Merge remote-tracking branch 'upstream/develop' into refactor-src-mer…

…ge-develop (#349)

* refactor(maw): refactor MAW conductance calculation for issue 305 (#310)

Add traps to catch 1) skin factors that are <= 0 when using the SKIN
conductance equation and 2) and negative saturated conductances values.

Closes #305

* feat(tableobj): Add a generic table object for lst file output (#303)

Full implementation for SFR package. Partial implementation for LAK, MAW, and UZF packages.

* feat(tableobj): update MAW package to use tableobj for data output (#315)

Also fix some budget reporting issues in the MAW package

* fix(auxmult): auxmult fix when auxmult and bound are in time series (#316)

* change order of time series interpolation so aux is done first in case it is an auxmult column
* partially addresses #314
* updated release notes

* refactor(BoundaryPackage): Add use of TableObject for print_flows option (#317)

* feat(lnf): update n-point geometry package data

* Revert "feat(lnf): update n-point geometry package data"

This reverts commit 3460cfb.

* fix(lak): revise the way outlet to-mvr flows are stored in budobj (#321)

* fix(lak): revise the way outlet to-mvr flows are stored in budobj

* updated release notes

* refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file (#329)

* refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file

* update release notes

* fix(maw): new headtable corrected to have mawwells rows instead of maxbound (#332)

* fix(sfr): Remove upstream_fraction check from PACKAGEDATA block (#334)

closes #324

* feat(transport): update develop with some general routines needed for transport (#339)

* feat(transport): update develop with some general routines needed for transport
* fix(mover): correct typo in error message
* closes #336
* refactor(disu): correct type in disu error message
* closes #635

* fix(csub): Allow interbed observations when no interbeds specified (#338)

DNODATA values reported if 1) delay interbed observations are specified
and no delay interbeds are specified and 2) interbed observations are
specified and the number of interbeds is zero. Added test of all
observation types to test_gwf_csub_sk01.py which has no interbeds.

closes #298

* ci(travis): update travis.yml to install miniconda instead of apt python (#346)

* refactor(mf6): standardize output to STDOUT to use istdout variable

* refactor(mf6): standardize output to STDOUT to use istdout variable

Modify mf5to6 to use standard SimVariables.f90 in mf6 src and add
ListType variables in original mf5to6 SimVariables.f90 file to
SimListVariables.f90 and update use statements.

* Merge remote-tracking branch 'upstream/develop' into refactor-src-merge-develop

# Conflicts:
#	autotest/simulation.py
#	msvs/mf6.vfproj
#	src/Model/GroundWaterFlow/gwf3csub8.f90
#	src/Solution/NumericalSolution.f90
#	src/Utilities/List.f90
#	src/Utilities/Sim.f90
#	src/Utilities/SimVariables.f90
#	src/mf6.f90
#	utils/mf5to6/src/Preproc/SimVariables.f90

Co-authored-by: langevin-usgs <langevin@usgs.gov>

doc/ReleaseNotes/ReleaseNotes.tex

@@ -118,6 +118,9 @@ \section{History}
 \item Version mf6.1.1--Release Candidate
 
 \underline{NEW FUNCTIONALITY}
+\begin{itemize}
+\item Added silent command line switch (-s or --silent) that sends all output to the screen (\texttt{STDOUT})  to a file (``mfsim.stdout'').
+\end{itemize}
 
 \underline{BASIC FUNCTIONALITY}
 \begin{itemize}

doc/mf6io/mf6switches.tex

@@ -9,6 +9,7 @@
  -v       --version         Display program version information.
  -dev     --develop         Display program develop option mode.
  -c       --compiler        Display compiler information.
+ -s       --silent          STDOUT output piped to mfsim.stdout file.
 
 Bug reporting and contributions are welcome from the community.
 Questions can be asked on the issues page[1]. Before creating a new

src/Utilities/List.f90

@@ -1,6 +1,7 @@
 module ListModule
   ! -- ListType implements a generic list.
   use KindModule, only: DP, I4B
+  use SimVariablesModule, only: istdout
   private
   public :: ListType, ListNodeType
 
@@ -204,14 +205,12 @@ function GetPreviousItem(this) result(resultobj)
   end function GetPreviousItem
 
   subroutine InsertAfter(this, objptr, indx)
-    use, intrinsic :: iso_fortran_env, only: output_unit
     implicit none
     ! -- dummy
     class(ListType), intent(inout) :: this
     class(*), pointer, intent(inout) :: objptr
     integer(I4B), intent(in) :: indx
     ! -- local
-    integer(I4B) :: istdout = output_unit
     integer(I4B) :: numnodes
     type(ListNodeType), pointer :: precedingNode => null()
     type(ListNodeType), pointer :: followingNode => null()

src/Utilities/Sim.f90

@@ -536,18 +536,26 @@ subroutine ustop(stopmess, ioutlocal)
 ! ------------------------------------------------------------------------------
   ! -- dummy
   character, optional, intent(in) :: stopmess*(*)
-  integer(I4B),   optional, intent(in) :: ioutlocal
+  integer(I4B), optional, intent(in) :: ioutlocal
 
-  !---------------------------------------------------------------------------  
+  !---------------------------------------------------------------------------
+  !
+  ! -- print the final message
   call print_final_message(stopmess, ioutlocal)
-
+  !
   ! -- return appropriate error codes when terminating the program
   call stop_with_error(ireturnerr)
 
-
 end subroutine ustop
 
 subroutine print_final_message(stopmess, ioutlocal)
+! ******************************************************************************
+! Print a final message and close all open files
+! ******************************************************************************
+!
+!    SPECIFICATIONS:
+! ------------------------------------------------------------------------------
+  ! -- dummy
   character, optional, intent(in) :: stopmess*(*)
   integer(I4B),   optional, intent(in) :: ioutlocal  
   ! -- local
@@ -589,8 +597,18 @@ subroutine print_final_message(stopmess, ioutlocal)
 end subroutine print_final_message
 
 subroutine stop_with_error(ierr)
+! ******************************************************************************
+! Stop the program and issue the correct return code 
+! ******************************************************************************
+!
+!    SPECIFICATIONS:
+! ------------------------------------------------------------------------------
+  ! -- modules
+  ! -- dummy
   integer(I4B), intent(in) :: ierr
-
+!-------------------------------------------------------------------------------
+  !
+  ! -- return the correct return code
   select case (ierr)
     case (0)
       stop
@@ -623,7 +641,7 @@ end subroutine converge_reset
 
   subroutine converge_check(hasConverged)
 ! ******************************************************************************
-! converge_check
+! convergence check
 ! ******************************************************************************
 !
 !    SPECIFICATIONS:
@@ -663,12 +681,13 @@ end subroutine converge_check
 
   subroutine final_message()
 ! ******************************************************************************
-! final_message
+! Create the appropriate final message and terminate the program
 ! ******************************************************************************
 !
 !    SPECIFICATIONS:
 ! ------------------------------------------------------------------------------
     ! -- modules
+    ! -- dummy
     use SimVariablesModule, only: isimcnvg, numnoconverge, ireturnerr
     ! -- formats
     character(len=*), parameter :: fmtnocnvg =                                 &
@@ -690,7 +709,6 @@ subroutine final_message()
     !
     ! -- Return or halt
     if (iforcestop == 1) call stop_with_error(ireturnerr)
-    return
 
   end subroutine final_message
 
@@ -720,11 +738,6 @@ subroutine sim_closefiles()
         cycle
       end if
       !
-      ! -- skip istdout if it has been opened
-      if (i == istdout) then
-        cycle
-      end if
-      !
       ! -- close file unit i
       close(i)
     end do

utils/mf5to6/msvs/mf5to6.vfproj

@@ -95,6 +95,7 @@
 		<File RelativePath="..\..\..\src\Utilities\kind.f90"/>
 		<File RelativePath="..\..\..\src\Utilities\List.f90"/>
 		<File RelativePath="..\..\..\src\Utilities\OpenSpec.f90"/>
+		<File RelativePath="..\..\..\src\Utilities\SimVariables.f90"/>
 		<File RelativePath="..\..\..\src\Utilities\version.f90"/></Filter></Filter>
 		<Filter Name="NWT">
 		<File RelativePath="..\src\NWT\gwf2hfb7_NWT.f"/>
@@ -125,7 +126,7 @@
 		<File RelativePath="..\src\Preproc\ObservePHMF.f90"/>
 		<File RelativePath="..\src\Preproc\Preproc.f90"/>
 		<File RelativePath="..\src\Preproc\SimPHMF.f90"/>
-		<File RelativePath="..\src\Preproc\SimVariables.f90"/>
+		<File RelativePath="..\src\Preproc\SimListVariables.f90"/>
 		<File RelativePath="..\src\Preproc\SimVariablesPHMF.f90"/>
 		<File RelativePath="..\src\Preproc\Utilities.f90"/></Filter>
 		<File RelativePath="..\src\ArrayReadersMF5.f90"/>

utils/mf5to6/pymake/extrafiles.txt

@@ -5,6 +5,7 @@
 ../../../src/Utilities/TimeSeries/TimeSeriesRecord.f90
 ../../../src/Utilities/BlockParser.f90
 ../../../src/Utilities/Constants.f90
+../../../src/Utilities/SimVariables.f90
 ../../../src/Utilities/genericutils.f90
 ../../../src/Utilities/InputOutput.f90
 ../../../src/Utilities/kind.f90

utils/mf5to6/src/ModelConverter.f90

@@ -36,7 +36,7 @@ module ModelConverterModule
   use GlobalVariablesModule, only: echo
   use SimModule, only: store_error, store_note, store_warning, ustop, &
                        write_message
-  use SimVariablesModule, only: SimMovers
+  use SimListVariablesModule, only: SimMovers
   use UpwSubsModule, only: GWF2UPW1AR
   use UtilitiesModule, only: GetArgs
 

utils/mf5to6/src/ModelPackage.f90

@@ -2,7 +2,7 @@ module ModelPackageModule
 
   use ConstantsModule, only: LENMODELNAME, LENPACKAGENAME
   use ListModule, only: ListType
-  use SimVariablesModule, only: ModelPacks
+  use SimListVariablesModule, only: ModelPacks
 
   implicit none
 

utils/mf5to6/src/MvrPackageWriter.f90

@@ -6,7 +6,7 @@ module MvrPackageWriterModule
   use ListModule, only: ListType
   use MoverModule, only: MoverType, AddMoverToList, GetMoverFromList
   use PackageWriterModule, only: PackageWriterType
-  use SimVariablesModule, only: SimMovers
+  use SimListVariablesModule, only: SimMovers
 
   implicit none
 

utils/mf5to6/src/PackageWriter.f90

@@ -14,7 +14,7 @@ module PackageWriterModule
   use MoverModule, only: MoverType, AddMoverToList
   use ObsWriterModule, only: ObsWriterType
   use SimModule, only: store_error, store_note, ustop
-  use SimVariablesModule, only: SimMovers
+  use SimListVariablesModule, only: SimMovers
   use UtilitiesModule, only: ConstantReal2D
 
   implicit none

utils/mf5to6/src/Preproc/SimListVariables.f90

@@ -0,0 +1,12 @@
+module SimListVariablesModule
+  use ListModule, only: ListType
+
+  implicit none
+
+  private
+  public :: ModelPacks, SimMovers
+
+  type(ListType), pointer :: SimMovers => null()
+  type(ListType) :: ModelPacks
+
+end module SimListVariablesModule

utils/mf5to6/src/SimFileWriter.f90

@@ -9,7 +9,7 @@ module SimFileWriterModule
   use ModelModule, only: ModelType
   use MoverModule, only: MoverType, AddMoverToList
   use MvrPackageWriterModule, only: MvrPackageWriterType
-  use SimVariablesModule, only: SimMovers
+  use SimListVariablesModule, only: SimMovers
 
   implicit none
 

utils/mf5to6/src/mf5to6.f90

@@ -18,7 +18,7 @@ program mf5to6
                                     AllSfrPkgWriters
   use SimFileWriterModule, only: SimFileWriterType
   use SimModule, only: ustop
-  use SimVariablesModule, only: SimMovers
+  use SimListVariablesModule, only: SimMovers
   use UtilitiesModule, only: GetArgs, ReadMf5to6Options, PhmfOption
   !
   implicit none