refactor(transport): updated with develop

* fix(ci): fix to pre-commit when working on a fork

* fix(update_flopy): there is a new flopy.dfn file that cannot be removed (#112)

* refactor(tests): to work with recent flopy changes (#113)

* refactor(tests): to work with recent flopy changes

* fix(test_gwf_utl02): added the time series filename due to possible bug in flopy

* fix(disvdfn): corrected top shape to (ncpl) (#115)

* refactor(test000_setup.py): cleaning up the build process using new pymake functionality (#117)

* fix(dis/disv):  terminate with error if all IDOMAIN values less than or equal to zero (#124)

* fix(dis/disv):  terminate with error if all IDOMAIN values less than or equal to zero

* couple fixes to get tests running with new flopy code

* refactor(make-release): refactor updates to version numbers (#126)

* test(test000_setup): fallback for when os.path.relpath throws (#45)

Happens on Windows only. It is only used for logging, so no functional change.

* test(idomain): add zero idomain autotest (#129)

* fix(mover): added better error trapping for mover entries (#131)

* fix(mover): added better error trapping for mover entries

* more refactoring to eliminate use of memory manager in the mover object

* added characters to error message line length in memory manager

* Added mover test with a variety of mover options active

* some final cleanups on this mover patch

closes #130 

This required some fairly substantial refactoring of the mover object.  Instead of looking up information in the memory manager, the mover object is now passed packagemover objects, which should be much more efficient.

* test(returncodes): add mf6 return codes and command args autotest (#132)

Add mf6 return codes and command args autotest. Update return codes to
use select case.

* feat(ims): Add no_ptc_option FIRST and ALL to no_ptc options keyword (#134)

Add no_ptc_option FIRST and ALL to no_ptc options keyword. Add autotest
(test_gwf_noptc01.py) to test new option against simulation with PTC.

* docs(gwf.tex): minor fix (#135)

* ci(z01/z02): minor change to look for examples with .git extension (#136)

* fix(z02): correcting mistake from last commit (#139)

* ci(slack): add slack notifications

* fix(auxiliary): corrected advanced package auxiliary variables (#146)

* fix(auxiliary): corrected inconsistencies and bugs advanced package aux variables

Added a new test to make sure the aux variables are being carried correctly into the binary budget files.

* More on the auxiliary fix

* Another fix to get MAW right

* fix(ims): Allow for optional nonlinear and linear block (#147)

* ci(travis): Add simple test of Newton-Raphson with known solution (#149)

* fix(oc): error message causing runtime error (#152)

Close #151

* Update gwf-dis.dfn

Corrected a dfn typo as first reported here: https://github.com/modflowpy/flopy/pull/574/files

* fix(mkdist): error output problem in the make distribution script (#162)

Close #154

* docs(disu.dfn): small typo fix

* fix(evt): fixed error in evapotranspiration rate calculation (#169)

Closes #168

* refact(sync dfns): Disu dfn synced with flopy. (#188)

* refactor(sfr): move SfrDataType members into flat arrays (#194)

* refactor(sfr): converted the first 12 entries of SfrDataType to flat arrays

* refactor(sfr): ustrf flattening

* refactor(sfr): ftotnd flattening

* refactor(sfr): usflow flattening

* refactor(sfr): dsflow flattening

* refactor(sfr): depth flattening

* refactor(sfr): stage and gwflow flattening

* refactor(sfr): simevap flattening

* refactor(sfr): simrunoff flattening

* refactor(sfr): stage0 flattening

* refactor(sfr): flattening usflow0

* refactor(sfr): ndiv flattening

*  refactor(gwf): cleaning up call statements and arguments(#202)

* refactor(gnc): removed mention of iasln as it was not used and named wrong

* refactor(gwf): cleaning up model%ia/ja confusion in gwf

* refactor(gwf): cleaning up call statements and arguments

* refactor(xt3d): minor comment cleanup

This is in preparation to be able to mask a primary connection between two model cells so that an interface model can be used to connect two models

autotest/test000_setup.py

@@ -107,7 +107,7 @@ def getmfexes(pth='.', version='', pltfrm=None):
  assets = {p: url + p for p in ['mac.zip', 'linux.zip',
  'win32.zip', 'win64.zip']}
  download_url = assets[zipname]
- pymake.download_and_unzip(download_url, pth, verify=False)
+ pymake.download_and_unzip(download_url, pth)
 
  return
 
@@ -232,12 +232,12 @@ def test_build_zonebudget():
 
 
 if __name__ == "__main__":
- #test_create_dirs()
- #getmfexes(pth=mfexe_pth, version=download_version)
- #test_build_modflow()
- #test_build_mfnwt()
- #test_build_usg()
- #test_build_lgr()
+ test_create_dirs()
+ test_getmfexes()
+ test_build_modflow()
+ test_build_mfnwt()
+ test_build_usg()
+ test_build_lgr()
  test_build_modflow6()
- #test_build_mf5to6()
- #test_build_zonebudget()
+ test_build_mf5to6()
+ test_build_zonebudget()

src/Exchange/GhostNode.f90

@@ -307,7 +307,7 @@ subroutine gnc_mc(this, iasln, jasln)
  return
  end subroutine gnc_mc
 
- subroutine gnc_fmsav(this, kiter, iasln, amatsln)
+ subroutine gnc_fmsav(this, kiter, amatsln)
 ! ******************************************************************************
 ! gnc_fmsav -- Store the n-m Picard conductance in cond prior to the Newton
 ! terms being added.
@@ -320,7 +320,6 @@ subroutine gnc_fmsav(this, kiter, iasln, amatsln)
  ! -- dummy
  class(GhostNodeType) :: this
  integer(I4B), intent(in) :: kiter
- integer(I4B), dimension(:), intent(in) :: iasln
  real(DP), dimension(:), intent(inout) :: amatsln
  ! -- local
  integer(I4B) :: ignc, ipos
@@ -343,7 +342,7 @@ subroutine gnc_fmsav(this, kiter, iasln, amatsln)
  return
  end subroutine gnc_fmsav
 
- subroutine gnc_fc(this, kiter, iasln, amatsln)
+ subroutine gnc_fc(this, kiter, amatsln)
 ! ******************************************************************************
 ! gnc_fc -- Fill matrix terms
 ! Subroutine: (1) Add the GNC terms to the solution amat or model rhs depending
@@ -357,7 +356,6 @@ subroutine gnc_fc(this, kiter, iasln, amatsln)
  ! -- dummy
  class(GhostNodeType) :: this
  integer(I4B), intent(in) :: kiter
- integer(I4B), dimension(:), intent(in) :: iasln
  real(DP), dimension(:), intent(inout) :: amatsln
  ! -- local
  integer(I4B) :: ignc, j, noden, nodem, ipos, jidx, iposjn, iposjm
@@ -366,7 +364,7 @@ subroutine gnc_fc(this, kiter, iasln, amatsln)
  !
  ! -- If this is a single model gnc (not an exchange across models), then
  ! pull conductances out of amatsln and store them in this%cond
- if(this%smgnc) call this%gnc_fmsav(kiter, iasln, amatsln)
+ if(this%smgnc) call this%gnc_fmsav(kiter, amatsln)
  !
  ! -- Add gnc terms to rhs or to amat depending on whether gnc is implicit
  ! or explicit

src/Exchange/GwfGwfExchange.f90

@@ -533,7 +533,7 @@ subroutine gwf_gwf_fc(this, kiter, iasln, amatsln, inwtflag)
  !
  ! -- Fill the gnc terms in the solution matrix
  if(this%ingnc > 0) then
- call this%gnc%gnc_fc(kiter, iasln, amatsln)
+ call this%gnc%gnc_fc(kiter, amatsln)
  endif
  !
  ! -- Call mvr fc routine

src/Model/GroundWaterFlow/gwf3.f90

@@ -321,18 +321,19 @@ subroutine gwf_df(this)
  !
  ! -- Define packages and utility objects
  call this%dis%dis_df()
- call this%npf%npf_df(this%xt3d, this%ingnc)
+ call this%npf%npf_df(this%dis, this%xt3d, this%ingnc)
  call this%oc%oc_df()
  call this%budget%budget_df(niunit, 'VOLUME', 'L**3')
  if(this%ingnc > 0) call this%gnc%gnc_df(this)
  !
  ! -- Assign or point model members to dis members
+ ! this%neq will be incremented if packages add additional unknowns
  this%neq = this%dis%nodes
  this%nja = this%dis%nja
  this%ia => this%dis%con%ia
  this%ja => this%dis%con%ja
  !
- ! -- Allocate model arrays, now that neq and nja are assigned
+ ! -- Allocate model arrays, now that neq and nja are known
  call this%allocate_arrays()
  !
  ! -- Define packages and assign iout for time series managers
@@ -365,12 +366,11 @@ subroutine gwf_ac(this, sparse)
  integer(I4B) :: ip
 ! ------------------------------------------------------------------------------
  !
- ! -- Add the internal connections of this model to sparse
+ ! -- Add the primary grid connections of this model to sparse
  call this%dis%dis_ac(this%moffset, sparse)
  !
  ! -- Add any additional connections that NPF may need
- if(this%innpf > 0) call this%npf%npf_ac(this%moffset, sparse, &
- this%dis%nodes, this%ia, this%ja)
+ if(this%innpf > 0) call this%npf%npf_ac(this%moffset, sparse)
  !
  ! -- Add any package connections
  do ip = 1, this%bndlist%Count()
@@ -407,8 +407,7 @@ subroutine gwf_mc(this, iasln, jasln)
  call this%dis%dis_mc(this%moffset, this%idxglo, iasln, jasln)
  !
  ! -- Map any additional connections that NPF may need
- if(this%innpf > 0) call this%npf%npf_mc(this%moffset, this%dis%nodes, &
- this%ia, this%ja, iasln, jasln)
+ if(this%innpf > 0) call this%npf%npf_mc(this%moffset, iasln, jasln)
  !
  ! -- Map any package connections
  do ip=1,this%bndlist%Count()
@@ -442,8 +441,7 @@ subroutine gwf_ar(this)
  !
  ! -- Allocate and read modules attached to model
  if(this%inic > 0) call this%ic%ic_ar(this%x)
- if(this%innpf > 0) call this%npf%npf_ar(this%dis, this%ic, &
- this%ibound, this%x)
+ if(this%innpf > 0) call this%npf%npf_ar(this%ic, this%ibound, this%x)
  if(this%inbuy > 0) call this%buy%buy_ar(this%dis, this%npf, this%ibound)
  if(this%inhfb > 0) call this%hfb%hfb_ar(this%ibound, this%xt3d, this%dis)
  if(this%insto > 0) call this%sto%sto_ar(this%dis, this%ibound)
@@ -604,19 +602,16 @@ subroutine gwf_fc(this, kiter, amatsln, njasln, inwtflag)
  endif
  !
  ! -- Fill standard conductance terms
- if(this%innpf > 0) call this%npf%npf_fc(kiter, this%dis%nodes, &
- this%nja, njasln, amatsln, &
- this%idxglo, this%rhs, this%x)
+ if(this%innpf > 0) call this%npf%npf_fc(kiter, njasln, amatsln, &
+ this%idxglo, this%rhs, this%x)
  if(this%inbuy > 0) call this%buy%buy_fc(kiter, njasln, amatsln, &
  this%idxglo, this%rhs, this%x)
- if(this%inhfb > 0) call this%hfb%hfb_fc(kiter, this%dis%nodes, &
- this%nja, njasln, amatsln, &
- this%idxglo, this%rhs, this%x)
- if(this%ingnc > 0) call this%gnc%gnc_fc(kiter, this%ia, amatsln)
+ if(this%inhfb > 0) call this%hfb%hfb_fc(kiter, njasln, amatsln, &
+ this%idxglo, this%rhs, this%x)
+ if(this%ingnc > 0) call this%gnc%gnc_fc(kiter, amatsln)
  if(this%insto > 0) then
- call this%sto%sto_fc(kiter, this%dis%nodes, this%xold, &
- this%x, this%nja, njasln, &
- amatsln, this%idxglo, this%rhs)
+ call this%sto%sto_fc(kiter, this%xold, this%x, njasln, amatsln, &
+ this%idxglo, this%rhs)
  end if
  if(this%inmvr > 0) call this%mvr%mvr_fc()
  do ip = 1, this%bndlist%Count()
@@ -627,8 +622,8 @@ subroutine gwf_fc(this, kiter, amatsln, njasln, inwtflag)
  !--Fill newton terms
  if(this%innpf > 0) then
  if(inwt /= 0) then
- call this%npf%npf_fn(kiter, this%dis%nodes, this%nja, njasln,  &
- amatsln, this%idxglo, this%rhs, this%x)
+ call this%npf%npf_fn(kiter, njasln, amatsln, this%idxglo, this%rhs, &
+ this%x)
  endif
  endif
  !
@@ -645,8 +640,8 @@ subroutine gwf_fc(this, kiter, amatsln, njasln, inwtflag)
  ! -- Fill newton terms for storage
  if(this%insto > 0) then
  if (inwtsto /= 0) then
- call this%sto%sto_fn(kiter, this%dis%nodes, this%xold, this%x, &
-  this%nja, njasln, amatsln, this%idxglo, this%rhs)
+ call this%sto%sto_fn(kiter, this%xold, this%x, njasln, amatsln, &
+ this%idxglo, this%rhs)
  end if
  end if
  !
@@ -913,11 +908,9 @@ subroutine gwf_cq(this, icnvg, isuppress_output)
  do i = 1, this%nja
  this%flowja(i) = DZERO
  enddo
- if(this%innpf > 0) call this%npf%npf_flowja(this%neq, this%nja, this%x, &
- this%flowja)
+ if(this%innpf > 0) call this%npf%npf_flowja(this%x, this%flowja)
  if(this%inbuy > 0) call this%buy%buy_flowja(this%x, this%flowja)
- if(this%inhfb > 0) call this%hfb%hfb_flowja(this%neq, this%nja, this%x, &
- this%flowja)
+ if(this%inhfb > 0) call this%hfb%hfb_flowja(this%x, this%flowja)
  if(this%ingnc > 0) call this%gnc%flowja(this%flowja)
  !
  ! -- Return
@@ -976,7 +969,7 @@ subroutine gwf_bd(this, icnvg, isuppress_output)
  !
  ! -- Node Property Flow
  if(this%innpf > 0) then
- call this%npf%npf_bdadj(this%nja, this%flowja, icbcfl, icbcun)
+ call this%npf%npf_bdadj(this%flowja, icbcfl, icbcun)
  endif
  !
  ! -- Clear obs
@@ -1041,7 +1034,7 @@ subroutine gwf_ot(this)
  if(ibudfl /= 0) then
  !
  ! -- NPF output
- if(this%innpf > 0) call this%npf%npf_ot(this%neq, this%nja, this%flowja)
+ if(this%innpf > 0) call this%npf%npf_ot(this%flowja)
  !
  ! -- GNC output
  if(this%ingnc > 0) &

src/Model/GroundWaterFlow/gwf3hfb8.f90

@@ -196,7 +196,7 @@ subroutine hfb_rp(this)
  return
  end subroutine hfb_rp
 
- subroutine hfb_fc(this, kiter, nodes, nja, njasln, amat, idxglo, rhs, hnew)
+ subroutine hfb_fc(this, kiter, njasln, amat, idxglo, rhs, hnew)
 ! ******************************************************************************
 ! hfb_fc -- Fill amatsln for the following conditions:
 ! 1. Not Newton, and
@@ -212,14 +212,13 @@ subroutine hfb_fc(this, kiter, nodes, nja, njasln, amat, idxglo, rhs, hnew)
  ! -- dummy
  class(GwfHfbType) :: this
  integer(I4B) :: kiter
- integer(I4B),intent(in) :: nodes
- integer(I4B),intent(in) :: nja
  integer(I4B),intent(in) :: njasln
  real(DP),dimension(njasln),intent(inout) :: amat
- integer(I4B),intent(in),dimension(nja) :: idxglo
- real(DP),intent(inout),dimension(nodes) :: rhs
- real(DP),intent(inout),dimension(nodes) :: hnew
+ integer(I4B),intent(in),dimension(:) :: idxglo
+ real(DP),intent(inout),dimension(:) :: rhs
+ real(DP),intent(inout),dimension(:) :: hnew
  ! -- local
+ integer(I4B) :: nodes, nja
  integer(I4B) :: ihfb, n, m
  integer(I4B) :: ipos
  integer(I4B) :: idiag, isymcon
@@ -229,6 +228,8 @@ subroutine hfb_fc(this, kiter, nodes, nja, njasln, amat, idxglo, rhs, hnew)
  real(DP) :: topn, topm, botn, botm
 ! ------------------------------------------------------------------------------
  !
+ nodes = this%dis%nodes
+ nja = this%dis%con%nja
  if (associated(this%xt3d%ixt3d)) then
  ixt3d = this%xt3d%ixt3d
  else
@@ -335,7 +336,7 @@ subroutine hfb_fc(this, kiter, nodes, nja, njasln, amat, idxglo, rhs, hnew)
  return
  end subroutine hfb_fc
 
- subroutine hfb_flowja(this, nodes, nja, hnew, flowja)
+ subroutine hfb_flowja(this, hnew, flowja)
 ! ******************************************************************************
 ! hfb_flowja -- flowja will automatically include the effects of the hfb
 ! for confined and newton cases when xt3d is not used. This method
@@ -348,10 +349,8 @@ subroutine hfb_flowja(this, nodes, nja, hnew, flowja)
  use ConstantsModule, only: DHALF, DZERO
  ! -- dummy
  class(GwfHfbType) :: this
- integer(I4B),intent(in) :: nodes
- integer(I4B),intent(in) :: nja
- real(DP),intent(inout),dimension(nodes) :: hnew
- real(DP),intent(inout),dimension(nja) :: flowja
+ real(DP),intent(inout),dimension(:) :: hnew
+ real(DP),intent(inout),dimension(:) :: flowja
  ! -- local
  integer(I4B) :: ihfb, n, m
  integer(I4B) :: ipos
@@ -405,7 +404,7 @@ subroutine hfb_flowja(this, nodes, nja, hnew, flowja)
  condhfb = this%hydchr(ihfb)
  endif
  ! -- Make hfb corrections for xt3d
- call this%xt3d%xt3d_flowjahfb(nodes, n, m, nja, hnew, flowja, condhfb)
+ call this%xt3d%xt3d_flowjahfb(n, m, hnew, flowja, condhfb)
  end do
  !
  else