modflowpy · jdhughes-dev · Jun 23, 2020 · Jun 11, 2020 · Jun 12, 2020 · Jun 17, 2020
diff --git a/README.md b/README.md
@@ -3,11 +3,11 @@
 
 ### Version 3.3.1 &mdash; release candidate
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 Introduction

diff --git a/autotest/get_exes.py b/autotest/get_exes.py
@@ -55,6 +55,16 @@ def list_exes():
 def test_download_and_unzip():
     pymake.getmfexes(exe_pth)
 
+    # move the exes from exe_pth to bindir
+    files = os.listdir(exe_pth)
+    for file in files:
+        if file.startswith('__'):
+            continue
+        src = os.path.join(exe_pth, file)
+        dst = os.path.join(bindir, file)
+        print('moving {} -> {}'.format(src, dst))
+        os.replace(src, dst)
+
 
 def test_cleanup():
     cleanup()
@@ -65,7 +75,7 @@ def test_list_download():
 
 
 def main():
-    pymake.getmfexes(exe_pth)
+    test_download_and_unzip()
 
     # clean up the download directory
     cleanup()

diff --git a/autotest/t065_test_gridintersect.py b/autotest/t065_test_gridintersect.py
@@ -841,6 +841,22 @@ def test_rect_grid_polygon_with_hole_shapely(rtree=True):
     return result
 
 
+def test_rect_grid_polygon_in_edge_in_cell(rtree=True):
+    # avoid test fail when shapely not available
+    try:
+        import shapely
+    except:
+        return
+    gr = get_rect_grid()
+    ix = GridIntersect(gr, method='vertex', rtree=rtree)
+    p = Polygon([(0., 5.), (3., 0.), (7., 0.),
+                 (10., 5.), (10., -1.), (0., -1.)])
+    result = ix.intersect_polygon(p)
+    assert len(result) == 1
+    assert result.areas.sum() == 15.
+    return result
+
+
 def test_tri_grid_polygon_outside(rtree=True):
     # avoid test fail when shapely not available
     try:

diff --git a/flopy/discretization/grid.py b/flopy/discretization/grid.py
@@ -51,7 +51,7 @@ class Grid(object):
     rotation : float
         rotation angle of model grid, as it is rotated around the origin point
 
-    Properties
+    Attributes
     ----------
     grid_type : enumeration
         type of model grid ('structured', 'vertex_layered',

diff --git a/flopy/mf6/data/dfn/gwf-chd.dfn b/flopy/mf6/data/dfn/gwf-chd.dfn
@@ -180,7 +180,7 @@ in_record true
 reader urword
 time_series true
 longname head value assigned to constant head
-description is the head at the boundary.
+description is the head at the boundary. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
 
 block period
 name aux

diff --git a/flopy/mf6/data/dfn/gwf-csub.dfn b/flopy/mf6/data/dfn/gwf-csub.dfn
@@ -405,6 +405,38 @@ optional false
 longname file keyword
 description name of the binary output file to write z-displacement information.
 
+block options
+name package_convergence_filerecord
+type record package_convergence fileout package_convergence_filename
+shape
+reader urword
+tagged true
+optional true
+longname
+description
+
+block options
+name package_convergence
+type keyword
+shape
+in_record true
+reader urword
+tagged true
+optional false
+longname package_convergence keyword
+description keyword to specify that record corresponds to the package convergence comma spaced values file.
+
+block options
+name package_convergence_filename
+type string
+shape
+in_record true
+reader urword
+tagged false
+optional false
+longname file keyword
+description name of the comma spaced values output file to write package convergence information.
+
 block options
 name ts_filerecord
 type record ts6 filein ts6_filename
@@ -544,7 +576,7 @@ description is the specific gravity of saturated sediments. If not specified, th
 block packagedata
 name packagedata
 type recarray icsubno cellid cdelay pcs0 thick_frac rnb ssv_cc sse_cr theta kv h0 boundname
-shape (ncsubcells)
+shape (ninterbeds)
 reader urword
 longname
 description
@@ -557,7 +589,7 @@ tagged false
 in_record true
 reader urword
 longname CSUB id number for this entry
-description integer value that defines the CSUB interbed number associated with the specified PACKAGEDATA data on the line. CSUBNO must be greater than zero and less than or equal to NCSUBCELLS.  CSUB information must be specified for every CSUB cell or the program will terminate with an error.  The program will also terminate with an error if information for a CSUB interbed number is specified more than once.
+description integer value that defines the CSUB interbed number associated with the specified PACKAGEDATA data on the line. CSUBNO must be greater than zero and less than or equal to NINTERBEDS.  CSUB information must be specified for every CSUB cell or the program will terminate with an error.  The program will also terminate with an error if information for a CSUB interbed number is specified more than once.
 numeric_index true
 
 block packagedata
@@ -577,7 +609,7 @@ shape
 tagged false
 in_record true
 reader urword
-longname initial water content
+longname delay type
 description character string that defines the subsidence delay type for the interbed. Possible subsidence package CDELAY strings include: NODELAY--character keyword to indicate that delay will not be simulated in the interbed.  DELAY--character keyword to indicate that delay will be simulated in the interbed.
 
 block packagedata
@@ -627,7 +659,7 @@ shape
 tagged false
 in_record true
 reader urword
-longname initial elastic interbed specific storage
+longname initial interbed elastic specific storage
 description is the initial elastic coarse-grained material specific storage or recompression index of the interbed. The recompression index is specified if COMPRESSION\_INDICES is specified in the OPTIONS block. Specified or calculated interbed elastic specific storage values are not adjusted from initial values if HEAD\_BASED is specified in the OPTIONS block.
 
 block packagedata
@@ -714,4 +746,4 @@ in_record true
 reader urword
 time_series true
 longname well stress offset
-description is the stress offset for the cell. SIG0 is added to the calculated geostatic stress for the cell. SIG0 is specified only if MAXSIG0 is specified to be greater than 0 in the DIMENSIONS block.
+description is the stress offset for the cell. SIG0 is added to the calculated geostatic stress for the cell. SIG0 is specified only if MAXSIG0 is specified to be greater than 0 in the DIMENSIONS block. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
diff --git a/flopy/mf6/data/dfn/gwf-disu.dfn b/flopy/mf6/data/dfn/gwf-disu.dfn
@@ -97,7 +97,7 @@ name idomain
 type integer
 shape (nodes)
 reader readarray
-layered true
+layered false
 optional true
 longname idomain existence array
 description is an optional array that characterizes the existence status of a cell.  If the IDOMAIN array is not specified, then all model cells exist within the solution.  If the IDOMAIN value for a cell is 0, the cell does not exist in the simulation.  Input and output values will be read and written for the cell, but internal to the program, the cell is excluded from the solution.  If the IDOMAIN value for a cell is 1, the cell exists in the simulation.  IDOMAIN values of -1 cannot be specified for the DISU Package.

diff --git a/flopy/mf6/data/dfn/gwf-drn.dfn b/flopy/mf6/data/dfn/gwf-drn.dfn
@@ -18,6 +18,15 @@ optional true
 longname name of auxiliary variable for multiplier
 description REPLACE auxmultname {'{#1}': 'drain conductance'}
 
+block options
+name auxdepthname
+type string
+shape
+reader urword
+optional true
+longname name of auxiliary variable for drainage depth
+description name of a variable listed in AUXILIARY that defines the depth at which drainage discharge will be scaled. If a positive value is specified for the AUXDEPTHNAME AUXILIARY variable, then ELEV is the elevation at which the drain starts to discharge and ELEV + DDRN (assuming DDRN is the AUXDEPTHNAME variable) is the elevation when the drain conductance (COND) scaling factor is 1. If a negative drainage depth value is specified for DDRN, then ELEV + DDRN is the elevation at which the drain starts to discharge and ELEV is the elevation when the conductance (COND) scaling factor is 1. A linear- or cubic-scaling is used to scale the drain conductance (COND) when the Standard or Newton-Raphson Formulation is used, respectively.
+
 block options
 name boundnames
 type keyword

diff --git a/flopy/mf6/data/dfn/gwf-evt.dfn b/flopy/mf6/data/dfn/gwf-evt.dfn
@@ -203,7 +203,7 @@ in_record true
 reader urword
 time_series true
 longname ET surface
-description is the elevation of the ET surface ($L$). A time-series name may be specified. 
+description is the elevation of the ET surface ($L$). If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
 
 block period
 name rate
@@ -214,7 +214,7 @@ in_record true
 reader urword
 time_series true
 longname maximum ET rate
-description is the maximum ET flux rate ($LT^{-1}$).  A time-series name may be specified. 
+description is the maximum ET flux rate ($LT^{-1}$). If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
 
 block period
 name depth
@@ -225,7 +225,7 @@ in_record true
 reader urword
 time_series true
 longname ET extinction depth
-description is the ET extinction depth ($L$).  A time-series name may be specified. 
+description is the ET extinction depth ($L$). If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
 
 block period
 name pxdp
@@ -236,7 +236,7 @@ in_record true
 reader urword
 time_series true
 longname proportion of ET extinction depth
-description is the proportion of the ET extinction depth at the bottom of a segment (dimensionless).  A time-series name may be specified. 
+description is the proportion of the ET extinction depth at the bottom of a segment (dimensionless). If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
 
 block period
 name petm
@@ -247,7 +247,7 @@ in_record true
 reader urword
 time_series true
 longname proportion of maximum ET rate
-description is the proportion of the maximum ET flux rate at the bottom of a segment (dimensionless).  A time-series name may be specified. 
+description is the proportion of the maximum ET flux rate at the bottom of a segment (dimensionless). If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
 
 block period
 name petm0
@@ -259,7 +259,7 @@ reader urword
 optional true
 time_series true
 longname proportion of maximum ET rate at ET surface
-description is the proportion of the maximum ET flux rate that will apply when head is at or above the ET surface (dimensionless). PETM0 is read only when the SURF\_RATE\_SPECIFIED option is used. A time-series name may be specified.
+description is the proportion of the maximum ET flux rate that will apply when head is at or above the ET surface (dimensionless). PETM0 is read only when the SURF\_RATE\_SPECIFIED option is used. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
 
 block period
 name aux

diff --git a/flopy/mf6/data/dfn/gwf-lak.dfn b/flopy/mf6/data/dfn/gwf-lak.dfn
@@ -127,6 +127,38 @@ optional false
 longname file keyword
 description name of the binary output file to write budget information.
 
+block options
+name package_convergence_filerecord
+type record package_convergence fileout package_convergence_filename
+shape
+reader urword
+tagged true
+optional true
+longname
+description
+
+block options
+name package_convergence
+type keyword
+shape
+in_record true
+reader urword
+tagged true
+optional false
+longname package_convergence keyword
+description keyword to specify that record corresponds to the package convergence comma spaced values file.
+
+block options
+name package_convergence_filename
+type string
+shape
+in_record true
+reader urword
+tagged false
+optional false
+longname file keyword
+description name of the comma spaced values output file to write package convergence information.
+
 block options
 name ts_filerecord
 type record ts6 filein ts6_filename
@@ -483,7 +515,7 @@ reader urword
 optional false
 tagged false
 longname table file name
-description character string that defines the path and filename for the file containing lake table data for the lake connection. The CTABNAME file includes the number of entries in the file and the relation between stage, surface area, and volume for each entry in the file. Lake table files for EMBEDDEDH and EMBEDDEDV lake-GWF connections also include lake-GWF exchange area data for each entry in the file. Input instructions for the CTABNAME file is included at the LAK package lake table file input instructions section.
+description character string that defines the path and filename for the file containing lake table data for the lake connection. The TAB6\_FILENAME file includes the number of entries in the file and the relation between stage, volume, and surface area for each entry in the file. Lake table files for EMBEDDEDH and EMBEDDEDV lake-GWF connections also include lake-GWF exchange area data for each entry in the file. Instructions for creating the TAB6\_FILENAME input file are provided in Lake Table Input File section.
 
 
 

diff --git a/flopy/mf6/data/dfn/gwf-maw.dfn b/flopy/mf6/data/dfn/gwf-maw.dfn
@@ -135,6 +135,14 @@ optional true
 longname deactivate well storage
 description keyword that deactivates inclusion of well storage contributions to the multi-aquifer well package continuity equation.
 
+block options
+name flow_correction
+type keyword
+reader urword
+optional true
+longname activate flow correction
+description keyword that activates flow corrections in cases where the head in a multi-aquifer well is below the bottom of the screen for a connection or the head in a convertible cell connected to a multi-aquifer well is below the cell bottom. When flow corrections are activated, unit head gradients are used to calculate the flow between a multi-aquifer well and a connected GWF cell. By default, flow corrections are not made.
+
 block options
 name flowing_wells
 type keyword
@@ -314,7 +322,7 @@ tagged false
 in_record true
 reader urword
 longname conductance equation
-description character string that defines the conductance equation that is used to calculate the saturated conductance for the multi-aquifer well. Possible multi-aquifer well CONDEQN strings include: SPECIFIED--character keyword to indicate the multi-aquifer well saturated conductance will be specified.  THIEM--character keyword to indicate the multi-aquifer well saturated conductance will be calculated using the Thiem equation, which considers the cell top and bottom, aquifer hydraulic conductivity, and effective cell and well radius.  SKIN--character keyword to indicate that the multi-aquifer well saturated conductance will be calculated using the cell top and bottom, aquifer and screen hydraulic conductivity, and well and skin radius.    CUMULATIVE--character keyword to indicate that the multi-aquifer well saturated conductance will be calculated using a combination of the Thiem and SKIN equations.  MEAN--character keyword to indicate the multi-aquifer well saturated conductance will be calculated using the aquifer and screen top and bottom, aquifer and screen hydraulic conductivity, and well and skin radius.
+description character string that defines the conductance equation that is used to calculate the saturated conductance for the multi-aquifer well. Possible multi-aquifer well CONDEQN strings include: SPECIFIED--character keyword to indicate the multi-aquifer well saturated conductance will be specified.  THIEM--character keyword to indicate the multi-aquifer well saturated conductance will be calculated using the Thiem equation, which considers the cell top and bottom, aquifer hydraulic conductivity, and effective cell and well radius.  SKIN--character keyword to indicate that the multi-aquifer well saturated conductance will be calculated using the cell top and bottom, aquifer and screen hydraulic conductivity, and well and skin radius.  CUMULATIVE--character keyword to indicate that the multi-aquifer well saturated conductance will be calculated using a combination of the Thiem and SKIN equations.  MEAN--character keyword to indicate the multi-aquifer well saturated conductance will be calculated using the aquifer and screen top and bottom, aquifer and screen hydraulic conductivity, and well and skin radius. The CUMULATIVE conductance equation is identical to the SKIN LOSSTYPE in the Multi-Node Well (MNW2) package for MODFLOW-2005. The program will terminate with an error condition if CONDEQN is SKIN or CUMULATIVE and the calculated saturated conductance is less than zero; if an error condition occurs, it is suggested that the THEIM or MEAN conductance equations be used for these multi-aquifer wells.
 
 block packagedata
 name ngwfnodes
@@ -419,7 +427,7 @@ tagged false
 in_record true
 reader urword
 longname skin data
-description value that defines the skin (filter pack) hydraulic conductivity (if CONDEQN for the multi-aquifer well is SKIN, CUMULATIVE, or MEAN) or conductance (if CONDEQN for the multi-aquifer well is SPECIFIED) for each GWF node connected to the multi-aquifer well (NGWFNODES). HK\_SKIN can be any value if CONDEQN is THIEM.
+description value that defines the skin (filter pack) hydraulic conductivity (if CONDEQN for the multi-aquifer well is SKIN, CUMULATIVE, or MEAN) or conductance (if CONDEQN for the multi-aquifer well is SPECIFIED) for each GWF node connected to the multi-aquifer well (NGWFNODES). If CONDEQN is SPECIFIED, HK\_SKIN must be greater than or equal to zero.  HK\_SKIN can be any value if CONDEQN is THIEM. Otherwise, HK\_SKIN must be greater than zero. If CONDEQN is SKIN, the contrast between the cell transmissivity (the product of geometric mean horizontal hydraulic conductivity and the cell thickness) and the well transmissivity (the product of HK\_SKIN and the screen thicknesses) must be greater than one in node CELLID or the program will terminate with an error condition; if an error condition occurs, it is suggested that the HK\_SKIN be reduced to a value less than K11 and K22 in node CELLID or the THEIM or MEAN conductance equations be used for these multi-aquifer wells.
 
 block connectiondata
 name radius_skin