Added VKD definition file and files needed to create the user guide V…

…KD information.

README.md

@@ -7,8 +7,8 @@
 
 ## Automated Testing Status on Travis-CI
 
-### Version 6.0.3 develop — build 13
-[![Build Status](https://travis-ci.org/MODFLOW-USGS/modflow6.svg?branch=develop)](https://travis-ci.org/MODFLOW-USGS/modflow6)
+### Version 6.0.3 vkd — build 8
+[![Build Status](https://travis-ci.org/MODFLOW-USGS/modflow6.svg?branch=vkd)](https://travis-ci.org/MODFLOW-USGS/modflow6)
 
 ## Introduction
 
@@ -31,7 +31,7 @@ MODFLOW 6 is the latest core version of MODFLOW. It synthesizes many of the capa
 
 #### ***Software/Code citation for MODFLOW 6:***
 
-[Langevin, C.D., Hughes, J.D., Banta, E.R., Provost, A.M., Niswonger, R.G., and Panday, Sorab, 2018, MODFLOW 6 Modular Hydrologic Model version 6.0.3 — develop: U.S. Geological Survey Software Release, 30 August 2018, https://doi.org/10.5066/F76Q1VQV](https://doi.org/10.5066/F76Q1VQV)
+[Langevin, C.D., Hughes, J.D., Banta, E.R., Provost, A.M., Niswonger, R.G., and Panday, Sorab, 2018, MODFLOW 6 Modular Hydrologic Model version 6.0.3 — vkd: U.S. Geological Survey Software Release, 06 September 2018, https://doi.org/10.5066/F76Q1VQV](https://doi.org/10.5066/F76Q1VQV)
 
 
 ## Instructions for building definition files for new packages

code.json

@@ -1,26 +1,26 @@
 [
     {
         "status": "Release Candidate", 
-        "languages": [
-            "Fortran2008"
-        ], 
+        "downloadURL": "https://code.usgs.gov/usgs/modflow/modflow6/archive/master.zip", 
         "repositoryURL": "https://code.usgs.gov/usgs/modflow/modflow6.git", 
         "disclaimerURL": "https://code.usgs.gov/usgs/modflow/modflow6/blob/master/DISCLAIMER.md", 
         "tags": [
             "MODFLOW", 
             "groundwater model"
         ], 
-        "vcs": "git", 
-        "name": "modflow6", 
-        "downloadURL": "https://code.usgs.gov/usgs/modflow/modflow6/archive/master.zip", 
+        "description": "MODFLOW is the USGS's modular hydrologic model. MODFLOW is considered an international standard for simulating and predicting groundwater conditions and groundwater/surface-water interactions.", 
         "contact": {
             "name": "Christian D. Langevin", 
             "email": "langevin@usgs.gov"
         }, 
+        "languages": [
+            "Fortran2008"
+        ], 
+        "vcs": "git", 
         "laborHours": -1, 
-        "version": "6.0.3.13", 
+        "version": "6.0.3.8", 
         "date": {
-            "metadataLastUpdated": "2018-08-30"
+            "metadataLastUpdated": "2018-09-06"
         }, 
         "organization": "U.S. Geological Survey", 
         "permissions": {
@@ -33,6 +33,6 @@
             "usageType": "openSource"
         }, 
         "homepageURL": "https://code.usgs.gov/usgs/modflow/modflow6/", 
-        "description": "MODFLOW is the USGS's modular hydrologic model. MODFLOW is considered an international standard for simulating and predicting groundwater conditions and groundwater/surface-water interactions."
+        "name": "modflow6"
     }
 ]

doc/mf6io/gwf/gwf.tex

@@ -85,6 +85,10 @@ \subsection{Observation (OBS) Utility for a GWF Model}
 \subsection{Node Property Flow (NPF) Package}
 \input{gwf/npf}
 
+\newpage
+\subsection{Variations in Hydraulic Conductivity with Depth (VKD) Package}
+\input{gwf/vkd}
+
 \newpage
 \subsection{Horizontal Flow Barrier (HFB) Package}
 \input{gwf/hfb}

doc/mf6io/gwf/vkd.tex

@@ -0,0 +1,20 @@
+Input to the Variations in Hydraulic Conductivity with Depth (VKD) Package is read from the file of type ``VKD6''.  The VKD Package is activated by specifying an option in the NPF options block.  Only one VKD Package can be specified for a GWF model.
+
+\vspace{5mm}
+\subsubsection{Structure of Blocks}
+\vspace{5mm}
+
+\noindent \textit{FOR EACH SIMULATION}
+\lstinputlisting[style=blockdefinition]{./mf6ivar/tex/gwf-vkd-options.dat}
+\lstinputlisting[style=blockdefinition]{./mf6ivar/tex/gwf-vkd-dimensions.dat}
+\lstinputlisting[style=blockdefinition]{./mf6ivar/tex/gwf-vkd-packagedata.dat}
+
+\vspace{5mm}
+\subsubsection{Explanation of Variables}
+\begin{description}
+\input{./mf6ivar/tex/gwf-vkd-desc.tex}
+\end{description}
+
+\vspace{5mm}
+\subsubsection{Example Input File}
+\lstinputlisting[style=inputfile]{./mf6ivar/examples/gwf-vkd-example.dat}

doc/mf6io/mf6ivar/dfn/gwf-npf.dfn

@@ -135,6 +135,49 @@ optional true
 longname keyword to save specific discharge
 description keyword to indicate that x, y, and z components of specific discharge will be calculated at cell centers and written to the cell-by-cell flow file, which is specified with ``BUDGET SAVE FILE'' in Output Control.
 
+block options
+name vkd_filerecord
+type record vkd6 filein vkd6_filename
+shape
+reader urword
+tagged true
+optional true
+longname
+description
+
+block options
+name vkd6
+type keyword
+shape
+in_record true
+reader urword
+tagged true
+optional false
+longname vkd keyword
+description keyword to specify that record corresponds to a vkd file.
+
+block options
+name filein
+type keyword
+shape
+in_record true
+reader urword
+tagged true
+optional false
+longname file keyword
+description keyword to specify that an input filename is expected next.
+
+block options
+name vkd6_filename
+type string
+preserve_case true
+in_record true
+tagged false
+reader urword
+optional false
+longname vkd6 input filename
+description is the file name of the VKD input file. This option should not be used unless the Variations in Hydraulic Conductivity with Depth (VKD) Package is needed for the simulation.
+
 
 # --------------------- gwf npf griddata ---------------------
 

doc/mf6io/mf6ivar/dfn/gwf-vkd.dfn

@@ -0,0 +1,69 @@
+# --------------------- gwf vkd options ---------------------
+
+block options
+name print_input
+type keyword
+reader urword
+optional true
+longname model print input to listing file
+description keyword to indicate that the list of VKD cells and information will be written to the listing file immediately after it is read.
+
+
+# --------------------- gwf vkd dimensions ---------------------
+
+block dimensions
+name numvkd
+type integer
+reader urword
+optional false
+longname number of VKD cells
+description integer value specifying the number of VKD cells. There must be NUMVKD entries in the PACKAGEDATA block.
+
+block dimensions
+name numelevs
+type integer
+reader urword
+optional false
+longname number of VKD inflections
+description integer value specifying the number of VKD inflections. There must be NUMELEVS entries for both EIP and KIP for every cell defined in PACKAGEDATA block.
+
+
+# --------------------- gwf vkd packagedata ---------------------
+
+block packagedata
+name packagedata
+type recarray cellid eip kip
+shape (numvkd)
+reader urword
+longname
+description
+
+block packagedata
+name cellid
+type integer
+shape (ncelldim)
+tagged false
+in_record true
+reader urword
+longname cell identifier
+description REPLACE cellid {}
+
+block packagedata
+name eip
+type double precision
+shape (numelevs)
+tagged false
+in_record true
+reader urword
+longname elevation of inflection point
+description elevation of VKD inflection point.  This number is an elevation (relative to the same datum used for cell tops and bottoms) in model length units.
+
+block packagedata
+name kip
+type double precision
+shape (numelevs)
+tagged false
+in_record true
+reader urword
+longname hydraulic conductivity factor
+description hydraulic conductivity factor at VKD inflection point.

doc/mf6io/mf6ivar/examples/gwf-vkd-example.dat

@@ -0,0 +1,13 @@
+BEGIN OPTIONS
+  PRINT_INPUT
+END OPTIONS
+
+BEGIN DIMENSIONS
+  NUMVKD 1
+  NUMELEVS 2
+END DIMENSIONS
+
+BEGIN PACKAGEDATA
+  # L  R  C EIP(1) EIP(2) KIP(1) KIP(2)
+    1  1  4   0.25    0.5    1.0    1.5
+END PACKAGEDATA

doc/mf6io/mf6ivar/md/mf6ivar.md

@@ -44,7 +44,7 @@
 | EXG | GWFGWF | EXCHANGEDATA | CELLIDM2 | INTEGER | is the cellid of the cell in model 2 as specified in the simulation name file. For a structured grid that uses the DIS input file, CELLIDM2 is the layer, row, and column numbers of the cell.   For a grid that uses the DISV input file, CELLIDM2 is the layer number and CELL2D number for the two cells.  If the model uses the unstructured discretization (DISU) input file, then CELLIDM2 is the node number for the cell. |
 | EXG | GWFGWF | EXCHANGEDATA | IHC | INTEGER | is an integer flag indicating the direction between node n and all of its m connections. If IHC = 0 then the connection is vertical.  If IHC = 1 then the connection is horizontal. If IHC = 2 then the connection is horizontal for a vertically staggered grid. |
 | EXG | GWFGWF | EXCHANGEDATA | CL1 | DOUBLE PRECISION | is the distance between the center of cell 1 and the its shared face with cell 2. |
-| EXG | GWFGWF | EXCHANGEDATA | CL2 | DOUBLE PRECISION | is the distance between the center of cell 1 and the its shared face with cell 2. |
+| EXG | GWFGWF | EXCHANGEDATA | CL2 | DOUBLE PRECISION | is the distance between the center of cell 2 and the its shared face with cell 1. |
 | EXG | GWFGWF | EXCHANGEDATA | HWVA | DOUBLE PRECISION | is the horizontal width of the flow connection between cell 1 and cell 2 if IHC $>$ 0, or it is the area perpendicular to flow of the vertical connection between cell 1 and cell 2 if IHC = 0. |
 | EXG | GWFGWF | EXCHANGEDATA | AUX | DOUBLE PRECISION (NAUX) | represents the values of the auxiliary variables for each GWFGWF Exchange. The values of auxiliary variables must be present for each exchange. The values must be specified in the order of the auxiliary variables specified in the OPTIONS block. |
 | SLN | IMS | OPTIONS | PRINT_OPTION | STRING | is a flag that controls printing of convergence information from the solver.  NONE means print nothing. SUMMARY means print only the total number of iterations and nonlinear residual reduction summaries. ALL means print linear matrix solver convergence information to the solution listing file and model specific linear matrix solver convergence information to each model listing file in addition to SUMMARY information. NONE is default if PRINT\_OPTION is not specified. |
@@ -154,6 +154,9 @@
 | GWF | NPF | OPTIONS | XT3D | KEYWORD | keyword indicating that the XT3D formulation will be used.  If the RHS keyword is also included, then the XT3D additional terms will be added to the right-hand side.  If the RHS keyword is excluded, then the XT3D terms will be put into the coefficient matrix.  Use of XT3D will substantially increase the computational effort, but will result in improved accuracy for anisotropic conductivity fields and for unstructured grids in which the CVFD requirement is violated.  XT3D requires additional information about the shapes of grid cells.  If XT3D is active and the DISU Package is used, then the user will need to provide in the DISU Package the angldegx array in the CONNECTIONDATA block and the VERTICES and CELL2D blocks. |
 | GWF | NPF | OPTIONS | RHS | KEYWORD | If the RHS keyword is also included, then the XT3D additional terms will be added to the right-hand side.  If the RHS keyword is excluded, then the XT3D terms will be put into the coefficient matrix. |
 | GWF | NPF | OPTIONS | SAVE_SPECIFIC_DISCHARGE | KEYWORD | keyword to indicate that x, y, and z components of specific discharge will be calculated at cell centers and written to the cell-by-cell flow file, which is specified with ``BUDGET SAVE FILE'' in Output Control. |
+| GWF | NPF | OPTIONS | VKD6 | KEYWORD | keyword to specify that record corresponds to a vkd file. |
+| GWF | NPF | OPTIONS | FILEIN | KEYWORD | keyword to specify that an input filename is expected next. |
+| GWF | NPF | OPTIONS | VKD6_FILENAME | STRING | is the file name of the VKD input file. This option should not be used unless the Variations in Hydraulic Conductivity with Depth (VKD) Package is needed for the simulation. |
 | GWF | NPF | GRIDDATA | ICELLTYPE | INTEGER (NODES) | flag for each cell that specifies how saturated thickness is treated.  0 means saturated thickness is held constant;  $>$0 means saturated thickness varies with computed head when head is below the cell top; $<$0 means saturated thickness varies with computed head unless the THICKSTRT option is in effect.  When THICKSTRT is in effect, a negative value of icelltype indicates that saturated thickness will be computed as STRT-BOT and held constant. |
 | GWF | NPF | GRIDDATA | K | DOUBLE PRECISION (NODES) | is the hydraulic conductivity.  For the common case in which the user would like to specify the horizontal hydraulic conductivity and the vertical hydraulic conductivity, then K should be assigned as the horizontal hydraulic conductivity, K33 should be assigned as the vertical hydraulic conductivity, and texttt{K22} and the three rotation angles should not be specified.  When more sophisticated anisotropy is required, then K corresponds to the K11 hydraulic conductivity axis.  All included cells (IDOMAIN $>$ 0) must have a K value greater than zero. |
 | GWF | NPF | GRIDDATA | K22 | DOUBLE PRECISION (NODES) | is the hydraulic conductivity of the second ellipsoid axis; for an unrotated case this is the hydraulic conductivity in the y direction.  If K22 is not included in the GRIDDATA block, then K22 is set equal to K.  For a regular MODFLOW grid (DIS Package is used) in which no rotation angles are specified, K22 is the hydraulic conductivity along columns in the y direction. For an unstructured DISU grid, the user must assign principal x and y axes and provide the angle for each cell face relative to the assigned x direction.  All included cells (IDOMAIN $>$ 0) must have a K22 value greater than zero. |
@@ -162,6 +165,12 @@
 | GWF | NPF | GRIDDATA | ANGLE2 | DOUBLE PRECISION (NODES) | is a rotation angle of the hydraulic conductivity tensor in degrees. The angle represents the second of three sequential rotations of the hydraulic conductivity ellipsoid. Following the rotation by ANGLE1 described above, ANGLE2 rotates the ellipsoid about its K22 axis (out of the x - y plane). An array can be specified for ANGLE2 only if ANGLE1 is also specified. A positive value of ANGLE2 represents clockwise rotation when viewed from any point on the positive K22 axis, looking toward the center of the ellipsoid. A value of zero indicates that the K11 axis lies within the x - y plane. If ANGLE2 is not specified, default values of zero are assigned to ANGLE2 and ANGLE3; connections that are not user-designated as vertical are assumed to be strictly horizontal (that is, to have no z component to their orientation); and connection lengths are based on horizontal distances. |
 | GWF | NPF | GRIDDATA | ANGLE3 | DOUBLE PRECISION (NODES) | is a rotation angle of the hydraulic conductivity tensor in degrees. The angle represents the third of three sequential rotations of the hydraulic conductivity ellipsoid. Following the rotations by ANGLE1 and ANGLE2 described above, ANGLE3 rotates the ellipsoid about its K11 axis. An array can be specified for ANGLE3 only if ANGLE1 and ANGLE2 are also specified. An array must be specified for ANGLE3 if ANGLE2 is specified. A positive value of ANGLE3 represents clockwise rotation when viewed from any point on the positive K11 axis, looking toward the center of the ellipsoid. A value of zero indicates that the K22 axis lies within the x - y plane. |
 | GWF | NPF | GRIDDATA | WETDRY | DOUBLE PRECISION (NODES) | is a combination of the wetting threshold and a flag to indicate which neighboring cells can cause a cell to become wet. If WETDRY $<$ 0, only a cell below a dry cell can cause the cell to become wet. If WETDRY $>$ 0, the cell below a dry cell and horizontally adjacent cells can cause a cell to become wet. If WETDRY is 0, the cell cannot be wetted. The absolute value of WETDRY is the wetting threshold. When the sum of BOT and the absolute value of WETDRY at a dry cell is equaled or exceeded by the head at an adjacent cell, the cell is wetted.  WETDRY must be specified if ``REWET'' is specified in the OPTIONS block.  If ``REWET'' is not specified in the options block, then WETDRY can be entered, and memory will be allocated for it, even though it is not used. |
+| GWF | VKD | OPTIONS | PRINT_INPUT | KEYWORD | keyword to indicate that the list of VKD cells and information will be written to the listing file immediately after it is read. |
+| GWF | VKD | DIMENSIONS | NUMVKD | INTEGER | integer value specifying the number of VKD cells. There must be NUMVKD entries in the PACKAGEDATA block. |
+| GWF | VKD | DIMENSIONS | NUMELEVS | INTEGER | integer value specifying the number of VKD inflections. There must be NUMELEVS entries for both EIP and KIP for every cell defined in PACKAGEDATA block. |
+| GWF | VKD | PACKAGEDATA | CELLID | INTEGER (NCELLDIM) | is the cell identifier, and depends on the type of grid that is used for the simulation.  For a structured grid that uses the DIS input file, CELLID is the layer, row, and column.   For a grid that uses the DISV input file, CELLID is the layer and CELL2D number.  If the model uses the unstructured discretization (DISU) input file, CELLID is the node number for the cell. |
+| GWF | VKD | PACKAGEDATA | EIP | DOUBLE PRECISION (NUMELEVS) | elevation of VKD inflection point.  This number is an elevation (relative to the same datum used for cell tops and bottoms) in model length units. |
+| GWF | VKD | PACKAGEDATA | KIP | DOUBLE PRECISION (NUMELEVS) | hydraulic conductivity factor at VKD inflection point. |
 | GWF | STO | OPTIONS | SAVE_FLOWS | KEYWORD | keyword to indicate that cell-by-cell flow terms will be written to the file specified with ``BUDGET SAVE FILE'' in Output Control. |
 | GWF | STO | OPTIONS | STORAGECOEFFICIENT | KEYWORD | keyword to indicate that the SS array is read as storage coefficient rather than specific storage. |
 | GWF | STO | GRIDDATA | ICONVERT | INTEGER (NODES) | is a flag for each cell that specifies whether or not a cell is convertible for the storage calculation. 0 indicates confined storage is used. $>$0 indicates confined storage is used when head is above cell top and a mixed formulation of unconfined and confined storage is used when head is below cell top. |

doc/mf6io/mf6ivar/mf6ivar.py

@@ -453,6 +453,7 @@ def write_appendix(texdir, allblocks):
                   'gwf-disu',    # dfn completed  tex updated
                   'gwf-ic',      # dfn completed  tex updated
                   'gwf-npf',     # dfn completed  tex updated
+                  'gwf-vkd',     # dfn completed  tex updated
                   'gwf-sto',     # dfn completed  tex updated
                   'gwf-hfb',     # dfn completed  tex updated
                   'gwf-chd',     # dfn completed  tex updated

doc/mf6io/mf6ivar/tex/appendixA.tex

@@ -66,6 +66,10 @@
 GWF & NPF & OPTIONS & yes \\ 
 GWF & NPF & GRIDDATA & no \\ 
 \hline
+GWF & VKD & OPTIONS & yes \\ 
+GWF & VKD & DIMENSIONS & yes \\ 
+GWF & VKD & PACKAGEDATA & yes \\ 
+\hline
 GWF & STO & OPTIONS & yes \\ 
 GWF & STO & GRIDDATA & no \\ 
 GWF & STO & PERIOD & yes \\ 

doc/mf6io/mf6ivar/tex/exg-gwfgwf-desc.tex

@@ -51,7 +51,7 @@
 
 \item \texttt{cl1}---is the distance between the center of cell 1 and the its shared face with cell 2.
 
-\item \texttt{cl2}---is the distance between the center of cell 1 and the its shared face with cell 2.
+\item \texttt{cl2}---is the distance between the center of cell 2 and the its shared face with cell 1.
 
 \item \texttt{hwva}---is the horizontal width of the flow connection between cell 1 and cell 2 if IHC $>$ 0, or it is the area perpendicular to flow of the vertical connection between cell 1 and cell 2 if IHC = 0.
 

doc/mf6io/mf6ivar/tex/gwf-npf-desc.tex

@@ -29,6 +29,12 @@
 
 \item \texttt{SAVE\_SPECIFIC\_DISCHARGE}---keyword to indicate that x, y, and z components of specific discharge will be calculated at cell centers and written to the cell-by-cell flow file, which is specified with ``BUDGET SAVE FILE'' in Output Control.
 
+\item \texttt{VKD6}---keyword to specify that record corresponds to a vkd file.
+
+\item \texttt{FILEIN}---keyword to specify that an input filename is expected next.
+
+\item \texttt{vkd6\_filename}---is the file name of the VKD input file. This option should not be used unless the Variations in Hydraulic Conductivity with Depth (VKD) Package is needed for the simulation.
+
 \end{description}
 \item \textbf{Block: GRIDDATA}
 

doc/mf6io/mf6ivar/tex/gwf-npf-options.dat

@@ -7,4 +7,5 @@ BEGIN OPTIONS
   [REWET WETFCT <wetfct> IWETIT <iwetit> IHDWET <ihdwet>]
   [XT3D [RHS]]
   [SAVE_SPECIFIC_DISCHARGE]
+  [VKD6 FILEIN <vkd6_filename>]
 END OPTIONS