refactor(gridgen): fixes and additions related to vertical pass through cells (#953)
* Gridgen fixes and additions - Added Gridgen's "vertical pass through" option to utils/gridgen.export(). - Fixed utils/gridgen.set_surface_interpolation() file paths for ASCIIGRID option. - Fixed grd variable definitions for ASCIIGRID surface interpolation option in utils/gridgen._builder_block(). These now use gridgen._asciigrid_dict where appropriate (default ascii grid names were causing errors). - Added docstring to utils/gridgen.get_disu(). - Minor edit to modflow/mfdisu.py docstring re: util3d / unstructured models. * docs(readme): autotest build_exes.py changed to get_exes.py * test(gridgen vertical pass through) * test(gridgen vertical pass through) * style(gridgen.py) * test(gridgen vertical pass through)develop
Chris Nicol
GitHub
parent
05ce3bc53d
commit
510b9f169f
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@ -66,7 +66,7 @@ Before you submit your Pull Request (PR) consider the following guidelines:
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```shell
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cd autotest
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nosetests -v build_exes.py
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nosetests -v get_exes.py
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nosetests -v
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```
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Note: the FloPy test suite requires the [nosetests](https://pypi.org/project/nose/) and [pymake](https://github.com/modflowpy/pymake) python packages. All the FloPy dependencies must also be installed for the tests to pass.
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@ -45,9 +45,17 @@ def test_gridgen():
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delr=delr,
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delc=delc, top=top, botm=botm)
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ms_u = flopy.modflow.Modflow(modelname = 'mymfusgmodel', model_ws = cpth,
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version = 'mfusg')
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dis_usg = flopy.modflow.ModflowDis(ms_u, nlay=nlay, nrow=nrow, ncol=ncol,
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delr=delr,
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delc=delc, top=top, botm=botm)
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gridgen_ws = cpth
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g = Gridgen(dis5, model_ws=gridgen_ws, exe_name=exe_name)
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g6 = Gridgen(dis6, model_ws=gridgen_ws, exe_name=exe_name)
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gu = Gridgen(dis_usg, model_ws=gridgen_ws, exe_name=exe_name,
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vertical_pass_through=True)
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rf0shp = os.path.join(gridgen_ws, 'rf0')
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xmin = 7 * delr
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@ -58,6 +66,7 @@ def test_gridgen():
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(xmin, ymin)]]]
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g.add_refinement_features(rfpoly, 'polygon', 1, range(nlay))
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g6.add_refinement_features(rfpoly, 'polygon', 1, range(nlay))
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gu.add_refinement_features(rfpoly, 'polygon', 1, range(nlay))
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rf1shp = os.path.join(gridgen_ws, 'rf1')
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xmin = 8 * delr
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@ -68,6 +77,7 @@ def test_gridgen():
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(xmin, ymin)]]]
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g.add_refinement_features(rfpoly, 'polygon', 2, range(nlay))
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g6.add_refinement_features(rfpoly, 'polygon', 2, range(nlay))
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gu.add_refinement_features(rfpoly, 'polygon', 2, range(nlay))
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rf2shp = os.path.join(gridgen_ws, 'rf2')
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xmin = 9 * delr
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@ -78,6 +88,19 @@ def test_gridgen():
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(xmin, ymin)]]]
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g.add_refinement_features(rfpoly, 'polygon', 3, range(nlay))
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g6.add_refinement_features(rfpoly, 'polygon', 3, range(nlay))
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gu.add_refinement_features(rfpoly, 'polygon', 3, range(nlay))
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# inactivate parts of mfusg layer 2 to test vertical-pass-through option
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xmin = 0 * delr
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xmax = 18 * delr
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ymin = 0 * delc
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ymax = 18 * delc
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adpoly2 = [[[(xmin, ymin), (xmax, ymin), (xmax, ymax), (xmin, ymax),
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(xmin, ymin)]]]
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gu.add_active_domain(adpoly2, layers = [1])
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adpoly1_3 = [[[(0., 0.), (Lx, 0.), (Lx, Ly), (0., Ly),
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(0., 0.)]]]
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gu.add_active_domain(adpoly1_3, layers = [0,2])
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# if gridgen executable is available then do the main part of the test
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if run:
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@ -126,6 +149,32 @@ def test_gridgen():
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assert os.path.isfile(fname), \
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'MF6 disv file not created: {}'.format(fname)
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# test mfusg with vertical pass-through (True above at instantiation)
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gu.build()
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disu_vp = gu.get_disu(ms_u)
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# -check that node 1 (layer 1) is connected to layer 3 but not layer 2:
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ja0 = disu_vp.ja[: disu_vp.iac[0]]
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msg = ("MFUSG node 1 (layer 1) is not connected to layer 3 but should "
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"be (with vertical pass through activated).")
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assert max(ja0) > sum(disu_vp.nodelay[:2]), msg
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# -check that node 1 (layer 1) is not connected to any layer 2 nodes
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msg = ("MFUSG node 1 (layer 1) is connected to layer 2 but should not "
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"be (with vertical pass through activated).")
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assert len(ja0[(ja0 > disu_vp.nodelay[0]) & \
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(ja0 <= sum(disu_vp.nodelay[:2]))]
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) == 0, msg
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#ms_u.disu.write_file()
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# test mfusg without vertical pass-through
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gu.vertical_pass_through = False
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gu.build()
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disu_vp = gu.get_disu(ms_u)
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# -check that node 1 (layer 1) is connected to layer 1 only:
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ja0 = disu_vp.ja[: disu_vp.iac[0]]
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msg = ("MFUSG node 1 (layer 1) is connected to layer 2 or 3 but "
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"should not be (without vertical pass through activated).")
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assert max(ja0) <= disu_vp.nodelay[0], msg
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return
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@ -184,9 +184,8 @@ class ModflowDisU(Package):
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Notes
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-----
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Does not work yet for multi-layer USG models because top and bot cannot
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be u3d instances until u3d is modified to handle multiple u2d instances
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of different size.
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Now works for multi-layer USG models since u3d was modified to handle
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multiple u2d instances of different size.
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Examples
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--------
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@ -121,6 +121,10 @@ class Gridgen(object):
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surface_interpolation : str
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Default gridgen method for interpolating elevations. Valid options
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include 'replicate' (default) and 'interpolate'
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vertical_pass_through : bool
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If true, Gridgen's GRID_TO_USGDATA command will connect layers
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where intermediate layers are inactive.
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(default is False)
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Notes
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-----
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@ -135,6 +139,7 @@ class Gridgen(object):
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model_ws=".",
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exe_name="gridgen",
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surface_interpolation="replicate",
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vertical_pass_through=False,
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):
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self.dis = dis
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if isinstance(dis, ModflowGwfdis):
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@ -170,6 +175,11 @@ class Gridgen(object):
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surface_interpolation for k in range(self.nlay + 1)
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]
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# Set export options
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self.vertical_pass_through = "False"
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if vertical_pass_through:
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self.vertical_pass_through = "True"
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# Set up a blank _active_domain list with None for each layer
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self._addict = {}
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self._active_domain = []
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@ -202,7 +212,8 @@ class Gridgen(object):
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Array that is used as an asciigrid. If elev is a string, then
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it is assumed to be the name of the asciigrid.
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elev_extent : list-like
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list of xmin, xmax, ymin, ymax extents of the elev grid.
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List of xmin, xmax, ymin, ymax extents of the elev grid.
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Must be specified for ASCIIGRID; optional otherwise.
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Returns
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-------
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@ -242,9 +253,10 @@ class Gridgen(object):
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self._asciigrid_dict[isurf] = nm
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elif isinstance(elev, str):
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if not os.path.isfile(elev):
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if not os.path.isfile(os.path.join(self.model_ws, elev)):
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raise Exception(
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"Error. elev is not a valid file: " "{}".format(elev)
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"Error. elev is not a valid file: "
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"{}".format(os.path.join(self.model_ws, elev))
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)
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self._asciigrid_dict[isurf] = elev
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else:
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@ -439,11 +451,18 @@ class Gridgen(object):
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"""
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Export the quadtree grid to shapefiles, usgdata, and vtk
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Parameters
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----------
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verbose : bool
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If true, print the results of the gridgen command to the terminal
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(default is False)
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Returns
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-------
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None
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"""
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# Create the export definition file
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fname = os.path.join(self.model_ws, "_gridgen_export.dfn")
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f = open(fname, "w")
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@ -635,6 +654,35 @@ class Gridgen(object):
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itmuni=4,
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lenuni=2,
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):
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"""
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Create a MODFLOW-USG DISU flopy object.
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Parameters
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----------
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model : Flopy model object
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The Flopy model object (of type :class:`flopy.modflow.mf.Modflow`)
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to which this package will be added.
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nper : int
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Number of model stress periods (default is 1).
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perlen : float or array of floats (nper)
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A single value or array of the stress period lengths
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(default is 1).
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nstp : int or array of ints (nper)
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Number of time steps in each stress period (default is 1).
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tsmult : float or array of floats (nper)
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Time step multiplier (default is 1.0).
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steady : boolean or array of boolean (nper)
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True or False indicating whether or not stress period is
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steady state (default is True).
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itmuni : int
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Time units, default is days (4)
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lenuni : int
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Length units, default is meters (2)
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Returns
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-------
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disu : Flopy ModflowDisU object.
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"""
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# nodes, nlay, ivsd, itmuni, lenuni, idsymrd, laycbd
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fname = os.path.join(self.model_ws, "qtg.nod")
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@ -1787,7 +1835,7 @@ class Gridgen(object):
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for k in range(self.nlay):
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if self.surface_interpolation[k] == "ASCIIGRID":
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grd = "_gridgen.lay{}.asc".format(k)
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grd = self._asciigrid_dict[k]
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else:
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grd = "basename"
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s += " TOP LAYER {} = {} {}\n".format(
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@ -1796,7 +1844,7 @@ class Gridgen(object):
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for k in range(self.nlay):
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if self.surface_interpolation[k + 1] == "ASCIIGRID":
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grd = "_gridgen.lay{}.asc".format(k + 1)
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grd = self._asciigrid_dict[k + 1]
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else:
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grd = "basename"
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s += " BOTTOM LAYER {} = {} {}\n".format(
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@ -1823,6 +1871,9 @@ class Gridgen(object):
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s += "BEGIN GRID_TO_USGDATA grid_to_usgdata\n"
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s += " GRID = quadtreegrid\n"
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s += " USG_DATA_PREFIX = qtg\n"
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s += " VERTICAL_PASS_THROUGH = {0}\n".format(
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self.vertical_pass_through
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)
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s += "END GRID_TO_USGDATA\n"
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s += "\n"
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s += "BEGIN GRID_TO_VTKFILE grid_to_vtk\n"
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