feat(mf6 checker): input data check for mf6 (#779)

* feat(input data check for mf6): refactored mf2005 input data check to support both mf2005 and mf6

* feat(input data check for mf6): refactor of mf2005 code to work with mf6

* feat(input data check for mf6): autotest updates

* feat(input data check for mf6)

* fix(codacy fixes)

* fix(check too complex)

* fix(codacy): simplified check code

autotest/t024_test.py

@@ -40,6 +40,7 @@ def test_bcs_check():
     ibound[1, 1, 1] = 1  # fully isolated cell
     ibound[0:2, 4, 4] = 1  # cell connected vertically to one other cell
     bas = flopy.modflow.ModflowBas(mf, ibound=ibound)
+    mf._mg_resync = True
     chk = bas.check()
     assert chk.summary_array['desc'][0] == 'isolated cells in ibound array'
     assert chk.summary_array.i[0] == 1 and chk.summary_array.i[0] == 1 and \

autotest/t504_test.py

@@ -49,7 +49,7 @@ def test001a_tharmonic():
 
     # load simulation
     sim = MFSimulation.load(model_name, 'mf6', exe_name, pth,
-                            verbosity_level=0)
+                            verbosity_level=0, verify_data=True)
     sim.simulation_data.mfpath.set_sim_path(run_folder)
 
     # write simulation to new location
@@ -150,7 +150,8 @@ def test003_gwfs_disv():
     array_util = PyListUtil()
 
     # load simulation
-    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth)
+    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth,
+                            verify_data=True)
 
     # make temp folder to save simulation
     sim.simulation_data.mfpath.set_sim_path(run_folder)
@@ -235,7 +236,7 @@ def test005_advgw_tidal():
 
     # load simulation
     sim = MFSimulation.load(model_name, 'mf6', exe_name, pth,
-                            verbosity_level=2)
+                            verbosity_level=2, verify_data=True)
 
     # test obs/ts package interface
     model = sim.get_model(model_name)
@@ -321,7 +322,8 @@ def test006_gwf3():
     array_util = PyListUtil()
 
     # load simulation
-    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth)
+    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth,
+                            verify_data=True)
 
     model = sim.get_model()
     disu = model.get_package('disu')
@@ -460,7 +462,8 @@ def test045_lake1ss_table():
     expected_head_file_b = os.path.join(expected_output_folder, 'lakeex1b_adj.hds')
 
     # load simulation
-    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth)
+    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth,
+                            verify_data=True)
 
     # make temp folder to save simulation
     sim.simulation_data.mfpath.set_sim_path(run_folder)
@@ -532,7 +535,7 @@ def test006_2models_mvr():
     expected_head_file_bb = os.path.join(expected_output_folder, 'model2_adj.hds')
 
     # load simulation
-    sim = MFSimulation.load(sim_name, 'mf6', exe_name, pth)
+    sim = MFSimulation.load(sim_name, 'mf6', exe_name, pth, verify_data=True)
 
     # make temp folder to save simulation
     sim.simulation_data.mfpath.set_sim_path(run_folder)
@@ -685,7 +688,8 @@ def test001e_uzf_3lay():
     expected_head_file_b = os.path.join(expected_output_folder, 'test001e_UZF_3lay_adj.hds')
 
     # load simulation
-    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth)
+    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth,
+                            verify_data=True)
 
     # make temp folder to save simulation
     sim.simulation_data.mfpath.set_sim_path(run_folder)
@@ -766,7 +770,8 @@ def test045_lake2tr():
                                         'lakeex2a_adj.hds')
 
     # load simulation
-    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth)
+    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth,
+                            verify_data=True)
 
     # write simulation to new location
     sim.simulation_data.mfpath.set_sim_path(run_folder)
@@ -824,7 +829,8 @@ def test036_twrihfb():
     expected_head_file_b = os.path.join(expected_output_folder, 'twrihfb2015_output_adj.hds')
 
     # load simulation
-    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth)
+    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth,
+                            verify_data = True)
 
     # make temp folder to save simulation
     sim.simulation_data.mfpath.set_sim_path(run_folder)
@@ -890,7 +896,8 @@ def test027_timeseriestest():
     expected_head_file_b = os.path.join(expected_output_folder, 'timeseriestest_adj.hds')
 
     # load simulation
-    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth)
+    sim = MFSimulation.load(model_name, 'mf6', exe_name, pth,
+                            verify_data=True)
 
     # make temp folder to save simulation
     sim.simulation_data.mfpath.set_sim_path(run_folder)

autotest/t505_test.py

@@ -74,8 +74,8 @@ def np001():
                             exe_name=exe_name, sim_ws=run_folder,
                             continue_=True, memory_print_option='summary')
     name = test_sim.name_file
-    assert name.continue_.get_data() == True
-    assert name.nocheck.get_data() == None
+    assert name.continue_.get_data()
+    assert name.nocheck.get_data() is None
     assert name.memory_print_option.get_data() == 'summary'
 
     kwargs = {}
@@ -289,8 +289,25 @@ def np001():
                                     stress_period_data=well_spd)
     except MFDataException:
         error_occurred = True
-
     assert error_occurred
+
+    # test error checking
+    drn_package = ModflowGwfdrn(model, print_input=True, print_flows=True,
+                                save_flows=True, maxbound=1,
+                                timeseries=[(0.0, 60.0), (100000.0, 60.0)],
+                                stress_period_data=[((100, 0, 0), np.nan,
+                                                     'drn_1'), ((0, 0, 0),
+                                                    10.0)])
+    npf_package = ModflowGwfnpf(model, save_flows=True,
+                                alternative_cell_averaging='logarithmic',
+                                icelltype=1, k=100001.0, k33=1e-12)
+    chk = sim.check()
+    summary = '.'.join(chk[0].summary_array.desc)
+    assert 'drn_1 package: invalid BC index' in summary
+    assert 'npf package: vertical hydraulic conductivity values below ' \
+           'checker threshold of 1e-11' in summary
+    assert 'npf package: horizontal hydraulic conductivity values above ' \
+           'checker threshold of 100000.0' in summary
     return
 
 
@@ -391,8 +408,8 @@ def np002():
         sim.run_simulation()
 
         sim2 = MFSimulation.load(sim_ws=run_folder)
-        model = sim2.get_model(model_name)
-        npf_package = model.get_package('npf')
+        model_ = sim2.get_model(model_name)
+        npf_package = model_.get_package('npf')
         k = npf_package.k.array
 
         # get expected results
@@ -426,6 +443,20 @@ def np002():
         # clean up
         sim.delete_output_files()
 
+    # test error checking
+    sto_package = ModflowGwfsto(model, save_flows=True, iconvert=1,
+                                ss=0.00000001, sy=0.6)
+    chd_package = ModflowGwfchd(model, print_input=True, print_flows=True,
+                                maxbound=1, stress_period_data=[((0, 0, 0),
+                                                                 np.nan)])
+    chk = sim.check()
+    summary = '.'.join(chk[0].summary_array.desc)
+    assert 'sto package: specific storage values below ' \
+           'checker threshold of 1e-06' in summary
+    assert 'sto package: specific yield values above ' \
+           'checker threshold of 0.5' in summary
+    assert 'Not a number' in summary
+
     return
 
 
@@ -954,6 +985,11 @@ def test005_advgw_tidal():
     # clean up
     sim.delete_output_files()
 
+    # check packages
+    chk = sim.check()
+    summary = '.'.join(chk[0].summary_array.desc)
+    assert summary == ''
+
     return
 
 

flopy/discretization/structuredgrid.py

@@ -55,9 +55,15 @@ def __init__(self, delc=None, delr=None, top=None, botm=None, idomain=None,
             assert self.__nrow * self.__ncol == len(np.ravel(top))
         if botm is not None:
             assert self.__nrow * self.__ncol == len(np.ravel(botm[0]))
+            if nlay is not None and nlay < len(botm):
+                self.__nlay_nocbd = nlay
+            else:
+                self.__nlay_nocbd = len(botm)
+
             self.__nlay = len(botm)
         else:
             self.__nlay = nlay
+            self.__nlay_nocbd = nlay
 
     ####################
     # Properties
@@ -75,6 +81,10 @@ def is_complete(self):
             return True
         return False
 
+    @property
+    def nlay_nocbd(self):
+        return self.__nlay_nocbd
+
     @property
     def nlay(self):
         return self.__nlay

flopy/discretization/unstructuredgrid.py

@@ -96,11 +96,16 @@ def nnodes(self):
     @property
     def ncpl(self):
         if self._ncpl is None:
-            return len(self._iverts)
+            if self._iverts is None:
+                return None
+            else:
+                return len(self._iverts)
         return self._ncpl
 
     @property
     def shape(self):
+        if self.ncpl is None:
+            return self.nnodes
         if isinstance(self.ncpl, (list, np.ndarray)):
             return self.nlay, self.ncpl[0]
         else:

flopy/export/netcdf.py

@@ -197,7 +197,8 @@ def __init__(self, output_filename, model, time_values=None,
         self.z_positive = z_positive
         if self.grid_units is None:
             self.grid_units = "unspecified"
-        assert self.grid_units in ["feet", "meters", "unspecified"], \
+        assert self.grid_units in ["feet", "meters", "unspecified",
+                                   "undefined"], \
             "unsupported length units: " + self.grid_units
 
         self.time_units = self.model_time.time_units