Fixes merge issues that removed HDF5 gridue capability

.gitignore

@@ -5,9 +5,13 @@ build/
 .idea/
 .DS_Store
 *~
+*.swp
 a.out
+PyUEDGE_tutorial/*
+*.swo
 pyscripts/__src__.py
 dist/uedge-8.0.0-py3.7-macosx-10.9-x86_64.egg
 uedge.egg-info
 *.egg
 *.c
+*.f

api/fimp.m

@@ -266,6 +266,8 @@ subroutine readmc(nzdf,mcfilename)
       character*256 mcfilename(*)
       character*256 fname
       Use(Multicharge)
+      Use(Math_problem_size)  # neqmx
+      Use(Lsode)        # iprint
       Use(Impdata)      #apidir
 
 c ... Function:
@@ -308,11 +310,15 @@ call xerrab("")
 *     un*formatted read for header data
       read (nget,'(2a8,i12,4x,a32)') idcod, idtyp, n, id1
       if (n .lt. 0 .and. iprt_imp_file == 1) then  
-        write(*,*) '***Impurity file using new 2012 format is ',mcfilename(i)
+        if (iprint .ne. 0) then
+            write(*,*) '***Impurity file using new 2012 format is ',mcfilename(i)
+        endif
         mcfformat(i) = 1
         iprt_imp_file = 0
       elseif (iprt_imp_file == 1) then
-        write(*,*) '***Impurity file using pre-2012 format is ',mcfilename(i)
+        if (iprint .ne. 0) then
+            write(*,*) '***Impurity file using pre-2012 format is ',mcfilename(i)
+        endif
         mcfformat(i) = 0
         iprt_imp_file = 0
       endif

api/sputt.m

@@ -40,6 +40,8 @@ SUBROUTINE SYLD96(MATT,MATP,CION,CIZB,CRMB)
 cdtr      include    'cyield'
 
       Use(Cyield)   # ceth,cetf,cq,ntars,cidata
+      Use(Math_problem_size) # neqmx
+      Use(Lsode)    # iprint
 
       real ETH(7,12), ETF(7,12), Q(7,12), EBD(12)
       LOGICAL IDATA(7,12)
@@ -199,9 +201,11 @@ ctdr      IF (CEBD.EQ.0.0 .AND. MATT.LE.12) CEBD = EBD(MATT)
       IF (CIZB.EQ.6) MATP = 5
       IF (CIZB.EQ.8) MATP = 7
 cdtr      IF (CNEUTD.EQ.1) MATP = CBOMBF
-      WRITE (*,*) 'TARGET MATERIAL IS     ' , TARMAT(MATT)
-      WRITE (*,*) 'BOMBARDING IONS ARE    ' , PLAMAT(MATP)
+      if (iprint .ne. 0) then
+        WRITE (*,*) 'TARGET MATERIAL IS     ' , TARMAT(MATT)
+        WRITE (*,*) 'BOMBARDING IONS ARE    ' , PLAMAT(MATP)
 cdtr      IF (CNEUTD.EQ.1) CALL PRI ('         WITH ZIMP', CBOMBZ)
+      endif
       RETURN
       END
 C

bbb/geometry.m

@@ -448,6 +448,7 @@ logical function tstguardc (ix, iy)
 
       implicit none
       Use(Dim)            # nx,ny
+      Use(Math_problem_size) # neqmx
       Use(Share)          # nxomit,nxc,nxleg,nxcore,geometry,ismpsym
       Use(Xpoint_indices) # ixpt1,ixpt2,iysptrx1,iysptrx2,iysptrx
       Use(RZ_grid_info)   # rm,zm,psi,br,bz,bpol,bphi,b
@@ -456,6 +457,7 @@ logical function tstguardc (ix, iy)
       Use(UEpar)          # thetar
       Use(Phyvar)         # pi
       Use(Bfield)         # b0old
+      Use(Lsode)          # iprint
       Use(Npes_mpi)       # mype
       Use(Comgeo)         # area_core
 *  -- local scalars --
@@ -487,7 +489,7 @@ c            write(6,*) "Calling flxrun in globalmesh."
          else
             fname = trim(GridFileName)
             call readgrid(fname, runid)
-            write(*,*) 'Read file "', fname, '" with runid:  ', runid
+            if (iprint*(1-isgriduehdf5) .ne. 0) write(*,*) 'Read file "', fname, '" with runid:  ', runid
             write(*,*)
          endif
       elseif (mhdgeo .eq. 2) then
@@ -497,23 +499,23 @@ call readgrid(fname, runid)
          else
             fname = trim(GridFileName)
             call readgrid(fname, runid)
-            write(*,*) 'Read file "', fname, '" with runid:  ', runid
+            if (iprint*(1-isgriduehdf5) .ne. 0) write(*,*) 'Read file "', fname, '" with runid:  ', runid
             write(*,*)
          endif
       elseif (mhdgeo .eq. 0) then
          call idealgrd
-         write(*,*) '**** mhdgeo=0: cylindrical grid generated *****'
+         if (iprint*(1-isgriduehdf5) .ne. 0) write(*,*) '**** mhdgeo=0: cylindrical grid generated *****'
       elseif (mhdgeo .eq. -1) then
          call idealgrd
-         write(*,*) '**** mhdgeo=-1: cartesian grid generated *****'
+         if (iprint*(1-isgriduehdf5) .ne. 0) write(*,*) '**** mhdgeo=-1: cartesian grid generated *****'
       elseif (mhdgeo .eq. -2) then
          call mirrorgrd
-         write(*,*) '**** mhdgeo=-2: mag mirror grid generated *****'
+         if (iprint*(1-isgriduehdf5) .ne. 0) write(*,*) '**** mhdgeo=-2: mag mirror grid generated *****'
       else
-         write(*,*) '**** mhdgeo < -1: reading grid from file *****'
+         if (iprint*(1-isgriduehdf5) .ne. 0) write(*,*) '**** mhdgeo < -1: reading grid from file *****'
          fname = trim(GridFileName)
          call readgrid(fname, runid)
-         write(*,*) 'Read file "', fname, '" with runid:  ', runid
+         if (iprint*(1-isgriduehdf5) .ne. 0) write(*,*) 'Read file "', fname, '" with runid:  ', runid
          write(*,*)
       endif
 
@@ -635,6 +637,7 @@ call s2copy (nx+2,ny+2,psi(0,0,ij),1,nx+2,psig(0,0,ij),1,nx+2)
       Use(Indices_domain_dcl) # ixmnbcl,ixmxbcl
       Use(Math_problem_size)  # neqmx
       Use(Npes_mpi)       # mype
+      Use(Lsode)          # iprint
 
 *  -- local scalars --
       integer nj, iu, ik, ij, jx, iysi, iyso, iyp1, ix_last_core_cell,
@@ -680,7 +683,7 @@ call remark('*** WARNING: ismmon.ne.0 BUT isnonog=0 ****')
          else
             fname = trim(GridFileName)
             call readgrid(fname, runid)
-            write(*,*) 'Read file "', fname, '" with runid:  ', runid
+            if (iprint*(1-isgriduehdf5) .ne. 0) write(*,*) 'Read file "', fname, '" with runid:  ', runid
 c ...  now that the grid is read in, we can manipulate dnull for nxomit>0
             if (geometry=="dnull" .and. nxpt==2) then
               if (nxomit >= ixlb(2)) then
@@ -702,7 +705,7 @@ call remark("*** nxomit>0: do outer quad as single-null")
          else
             fname = trim(GridFileName)
             call readgrid(fname, runid)
-            write(*,*) 'Read file "', fname, '" with runid:  ', runid
+            if (iprint*(1-isgriduehdf5) .ne. 0) write(*,*) 'Read file "', fname, '" with runid:  ', runid
             write(*,*)
          endif
       elseif (mhdgeo .eq. 0) then
@@ -718,7 +721,7 @@ call readgrid(fname, runid)
          write(*,*) '**** mhdgeo < -1: reading grid from file *****'
          fname = trim(GridFileName)
          call readgrid(fname, runid)
-         write(*,*) 'Read file "', fname, '" with runid:  ', runid
+         if (iprint*(1-isgriduehdf5) .ne. 0) write(*,*) 'Read file "', fname, '" with runid:  ', runid
          write(*,*)
       endif
 

bbb/oderhs.m

@@ -8438,8 +8438,6 @@ cc      real(Size4) ranf
 c ... Pause from BASIS if a ctrl_c is typed
       call ruthere
 
-c ... Count Jacobian evaluations, both for total and for this case
-      ijactot = ijactot + 1   #note: ijactot set 0 in exmain if icntnunk=0
       ijac(ig) = ijac(ig) + 1
 
       if (svrpkg.eq.'nksol') write(*,*) ' Updating Jacobian, npe =  ', 
@@ -8593,6 +8591,9 @@ ccc            call pandf1 (xc, yc, iv, neq, t, yl, wk)
 c     sparse row format.
       call csrcsc (neq, 1, 1, rcsc, icsc, jcsc, jac, ja, ia)
 
+c ... Count Jacobian evaluations, both for total and for this case
+      ijactot = ijactot + 1   #note: ijactot set 0 in exmain if icntnunk=0
+
 c ... Accumulate cpu time spent here.
       if (istimingon .eq. 1) ttjstor = ttjstor + gettime(sec4) - tsjstor
       return

bbb/odesetup.m

@@ -6492,7 +6492,7 @@ c_mpi       call MPI_BCAST(area_core,1,MPI_DOUBLE_PRECISION,0,uedgeComm,ierr)
       Use(Npes_mpi)            # npes,mype,ispmion
       Use(UEint)               # isallloc
       Use(Rccoef)              # isoutwall
-      Use(Coefeq)              # jhswitch, oldseec
+      Use(Coefeq)              # oldseec, override
 c_mpi      Use(MpiVars)  #module defined in com/mpivarsmod.F.in
 
       integer ifake  #forces Forthon scripts to put implicit none above here

bbb/odesolve.m

@@ -21,6 +21,7 @@
       Use(Compla)   # ni,up,vy,te,ti,phi,zeff,nil,upl,tel,til,ngl,phil
       Use(Grid)     # ngrid,ig,imeth,ijac,iyld,yldmax
       Use(Stat)
+      Use(Ident_vars) # exmain_evals
       Use(Ynorm)    # suscal,sfscal
       Use(Ident_vars) # exmain_evals
       Use(Oldpla)

grd/grddriv.m

@@ -41,9 +41,9 @@ call gallot("Argfc",0)	#uses npts,nconst,nwdim,niwdim
 
       call ingrd
       call grdgen
+      write(*,*) '***** Grid generation has been completed'
       call writeue
 
-      write(*,*) '***** Grid generation has been completed'
 
       return
       end

grd/grdread.m

@@ -153,6 +153,9 @@ subroutine readgridpars(fname, runid)
       real simagxs_tmp, sibdrys_tmp
       external freeus,remark,xerrab,gallot,rdgrid
 
+      if (isgriduehdf5 .eq. 1) then
+        call parsestr('import uedge.gridue as gue;gue.read_gridpars()')
+      else
 c     Read mesh parameters from a UEDGE code grid data file
       simagxs_tmp=0
       sibdrys_tmp=0
@@ -185,6 +188,7 @@ call xerrab("**** requested grid data file not found")
       close (nuno)
 
  1999 format(5i4)
+      endif
 
       return
       end
@@ -193,14 +197,18 @@ call xerrab("**** requested grid data file not found")
 
       subroutine readgrid(fname, runid)
       implicit none
-Use(Share)            # geometry
+Use(Share)            # geometry, isgriduehdf5
 Use(Dim)              # nxm,nym
 Use(Xpoint_indices)   # ixlb,ixpt1,ixmdp,ixpt2,ixrb,iysptrx1,iysptrx2
       character*(*) fname, runid
       integer nuno,ios
       real simagxs_tmp, sibdrys_tmp
       external freeus,remark,xerrab,gallot,rdgrid
 
+      if (isgriduehdf5 .eq. 1) then
+        call parsestr('import uedge.gridue as gue;gue.read_gridue()')
+      else
+
 c     Read a UEDGE code grid data file
       simagxs_tmp=0
       sibdrys_tmp=0
@@ -234,6 +242,7 @@ call gallot("RZ_grid_info",0)
       call rdgrid(nuno, runid)
 
       close (nuno)
+      endif # end isgriduehdf5 check
 
       return
       end

grd/grdwrit.m

@@ -150,7 +150,11 @@ call mapdnbot2dnull(ixpt1t,ixtopt,ixpt2t,nxmt,iysptrxt,nymt)
          call add_guardc_tp
          call magnetics(0,nxm+1,1,nym)
          call symmetrize_magnetics
-         call writednf (fname, runidarg)
+         if (isgriduehdf5 .eq. 1) then
+            call parsestr('import uedge.gridue as gue;gue.write_gridue()')
+         else
+            call writednf (fname, runidarg)
+         endif
       else
 c        write the outboard half of the full double null geometry,
 c        excluding the PLANET guard cells near the x-points.
@@ -426,7 +430,11 @@ call xerrab("*** ix indexing error in subroutine wrdndata ***")
       call magnetics(1,nxm,1,nym)
 
 #     Finally, write out the data --
-      call writedata (fname, runidarg)
+      if (isgriduehdf5 .eq. 1) then
+        call parsestr('import uedge.gridue as gue;gue.write_gridue()')
+      else
+        call writedata (fname, runidarg)
+      endif
 
       return
       end
@@ -441,7 +449,7 @@ subroutine writesn (fname, runidarg)
 Use(Dimensions)
 Use(Inmesh)
 Use(Linkco)
-Use(Share)        # nxxpt
+Use(Share)        # nxxpt, isgriduehdf5
       character*(*) fname, runidarg
       external gallot, wrsndata
 
@@ -579,7 +587,12 @@ call xerrab("*** ix indexing error in subroutine wrsndata ***")
       call magnetics(ixmin,nxm,1,nym)
 
 #     Finally, write out the data --
-      call writedata (fname, runidarg)
+
+      if (isgriduehdf5 .eq. 1) then
+        call parsestr('import uedge.gridue as gue;gue.write_gridue()')
+      else
+        call writedata (fname, runidarg)
+      endif
 
       return
       end