Simplify time stepping schemes and add type hints and documentation (#…

…572)

* Improve naming in time stepping schemes.
* Add documentation and type hints. Remove support for monolithic problem to simplify code.
* Tidy up and improve inheritance and documentation.
* Do not instantiate objects from problemDefinition

oscillator/solver-python/mypy.ini

@@ -0,0 +1,7 @@
+[mypy]
+
+[mypy-scipy.*]
+ignore_missing_imports = True
+
+[mypy-precice.*]
+ignore_missing_imports = True

oscillator/solver-python/oscillator.py

@@ -7,9 +7,10 @@
 from enum import Enum
 import csv
 import os
+from typing import Type
 
 import problemDefinition
-import timeSteppers
+from timeSteppers import TimeStepper, TimeSteppingSchemes, GeneralizedAlpha, RungeKutta4, RadauIIA
 
 
 class Participant(Enum):
@@ -25,20 +26,24 @@ class Participant(Enum):
     help="Time stepping scheme being used.",
     type=str,
     choices=[
-        s.value for s in timeSteppers.TimeSteppingSchemes],
-    default=timeSteppers.TimeSteppingSchemes.NEWMARK_BETA.value)
+        s.value for s in TimeSteppingSchemes],
+    default=TimeSteppingSchemes.NEWMARK_BETA.value)
 args = parser.parse_args()
 
 participant_name = args.participantName
 
+this_mass: Type[problemDefinition.Mass]
+other_mass: Type[problemDefinition.Mass]
+this_spring: Type[problemDefinition.Spring]
+connecting_spring = problemDefinition.SpringMiddle
+
 if participant_name == Participant.MASS_LEFT.value:
     write_data_name = 'Force-Left'
     read_data_name = 'Force-Right'
     mesh_name = 'Mass-Left-Mesh'
 
     this_mass = problemDefinition.MassLeft
     this_spring = problemDefinition.SpringLeft
-    connecting_spring = problemDefinition.SpringMiddle
     other_mass = problemDefinition.MassRight
 
 elif participant_name == Participant.MASS_RIGHT.value:
@@ -48,7 +53,6 @@ class Participant(Enum):
 
     this_mass = problemDefinition.MassRight
     this_spring = problemDefinition.SpringRight
-    connecting_spring = problemDefinition.SpringMiddle
     other_mass = problemDefinition.MassLeft
 
 else:
@@ -89,25 +93,19 @@ class Participant(Enum):
 a = a0
 t = 0
 
-if args.time_stepping == timeSteppers.TimeSteppingSchemes.GENERALIZED_ALPHA.value:
-    time_stepper = timeSteppers.GeneralizedAlpha(stiffness=stiffness, mass=mass, alpha_f=0.4, alpha_m=0.2)
-elif args.time_stepping == timeSteppers.TimeSteppingSchemes.NEWMARK_BETA.value:
-    time_stepper = timeSteppers.GeneralizedAlpha(stiffness=stiffness, mass=mass, alpha_f=0.0, alpha_m=0.0)
-elif args.time_stepping == timeSteppers.TimeSteppingSchemes.RUNGE_KUTTA_4.value:
-    ode_system = np.array([
-        [0, 1],  # du
-        [-stiffness / mass, 0],  # dv
-    ])
-    time_stepper = timeSteppers.RungeKutta4(ode_system=ode_system)
-elif args.time_stepping == timeSteppers.TimeSteppingSchemes.Radau_IIA.value:
-    ode_system = np.array([
-        [0, 1],  # du
-        [-stiffness / mass, 0],  # dv
-    ])
-    time_stepper = timeSteppers.RadauIIA(ode_system=ode_system)
+time_stepper: TimeStepper
+
+if args.time_stepping == TimeSteppingSchemes.GENERALIZED_ALPHA.value:
+    time_stepper = GeneralizedAlpha(stiffness=stiffness, mass=mass, alpha_f=0.4, alpha_m=0.2)
+elif args.time_stepping == TimeSteppingSchemes.NEWMARK_BETA.value:
+    time_stepper = GeneralizedAlpha(stiffness=stiffness, mass=mass, alpha_f=0.0, alpha_m=0.0)
+elif args.time_stepping == TimeSteppingSchemes.RUNGE_KUTTA_4.value:
+    time_stepper = RungeKutta4(stiffness=stiffness, mass=mass)
+elif args.time_stepping == TimeSteppingSchemes.Radau_IIA.value:
+    time_stepper = RadauIIA(stiffness=stiffness, mass=mass)
 else:
     raise Exception(
-        f"Invalid time stepping scheme {args.time_stepping}. Please use one of {[ts.value for ts in timeSteppers.TimeSteppingSchemes]}")
+        f"Invalid time stepping scheme {args.time_stepping}. Please use one of {[ts.value for ts in TimeSteppingSchemes]}")
 
 
 positions = []
@@ -133,34 +131,32 @@ class Participant(Enum):
     precice_dt = participant.get_max_time_step_size()
     dt = np.min([precice_dt, my_dt])
 
-    def f(t): return participant.read_data(mesh_name, read_data_name, vertex_ids, t)[0]
+    def f(t: float) -> float: return participant.read_data(mesh_name, read_data_name, vertex_ids, t)[0]
 
     # do time step, write data, and advance
-    # performs adaptive time stepping with dense output; multiple write calls per time step
-    if args.time_stepping == timeSteppers.TimeSteppingSchemes.Radau_IIA.value:
-        u_new, v_new, a_new, sol = time_stepper.do_step(u, v, a, f, dt)
-        t_new = t + dt
+    u_new, v_new, a_new = time_stepper.do_step(u, v, a, f, dt)
+
+    t_new = t + dt
+
+    # RadauIIA time stepper provides dense output. Do multiple write calls per time step.
+    if isinstance(time_stepper, RadauIIA):
         # create n samples_per_step of time stepping scheme. Degree of dense
         # interpolating function is usually larger 1 and, therefore, we need
         # multiple samples per step.
         samples_per_step = 5
-        n_time_steps = len(sol.ts)  # number of time steps performed by adaptive time stepper
+        n_time_steps = len(time_stepper.dense_output.ts)  # number of time steps performed by adaptive time stepper
         n_pseudo = samples_per_step * n_time_steps  # samples_per_step times no. time steps per window.
-
         t_pseudo = 0
         for i in range(n_pseudo):
             # perform n_pseudo pseudosteps
             dt_pseudo = dt / n_pseudo
             t_pseudo += dt_pseudo
-            write_data = [connecting_spring.k * sol(t_pseudo)[0]]
+            write_data = np.array([connecting_spring.k * time_stepper.dense_output(t_pseudo)[0]])
             participant.write_data(mesh_name, write_data_name, vertex_ids, write_data)
             participant.advance(dt_pseudo)
 
     else:  # simple time stepping without dense output; only a single write call per time step
-        u_new, v_new, a_new = time_stepper.do_step(u, v, a, f, dt)
-        t_new = t + dt
-
-        write_data = [connecting_spring.k * u_new]
+        write_data = np.array([connecting_spring.k * u_new])
         participant.write_data(mesh_name, write_data_name, vertex_ids, write_data)
         participant.advance(dt)
 

oscillator/solver-python/problemDefinition.py

@@ -1,20 +1,33 @@
 import numpy as np
 from numpy.linalg import eig
+from typing import Callable
 
 
-class SpringLeft:
+class Spring:
+    k: float
+
+
+class SpringLeft(Spring):
     k = 4 * np.pi**2
 
 
-class SpringMiddle:
+class SpringMiddle(Spring):
     k = 16 * (np.pi**2)
 
 
-class SpringRight:
+class SpringRight(Spring):
     k = 4 * np.pi**2
 
 
-class MassLeft:
+class Mass:
+    m: float
+    u0: float
+    v0: float
+    u_analytical: Callable[[float | np.ndarray], float | np.ndarray]
+    v_analytical: Callable[[float | np.ndarray], float | np.ndarray]
+
+
+class MassLeft(Mass):
     # mass
     m = 1
 
@@ -23,10 +36,8 @@ class MassLeft:
     u0 = 1.0
     v0 = 0.0
 
-    u_analytical, v_analytical = None, None  # will be defined below
-
 
-class MassRight:
+class MassRight(Mass):
     # mass
     m = 1
 
@@ -35,8 +46,6 @@ class MassRight:
     u0 = 0.0
     v0 = 0.0
 
-    u_analytical, v_analytical = None, None  # will be defined below
-
 
 # Mass matrix
 M = np.array([