Renaming of classes + files (and some function) in DAE project (#463)

* Rename ProblemDAE.py -> problemDAE.py with renaming of class ptype_dae -> ProblemDAE

* Renaming of the rest..

* Renaming of rest rest - Having consistency feels more comfortable now.

pySDC/playgrounds/DAE/DiscontinuousTestDAE.py

@@ -3,8 +3,8 @@
 import matplotlib.pyplot as plt
 
 from pySDC.helpers.stats_helper import get_sorted
-from pySDC.projects.DAE.sweepers.SemiImplicitDAE import SemiImplicitDAE
-from pySDC.projects.DAE.problems.DiscontinuousTestDAE import DiscontinuousTestDAE
+from pySDC.projects.DAE.sweepers.semiImplicitDAE import SemiImplicitDAE
+from pySDC.projects.DAE.problems.discontinuousTestDAE import DiscontinuousTestDAE
 from pySDC.implementations.controller_classes.controller_nonMPI import controller_nonMPI
 
 from pySDC.implementations.hooks.log_solution import LogSolution

pySDC/playgrounds/DAE/LinearTestDAEMinion.py → pySDC/playgrounds/DAE/linearTestDAEMinion.py

@@ -1,11 +1,11 @@
 import numpy as np
 
 from pySDC.core.problem import WorkCounter
-from pySDC.projects.DAE.misc.ProblemDAE import ptype_dae
+from pySDC.projects.DAE.misc.problemDAE import ProblemDAE
 from pySDC.core.errors import ProblemError
 
 
-class LinearTestDAEMinion(ptype_dae):
+class LinearTestDAEMinion(ProblemDAE):
     r"""
     This class implements a linear stiff DAE problem from [1]_ that is given by
 

pySDC/playgrounds/DAE/log_residual_components.py

@@ -7,19 +7,19 @@ class LogResidualComponentsPostIter(Hooks):
 
     Parameters
     ----------
-    Hooks : _type_
-        _description_
+    Hooks : pySDC.core.hooks.Hooks
+        Hook base class.
     """
 
     def post_iteration(self, step, level_number):
         r"""
-        Default routine called after each step.
+        Default routine called after each iteration.
 
         Parameters
         ----------
-        step : pySDC.core.Step
+        step : pySDC.core.step.Step
             Current step.
-        level_number : pySDC.core.level
+        level_number : pySDC.core.level.Level
             Current level number.
         """
 

pySDC/playgrounds/DAE/playground_MPI.py

@@ -1,8 +1,8 @@
 from mpi4py import MPI
 from pathlib import Path
 
-from pySDC.projects.DAE.sweepers.SemiImplicitDAEMPI import SemiImplicitDAEMPI
-from pySDC.projects.DAE.problems.DiscontinuousTestDAE import DiscontinuousTestDAE
+from pySDC.projects.DAE.sweepers.semiImplicitDAEMPI import SemiImplicitDAEMPI
+from pySDC.projects.DAE.problems.discontinuousTestDAE import DiscontinuousTestDAE
 from pySDC.implementations.controller_classes.controller_nonMPI import controller_nonMPI
 
 from pySDC.playgrounds.DAE.DiscontinuousTestDAE import plotSolution

pySDC/projects/DAE/README.rst

@@ -8,11 +8,11 @@ To run the scripts contained in this project a standard installation of pySDC sh
 Project overview 
 ----------------
 - misc
-    - | ``DAEMesh.py``
+    - | ``meshDAE.py``
       | Datatype for semi-explicit DAE problem classes differential and algebraic parts to have a clean treatment.
-    - | ``HookClass_DAE.py``
+    - | ``hooksDAE.py``
       | Simple hook classes to read out the approximate solution and error after each time step.
-    - | ``ProblemDAE.py``
+    - | ``problemDAE.py``
       | Parent class for DAE problems containing the method to solve the (non)-linear system at each node/stage.
 
 - plotting
@@ -24,19 +24,19 @@ Project overview
       | Reads a previously generated data file in `.npy` format and generates a plot on logarithmic y-axis and linear x-axis. 
 
 - problems
-    - | ``DiscontinousTestDAE``
+    - | ``discontinousTestDAE.py``
       | Simple nonlinear semi-explicit index-1 DAE with discrete state event whose event time is known.
     - | ``pendulum2D.py``
       | Example of the pendulum described by a semi-implicit DAE of index 3.
     - | ``problematicF.py``
       | Fully-implicit DAE of index 2 which is not solvable for numerically solvable for certain choices of parameter :math:`\eta`.
-    - | ``simple_DAE.py`` 
+    - | ``simpleDAE.py`` 
       | Linear semi-explicit index-2 system of Hessenberg form with known analytical solution.
-    - | ``synchronous_machine.py`` 
+    - | ``synchronousMachine.py`` 
       | Synchronous machine model attached to an infinite bus undergoing torque disturbance test. Results in an index-1 system. 
-    - | ``transistor_amplifier.py``
+    - | ``transistorAmplifier.py``
       | A two transistor amplifier model that results in an index-1 differential algebraic system. A nice example of a system resulting from a common real world situation.
-    - | ``WSCC9BusSystem.py``
+    - | ``wscc9BusSystem.py``
       | Large power system test case with three reduced model synchronous machines and nine buses. It is also part of the `PinTSimE project <https://github.com/Parallel-in-Time/pySDC/tree/master/pySDC/projects/PinTSimE>`_.
 
 - run
@@ -52,15 +52,15 @@ Project overview
       | Script checking the order of accuracy of MPI sweepers for DAEs of different indices.
 
 - sweepers
-    - | ``fully_implicit_DAE.py`` 
+    - | ``fullyImplicitDAE.py`` 
       | Sweeper that accepts a fully implicit formulation of a system of differential equations and applies to it a modified version of spectral deferred correction
-    - | ``SemiImplicitDAE.py``
+    - | ``semiImplicitDAE.py``
       | SDC sweeper especially for semi-explicit DAEs. This sweeper is based on ideas mentioned in `Huang et al. (2007) <https://www.sciencedirect.com/science/article/abs/pii/S0021999106003147>`_.
-    - | ``fully_implicit_DAE_MPI.py``
+    - | ``fullyImplicitDAEMPI.py``
       | MPI version of fully-implicit SDC-DAE sweeper.
-    - | ``SemiImplicitDAEMPI.py``
+    - | ``semiImplicitDAEMPI.py``
       | MPI version of semi-implicit SDC-DAE sweeper.
-    - | ``RungeKuttaDAE.py``
+    - | ``rungeKuttaDAE.py``
       | Runge-Kutta methods that can be used to solve DAEs in pySDC in a fully-implicit description.
 
 - tests
@@ -173,9 +173,9 @@ which is of the general form
 
 .. literalinclude:: ../../../pySDC/projects/DAE/problems/problematicF.py
 
-The imports for the classes ``ptype_dae`` and ``mesh`` are necessary for implementing this problem.
+The imports for the classes ``ProblemDAE`` and ``mesh`` are necessary for implementing this problem.
 
-The problem class inherits from the parent ``ptype_dae`` that
+The problem class inherits from the parent ``ProblemDAE`` that
 has the ``solve_system`` method solving the (non)-linear system to find the root, i.e., updating the values of the unknown derivative. All DAE problem classes should therefore inherit from this class.
 For this general type of DAEs the datatype ``mesh`` is used here for both, ``u`` and ``f``.
 Further, the constructor requires at least the parameter ``newton_tol``, the tolerance passed to the root solver. It is possible to set a default value (which is set to ``1e-8`` in the example above).
@@ -208,16 +208,16 @@ We want to implement such an equation and consider the example
   0 &= (t + 2) u_1 (t) + (t^2 - 4) u_2 (t) - (t^2 + t - 2) e^t.
 
 This example has two differential variables :math:`u_1`, :math:`u_2` (two differential equations) and one algebraic variable :math:`z` (thus one algebraic equation).
-In ``pySDC`` defining a problem class for semi-explicit DAEs is slightly different to those of fully-implicit form. Additionally to ``numpy`` for the example the imports for the classes ``ptype_dae`` and ``DAEMesh`` are needed.
+In ``pySDC`` defining a problem class for semi-explicit DAEs is slightly different to those of fully-implicit form. Additionally to ``numpy`` for the example the imports for the classes ``ProblemDAE`` and ``MeshDAE`` are needed.
 
-.. literalinclude:: ../../../pySDC/projects/DAE/problems/simple_DAE.py
+.. literalinclude:: ../../../pySDC/projects/DAE/problems/simpleDAE.py
 
-This problem class inherits again from ``ptype_dae``. In contrast, for the solution ``u`` and the right-hand side of the ``f``
-a different datatype ``DAEMesh`` is used that allows to separate between the differential variables and the algebraic variables as well
+This problem class inherits again from ``ProblemDAE``. In contrast, for the solution ``u`` and the right-hand side of the ``f``
+a different datatype ``MeshDAE`` is used that allows to separate between the differential variables and the algebraic variables as well
 as for the equations. The tolerance for the root solver is passed with a default value of ``1e-10`` and the number of unknowns is :math:`3`, i.e., ``nvars=3``.
 The problem-specific parameter ``a`` has a default value of ``10.0``.
 
-In the ``eval_f`` method the equations and the variables are now separated using the components of the ``DAEMesh``. Recall that ``eval_f`` returns the right-hand side function so that we have a root problem. However, for this semi-explicit DAE this is not the case, but we can change that by rewriting the system to
+In the ``eval_f`` method the equations and the variables are now separated using the components of the ``MeshDAE``. Recall that ``eval_f`` returns the right-hand side function so that we have a root problem. However, for this semi-explicit DAE this is not the case, but we can change that by rewriting the system to
 
 .. math::
 

pySDC/projects/DAE/misc/HookClass_DAE.py → pySDC/projects/DAE/misc/hooksDAE.py

@@ -13,9 +13,9 @@ def post_step(self, step, level_number):
 
         Parameters
         ----------
-        step : pySDC.core.Step
+        step : pySDC.core.step.Step
             Current step.
-        level_number : pySDC.core.level
+        level_number : pySDC.core.level.Level
             Current level number.
         """
 
@@ -46,7 +46,7 @@ def post_step(self, step, level_number):
 
 class LogGlobalErrorPostStepAlgebraicVariable(Hooks):
     """
-    Logs the global error in the algebraic variable
+    Logs the global error in the algebraic variable after each step.
     """
 
     def post_step(self, step, level_number):
@@ -55,9 +55,9 @@ def post_step(self, step, level_number):
 
         Parameters
         ----------
-        step : pySDC.core.Step
+        step : pySDC.core.step.Step
             Current step.
-        level_number : pySDC.core.level
+        level_number : pySDC.core.level.Level
             Current level number.
         """
 

pySDC/projects/DAE/misc/DAEMesh.py → pySDC/projects/DAE/misc/meshDAE.py

@@ -1,7 +1,7 @@
 from pySDC.implementations.datatype_classes.mesh import MultiComponentMesh
 
 
-class DAEMesh(MultiComponentMesh):
+class MeshDAE(MultiComponentMesh):
     r"""
     Datatype for DAE problems. The solution of the problem can be splitted in the differential part
     and in an algebraic part.

pySDC/projects/DAE/misc/ProblemDAE.py → pySDC/projects/DAE/misc/problemDAE.py

@@ -2,10 +2,10 @@
 from scipy.optimize import root
 
 from pySDC.core.problem import Problem, WorkCounter
-from pySDC.projects.DAE.misc.DAEMesh import DAEMesh
+from pySDC.projects.DAE.misc.meshDAE import MeshDAE
 
 
-class ptype_dae(Problem):
+class ProblemDAE(Problem):
     r"""
     This class implements a generic DAE class and illustrates the interface class for DAE problems.
     It ensures that all parameters are passed that are needed by DAE sweepers.
@@ -25,8 +25,8 @@ class ptype_dae(Problem):
         in work_counters['rhs']
     """
 
-    dtype_u = DAEMesh
-    dtype_f = DAEMesh
+    dtype_u = MeshDAE
+    dtype_f = MeshDAE
 
     def __init__(self, nvars, newton_tol):
         """Initialization routine"""

pySDC/projects/DAE/problems/DiscontinuousTestDAE.py → pySDC/projects/DAE/problems/discontinuousTestDAE.py

@@ -1,10 +1,10 @@
 import numpy as np
 
 from pySDC.core.problem import WorkCounter
-from pySDC.projects.DAE.misc.ProblemDAE import ptype_dae
+from pySDC.projects.DAE.misc.problemDAE import ProblemDAE
 
 
-class DiscontinuousTestDAE(ptype_dae):
+class DiscontinuousTestDAE(ProblemDAE):
     r"""
     This class implements a scalar test discontinuous differential-algebraic equation (DAE) similar to [1]_. The event function
     is defined as :math:`h(y):= 2y - 100`. Then, the discontinuous DAE model reads:

pySDC/projects/DAE/problems/pendulum2D.py

@@ -1,7 +1,7 @@
-from pySDC.projects.DAE.misc.ProblemDAE import ptype_dae
+from pySDC.projects.DAE.misc.problemDAE import ProblemDAE
 
 
-class pendulum_2d(ptype_dae):
+class Pendulum2D(ProblemDAE):
     r"""
     Example implementing the well known 2D pendulum as a first order differential-algebraic equation (DAE) of index 3.
     The DAE system is given by the equations

pySDC/projects/DAE/problems/problematicF.py

@@ -1,10 +1,10 @@
 import numpy as np
 
-from pySDC.projects.DAE.misc.ProblemDAE import ptype_dae
+from pySDC.projects.DAE.misc.problemDAE import ProblemDAE
 from pySDC.implementations.datatype_classes.mesh import mesh
 
 
-class problematic_f(ptype_dae):
+class ProblematicF(ProblemDAE):
     r"""
     Standard example of a very simple fully implicit index-2 differential algebraic equation (DAE) that is not
     numerically solvable for certain choices of the parameter :math:`\eta`. The DAE system is given by

pySDC/projects/DAE/problems/simple_DAE.py → pySDC/projects/DAE/problems/simpleDAE.py

@@ -1,9 +1,9 @@
 import numpy as np
 
-from pySDC.projects.DAE.misc.ProblemDAE import ptype_dae
+from pySDC.projects.DAE.misc.problemDAE import ProblemDAE
 
 
-class simple_dae_1(ptype_dae):
+class SimpleDAE(ProblemDAE):
     r"""
     Example implementing a smooth linear index-2 differential-algebraic equation (DAE) with known analytical solution.
     The DAE system is given by

pySDC/projects/DAE/problems/synchronous_machine.py → pySDC/projects/DAE/problems/synchronousMachine.py

@@ -2,11 +2,10 @@
 import warnings
 from scipy.interpolate import interp1d
 
-from pySDC.projects.DAE.misc.ProblemDAE import ptype_dae
-from pySDC.implementations.datatype_classes.mesh import mesh
+from pySDC.projects.DAE.misc.problemDAE import ProblemDAE
 
 
-class synchronous_machine_infinite_bus(ptype_dae):
+class SynchronousMachineInfiniteBus(ProblemDAE):
     r"""
     Synchronous machine model from Kundur (equiv. circuits fig. 3.18 in [1]_) attached to infinite bus. The machine can be
     represented as two different circuits at the direct-axis and the quadrature-axis. Detailed information can be found in

pySDC/projects/DAE/problems/transistor_amplifier.py → pySDC/projects/DAE/problems/transistorAmplifier.py

@@ -2,7 +2,7 @@
 import numpy as np
 from scipy.interpolate import interp1d
 
-from pySDC.projects.DAE.misc.ProblemDAE import ptype_dae
+from pySDC.projects.DAE.misc.problemDAE import ProblemDAE
 from pySDC.implementations.datatype_classes.mesh import mesh
 
 
@@ -11,7 +11,7 @@ def _transistor(u_in):
     return 1e-6 * (np.exp(u_in / 0.026) - 1)
 
 
-class one_transistor_amplifier(ptype_dae):
+class OneTransistorAmplifier(ProblemDAE):
     r"""
     The one transistor amplifier example from pg. 377 in [1]_. The problem is an index-1 differential-algebraic equation
     (DAE) having the equations
@@ -138,7 +138,7 @@ def u_exact(self, t):
         return me
 
 
-class two_transistor_amplifier(ptype_dae):
+class TwoTransistorAmplifier(ProblemDAE):
     r"""
     The two transistor amplifier example from page 108 in [1]_. The problem is an index-1 differential-algebraic equation
     (DAE) having the equations

pySDC/projects/DAE/problems/WSCC9BusSystem.py → pySDC/projects/DAE/problems/wscc9BusSystem.py

@@ -1,5 +1,5 @@
 import numpy as np
-from pySDC.projects.DAE.misc.ProblemDAE import ptype_dae
+from pySDC.projects.DAE.misc.problemDAE import ProblemDAE
 from pySDC.core.errors import ParameterError
 
 
@@ -573,7 +573,7 @@ def get_event_Ybus():
 #     return ppc['Ybus']()
 
 
-class WSCC9BusSystem(ptype_dae):
+class WSCC9BusSystem(ProblemDAE):
     r"""
     Example implementing the WSCC 9 Bus system [1]_. For this complex model, the equations can be found in [2]_, and
     sub-transient and turbine parameters are taken from [3]_. The network data of the system are taken from MATPOWER [4]_.

pySDC/projects/DAE/run/accuracy_check_MPI.py

@@ -2,7 +2,7 @@
 from mpi4py import MPI
 
 from pySDC.implementations.controller_classes.controller_nonMPI import controller_nonMPI
-from pySDC.projects.DAE.misc.HookClass_DAE import (
+from pySDC.projects.DAE.misc.hooksDAE import (
     LogGlobalErrorPostStepDifferentialVariable,
     LogGlobalErrorPostStepAlgebraicVariable,
 )
@@ -36,26 +36,26 @@ def run(dt, num_nodes, use_MPI, semi_implicit, residual_type, index_case, initia
 
     if not semi_implicit:
         if use_MPI:
-            from pySDC.projects.DAE.sweepers.fully_implicit_DAE_MPI import fully_implicit_DAE_MPI as sweeper
+            from pySDC.projects.DAE.sweepers.fullyImplicitDAEMPI import FullyImplicitDAEMPI as sweeper
 
         else:
-            from pySDC.projects.DAE.sweepers.fully_implicit_DAE import fully_implicit_DAE as sweeper
+            from pySDC.projects.DAE.sweepers.fullyImplicitDAE import FullyImplicitDAE as sweeper
 
     else:
         if use_MPI:
-            from pySDC.projects.DAE.sweepers.SemiImplicitDAEMPI import SemiImplicitDAEMPI as sweeper
+            from pySDC.projects.DAE.sweepers.semiImplicitDAEMPI import SemiImplicitDAEMPI as sweeper
 
         else:
-            from pySDC.projects.DAE.sweepers.SemiImplicitDAE import SemiImplicitDAE as sweeper
+            from pySDC.projects.DAE.sweepers.semiImplicitDAE import SemiImplicitDAE as sweeper
 
     if index_case == 1:
-        from pySDC.projects.DAE.problems.DiscontinuousTestDAE import DiscontinuousTestDAE as problem
+        from pySDC.projects.DAE.problems.discontinuousTestDAE import DiscontinuousTestDAE as problem
 
         t0 = 1.0
         Tend = 1.5
 
     elif index_case == 2:
-        from pySDC.projects.DAE.problems.simple_DAE import simple_dae_1 as problem
+        from pySDC.projects.DAE.problems.simpleDAE import SimpleDAE as problem
 
         t0 = 0.0
         Tend = 0.4

pySDC/projects/DAE/run/fully_implicit_dae_playground.py

@@ -3,8 +3,8 @@
 import pickle
 
 from pySDC.implementations.controller_classes.controller_nonMPI import controller_nonMPI
-from pySDC.projects.DAE.problems.problematicF import problematic_f
-from pySDC.projects.DAE.sweepers.fully_implicit_DAE import fully_implicit_DAE
+from pySDC.projects.DAE.problems.problematicF import ProblematicF
+from pySDC.projects.DAE.sweepers.fullyImplicitDAE import FullyImplicitDAE
 from pySDC.implementations.hooks.log_errors import LogGlobalErrorPostStep
 from pySDC.helpers.stats_helper import get_sorted
 from pySDC.implementations.hooks.log_solution import LogSolution
@@ -39,9 +39,9 @@ def main():
 
     # Fill description dictionary for easy hierarchy creation
     description = dict()
-    description['problem_class'] = problematic_f
+    description['problem_class'] = ProblematicF
     description['problem_params'] = problem_params
-    description['sweeper_class'] = fully_implicit_DAE
+    description['sweeper_class'] = FullyImplicitDAE
     description['sweeper_params'] = sweeper_params
     description['level_params'] = level_params
     description['step_params'] = step_params