update(ModflowFlwob and ModflowHob): added "no_print", "options", and… (

#414)

* update(ModflowFlwob and ModflowHob): added "no_print", "options", and "filenames" kwargs.

*  refactor(modpath): refactor MODPATH 7 particle classes

Refactor MODPATH 7 particle classes to make a clear distinction between
particle groups and particle data (locations, etc.).

* Changes to LKT for dealing with multi-species simulations that include lakes (#412)

* Explicit cast to np.array isn't preserved

* Fixes issue in LAK package _init_ routines when only a single lake is active

* Previous alteration worked for one lake, but didn't handle one stage for multiple lakes.  This should account for that condition

* Fix mis-statement

* LMT: Lacking support for keyword 'ALL' following Package_Flows keyword

* Add precision for variable thkmin

* PERLEN variable getting trucated by use of "G" (general form) when number of significant digits was > 4.

* Switching printing of PERLEN in BTN from 10.6G to 10G

* Fix for issue #402 including a new test for checking mtlkt.py

* Remove apostrophe from comment (interferes with Travis build)

* Rename test, another recent commit had the same name

* Remove argument from call to test

* refactor(modpath): refactor particledata (#416)

Refactor ParticleData (input style 1) so that it is the same as the 
node template (input style 3). Refactor NodeParticleTemplates 
particles into a single class. Add starting particle location data 
input style 2.

* New jupyter notebook for MT3D-USGS (#415)

* Explicit cast to np.array isn't preserved

* Fixes issue in LAK package _init_ routines when only a single lake is active

* Previous alteration worked for one lake, but didn't handle one stage for multiple lakes.  This should account for that condition

* Fix mis-statement

* LMT: Lacking support for keyword 'ALL' following Package_Flows keyword

* Add precision for variable thkmin

* PERLEN variable getting trucated by use of "G" (general form) when number of significant digits was > 4.

* Switching printing of PERLEN in BTN from 10.6G to 10G

* Fix for issue #402 including a new test for checking mtlkt.py

* Remove apostrophe from comment (interferes with Travis build)

* Rename test, another recent commit had the same name

* Remove argument from call to test

* Adding new example notebook for MT3D-USGS that uses SFT, LKT, and UZT, including connections between them

* Fixed a typo, added link for docs/notebook_examples.md in a reasonable section of the document

* An errant capital letter in the new notebook, switched to lowercase

* docs: update documentation (#417)

Update docstrings for MFGridFile class. Update README.md and
CONTRIBUTING.md. Update pre-commit.py to use develop branch for
branches with "-" or ":" in the branch name (it is assumed these
are bug fix or feature branches for the develop branch.

* refactor(lgrutil.py) : redesign of the hidden lgrutil gem

Unfortunately, this breaks backward compatibility (if anyone was using this).  But the new implementation should be a little easier to use.  Still  need to implement ghost nodes.

* Removed old newline character before "NOPRINT".

* docs: update docstrings (#418)

Update docstrings for HeadObservation, ModflowHobs, and ModflowFlwob
classes.

Closed #406

* docs: update docstrings (#419)

Update docstrings for sphinx.

* refactor(Modflow): Forgive loading models with an incomplete BAS6 package (#420)

* raise IOError if external file does not exist

* remove requirement that BAS6 needs to be loaded in full

* update(ModflowFlwob and ModflowHob): add condition test to check for user-specified output file names.

* update(ModflowFlwob and ModflowHob): reworked additional code again after refactorization of upstream branch.

* update(ModflowFlwob and ModflowHob): reordered kwargs in __init__ to reflect order in docstring.

* update(ModflowFlwob and ModflowHob): reworked additional code again after refactorization of upstream branch.

* update(ModflowFlwob and ModflowHob): pass list of filenames to Package.__init__() to achieve desired output file names.

* update(ModflowFlwob and ModflowHob): updated HOB test and added new code to test FLWOBS.

* update(ModflowFlwob and ModflowHob): pass mf executable name to new model upon load.

autotest/t041_test.py

@@ -36,7 +36,7 @@ def test_hob_simple():
     ib = np.ones(shape3d, dtype=np.int)
     ib[0, 0, 0] = -1
     m = flopy.modflow.Modflow(modelname=modelname, model_ws=pth,
-                              verbose=True, exe_name=exe_name, )
+                              verbose=False, exe_name=exe_name, )
     dis = flopy.modflow.ModflowDis(m, nlay=1, nrow=11, ncol=11, nper=2,
                                    perlen=[1, 1])
 
@@ -204,7 +204,87 @@ def test_obs_create_and_write():
             raise ValueError('could not load new HOB output file')
 
 
+def test_hob_options():
+    """
+    test041 load and run a simple MODFLOW-2005 OBS example with specified filenames
+    """
+    print('test041 load and run a simple MODFLOW-2005 OBS example with specified filenames')
+    pth = os.path.join(cpth, 'simple')
+    modelname = 'hob_simple'
+    pkglst = ['dis', 'bas6', 'pcg', 'lpf']
+    m = flopy.modflow.Modflow.load(modelname + '.nam', model_ws=pth, check=False,
+                                   load_only=pkglst, verbose=False, exe_name=exe_name)
+
+    obs = flopy.modflow.HeadObservation(m, layer=0, row=5, column=5,
+                                        time_series_data=[[1., 54.4],
+                                                          [2., 55.2]])
+    f_in = modelname + '_custom_fname.hob'
+    f_out = modelname + '_custom_fname.hob.out'
+    filenames = [f_in, f_out]
+    hob = flopy.modflow.ModflowHob(m, iuhobsv=51, hobdry=-9999.,
+                                   obs_data=[obs], options=['NOPRINT'],
+                                   filenames=filenames)
+
+
+    # add DRN package
+    spd = {0: [[0, 5, 5, .5, 8e6],
+               [0, 8, 8, .7, 8e6]]}
+    drn = flopy.modflow.ModflowDrn(m, 53, stress_period_data=spd)
+
+    # flow observation
+
+    # Lists of length nqfb
+    nqobfb = [1, 1]
+    nqclfb = [1, 1]
+
+    # Lists of length nqtfb
+    obsnam = ['drob_1', 'drob_2']
+    irefsp = [1, 1]
+    toffset = [0, 0]
+    flwobs = [0., 0.]
+
+    # Lists of length (nqfb, nqclfb)
+    layer = [[1], [1]]
+    row = [[6], [9]]
+    column = [[6], [9]]
+    factor = [[1.], [1.]]
+
+    drob = flopy.modflow.ModflowFlwob(m,
+                                      nqfb=len(nqclfb),
+                                      nqcfb=np.sum(nqclfb),
+                                      nqtfb=np.sum(nqobfb),
+                                      nqobfb=nqobfb,
+                                      nqclfb=nqclfb,
+                                      obsnam=obsnam,
+                                      irefsp=irefsp,
+                                      toffset=toffset,
+                                      flwobs=flwobs,
+                                      layer=layer,
+                                      row=row,
+                                      column=column,
+                                      factor=factor,
+                                      flowtype='drn',
+                                      options=['NOPRINT'],
+                                      filenames=['flwobs_simple.drob',
+                                                 'flwobs_simple.obd'])
+    # Write the model input files
+    m.write_input()
+
+    assert m.get_output(unit=51) == f_out, 'output filename ({}) does \
+                                                not match specified name'.format(m.get_output(unit=51))
+
+    assert os.path.isfile(os.path.join(pth, f_in)), 'specified HOB input file not found'
+
+    # run the modflow-2005 model
+    if run:
+        success, buff = m.run_model(silent=False)
+        assert success, 'could not run simple MODFLOW-2005 model'
+
+    return
+
+
 if __name__ == '__main__':
     test_hob_simple()
     test_obs_create_and_write()
     test_obs_load_and_write()
+    test_hob_options()

flopy/mbase.py

@@ -349,7 +349,8 @@ def add_output_file(self, unit, fname=None, extension='cbc',
             # determine if the file is in external_units
             if abs(unit) in self.external_units:
                 idx = self.external_units.index(abs(unit))
-                fname = os.path.basename(self.external_fnames[idx])
+                if fname is None:
+                    fname = os.path.basename(self.external_fnames[idx])
                 binflag = self.external_binflag[idx]
                 self.remove_external(unit=abs(unit))
             # determine if the unit exists in the output data

flopy/modflow/mfflwob.py

@@ -63,9 +63,25 @@ class ModflowFlwob(Package):
         Filename extension. If extension is None, extension is set to
         ['chob','obc','gbob','obg','drob','obd', 'rvob','obr']
         (default is None).
+    no_print : boolean
+        When True or 1, a list of flow observations will not be
+        written to the Listing File (default is False)
+    options : list of strings
+        Package options (default is None).
     unitnumber : list of int
         File unit number. If unitnumber is None, unitnumber is set to
         [40, 140, 41, 141, 42, 142, 43, 143] (default is None).
+    filenames : str or list of str
+        Filenames to use for the package and the output files. If
+        filenames=None the package name will be created using the model name
+        and package extension and the flwob output name will be created using
+        the model name and .out extension (for example,
+        modflowtest.out), if iufbobsv is a number greater than zero.
+        If a single string is passed the package will be set to the string
+        and flwob output name will be created using the model name and .out
+        extension, if iufbobsv is a number greater than zero. To define the
+        names for all package files (input and output) the length of the list
+        of strings should be 2. Default is None.
 
 
     Attributes
@@ -88,7 +104,8 @@ def __init__(self, model, nqfb=0, nqcfb=0, nqtfb=0, iufbobsv=0,
                  tomultfb=1.0, nqobfb=None, nqclfb=None, obsnam=None,
                  irefsp=None, toffset=None, flwobs=None, layer=None,
                  row=None, column=None, factor=None, flowtype=None,
-                 extension=None, unitnumber=None):
+                 extension=None, no_print=False, options=None,
+                 filenames=None, unitnumber=None):
 
         """
         Package constructor
@@ -151,9 +168,19 @@ def __init__(self, model, nqfb=0, nqcfb=0, nqtfb=0, iufbobsv=0,
             msg = 'ModflowFlwob: flowtype must be CHD, GHB, DRN, or RIV'
             raise KeyError(msg)
 
+        # set filenames
+        if filenames is None:
+            filenames = [None, None]
+        elif isinstance(filenames, str):
+            filenames = [filenames, None]
+        elif isinstance(filenames, list):
+            if len(filenames) < 2:
+                filenames.append(None)
+
         # call base package constructor
-        Package.__init__(self, model, extension, name, unitnumber,
-                         allowDuplicates=True)
+        Package.__init__(self, model, extension=extension, name=name,
+                         unit_number=unitnumber,
+                         allowDuplicates=True, filenames=filenames)
 
         self.nqfb = nqfb
         self.nqcfb = nqcfb
@@ -198,6 +225,14 @@ def __init__(self, model, nqfb=0, nqcfb=0, nqtfb=0, iufbobsv=0,
 
         # add more checks here
 
+        self.no_print = no_print
+        self.np = 0
+        if options is None:
+            options = []
+        if self.no_print:
+            options.append('NOPRINT')
+        self.options = options
+
         # add checks for input compliance (obsnam length, etc.)
         self.parent.add_package(self)
 
@@ -220,7 +255,10 @@ def write_file(self):
         line = '{:10d}'.format(self.nqfb)
         line += '{:10d}'.format(self.nqcfb)
         line += '{:10d}'.format(self.nqtfb)
-        line += '{:10d}\n'.format(self.iufbobsv)
+        line += '{:10d}'.format(self.iufbobsv)
+        if self.no_print or 'NOPRINT' in self.options:
+            line += '{: >10}'.format('NOPRINT')
+        line += '\n'
         f_fbob.write(line)
         f_fbob.write('{:10e}\n'.format(self.tomultfb))
 

flopy/modflow/mfhob.py

@@ -35,6 +35,11 @@ class ModflowHob(Package):
         will be used (default is None).
     extension : string
         Filename extension (default is hob)
+    no_print : boolean
+        When True or 1, a list of head observations will not be
+        written to the Listing File (default is False)
+    options : list of strings
+        Package options (default is None).
     unitnumber : int
         File unit number (default is None)
     filenames : str or list of str
@@ -77,8 +82,9 @@ class ModflowHob(Package):
     """
 
     def __init__(self, model, iuhobsv=None, hobdry=0, tomulth=1.0,
-                 obs_data=None, hobname=None,
-                 extension='hob', unitnumber=None, filenames=None):
+                 obs_data=None, hobname=None, extension='hob',
+                 no_print=False, options=None,
+                 unitnumber=None, filenames=None):
         """
         Package constructor
         """
@@ -140,6 +146,14 @@ def __init__(self, model, iuhobsv=None, hobdry=0, tomulth=1.0,
         # set self.obs_data
         self.obs_data = obs_data
 
+        self.no_print = no_print
+        self.np = 0
+        if options is None:
+            options = []
+        if self.no_print:
+            options.append('NOPRINT')
+        self.options = options
+
         # add checks for input compliance (obsnam length, etc.)
         self.parent.add_package(self)
 
@@ -194,7 +208,10 @@ def write_file(self):
         f.write('{:10d}'.format(self.mobs))
         f.write('{:10d}'.format(self.maxm))
         f.write('{:10d}'.format(self.iuhobsv))
-        f.write('{:10.4g}\n'.format(self.hobdry))
+        f.write('{:10.4g}'.format(self.hobdry))
+        if self.no_print or 'NOPRINT' in self.options:
+            f.write('{: >10}'.format('NOPRINT'))
+        f.write('\n')
 
         # write dataset 2
         f.write('{:10.4g}\n'.format(self.tomulth))