignment_true.gif",
+    fps=10,
+    initial_time=10,
+)

tests/test_str.py

@@ -3,10 +3,10 @@
 
 
 def test_geometry_str():
-    geo = Geometry(1, 1, 1, 1, 1, 1, False)
+    geo = Geometry(1, 1, 1, 1, 1, 1, 1, False)
     assert (
         str(geo)
-        == "Geometry parameters:  Nx:1,  Ny:1, Lx:1, Ly:1, dt:1, T:1, y-periodicity:False"
+        == "Geometry parameters:  Nx:1,  Ny:1, Lx:1, Ly:1, dt:1, T:1, t_init:1, y-periodicity:False"
     )