Merge pull request #122 from mbakker7/dev

Release 6.6.0: refactor cross-sections

docs/01howto/getting_started/cross_sections.rst

@@ -6,11 +6,11 @@ infinitely long line-sinks, and infinitely long line-doublets. The cross-section
 parallel to the x-axis. Strip inhomogeneities may extend to infinity. The following
 elements are available:
 
-1. :class:`~timml.inhomogeneity1d.StripInhomMaq` is a strip aquifer consisting of a
+1. :class:`~timml.inhomogeneity1d.XsectionMaq` is a strip aquifer consisting of a
    regular sequence of aquifer - leaky layer - aquifer - leaky layer, aquifer, etc., like
    a ModelMaq.
 
-2. :class:`~timml.inhomogeneity1d.StripInhom3D` is a strip aquifer consisting of a
+2. :class:`~timml.inhomogeneity1d.Xsection3D` is a strip aquifer consisting of a
    stack of aquifer layers.
 
 3. :class:`~timml.linesink1d.LineSink1D` is an infinitely long line-sink for which the
@@ -22,5 +22,5 @@ elements are available:
 5. :class:`~timml.linedoublet1d.LeakyLineDoublet1D` is an infinitely long leaky wall.
    An impermeable wall is created by specifying an infinitely large resistance
 
-6. :class:`~timml.stripareasink.StripAreaSink` is a strip area-sink, which can only be
+6. :class:`~timml.stripareasink.XsectionAreaSink` is a strip area-sink, which can only be
    added when the topboundary is confined (topboundary='conf').

timml/__init__.py

@@ -3,17 +3,26 @@
 Mark Bakker, Delft University of Technology
 mark dot bakker at tudelft dot nl
 
-TimML is a computer program for the simulation of steady-state multiaquifer flow with
+TimML is a computer program for the simulation of steady-state multi-aquifer flow with
 analytic elements and consists of a library of Python scripts and FORTRAN extensions.
 """
-# ruff: noqa: F401
-# from __future__ import division, print_function, absolute_import
 
+# ruff: noqa: F401
 # --version number
-__name__ = "timml"
 __author__ = "Mark Bakker"
 # Import all classes and functions
-from timml.inhomogeneity1d import StripInhom3D, StripInhomMaq
+from timml import bessel
+from timml.circareasink import CircAreaSink
+from timml.constant import Constant, ConstantStar
+from timml.inhomogeneity import (
+    BuildingPit3D,
+    BuildingPitMaq,
+    LeakyBuildingPit3D,
+    LeakyBuildingPitMaq,
+    PolygonInhom3D,
+    PolygonInhomMaq,
+)
+from timml.inhomogeneity1d import StripInhom3D, StripInhomMaq, Xsection3D, XsectionMaq
 from timml.linedoublet import (
     ImpLineDoublet,
     ImpLineDoubletString,
@@ -31,65 +40,12 @@
     LineSinkDitchString,
 )
 from timml.linesink1d import HeadLineSink1D, LineSink1D
-from timml.model import Model, Model3D, ModelMaq
-from timml.stripareasink import StripAreaSink
+from timml.model import Model, Model3D, ModelMaq, ModelXsection
+from timml.stripareasink import XsectionAreaSink
 from timml.trace import timtraceline, timtracelines
 from timml.uflow import Uflow
-from timml.version import __version__
+from timml.version import __version__, show_versions
 from timml.well import HeadWell, LargeDiameterWell, Well, WellBase
 
-from . import bessel
-from .circareasink import CircAreaSink
-from .constant import Constant, ConstantStar
-from .inhomogeneity import (
-    BuildingPit3D,
-    BuildingPitMaq,
-    LeakyBuildingPit3D,
-    LeakyBuildingPitMaq,
-    PolygonInhom3D,
-    PolygonInhomMaq,
-)
-
-__all__ = [
-    "CircAreaSink",
-    "Constant",
-    "ConstantStar",
-    "BuildingPit3D",
-    "BuildingPitMaq",
-    "LeakyBuildingPit3D",
-    "LeakyBuildingPitMaq",
-    "PolygonInhom3D",
-    "PolygonInhomMaq",
-    "StripInhom3D",
-    "StripInhomMaq",
-    "ImpLineDoublet",
-    "ImpLineDoubletString",
-    "LeakyLineDoublet",
-    "LeakyLineDoubletString",
-    "ImpLineDoublet1D",
-    "LeakyLineDoublet1D",
-    "HeadLineSink",
-    "HeadLineSinkContainer",
-    "HeadLineSinkString",
-    "HeadLineSinkZero",
-    "LineSinkBase",
-    "LineSinkDitch",
-    "LineSinkDitchString",
-    "HeadLineSink1D",
-    "LineSink1D",
-    "Model",
-    "Model3D",
-    "ModelMaq",
-    "StripAreaSink",
-    "timtraceline",
-    "timtracelines",
-    "Uflow",
-    "__version__",
-    "HeadWell",
-    "LargeDiameterWell",
-    "Well",
-    "WellBase",
-]
-
 # default bessel module is numba
 bessel.set_bessel_method(method="numba")

timml/aquifer.py

@@ -127,7 +127,7 @@ def findlayer(self, z):
 
 class Aquifer(AquiferData):
     def __init__(self, model, kaq, c, z, npor, ltype):
-        AquiferData.__init__(self, model, kaq, c, z, npor, ltype)
+        super().__init__(model, kaq, c, z, npor, ltype)
         self.inhomlist = []
         self.area = 1e300  # Needed to find smallest inhom
 
@@ -150,11 +150,30 @@ def find_aquifer_data(self, x, y):
                 if inhom.area < rv.area:
                     rv = inhom
         return rv
-        # Not used anymore I think 5 Nov 2015
-        # def find_aquifer_number(self, x, y):
-        #    rv = -1
-        #    for i,inhom in enumerate(self.inhomlist):
-        #        if inhom.isinside(x, y):
-        #            if inhom.area < rv.area:
-        #                rv = i
-        #    return rv
+
+
+class SimpleAquifer(Aquifer):
+    """Simple aquifer for cross-section models.
+
+    Only the number of aquifers has to be specified.
+
+    Parameters
+    ----------
+    naq : int
+        Number of aquifers.
+    """
+
+    def __init__(self, naq):
+        self.naq = naq
+        self.inhomlist = []
+        self.area = 1e300  # Needed to find smallest inhomogeneity
+        self.elementlist = []
+
+    def __repr__(self):
+        return f"Simple Aquifer: {self.naq} aquifer(s)"
+
+    def initialize(self):
+        for inhom in self.inhomlist:
+            inhom.initialize()
+        for inhom in self.inhomlist:
+            inhom.create_elements()

timml/inhomogeneity1d.py

@@ -1,30 +1,78 @@
 import inspect  # user for storing the input
+import warnings
 
 import numpy as np
 
-from .aquifer import AquiferData
-from .aquifer_parameters import param_3d, param_maq
-from .constant import ConstantStar
-from .linesink1d import FluxDiffLineSink1D, HeadDiffLineSink1D
-from .stripareasink import StripAreaSinkInhom
+from timml.aquifer import AquiferData
+from timml.aquifer_parameters import param_3d, param_maq
+from timml.constant import ConstantStar
+from timml.linesink1d import FluxDiffLineSink1D, HeadDiffLineSink1D
+from timml.stripareasink import XsectionAreaSinkInhom
 
-__all__ = ["StripInhomMaq", "StripInhom3D"]
+__all__ = ["XsectionMaq", "Xsection3D"]
 
 
-class StripInhom(AquiferData):
+class Xsection(AquiferData):
+    """Base class for cross-section inhomogeneities.
+
+    Parameters
+    ----------
+    model : Model object
+        model to which the element is added, usually an instance of ModelXsection
+    x1 : float
+        left boundary of inhomogeneity (may be -np.inf if extends to infinity)
+    x2 : float
+        right boundary of inhomogeneity (may be np.inf if extends to infinity)
+    kaq : float, array or list
+        hydraulic conductivity of each layer from the top down
+    c : float, array or list
+        resistance of leaky layers from the top down
+    z : array or list
+        elevation tops and bottoms of the layers from the top down,
+        leaky layers may have zero thickness
+    npor : float, array or list
+        porosity of all aquifer layers from the top down
+    ltype : string, array or list
+        type of the layers: 'a' for aquifer, 'l' for leaky layer
+    hstar : float, optional
+        head value above semi-confining top, only read if topboundary='semi'
+    N : float, optional
+        infiltration rate, only read if topboundary='conf'
+    name : string, optional
+        name of the inhomogeneity
+    """
+
     tiny = 1e-12
 
-    def __init__(self, model, x1, x2, kaq, c, z, npor, ltype, hstar, N):
-        AquiferData.__init__(self, model, kaq, c, z, npor, ltype)
+    def __init__(self, model, x1, x2, kaq, c, z, npor, ltype, hstar, N, name=None):
+        super().__init__(model, kaq, c, z, npor, ltype)
         self.x1 = x1
         self.x2 = x2
         self.hstar = hstar
         self.N = N
         self.inhom_number = self.model.aq.add_inhom(self)
+        if name is None:
+            self.name = f"inhom{self.inhom_number:02g}"
+        else:
+            self.name = name
         self.addlinesinks = True  # Set to False not to add line-sinks
 
     def __repr__(self):
-        return "Inhom1D: " + str([self.x1, self.x2])
+        if self.hstar is not None:
+            hstar = f" with h* = {self.hstar}"
+        else:
+            hstar = ""
+        if self.N is not None:
+            inf = f" with N = {self.N}"
+        else:
+            inf = ""
+
+        return (
+            f"{self.name}: {self.__class__.__name__} "
+            + str([self.x1, self.x2])
+            + hstar
+            + inf
+        )
 
     def isinside(self, x, y):
         return (x >= self.x1) and (x < self.x2)
@@ -72,15 +120,15 @@ def create_elements(self):
                 assert (
                     aqin.ilap
                 ), "Error: infiltration can only be added if topboundary='conf'"
-                StripAreaSinkInhom(self.model, self.x1, self.x2, self.N, layer=0)
+                XsectionAreaSinkInhom(self.model, self.x1, self.x2, self.N, layer=0)
         if aqin.ltype[0] == "l":
             assert self.hstar is not None, "Error: hstar needs to be set"
             c = ConstantStar(self.model, self.hstar, aq=aqin)
             c.inhomelement = True
 
 
-class StripInhomMaq(StripInhom):
-    """Create a strip inhomogeneity for a mult-aquifer sequence of aquifer-leaky layer.
+class XsectionMaq(Xsection):
+    """Cross-section inhomogeneity for a multi-aquifer sequence.
 
     Parameters
     ----------
@@ -130,6 +178,7 @@ def __init__(
         topboundary="conf",
         hstar=None,
         N=None,
+        name=None,
     ):
         if c is None:
             c = []
@@ -142,11 +191,11 @@ def __init__(
             npor,
             ltype,
         ) = param_maq(kaq, z, c, npor, topboundary)
-        StripInhom.__init__(self, model, x1, x2, kaq, c, z, npor, ltype, hstar, N)
+        super().__init__(model, x1, x2, kaq, c, z, npor, ltype, hstar, N, name=name)
 
 
-class StripInhom3D(StripInhom):
-    """Strip inhomogeneity for a multi-layer model consisting of stacked aquifer layers.
+class Xsection3D(Xsection):
+    """Cross-section inhomogeneity consisting of stacked aquifer layers.
 
     The resistance between the layers is computed from the vertical hydraulic
     conductivity of the layers.
@@ -189,6 +238,8 @@ class StripInhom3D(StripInhom):
         head value above semi-confining top, only read if topboundary='semi'
     N : float (default is None)
         infiltration rate, only read if topboundary='conf'
+    name : string, optional
+        name of the inhomogeneity
     """
 
     def __init__(
@@ -205,6 +256,7 @@ def __init__(
         topres=None,
         topthick=0.0,
         N=None,
+        name=None,
     ):
         if z is None:
             z = [1, 0]
@@ -217,4 +269,76 @@ def __init__(
         ) = param_3d(kaq, z, kzoverkh, npor, topboundary, topres)
         if topboundary == "semi":
             z = np.hstack((z[0] + topthick, z))
-        StripInhom.__init__(self, model, x1, x2, kaq, c, z, npor, ltype, hstar, N)
+        super().__init__(model, x1, x2, kaq, c, z, npor, ltype, hstar, N, name=name)
+
+
+class StripInhom(Xsection):
+    def __init__(self, model, x1, x2, kaq, c, z, npor, ltype, hstar, N, name=None):
+        warnings.warn(
+            "'StripInhom' is deprecated and has been renamed to 'Xsection'",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        super().__init__(model, x1, x2, kaq, c, z, npor, ltype, hstar, N, name=name)
+
+
+class StripInhomMaq(XsectionMaq):
+    def __init__(
+        self,
+        model,
+        x1,
+        x2,
+        kaq=1,
+        z=None,
+        c=None,
+        npor=0.3,
+        topboundary="conf",
+        hstar=None,
+        N=None,
+        name=None,
+    ):
+        warnings.warn(
+            "'StripInhomMaq' is deprecated and has been renamed to 'XsectionMaq'",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        super().__init__(model, x1, x2, kaq, z, c, npor, topboundary, hstar, N, name)
+
+
+class StripInhom3D(Xsection3D):
+    def __init__(
+        self,
+        model,
+        x1,
+        x2,
+        kaq,
+        z=None,
+        kzoverkh=1,
+        npor=0.3,
+        topboundary="conf",
+        hstar=None,
+        topres=None,
+        topthick=0.0,
+        N=None,
+        name=None,
+    ):
+        warnings.warn(
+            "'StripInhom3D' is deprecated and has been renamed to 'Xsection3D'",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        super().__init__(
+            model,
+            x1,
+            x2,
+            kaq,
+            z,
+            kzoverkh,
+            npor,
+            topboundary,
+            hstar,
+            topres,
+            topthick,
+            N,
+            name,
+        )