solver updates (#223)

* merge fix

* Remove obsolete F0, F1 from generic_solvers

* Another r string warning removal

* Removing obsolete Unknown attributes on the generic solver

* Getting rid of the problem_description method in every solver

* Removing some commented out code.

* Clean up the expression's initialisation code

* simplifying the uw_counter_object idea to keep a total_instances and instance_number

* Removing the metaclass counter idea - now simpler. Need to add a stress test

* Adding _version.py file.

Also starting a runtime record class, currently in __init__.py

* Object counter function to class function + property

* Introducting uw_record.

uw_record gives information on the installation and runtime

Access via:
import underworld3 as uw
uw.auditor.get_installation_data
uw.auditor.get_runtime_data

* uw_record lives in underworld/utilities/__init__.py
* uw_record collects data only on proc 0 and broadcasts to all procs.
  For get_runtime_data be aware of this design. As calling often could cause
  an operational overhead. While get_installation_data only bcasts at initialisation.
* Coming idea is to serialised the output get_installation_data into
  hdf5 files

* Rename uw_record -> auditor

* access via underworld3.auditor
* test included in test_0005_utils.py

* Modify test script name for uw_counter

* Clean up the interface of 'auditor'

* Removing the uw_count class

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = underworld3
-version = 0.98b
+version = attr: underworld3.__version__
 
 #[build_ext]
 #inplace = True
@@ -20,6 +20,7 @@ install_requires =
   pint
   psutil
   typing_extensions
+
 package_dir =
     = src
 packages = find:

src/underworld3/__init__.py

@@ -75,6 +75,10 @@
 
 PETSc.Sys.popErrorHandler()
 
+try:
+    from ._version import __version__
+except ImportError:
+    __version__ = "Unknown" # check src/underworld3/_version.py
 
 def view():
     from IPython.display import Latex, Markdown, display
@@ -97,8 +101,11 @@ def view():
 from ._var_types import *
 from .utilities._petsc_tools import *
 from .utilities._nb_tools import *
+from .utilities._utils import auditor
 
-from underworld3.utilities import _api_tools
+from .utilities import _api_tools
+#from underworld3.utilities import _api_tools
+from .utilities._utils import auditor
 
 import underworld3.adaptivity
 import underworld3.coordinates
@@ -131,31 +138,6 @@ def view():
 _libdirs = _OD()
 _incdirs = _OD({_np.get_include(): None})
 
-
-# def _is_notebook() -> bool:
-#     """
-#     Function to determine if the python environment is a Notebook or not.
-
-#     Returns 'True' if executing in a notebook, 'False' otherwise
-
-#     Script taken from https://stackoverflow.com/a/39662359/8106122
-#     """
-
-#     try:
-#         shell = get_ipython().__class__.__name__
-#         if shell == "ZMQInteractiveShell":
-#             return True  # Jupyter notebook or qtconsole
-#         elif shell == "TerminalInteractiveShell":
-#             return False  # Terminal running IPython
-#         else:
-#             return False  # Other type (?)
-#     except NameError:
-#         return False  # Probably standard Python interpreter
-
-
-# is_notebook = _is_notebook()
-
-
 ## -------------------------------------------------------------
 
 # pdoc3 over-rides. pdoc3 has a strange path-traversal algorithm
@@ -175,6 +157,3 @@ def view():
 # child class modifications
 
 __pdoc__["systems.constitutive_models.Constitutive_Model.Parameters"] = False
-
-
-## Add an options dictionary for arbitrary underworld things

src/underworld3/_version.py

@@ -0,0 +1 @@
+__version__ = "0.98.1b"

src/underworld3/cython/petsc_generic_snes_solvers.pyx

@@ -3,7 +3,7 @@ from xmlrpc.client import Boolean
 import sympy
 from sympy import sympify
 
-from typing import Optional, Union
+from typing import Optional, Union, TypeAlias
 from petsc4py import PETSc
 
 import underworld3
@@ -37,14 +37,6 @@ class SolverBaseClass(uw_object):
 
         self.Unknowns = self._Unknowns(self)
 
-        self._u = self.Unknowns.u
-        self._DuDt = self.Unknowns.DuDt
-        self._DFDt = self.Unknowns.DFDt
-
-        self._L = self.Unknowns.L # grad(u)
-        self._E = self.Unknowns.E # sym part
-        self._W = self.Unknowns.W # asym part
-
         self._order = 0
         self._constitutive_model = None
 
@@ -190,6 +182,11 @@ class SolverBaseClass(uw_object):
         return
 
 
+    # Deprecate in favour of properties for solver.F0, solver.F1
+    @timing.routine_timer_decorator
+    def _setup_problem_description(self):
+        raise RuntimeError("Contact Developers - shouldn't be calling SolverBaseClass _setup_problem_description")
+
     @timing.routine_timer_decorator
     def add_condition(self, f_id, c_type, conds, label, components=None):
         """
@@ -201,6 +198,7 @@ class SolverBaseClass(uw_object):
         ----------
         f_id: int
             Index of the solver's field (equation) to apply the condition.
+            Note: The solvers field id is usually different to the mesh's field ids.
         c_type: string
             BC type. Either dirichlet (essential) or neumann (natural) conditions.
         conds: array_like of floats or a sympy.Matrix
@@ -289,30 +287,13 @@ class SolverBaseClass(uw_object):
         """
         self.add_condition(0, 'dirichlet', conds, boundary, components)
 
-
-    ## Properties that are common to all solvers
-    ## F0 and F1 are the force / flux terms, respectively
-    ## Solvers over-ride these to describe the problem type
     @property
     def F0(self):
-
-        f0 = uw.function.expression(
-            r"\mathbf{f}_0\left( \mathbf{u} \right)",
-            None,
-            "Pointwise force term: f_0(u)",
-        )
-
-        return f0
+        raise RuntimeError("Contact Developers - SolverBaseClass F0 is being used")
 
     @property
     def F1(self):
-        f1 = uw.function.expression(
-            r"\mathbf{F}_1\left( \mathbf{u} \right)",
-            None,
-            "Pointwise flux term: F_1(u)",
-        )
-
-        return f1
+        raise RuntimeError("Contact Developers - SolverBaseClass F0 is being used")
 
     @property
     def u(self):
@@ -439,16 +420,11 @@ class SNES_Scalar(SolverBaseClass):
         self.Unknowns.DuDt = DuDt
         self.Unknowns.DFDt = DFDt
 
-        # self.u = u_Field
-        # self.DuDt = DuDt
-        # self.DFDt = DFDt
-
         self.name = solver_name
         self.verbose = verbose
         self._tolerance = 1.0e-4
 
         ## Todo: this is obviously not particularly robust
-
         if solver_name != "" and not solver_name.endswith("_"):
             self.petsc_options_prefix = solver_name+"_"
         else:
@@ -488,8 +464,6 @@ class SNES_Scalar(SolverBaseClass):
             self.petsc_options.delValue("snes_monitor_short")
             self.petsc_options.delValue("snes_converged_reason")
 
-        self._F0 = sympy.Matrix.zeros(1,1)
-        self._F1 = sympy.Matrix.zeros(1,mesh.dim)
         self.dm = None
 
 
@@ -508,7 +482,6 @@ class SNES_Scalar(SolverBaseClass):
         self.mesh._equation_systems_register.append(self)
 
         self.is_setup = False
-        # super().__init__()
 
     @property
     def tolerance(self):
@@ -1085,8 +1058,6 @@ class SNES_Vector(SolverBaseClass):
                         vtype=uw.VarType.VECTOR, degree=degree )
 
 
-        self._F0 = sympy.Matrix.zeros(1, self.mesh.dim)
-        self._F1 = sympy.Matrix.zeros(self.mesh.dim, self.mesh.dim)
         self.dm = None
 
         ## sympy.Matrix
@@ -1111,8 +1082,6 @@ class SNES_Vector(SolverBaseClass):
 
         self.mesh._equation_systems_register.append(self)
 
-        # super().__init__()
-
     @property
     def tolerance(self):
         return self._tolerance

src/underworld3/discretisation.py

@@ -1650,7 +1650,7 @@ def __init__(
         self.symbol = symbol
 
         if mesh.instance_number > 1:
-            invisible = "\,\!" * mesh.instance_number
+            invisible = r"\,\!" * mesh.instance_number
             self.symbol = f"{{ {{ {invisible} }} {symbol} }}"
 
         self.clean_name = re.sub(r"[^a-zA-Z0-9_]", "", name)

src/underworld3/function/expressions.py

@@ -87,7 +87,7 @@ class UWexpression(Symbol, uw_object):
     ```{python}
         alpha = UWexpression(
                         r'\\alpha',
-                        value=3.0e-5,
+                        sym=3.0e-5,
                         description="thermal expansivity"
                             )
         print(alpha.sym)
@@ -96,17 +96,22 @@ class UWexpression(Symbol, uw_object):
 
     """
 
-    def __new__(cls, name, value, description="No description provided"):
+    def __new__(cls, name, *args, **kwargs,):
 
         obj = Symbol.__new__(cls, name)
-        obj.sym = sympy.sympify(value)
-        obj.symbol = name
         return obj
 
-    def __init__(self, name, value, description="No description provided"):
-
-        self._sym = sympy.sympify(value)
-        self._description = description
+    def __init__(self, name, sym=None, description="No description provided", value=None):
+        if value is not None and sym is None:
+            import warnings;
+            warnings.warn(message=f"DEPRECATION warning, don't use 'value' attribute for expression: {value}, please use 'sym' attribute")
+            sym = value
+        if value is not None and sym is not None:
+            raise ValueError("Both 'sym' and 'value' attributes are provided, please use one")
+
+        self.sym = sympy.sympify(sym)
+        self.symbol = name
+        self.description = description
 
         return
 

src/underworld3/systems/solvers.py

@@ -81,9 +81,6 @@ def __init__(
         if solver_name == "":
             solver_name = "Poisson_{}_".format(self.instance_number)
 
-        # Register the problem setup function
-        self._setup_problem_description = self.poisson_problem_description
-
         # default values for properties
         self.f = sympy.Matrix.zeros(1, 1)
 
@@ -210,9 +207,6 @@ def __init__(
         if solver_name == "":
             self.solver_name = "Darcy_{}_".format(self.instance_number)
 
-        # Register the problem setup function
-        self._setup_problem_description = self.darcy_problem_description
-
         # default values for properties
         self._f = sympy.Matrix([0])
         self._k = 1
@@ -458,8 +452,6 @@ def __init__(
 
         self._bodyforce = sympy.Matrix([[0] * self.mesh.dim])
 
-        self._setup_problem_description = self.stokes_problem_description
-
         # this attrib records if we need to setup the problem (again)
         self.is_setup = False
 
@@ -842,7 +834,6 @@ def __init__(
         if solver_name == "":
             self.name = "SProj_{}_".format(self.instance_number)
 
-        self._setup_problem_description = self.projection_problem_description
         self.is_setup = False
         self._smoothing = 0.0
         self._uw_weighting_function = 1.0
@@ -974,7 +965,6 @@ def __init__(
         if solver_name == "":
             solver_name = "VProj{}_".format(self.instance_number)
 
-        self._setup_problem_description = self.projection_problem_description
         self.is_setup = False
         self._smoothing = 0.0
         self._penalty = 0.0
@@ -1298,8 +1288,6 @@ def __init__(
         self.is_setup = False
 
         self.restore_points_to_domain_func = restore_points_func
-        self._setup_problem_description = self.adv_diff_slcn_problem_description
-
         ### Setup the history terms ... This version should not build anything
         ### by default - it's the template / skeleton
 
@@ -1636,8 +1624,6 @@ def __init__(
         )
 
         self.restore_points_to_domain_func = restore_points_func
-        self._setup_problem_description = self.navier_stokes_problem_description
-
         self._bodyforce = sympy.Matrix([[0] * self.mesh.dim])
         self._constitutive_model = None
 

src/underworld3/utilities/__init__.py

@@ -16,8 +16,7 @@ def _append_petsc_path():
 
 from .uw_petsc_gen_xdmf import Xdmf, generateXdmf, generate_uw_Xdmf
 from .uw_swarmIO import swarm_h5, swarm_xdmf
-from ._utils import CaptureStdout, h5_scan, mem_footprint, gather_data
+from ._utils import CaptureStdout, h5_scan, mem_footprint, gather_data, auditor
 
 from .read_medit_ascii import read_medit_ascii, print_medit_mesh_info
 from .create_dmplex_from_medit import create_dmplex_from_medit
-