Merge pull request #23 from holm10/hdf5grid

Implementing HDF5 grid files for UEDGE

.gitignore

@@ -5,11 +5,15 @@ build/
 .idea/
 .DS_Store
 *~
-pyscripts/__src__.py
+*.swp
 a.out
+PyUEDGE_tutorial/*
+*.swo
+*.egg
 pyscripts/__src__.py
+uedge.egg-info/
 dist/uedge-8.0.0-py3.7-macosx-10.9-x86_64.egg
 uedge.egg-info
-pyscripts/__src__.py
-*.egg
-*.swp
+*.c
+*.f
+

aph/Package

@@ -3,6 +3,6 @@ POINTER = cray
 
 VDF = aph.v
 
-NVDF = ../com/com.v
+NVDF = ../com/com_basis.v
 
 SM = aphrates.m aphread.m

api/Package

@@ -3,7 +3,7 @@ POINTER = cray
 
 VDF = api_basis.v
 
-NVDF = ../com/com.v
+NVDF = ../com/com_basis.v ../bbb/bbb_basis.v
 
 SM = apifcn.m apip93.m apisorc.m fimp.m inelrates.m fmombal.m sputt.m
 

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/Package

@@ -3,7 +3,7 @@ POINTER = cray
 
 VDF = bbb_basis.v
 
-NVDF = ../com/com.v
+NVDF = ../com/com_basis.v
 
 SM = boundary.m convert.m geometry.m griddubl.m \
      oderhs.m odesetup.m odesolve.m potencur.m turbulence.m \

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/odesetup.m

@@ -6596,7 +6596,7 @@ call gchange("Interp",0)
                   call comp_vertex_vals  # gen plasma/neut values at rm,zm(,,4)
                endif
             endif
-         write(6,*) "Interpolants created; mype =", mype
+         if (iprint .ge. 1) write(6,*) "Interpolants created; mype =", mype
          endif
 
   100 continue

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)

com/Package

@@ -2,7 +2,7 @@ LANGUAGE = C
 PKG = com
 POINTER = cray
 
-VDF = com.v
+VDF = com_basis.v
 
 NVDF = ../aph/aph.v ../api/api_basis.v ../bbb/bbb_basis.v ../grd/grd_basis.v\
        ../flx/flx_basis.v  ../wdf/wdf.v

com/com.v

@@ -251,6 +251,7 @@ nxxpt
 nyomitmx	integer /0/
    # number of y-cells to omit from iy=ny; used to do core only for fluid eqns
 igrid		integer	/1/	# loop index for which grid; e.g., nysol(igrid)
+isgriduehdf5   integer /0/  
 geometry	character*16 /"snull"/
 				# specifies magnetic configuration, e.g.,
 				# ='snull' for lower single null