docs(releasenotes): more cleanup for 6.5.0 release (#1838)

* docs(releasenotes): more cleanup for 6.5.0 release

* fix ftype table links in mf6io

Author: christianlangevin

doc/ReleaseNotes/ReleaseNotes.tex

@@ -202,7 +202,7 @@ \section{Known Issues and Incompatibilities}
 \begin{enumerate}
 
 \item
-The READARRAY utility is used by some packages to read arrays of numeric values provided by the user.  The READARRAY utility has an IPRN option (as described in the MODFLOW 6 Description of Input and Output), which will cause the array to be written to the model listing file.  Support for the IPRN option has been removed for some packages and will ultimately be removed for all packages.  An alternative for IPRN functionality is presently under development.
+The READARRAY utility is used by some packages to read arrays of numeric values provided by the user.  The READARRAY utility has an IPRN option (as described in the MODFLOW 6 Description of Input and Output), which will cause the array to be written to the model listing file.  Support for the IPRN option has been removed for some packages and will ultimately be removed for all packages.  A new option, called ``EXPORT\_ARRAY\_ASCII'' has been implemented for some packages to support writing of gridded data to external text files.  This option has been implemented to replace the IPRN functionality.
 
 \item
 The capability to use Unsaturated Zone Flow (UZF) routing beneath lakes and streams has not been implemented.
@@ -235,10 +235,7 @@ \section{Known Issues and Incompatibilities}
 
 % -------------------------------------------------
 \section{Distribution File}
-The following distribution file is for use on personal computers: \texttt{\modflowversion\_[ostag].zip}.  The distribution file is a compressed zip file. The following directory structure is incorporated in the zip file:
-
-% folder structured created by python script
-\input{folder_struct.tex}
+The distribution is provided in the form of a compressed zip file.  Distributions are available for several different operating systems, including Windows, Mac, and Linux.  Distributions are marked with an operating system tag, called ``ostag''.  Values for ``ostag'' include ``win64'', ``mac'', and ``linux'', for example.  Distribution files for this release are labeled as \texttt{\modflowversion\_[ostag].zip}.  Thus, the distribution file for Windows for this release is  \texttt{\modflowversion\_win64.zip}.
 
 It is recommended that no user files are kept in the release directory.  If you do plan to put your own files in the release directory, do so only by creating additional subdirectories.
 

doc/SuppTechInfo/mf6suptechinfo.bbl

@@ -1,22 +1,52 @@
-\begin{thebibliography}{21}
+\begin{thebibliography}{30}
 \providecommand{\natexlab}[1]{#1}
 \expandafter\ifx\csname urlstyle\endcsname\relax
-  \providecommand{\doi}[1]{doi:\discretionary{}{}{}#1}\else
-  \providecommand{\doi}{doi:\discretionary{}{}{}\begingroup
+  \providecommand{\doiagency}[1]{doi:\discretionary{}{}{}#1}\else
+  \providecommand{\doiagency}{doi:\discretionary{}{}{}\begingroup
   \urlstyle{rm}\Url}\fi
 
+\bibitem[{Bakker and others(2016)Bakker, Post, Langevin, Hughes, White, Starn,
+  and Fienen}]{bakker2016flopy}
+Bakker, M., Post, V., Langevin, C.D., Hughes, J.D., White, J.T., Starn, J.J.,
+  and Fienen, M.N., 2016, Scripting modflow model development using python and
+  flopy: Groundwater, \url{https://doi.org/https://doi.org/10.1111/gwat.12413}.
+
+\bibitem[{Bakker and others(2024)Bakker, Post, Hughes, Langevin, White, Leaf,
+  Paulinski, Bellino, Morway, Toews, Larsen, Fienen, Starn, Brenhoff, and
+  Bonelli}]{flopysoftware}
+Bakker, M., Post, V., Hughes, J.D., Langevin, C.D., White, J.T., Leaf, A.T.,
+  Paulinski, S.R., Bellino, J.C., Morway, E.D., Toews, M.W., Larsen, J.D.,
+  Fienen, M.N., Starn, J.J., Brenhoff, D.A., and Bonelli, W.P., 2024, FloPy
+  v3.7.0dev0 (preliminary): {U.S. Geological Survey Software Release},
+  \url{https://doi.org/10.5066/F7BK19FH}.
+
+\bibitem[{Bedekar and others(2016)Bedekar, Morway, Langevin, and
+  Tonkin}]{mt3dusgs}
+Bedekar, V., Morway, E.D., Langevin, C.D., and Tonkin, M.J., 2016, MT3D-USGS
+  version 1: A U.S. Geological Survey release of MT3DMS updated with new and
+  expanded transport capabilities for use with MODFLOW: {U.S. Geological Survey
+  Techniques and Methods, book 6, chap. A53, 69 p.},
+  \url{https://doi.org/10.3133/tm6a53}, \url{http://dx.doi.org/10.3133/tm6A53}.
+
 \bibitem[{Campbell and others(1994)Campbell, Jungbauer, Bidlake, and
   Hungerford}]{campbell1994}
 Campbell, G.S., Jungbauer, J.D., Bidlake, W.R., and Hungerford, R.D., 1994,
   Predicting the effect of temperature on soil thermal conductivity: Soil
   Science, v. 158, no.~5, p.~307--313.
 
+\bibitem[{Cordes and Kinzelbach(1992)}]{cordes1992}
+Cordes, C., and Kinzelbach, W., 1992, Continuous groundwater velocity fields
+  and path lines in linear, bilinear, and trilinear finite elements: Water
+  Resources Research, v.~28, p.~2903--2911,
+  \url{https://doi.org/10.1029/92WR01686}.
+
 \bibitem[{Guo and Langevin(2002)}]{langevin2002seawat}
-Guo, Weixing, and Langevin, C.D., 2002, User's Guide to SEAWAT: A Computer
-  Program for Simulation of Three-Dimensional Variable-Density Ground-Water
-  Flow: {U.S. Geological Survey Techniques of Water-Resources Investigations
-  book 6, Chapter A7, 77 p.}, accessed July 25, 2019, at
-  \url{https://pubs.er.usgs.gov/publication/ofr03426}.
+Guo, W., and Langevin, C.D., 2002, User's Guide to SEAWAT: A Computer Program
+  for Simulation of Three-Dimensional Variable-Density Ground-Water Flow: {U.S.
+  Geological Survey Techniques of Water-Resources Investigations book 6,
+  Chapter A7, 77 p.}, accessed July 25, 2019, at
+  \url{https://doi.org/https://doi.org/10.3133/twri06A7}, at
+  \url{https://pubs.usgs.gov/publication/twri06A7}.
 
 \bibitem[{Harbaugh(2005)}]{modflow2005}
 Harbaugh, A.W., 2005, MODFLOW-2005, the U.S. Geological Survey modular
@@ -52,9 +82,16 @@ Hughes, J.D., Langevin, C.D., and Banta, E.R., 2017, Documentation for the
   MODFLOW 6 framework: {U.S. Geological Survey Techniques and Methods, book 6,
   chap. A57, 36 p.}, \url{https://doi.org/10.3133/tm6A57}.
 
+\bibitem[{Hughes and others(2024)Hughes, Langevin, Paulinski, Larsen, and
+  Brakenhoff}]{hughes2023flopy}
+Hughes, J.D., Langevin, C.D., Paulinski, S.R., Larsen, J.D., and Brakenhoff,
+  D., 2024, {FloPy} workflows for creating structured and unstructured
+  {MODFLOW} models: Groundwater, v.~62, no.~1, p.~124--139,
+  \url{https://doi.org/10.1111/gwat.13327}.
+
 \bibitem[{Kavetski and Kuczera(2007)}]{doi:10.1029/2006WR005195}
-Kavetski, Dmitri, and Kuczera, George, 2007, Model smoothing strategies to
-  remove microscale discontinuities and spurious secondary optima in objective
+Kavetski, D., and Kuczera, G., 2007, Model smoothing strategies to remove
+  microscale discontinuities and spurious secondary optima in objective
   functions in hydrological calibration: Water Resources Research, v.~43,
   no.~3, \url{https://doi.org/10.1029/2006WR005195},
   \url{https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2006WR005195}.
@@ -67,30 +104,30 @@ Kipp, K.L., 1987, HST3D: A Computer Code for Simulation of Heat and Solute
 
 \bibitem[{Langevin and others(2008)Langevin, Thorne~Jr, Dausman, Sukop, and
   Guo}]{langevin2008seawat}
-Langevin, C.D., Thorne~Jr, D.T., Dausman, A.M., Sukop, M.C., and Guo, Weixing,
-  2008, {SEAWAT} Version 4---A computer program for simulation of multi-species
+Langevin, C.D., Thorne~Jr, D.T., Dausman, A.M., Sukop, M.C., and Guo, W., 2008,
+  {SEAWAT} Version 4---A computer program for simulation of multi-species
   solute and heat transport: {U.S. Geological Survey Techniques and Methods,
   book 6, chap. A22, 39 p.}, accessed June 27, 2017, at
   \url{https://pubs.er.usgs.gov/publication/tm6A22}.
 
 \bibitem[{Langevin and others(2017)Langevin, Hughes, Provost, Banta, Niswonger,
   and Panday}]{modflow6gwf}
 Langevin, C.D., Hughes, J.D., Provost, A.M., Banta, E.R., Niswonger, R.G., and
-  Panday, Sorab, 2017, Documentation for the MODFLOW 6 Groundwater Flow (GWF)
+  Panday, S., 2017, Documentation for the MODFLOW 6 Groundwater Flow (GWF)
   Model: {U.S. Geological Survey Techniques and Methods, book 6, chap. A55, 197
   p.}, \url{https://doi.org/10.3133/tm6A55}.
 
 \bibitem[{Langevin and others(2022)Langevin, Provost, Panday, and
   Hughes}]{modflow6gwt}
-Langevin, C.D., Provost, A.M., Panday, Sorab, and Hughes, J.D., 2022,
+Langevin, C.D., Provost, A.M., Panday, S., and Hughes, J.D., 2022,
   Documentation for the MODFLOW 6 Groundwater Transport (GWT) Model: {U.S.
   Geological Survey Techniques and Methods, book 6, chap. A61, 56 p.},
   \url{https://doi.org/10.3133/tm6A61}.
 
 \bibitem[{Ma and Zheng(2010)}]{mazheng2010}
-Ma, Rui, and Zheng, Chunmiao, 2010, Effects of density and viscosity in
-  modeling heat as a groundwater tracer: Groundwater, v.~48, no.~3,
-  p.~380--389, \url{https://doi.org/10.1111/j.1745-6584.2009.00660.x}.
+Ma, R., and Zheng, C., 2010, Effects of density and viscosity in modeling heat
+  as a groundwater tracer: Groundwater, v.~48, no.~3, p.~380--389,
+  \url{https://doi.org/10.1111/j.1745-6584.2009.00660.x}.
 
 \bibitem[{Maidment(1993)}]{maidment1993}
 Maidment, D.R., 1993, Handbook of Hydrology: New York, USA, McGraw-Hill.
@@ -103,23 +140,38 @@ Markle, J.M., Schincariol, R.A., Sass, J.H., and Molson, J.W., 2006,
   no.~4, p.~1281--1294,
   \url{https://doi.org/https://doi.org/10.2136/sssaj2005.0293}.
 
+\bibitem[{Panday(2019)}]{panday2019bct}
+Panday, S., 2019, USG-Transport Version 1.4.0: The Block-Centered Transport
+  Process for MODFLOW-USG: ,
+  \url{http://gmsdocs.aquaveo.com.s3.amazonaws.com/GWT_v1-4-0.pdf}.
+
 \bibitem[{Panday and others(2013)Panday, Langevin, Niswonger, Ibaraki, and
   Hughes}]{modflowusg}
-Panday, Sorab, Langevin, C.D., Niswonger, R.G., Ibaraki, Motomu, and Hughes,
-  J.D., 2013, MODFLOW-USG version 1---An unstructured grid version of MODFLOW
-  for simulating groundwater flow and tightly coupled processes using a control
+Panday, S., Langevin, C.D., Niswonger, R.G., Ibaraki, M., and Hughes, J.D.,
+  2013, MODFLOW-USG version 1---An unstructured grid version of MODFLOW for
+  simulating groundwater flow and tightly coupled processes using a control
   volume finite-difference formulation: {U.S. Geological Survey Techniques and
   Methods, book 6, chap. A45, 66 p.}, accessed June 27, 2017, at
   \url{https://pubs.usgs.gov/tm/06/a45/}.
 
+\bibitem[{Pollock(2015)}]{pollock2015}
+Pollock, D.W., 2015, Extending the modpath algorithm to rectangular
+  unstructured grids: Groundwater, v.~54, p.~121--125,
+  \url{https://doi.org/10.1111/gwat.12328}.
+
+\bibitem[{Pollock(2016)}]{pollock2016modpath7}
+Pollock, D.W., 2016, User guide for MODPATH Version 7---A particle-tracking
+  model for MODFLOW: {U.S. Geological Survey Open-File Report 2016--1086, 35
+  p.}, accessed June 27, 2017, at \url{https://doi.org/10.3133/ofr20161086}.
+
 \bibitem[{Provost and others(2017)Provost, Langevin, and Hughes}]{modflow6xt3d}
 Provost, A.M., Langevin, C.D., and Hughes, J.D., 2017, Documentation for the
   ``XT3D'' Option in the Node Property Flow (NPF) Package of MODFLOW 6: {U.S.
   Geological Survey Techniques and Methods, book 6, chap. A56, 46 p.},
   \url{https://doi.org/10.3133/tm6A56}.
 
 \bibitem[{Thorne and others(2006)Thorne, Langevin, and Sukop}]{thorne2006}
-Thorne, Danny, Langevin, C.D., and Sukop, M.C., 2006, Addition of simultaneous
+Thorne, D., Langevin, C.D., and Sukop, M.C., 2006, Addition of simultaneous
   heat and solute transport and variable fluid viscosity to seawat: Computers
   and Geosciences, v.~32, no.~10, p.~1758--1768,
   \url{https://doi.org/https://doi.org/10.1016/j.cageo.2006.04.005}.
@@ -130,12 +182,17 @@ Voss, C.I., 1984, SUTRA---A finite-element simulation model for
   transport or chemically-reactive single-species solute transport: {U.S.
   Geological Survey Water-Resources Investigations Report 84--4369, 409 p.}
 
+\bibitem[{Zhang and others(2012)Zhang, King, and Datta-Gupta}]{zhang2012}
+Zhang, Y., King, M.J., and Datta-Gupta, A., 2012, Robust streamline tracing
+  using inter-cell fluxes in locally refined and unstructured grids: Water
+  Resources Research, v.~48, \url{https://doi.org/10.1029/2011WR011396}.
+
 \bibitem[{Zheng(2010)}]{zheng2010supplemental}
-Zheng, Chunmiao, 2010, MT3DMS v5.3, Supplemental User's Guide: {Technical
-  Report Prepared for the U.S. Army Corps of Engineers, 51 p.}
+Zheng, C., 2010, MT3DMS v5.3, Supplemental User's Guide: {Technical Report
+  Prepared for the U.S. Army Corps of Engineers, 51 p.}
 
 \bibitem[{Zheng and Wang(1999)}]{zheng1999mt3dms}
-Zheng, Chunmiao, and Wang, P.P., 1999, MT3DMS---A modular three-dimensional
+Zheng, C., and Wang, P.P., 1999, MT3DMS---A modular three-dimensional
   multi-species transport model for simulation of advection, dispersion and
   chemical reactions of contaminants in groundwater systems; Documentation and
   user's guide: {Contract report SERDP--99--1: Vicksburg, Miss., U.S. Army

doc/mf6io/gwe/namefile.tex

@@ -41,7 +41,7 @@ \subsubsection{Explanation of Variables}
 OBS6 & Observations Option \\
 \hline 
 \end{tabular*}
-\label{table:ftype}
+\label{table:ftype-gwe}
 \end{center}
 \normalsize
 \end{table}

doc/mf6io/gwf/namefile.tex

@@ -49,7 +49,7 @@ \subsubsection{Explanation of Variables}
 OBS6 & Observations Option \\
 \hline 
 \end{tabular*}
-\label{table:ftype}
+\label{table:ftype-gwf}
 \end{center}
 \normalsize
 \end{table}

doc/mf6io/gwt/namefile.tex

@@ -43,7 +43,7 @@ \subsubsection{Explanation of Variables}
 OBS6 & Observations Option \\
 \hline 
 \end{tabular*}
-\label{table:ftype}
+\label{table:ftype-gwt}
 \end{center}
 \normalsize
 \end{table}

doc/mf6io/mf6ivar/dfn/gwe-est.dfn

@@ -61,7 +61,7 @@ shape (nodes)
 reader readarray
 layered true
 longname density of aquifer material
-description is a user-specified value of the density of aquifer material not considering the voids. Value will remain fixed for the entire simulation.  For example, if working in SI units, values may be entered as kg/m3. 
+description is a user-specified value of the density of aquifer material not considering the voids. Value will remain fixed for the entire simulation.  For example, if working in SI units, values may be entered as kilograms per cubic meter. 
 
 # --------------------- gwe est packagedata ---------------------
 
@@ -91,7 +91,7 @@ tagged false
 in_record true
 reader urword
 longname density of water
-description is a user-specified value of the density of water. Value will remain fixed for the entire simulation.  For example, if working in SI units, values may be entered as kg/m3. 
+description is a user-specified value of the density of water. Value will remain fixed for the entire simulation.  For example, if working in SI units, values may be entered as kilograms per cubic meter. 
 
 
 block packagedata

doc/mf6io/mf6ivar/dfn/gwe-nam.dfn

@@ -50,7 +50,7 @@ type string
 tagged false
 reader urword
 longname package type
-description is the file type, which must be one of the following character values shown in table~\ref{table:ftype}. Ftype may be entered in any combination of uppercase and lowercase.
+description is the file type, which must be one of the following character values shown in table~\ref{table:ftype-gwe}. Ftype may be entered in any combination of uppercase and lowercase.
 
 block packages
 name fname

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

@@ -75,7 +75,7 @@ type string
 tagged false
 reader urword
 longname package type
-description is the file type, which must be one of the following character values shown in table~\ref{table:ftype}. Ftype may be entered in any combination of uppercase and lowercase.
+description is the file type, which must be one of the following character values shown in table~\ref{table:ftype-gwf}. Ftype may be entered in any combination of uppercase and lowercase.
 
 block packages
 name fname

doc/mf6io/mf6ivar/dfn/gwt-nam.dfn

@@ -50,7 +50,7 @@ type string
 tagged false
 reader urword
 longname package type
-description is the file type, which must be one of the following character values shown in table~\ref{table:ftype}. Ftype may be entered in any combination of uppercase and lowercase.
+description is the file type, which must be one of the following character values shown in table~\ref{table:ftype-gwt}. Ftype may be entered in any combination of uppercase and lowercase.
 
 block packages
 name fname

doc/mf6io/mf6ivar/dfn/prt-nam.dfn

@@ -49,7 +49,7 @@ type string
 tagged false
 reader urword
 longname package type
-description is the file type, which must be one of the following character values shown in table~\ref{table:ftype}. Ftype may be entered in any combination of uppercase and lowercase.
+description is the file type, which must be one of the following character values shown in table~\ref{table:ftype-prt}. Ftype may be entered in any combination of uppercase and lowercase.
 
 block packages
 name fname